From 65b734a7f9feafeb19216384b46677558f8c0c04 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Fri, 6 Sep 2024 14:57:13 -0700
Subject: [PATCH 01/90] [maven-release-plugin] prepare for next development
 iteration

---
 biojava-aa-prop/pom.xml                 |  6 +++---
 biojava-alignment/pom.xml               |  4 ++--
 biojava-core/pom.xml                    |  2 +-
 biojava-genome/pom.xml                  |  6 +++---
 biojava-integrationtest/pom.xml         |  4 ++--
 biojava-modfinder/pom.xml               |  4 ++--
 biojava-ontology/pom.xml                |  2 +-
 biojava-protein-comparison-tool/pom.xml | 10 +++++-----
 biojava-protein-disorder/pom.xml        |  4 ++--
 biojava-structure-gui/pom.xml           |  6 +++---
 biojava-structure/pom.xml               |  6 +++---
 biojava-survival/pom.xml                |  2 +-
 biojava-ws/pom.xml                      |  4 ++--
 pom.xml                                 |  4 ++--
 14 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index b90d4e549d..474d4e32cf 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.3</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.3</version>
+			<version>7.1.4-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.3</version>
+			<version>7.1.4-SNAPSHOT</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index 2f7b2f8c54..d0024aaf6f 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.3</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.3</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 3c9aeb4724..9b8af63ea1 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.3</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 89ff5eb825..5de6f9ec8a 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.3</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -70,13 +70,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.3</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.3</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index f52bfae964..f0be361c82 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>7.1.3</version>
+    <version>7.1.4-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -40,7 +40,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>7.1.3</version>
+    	<version>7.1.4-SNAPSHOT</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index 7e2ef39ce0..2a8b240f62 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.3</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-modfinder</artifactId>
 	<name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.3</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<type>jar</type>
 			<scope>compile</scope>
 		</dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 5f26925d6d..43e55d9d11 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>7.1.3</version>
+    <version>7.1.4-SNAPSHOT</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml
index 86280e7e43..d5815b33b3 100644
--- a/biojava-protein-comparison-tool/pom.xml
+++ b/biojava-protein-comparison-tool/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.3</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>biojava-protein-comparison-tool</artifactId>
@@ -36,23 +36,23 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.3</version>
+			<version>7.1.4-SNAPSHOT</version>
 
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.3</version>
+			<version>7.1.4-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.3</version>
+			<version>7.1.4-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure-gui</artifactId>
-			<version>7.1.3</version>
+			<version>7.1.4-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>net.sourceforge.jmol</groupId>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 59ad785ce2..2c31c5b87f 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.3</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.3</version>
+			<version>7.1.4-SNAPSHOT</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or
 			scopes here) -->
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index 82e81ca96d..d60945af3d 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-		<version>7.1.3</version>
+		<version>7.1.4-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -27,13 +27,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-			<version>7.1.3</version>
+			<version>7.1.4-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-			<version>7.1.3</version>
+			<version>7.1.4-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index a87300b8fa..7572967f73 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.3</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -51,13 +51,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.3</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.3</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index c14bebebc3..8827137d94 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>7.1.3</version>
+        <version>7.1.4-SNAPSHOT</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index e3df9b3aa3..e02301197a 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.3</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.3</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 006f1d2133..85e22b680c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>7.1.3</version>
+	<version>7.1.4-SNAPSHOT</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the
@@ -51,7 +51,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>biojava-7.1.3</tag>
+		<tag>HEAD</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list

From d69435b698cca7111544babf6799e93aac7ffd4f Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Fri, 6 Sep 2024 15:23:24 -0700
Subject: [PATCH 02/90] Updating after release

---
 CHANGELOG.md | 5 +++++
 README.md    | 4 ++--
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e34223eba2..14fb2b0610 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,11 @@
 BioJava Changelog
 -----------------
 
+BioJava 7.1.3
+==============================
+### Fixed
+* Bug in symmetry detection #1101 and rcsb/symmetry#118
+
 BioJava 7.1.2
 ==============================
 ### Fixed
diff --git a/README.md b/README.md
index bac2e659d0..92473664be 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 # Welcome to <img src="logo-full.png" height="35"/>
 
 ![Build](https://github.com/biojava/biojava/actions/workflows/master.yml/badge.svg)
-[![Version](http://img.shields.io/badge/version-7.1.2-blue.svg?style=flat)](https://github.com/biojava/biojava/releases/tag/biojava-7.1.2) [![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/biojava/biojava/blob/master/LICENSE) [![Join the chat at https://gitter.im/biojava/biojava](https://badges.gitter.im/biojava/biojava.svg)](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+[![Version](http://img.shields.io/badge/version-7.1.3-blue.svg?style=flat)](https://github.com/biojava/biojava/releases/tag/biojava-7.1.3) [![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/biojava/biojava/blob/master/LICENSE) [![Join the chat at https://gitter.im/biojava/biojava](https://badges.gitter.im/biojava/biojava.svg)](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 
 
 BioJava is an open-source project dedicated to providing a Java framework for **processing biological data**. It provides analytical and statistical routines, parsers for common file formats, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.
@@ -29,7 +29,7 @@ If you are using Maven you can add the BioJava repository by adding the followin
       <dependency>
         <groupId>org.biojava</groupId>
         <artifactId>biojava-core</artifactId>
-        <version>7.1.2</version>
+        <version>7.1.3</version>
       </dependency>
       <!-- other biojava modules as needed -->
     </dependencies>

From 5ed782bf2c4d30da89aaf35d633854df124c6af3 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Fri, 3 Jan 2025 10:17:05 -0800
Subject: [PATCH 03/90] Use official url instead of github

---
 .../biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java   | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java
index e362c2a35f..5190bd38c1 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java
@@ -354,8 +354,8 @@ private void checkBioAssemblies1(Structure structOne, Structure structTwo) throw
 
 	@Test
 	public void testStructWithBranchedEntitiesRoundTrip() throws IOException {
-		// Example carbohydrate remediation file to be released in July 2020
-		URL url = new URL("https://raw.githubusercontent.com/pdbxmmcifwg/carbohydrate-extension/master/examples/models/1B5F-carb.cif");
+		// Example carbohydrate remediation, remediated in July 2020
+		URL url = new URL("https://files.rcsb.org/download/1B5F.cif.gz");
 		InputStream inStream = url.openStream();
 
 		Structure structure = CifStructureConverter.fromInputStream(inStream);
@@ -366,7 +366,7 @@ public void testStructWithBranchedEntitiesRoundTrip() throws IOException {
 		new StructureDataToAdapter(writerToEncoder, mmtfStructureReader);
 		Structure structure2 = mmtfStructureReader.getStructure();
 
-		assertEquals(7, structure2.getEntityInfos().size());
+		assertEquals(6, structure2.getEntityInfos().size());
 
 		assertEquals(2, structure2.getEntityById(1).getChains().size());
 		assertEquals(2, structure2.getEntityById(2).getChains().size());

From 26e1a4d6bfd9dfab84426e22156422f27ff1da49 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Fri, 3 Jan 2025 10:43:21 -0800
Subject: [PATCH 04/90] Plugin update: site and javadoc. Removed deprecated
 findbugs that was producing errors on `mvn site`

---
 pom.xml | 22 +++++++---------------
 1 file changed, 7 insertions(+), 15 deletions(-)

diff --git a/pom.xml b/pom.xml
index 85e22b680c..4e486ea368 100644
--- a/pom.xml
+++ b/pom.xml
@@ -275,11 +275,6 @@
 					</executions>
 
 				</plugin>
-				<plugin>
-					<groupId>org.codehaus.mojo</groupId>
-					<artifactId>findbugs-maven-plugin</artifactId>
-					<version>3.0.5</version>
-				</plugin>
 
 				<plugin>
 					<groupId>org.codehaus.mojo</groupId>
@@ -324,10 +319,16 @@
 					<version>3.0.0-M1</version>
 				</plugin>
 
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-javadoc-plugin</artifactId>
+					<version>3.11.2</version>
+				</plugin>
+
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-site-plugin</artifactId>
-					<version>3.9.1</version>
+					<version>3.21.0</version>
 				</plugin>
 
 				<plugin>
@@ -375,10 +376,6 @@
 
 			</plugin>
 
-			<plugin>
-				<groupId>org.codehaus.mojo</groupId>
-				<artifactId>findbugs-maven-plugin</artifactId>
-			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-checkstyle-plugin</artifactId>
@@ -512,10 +509,6 @@
 					</reportSet>
 				</reportSets>
 			</plugin>
-			<plugin>
-				<groupId>org.codehaus.mojo</groupId>
-				<artifactId>findbugs-maven-plugin</artifactId>
-			</plugin>
 
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
@@ -608,7 +601,6 @@
 					<plugin>
 						<groupId>org.apache.maven.plugins</groupId>
 						<artifactId>maven-javadoc-plugin</artifactId>
-						<version>3.2.0</version>
 						<executions>
 							<execution>
 								<id>attach-javadocs</id>

From 27a88ff9780f0c67561b046ad44540f779ff4c02 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Fri, 3 Jan 2025 10:45:17 -0800
Subject: [PATCH 05/90] Javadoc fix: <p>

---
 .../java/org/biojava/nbio/aaproperties/Constraints.java    | 2 +-
 .../org/biojava/nbio/aaproperties/IPeptideProperties.java  | 2 +-
 .../nbio/aaproperties/profeat/IProfeatProperties.java      | 2 +-
 .../nbio/aaproperties/profeat/convertor/Convertor.java     | 2 +-
 .../nbio/aaproperties/profeat/convertor/package-info.java  | 2 +-
 .../java/org/biojava/nbio/core/util/FlatFileCache.java     | 2 +-
 .../main/java/org/biojava/nbio/core/util/SoftHashMap.java  | 7 ++++---
 .../main/java/org/biojava/nbio/core/util/XMLWriter.java    | 2 +-
 .../ws/alignment/qblast/BlastAlignmentParameterEnum.java   | 2 +-
 .../alignment/qblast/BlastOutputAlignmentFormatEnum.java   | 2 +-
 .../nbio/ws/alignment/qblast/BlastOutputFormatEnum.java    | 2 +-
 .../nbio/ws/alignment/qblast/BlastOutputParameterEnum.java | 2 +-
 .../biojava/nbio/ws/alignment/qblast/BlastProgramEnum.java | 2 +-
 .../ws/alignment/qblast/NCBIQBlastAlignmentProperties.java | 2 +-
 .../ws/alignment/qblast/NCBIQBlastOutputProperties.java    | 2 +-
 .../nbio/ws/alignment/qblast/NCBIQBlastService.java        | 4 ++--
 16 files changed, 20 insertions(+), 19 deletions(-)

diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java
index d525c6bfe8..cecd981223 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java
@@ -30,7 +30,7 @@
 /**
  * This class is used to support the implementation of properties stated in IPeptideProperties.
  * It initializes several values that would be needed for the computation of properties such as
- * <p/>
+ * <p>
  * Molecular weight<br/>
  * Instability index<br/>
  * Hydropathy value<br/>
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java
index e90e7bd568..5e7ea3b6f1 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java
@@ -35,7 +35,7 @@
 /**
  * An interface to generate some basic physico-chemical properties of protein sequences.<br/>
  * The following properties could be generated:
- * <p/>
+ * <p>
  * Molecular weight<br/>
  * Absorbance<br/>
  * Extinction coefficient<br/>
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java
index 0fab96f94a..864cb0ce78 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java
@@ -28,7 +28,7 @@ public interface IProfeatProperties {
 	/**
 	 * Based on Table 2 of http://nar.oxfordjournals.org/content/34/suppl_2/W32.full.pdf<br/>
 	 * An interface class to generate the properties of a protein sequence based on its converted attributes.<br/>
-	 * The seven different attributes are<p/>
+	 * The seven different attributes are<p>
 	 * Hydrophobicity (Polar, Neutral, Hydrophobicity)<br/>
 	 * Normalized van der Waals volume (Range 0 - 2.78, 2.95 - 4.0, 4.03 - 8.08)<br/>
 	 * Polarity (Value 4.9 - 6.2, 8.0 - 9.2, 10.4 - 13.0)<br/>
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java
index a88d93add3..e298ab2520 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java
@@ -28,7 +28,7 @@ public abstract class Convertor {
 	/**
 	 * Based on Table 2 of http://nar.oxfordjournals.org/content/34/suppl_2/W32.full.pdf<br/>
 	 * An abstract class to convert a protein sequence into representation of different attribute with each attribute having 3 groups.<br/>
-	 * The seven different attributes are<p/>
+	 * The seven different attributes are<p>
 	 * Hydrophobicity (Polar, Neutral, Hydrophobicity)<br/>
 	 * Normalized van der Waals volume (Range 0 - 2.78, 2.95 - 4.0, 4.03 - 8.08)<br/>
 	 * Polarity (Value 4.9 - 6.2, 8.0 - 9.2, 10.4 - 13.0)<br/>
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/package-info.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/package-info.java
index 22143b53cb..a28076aa41 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/package-info.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/package-info.java
@@ -20,7 +20,7 @@
  */
 /**
  * Set of classes that enable the conversion protein sequences into various attributes.
- * The seven different attributes are<p/>
+ * The seven different attributes are<p>
  * Hydrophobicity (Polar, Neutral, Hydrophobicity)<br/>
  * Normalized van der Waals volume (Range 0 - 2.78, 2.95 - 4.0, 4.03 - 8.08)<br/>
  * Polarity (Value 4.9 - 6.2, 8.0 - 9.2, 10.4 - 13.0)<br/>
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java
index 09f8a6760d..110c355b4a 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java
@@ -58,7 +58,7 @@ private FlatFileCache(){
 
 	/**
 	 * The file is read and the bytes stored immediately.
-	 * <p/> 
+	 * <p> 
 	 * Once added, {@code fileToCache} can be modified or deleted and the cached values will not change.
 	 * @param key
 	 * @param fileToCache A readable file, of Integer.MAX bytes length or less.
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java
index f3bcef0468..b93c38277e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java
@@ -31,12 +31,13 @@
 import org.slf4j.LoggerFactory;
 
 
-/** A in memory cache using soft references. (can be garbage collected)
+/**
+ * An in memory cache using soft references. (can be garbage collected)
  * This code is based on: http://java-interview-faqs.blogspot.com/2008/09/building-faster-and-efficient-cache.html
- * <p/>
+ * <p>
  * Note that entrySet() is not implemented and therefore many methods such as keySet(),
  * containsKey(), values() etc do not work.
- * <p/>
+ * <p>
  * This class is therefore best used as a cache simply to put and get items by a known key
  */
 public class SoftHashMap<K, V> extends AbstractMap<K, V> {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLWriter.java
index 141ddba640..7b799818df 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLWriter.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLWriter.java
@@ -113,7 +113,7 @@ public interface XMLWriter {
 	 * avoid namespaces that are used only in leaf-nodes of a tree being re-defined
 	 * every time they are used. The XMLWriter will generally try to use the
 	 * suggested prefix for this namespace, but there is no guarantee of this.
-	 * <p/>
+	 * <p>
 	 * 
 	 * In particular, if the namespace is already in use, the current prefix will still
 	 * be used. Similarly if the suggested prefix has already been used for another
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastAlignmentParameterEnum.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastAlignmentParameterEnum.java
index 061475071a..d6389dba98 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastAlignmentParameterEnum.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastAlignmentParameterEnum.java
@@ -26,7 +26,7 @@
 /**
  * Alignment request parameters accepted by QBlast service.<br/>
  * Not all are mandatory. Certain parameters only work with a subset of other parameters in the list.
- * <p/>
+ * <p>
  * Taken from <a href=https://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node9.html>Blast URL API</a>
  *
  * @author Gediminas Rimsa
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputAlignmentFormatEnum.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputAlignmentFormatEnum.java
index f414fb475d..13be691e5c 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputAlignmentFormatEnum.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputAlignmentFormatEnum.java
@@ -25,7 +25,7 @@
 
 /**
  * Enum representing available output alignment types.
- * <p/>
+ * <p>
  * Values as used in QBlast URL API.
  *
  * @author Gediminas Rimsa
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputFormatEnum.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputFormatEnum.java
index 032d7e800a..3ccb1096e6 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputFormatEnum.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputFormatEnum.java
@@ -25,7 +25,7 @@
 
 /**
  * Enum representing available output formats.
- * <p/>
+ * <p>
  * Values are as used by QBlast URL API.
  *
  * @author Gediminas Rimsa
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputParameterEnum.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputParameterEnum.java
index dfa144864d..b0ed9354fa 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputParameterEnum.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputParameterEnum.java
@@ -26,7 +26,7 @@
 /**
  * Output parameters accepted by QBlast service. <br/>
  * Not all are mandatory. Certain parameters only work with a subset of other parameters in the list.
- * <p/>
+ * <p>
  * Taken from <a href=https://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node9.html>Blast URL API</a>
  *
  * @author Gediminas Rimsa
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastProgramEnum.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastProgramEnum.java
index 90c0557c78..ee020bc38d 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastProgramEnum.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastProgramEnum.java
@@ -25,7 +25,7 @@
 
 /**
  * Enum representing available blast programs.
- * <p/>
+ * <p>
  * Values are as used by QBlast URL API.
  *
  * @author Gediminas Rimsa
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java
index 196dc30c90..5976f9e915 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java
@@ -36,7 +36,7 @@
  * This class wraps a QBlast search request parameter {@code Map} by adding several convenient parameter addition
  * methods. Other QBlast URL API parameters should be added using
  * {@link #setAlignmentOption(BlastAlignmentParameterEnum, String)}
- * <p/>
+ * <p>
  * Required parameters are {@code PROGRAM} and {@code DATABASE}, other parameters are optional
  *
  * @author Sylvain Foisy, Diploide BioIT
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastOutputProperties.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastOutputProperties.java
index 3c38328ae6..6c4b92eb87 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastOutputProperties.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastOutputProperties.java
@@ -119,7 +119,7 @@ public String getOutputFormat() {
 
 	/**
 	 * Sets the stream output format to get from the QBlast service
-	 * <p/>
+	 * <p>
 	 * If {@code HTML} format is selected, also adds the following parameters (which are removed if another output
 	 * format is chosen):
 	 *
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java
index 42fafb0155..5826949426 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java
@@ -248,7 +248,7 @@ public boolean isReady(String id) throws Exception {
 
 	/**
 	 * Checks for completion of request.
-	 * <p/>
+	 * <p>
 	 * If expected execution time (RTOE) is available for request, this method will always return false until that time
 	 * passes. This is done to prevent sending unnecessary requests to the server.
 	 *
@@ -307,7 +307,7 @@ public boolean isReady(String id, long present) throws Exception {
 	/**
 	 * Extracts the actual Blast report for given request id according to options provided in {@code outputProperties}
 	 * argument.
-	 * <p/>
+	 * <p>
 	 * If the results are not ready yet, sleeps until they are available. If sleeping is not desired, call this method
 	 * after {@code isReady} returns true
 	 *

From 193287b7bff37997d72da9ab188261667f1b1f21 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Fri, 3 Jan 2025 11:00:23 -0800
Subject: [PATCH 06/90] Javadoc fix: param fixes

---
 .../nbio/core/alignment/SimpleAlignedSequence.java     |  1 +
 .../nbio/core/alignment/template/AlignedSequence.java  |  1 +
 .../alignment/template/MutableAlignedSequence.java     |  1 +
 .../main/java/org/biojava/nbio/core/search/io/Hsp.java |  5 +++--
 .../sequence/io/FileProxyProteinSequenceCreator.java   |  2 +-
 .../biojava/nbio/core/sequence/io/GenbankReader.java   |  3 ++-
 .../io/template/FastaHeaderFormatInterface.java        |  5 ++++-
 .../io/template/GenbankHeaderFormatInterface.java      | 10 ++++++----
 .../sequence/io/template/SequenceCreatorInterface.java |  1 +
 .../io/template/SequenceHeaderParserInterface.java     |  2 ++
 .../core/sequence/loader/SequenceFileProxyLoader.java  |  2 +-
 .../sequence/loader/StringProxySequenceReader.java     |  3 +--
 .../core/sequence/storage/ArrayListSequenceReader.java |  2 +-
 .../nbio/core/sequence/template/AbstractSequence.java  |  2 +-
 .../java/org/biojava/nbio/core/util/SoftHashMap.java   |  2 ++
 15 files changed, 28 insertions(+), 14 deletions(-)

diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java
index 85d0a03c26..331480bbef 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java
@@ -44,6 +44,7 @@
  *
  * @author Mark Chapman
  * @param <C> each element of the {@link Sequence} is a {@link Compound} of type C
+ * @param <S> the sequence type
  */
 public class SimpleAlignedSequence<S extends Sequence<C>, C extends Compound> implements Serializable, AlignedSequence<S, C> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java
index bc64496810..92fd972ec7 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java
@@ -34,6 +34,7 @@
  * @author Mark Chapman
  * @author Paolo Pavan
  * @param <C> each element of the {@link Sequence} is a {@link Compound} of type C
+ * @param <S> the sequence type
  */
 public interface AlignedSequence<S extends Sequence<C>, C extends Compound> extends Sequence<C> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableAlignedSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableAlignedSequence.java
index cfe85f7d33..edef1d54b7 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableAlignedSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableAlignedSequence.java
@@ -34,6 +34,7 @@
  * @author Mark Chapman
  * @author Paolo Pavan
  * @param <C> each element of the {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <S> the sequence type
  */
 public interface MutableAlignedSequence<S extends Sequence<C>, C extends Compound> extends AlignedSequence<S, C> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java
index 7a27828feb..832997bb2b 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java
@@ -40,15 +40,16 @@
 /**
  * This class models a search Hsp.
  * You will retrieve a list of this using iterator of a Hit
- *
+ * <p>
  * Designed by Paolo Pavan.
  * You may want to find my contacts on Github and LinkedIn for code info
  * or discuss major changes.
  * https://github.com/paolopavan
  *
  * @author Paolo Pavan
+ * @param <C> the compound type
+ * @param <S> the sequence type
  */
-
 public abstract class Hsp <S extends Sequence<C>, C extends Compound> {
 	private static final Logger logger = LoggerFactory.getLogger(Hsp.class);
 	private Integer hspNum;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java
index e45907a2ed..f7e1cc7ab6 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java
@@ -55,7 +55,7 @@ public class FileProxyProteinSequenceCreator implements SequenceCreatorInterface
 
 	/**
 	 * Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
-	 * @param fastaFile
+	 * @param file
 	 * @param compoundSet
 	 */
 	public FileProxyProteinSequenceCreator(File file, CompoundSet<AminoAcidCompound> compoundSet, SequenceParserInterface sequenceParser ) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java
index e2f4e8bf25..31f99eab8a 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java
@@ -53,7 +53,8 @@
 /**
  * Use {@link GenbankReaderHelper} as an example of how to use this class where {@link GenbankReaderHelper} should be the
  * primary class used to read Genbank files
- *
+ * @param <S> the sequence type
+ * @param <C> the compound type
  */
 public class GenbankReader<S extends AbstractSequence<C>, C extends Compound> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/FastaHeaderFormatInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/FastaHeaderFormatInterface.java
index a0bb6af6d3..51f5898f9f 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/FastaHeaderFormatInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/FastaHeaderFormatInterface.java
@@ -28,12 +28,15 @@
 /**
  *
  * @author Scooter Willis <willishf at gmail dot com>
+ * @param <C> the compound type
+ * @param <S> the sequence type
  */
 public interface FastaHeaderFormatInterface<S extends Sequence<?>, C extends Compound> {
+
 	/**
 	 *
 	 * @param sequence
 	 * @return
 	 */
-	public String getHeader(S sequence);
+	String getHeader(S sequence);
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.java
index 5e08a424bf..0dff2d40eb 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.java
@@ -28,16 +28,18 @@
 
 /**
  * @author mckeee1
- *
+ * @param <C> the compound type
+ * @param <S> the sequence type
  */
 public interface GenbankHeaderFormatInterface<S extends Sequence<?>, C extends Compound> {
+
+	public static final String UNKNOWN_DNA = "UNK";
+
 	/**
 	 *
 	 * @param sequence
 	 * @return
 	 */
-	public static final String UNKNOWN_DNA = "UNK";
-
-	public String getHeader(S sequence);
+	String getHeader(S sequence);
 
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceCreatorInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceCreatorInterface.java
index 9ec26dc225..b2277aecea 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceCreatorInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceCreatorInterface.java
@@ -33,6 +33,7 @@
 /**
  *
  * @author Scooter Willis <willishf at gmail dot com>
+ * @param <C> the compound type
  */
 public interface SequenceCreatorInterface<C extends Compound> {
 	/**
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceHeaderParserInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceHeaderParserInterface.java
index dba9d7ca3d..41a63ccf90 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceHeaderParserInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceHeaderParserInterface.java
@@ -28,6 +28,8 @@
 /**
  *
  * @author Scooter Willis <willishf at gmail dot com>
+ * @param <C> the compound type
+ * @param <S> the sequence type
  */
 public interface SequenceHeaderParserInterface<S extends Sequence<?>, C extends Compound> {
 	/**
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java
index 61df84f46d..6dad329743 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java
@@ -51,7 +51,7 @@
  *
  *
  * @author Scooter Willis <willishf at gmail dot com>
- * @param <C>
+ * @param <C> the compound type
  */
 public class SequenceFileProxyLoader<C extends Compound> implements ProxySequenceReader<C> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java
index b97ad43bb9..b9c0a70a9d 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java
@@ -39,9 +39,8 @@
 /**
  * An example of a ProxySequenceReader that is created from a String. Used for testing
  * @author Scooter Willis <willishf at gmail dot com>
- * @param <C>
+ * @param <C> the compound type
  */
-
 public class StringProxySequenceReader<C extends Compound> implements ProxySequenceReader<C> {
 
 	private String sequence;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java
index 5e499261c1..1cfc068fbb 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java
@@ -39,7 +39,7 @@
 /**
  * Stores a Sequence as a collection of compounds in an ArrayList
  *
- * @param <C>
+ * @param <C> the compound type
  */
 public class ArrayListSequenceReader<C extends Compound> implements SequenceReader<C> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java
index b5b2d29740..38cf55d09c 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java
@@ -47,7 +47,7 @@
 /**
  *
  * The base class for DNA, RNA and Protein sequences.
- * @param <C>
+ * @param <C> the compound type
  */
 public abstract class AbstractSequence<C extends Compound> implements Sequence<C> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java
index b93c38277e..2c10948b55 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java
@@ -39,6 +39,8 @@
  * containsKey(), values() etc do not work.
  * <p>
  * This class is therefore best used as a cache simply to put and get items by a known key
+ * @param <K> the key type
+ * @param <V> the value type
  */
 public class SoftHashMap<K, V> extends AbstractMap<K, V> {
 

From d10480957234d8591f79381f962a985aec1a2c74 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Fri, 3 Jan 2025 11:02:20 -0800
Subject: [PATCH 07/90] Javadoc fix: html-like tag not allowed

---
 .../org/biojava/nbio/core/exceptions/ParserException.java     | 2 +-
 .../org/biojava/nbio/core/search/io/blast/BlastXMLParser.java | 2 +-
 .../java/org/biojava/nbio/core/sequence/CDSComparator.java    | 2 +-
 .../main/java/org/biojava/nbio/core/sequence/DataSource.java  | 2 +-
 .../java/org/biojava/nbio/core/sequence/ExonComparator.java   | 2 +-
 .../main/java/org/biojava/nbio/core/sequence/RNASequence.java | 2 +-
 .../org/biojava/nbio/core/sequence/SequenceComparator.java    | 2 +-
 .../biojava/nbio/core/sequence/features/AbstractFeature.java  | 2 +-
 .../biojava/nbio/core/sequence/features/DBReferenceInfo.java  | 2 +-
 .../core/sequence/features/DatabaseReferenceInterface.java    | 2 +-
 .../biojava/nbio/core/sequence/features/FeatureInterface.java | 2 +-
 .../nbio/core/sequence/features/FeaturesKeyWordInterface.java | 2 +-
 .../biojava/nbio/core/sequence/features/QuantityFeature.java  | 2 +-
 .../org/biojava/nbio/core/sequence/features/TextFeature.java  | 2 +-
 .../org/biojava/nbio/core/sequence/io/DNASequenceCreator.java | 2 +-
 .../org/biojava/nbio/core/sequence/io/FastaGeneWriter.java    | 2 +-
 .../org/biojava/nbio/core/sequence/io/FastaReaderHelper.java  | 2 +-
 .../biojava/nbio/core/sequence/io/FastaSequenceParser.java    | 2 +-
 .../java/org/biojava/nbio/core/sequence/io/FastaWriter.java   | 2 +-
 .../org/biojava/nbio/core/sequence/io/FastaWriterHelper.java  | 2 +-
 .../nbio/core/sequence/io/FileProxyDNASequenceCreator.java    | 2 +-
 .../nbio/core/sequence/io/FileProxyRNASequenceCreator.java    | 2 +-
 .../biojava/nbio/core/sequence/io/GenbankReaderHelper.java    | 2 +-
 .../nbio/core/sequence/io/GenericFastaHeaderFormat.java       | 2 +-
 .../nbio/core/sequence/io/GenericFastaHeaderParser.java       | 2 +-
 .../biojava/nbio/core/sequence/io/ProteinSequenceCreator.java | 2 +-
 .../org/biojava/nbio/core/sequence/io/RNASequenceCreator.java | 2 +-
 .../core/sequence/io/template/FastaHeaderFormatInterface.java | 2 +-
 .../core/sequence/io/template/SequenceCreatorInterface.java   | 2 +-
 .../sequence/io/template/SequenceHeaderParserInterface.java   | 2 +-
 .../core/sequence/io/template/SequenceParserInterface.java    | 2 +-
 .../nbio/core/sequence/loader/SequenceFileProxyLoader.java    | 2 +-
 .../nbio/core/sequence/loader/StringProxySequenceReader.java  | 2 +-
 .../biojava/nbio/core/sequence/location/SequenceLocation.java | 2 +-
 .../nbio/core/sequence/storage/SequenceAsStringHelper.java    | 2 +-
 .../org/biojava/nbio/core/sequence/io/FastaReaderTest.java    | 2 +-
 .../biojava/nbio/core/sequence/io/GenbankCookbookTest.java    | 2 +-
 .../org/biojava/nbio/core/sequence/io/GenbankReaderTest.java  | 2 +-
 .../nbio/core/sequence/io/GenericFastaHeaderParserTest.java   | 4 ++--
 .../main/java/org/biojava/nbio/genome/GeneFeatureHelper.java  | 2 +-
 .../org/biojava/nbio/genome/homology/BlastHomologyHits.java   | 2 +-
 .../nbio/genome/homology/GFF3FromUniprotBlastHits.java        | 2 +-
 .../biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.java   | 2 +-
 .../org/biojava/nbio/genome/parsers/gff/FeatureHelper.java    | 2 +-
 .../java/org/biojava/nbio/genome/parsers/gff/GCStats.java     | 2 +-
 .../java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java  | 2 +-
 .../java/org/biojava/nbio/genome/query/BlastXMLQuery.java     | 2 +-
 .../java/org/biojava/nbio/genome/query/OutputHitsGFF.java     | 2 +-
 .../main/java/org/biojava/nbio/genome/util/SplitFasta.java    | 2 +-
 .../java/org/biojava/nbio/genome/GeneFeatureHelperTest.java   | 2 +-
 .../src/main/java/org/biojava/nbio/survival/cox/CoxCC.java    | 2 +-
 .../java/org/biojava/nbio/survival/cox/CoxCoefficient.java    | 2 +-
 .../main/java/org/biojava/nbio/survival/cox/CoxHelper.java    | 2 +-
 .../src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java  | 2 +-
 .../src/main/java/org/biojava/nbio/survival/cox/CoxMart.java  | 2 +-
 .../main/java/org/biojava/nbio/survival/cox/CoxMethod.java    | 2 +-
 .../src/main/java/org/biojava/nbio/survival/cox/CoxR.java     | 2 +-
 .../src/main/java/org/biojava/nbio/survival/cox/CoxScore.java | 2 +-
 .../main/java/org/biojava/nbio/survival/cox/CoxVariables.java | 2 +-
 .../java/org/biojava/nbio/survival/cox/ResidualsCoxph.java    | 2 +-
 .../src/main/java/org/biojava/nbio/survival/cox/RiskInfo.java | 2 +-
 .../main/java/org/biojava/nbio/survival/cox/StrataInfo.java   | 2 +-
 .../main/java/org/biojava/nbio/survival/cox/SurvFitInfo.java  | 2 +-
 .../main/java/org/biojava/nbio/survival/cox/SurvivalInfo.java | 2 +-
 .../org/biojava/nbio/survival/cox/SurvivalInfoHelper.java     | 2 +-
 .../java/org/biojava/nbio/survival/cox/SurvivalInfoIndex.java | 2 +-
 .../src/main/java/org/biojava/nbio/survival/cox/WaldTest.java | 2 +-
 .../main/java/org/biojava/nbio/survival/cox/WaldTestInfo.java | 2 +-
 .../nbio/survival/cox/comparators/CoxComparatorInterface.java | 2 +-
 .../comparators/CoxVariablesOverallModelFitComparator.java    | 2 +-
 .../cox/comparators/CoxVariablesVariableComparator.java       | 2 +-
 .../nbio/survival/cox/comparators/MeanModelComparator.java    | 2 +-
 .../nbio/survival/cox/comparators/SurvivalInfoComparator.java | 2 +-
 .../survival/cox/comparators/SurvivalInfoValueComparator.java | 2 +-
 .../java/org/biojava/nbio/survival/cox/stats/AgScore.java     | 2 +-
 .../main/java/org/biojava/nbio/survival/cox/stats/ChiSq.java  | 2 +-
 .../java/org/biojava/nbio/survival/cox/stats/Cholesky2.java   | 2 +-
 .../java/org/biojava/nbio/survival/cox/stats/Chsolve2.java    | 2 +-
 .../main/java/org/biojava/nbio/survival/data/ChangeValue.java | 2 +-
 .../org/biojava/nbio/survival/data/CompactCharSequence.java   | 2 +-
 .../main/java/org/biojava/nbio/survival/data/HeaderInfo.java  | 2 +-
 .../main/java/org/biojava/nbio/survival/data/WorkSheet.java   | 2 +-
 .../nbio/survival/kaplanmeier/figure/ExpressionFigure.java    | 2 +-
 .../nbio/survival/kaplanmeier/figure/GroupResults.java        | 2 +-
 .../nbio/survival/kaplanmeier/figure/KMFigureInfo.java        | 2 +-
 .../nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java   | 2 +-
 .../nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java  | 2 +-
 .../biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.java   | 2 +-
 .../kaplanmeier/metadata/ClinicalMetaDataOutcome.java         | 2 +-
 .../kaplanmeier/metadata/DiscreteQuantizerInterface.java      | 2 +-
 .../nbio/survival/kaplanmeier/metadata/MeanQuantizer.java     | 2 +-
 .../nbio/survival/kaplanmeier/metadata/MetaDataInfo.java      | 2 +-
 92 files changed, 93 insertions(+), 93 deletions(-)

diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/exceptions/ParserException.java b/biojava-core/src/main/java/org/biojava/nbio/core/exceptions/ParserException.java
index acd8cc47fb..5afaa7c412 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/exceptions/ParserException.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/exceptions/ParserException.java
@@ -23,7 +23,7 @@
  */
 /**
  * General abstraction of different parsing errors
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class ParserException extends RuntimeException {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java
index 73932d9147..5ccd89f459 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java
@@ -43,7 +43,7 @@
 
 /**
  * Re-designed by Paolo Pavan on the footprint of:
- * org.biojava.nbio.genome.query.BlastXMLQuery by Scooter Willis <willishf at gmail dot com>
+ * org.biojava.nbio.genome.query.BlastXMLQuery by Scooter Willis 
  *
  * You may want to find my contacts on Github and LinkedIn for code info
  * or discuss major changes.
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSComparator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSComparator.java
index 8acb7a7e83..0342ec7a46 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSComparator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSComparator.java
@@ -18,7 +18,7 @@
  *      http://www.biojava.org/
  *
  * Created on 3/1/2010
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 
 package org.biojava.nbio.core.sequence;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/DataSource.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/DataSource.java
index 000adce936..367c00a889 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/DataSource.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/DataSource.java
@@ -36,7 +36,7 @@
  * NCBI Reference Sequence           ref|accession|locus
  * Local Sequence identifier         lcl|identifier
  * </pr>
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 
 public enum DataSource {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ExonComparator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ExonComparator.java
index 64495b251f..43389f433c 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ExonComparator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ExonComparator.java
@@ -30,7 +30,7 @@
 /**
  * Sort Exon where it is a little confusing if exons should always be ordered left to right
  * where a negative stranded gene should go the other direction. Need to think about this?
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class ExonComparator implements Comparator<ExonSequence>, Serializable{
 	private static final long serialVersionUID = 1;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/RNASequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/RNASequence.java
index a3e706716b..318df7cf9f 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/RNASequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/RNASequence.java
@@ -39,7 +39,7 @@
 
 /**
  * RNASequence where RNACompoundSet are the allowed values
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 
 public class RNASequence extends AbstractSequence<NucleotideCompound> {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/SequenceComparator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/SequenceComparator.java
index 066aa930de..742b47bfce 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/SequenceComparator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/SequenceComparator.java
@@ -29,7 +29,7 @@
 
 /**
  * Used to sort sequences in ascending order of  bioBegin property.
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class SequenceComparator implements Comparator<AbstractSequence<?>>, Serializable{
 	private static final long serialVersionUID = 1;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/AbstractFeature.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/AbstractFeature.java
index 16e894697c..5f0ed8043f 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/AbstractFeature.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/AbstractFeature.java
@@ -36,7 +36,7 @@
  * A feature is currently any descriptive item that can be associated with a sequence position(s)
  * A feature has a type and a source which is currently a string to allow flexibility for the user
  * Ideally well defined features should have a class to describe attributes of that feature
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public abstract class AbstractFeature<S extends AbstractSequence<C>, C extends Compound>
 		implements FeatureInterface<S, C> {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DBReferenceInfo.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DBReferenceInfo.java
index 7598f77f33..3cc8b8897a 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DBReferenceInfo.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DBReferenceInfo.java
@@ -34,7 +34,7 @@
  * Currently implement when the {@link UniprotProxySequenceReader} is used
  * to load a protein sequence
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  * @author Paolo Pavan
  */
 public class DBReferenceInfo extends Qualifier {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DatabaseReferenceInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DatabaseReferenceInterface.java
index 20c00034dd..a302d08857 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DatabaseReferenceInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DatabaseReferenceInterface.java
@@ -30,7 +30,7 @@
 /**
  * If a SequenceProxyReader implements this interface then that external source
  * has a list of cross reference id(s)
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public interface DatabaseReferenceInterface {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureInterface.java
index 47564bcefa..c7b05cf5b9 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureInterface.java
@@ -37,7 +37,7 @@
  * A feature can contain features to handle cases where a domain is a feature and the secondary structures covered by that domain
  * and other requirements for grouping.
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  * @author Paolo Pavan
  */
 public interface FeatureInterface<S extends AbstractSequence<C>, C extends Compound> {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeaturesKeyWordInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeaturesKeyWordInterface.java
index 1b1acd994e..e7bef35d6c 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeaturesKeyWordInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeaturesKeyWordInterface.java
@@ -28,7 +28,7 @@
  * Models the keywords that are annotated for a protein sequence at Uniprot. If a ProxySequenceReader
  * implements this interface then the sequence will call this method
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public interface FeaturesKeyWordInterface {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/QuantityFeature.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/QuantityFeature.java
index 524bdfdaa3..3e6304c5c6 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/QuantityFeature.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/QuantityFeature.java
@@ -31,7 +31,7 @@
  * It is common to have a numerical value or values associated with a feature. This can then
  * be used in heat maps or other visual indicators when viewing a sequence. Multiple quantities
  * could represent a time corse study and display a color gradient
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class QuantityFeature<S extends AbstractSequence<C>, C extends Compound> extends AbstractFeature<S, C> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/TextFeature.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/TextFeature.java
index 2b8cf26b59..5634e065a9 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/TextFeature.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/TextFeature.java
@@ -26,7 +26,7 @@
 
 /**
  * A implmentation of AbstractFeature
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class TextFeature<S extends AbstractSequence<C>, C extends Compound> extends AbstractFeature<S, C> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/DNASequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/DNASequenceCreator.java
index 78a5dd4832..64a9467f3e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/DNASequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/DNASequenceCreator.java
@@ -37,7 +37,7 @@
  * A helper class that allows different ways to read a string and create a DNA sequence. Used in FastaReaderHelper
  * and probably a layer that isn't needed
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class DNASequenceCreator implements
 		SequenceCreatorInterface<NucleotideCompound> {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaGeneWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaGeneWriter.java
index 2297e5e070..065bfff79a 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaGeneWriter.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaGeneWriter.java
@@ -35,7 +35,7 @@
  * A Gene sequence has a Positive or Negative Strand where we want to write out to a stream the 5 to 3 prime version.
  * It is also an option to write out the gene sequence where the exon regions are upper case
  * 6/22/2010 FastaWriter needs to be sequence aware to handle writing out a GeneSequence which is negative Strand with the proper sequence
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class FastaGeneWriter {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java
index 4493766202..973a2813c6 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java
@@ -39,7 +39,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class FastaReaderHelper {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaSequenceParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaSequenceParser.java
index 35043c93bc..7140c094c5 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaSequenceParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaSequenceParser.java
@@ -28,7 +28,7 @@
 
 /**
  * Used to parse a stream of a fasta file to get the sequence
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class FastaSequenceParser implements SequenceParserInterface {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriter.java
index ff425bde49..f0fc191ff2 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriter.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriter.java
@@ -44,7 +44,7 @@
  * and that is used when writing to the stream. This behavior can be overwritten by implementing
  * a custom FastaHeaderFormatInterface.
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class FastaWriter<S extends Sequence<?>, C extends Compound> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java
index dfeae8a642..b4200b89c2 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java
@@ -39,7 +39,7 @@
 
 /**
  * The class that should be used to write out fasta file of a sequence collection
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class FastaWriterHelper {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java
index 21b0699ab6..52d11f9953 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java
@@ -45,7 +45,7 @@
  * Same approach can be used for genome sequence data stored in a local fasta file, in a database or via http
  * interface to a remote server
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class FileProxyDNASequenceCreator implements
 		SequenceCreatorInterface<NucleotideCompound> {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java
index 58fe3f98d7..d5c9b45f0e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java
@@ -45,7 +45,7 @@
  * Same approach can be used for genome sequence data stored in a local fasta file, in a database or via http
  * interface to a remote server
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class FileProxyRNASequenceCreator implements
 		SequenceCreatorInterface<NucleotideCompound> {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java
index 5146310591..7d382ce6b9 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java
@@ -41,7 +41,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class GenbankReaderHelper {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderFormat.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderFormat.java
index a007af0a61..c26b8362da 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderFormat.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderFormat.java
@@ -32,7 +32,7 @@
  * use the accession id. This allows the implementation by the user to write out complex header
  * with id notes etc without rewriting the fasta writer
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class GenericFastaHeaderFormat<S extends AbstractSequence<?>, C extends Compound> implements FastaHeaderFormatInterface<S, C> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParser.java
index 1556bf838e..f4c8ea3416 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParser.java
@@ -59,7 +59,7 @@
  * NCBI Reference Sequence           ref|accession|locus
  * Local Sequence identifier         lcl|identifier
  *</pre>
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class GenericFastaHeaderParser<S extends AbstractSequence<C>, C extends Compound> implements SequenceHeaderParserInterface<S,C> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ProteinSequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ProteinSequenceCreator.java
index 1efebed609..6f4e839ca7 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ProteinSequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ProteinSequenceCreator.java
@@ -37,7 +37,7 @@
  * Used to create a ProteinSequence from a String to allow for details
  * about the location of the sequence etc.
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class ProteinSequenceCreator implements
 		SequenceCreatorInterface<AminoAcidCompound> {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/RNASequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/RNASequenceCreator.java
index 0a691f1afa..16f69cbf74 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/RNASequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/RNASequenceCreator.java
@@ -35,7 +35,7 @@
 /**
  * Used to create a RNA sequence
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class RNASequenceCreator implements
 		SequenceCreatorInterface<NucleotideCompound> {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/FastaHeaderFormatInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/FastaHeaderFormatInterface.java
index 51f5898f9f..bfd3092357 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/FastaHeaderFormatInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/FastaHeaderFormatInterface.java
@@ -27,7 +27,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  * @param <C> the compound type
  * @param <S> the sequence type
  */
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceCreatorInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceCreatorInterface.java
index b2277aecea..c03900055b 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceCreatorInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceCreatorInterface.java
@@ -32,7 +32,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  * @param <C> the compound type
  */
 public interface SequenceCreatorInterface<C extends Compound> {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceHeaderParserInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceHeaderParserInterface.java
index 41a63ccf90..a49e27c754 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceHeaderParserInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceHeaderParserInterface.java
@@ -27,7 +27,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  * @param <C> the compound type
  * @param <S> the sequence type
  */
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java
index fd536e2802..9950c450eb 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java
@@ -27,7 +27,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public interface SequenceParserInterface {
 	/**
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java
index 6dad329743..ef4bf016cb 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java
@@ -50,7 +50,7 @@
  * data was loaded and then after X amount of time clear the contents to free up memory.
  *
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  * @param <C> the compound type
  */
 public class SequenceFileProxyLoader<C extends Compound> implements ProxySequenceReader<C> {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java
index b9c0a70a9d..86323d1289 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java
@@ -38,7 +38,7 @@
 
 /**
  * An example of a ProxySequenceReader that is created from a String. Used for testing
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  * @param <C> the compound type
  */
 public class StringProxySequenceReader<C extends Compound> implements ProxySequenceReader<C> {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SequenceLocation.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SequenceLocation.java
index 443f7d9f06..beb03e3be7 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SequenceLocation.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SequenceLocation.java
@@ -31,7 +31,7 @@
 import java.util.List;
 /**
  * A location in a sequence that keeps a reference to its parent sequence
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  * @author Paolo Pavan
  */
 public class SequenceLocation<S extends AbstractSequence<C>, C extends Compound> extends SimpleLocation {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SequenceAsStringHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SequenceAsStringHelper.java
index 995a358ef0..c2b02debee 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SequenceAsStringHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SequenceAsStringHelper.java
@@ -29,7 +29,7 @@
 /**
  * This is a common method that can be used across multiple storage/proxy implementations to
  * handle Negative strand and other interesting elements of sequence data.
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class SequenceAsStringHelper<C extends Compound> {
 
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaReaderTest.java
index 7981d8e6e3..466cabaa94 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaReaderTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaReaderTest.java
@@ -35,7 +35,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class FastaReaderTest {
 
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
index 132a36d816..06459579a7 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
@@ -37,7 +37,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class GenbankCookbookTest {
 
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
index e813f863a8..0a03c85586 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
@@ -43,7 +43,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  * @author Jacek Grzebyta
  * @author Philippe Soares
  */
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParserTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParserTest.java
index 4d8ae7e8bd..b5e5598722 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParserTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParserTest.java
@@ -32,7 +32,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class GenericFastaHeaderParserTest {
 
@@ -52,7 +52,7 @@ public class GenericFastaHeaderParserTest {
 	 * NCBI Reference Sequence           ref|accession|locus
 	 * Local Sequence identifier         lcl|identifier
 	 *
-	 * @author Scooter Willis <willishf at gmail dot com>
+	 * @author Scooter Willis 
 	 */
 	@Test
 	public void testParseHeader() throws CompoundNotFoundException {
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java
index 0090ce7786..c9786b3ad0 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java
@@ -36,7 +36,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class GeneFeatureHelper {
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/BlastHomologyHits.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/BlastHomologyHits.java
index 0d40fe835c..9fb2ebce48 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/BlastHomologyHits.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/BlastHomologyHits.java
@@ -28,7 +28,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class BlastHomologyHits {
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java
index bc6893d19d..67e22bd992 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java
@@ -46,7 +46,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  * @author Mark Chapman
  */
 public class GFF3FromUniprotBlastHits {
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.java
index b68074e080..dc6a97e702 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.java
@@ -37,7 +37,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class GeneIDXMLReader {
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureHelper.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureHelper.java
index bcdc0bc32b..f18c14a098 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureHelper.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureHelper.java
@@ -25,7 +25,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class FeatureHelper {
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GCStats.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GCStats.java
index 2974a13c9c..8ee0881551 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GCStats.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GCStats.java
@@ -26,7 +26,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class GCStats {
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java
index 7432729d97..88af970928 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java
@@ -31,7 +31,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class GFF3Writer {
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/query/BlastXMLQuery.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/query/BlastXMLQuery.java
index 06d65933a9..98f36dd22f 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/query/BlastXMLQuery.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/query/BlastXMLQuery.java
@@ -33,7 +33,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class BlastXMLQuery {
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/query/OutputHitsGFF.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/query/OutputHitsGFF.java
index f7ac399455..5ab5e8f13a 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/query/OutputHitsGFF.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/query/OutputHitsGFF.java
@@ -33,7 +33,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class OutputHitsGFF {
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/SplitFasta.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/SplitFasta.java
index 374dd378a1..a618443d0f 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/SplitFasta.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/SplitFasta.java
@@ -35,7 +35,7 @@
 
 /**
  * Utility to write each Fasta entry to a unique file
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class SplitFasta {
 
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/GeneFeatureHelperTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/GeneFeatureHelperTest.java
index e5e1a8379d..3c81c50916 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/GeneFeatureHelperTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/GeneFeatureHelperTest.java
@@ -43,7 +43,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class GeneFeatureHelperTest {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCC.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCC.java
index a6e4779a44..ccd9d1f238 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCC.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCC.java
@@ -30,7 +30,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class CoxCC {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCoefficient.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCoefficient.java
index a8023284b5..d95f85ca76 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCoefficient.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCoefficient.java
@@ -25,7 +25,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class CoxCoefficient {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxHelper.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxHelper.java
index dfc149c54e..4430922993 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxHelper.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxHelper.java
@@ -30,7 +30,7 @@
  * Given the number of options for adjusting the calculations using weighting, strata, clustering etc the helper class can be used to hide
  * the complexity for typical use case.
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class CoxHelper {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java
index 7bfafba710..c9f4f18056 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java
@@ -32,7 +32,7 @@
 
 /**
  * Holds the results of a cox analysis where calling dump(), toString() will give an output similar to R
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class CoxInfo {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxMart.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxMart.java
index d49545efa6..9c54c37618 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxMart.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxMart.java
@@ -44,7 +44,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class CoxMart {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxMethod.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxMethod.java
index 64cfe1fdde..fe26661fd8 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxMethod.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxMethod.java
@@ -22,7 +22,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public enum CoxMethod{
 	/**
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java
index 943dde980d..d2ac87e87a 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java
@@ -106,7 +106,7 @@
  * <p>
  * the data must be sorted by ascending time within strata
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class CoxR {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxScore.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxScore.java
index cc51ec4d3f..3de88ec20a 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxScore.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxScore.java
@@ -24,7 +24,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class CoxScore {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxVariables.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxVariables.java
index 7a99f4db02..6b477cb496 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxVariables.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxVariables.java
@@ -25,7 +25,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class CoxVariables {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java
index 94baf9dce8..42b34905cc 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java
@@ -29,7 +29,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class ResidualsCoxph {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/RiskInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/RiskInfo.java
index 9e050b62da..6a8b9c4316 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/RiskInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/RiskInfo.java
@@ -22,7 +22,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class RiskInfo {
 	double weight;
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/StrataInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/StrataInfo.java
index 5cf88613ab..8a50d559fb 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/StrataInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/StrataInfo.java
@@ -27,7 +27,7 @@
 /**
  * Information needed to represent a survival curve
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class StrataInfo {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvFitInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvFitInfo.java
index c22e6fb9b5..fa3d30f756 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvFitInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvFitInfo.java
@@ -25,7 +25,7 @@
 /**
  * Contains info for graphing km figures
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class SurvFitInfo {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfo.java
index c1ed799293..c60d197682 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfo.java
@@ -29,7 +29,7 @@
  * The code handles figuring out if a variables is continuous or categorical. If categorical will
  * convert to numerical values.
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class SurvivalInfo implements Comparable<SurvivalInfo> {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoHelper.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoHelper.java
index 6e292d1633..bf89f51fc8 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoHelper.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoHelper.java
@@ -27,7 +27,7 @@
 
 /**
  * Used to work with SurvivalInfo
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class SurvivalInfoHelper {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoIndex.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoIndex.java
index 51c443b0b7..1a87f906f4 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoIndex.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoIndex.java
@@ -22,7 +22,7 @@
 
 /**
  * Not used and probably should be deleted
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class SurvivalInfoIndex implements Comparable<SurvivalInfoIndex> {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/WaldTest.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/WaldTest.java
index fb011e3cf4..b0996e80e6 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/WaldTest.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/WaldTest.java
@@ -25,7 +25,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class WaldTest {
 //coxph_wtest, df=as.integer(nvar),as.integer(ntest),as.double(var),tests= as.double(b),solve= double(nvar*ntest),as.double(toler.chol))
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/WaldTestInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/WaldTestInfo.java
index f5f09d8b03..30cdd1e3f3 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/WaldTestInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/WaldTestInfo.java
@@ -24,7 +24,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class WaldTestInfo {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxComparatorInterface.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxComparatorInterface.java
index 703936e751..fa012ead4d 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxComparatorInterface.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxComparatorInterface.java
@@ -27,7 +27,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public interface CoxComparatorInterface extends Comparator<CoxVariables> {
 	public String getDescription();
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesOverallModelFitComparator.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesOverallModelFitComparator.java
index 964b1e254f..4ec710d6c1 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesOverallModelFitComparator.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesOverallModelFitComparator.java
@@ -28,7 +28,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class CoxVariablesOverallModelFitComparator implements Comparator<CoxVariables>, Serializable {
 	private static final long serialVersionUID = 1;
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesVariableComparator.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesVariableComparator.java
index 1c48b2dcf0..3c7e2c16d8 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesVariableComparator.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesVariableComparator.java
@@ -25,7 +25,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class CoxVariablesVariableComparator implements CoxComparatorInterface {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/MeanModelComparator.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/MeanModelComparator.java
index 5f61766a25..4ac6a3f402 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/MeanModelComparator.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/MeanModelComparator.java
@@ -28,7 +28,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class MeanModelComparator implements Comparator<CoxVariables>, Serializable {
 	private static final long serialVersionUID = 1;
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/SurvivalInfoComparator.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/SurvivalInfoComparator.java
index f8415af304..899e5e0cb4 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/SurvivalInfoComparator.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/SurvivalInfoComparator.java
@@ -27,7 +27,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class SurvivalInfoComparator implements Comparator<SurvivalInfo>, Serializable {
 	private static final long serialVersionUID = 1;
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/SurvivalInfoValueComparator.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/SurvivalInfoValueComparator.java
index 81098c46cf..f639be0079 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/SurvivalInfoValueComparator.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/SurvivalInfoValueComparator.java
@@ -27,7 +27,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class SurvivalInfoValueComparator implements Comparator<SurvivalInfo>, Serializable {
 	private static final long serialVersionUID = 1;
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/AgScore.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/AgScore.java
index 7760cbe23d..1a3488b1ec 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/AgScore.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/AgScore.java
@@ -28,7 +28,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class AgScore {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/ChiSq.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/ChiSq.java
index 4ad714f549..d193e6104b 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/ChiSq.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/ChiSq.java
@@ -22,7 +22,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class ChiSq {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/Cholesky2.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/Cholesky2.java
index 8c4f81af3b..8ce9f73ff5 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/Cholesky2.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/Cholesky2.java
@@ -22,7 +22,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class Cholesky2 {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/Chsolve2.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/Chsolve2.java
index dad7d06688..8f62db56c3 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/Chsolve2.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/Chsolve2.java
@@ -22,7 +22,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class Chsolve2 {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/ChangeValue.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/ChangeValue.java
index b5841d9f63..5e734a27ba 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/ChangeValue.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/ChangeValue.java
@@ -23,7 +23,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public interface ChangeValue {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/CompactCharSequence.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/CompactCharSequence.java
index 68cf58c0a8..eb029560cb 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/CompactCharSequence.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/CompactCharSequence.java
@@ -25,7 +25,7 @@
 
 /**
  *http://www.javamex.com/tutorials/memory/ascii_charsequence.shtml
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class CompactCharSequence implements CharSequence, Serializable {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/HeaderInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/HeaderInfo.java
index 7357eca3a3..71408271db 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/HeaderInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/HeaderInfo.java
@@ -22,7 +22,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class HeaderInfo {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java
index 9e4de21fcc..9e1f4b6fd2 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java
@@ -27,7 +27,7 @@
  * Need to handle very large spreadsheets of expression data so keep memory
  * footprint low
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class WorkSheet {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.java
index d8d120aee7..51142aeab0 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.java
@@ -35,7 +35,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class ExpressionFigure extends JPanel {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/GroupResults.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/GroupResults.java
index abdfe810b6..6c2e0b1b90 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/GroupResults.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/GroupResults.java
@@ -24,7 +24,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class GroupResults {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.java
index d17d6afa51..c3b9bed262 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.java
@@ -27,7 +27,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class KMFigureInfo {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java
index f1e8877f97..21e68ccdd0 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java
@@ -36,7 +36,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class KaplanMeierFigure extends JPanel {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java
index dc3e57994e..c4578f1c8b 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java
@@ -31,7 +31,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class NumbersAtRiskPanel extends JPanel {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.java
index 764c8af76f..0167aa591a 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.java
@@ -34,7 +34,7 @@
  * Ported from survfitKM.S When combining multiple entries with same time not
  * sure how the weighting adds up
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class SurvFitKM {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/ClinicalMetaDataOutcome.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/ClinicalMetaDataOutcome.java
index 3b1ca8fe15..b507f41f97 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/ClinicalMetaDataOutcome.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/ClinicalMetaDataOutcome.java
@@ -27,7 +27,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class ClinicalMetaDataOutcome {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/DiscreteQuantizerInterface.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/DiscreteQuantizerInterface.java
index 5c80054a72..4d48bd71c3 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/DiscreteQuantizerInterface.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/DiscreteQuantizerInterface.java
@@ -25,7 +25,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public interface DiscreteQuantizerInterface {
 	/**
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MeanQuantizer.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MeanQuantizer.java
index 964a365cdc..ba64cf1727 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MeanQuantizer.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MeanQuantizer.java
@@ -25,7 +25,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class MeanQuantizer implements DiscreteQuantizerInterface {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.java
index bad051b590..75af37ca57 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.java
@@ -26,7 +26,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class MetaDataInfo {
 

From 2fab7b03503a48faff1dde8a86254e1b287dd063 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Fri, 3 Jan 2025 11:21:46 -0800
Subject: [PATCH 08/90] Javadoc fix: html escaping

---
 .../matrices/SubstitutionMatrixHelper.java    | 32 +++++++++----------
 .../nbio/core/alignment/template/Profile.java | 22 ++++++-------
 .../core/alignment/template/SequencePair.java | 12 +++----
 .../template/SubstitutionMatrix.java          |  2 +-
 .../sequence/location/LocationHelper.java     |  2 +-
 .../storage/JoiningSequenceReader.java        |  6 ++--
 .../sequence/template/LightweightProfile.java |  4 +--
 .../core/sequence/template/SequenceMixin.java |  6 ++--
 .../nbio/core/util/FileDownloadUtils.java     |  4 +--
 .../core/util/StringManipulationHelper.java   |  8 ++---
 10 files changed, 49 insertions(+), 49 deletions(-)

diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java
index 3f55a3897a..ab737b536e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java
@@ -78,7 +78,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getIdentity() {
 	}
 
 	/**
-	 * Returns Blosum 100 matrix by Henikoff & Henikoff
+	 * Returns Blosum 100 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 100 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum100() {
@@ -86,7 +86,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum100() {
 	}
 
 	/**
-	 * Returns Blosum 30 matrix by Henikoff & Henikoff
+	 * Returns Blosum 30 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 30 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum30() {
@@ -94,7 +94,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum30() {
 	}
 
 	/**
-	 * Returns Blosum 35 matrix by Henikoff & Henikoff
+	 * Returns Blosum 35 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 35 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum35() {
@@ -102,7 +102,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum35() {
 	}
 
 	/**
-	 * Returns Blosum 40 matrix by Henikoff & Henikoff
+	 * Returns Blosum 40 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 40 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum40() {
@@ -110,7 +110,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum40() {
 	}
 
 	/**
-	 * Returns Blosum 45 matrix by Henikoff & Henikoff
+	 * Returns Blosum 45 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 45 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum45() {
@@ -118,7 +118,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum45() {
 	}
 
 	/**
-	 * Returns Blosum 50 matrix by Henikoff & Henikoff
+	 * Returns Blosum 50 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 50 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum50() {
@@ -126,7 +126,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum50() {
 	}
 
 	/**
-	 * Returns Blosum 55 matrix by Henikoff & Henikoff
+	 * Returns Blosum 55 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 55 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum55() {
@@ -134,7 +134,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum55() {
 	}
 
 	/**
-	 * Returns Blosum 60 matrix by Henikoff & Henikoff
+	 * Returns Blosum 60 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 60 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum60() {
@@ -142,7 +142,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum60() {
 	}
 
 	/**
-	 * Returns Blosum 62 matrix by Henikoff & Henikoff
+	 * Returns Blosum 62 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 62 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum62() {
@@ -150,7 +150,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum62() {
 	}
 
 	/**
-	 * Returns Blosum 65 matrix by Henikoff & Henikoff
+	 * Returns Blosum 65 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 65 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum65() {
@@ -158,7 +158,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum65() {
 	}
 
 	/**
-	 * Returns Blosum 70 matrix by Henikoff & Henikoff
+	 * Returns Blosum 70 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 70 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum70() {
@@ -166,7 +166,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum70() {
 	}
 
 	/**
-	 * Returns Blosum 75 matrix by Henikoff & Henikoff
+	 * Returns Blosum 75 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 75 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum75() {
@@ -174,7 +174,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum75() {
 	}
 
 	/**
-	 * Returns Blosum 80 matrix by Henikoff & Henikoff
+	 * Returns Blosum 80 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 80 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum80() {
@@ -182,7 +182,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum80() {
 	}
 
 	/**
-	 * Returns Blosum 85 matrix by Henikoff & Henikoff
+	 * Returns Blosum 85 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 85 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum85() {
@@ -190,7 +190,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum85() {
 	}
 
 	/**
-	 * Returns Blosum 90 matrix by Henikoff & Henikoff
+	 * Returns Blosum 90 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 90 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum90() {
@@ -198,7 +198,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum90() {
 	}
 
 	/**
-	 * Returns PAM 250 matrix by Gonnet, Cohen & Benner
+	 * Returns PAM 250 matrix by Gonnet, Cohen &amp; Benner
 	 * @return Gonnet 250 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getGonnet250() {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java
index 811de73b31..62575a1bf2 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java
@@ -58,7 +58,7 @@ enum StringFormat {
 	 *
 	 * @param listIndex index of sequence in profile
 	 * @return desired sequence
-	 * @throws IndexOutOfBoundsException if listIndex < 1 or listIndex > number of sequences
+	 * @throws IndexOutOfBoundsException if listIndex &lt; 1 or listIndex &gt; number of sequences
 	 */
 	AlignedSequence<S, C> getAlignedSequence(int listIndex);
 
@@ -101,8 +101,8 @@ enum StringFormat {
 	 * @param listIndex index of sequence in profile
 	 * @param alignmentIndex column index within an alignment
 	 * @return the sequence element
-	 * @throws IndexOutOfBoundsException if listIndex < 1, listIndex > number of sequences, alignmentIndex < 1, or
-	 *     alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if listIndex &lt; 1, listIndex &gt; number of sequences, alignmentIndex &lt; 1, or
+	 *     alignmentIndex &gt; {@link #getLength()}
 	 */
 	C getCompoundAt(int listIndex, int alignmentIndex);
 
@@ -113,7 +113,7 @@ enum StringFormat {
 	 * @param sequence either an {@link AlignedSequence} or an original {@link Sequence}
 	 * @param alignmentIndex column index within an alignment
 	 * @return the sequence element
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	C getCompoundAt(S sequence, int alignmentIndex);
 
@@ -122,7 +122,7 @@ enum StringFormat {
 	 *
 	 * @param alignmentIndex column index within an alignment
 	 * @return list of counts
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	int[] getCompoundCountsAt(int alignmentIndex);
 
@@ -132,7 +132,7 @@ enum StringFormat {
 	 * @param alignmentIndex column index within an alignment
 	 * @param compounds list of compounds to count
 	 * @return corresponding list of counts
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	int[] getCompoundCountsAt(int alignmentIndex, List<C> compounds);
 
@@ -141,7 +141,7 @@ enum StringFormat {
 	 *
 	 * @param alignmentIndex column index within an alignment
 	 * @return the sequence elements
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	List<C> getCompoundsAt(int alignmentIndex);
 
@@ -157,7 +157,7 @@ enum StringFormat {
 	 *
 	 * @param alignmentIndex column index within an alignment
 	 * @return list of fractional weights
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	float[] getCompoundWeightsAt(int alignmentIndex);
 
@@ -167,7 +167,7 @@ enum StringFormat {
 	 * @param alignmentIndex column index within an alignment
 	 * @param compounds list of compounds to count
 	 * @return corresponding list of fractional weights
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	float[] getCompoundWeightsAt(int alignmentIndex, List<C> compounds);
 
@@ -177,7 +177,7 @@ enum StringFormat {
 	 *
 	 * @param alignmentIndex column index within an alignment
 	 * @return the sequence indices
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	int[] getIndicesAt(int alignmentIndex);
 
@@ -236,7 +236,7 @@ enum StringFormat {
 	 *
 	 * @param alignmentIndex column index within an alignment
 	 * @return true if any {@link AlignedSequence} has a gap at the given index
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	boolean hasGap(int alignmentIndex);
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java
index 24f2315e00..1367fb6be9 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java
@@ -41,7 +41,7 @@ public interface SequencePair<S extends Sequence<C>, C extends Compound> extends
 	 *
 	 * @param alignmentIndex column index in alignment
 	 * @return the query sequence element
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	C getCompoundInQueryAt(int alignmentIndex);
 
@@ -50,7 +50,7 @@ public interface SequencePair<S extends Sequence<C>, C extends Compound> extends
 	 *
 	 * @param alignmentIndex column index in alignment
 	 * @return the target sequence element
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	C getCompoundInTargetAt(int alignmentIndex);
 
@@ -59,7 +59,7 @@ public interface SequencePair<S extends Sequence<C>, C extends Compound> extends
 	 *
 	 * @param alignmentIndex column index in alignment
 	 * @return index in query {@link Sequence}
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	int getIndexInQueryAt(int alignmentIndex);
 
@@ -68,7 +68,7 @@ public interface SequencePair<S extends Sequence<C>, C extends Compound> extends
 	 *
 	 * @param targetIndex index in target {@link Sequence}
 	 * @return index in query {@link Sequence}
-	 * @throws IndexOutOfBoundsException if targetIndex < 1 or targetIndex > {@link #getTarget()}.getLength()
+	 * @throws IndexOutOfBoundsException if targetIndex &lt; 1 or targetIndex &gt; {@link #getTarget()}.getLength()
 	 */
 	int getIndexInQueryForTargetAt(int targetIndex);
 
@@ -77,7 +77,7 @@ public interface SequencePair<S extends Sequence<C>, C extends Compound> extends
 	 *
 	 * @param alignmentIndex column index in alignment
 	 * @return index in target {@link Sequence}
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	int getIndexInTargetAt(int alignmentIndex);
 
@@ -86,7 +86,7 @@ public interface SequencePair<S extends Sequence<C>, C extends Compound> extends
 	 *
 	 * @param queryIndex index in query {@link Sequence}
 	 * @return index in target {@link Sequence}
-	 * @throws IndexOutOfBoundsException if queryIndex < 1 or queryIndex > {@link #getQuery()}.getLength()
+	 * @throws IndexOutOfBoundsException if queryIndex &lt; 1 or queryIndex &gt; {@link #getQuery()}.getLength()
 	 */
 	int getIndexInTargetForQueryAt(int queryIndex);
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SubstitutionMatrix.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SubstitutionMatrix.java
index 22a8de5f5c..436fc7a44b 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SubstitutionMatrix.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SubstitutionMatrix.java
@@ -103,7 +103,7 @@ public interface SubstitutionMatrix<C extends Compound> {
 	 * Rescales the matrix so that to {@link #getMaxValue()} - {@link #getMinValue()} = scale.
 	 *
 	 * @param scale new normalization scale of this matrix
-	 * @throws IllegalArgumentException if scale < 1
+	 * @throws IllegalArgumentException if scale &lt; 1
 	 */
 	SubstitutionMatrix<C> normalizeMatrix(short scale);
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java
index d36d882c98..f164e5b7b8 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java
@@ -307,7 +307,7 @@ public static Strand detectStrand(List<Location> subLocations) {
 	}
 
 	/**
-	 * Assumes that the first element is the start & clones it
+	 * Assumes that the first element is the start &amp; clones it
 	 */
 	public static Point detectStart(List<Location> subLocations) {
 		return subLocations.get(0).getStart().clonePoint();
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java
index 46a0501b8a..ae1471b52c 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java
@@ -56,7 +56,7 @@ public class JoiningSequenceReader<C extends Compound> implements ProxySequenceR
 	private int[] minSequenceIndex;
 
 	/**
-	 * Allows creation of the store from Vargs Sequence<C> objects. CompoundSet
+	 * Allows creation of the store from Vargs {@link Sequence<C>} objects. CompoundSet
 	 * defaults to the first element of the array (assuming there are elements
 	 * available during construction otherwise we will throw an illegal
 	 * state exception).
@@ -66,7 +66,7 @@ public JoiningSequenceReader(Sequence<C>... sequences) {
 	}
 
 	/**
-	 * Allows creation of the store from List<Sequence<C>>. CompoundSet
+	 * Allows creation of the store from {@link List<Sequence<C>>}. CompoundSet
 	 * defaults to the first element of the List (assuming there are elements
 	 * available during construction otherwise we will throw an illegal
 	 * state exception).
@@ -217,7 +217,7 @@ else if (midMinPosition > position && midMaxPosition > position) {
 
 	/**
 	 * Iterator implementation which attempts to move through the 2D structure
-	 * attempting to skip onto the next sequence as & when it is asked to
+	 * attempting to skip onto the next sequence as &amp; when it is asked to
 	 */
 
 	@Override
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/LightweightProfile.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/LightweightProfile.java
index e6f632224b..033fa84e85 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/LightweightProfile.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/LightweightProfile.java
@@ -52,7 +52,7 @@ enum StringFormat {
 	 *
 	 * @param listIndex index of sequence in profile
 	 * @return desired sequence
-	 * @throws IndexOutOfBoundsException if listIndex < 1 or listIndex > number of sequences
+	 * @throws IndexOutOfBoundsException if listIndex &lt; 1 or listIndex &gt; number of sequences
 	 */
 	S getAlignedSequence(int listIndex);
 
@@ -68,7 +68,7 @@ enum StringFormat {
 	 *
 	 * @param alignmentIndex column index within an alignment
 	 * @return the sequence elements
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	List<C> getCompoundsAt(int alignmentIndex);
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java
index c3dec3d0bd..3d75261d87 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java
@@ -285,7 +285,7 @@ public static <C extends Compound> List<SequenceView<C>> nonOverlappingKmers(Seq
 
 	/**
 	 * Used to generate overlapping k-mers such i.e. ATGTA will give rise to
-	 * ATG, TGT & GTA
+	 * ATG, TGT &amp; GTA
 	 *
 	 * @param <C> Compound to use
 	 * @param sequence Sequence to build from
@@ -343,7 +343,7 @@ public static <C extends Compound> SequenceView<C> inverse(Sequence<C> sequence)
 	/**
 	 * A case-insensitive manner of comparing two sequence objects together.
 	 * We will throw out any compounds which fail to match on their sequence
-	 * length & compound sets used. The code will also bail out the moment
+	 * length &amp; compound sets used. The code will also bail out the moment
 	 * we find something is wrong with a Sequence. Cost to run is linear to
 	 * the length of the Sequence.
 	 *
@@ -359,7 +359,7 @@ public static <C extends Compound> boolean sequenceEqualityIgnoreCase(Sequence<C
 	/**
 	 * A case-sensitive manner of comparing two sequence objects together.
 	 * We will throw out any compounds which fail to match on their sequence
-	 * length & compound sets used. The code will also bail out the moment
+	 * length &amp; compound sets used. The code will also bail out the moment
 	 * we find something is wrong with a Sequence. Cost to run is linear to
 	 * the length of the Sequence.
 	 *
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
index 3259676ef0..00cb2c923f 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
@@ -350,7 +350,7 @@ public static URLConnection prepareURLConnection(String url, int timeout) throws
 	}
 
 	/**
-	 * Recursively delete a folder & contents
+	 * Recursively delete a folder &amp; contents
 	 *
 	 * @param dir directory to delete
 	 */
@@ -375,7 +375,7 @@ public FileVisitResult postVisitDirectory(Path dir, IOException e) throws IOExce
 	    });
 	}
 	/**
-	 * Recursively delete a folder & contents
+	 * Recursively delete a folder &amp; contents
 	 *
 	 * @param dir directory to delete
 	 */
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java
index 1fe985d0ba..c7b27cc752 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java
@@ -202,9 +202,9 @@ public static boolean equalsToXml(String expected, String actual) {
 	/**
 	 * Adds padding to left of supplied string
 	 * @param s The String to pad
-	 * @param n an integer >= 1
+	 * @param n an integer &gt;= 1
 	 * @return The left-padded string. 
-	 * @throws IllegalArgumentException if n <= 0
+	 * @throws IllegalArgumentException if n &lt;= 0
 	 */
 	public static String padLeft(String s, int n) {
 		validatePadding(n);
@@ -214,9 +214,9 @@ public static String padLeft(String s, int n) {
 	/**
 	 * Adds padding to right of supplied string
 	 * @param s The String to pad
-	 * @param n an integer >= 1
+	 * @param n an integer &gt;= 1
 	 * @return The right-padded string. 
-	 * @throws IllegalArgumentException if n <= 0
+	 * @throws IllegalArgumentException if n &lt;= 0
 	 */
 	public static String padRight(String s, int n) {
 		validatePadding(n);

From 1c8d58788845e1418b83683734eef997951734c5 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Fri, 3 Jan 2025 11:22:22 -0800
Subject: [PATCH 09/90] Javadoc fix: bad tags

---
 .../biojava/nbio/core/sequence/reference/AbstractReference.java | 2 +-
 .../biojava/nbio/core/sequence/reference/GenbankReference.java  | 2 +-
 .../nbio/core/sequence/reference/ReferenceInterface.java        | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/reference/AbstractReference.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/reference/AbstractReference.java
index 64c9792a0b..3c9958cb5c 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/reference/AbstractReference.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/reference/AbstractReference.java
@@ -22,7 +22,7 @@
 
 /**
  * @since 5.0.0
- * @Author Jim Tang
+ * @author Jim Tang
  */
 public abstract class AbstractReference implements ReferenceInterface {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/reference/GenbankReference.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/reference/GenbankReference.java
index 9e67dcb0fa..ff8db13727 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/reference/GenbankReference.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/reference/GenbankReference.java
@@ -24,7 +24,7 @@
  * For Genbank format file only.
  *
  * @since 5.0.0
- * @Author Jim Tang
+ * @author Jim Tang
  */
 public class GenbankReference extends AbstractReference {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/reference/ReferenceInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/reference/ReferenceInterface.java
index 2c3b8fa457..6c86cca96d 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/reference/ReferenceInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/reference/ReferenceInterface.java
@@ -22,7 +22,7 @@
 
 /**
  * @since 5.0.0
- * @Author Jim Tang
+ * @author Jim Tang
  */
 public interface ReferenceInterface {
 

From 13e3afef7566de8d5662eac8438c3dfa9edefa42 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Fri, 3 Jan 2025 14:52:33 -0800
Subject: [PATCH 10/90] Javadoc fix: all other errors in core module

---
 .../src/main/java/demo/UncompressFile.java    |  2 +-
 .../nbio/core/alignment/SimpleProfile.java    |  2 +-
 .../alignment/template/AlignedSequence.java   |  8 +--
 .../nbio/core/search/io/ResultFactory.java    |  7 +-
 .../biojava/nbio/core/search/io/SearchIO.java |  1 -
 .../nbio/core/sequence/CDSSequence.java       |  6 +-
 .../nbio/core/sequence/DataSource.java        |  2 +-
 .../nbio/core/sequence/edits/Edit.java        |  2 +-
 .../features/FeatureDbReferenceInfo.java      |  2 +-
 .../sequence/features/FeatureInterface.java   | 64 ++++++++-----------
 .../nbio/core/sequence/io/ABITrace.java       |  4 +-
 .../sequence/io/BufferedReaderBytesRead.java  |  4 +-
 .../CasePreservingProteinSequenceCreator.java | 15 +++--
 .../core/sequence/io/FastaWriterHelper.java   |  2 +-
 .../io/FileProxyDNASequenceCreator.java       |  3 +-
 .../io/FileProxyRNASequenceCreator.java       |  2 +-
 .../nbio/core/sequence/io/GenbankReader.java  |  2 +-
 .../sequence/io/GenbankSequenceParser.java    |  2 +-
 .../nbio/core/sequence/io/GenbankWriter.java  |  3 -
 .../io/GenericGenbankHeaderParser.java        |  2 +-
 .../nbio/core/sequence/io/IUPACParser.java    |  8 +--
 .../core/sequence/io/embl/EmblRecord.java     | 30 ++++-----
 .../io/template/SequenceParserInterface.java  |  6 +-
 .../nbio/core/sequence/io/util/IOUtils.java   |  4 +-
 .../loader/GenbankProxySequenceReader.java    |  6 +-
 .../loader/UniprotProxySequenceReader.java    |  1 -
 .../sequence/location/LocationHelper.java     |  2 +-
 .../sequence/location/template/Location.java  |  8 +--
 .../sequence/storage/BitSequenceReader.java   |  4 +-
 .../storage/SingleCompoundSequenceReader.java |  2 +-
 .../nbio/core/sequence/template/Compound.java | 20 +++---
 .../core/sequence/template/SequenceMixin.java |  4 +-
 .../core/sequence/transcription/Table.java    |  4 +-
 .../transcription/TranscriptionEngine.java    |  6 +-
 .../nbio/core/util/FileDownloadUtils.java     |  4 +-
 .../biojava/nbio/core/util/FlatFileCache.java |  2 +-
 .../core/util/StringManipulationHelper.java   |  2 +-
 .../org/biojava/nbio/core/util/XMLHelper.java |  2 +-
 .../SimpleGenbankProxySequenceReaderTest.java |  1 -
 39 files changed, 119 insertions(+), 132 deletions(-)

diff --git a/biojava-core/src/main/java/demo/UncompressFile.java b/biojava-core/src/main/java/demo/UncompressFile.java
index bd36ee5983..7258d6d18b 100644
--- a/biojava-core/src/main/java/demo/UncompressFile.java
+++ b/biojava-core/src/main/java/demo/UncompressFile.java
@@ -38,7 +38,7 @@ public class UncompressFile {
 	 * Reads a file, uncompresses it, and sends the result to stdout.
 	 * Also writes trivial statistics to stderr.
 	 * @param args An array with one String element, the name of the file to read.
-	 * @throws IOException for any failure
+	 * @throws Exception for any failure
 	 */
 	public static void main(String[] args) throws Exception {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java
index 4b853fcb37..7cfdb7dedc 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java
@@ -159,7 +159,7 @@ protected SimpleProfile(Profile<S, C> query, Profile<S, C> target, List<Step> sx
 	 /**
 	 * Creates a profile for the already aligned sequences.
 	 * @param alignedSequences the already aligned sequences
-	 * @throws IllegalArgument if aligned sequences differ in length or
+	 * @throws IllegalArgumentException if aligned sequences differ in length or
 	 * collection is empty.
 	 */
 	public SimpleProfile(Collection<AlignedSequence<S,C>> alignedSequences) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java
index 92fd972ec7..cbb959fd25 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java
@@ -39,7 +39,7 @@
 public interface AlignedSequence<S extends Sequence<C>, C extends Compound> extends Sequence<C> {
 
 	/**
-	 * Defines an alignment step in order to pass alignment information from an {@link Aligner} to a constructor.
+	 * Defines an alignment step in order to pass alignment information from an Aligner to a constructor.
 	 */
 	enum Step { COMPOUND, GAP }
 
@@ -66,7 +66,7 @@ enum Step { COMPOUND, GAP }
 	 *
 	 * @param sequenceIndex index in the original {@link Sequence}
 	 * @return column index within an alignment
-	 * @throws IndexOutOfBoundsException if sequenceIndex < 1 or sequenceIndex >
+	 * @throws IndexOutOfBoundsException if sequenceIndex &lt; 1 or sequenceIndex >
 	 *         {@link #getOriginalSequence()}.{@link #getLength()}
 	 */
 	int getAlignmentIndexAt(int sequenceIndex);
@@ -131,7 +131,7 @@ enum Step { COMPOUND, GAP }
 	 *
 	 * @param alignmentIndex column index within an alignment
 	 * @return index in the original {@link Sequence}
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	int getSequenceIndexAt(int alignmentIndex);
 
@@ -155,7 +155,7 @@ enum Step { COMPOUND, GAP }
 	 *
 	 * @param alignmentIndex column index within an alignment
 	 * @return true if this column has a gap
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	boolean isGap(int alignmentIndex);
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/ResultFactory.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/ResultFactory.java
index 479df1ac4d..d9279b8cce 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/ResultFactory.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/ResultFactory.java
@@ -34,7 +34,6 @@
  *
  * @author Paolo Pavan
  */
-
 public interface ResultFactory {
 	/**
 	 * returns a list of file extensions associated to this ResultFactory
@@ -49,7 +48,8 @@ public interface ResultFactory {
 	 *
 	 * @param maxEScore
 	 * @return
-	 * @throws Exception
+	 * @throws IOException
+	 * @throws ParseException
 	 */
 	List<Result> createObjects(double maxEScore) throws IOException, ParseException;
 	/**
@@ -57,7 +57,8 @@ public interface ResultFactory {
 	 * to a file in the same format that it is able to read.
 	 *
 	 * @param results
-	 * @throws Exception
+	 * @throws IOException
+	 * @throws ParseException
 	 */
 	void storeObjects(List<Result> results) throws IOException, ParseException;
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java
index 95ffb9fcfc..e864068afd 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java
@@ -64,7 +64,6 @@ public class SearchIO implements Iterable<Result>{
 	 * file extension.
 	 *
 	 * @param f
-	 * @throws Exception
 	 */
 	public SearchIO (File f)  throws IOException, ParseException{
 		factory = guessFactory(f);
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java
index f897622f3c..2fbd638b82 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java
@@ -32,7 +32,7 @@
  * Represents a exon or coding sequence in a gene. It has a parent {@link TranscriptSequence}
  * where a TranscriptSequence is the child of a GeneSequence
  * Not important for protein construction but the phase is used if outputting the gene
- * to a gff3 file. {@link http://www.sequenceontology.org/gff3.shtml}
+ * to a gff3 file. <a href="http://www.sequenceontology.org/gff3.shtml">http://www.sequenceontology.org/gff3.shtml</a>
  * @author Scooter Willis
  */
 public class CDSSequence extends DNASequence {
@@ -90,8 +90,8 @@ public Strand getStrand() {
 	 * A CDS sequence if negative stranded needs to be reverse complement
 	 * to represent the actual coding sequence. When getting a ProteinSequence
 	 * from a TranscriptSequence this method is callled for each CDSSequence
-	 * {@link http://www.sequenceontology.org/gff3.shtml}
-	 * {@link http://biowiki.org/~yam/bioe131/GFF.ppt}
+	 * <a href="http://www.sequenceontology.org/gff3.shtml">http://www.sequenceontology.org/gff3.shtml</a>
+	 * <a href="http://biowiki.org/~yam/bioe131/GFF.ppt">http://biowiki.org/~yam/bioe131/GFF.ppt</a>
 	 * @return coding sequence
 	 */
 	public String getCodingSequence() {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/DataSource.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/DataSource.java
index 367c00a889..9086382155 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/DataSource.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/DataSource.java
@@ -35,7 +35,7 @@
  * General database identifier       gnl|database|identifier
  * NCBI Reference Sequence           ref|accession|locus
  * Local Sequence identifier         lcl|identifier
- * </pr>
+ * </pre>
  * @author Scooter Willis 
  */
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/edits/Edit.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/edits/Edit.java
index edf891c4f7..e0d06eb0c7 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/edits/Edit.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/edits/Edit.java
@@ -114,7 +114,7 @@ protected void setSequence(Sequence<C> sequence) {
 		 * @param editingSequence Asked for in-case we need to do String to
 		 * Sequence conversion so we need a CompoundSet which is given
 		 * by the Sequence we are editing
-		 * @return The Sequence<C> object we wish to insert
+		 * @return The {@link Sequence<C>} object we wish to insert
 		 */
 		public Sequence<C> getTargetSequence(Sequence<C> editingSequence) {
 			if (sequence == null && stringSequence != null) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureDbReferenceInfo.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureDbReferenceInfo.java
index 3b49341d22..68b518b051 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureDbReferenceInfo.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureDbReferenceInfo.java
@@ -11,7 +11,7 @@
  * Copyright for this code is held jointly by the individual
  * authors.  These should be listed in @author doc comments.
  *
- * @author Jacek Grzebyta <github:jgrzebyta>
+ * @author Jacek Grzebyta &lt;github:jgrzebyta&gt;
  *
  * For more information on the BioJava project and its aims,
  * or to join the biojava-l mailing list, visit the home page
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureInterface.java
index c7b05cf5b9..8976953fd0 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureInterface.java
@@ -33,7 +33,7 @@
  * the surface of a protein where different sequence positions make up that feature. Ligand binding pocket is another example.
  * The location in its current form knows the start and stop position in a sequence and thus should contain knowledge about the
  * actual sequence.
- *
+ * <p>
  * A feature can contain features to handle cases where a domain is a feature and the secondary structures covered by that domain
  * and other requirements for grouping.
  *
@@ -46,32 +46,26 @@ public interface FeatureInterface<S extends AbstractSequence<C>, C extends Compo
 	 * Get the short description that can be used to describe the feature
 	 * @return
 	 */
-
-	public String getShortDescription();
+	String getShortDescription();
 
 	/**
 	 * Set the short description that can be used to describe the feature
 	 * @param shortDescription
 	 */
+	void setShortDescription(String shortDescription);
 
-	public void setShortDescription(String shortDescription);
-
-	  /**
+	 /**
 	 * Get the description that can be used to describe the feature
 	 * @return
 	 */
+	String getDescription();
 
-	public String getDescription();
-
-
-	  /**
+	 /**
 	 * Set the description that can be used to describe the feature
-	 * @return
 	 */
+	void setDescription(String description);
 
-	public void setDescription(String description);
-
-		/**
+	/**
 	 * The location(s) of this feature where the location should contain a reference to parent and sequence etc.
 	 * <p>
 	 * The location may be complicated, or simply a range.
@@ -80,7 +74,7 @@ public interface FeatureInterface<S extends AbstractSequence<C>, C extends Compo
 	 *
 	 * @return a Location anchoring this feature
 	 */
-	public AbstractLocation getLocations();
+	AbstractLocation getLocations();
 
 		/**
 	 * The new location for this feature.
@@ -93,14 +87,14 @@ public interface FeatureInterface<S extends AbstractSequence<C>, C extends Compo
 	 * @param loc the new Location for this feature
 	 *
 	 */
-	public void setLocation(AbstractLocation loc);
+	void setLocation(AbstractLocation loc);
 
-		/**
+	/**
 	 * The type of the feature.
 	 *
 	 * @return the type of this sequence
 	 */
-	public String getType();
+	String getType();
 
 	/**
 	 * Change the type of this feature.
@@ -108,15 +102,15 @@ public interface FeatureInterface<S extends AbstractSequence<C>, C extends Compo
 	 * @param type  new type String
 	 *
 	 */
-	public void setType(String type);
+	void setType(String type);
 
 
-		/**
+	/**
 	 * The source of the feature. This may be a program or process.
 	 *
 	 * @return the source, or generator
 	 */
-	public String getSource();
+	String getSource();
 
 	/**
 	 * Change the source of the FeatureInterface.
@@ -124,66 +118,60 @@ public interface FeatureInterface<S extends AbstractSequence<C>, C extends Compo
 	 * @param source the new source String
 	 *
 	 */
-	public void setSource(String source);
+	void setSource(String source);
 
 	/**
 	 * Set the parent feature
 	 * @param feature
 	 */
-
-	public void setParentFeature(FeatureInterface<S, C> feature);
+	void setParentFeature(FeatureInterface<S, C> feature);
 
 	/**
 	 * Get the parent feature
 	 * @return
 	 */
-
-	public FeatureInterface<S, C> getParentFeature();
+	FeatureInterface<S, C> getParentFeature();
 
 	/**
 	 * Get the features contained by this feature
 	 * @return
 	 */
-
-	public List<FeatureInterface<S, C>> getChildrenFeatures();
+	List<FeatureInterface<S, C>> getChildrenFeatures();
 
 	/**
 	 * Set the children features
 	 * @param features
 	 */
+	void setChildrenFeatures(List<FeatureInterface<S, C>> features);
 
-	public void setChildrenFeatures(List<FeatureInterface<S, C>> features);
 
-
-		/**
+	/**
 	 * @return the userObject
 	 */
-	public Object getUserObject();
+	Object getUserObject();
 
 	/**
 	 * @param userObject the userObject to set
 	 */
-	public void setUserObject(Object userObject);
-
+	void setUserObject(Object userObject);
 
 	/**
 	 * Get the qualifiers for this feature
 	 * @return
 	 */
 
-	public Map<String, List<Qualifier>> getQualifiers();
+	Map<String, List<Qualifier>> getQualifiers();
 
 	/**
 	 * Set the qualifiers
 	 * @param qualifiers
 	 */
+	void setQualifiers(Map<String, List<Qualifier>> qualifiers);
 
-	public void setQualifiers(Map<String, List<Qualifier>> qualifiers);
 	/**
 	 * Add a qualifier
 	 * @param qualifier
 	 */
-
-	public void addQualifier(String key, Qualifier qualifier);
+	void addQualifier(String key, Qualifier qualifier);
 
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java
index ea6f9abe1c..9561e21660 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java
@@ -171,9 +171,9 @@ public int[] getQcalls() {
 	}
 
 	/**
-	 * Returns the original programmatically determined (unedited) sequence as a <code>AbstractSequence<NucleotideCompound></code>.
+	 * Returns the original programmatically determined (unedited) sequence as a {@link AbstractSequence<NucleotideCompound>}.
 	 *
-	 * @return AbstractSequence<NucleotideCompound> sequence
+	 * @return sequence
 	 */
 	public AbstractSequence<NucleotideCompound> getSequence() throws CompoundNotFoundException {
 		DNASequenceCreator creator = new DNASequenceCreator(ABITracerCompoundSet.getABITracerCompoundSet());
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.java
index 998bbada13..30aa52c5d7 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.java
@@ -174,7 +174,7 @@ private void fill() throws IOException {
 	 * Reads a single character.
 	 *
 	 * @return The character read, as an integer in the range
-	 *         0 to 65535 (<tt>0x00-0xffff</tt>), or -1 if the
+	 *         0 to 65535 (<code>0x00-0xffff</code>), or -1 if the
 	 *         end of the stream has been reached
 	 * @exception  IOException  If an I/O error occurs
 	 */
@@ -521,7 +521,7 @@ public boolean markSupported() {
 	 *                         whose size is no smaller than limit.
 	 *                         Therefore large values should be used with care.
 	 *
-	 * @exception  IllegalArgumentException  If readAheadLimit is < 0
+	 * @exception  IllegalArgumentException  If readAheadLimit is &lt; 0
 	 * @exception  IOException  If an I/O error occurs
 	 */
 	@Override
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.java
index 94b2a6d918..0fb731ab10 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.java
@@ -41,14 +41,15 @@
  * <p>The user collection will be the same length as the resulting ProteinSequence.
  * Each object can be cast to a Boolean. If true, the corresponding position in
  * the input file was uppercase.
- *
- * <h3>Example</h3>
- * <code><pre>CasePreservingProteinSequenceCreator creator =
+ * <p>
+ * Example
+ * <code>
+ *    CasePreservingProteinSequenceCreator creator =
  *    new CasePreservingProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet());
- *AbstractSequence<AminoAcidCompound> seq = creator.getSequence("aaAA",0);
- *System.out.println(seq.getSequenceAsString()); //"AAAA"
- *System.out.println(seq.getUserCollection()); //"[false, false, true, true]"
- *</code></pre>
+ *    AbstractSequence&lt;AminoAcidCompound&gt; seq = creator.getSequence("aaAA",0);
+ *    System.out.println(seq.getSequenceAsString()); //"AAAA"
+ *    System.out.println(seq.getUserCollection()); //"[false, false, true, true]"
+ * </code>
  */
 public class CasePreservingProteinSequenceCreator extends ProteinSequenceCreator {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java
index b4200b89c2..364260d9a2 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java
@@ -96,7 +96,7 @@ public static void writeGeneSequence(File file, Collection<GeneSequence> geneSeq
 	/**
 	 * Write a collection of GeneSequences to a file where if the gene is negative strand it will flip and complement the sequence
 	 * @param outputStream
-	 * @param dnaSequences
+	 * @param geneSequences
 	 * @throws Exception
 	 */
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java
index 52d11f9953..96317cecdd 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java
@@ -56,8 +56,9 @@ public class FileProxyDNASequenceCreator implements
 
 	/**
 	 * Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
-	 * @param fastaFile
+	 * @param file
 	 * @param compoundSet
+	 * @param sequenceParser
 	 */
 	public FileProxyDNASequenceCreator(File file,
 			CompoundSet<NucleotideCompound> compoundSet,
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java
index d5c9b45f0e..53de88bb06 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java
@@ -56,7 +56,7 @@ public class FileProxyRNASequenceCreator implements
 
 	/**
 	 * Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
-	 * @param fastaFile
+	 * @param file
 	 * @param compoundSet
 	 */
 	public FileProxyRNASequenceCreator(File file,
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java
index 31f99eab8a..7f67918377 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java
@@ -12,7 +12,7 @@
  * authors.  These should be listed in @author doc comments.
  *
  * @author Scooter Willis ;lt;willishf at gmail dot com&gt;
- * @author Karl Nicholas <github:karlnicholas>
+ * @author Karl Nicholas &lt;github:karlnicholas&gt;
  * @author Paolo Pavan
  *
  * For more information on the BioJava project and its aims,
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java
index 90653612e7..7b7f0e1450 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java
@@ -17,7 +17,7 @@
  * @author Bubba Puryear
  * @author George Waldon
  * @author Deepak Sheoran
- * @author Karl Nicholas <github:karlnicholas>
+ * @author Karl Nicholas &lt;github:karlnicholas&gt;
  * @author Jacek Grzebyta
  * @author Paolo Pavan
  *
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriter.java
index c99a9c23fd..9d47db3bbd 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriter.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriter.java
@@ -69,7 +69,6 @@ public GenbankWriter(OutputStream os, Collection<S> sequences,
 	 * @param headerFormat
 	 * @param lineLength
 	 */
-
 	public GenbankWriter(OutputStream os, Collection<S> sequences,
 			GenbankHeaderFormatInterface<S, C> headerFormat, int lineLength) {
 		this.os = os;
@@ -82,9 +81,7 @@ public GenbankWriter(OutputStream os, Collection<S> sequences,
 	 * Allow an override of operating system line separator for programs that
 	 * needs a specific CRLF or CR or LF option
 	 *
-	 * @param lineSeparator
 	 */
-
 	public void process() throws Exception {
 		// Loosely based on code from Howard Salis
 		// TODO - Force lower case?
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java
index 7b1dc0524d..4fd6354110 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java
@@ -11,7 +11,7 @@
  * Copyright for this code is held jointly by the individual
  * authors.  These should be listed in @author doc comments.
  *
- * @author Karl Nicholas <github:karlnicholas>
+ * @author Karl Nicholas &lt;github:karlnicholas&gt;
  *
  * For more information on the BioJava project and its aims,
  * or to join the biojava-l mailing list, visit the home page
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java
index 0f9b3ca950..65e9d96830 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java
@@ -266,7 +266,7 @@ public boolean isStart(AminoAcidCompound compound) {
 		 * @param aminoAcids The target amino acid compounds objects
 		 */
 				@Override
-		public List<Codon> getCodons(CompoundSet<NucleotideCompound> nucelotides,
+		public List<Codon> getCodons(CompoundSet<NucleotideCompound> nucleotides,
 				CompoundSet<AminoAcidCompound> aminoAcids) {
 
 			if (this.codons.isEmpty()) {
@@ -277,9 +277,9 @@ public List<Codon> getCodons(CompoundSet<NucleotideCompound> nucelotides,
 				for (int i = 0; i < aminoAcidStrings.size(); i++) {
 
 					List<String> codonString    = codonStrings.get(i);
-					NucleotideCompound one      = getCompound(codonString, 0, nucelotides);
-					NucleotideCompound two      = getCompound(codonString, 1, nucelotides);
-					NucleotideCompound three    = getCompound(codonString, 2, nucelotides);
+					NucleotideCompound one      = getCompound(codonString, 0, nucleotides);
+					NucleotideCompound two      = getCompound(codonString, 1, nucleotides);
+					NucleotideCompound three    = getCompound(codonString, 2, nucleotides);
 					boolean start               = ("M".equals(startCodonStrings.get(i)));
 					boolean stop                = ("*".equals(aminoAcidStrings.get(i)));
 					AminoAcidCompound aminoAcid = aminoAcids
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblRecord.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblRecord.java
index 1e84382b54..46497b5a0d 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblRecord.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblRecord.java
@@ -64,7 +64,7 @@ public class EmblRecord {
 	 * 6. Taxonomic division
 	 * 7. Sequence length
 	 *
-	 * @return EmblId
+	 * @return
 	 */
 	public EmblId getEmblId() {
 		return emblId;
@@ -80,7 +80,7 @@ public void setEmblId(EmblId emblId) {
 	 * The citations provide access to the papers from which the data has been
 	 * abstracted.
 	 *
-	 * @return EmblReference
+	 * @return
 	 */
 	public List<EmblReference> getEmblReference() {
 		return emblReference;
@@ -94,7 +94,7 @@ public void setEmblReference(List<EmblReference> emblReference) {
 	 * The AC (Accession number) line lists the accession numbers associated with
 	 * the entry.
 	 *
-	 * @return List<String>
+	 * @return
 	 */
 	public List<String> getAccessionNumber() {
 		return accessionNumber;
@@ -119,7 +119,7 @@ public void setProjectIdentifier(String projectIdentifier) {
 	 * The OG (OrGanelle) linetype indicates the sub-cellular location of non-nuclear
 	 * sequences.
 	 *
-	 * @return String
+	 * @return
 	 */
 	public String getOrGanelle() {
 		return orGanelle;
@@ -132,7 +132,7 @@ public void setOrGanelle(String orGanelle) {
 	/**
 	 * The DT  line shows when an entry first appeared in the database
 	 *
-	 * @return String
+	 * @return
 	 */
 	public String getCreatedDate() {
 		return createdDate;
@@ -146,7 +146,7 @@ public void setCreatedDate(String createdDate) {
 	 * The FH (Feature Header) lines are present only to improve readability of
 	 * an entry when it is printed or displayed on a terminal screen.
 	 *
-	 * @return String
+	 * @return
 	 */
 	public String getFeatureHeader() {
 		return featureHeader;
@@ -161,7 +161,7 @@ public void setFeatureHeader(String featureHeader) {
 	 * sequence data. Regions or sites in the sequence which are of interest are
 	 * listed in the table.
 	 *
-	 * @return String
+	 * @return
 	 */
 	public String getFeatureTable() {
 		return featureTable;
@@ -190,7 +190,7 @@ public void setLastUpdatedDate(String lastUpdatedDate) {
 	 * sequence codes, the region of the genome from which it is derived, or other
 	 * information which helps to identify the sequence.
 	 *
-	 * @return String
+	 * @return
 	 */
 	public String getSequenceDescription() {
 		return sequenceDescription;
@@ -205,7 +205,7 @@ public void setSequenceDescription(String sequenceDescription) {
 	 * cross-reference indexes of the sequence entries based on functional,
 	 * structural, or other categories deemed important.
 	 *
-	 * @return List<String>
+	 * @return
 	 */
 	public List<String> getKeyword() {
 		return keyword;
@@ -235,7 +235,7 @@ public void setOrganismSpecies(String organismSpecies) {
 	 * The OC (Organism Classification) lines contain the taxonomic classification
 	 * Of the source organism
 	 *
-	 * @return String
+	 * @return
 	 */
 	public String getOrganismClassification() {
 		return organismClassification;
@@ -249,7 +249,7 @@ public void setOrganismClassification(String organismClassification) {
 	 * The DR (Database Cross-reference) line cross-references other databases which
 	 * contain information related to the entry in which the DR line appears.
 	 *
-	 * @return String
+	 * @return
 	 */
 	public String getDatabaseCrossReference() {
 		return databaseCrossReference;
@@ -262,7 +262,7 @@ public void setDatabaseCrossReference(String databaseCrossReference) {
 	/**
 	 * The AH (Assembly Header) line provides column headings for the assembly information.
 	 *
-	 * @return String
+	 * @return
 	 */
 	public String getAssemblyHeader() {
 		return assemblyHeader;
@@ -290,7 +290,7 @@ public void setAssemblyInformation(String assemblyInformation) {
 	 * Con(structed) sequences in the CON data classes represent complete
 	 * chromosomes, genomes and other long sequences constructed from segment entries.
 	 *
-	 * @return String
+	 * @return
 	 */
 	public String getConstructedSequence() {
 		return constructedSequence;
@@ -304,7 +304,7 @@ public void setConstructedSequence(String constructedSequence) {
 	 * The SQ (SeQuence header) line marks the beginning of the sequence data and
 	 * Gives a summary of its content.
 	 *
-	 * @return String
+	 * @return
 	 */
 	public String getSequenceHeader() {
 		return sequenceHeader;
@@ -317,7 +317,7 @@ public void setSequenceHeader(String sequenceHeader) {
 	/**
 	 * The Sequence Data Line
 	 *
-	 * @return String
+	 * @return
 	 */
 	public String getSequence() {
 		return sequence;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java
index 9950c450eb..82b2cab38b 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java
@@ -32,10 +32,10 @@
 public interface SequenceParserInterface {
 	/**
 	 *
-	 * @param dataInput
+	 * @param bufferedReader
 	 * @param sequenceLength
 	 * @return
-	 * @throws Exception
+	 * @throws IOException
 	 */
-	public String getSequence(BufferedReader bufferedReader,int sequenceLength) throws IOException;
+	String getSequence(BufferedReader bufferedReader,int sequenceLength) throws IOException;
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java
index b60bc9eb00..fe3dfcd42a 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java
@@ -157,7 +157,7 @@ public static List<String> getList(File file) throws IOException {
 	 *
 	 * @param file File which may or may not be GZipped
 	 * @return The final stream
-	 * @throws IOExceptio n
+	 * @throws IOException
 	 */
 	public static InputStream openFile(File file) throws IOException {
 		final InputStream is;
@@ -178,7 +178,7 @@ public static InputStream openFile(File file) throws IOException {
 
 	/**
 	 * Closure interface used when working with
-	 * {@link IOUtils#processReader(String)}. Each time a line is encountered
+	 * {@link IOUtils#processReader(BufferedReader, ReaderProcessor)}. Each time a line is encountered
 	 * the object that implements this interface will be invoked.
 	 *
 	 * @author ayates
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
index d3e6c52661..f443472aad 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
@@ -11,7 +11,7 @@
  * Copyright for this code is held jointly by the individual
  * authors.  These should be listed in @author doc comments.
  *
- * @author Karl Nicholas <github:karlnicholas>
+ * @author Karl Nicholas &lt;github:karlnicholas&gt;
  *
  * For more information on the BioJava project and its aims,
  * or to join the biojava-l mailing list, visit the home page
@@ -42,8 +42,8 @@
 import java.util.Map;
 
 /**
- * @author Karl Nicholas <github:karlnicholas>
- * @author Jacek Grzebyta <github:jgrzebyta>
+ * @author Karl Nicholas &lt;github:karlnicholas&gt;
+ * @author Jacek Grzebyta &lt;github:jgrzebyta&gt;
  */
 public class GenbankProxySequenceReader<C extends Compound> extends StringProxySequenceReader<C> implements FeaturesKeyWordInterface, DatabaseReferenceInterface, FeatureRetriever {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java
index f1cd7a7471..38feabdbf5 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java
@@ -120,7 +120,6 @@ public UniprotProxySequenceReader(Document document, CompoundSet<C> compoundSet)
 	 * @param xml
 	 * @param compoundSet
 	 * @return UniprotProxySequenceReader
-	 * @throws Exception
 	 */
 	public static <C extends Compound> UniprotProxySequenceReader<C> parseUniprotXMLString(String xml, CompoundSet<C> compoundSet) {
 		try {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java
index f164e5b7b8..38f96d7d08 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java
@@ -113,7 +113,7 @@ public static Location location(int start, int end, Strand strand, int length) {
 	 * other location builder this allows you to express your input
 	 * location on the reverse strand
 	 *
-	 * @param location The location which currently expresses the outer
+	 * @param start The location which currently expresses the outer
 	 * bounds of a circular location.
 	 * @param length The length of the circular genomic unit
 	 * @return The circular location; can optionally return a normal non
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java
index b0887bf706..266f9a6f1b 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java
@@ -71,7 +71,7 @@ public interface Location extends Iterable<Location>, Accessioned {
 	/**
 	 * Gives access to the sub locations for this location. However this does
 	 * not return sub-locations of sub-locations. For that functionality use
-	 * {@link #getAllSubLocations()}.
+	 * {@link #getRelevantSubLocations()}.
 	 *
 	 * @return A list of a single level of sub-locations
 	 */
@@ -107,7 +107,7 @@ public interface Location extends Iterable<Location>, Accessioned {
 	 * Will return a SequenceReader object which represents the outer bounds
 	 * of this Location
 	 *
-	 * @param &lt;C&gt; The type of compound to use
+	 * @param <C> The type of compound to use
 	 * @param sequence The sequence object to work with
 	 * @return The sequence
 	 */
@@ -118,7 +118,7 @@ public interface Location extends Iterable<Location>, Accessioned {
 	 * locations i.e. those locations which are not complex and define the
 	 * true Sequence represented
 	 *
-	 * @param &lt;C&gt; The type of compound to use
+	 * @param <C> The type of compound to use
 	 * @param sequence The sequence object to work with
 	 * @return The full assembled sequence
 	 */
@@ -166,7 +166,7 @@ public static Location location(int start, int end, Strand strand, int length) {
 		 * other location builder this allows you to express your input
 		 * location on the reverse strand
 		 *
-		 * @param location The location which currently expresses the outer
+		 * @param start The location which currently expresses the outer
 		 * bounds of a circular location.
 		 * @param length The length of the circular genomic unit
 		 * @return The circular location; can optionally return a normal non
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java
index 4c1f064ea6..8ca85aeec3 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java
@@ -64,7 +64,7 @@ public BitSequenceReader(BitArrayWorker<C> worker, AccessionID accession) {
 	}
 
 	/**
-	 * Class is immutable & so this is unsupported
+	 * Class is immutable, so this is unsupported
 	 */
 	@Override
 	public void setCompoundSet(CompoundSet<C> compoundSet) {
@@ -72,7 +72,7 @@ public void setCompoundSet(CompoundSet<C> compoundSet) {
 	}
 
 	/**
-	 * Class is immutable & so this is unsupported
+	 * Class is immutable, so this is unsupported
 	 */
 	@Override
 	public void setContents(String sequence) throws CompoundNotFoundException {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java
index b02c1e0c77..fd492f1bf9 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java
@@ -168,7 +168,7 @@ public AccessionID getAccession() {
 	}
 
 	/**
-	 * Delegates to {@link SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[]) }
+	 * Delegates to {@link SequenceMixin#countCompounds}
 	 */
 
 	@Override
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/Compound.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/Compound.java
index 6dbeda2208..aa04cb8c8a 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/Compound.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/Compound.java
@@ -28,21 +28,23 @@
 
 public interface Compound {
 
-	public boolean equalsIgnoreCase(Compound compound);
+	boolean equalsIgnoreCase(Compound compound);
 
-	public String getDescription();
+	String getDescription();
 
-	public void setDescription(String description);
+	void setDescription(String description);
 
-	public String getShortName();
+	String getShortName();
 
-	public void setShortName(String shortName);
+	void setShortName(String shortName);
 
-	public String getLongName();
+	String getLongName();
 
-	public void setLongName(String longName);
+	void setLongName(String longName);
 
-	public Float getMolecularWeight();
+	Float getMolecularWeight();
 
-	public void setMolecularWeight(Float molecularWeight);
+	void setMolecularWeight(Float molecularWeight);
+
+	String toString();
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java
index 3d75261d87..a71c9ba6f8 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java
@@ -150,7 +150,7 @@ public static <C extends Compound> Map<C, Integer> getComposition(Sequence<C> se
 	 * converting to a full length String and then writing the data out
 	 *
 	 * @param <C> Type of compound
-	 * @param writer The writer to send data to
+	 * @param appendable The writer to send data to
 	 * @param sequence The sequence to write out
 	 * @throws IOException Thrown if we encounter a problem
 	 */
@@ -244,7 +244,7 @@ public static <C extends Compound> SequenceView<C> createSubSequence(
 	 * Implements sequence shuffling by first materializing the given
 	 * {@link Sequence} into a {@link List}, applying
 	 * {@link Collections#shuffle(List)} and then returning the shuffled
-	 * elements in a new instance of {@link SequenceBackingStore} which behaves
+	 * elements in a new instance of {@link Sequence} which behaves
 	 * as a {@link Sequence}.
 	 */
 	public static <C extends Compound> Sequence<C> shuffle(Sequence<C> sequence) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Table.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Table.java
index 7d75a10d6a..bb86de83c9 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Table.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Table.java
@@ -57,8 +57,8 @@ CompoundSet<Codon> getCodonCompoundSet(
 	/**
 	 * Instance of a Codon which is 3 {@link NucleotideCompound}s, its
 	 * corresponding {@link AminoAcidCompound} and if it is a start or stop codon.
-	 * The object implements hashCode & equals but according to the nucleotide
-	 * compounds & not to the designation of it being a start, stop & amino
+	 * The object implements hashCode &amp; equals but according to the nucleotide
+	 * compounds &amp; not to the designation of it being a start, stop &amp; amino
 	 * acid compound
 	 *
 	 * @author ayates
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.java
index 162d760f05..f79bd0465e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.java
@@ -39,7 +39,7 @@
  * Protein sequence.
  *
  * In order to build one look at @ TranscriptionEngine.Builder} which provides
- * intelligent defaults & allows you to build an engine which is nearly the same
+ * intelligent defaults and allows you to build an engine which is nearly the same
  * as the default one but with a few changes. All of the engine is customisable.
  *
  * By default the code will attempt to:
@@ -48,7 +48,7 @@
  * <li>Trim Stops</li>
  * <li>Convert initiating codons to M</li>
  * <li>Allow for the fuzzy translation of Codons i.e. if it contains an N that
- * produces a {@link Sequence}&lt;{@link{AminoAcidCompound}&gt; with an X at
+ * produces a {@link Sequence<AminoAcidCompound>} with an X at
  * that position
  * </ul>
  *
@@ -170,7 +170,7 @@ public CompoundSet<AminoAcidCompound> getAminoAcidCompounds() {
 	}
 
 	/**
-	 * This class is the way to create a {@link TranslationEngine}.
+	 * This class is the way to create a {@link TranscriptionEngine}.
 	 */
 	public static class Builder {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
index 00cb2c923f..0b132b180e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
@@ -336,8 +336,8 @@ public static boolean ping(String url, int timeout) {
 	 * </code>
 	 * <p>
 	 *
-	 * <bold>NB. User should execute connect() method before getting input
-	 * stream.</bold>
+	 * <strong>NB. User should execute connect() method before getting input
+	 * stream.</strong>
 	 * @return
 	 * @throws IOException
 	 * @author Jacek Grzebyta
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java
index 110c355b4a..5df00ea661 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java
@@ -123,7 +123,7 @@ public  static InputStream getInputStream(String key){
 
 	/**
 	 * Returns the number of items in the cache.
-	 * If the cache is {@}, returns -1
+	 * If the cache is empty, returns -1
 	 * @return
 	 */
 	public static int size() {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java
index c7b27cc752..1ddadf695c 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java
@@ -77,7 +77,7 @@ private StringManipulationHelper() {
 	 * <li> Any IOException reading the stream is 'squashed' and not made
 	 *   available to caller
 	 * <li> An additional newline is appended at the end of the string.
-	 * <ul>
+	 * </ul>
 	 * @author andreas
 	 * @param stream
 	 * @return a possibly empty but non-null String
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLHelper.java
index 64aee3849a..9b895ef492 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLHelper.java
@@ -164,7 +164,7 @@ public static Element selectParentElement(Element element, String parentName) {
 	/**
 	 * If {@code}xpathExpression{@code} is a plain string with no '/' characterr, this is 
 	 * interpreted as a child element name to search for. 
-	 * <b/>
+	 * <p>
 	 * If {@code}xpathExpression{@code} is an XPath expression, this is evaluated and is assumed
 	 * to identify a single element.
 	 * @param element
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java
index 4150e90ffc..072e25a1e4 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java
@@ -34,7 +34,6 @@
  *
  * @author Jacek Grzebyta
  * @author Paolo Pavan
- * @see InfoTask
  */
 public class SimpleGenbankProxySequenceReaderTest {
 

From 71fe179011fbd17a04876da57a4e4f49f0845338 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Fri, 3 Jan 2025 15:30:12 -0800
Subject: [PATCH 11/90] Javadoc fix: all error in alignment module

---
 .../biojava/nbio/alignment/Alignments.java    | 26 +++++++-------
 .../alignment/FractionalIdentityScorer.java   |  2 +-
 .../alignment/FractionalSimilarityScorer.java |  2 +-
 .../SimpleProfileProfileAligner.java          |  2 +-
 .../alignment/io/StockholmFileAnnotation.java |  2 +-
 .../nbio/alignment/io/StockholmStructure.java | 11 ++++--
 .../AnchoredPairwiseSequenceAligner.java      |  4 +--
 .../alignment/routines/GuanUberbacher.java    |  2 +-
 .../template/AbstractMatrixAligner.java       |  2 +-
 .../AbstractPairwiseSequenceAligner.java      |  2 +-
 .../AbstractProfileProfileAligner.java        |  2 +-
 .../nbio/alignment/template/Aligner.java      |  2 +-
 .../CallablePairwiseSequenceAligner.java      |  2 +-
 .../CallableProfileProfileAligner.java        |  4 +--
 .../alignment/template/MatrixAligner.java     |  4 +--
 .../template/PairInProfileScorer.java         |  2 +-
 .../template/PairwiseSequenceAligner.java     |  2 +-
 .../alignment/template/PartitionRefiner.java  |  6 ++--
 .../template/ProfileProfileAligner.java       |  6 ++--
 .../template/ProfileProfileScorer.java        |  2 +-
 .../alignment/template/RescoreRefiner.java    |  6 ++--
 .../org/biojava/nbio/phylo/Comparison.java    |  4 +--
 .../nbio/phylo/DistanceMatrixCalculator.java  | 36 +++++++++----------
 23 files changed, 69 insertions(+), 64 deletions(-)

diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java
index 6cc2eb3f35..b389504826 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java
@@ -122,7 +122,7 @@ private Alignments() { }
 	 * {@link ConcurrencyTools} utility.
 	 *
 	 * @param <S> each {@link Sequence} of an alignment pair is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param sequences the {@link List} of {@link Sequence}s to align
 	 * @param type chosen type from list of pairwise sequence alignment routines
 	 * @param gapPenalty the gap penalties used during alignment
@@ -203,7 +203,7 @@ public static <S extends Sequence<C>, C extends Compound> Profile<S, C> getMulti
 	 * Factory method which computes a sequence alignment for the given {@link Sequence} pair.
 	 *
 	 * @param <S> each {@link Sequence} of the pair is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param query the first {@link Sequence}s to align
 	 * @param target the second {@link Sequence}s to align
 	 * @param type chosen type from list of pairwise sequence alignment routines
@@ -223,7 +223,7 @@ public static <S extends Sequence<C>, C extends Compound> SequencePair<S, C> get
 	 * Factory method which sets up a sequence alignment for all {@link Sequence} pairs in the given {@link List}.
 	 *
 	 * @param <S> each {@link Sequence} of an alignment pair is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param sequences the {@link List} of {@link Sequence}s to align
 	 * @param type chosen type from list of pairwise sequence alignment routines
 	 * @param gapPenalty the gap penalties used during alignment
@@ -309,7 +309,7 @@ static <E> List<E> getListFromFutures(List<Future<E>> futures) {
 	 * Factory method which constructs a pairwise sequence aligner.
 	 *
 	 * @param <S> each {@link Sequence} of an alignment pair is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param query the first {@link Sequence} to align
 	 * @param target the second {@link Sequence} to align
 	 * @param type chosen type from list of pairwise sequence alignment routines
@@ -399,7 +399,7 @@ static <S extends Sequence<C>, C extends Compound> PairwiseSequenceScorer<S, C>
 	 * Factory method which constructs a profile-profile aligner.
 	 *
 	 * @param <S> each {@link Sequence} of an alignment profile is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param profile1 the first {@link Profile} to align
 	 * @param profile2 the second {@link Profile} to align
 	 * @param type chosen type from list of profile-profile alignment routines
@@ -429,7 +429,7 @@ static <S extends Sequence<C>, C extends Compound> ProfileProfileAligner<S, C> g
 	 * Factory method which constructs a profile-profile aligner.
 	 *
 	 * @param <S> each {@link Sequence} of an alignment profile is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param profile1 the first {@link Profile} to align
 	 * @param profile2 the second {@link Profile} to align
 	 * @param type chosen type from list of profile-profile alignment routines
@@ -459,7 +459,7 @@ static <S extends Sequence<C>, C extends Compound> ProfileProfileAligner<S, C> g
 	 * Factory method which constructs a profile-profile aligner.
 	 *
 	 * @param <S> each {@link Sequence} of an alignment profile is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param profile1 the first {@link Profile} to align
 	 * @param profile2 the second {@link Profile} to align
 	 * @param type chosen type from list of profile-profile alignment routines
@@ -489,7 +489,7 @@ static <S extends Sequence<C>, C extends Compound> ProfileProfileAligner<S, C> g
 	 * Factory method which constructs a profile-profile aligner.
 	 *
 	 * @param <S> each {@link Sequence} of an alignment profile is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param profile1 the first {@link Profile} to align
 	 * @param profile2 the second {@link Profile} to align
 	 * @param type chosen type from list of profile-profile alignment routines
@@ -519,7 +519,7 @@ static <S extends Sequence<C>, C extends Compound> ProfileProfileAligner<S, C> g
 	 * Factory method which computes a profile alignment for the given {@link Profile} pair.
 	 *
 	 * @param <S> each {@link Sequence} of the {@link Profile} pair is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param profile1 the first {@link Profile} to align
 	 * @param profile2 the second {@link Profile} to align
 	 * @param type chosen type from list of profile-profile alignment routines
@@ -539,7 +539,7 @@ static <S extends Sequence<C>, C extends Compound> ProfilePair<S, C> getProfileP
 	 * of the {@link ConcurrencyTools} utility.
 	 *
 	 * @param <S> each {@link Sequence} of the {@link Profile} pair is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param tree guide tree to follow aligning profiles from leaves to root
 	 * @param type chosen type from list of profile-profile alignment routines
 	 * @param gapPenalty the gap penalties used during alignment
@@ -592,7 +592,7 @@ public static <S extends Sequence<C>, C extends Compound> Profile<S, C> getProgr
 	 * submitting all of the alignment tasks to the shared thread pool of the {@link ConcurrencyTools} utility.
 	 *
 	 * @param <S> each {@link Sequence} of an alignment pair is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param aligners list of alignments to run
 	 * @return list of {@link SequencePair} results from running alignments
 	 */
@@ -612,7 +612,7 @@ public static <S extends Sequence<C>, C extends Compound> Profile<S, C> getProgr
 	 * all of the scoring tasks to the shared thread pool of the {@link ConcurrencyTools} utility.
 	 *
 	 * @param <S> each {@link Sequence} of an alignment pair is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param scorers list of scorers to run
 	 * @return list of score results from running scorers
 	 */
@@ -637,7 +637,7 @@ public static <S extends Sequence<C>, C extends Compound> double[] runPairwiseSc
 	 * submitting all of the alignment tasks to the shared thread pool of the {@link ConcurrencyTools} utility.
 	 *
 	 * @param <S> each {@link Sequence} of the {@link Profile} pair is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param aligners list of alignments to run
 	 * @return list of {@link ProfilePair} results from running alignments
 	 */
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java
index 4b494db779..d66105681d 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java
@@ -34,7 +34,7 @@
  *
  * @author Mark Chapman
  * @param <S> each {@link Sequence} of the alignment pair is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public class FractionalIdentityScorer<S extends Sequence<C>, C extends Compound> extends AbstractScorer
 		implements PairwiseSequenceScorer<S, C> {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java
index 05911367f8..e9581f1f96 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java
@@ -34,7 +34,7 @@
  *
  * @author Mark Chapman
  * @param <S> each {@link Sequence} of the alignment pair is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public class FractionalSimilarityScorer<S extends Sequence<C>, C extends Compound> extends AbstractScorer
 		implements PairwiseSequenceScorer<S, C> {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java
index 47fb7976e0..ff94041bb8 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java
@@ -41,7 +41,7 @@
  *
  * @author Mark Chapman
  * @param <S> each {@link Sequence} in the pair of alignment {@link Profile}s is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public class SimpleProfileProfileAligner<S extends Sequence<C>, C extends Compound>
 		extends AbstractProfileProfileAligner<S, C> {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileAnnotation.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileAnnotation.java
index f0ca2bfa23..5b7ff9899b 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileAnnotation.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileAnnotation.java
@@ -160,7 +160,7 @@ public void setDbReferences(Set<DatabaseReference> dbReferences) {
 		this.dbReferences = dbReferences;
 	}
 	/**
-	 * @param dbReference the string without the initial annotation identifier ( #=GS DR )
+	 * @param dbReferenceRepresentingString the string without the initial annotation identifier ( #=GS DR )
 	 */
 	public void addDBReference(String dbReferenceRepresentingString) {
 		if (this.dbReferences == null) {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java
index d95a2bfa97..a70e751df5 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java
@@ -38,7 +38,8 @@
  * In general, Stockholm File contains the alignment mark-up lines.<br>
  * <br>
  *
- * <Table border="1" align="center">
+ * <table>
+ * <caption></caption>
  * <tr>
  * <td><b>Header Section</b></td>
  * </tr>
@@ -56,18 +57,24 @@
  * Sequence letters may include any characters except whitespace. Gaps may be indicated by "." or "-".<br>
  * Mark-up lines may include any characters except whitespace. Use underscore ("_") instead of space.<br>
  *
- * <Table border="1">
+ * <table>
+ * <caption></caption>
+ * <tr>
  * <th>section field</th>
  * <th>preferred location</th>
+ * </tr>
  * <tr>
  * <td>#=GF &lt;feature&gt; &lt;Generic per-File annotation, free text&gt;</td>
  * <td>Above the alignment</td>
+ * </tr>
  * <tr>
  * <td>#=GC &lt;feature&gt; &lt;Generic per-Column annotation, exactly 1 char per column&gt;</td>
  * <td>Below the alignment</td>
+ * </tr>
  * <tr>
  * <td>#=GS &lt;seqname&gt; &lt;feature&gt; &lt;Generic per-Sequence annotation, free text&gt;</td>
  * <td>Above the alignment or just below the corresponding sequence</td>
+ * </tr>
  * <tr>
  * <td>#=GR &lt;seqname&gt; &lt;feature&gt; &lt;Generic per-Residue annotation, exactly 1 char per residue&gt;</td>
  * <td>Just below the corresponding sequence</td>
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java
index 95d5264f1e..8533ecc91e 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java
@@ -42,7 +42,7 @@
  * will connect the query sequence to the target sequence at the <em>anchors</em>.  This class performs such global
  * sequence comparisons efficiently by dynamic programming with a space requirement reduced from quadratic (a multiple
  * of query sequence length times target sequence length) to only linear (a multiple of query sequence length).  The
- * counterpoint to this reduction in space complexity is a modest (a multiple < 2) increase in time.
+ * counterpoint to this reduction in space complexity is a modest (a multiple &lt; 2) increase in time.
  *
  * @author Mark Chapman
  * @author Daniel Cameron
@@ -67,7 +67,6 @@ public AnchoredPairwiseSequenceAligner() {
 	 * @param target the second {@link Sequence} of the pair to align
 	 * @param gapPenalty the gap penalties used during alignment
 	 * @param subMatrix the set of substitution scores used during alignment
-	 * @param cutsPerSection the number of cuts added to each section during each pass
 	 */
 	public AnchoredPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix) {
 		this(query, target, gapPenalty, subMatrix, null);
@@ -80,7 +79,6 @@ public AnchoredPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty,
 	 * @param target the second {@link Sequence} of the pair to align
 	 * @param gapPenalty the gap penalties used during alignment
 	 * @param subMatrix the set of substitution scores used during alignment
-	 * @param cutsPerSection the number of cuts added to each section during each pass
 	 * @param anchors the initial list of anchors
 	 */
 	public AnchoredPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix, int[] anchors) {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java
index 3ff44d8a8c..7e2d739db9 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java
@@ -34,7 +34,7 @@
  * {@link Compound} of each {@link Sequence}).  This class performs such global sequence comparisons efficiently by
  * dynamic programming with a space requirement reduced from quadratic (a multiple of query sequence length times
  * target sequence length) to only linear (a multiple of query sequence length).  The counterpoint to this reduction in
- * space complexity is a modest (a multiple < 2) increase in time.
+ * space complexity is a modest (a multiple &lt; 2) increase in time.
  *
  * @author Mark Chapman
  * @param <S> each {@link Sequence} of the alignment pair is of type S
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java
index 19fcc9c98f..1ea2e0de81 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java
@@ -46,7 +46,7 @@
  * @author Mark Chapman
  * @author Daniel Cameron
  * @param <S> each element of the alignment {@link Profile} is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public abstract class AbstractMatrixAligner<S extends Sequence<C>, C extends Compound> extends AbstractScorer
 		implements MatrixAligner<S, C> {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.java
index 8c86470608..699ff77d36 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.java
@@ -37,7 +37,7 @@
  *
  * @author Mark Chapman
  * @param <S> each {@link Sequence} of the alignment pair is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public abstract class AbstractPairwiseSequenceAligner<S extends Sequence<C>, C extends Compound>
 		extends AbstractMatrixAligner<S, C> implements PairwiseSequenceAligner<S, C> {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java
index 01cba48463..140627de9c 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java
@@ -43,7 +43,7 @@
  *
  * @author Mark Chapman
  * @param <S> each {@link Sequence} in the pair of alignment {@link Profile}s is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public abstract class AbstractProfileProfileAligner<S extends Sequence<C>, C extends Compound>
 		extends AbstractMatrixAligner<S, C> implements ProfileProfileAligner<S, C> {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/Aligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/Aligner.java
index 75ec8b4df8..76e735c031 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/Aligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/Aligner.java
@@ -32,7 +32,7 @@
  *
  * @author Mark Chapman
  * @param <S> each element of the alignment {@link Profile} is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public interface Aligner<S extends Sequence<C>, C extends Compound> extends Scorer {
 
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.java
index e1c4616620..7201513800 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.java
@@ -34,7 +34,7 @@
  *
  * @author Mark Chapman
  * @param <S> each {@link Sequence} of the alignment pair is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public class CallablePairwiseSequenceAligner<S extends Sequence<C>, C extends Compound>
 		implements Callable<SequencePair<S, C>> {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java
index 063426a91a..042138f144 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java
@@ -33,8 +33,8 @@
  * Implements a concurrency wrapper for a {@link ProfileProfileAligner}.
  *
  * @author Mark Chapman
- * @param <S> each {@link Sequence} of the {@link Profile} pair is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <S> each {@link Sequence} of the profile pair is of type S
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public class CallableProfileProfileAligner<S extends Sequence<C>, C extends Compound>
 		implements Callable<ProfilePair<S, C>> {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java
index 87f9f504ce..dd8e38ceeb 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java
@@ -30,8 +30,8 @@
  * Defines an {@link Aligner} which builds a score matrix during computation.
  *
  * @author Mark Chapman
- * @param <S> each element of the alignment {@link Profile} is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <S> each element of the alignment profile is of type S
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public interface MatrixAligner<S extends Sequence<C>, C extends Compound> extends Aligner<S, C> {
 
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairInProfileScorer.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairInProfileScorer.java
index 094a18bead..4166bcfef4 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairInProfileScorer.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairInProfileScorer.java
@@ -32,7 +32,7 @@
  *
  * @author Mark Chapman
  * @param <S> each {@link Sequence} of the alignment pair is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public interface PairInProfileScorer<S extends Sequence<C>, C extends Compound> extends PairwiseSequenceScorer<S, C> {
 
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairwiseSequenceAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairwiseSequenceAligner.java
index 696ff6ecd8..960c3a527b 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairwiseSequenceAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairwiseSequenceAligner.java
@@ -32,7 +32,7 @@
  *
  * @author Mark Chapman
  * @param <S> each {@link Sequence} of the alignment pair is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public interface PairwiseSequenceAligner<S extends Sequence<C>, C extends Compound> extends Aligner<S, C>,
 		PairwiseSequenceScorer<S, C> {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java
index 573944b413..124f2ff132 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java
@@ -28,11 +28,11 @@
 import org.biojava.nbio.core.sequence.template.Sequence;
 
 /**
- * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning.
+ * Defines an algorithm which computes a new alignment profile by splitting a current alignment and realigning.
  *
  * @author Mark Chapman
- * @param <S> each element of the alignment {@link Profile} is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <S> each element of the alignment profile is of type S
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public interface PartitionRefiner<S extends Sequence<C>, C extends Compound> extends Aligner<S, C>,
 		ProfileProfileScorer<S, C> {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java
index 6df23e0909..1e6fe7cccf 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java
@@ -28,11 +28,11 @@
 import org.biojava.nbio.core.sequence.template.Sequence;
 
 /**
- * Defines an {@link Aligner} for a pair of {@link Profile}s.
+ * Defines an {@link Aligner} for a pair of profiles.
  *
  * @author Mark Chapman
- * @param <S> each {@link Sequence} in the pair of alignment {@link Profile}s is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <S> each {@link Sequence} in the pair of alignment profiles is of type S
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public interface ProfileProfileAligner<S extends Sequence<C>, C extends Compound> extends Aligner<S, C>,
 		ProfileProfileScorer<S, C> {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileScorer.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileScorer.java
index 1d114841ee..c525b9c75a 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileScorer.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileScorer.java
@@ -32,7 +32,7 @@
  *
  * @author Mark Chapman
  * @param <S> each {@link Sequence} in the pair of alignment {@link Profile}s is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public interface ProfileProfileScorer<S extends Sequence<C>, C extends Compound> extends Scorer {
 
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java
index dba02a028c..f93c000380 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java
@@ -29,12 +29,12 @@
 import org.biojava.nbio.core.sequence.template.Sequence;
 
 /**
- * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and
+ * Defines an algorithm which computes a new alignment profile by rescoring all pairs in an alignment and
  * realigning.
  *
  * @author Mark Chapman
- * @param <S> each element of the alignment {@link Profile} is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <S> each element of the alignment profile is of type S
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public interface RescoreRefiner<S extends Sequence<C>, C extends Compound> extends Aligner<S, C> {
 
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java
index dc8ead79a7..9cae7734cb 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java
@@ -38,9 +38,9 @@ public class Comparison {
 	/**
 	 * this is a gapped PID calculation
 	 *
-	 * @param s1
+	 * @param seq1
 	 *            SequenceI
-	 * @param s2
+	 * @param seq2
 	 *            SequenceI
 	 * @return float
 	 */
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java
index d0464bae8b..922f301a8c 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java
@@ -54,9 +54,9 @@ private DistanceMatrixCalculator() {}
 	 * that differ between two aligned sequences. The percentage of identity
 	 * (PID) is the fraction of identical sites between two aligned sequences.
 	 *
-	 * <pre>
+	 * <code>
 	 * D = 1 - PID
-	 * </pre>
+	 * </code>
 	 *
 	 * The gapped positons in the alignment are ignored in the calculation. This
 	 * method is a wrapper to the forester implementation of the calculation:
@@ -65,7 +65,7 @@ private DistanceMatrixCalculator() {}
 	 * @param msa
 	 *            MultipleSequenceAlignment
 	 * @return DistanceMatrix
-	 * @throws Exception
+	 * @throws IOException
 	 */
 	public static <C extends Sequence<D>, D extends Compound> DistanceMatrix fractionalDissimilarity(
 			MultipleSequenceAlignment<C, D> msa) throws IOException {
@@ -81,9 +81,9 @@ public static <C extends Sequence<D>, D extends Compound> DistanceMatrix fractio
 	 * The Poisson (correction) evolutionary distance (d) is a function of the
 	 * fractional dissimilarity (D), given by:
 	 *
-	 * <pre>
+	 * <code>
 	 * d = -log(1 - D)
-	 * </pre>
+	 * </code>
 	 *
 	 * The gapped positons in the alignment are ignored in the calculation. This
 	 * method is a wrapper to the forester implementation of the calculation:
@@ -109,14 +109,14 @@ public static <C extends Sequence<D>, D extends Compound> DistanceMatrix poisson
 	 * dissimilarity (D) specially needed for large evolutionary distances. It
 	 * is given by:
 	 *
-	 * <pre>
+	 * <code>
 	 * d = -log(1 - D - 0.2 * D<sup>2</sup>)
-	 * </pre>
+	 * </code>
 	 *
 	 * The equation is derived by fitting the relationship between the
 	 * evolutionary distance (d) and the fractional dissimilarity (D) according
 	 * to the PAM model of evolution (it is an empirical approximation for the
-	 * method {@link #pamDistance(MultipleSequenceAlignment}). The gapped
+	 * method {@link #pamMLdistance(MultipleSequenceAlignment)}). The gapped
 	 * positons in the alignment are ignored in the calculation. This method is
 	 * a wrapper to the forester implementation of the calculation:
 	 * {@link PairwiseDistanceCalculator#calcKimuraDistances(Msa)}.
@@ -190,9 +190,9 @@ public static <C extends Sequence<D>, D extends Compound> DistanceMatrix percent
 	 * The fractional dissimilarity score (Ds) is a relative measure of the
 	 * dissimilarity between two aligned sequences. It is calculated as:
 	 *
-	 * <pre>
+	 * <code>
 	 * Ds = sum( max(M) - M<sub>ai,bi</sub> ) / (max(M)-min(M)) ) / L
-	 * </pre>
+	 * </code>
 	 *
 	 * Where the sum through i runs for all the alignment positions, ai and bi
 	 * are the AA at position i in the first and second aligned sequences,
@@ -270,9 +270,9 @@ public static <C extends Sequence<D>, D extends Compound> DistanceMatrix fractio
 	 * maximum similarity score between self-alignments (each sequence against
 	 * itself). Calculation of the score is as follows:
 	 *
-	 * <pre>
+	 * <code>
 	 * Ds = maxScore - sum<sub>i</sub>(M<sub>ai,bi</sub>)
-	 * </pre>
+	 * </code>
 	 *
 	 * It is recommended to use the method
 	 * {@link #fractionalDissimilarityScore(MultipleSequenceAlignment, SubstitutionMatrix)}
@@ -362,9 +362,9 @@ public static <C extends Sequence<D>, D extends Compound> DistanceMatrix dissimi
 	 * substitution rate of 1% per site. The fractional dissimilarity (D) of two
 	 * aligned sequences is related with the PAM distance (d) by the equation:
 	 *
-	 * <pre>
+	 * <code>
 	 * D = sum(fi * (1 - M<sub>ii</sub><sup>d</sup>))
-	 * </pre>
+	 * </code>
 	 *
 	 * Where the sum is for all 20 AA, fi denotes the natural fraction of the
 	 * given AA and M is the substitution matrix (in this case the PAM1 matrix).
@@ -373,9 +373,9 @@ public static <C extends Sequence<D>, D extends Compound> DistanceMatrix dissimi
 	 * likelihood (ML) approach is used, which consists in finding d that
 	 * maximazies the function:
 	 *
-	 * <pre>
+	 * <code>
 	 * L(d) = product(f<sub>ai</sub> * (1 - M<sub>ai,bi</sub><sup>d</sup>))
-	 * </pre>
+	 * </code>
 	 *
 	 * Where the product is for every position i in the alignment, and ai and bi
 	 * are the AA at position i in the first and second aligned sequences,
@@ -400,11 +400,11 @@ public static <C extends Sequence<D>, D extends Compound> DistanceMatrix pamMLdi
 	 * strutures. It is based on the diffusive model for protein fold evolution
 	 * (Grishin 1995). The structural deviations are captured as RMS deviations.
 	 *
-	 * <pre>
+	 * <code>
 	 * d<sub>Sij</sub> = (rmsd<sub>max</sub><sup>2</sup> / alpha<sup>2</sup>) *
 	 *        ln( (rmsd<sub>max</sub><sup>2</sup> - rmsd<sub>0</sub><sup>2</sup>) /
 	 *        (rmsd<sub>max</sub><sup>2</sup> - (rmsd<sub>ij</sub><sup>2</sup>) )
-	 * </pre>
+	 * </code>
 	 *
 	 * @param rmsdMat
 	 *            RMSD matrix for all structure pairs (symmetric matrix)

From ed7ab8e32d958730568898f733fccd0f0d42273d Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Fri, 3 Jan 2025 15:42:32 -0800
Subject: [PATCH 12/90] Javadoc fix: a few errors from structure module

---
 .../main/java/org/biojava/nbio/structure/BondImpl.java    | 4 ++--
 .../src/main/java/org/biojava/nbio/structure/Calc.java    | 4 ++--
 .../src/main/java/org/biojava/nbio/structure/Chain.java   | 8 +++++---
 .../org/biojava/nbio/structure/align/multiple/Block.java  | 3 +--
 .../biojava/nbio/structure/align/multiple/BlockImpl.java  | 2 --
 .../nbio/structure/align/multiple/BlockSetImpl.java       | 2 --
 .../java/org/biojava/nbio/structure/io/BondMaker.java     | 2 ++
 .../nbio/structure/io/StructureSequenceMatcher.java       | 5 ++---
 .../nbio/structure/quaternary/BioAssemblyTools.java       | 5 ++---
 .../structure/quaternary/BiologicalAssemblyBuilder.java   | 2 ++
 .../biojava/nbio/structure/symmetry/internal/CeSymm.java  | 3 +--
 11 files changed, 19 insertions(+), 21 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java
index 3c5fd7af68..78d38559f7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java
@@ -44,7 +44,7 @@ public class BondImpl implements Bond {
 	 * Note that by forming a bond between atoms 'A' and 'B' with this
 	 * constructor, atoms 'A' and 'B' will be updated to have this bond in their
 	 * list of bonds. If you do not want this automatic updating, instead use
-	 * {@link #Bond(Atom, Atom, int, boolean)} with the
+	 * {@link Bond(Atom, Atom, int, boolean)} with the
 	 * <code>addSelfToAtoms</code> flag set to <code>false</code>.
 	 *
 	 * @param atomA one of the atoms in this bond
@@ -83,7 +83,7 @@ public BondImpl(Atom atomA, Atom atomB, int bondOrder, boolean addSelfToAtoms) {
 	 * include this bond.
 	 * <p>
 	 * If you created your Bond with the constructor
-	 * {@link #Bond(Atom, Atom, int)}, this method has already been called for
+	 * {@link Bond(Atom, Atom, int)}, this method has already been called for
 	 * you and should not be called again.
 	 */
 	// TODO first check if those bonds haven't been made already
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
index b6fde44843..8c92f876f0 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
@@ -327,9 +327,9 @@ public static final double getPsi(AminoAcid a, AminoAcid b)
 	}
 
 	/**
-	 * Test if two amino acids are connected, i.e. if the distance from C to N <
+	 * Test if two amino acids are connected, i.e. if the distance from C to N &lt;
 	 * 2.5 Angstrom.
-	 *
+	 * <p>
 	 * If one of the AminoAcids has an atom missing, returns false.
 	 *
 	 * @param a
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java
index 6ceba9fd61..0d067373ca 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java
@@ -199,7 +199,7 @@ public interface Chain extends Serializable {
 	 * @return the length
 	 * @see #getAtomGroup(int)
 	 * @see #getAtomGroups()
-	 * @see #getSeqResLength())
+	 * @see #getSeqResLength()
 	 */
 	int getAtomLength();
 
@@ -346,18 +346,20 @@ public interface Chain extends Serializable {
 
 	/**
 	 * Get the predominant {@link GroupType} for a given Chain, following these
-	 * rules: <li>if the ratio of number of residues of a certain
+	 * rules:
+	 * <ul>
+	 * <li>if the ratio of number of residues of a certain
 	 * {@link GroupType} to total non-water residues is above the threshold
 	 * {@value org.biojava.nbio.structure.StructureTools#RATIO_RESIDUES_TO_TOTAL}, then that {@link GroupType} is
 	 * returned</li> <li>if there is no {@link GroupType} that is above the
 	 * threshold then the {@link GroupType} with most members is chosen, logging
 	 * it</li>
+	 * </ul>
 	 * <p>
 	 * See also {@link ChemComp#getPolymerType()} and
 	 * {@link ChemComp#getResidueType()} which follow the PDB chemical component
 	 * dictionary and provide a much more accurate description of groups and
 	 * their linking.
-	 * </p>
 	 *
 	 * @return the predominant group type
 	 */
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java
index c41e31e1c5..2bf5df80c6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java
@@ -72,7 +72,7 @@ public interface Block extends ScoresCache {
 	 * alignRes.get(structure).get(residue) = alignRes.get(size).get(length).
 	 *
 	 * @return List a double List of aligned residues for each structure.
-	 * @see #setAlignRes()
+	 * @see #setAlignRes(List)
 	 */
 	public List<List<Integer>> getAlignRes();
 
@@ -108,7 +108,6 @@ public interface Block extends ScoresCache {
 	 * Block.
 	 *
 	 * @return int number of aligned residues.
-	 * @see #updateCoreLength()
 	 * @see #length()
 	 * @see #size()
 	 */
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java
index becc817e85..e0423b6f8f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java
@@ -52,7 +52,6 @@ public class BlockImpl extends AbstractScoresCache implements Serializable,
 	 *
 	 * @param blockSet
 	 *            the parent BlockSet of the BlockImpl instance.
-	 * @return BlockImpl a BlockImpl instance linked to its parent BlockSet.
 	 */
 	public BlockImpl(BlockSet blockSet) {
 
@@ -69,7 +68,6 @@ public BlockImpl(BlockSet blockSet) {
 	 *
 	 * @param b
 	 *            BlockImpl object to be copied.
-	 * @return BlockImpl an identical copy of the input BlockImpl object.
 	 */
 	public BlockImpl(BlockImpl b) {
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java
index 5282f83b31..cbbb3ae895 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java
@@ -55,7 +55,6 @@ public class BlockSetImpl extends AbstractScoresCache implements Serializable,
 	 *
 	 * @param alignment
 	 *            MultipleAlignment parent of the BlockSet.
-	 * @return BlockSet an instance linked to the parent alignment.
 	 */
 	public BlockSetImpl(MultipleAlignment alignment) {
 
@@ -76,7 +75,6 @@ public BlockSetImpl(MultipleAlignment alignment) {
 	 *
 	 * @param bs
 	 *            BlockSet object to be copied.
-	 * @return BlockSet an identical copy of the input object.
 	 */
 	public BlockSetImpl(BlockSetImpl bs) {
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java
index a582f922d2..e6b8548025 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java
@@ -89,6 +89,7 @@ public BondMaker(Structure structure, FileParsingParameters params) {
 
 	/**
 	 * Creates bond objects and corresponding references in Atom objects:
+	 * <ul>
 	 * <li>
 	 * peptide bonds: inferred from sequence and distances
 	 * </li>
@@ -98,6 +99,7 @@ public BondMaker(Structure structure, FileParsingParameters params) {
 	 * <li>
 	 * intra-group (residue) bonds: read from the chemical component dictionary, via {@link org.biojava.nbio.structure.chem.ChemCompProvider}
 	 * </li>
+	 * </ul>
 	 */
 	public void makeBonds() {
 		logger.debug("Going to start making bonds");
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java
index fd06080118..fbc12ec9d3 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java
@@ -59,8 +59,7 @@ public class StructureSequenceMatcher {
 	 * @param sequence The input protein sequence
 	 * @param wholeStructure The structure from which to take a substructure
 	 * @return The resulting structure
-	 * @throws StructureException
-	 * @see {@link #matchSequenceToStructure(ProteinSequence, Structure)}
+	 * @see #matchSequenceToStructure(ProteinSequence, Structure)
 	 */
 	public static Structure getSubstructureMatchingProteinSequence(ProteinSequence sequence, Structure wholeStructure) {
 		ResidueNumber[] rns = matchSequenceToStructure(sequence, wholeStructure);
@@ -104,7 +103,7 @@ public static Structure getSubstructureMatchingProteinSequence(ProteinSequence s
 	 * @return A ProteinSequence with the full sequence of struct. Chains are
 	 *  concatenated in the same order as the input structures
 	 *
-	 * @see {@link SeqRes2AtomAligner#getFullAtomSequence(List, Map)}, which
+	 * @see SeqRes2AtomAligner#getFullAtomSequence(List, Map, boolean), which
 	 * 	does the heavy lifting.
 	 *
 	 */
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
index 95bcf1b402..7c359121de 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
@@ -262,12 +262,11 @@ public static double getBiologicalMoleculeMaximumExtend( final Structure structu
 
 	/**
 	 * Returns the centroid of the biological molecule.
-	 * @param structure
+	 * @param asymUnit
 	 * @return centroid
 	 * @throws IllegalArgumentException if structure is null
 	 */
-
-	public static double[] getBiologicalMoleculeCentroid( final Structure asymUnit,List<BiologicalAssemblyTransformation> transformations ) {
+	public static double[] getBiologicalMoleculeCentroid( final Structure asymUnit, List<BiologicalAssemblyTransformation> transformations ) {
 		if ( asymUnit == null ) {
 			throw new IllegalArgumentException( "null structure" );
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java
index f9597bbb7d..c6ec6bc8ff 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java
@@ -75,6 +75,7 @@ public BiologicalAssemblyBuilder(){
 	 * Builds a Structure object containing the quaternary structure built from given asymUnit and transformations,
 	 * by adding symmetry partners as new models.
 	 * The output Structure will be different depending on the multiModel parameter:
+	 * <ul>
 	 * <li>
 	 * the symmetry-expanded chains are added as new models, one per transformId. All original models but
 	 * the first one are discarded.
@@ -83,6 +84,7 @@ public BiologicalAssemblyBuilder(){
 	 * as original with symmetry-expanded chains added with renamed chain ids and names (in the form
 	 * originalAsymId_transformId and originalAuthId_transformId)
 	 * </li>
+	 * </ul>
 	 * @param asymUnit
 	 * @param transformations
 	 * @param useAsymIds if true use {@link Chain#getId()} to match the ids in the BiologicalAssemblyTransformation (needed if data read from mmCIF),
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java
index 43ee89c234..b8ea01d6a1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java
@@ -82,7 +82,6 @@ public class CeSymm {
 	 * <li>2.2 - run multiple symmetry levels recursively to find PG and
 	 * hierarchical symmetries.
 	 * </ul>
-	 * </li>
 	 */
 	public static final String version = "2.2";
 	public static final String algorithmName = "jCE-symm";
@@ -364,7 +363,7 @@ public static CeSymmResult analyze(Atom[] atoms) throws StructureException {
 	 *
 	 * @param atoms
 	 *            representative Atom array of the Structure
-	 * @param param
+	 * @param params
 	 *            CeSymmParameters bean
 	 * @return CeSymmResult
 	 * @throws StructureException

From 280f2398e7e287c8e3c41d3e09750fb9e0d285d8 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Fri, 3 Jan 2025 15:46:52 -0800
Subject: [PATCH 13/90] Javadoc fix: some more errors from structure module

---
 .../nbio/structure/align/ce/CeParameters.java | 19 ++++++++++++-------
 .../nbio/structure/align/multiple/Block.java  |  2 +-
 .../structure/align/multiple/BlockSet.java    |  2 +-
 .../nbio/structure/ecod/EcodInstallation.java |  4 ++--
 .../nbio/structure/geometry/CalcPoint.java    |  2 +-
 5 files changed, 17 insertions(+), 12 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java
index 106aa08090..b2e7177244 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java
@@ -342,7 +342,8 @@ public void setDistanceIncrement(Double distanceIncrement)
 
 
 
-	/** Get the Original RMSD threshold from which the alignment optimization is started
+	/**
+	 * Get the Original RMSD threshold from which the alignment optimization is started
 	 *
 	 * @return oRMSDThreshold
 	 */
@@ -353,7 +354,8 @@ public Double getORmsdThr()
 
 
 
-	/** Set the Original RMSD threshold from which the alignment optimization is started
+	/**
+	 * Set the Original RMSD threshold from which the alignment optimization is started
 	 *
 	 * @param oRmsdThr the threshold
 	 */
@@ -363,16 +365,17 @@ public void setORmsdThr(Double oRmsdThr)
 	}
 
 
-	/** Get the maximum nr of times the (slow) optimiziation of alignment should iterate. Default: unlimited
+	/**
+	 * Get the maximum nr of times the (slow) optimiziation of alignment should iterate. Default: unlimited
 	 *
-	 * @param maxNrIterationsForOptimization
 	 */
 	public int getMaxNrIterationsForOptimization() {
 		return maxNrIterationsForOptimization;
 	}
 
 
-	/** Set the maximum nr of times the (slow) optimiziation of alignment should iterate. Default: unlimited
+	/**
+	 * Set the maximum nr of times the (slow) optimiziation of alignment should iterate. Default: unlimited
 	 *
 	 * @param maxNrIterationsForOptimization
 	 */
@@ -381,7 +384,8 @@ public void setMaxNrIterationsForOptimization(int maxNrIterationsForOptimization
 	}
 
 
-	/** Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much.
+	/**
+	 * Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much.
 	 *  By default this is set to 0, meaning no contribution of the sequence alignment score.
 	 *
 	 * @return seqWeight the weight factor (default 0)
@@ -392,7 +396,8 @@ public double getSeqWeight() {
 	}
 
 
-	/** Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much.
+	/**
+	 * Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much.
 	 *  By default this is set to 0, meaning no contribution of the sequence alignment score.
 	 *
 	 * @param seqWeight the weight factor (default 0)
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java
index 2bf5df80c6..802d016c68 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java
@@ -89,7 +89,7 @@ public interface Block extends ScoresCache {
 	 * Returns the total number of aligned positions (columns) in the Block.
 	 *
 	 * @return int number of aligned residues.
-	 * @see #getCoreLength();
+	 * @see #getCoreLength()
 	 * @see #size()
 	 */
 	public int length();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSet.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSet.java
index 4fdf318c61..ed46d6bbe7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSet.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSet.java
@@ -111,7 +111,7 @@ public interface BlockSet extends ScoresCache {
 	 * This may trigger other properties to update which depend on the
 	 * superposition.
 	 *
-	 * @param matrices
+	 * @param transformations
 	 */
 	public void setTransformations(List<Matrix4d> transformations);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
index 2f9d27997a..f4be5cd4f5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
@@ -97,7 +97,7 @@ public class EcodInstallation implements EcodDatabase {
 	 * installations at the same path can lead to race conditions when downloading
 	 * files.
 	 * @param cacheLocation Location to save files, typically from the PDB_CACHE_DIR parameter
-	 * @param requestedVersion ECOD requestedVersion to fetch
+	 * @param version ECOD requestedVersion to fetch
 	 */
 	public EcodInstallation(String cacheLocation, String version) {
 		domainsFileLock = new ReentrantReadWriteLock();
@@ -295,7 +295,7 @@ public String getUrl() {
 
 	/**
 	 * Specify a different mirror for the ECOD server.
-	 * @param urlFormat the urlFormat to set
+	 * @param url the urlFormat to set
 	 */
 	public void setUrl(String url) {
 		this.url = url;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/CalcPoint.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/CalcPoint.java
index c1cfeb73e1..b0e440af31 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/CalcPoint.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/CalcPoint.java
@@ -40,7 +40,7 @@ private CalcPoint() {
 	}
 
 	/**
-	 * Center a cloud of points. This means subtracting the {@lin
+	 * Center a cloud of points. This means subtracting the {@link
 	 * #centroid(Point3d[])} of the cloud to each point.
 	 *
 	 * @param x

From 52d10538768889d97e23e5fe245434c956723091 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Fri, 3 Jan 2025 16:11:21 -0800
Subject: [PATCH 14/90] Javadoc fix: some more errors from structure module

---
 .../org/biojava/nbio/structure/Structure.java |  6 ------
 .../align/fatcat/calc/AFPChainer.java         |  6 +++---
 .../structure/align/util/AlignmentTools.java  | 19 ++++++++++---------
 .../structure/geometry/SuperPositionQCP.java  |  6 +++---
 .../biojava/nbio/structure/jama/Matrix.java   |  2 +-
 5 files changed, 17 insertions(+), 22 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java
index 5a31f407e2..8521044de7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java
@@ -65,7 +65,6 @@
  *
  *
  * <hr/>
- * </hr>
  * <p>
  * Q: How can I get a Structure object from a PDB file?
  * </p>
@@ -88,7 +87,6 @@
  *  </pre>
  *
  * <hr>
- * </hr>
  * <p>
  * Q: How can I calculate Phi and Psi angles of AminoAcids?
  * </p>
@@ -157,10 +155,6 @@
  * 		}
  * </pre>
  * <hr>
- * </hr>
- *
- *
- *
  *
  * @author Andreas Prlic
  * @since 1.4
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java
index 1d1628b51e..1e9e1cf7d7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java
@@ -39,17 +39,17 @@
 
 import javax.vecmath.Matrix4d;
 
-/** a class to chain AFPs to an alignment
+/**
+ * A class to chain AFPs to an alignment
  *
  * @author Andreas Prlic
- *
  */
 public class AFPChainer
 {
 	public static final boolean debug = FatCatAligner.debug;
 	// private static final boolean showAlig = false;
 
-	/**
+	/*
 	// Key function: chain (assembly) the AFPs
 	// a AFP (k) is defined as (i, j, k), with i and j are staring points
 	// AFP extension (eg. AFP(k-1) -> AFP(k) ) requiring
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
index 82d38d010c..f43a97392f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
@@ -72,7 +72,7 @@ public class AlignmentTools {
 	 * Since algorithms which create non-sequential alignments split the
 	 * alignment into multiple blocks, some computational time can be saved
 	 * by only checking block boundaries for sequentiality. Setting
-	 * <tt>checkWithinBlocks</tt> to <tt>true</tt> makes this function slower,
+	 * <code>checkWithinBlocks</code> to <code>true</code> makes this function slower,
 	 * but detects AFPChains with non-sequential blocks.
 	 *
 	 * Note that this method should give the same results as
@@ -209,7 +209,7 @@ public static <T> Map<T,T> applyAlignment(Map<T, T> alignmentMap, int k) {
 	 * @param <T>
 	 * @param alignmentMap The input function, as a map (see {@link AlignmentTools#alignmentAsMap(AFPChain)})
 	 * @param identity An identity-like function providing the isomorphism between
-	 *  the codomain of alignmentMap (of type <T>) and the domain (type <S>).
+	 *  the codomain of alignmentMap (of type T) and the domain (type S).
 	 * @param k The number of times to apply the alignment
 	 * @return A new alignment. If the input function is not automorphic
 	 *  (one-to-one), then some inputs may map to null, indicating that the
@@ -303,7 +303,7 @@ public static int getSymmetryOrder(Map<Integer, Integer> alignment,
 	 * identity. If <i>n</i> corresponds to the intrinsic order of the alignment,
 	 * this will be small. This algorithm tries increasing values of <i>n</i>
 	 * and looks for abrupt decreases in the root mean squared offset.
-	 * If none are found at <i>n</i><=maxSymmetry, the alignment is reported as
+	 * If none are found at <i>n</i>&lt;=maxSymmetry, the alignment is reported as
 	 * non-symmetric.
 	 *
 	 * @param alignment The alignment to test for symmetry
@@ -314,7 +314,7 @@ public static int getSymmetryOrder(Map<Integer, Integer> alignment,
 	 *  the calculation time and can lead to overfitting.
 	 * @param minimumMetricChange Percent decrease in root mean squared offsets
 	 *  in order to declare symmetry. 0.4f seems to work well for CeSymm.
-	 * @return The order of symmetry of alignment, or 1 if no order <=
+	 * @return The order of symmetry of alignment, or 1 if no order &lt;=
 	 *  maxSymmetry is found.
 	 *
 	 * @see IdentityMap For a simple identity function
@@ -472,7 +472,8 @@ public static Map<Integer, Integer> guessSequentialAlignment(
 	 * {@link AFPChain#getOptAln()}, but has the correct size().
 	 * <pre>
 	 * List<List<List<Integer>>> aln = getOptAlnAsList(AFPChain afpChain);
-	 * aln.get(blockNum).get(structureNum={0,1}).get(pos)</pre>
+	 * aln.get(blockNum).get(structureNum={0,1}).get(pos)
+	 * </pre>
 	 *
 	 * @param afpChain
 	 * @return
@@ -850,7 +851,7 @@ public static AFPChain replaceOptAln(AFPChain afpChain, Atom[] ca1, Atom[] ca2,
 	 * @param ca1
 	 * @param ca2 Second set of ca atoms. Will be modified based on the superposition
 	 * @throws StructureException
-	 * @see {@link CECalculator#calc_rmsd(Atom[], Atom[], int, boolean)}
+	 * @see CECalculator#calc_rmsd(Atom[], Atom[], int, boolean)
 	 *  contains much of the same code, but stores results in a CECalculator
 	 *  instance rather than an AFPChain
 	 */
@@ -979,12 +980,13 @@ public static Object resizeArray (Object oldArray, int newSize) {
 	 * <p>Note that more concise representations may be possible.</p>
 	 *
 	 * Examples:
+	 * <ul>
 	 * <li>1>2>3>1</li>
 	 * <li>1>2>3>2 4>3</li>
-	 *
+	 * </ul>
 	 * @param alignment The input function, as a map (see {@link AlignmentTools#alignmentAsMap(AFPChain)})
 	 * @param identity An identity-like function providing the isomorphism between
-	 *  the codomain of alignment (of type <T>) and the domain (type <S>).
+	 *  the codomain of alignment (of type T) and the domain (type S).
 	 * @return
 	 */
 	public static <S,T> String toConciseAlignmentString(Map<S,T> alignment, Map<T,S> identity) {
@@ -1197,7 +1199,6 @@ public static void alignmentToSIF(Writer out,AFPChain afpChain,
 	 * Does NOT rotate anything.
 	 * @param ca
 	 * @return a list of Chains that is built up from the Atoms in the ca array
-	 * @throws StructureException
 	 */
 	public static final List<Chain> getAlignedModel(Atom[] ca){
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQCP.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQCP.java
index bfb029bbe1..a36854a711 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQCP.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQCP.java
@@ -74,12 +74,12 @@
  * <p>
  * Citations:
  * <p>
- * Liu P, Agrafiotis DK, & Theobald DL (2011) Reply to comment on: "Fast
+ * Liu P, Agrafiotis DK, &amp; Theobald DL (2011) Reply to comment on: "Fast
  * determination of the optimal rotation matrix for macromolecular
  * superpositions." Journal of Computational Chemistry 32(1):185-186.
  * [http://dx.doi.org/10.1002/jcc.21606]
  * <p>
- * Liu P, Agrafiotis DK, & Theobald DL (2010) "Fast determination of the optimal
+ * Liu P, Agrafiotis DK, &amp; Theobald DL (2010) "Fast determination of the optimal
  * rotation matrix for macromolecular superpositions." Journal of Computational
  * Chemistry 31(7):1561-1563. [http://dx.doi.org/10.1002/jcc.21439]
  * <p>
@@ -96,7 +96,7 @@
  * <p>
  * dtheobald@brandeis.edu
  * <p>
- * Pu Liu Johnson & Johnson Pharmaceutical Research and Development, L.L.C. 665
+ * Pu Liu Johnson &amp; Johnson Pharmaceutical Research and Development, L.L.C. 665
  * Stockton Drive Exton, PA 19341 USA
  * <p>
  * pliu24@its.jnj.com
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/Matrix.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/Matrix.java
index 15bd130b99..2abdd1c972 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/Matrix.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/Matrix.java
@@ -53,7 +53,7 @@
  * 	decomposition classes.  These decompositions are accessed by the Matrix
  * 	class to compute solutions of simultaneous linear equations, determinants,
  * 	inverses and other matrix functions.  The five decompositions are:
- * <P><UL>
+ * <UL>
  * 	<LI>Cholesky Decomposition of symmetric, positive definite matrices.
  * 	<LI>LU Decomposition of rectangular matrices.
  * 	<LI>QR Decomposition of rectangular matrices.

From 5a5052428c88669d7bb31a92dcd2718c3cbb9788 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Mon, 6 Jan 2025 15:13:04 -0800
Subject: [PATCH 15/90] More lenient parsing if some fields are missing (e.g.
 in files output by Gemmi)

---
 .../nbio/structure/io/cif/CifStructureConsumerImpl.java   | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
index ca3906e4b2..b204687762 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
@@ -972,9 +972,9 @@ public void consumeStructRefSeq(StructRefSeq structRefSeq) {
 
             DBRef dbRef = new DBRef();
 
-            dbRef.setIdCode(structRefSeq.getPdbxPDBIdCode().get(rowIndex));
-            dbRef.setDbAccession(structRefSeq.getPdbxDbAccession().get(rowIndex));
-            dbRef.setDbIdCode(structRefSeq.getPdbxDbAccession().get(rowIndex));
+            dbRef.setIdCode(structRefSeq.getPdbxPDBIdCode().isDefined()? structRefSeq.getPdbxPDBIdCode().get(rowIndex):null);
+            dbRef.setDbAccession(structRefSeq.getPdbxDbAccession().isDefined()? structRefSeq.getPdbxDbAccession().get(rowIndex):null);
+            dbRef.setDbIdCode(structRefSeq.getPdbxDbAccession().isDefined()? structRefSeq.getPdbxDbAccession().get(rowIndex):null);
             dbRef.setChainName(structRefSeq.getPdbxStrandId().get(rowIndex));
 
             OptionalInt structRefRowIndex = IntStream.range(0, structRef.getRowCount())
@@ -1330,7 +1330,7 @@ private String getEntityType(String entityId) {
     private String getEntityDescription(String entityId) {
         return IntStream.range(0, entity.getRowCount())
                 .filter(i -> entity.getId().get(i).equals(entityId))
-                .mapToObj(i -> entity.getPdbxDescription().get(i))
+                .mapToObj(i -> entity.getPdbxDescription().isDefined()? entity.getPdbxDescription().get(i):"")
                 .findFirst()
                 .orElseThrow(() -> new NoSuchElementException("could not find entity with id " + entityId));
     }

From 2b33a56bd2fa555c62197ad8f81fff1f46722731 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Mon, 6 Jan 2025 15:27:11 -0800
Subject: [PATCH 16/90] Javadoc fix: many errors in struct align package

---
 .../align/multiple/MultipleAlignmentEnsemble.java      |  3 ---
 .../align/multiple/MultipleAlignmentEnsembleImpl.java  |  4 ----
 .../align/multiple/MultipleAlignmentImpl.java          |  3 ---
 .../structure/align/multiple/mc/MultipleMcMain.java    |  6 +++---
 .../align/multiple/mc/MultipleMcOptimizer.java         |  3 +--
 .../align/multiple/util/MultipleAlignmentScorer.java   |  4 ++--
 .../align/multiple/util/MultipleAlignmentTools.java    | 10 +++++-----
 .../align/multiple/util/MultipleAlignmentWriter.java   |  4 ++--
 8 files changed, 13 insertions(+), 24 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java
index d6358a825d..be1c46631c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java
@@ -147,7 +147,6 @@ public interface MultipleAlignmentEnsemble extends ScoresCache {
 	 * structure.
 	 *
 	 * @return List of Matrix interatomic distance matrices.
-	 * @see #updateDistanceMatrix()
 	 */
 	public List<Matrix> getDistanceMatrix();
 
@@ -155,7 +154,6 @@ public interface MultipleAlignmentEnsemble extends ScoresCache {
 	 * Returns the List of MultipleAlignments in the ensemble.
 	 *
 	 * @return List of MultipleAlignment in the ensemble.
-	 * @see #setMultipleAlignments()
 	 */
 	public List<MultipleAlignment> getMultipleAlignments();
 
@@ -165,7 +163,6 @@ public interface MultipleAlignmentEnsemble extends ScoresCache {
 	 * accessing an index of a List
 	 *
 	 * @return MultipleAlignment at the index in the ensemble.
-	 * @see #setMultipleAlignments()
 	 */
 	public MultipleAlignment getMultipleAlignment(int index);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java
index a6df171705..0f0b442a63 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java
@@ -67,7 +67,6 @@ public class MultipleAlignmentEnsembleImpl extends AbstractScoresCache
 	/**
 	 * Default Constructor. Empty ensemble, no structures assigned.
 	 *
-	 * @return MultipleAlignmentEnsemble an empty ensemble instance.
 	 */
 	public MultipleAlignmentEnsembleImpl() {
 
@@ -88,7 +87,6 @@ public MultipleAlignmentEnsembleImpl() {
 	 * @param structureIdentifiers
 	 *            List of Structure names, that can be parsed by
 	 *            {@link AtomCache}.
-	 * @return MultipleAlignmentEnsemble an ensemble with the structures.
 	 */
 	public MultipleAlignmentEnsembleImpl(
 			List<StructureIdentifier> structureIdentifiers) {
@@ -102,7 +100,6 @@ public MultipleAlignmentEnsembleImpl(
 	 *
 	 * @param e
 	 *            MultipleAlignmentEnsemble to copy.
-	 * @return MultipleAlignmentEnsemble identical copy of the input ensemble.
 	 */
 	public MultipleAlignmentEnsembleImpl(MultipleAlignmentEnsembleImpl e) {
 
@@ -153,7 +150,6 @@ public MultipleAlignmentEnsembleImpl(MultipleAlignmentEnsembleImpl e) {
 	 *            Atoms of the second structure
 	 * @param flexible
 	 *            true if the alignment is flexible (use BlockSets)
-	 * @return MultipleAlignmentEnsemble an ensemble
 	 */
 	public MultipleAlignmentEnsembleImpl(AFPChain afp, Atom[] ca1, Atom[] ca2,
 			boolean flexible) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java
index 7f55f1c2f0..f858f3082e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java
@@ -53,7 +53,6 @@ public class MultipleAlignmentImpl extends AbstractScoresCache implements
 	/**
 	 * Default Constructor. Empty alignment. No structures assigned.
 	 *
-	 * @return MultipleAlignment an empty MultipleAlignment instance.
 	 */
 	public MultipleAlignmentImpl() {
 		this(new MultipleAlignmentEnsembleImpl()); // assign an empty ensemble.
@@ -65,7 +64,6 @@ public MultipleAlignmentImpl() {
 	 *
 	 * @param ensemble
 	 *            parent MultipleAlignmentEnsemble.
-	 * @return MultipleAlignment an alignment instance part of an ensemble.
 	 */
 	public MultipleAlignmentImpl(MultipleAlignmentEnsemble ensemble) {
 
@@ -87,7 +85,6 @@ public MultipleAlignmentImpl(MultipleAlignmentEnsemble ensemble) {
 	 *
 	 * @param ma
 	 *            MultipleAlignmentImpl to copy.
-	 * @return MultipleAlignmentImpl identical copy of the alignment.
 	 */
 	public MultipleAlignmentImpl(MultipleAlignmentImpl ma) {
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.java
index 702ed1d6a5..e68cbe384e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.java
@@ -91,7 +91,7 @@ public class MultipleMcMain implements MultipleStructureAligner {
 	/**
 	 * Default constructor.
 	 * Default parameters are used.
-	 * @param pairwise the pairwise structure alignment used to generate the
+	 * @param pairwiseAlgo the pairwise structure alignment used to generate the
 	 * 			multiple alignment seed.
 	 */
 	public MultipleMcMain(StructureAlignment pairwiseAlgo){
@@ -177,7 +177,7 @@ private MultipleAlignment generateSeed(List<Atom[]> atomArrays)
 	 * lowest average RMSD against all others.
 	 * The index of this structure is returned.
 	 *
-	 * @param alignments List double containing all-to-all pairwise alignments
+	 * @param afpAlignments List double containing all-to-all pairwise alignments
 	 * @return int reference index
 	 */
 	private static int chooseReferenceRMSD(List<List<AFPChain>> afpAlignments){
@@ -209,7 +209,7 @@ private static int chooseReferenceRMSD(List<List<AFPChain>> afpAlignments){
 	 * It uses the blocks in AFPChain as {@link Block}s in the
 	 * MultipleAlignment, so considers non-topological
 	 * alignments, if the alignment is rigid. If the alignment is flexible,
-	 * it considers the blocks as {@link BlockSets}.
+	 * it considers the blocks as {@link BlockSet}s.
 	 *
 	 * @param afpList the list of pairwise alignments to the reference
 	 * @param atomArrays List of Atoms of the structures
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
index 664f251899..052f147fc6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
@@ -108,7 +108,6 @@ public class MultipleMcOptimizer implements Callable<MultipleAlignment> {
 	 *            the parameter beam
 	 * @param reference
 	 *            the index of the most similar structure to all others
-	 * @throws StructureException
 	 */
 	public MultipleMcOptimizer(MultipleAlignment seedAln,
 			MultipleMcParameters params, int reference) {
@@ -235,7 +234,7 @@ private void initialize() throws StructureException {
 	 * <li>Shrink Block: move a block column to the freePool.
 	 * <li>Insert gap: insert a gap in a random position of the alignment.
 	 * </ul>
-	 * </li>
+	 *
 	 */
 	public MultipleAlignment optimize() throws StructureException {
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java
index 1a9642e251..b17c5ae8f3 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java
@@ -304,7 +304,7 @@ public static double getAvgTMScore(List<Atom[]> transformed,
 	 * length.
 	 *
 	 * @param alignment
-	 * @param reference
+	 * @param ref
 	 *            Index of the reference structure
 	 * @return
 	 * @throws StructureException
@@ -427,7 +427,7 @@ public static double getMCScore(MultipleAlignment alignment,
 	 * Complexity: T(n,l) = O(l*n^2), if n=number of structures and l=alignment
 	 * length.
 	 *
-	 * @param transformed
+	 * @param trans
 	 *            List of transformed Atom arrays
 	 * @param d0
 	 *            parameter for the half-score distance
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java
index 52f926a5c6..7e46d3f115 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java
@@ -309,7 +309,7 @@ public static List<String> getSequenceAlignment(
 	 * Blocks is indicated by a gap in all positions, meaning that there is a
 	 * possible discontinuity.
 	 *
-	 * @param alignment
+	 * @param msa
 	 *            input MultipleAlignment
 	 * @return String for each row in the alignment, giving the 1-letter code
 	 *         for each aligned residue.
@@ -466,7 +466,7 @@ else if (previousPos[str] + 1 == residue) {
 	 * gap in all positions, meaning that there is something unaligned
 	 * inbetween.
 	 *
-	 * @param alignment
+	 * @param ma
 	 *            input MultipleAlignment
 	 * @return String for each row in the alignment, giving the 1-letter code
 	 *         for each aligned residue.
@@ -479,7 +479,7 @@ public static List<String> getBlockSequenceAlignment(MultipleAlignment ma) {
 	 * Returns the Atom of the specified structure that is aligned in the
 	 * sequence alignment position specified.
 	 *
-	 * @param multAln
+	 * @param msa
 	 *            the MultipleAlignment object from where the sequence alignment
 	 *            has been generated
 	 * @param mapSeqToStruct
@@ -568,7 +568,7 @@ public static int getBlockForSequencePosition(MultipleAlignment multAln,
 	 * Complexity: T(n,l) = O(l*n^2), if n=number of structures and l=alignment
 	 * length.
 	 *
-	 * @param alignment
+	 * @param msa
 	 *            MultipleAlignment
 	 * @return Matrix containing all average residue distances
 	 */
@@ -644,7 +644,7 @@ public static Matrix getAverageResidueDistances(List<Atom[]> transformed) {
 	 * <p>
 	 * For each structure in the alignment, returns an atom for each
 	 * representative atom in the aligned columns, omitting unaligned residues
-	 * (i.e. an array of length <tt>alignment.length()</tt> ).
+	 * (i.e. an array of length <code>alignment.length()</code> ).
 	 * <p>
 	 * All blocks are concatenated together, so Atoms may not appear in the same
 	 * order as in their parent structure. If the alignment blocks contain null
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java
index 7db5d2e714..771b8b5f68 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java
@@ -194,7 +194,7 @@ public static String toAlignedResidues(MultipleAlignment multAln) {
 	 * Converts the transformation Matrices of the alignment into a String
 	 * output.
 	 *
-	 * @param afpChain
+	 * @param alignment
 	 * @return String transformation Matrices
 	 */
 	public static String toTransformMatrices(MultipleAlignment alignment) {
@@ -289,7 +289,7 @@ public static String toXML(MultipleAlignmentEnsemble ensemble)
 	 * ATOM   2004  CA  ARG     4      32.662 -25.111   7.172  132 ARG
 	 * ATOM   2005  CA  GLY     5      29.121 -25.194   8.602  133 ARG
 	 *
-	 * Column 1 -30: Atom & Residue records of query sequence.
+	 * Column 1 -30: Atom and Residue records of query sequence.
 	 * Column 31-54: Coordinates of atoms in query copied from corresponding atoms in template.
 	 * Column 55-59: Corresponding residue number in template based on alignment
 	 * Column 60-64: Corresponding residue name in template

From d2053f30741f1361ab5cf377f8e0da240a7ba59f Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Mon, 6 Jan 2025 16:03:37 -0800
Subject: [PATCH 17/90] Javadoc fix: many errors in struct align package

---
 .../nbio/structure/BioAssemblyIdentifier.java    |  2 +-
 .../org/biojava/nbio/structure/StructureIO.java  |  6 ++++--
 .../nbio/structure/StructureIdentifier.java      |  5 ++---
 .../biojava/nbio/structure/StructureImpl.java    |  2 +-
 .../biojava/nbio/structure/URLIdentifier.java    |  2 +-
 .../nbio/structure/align/ce/CeCPMain.java        |  2 +-
 .../align/multiple/MultipleAlignmentImpl.java    |  1 -
 .../multiple/util/MultipleAlignmentTools.java    |  1 -
 .../nbio/structure/align/util/AtomCache.java     |  4 ++--
 .../nbio/structure/align/util/RotationAxis.java  |  6 ++----
 .../nbio/structure/asa/AsaCalculator.java        |  2 +-
 .../structure/chem/DownloadChemCompProvider.java |  2 ++
 .../biojava/nbio/structure/chem/PolymerType.java | 10 +++++-----
 .../biojava/nbio/structure/contact/GridCell.java |  3 ---
 .../contact/StructureInterfaceList.java          |  2 +-
 .../structure/geometry/SuperPositionQCP.java     |  6 ++----
 .../structure/io/FastaAFPChainConverter.java     |  6 +++---
 .../structure/io/StructureSequenceMatcher.java   |  3 +--
 .../biojava/nbio/structure/math/SymbolTable.java | 16 ++++++++--------
 .../nbio/structure/secstruc/SecStrucState.java   |  2 +-
 .../nbio/structure/symmetry/core/Helix.java      |  2 --
 .../symmetry/core/QuatSuperpositionScorer.java   |  2 +-
 .../nbio/structure/symmetry/core/Rotation.java   |  2 +-
 .../structure/symmetry/core/Stoichiometry.java   |  2 +-
 .../structure/symmetry/geometry/Icosahedron.java |  4 ++--
 .../structure/symmetry/geometry/Octahedron.java  |  7 ++-----
 .../nbio/structure/symmetry/geometry/Prism.java  |  2 +-
 .../symmetry/geometry/RectangularPrism.java      |  3 ---
 .../structure/symmetry/geometry/Tetrahedron.java |  7 ++-----
 .../internal/AngleOrderDetectorPlus.java         |  6 +++---
 .../symmetry/internal/ResidueGroup.java          |  2 +-
 .../symmetry/internal/SymmOptimizer.java         |  5 ++---
 .../nbio/structure/xtal/SymoplibParser.java      |  4 ++--
 33 files changed, 56 insertions(+), 75 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java
index 194368d763..eef6de2457 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java
@@ -58,7 +58,7 @@ public BioAssemblyIdentifier(String pdbCode, int biolNr) {
 	}
 
 	/**
-	 * @param pdbCode
+	 * @param pdbId
 	 * @param biolNr
 	 */
 	public BioAssemblyIdentifier(PdbId pdbId, int biolNr) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
index 9b96705c91..b08f52aba1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
@@ -81,7 +81,7 @@ public class StructureIO {
 	 *  <ul>
 	 *  <li>If only a PDB code is provided, the whole structure will be return including ligands, but the first model only (for NMR).
 	 *	<li>Chain IDs are case sensitive, PDB ids are not. To specify a particular chain write as: 4hhb.A or 4HHB.A </li>
-	 *  <li>To specify a SCOP domain write a scopId e.g. d2bq6a1. Some flexibility can be allowed in SCOP domain names, see {@link #setStrictSCOP(boolean)}</li>
+	 *  <li>To specify a SCOP domain write a scopId e.g. d2bq6a1</li>
 	 *  <li>URLs are accepted as well</li>
 	 *  </ul>
 	 *
@@ -116,6 +116,7 @@ public static AtomCache getAtomCache() {
 	 * Returns the first biological assembly that is available for the given PDB id.
 	 * <p>
 	 * The output Structure will be different depending on the multiModel parameter:
+	 * <ul>
 	 * <li>
 	 * the symmetry-expanded chains are added as new models, one per transformId. All original models but
 	 * the first one are discarded.
@@ -124,9 +125,10 @@ public static AtomCache getAtomCache() {
 	 * as original with symmetry-expanded chains added with renamed chain ids and names (in the form
 	 * originalAsymId_transformId and originalAuthId_transformId)
 	 * </li>
+	 * </ul>
 	 * <p>
 	 * For more documentation on quaternary structures see:
-	 * {@link http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies}
+	 * <a href="http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies">http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies</a>
 	 *
 	 *
 	 * @param pdbId
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java
index cc7d8109b2..2b8cb669cf 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java
@@ -48,7 +48,7 @@ public interface StructureIdentifier extends Serializable {
 	/**
 	 * Get the String form of this identifier.
 	 *
-	 * It is recommended that the {@link #toString()} method also return the
+	 * It is recommended that the toString() method also return the
 	 * identifier, for consistency during serialization.
 	 * @return The String form of this identifier
 	 */
@@ -63,7 +63,7 @@ public interface StructureIdentifier extends Serializable {
 	 * It is recommended that the most complete structure available be returned
 	 * (e.g. the full PDB) to allow processing of unselected portions where
 	 * appropriate.
-	 * @param AtomCache A potential sources of structures
+	 * @param cache A potential sources of structures
 	 * @return A Structure containing at least the atoms identified by this,
 	 *  or null if Structures are not applicable.
 	 * @throws StructureException For errors loading and parsing the structure
@@ -92,7 +92,6 @@ public interface StructureIdentifier extends Serializable {
 	 * ID should match that returned by getPdbId(), if applicable.
 	 * @return
 	 * @throws StructureException
-	 * @see StructureTools#getReducedStructure(Structure, String)
 	 */
 	Structure reduce(Structure input) throws StructureException;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
index 4fce5b853e..ae00c8f7f3 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
@@ -1015,7 +1015,7 @@ public String  getPDBCode () {
 	}
 	
 	/** {@inheritDoc} 
-	 * @deprecated use {@link #setPDBCode(PdbId)}
+	 * @deprecated use {@link #setPdbId(PdbId)}
 	 * */
 	@Deprecated
 	@Override
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java
index 796362809f..016d1f592c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java
@@ -75,7 +75,7 @@ public class URLIdentifier implements StructureIdentifier {
 	//TODO: should this get renamed to chainname or asymid?
 	public static final String CHAINID_PARAM = "chainid";
 	/**
-	 * URL parameter specifying residue ranges to include, e.g. <tt>residues=A:1-70</tt>
+	 * URL parameter specifying residue ranges to include, e.g. <code>residues=A:1-70</code>
 	 * @see SubstructureIdentifier
 	 */
 	public static final String RESIDUES_PARAM = "residues";
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java
index 881fc224b4..e40bdce47c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java
@@ -61,7 +61,7 @@ public class CeCPMain extends CeMain {
 	/**
 	 *  version history:
 	 *  1.5 - Added more parameters to the command line, including -maxOptRMSD
-	 *  1.4 - Added DuplicationHint parameter & default to duplicating the shorter chain
+	 *  1.4 - Added DuplicationHint parameter and default to duplicating the shorter chain
 	 *  1.3 - Short CPs are now discarded
 	 *  1.2 - now supports check AlignmentTools.isSequentialAlignment. XML protocol
 	 *  1.1 - skipped, (trying to avoid confusion with jfatcat in all vs. all comparisons)
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java
index f858f3082e..738eee30c5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java
@@ -237,7 +237,6 @@ protected void updateCoreLength() {
 	/**
 	 * Updates all cached properties
 	 *
-	 * @throws StructureException
 	 */
 	protected void updateCache() {
 		updateCoreLength();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java
index 7e46d3f115..543aaa8405 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java
@@ -940,7 +940,6 @@ public static Phylogeny getHSDMTree(MultipleAlignment msta)
 	 * @param msta
 	 *            MultipleAlignment of protein structures
 	 * @return Phylogeny phylogenetic tree
-	 * @throws CompoundNotFoundException
 	 */
 	public static Phylogeny getStructuralTree(MultipleAlignment msta) {
 		double[][] rmsdMat = MultipleAlignmentTools.getRMSDMatrix(msta)
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
index 63fc089a97..fe5bfb0f2e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
@@ -670,14 +670,14 @@ public void setFileParsingParams(FileParsingParameters params) {
 	 *   Load the requested ID from the PDB's obsolete repository
 	 * <li>{@link ObsoleteBehavior#FETCH_CURRENT FETCH_CURRENT}
 	 *   Load the most recent version of the requested structure
+	 * </ul>
 	 *
 	 * <p>This setting may be silently ignored by implementations which do not have
 	 * access to the server to determine whether an entry is obsolete, such as
 	 * if {@link #isAutoFetch()} is false. Note that an obsolete entry may still be
 	 * returned even this is FETCH_CURRENT if the entry is found locally.
 	 *
-	 * @param fetchFileEvenIfObsolete Whether to fetch obsolete records
-	 * @see #setFetchCurrent(boolean)
+	 * @param behavior Whether to fetch obsolete records
 	 * @since 4.0.0
 	 */
 	public void setObsoleteBehavior(ObsoleteBehavior behavior) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/RotationAxis.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/RotationAxis.java
index 6e00e1d434..859f944645 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/RotationAxis.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/RotationAxis.java
@@ -374,8 +374,7 @@ private void calculateTranslationalAxis(Matrix rotation, Atom translation) {
 	 * @param atoms Some atoms from the protein, used for determining the bounds
 	 *  	  of the axis.
 	 *
-	 * @return The Jmol script, suitable for calls to
-	 * {@link org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol#evalString() jmol.evalString()}
+	 * @return The Jmol script
 	 */
 	public String getJmolScript(Atom[] atoms){
 		return getJmolScript(atoms, 0);
@@ -442,8 +441,7 @@ public Pair<Atom> getAxisEnds(Atom[] atoms) {
 	 * @param axisID in case of representing more than one axis in the same jmol
 	 * 		  panel, indicate the ID number.
 	 *
-	 * @return The Jmol script, suitable for calls to
-	 * {@link org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol#evalString() jmol.evalString()}
+	 * @return The Jmol script
 	 */
 	public String getJmolScript(Atom[] atoms, int axisID){
 		final double width=.5;// width of JMol object
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
index 956bbe90a4..84effc3e44 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
@@ -618,7 +618,7 @@ private static double getRadiusForNucl(NucleotideImpl nuc, Atom atom) {
 	 *
 	 * If atom is neither part of a nucleotide nor of a standard aminoacid,
 	 * the default vdw radius for the element is returned. If atom is of
-	 * unknown type (element) the vdw radius of {@link Element().N} is returned
+	 * unknown type (element) the vdw radius of {@link Element#N} is returned
 	 *
 	 * @param atom
 	 * @return
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/DownloadChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/DownloadChemCompProvider.java
index 5e0a055a39..9eb9c7c6cf 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/DownloadChemCompProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/DownloadChemCompProvider.java
@@ -109,11 +109,13 @@ public static void setServerBaseUrl(String serverBaseUrl) {
     /**
      * Set the path to append to the serverBaseUrl (settable in {@link #setServerBaseUrl(String)}).
      * The string can contain placeholders that will be expanded at runtime:
+     * <ul>
      * <li>"{ccd_id}" to be replaced by the chemical component identifier, in capitals</li>
      * <li>"{ccd_id:beginIndex-endIndex}" to be replaced by a substring of the chemical component identifier in capitals,
      * with indices following the same convention as {@link String#substring(int, int)} </li>
      * <li>"{ccd_id:index}" to be replaced by a substring of the chemical component identifier in capitals,
      * with index either a positive or negative integer to substring from left or right of the string respectively.</li>
+     * </ul>
      * If any of the indices are off-bounds, then the full chemical component identifier is replaced
      */
     public static void setChemCompPathUrlTemplate(String chemCompPathUrlTemplate) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/PolymerType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/PolymerType.java
index 78bae77f86..8066044a43 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/PolymerType.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/PolymerType.java
@@ -106,22 +106,22 @@ public static PolymerType polymerTypeFromString(String polymerTypeString) {
     }
 
     /**
-     * Convenience <tt>Set</tt> of polymer types classified as protein.  This only contains {@link #peptide}
+     * Convenience <code>Set</code> of polymer types classified as protein.  This only contains {@link #peptide}
      */
     public static final Set<PolymerType> PROTEIN_ONLY;
 
     /**
-     * Convenience <tt>Set</tt> of polymer types classified as DNA.  This only contains {@link #dna}
+     * Convenience <code>Set</code> of polymer types classified as DNA.  This only contains {@link #dna}
      */
     public static final Set<PolymerType> DNA_ONLY;
 
     /**
-     * Convenience <tt>Set</tt> of polymer types classified as RNA.  This only contains {@link #rna}
+     * Convenience <code>Set</code> of polymer types classified as RNA.  This only contains {@link #rna}
      */
     public static final Set<PolymerType> RNA_ONLY;
 
     /**
-     * Convenience <tt>Set</tt> of polymer types classified as DNA.  This contains:
+     * Convenience <code>Set</code> of polymer types classified as DNA.  This contains:
      * <ul>
      * <li>{@link #dna}</li>
      * <li>{@link #rna}</li>
@@ -131,7 +131,7 @@ public static PolymerType polymerTypeFromString(String polymerTypeString) {
     public static final Set<PolymerType> POLYNUCLEOTIDE_ONLY;
 
     /**
-     * Convenience <tt>Set</tt> of all polymer types.
+     * Convenience <code>Set</code> of all polymer types.
      */
     public static final Set<PolymerType> ALL_POLYMER_TYPES;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GridCell.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GridCell.java
index 11e2a59283..6028110eb6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GridCell.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GridCell.java
@@ -103,9 +103,6 @@ public List<Contact> getContactsWithinCell(){
 	 * within the given cutoff as a list of Contacts containing the indices of the pair and the calculated distance.
 	 *
 	 * @param otherCell
-	 * @param iAtoms the first set of atom coordinates to which the iIndices correspond
-	 * @param jAtoms the second set of atom coordinates to which the jIndices correspond, if null distances are within the iAtoms only
-	 * @param cutoff
 	 * @return
 	 */
 	public List<Contact> getContactsToOtherCell(GridCell otherCell){
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java
index 5af5a61bc3..60f7c3a91b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java
@@ -52,7 +52,7 @@ public class StructureInterfaceList implements Serializable, Iterable<StructureI
 	/**
 	 * Default minimum area for a contact between two chains to be considered a
 	 * valid interface.
-	 * @see #removeInterfacesBelowArea(double);
+	 * @see #removeInterfacesBelowArea(double)
 	 */
 	public static final double DEFAULT_MINIMUM_INTERFACE_AREA = 35.0;
 	/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQCP.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQCP.java
index a36854a711..c96f2f7125 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQCP.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQCP.java
@@ -587,7 +587,7 @@ public Matrix4d superpose(Point3d[] fixed, Point3d[] moved) {
 	 * @param fixed
 	 * @param moved
 	 * @param weight
-	 *            array of weigths for each equivalent point position
+	 *            array of weights for each equivalent point position
 	 * @return weighted RMSD.
 	 */
 	public double getWeightedRmsd(Point3d[] fixed, Point3d[] moved, double[] weight) {
@@ -598,13 +598,11 @@ public double getWeightedRmsd(Point3d[] fixed, Point3d[] moved, double[] weight)
 	/**
 	 * The QCP method can be used as a two-step calculation: first compute the
 	 * RMSD (fast) and then compute the superposition.
-	 *
+	 * <p>
 	 * This method assumes that the RMSD of two arrays of points has been
 	 * already calculated using {@link #getRmsd(Point3d[], Point3d[])} method
 	 * and calculates the transformation of the same two point arrays.
 	 *
-	 * @param fixed
-	 * @param moved
 	 * @return transformation matrix as a Matrix4d to superpose moved onto fixed
 	 *         point arrays
 	 */
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java
index 81bf601ab6..1b8278125e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java
@@ -51,7 +51,7 @@
 import java.util.*;
 
 /**
- * A collection of static utilities to convert between {@link AFPChain AFPChains} and {@link FastaSequence FastaSequences}.
+ * A collection of static utilities to convert between {@link AFPChain AFPChains} and FastaSequences.
  *
  * @author dmyersturnbull
  * @see StructureSequenceMatcher
@@ -73,7 +73,7 @@ public static AFPChain cpFastaToAfpChain(String first, String second, Structure
 
 	/**
 	 * Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site
-	 * {@link cpSite} residues to the right.
+	 * <code>cpSite</code> residues to the right.
 	 *
 	 * @param fastaFile A FASTA file containing exactly 2 sequences, the first unpermuted and the second permuted
 	 * @param cpSite
@@ -97,7 +97,7 @@ public static AFPChain cpFastaToAfpChain(File fastaFile, Structure structure, in
 
 	/**
 	 * Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site
-	 * {@link cpSite} residues to the right.
+	 * <code>cpSite</code> residues to the right.
 	 *
 	 * @param first The unpermuted sequence
 	 * @param second The sequence permuted by cpSite
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java
index fbc12ec9d3..529526e2e0 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java
@@ -103,8 +103,7 @@ public static Structure getSubstructureMatchingProteinSequence(ProteinSequence s
 	 * @return A ProteinSequence with the full sequence of struct. Chains are
 	 *  concatenated in the same order as the input structures
 	 *
-	 * @see SeqRes2AtomAligner#getFullAtomSequence(List, Map, boolean), which
-	 * 	does the heavy lifting.
+	 * @see SeqRes2AtomAligner#getFullAtomSequence(List, Map, boolean)
 	 *
 	 */
 	public static ProteinSequence getProteinSequenceForStructure(Structure struct, Map<Integer,Group> groupIndexPosition ) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SymbolTable.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SymbolTable.java
index 0f9066b323..960e18b019 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SymbolTable.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SymbolTable.java
@@ -35,7 +35,7 @@
  *  Does not allow duplicate keys.
  *
  *  This class represents an ordered symbol table. It assumes that
- *  the elements are <tt>Comparable</tt>.
+ *  the elements are <code>Comparable</code>.
  *  It supports the usual <em>put</em>, <em>get</em>, <em>contains</em>,
  *  and <em>delete</em> methods.
  *  It also provides ordered methods for finding the <em>minimum</em>,
@@ -111,9 +111,9 @@ public int size() {
 	}
 
 	/**
-	 * Return an <tt>Iterator</tt> for the keys in the table.
-	 * To iterate over all of the keys in the symbol table <tt>st</tt>, use the
-	 * foreach notation: <tt>for (Key key : st)</tt>.
+	 * Return an <code>Iterator</code> for the keys in the table.
+	 * To iterate over all of the keys in the symbol table <code>st</code>, use the
+	 * foreach notation: <code>for (Key key : st)</code>.
 	 */
 	@Override
 	public Iterator<Key> iterator() {
@@ -121,9 +121,9 @@ public Iterator<Key> iterator() {
 	}
 
 	/**
-	 * Return an <tt>Iterable</tt> for the keys in the table.
-	 * To iterate over all of the keys in the symbol table <tt>st</tt>, use the
-	 * foreach notation: <tt>for (Key key : st.keys())</tt>.
+	 * Return an <code>Iterable</code> for the keys in the table.
+	 * To iterate over all of the keys in the symbol table <code>st</code>, use the
+	 * foreach notation: <code>for (Key key : st.keys())</code>.
 	 */
 	public Iterable<Key> keys() {
 		return st.keySet();
@@ -153,7 +153,7 @@ public Key ceil(Key k) {
 	}
 
 	/**
-	 * Return the largest key in the table <= k.
+	 * Return the largest key in the table &lt;= k.
 	 */
 	public Key floor(Key k) {
 		if (st.containsKey(k)) return k;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucState.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucState.java
index 33bdc7c931..6faebae39c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucState.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucState.java
@@ -107,7 +107,7 @@ public char[] getTurn() {
 
 	/**
 	 * Set the turn column corresponding to 3,4 or 5 helix patterns. If starting
-	 * > or ending < was set and the opposite is being set, the value will be
+	 * &gt; or ending &lt; was set and the opposite is being set, the value will be
 	 * converted to X. If a number was set, it will be overwritten by the new
 	 * character.
 	 *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Helix.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Helix.java
index 4dabe0c0ac..2c399185f1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Helix.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Helix.java
@@ -101,7 +101,6 @@ public void setRise(double rise) {
 
 	/**
 	 * Returns the pitch angle of the helix
-	 * @param transformation helix transformation
 	 * @return
 	 */
 	public double getAngle() {
@@ -110,7 +109,6 @@ public double getAngle() {
 
 	/**
 	 * Returns the AxisAngle of the helix transformation
-	 * @param transformation helix transformation
 	 * @return
 	 */
 	public AxisAngle4d getAxisAngle() {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.java
index 5df1278563..1964132a0d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.java
@@ -40,7 +40,7 @@ public class QuatSuperpositionScorer {
 	 * TM score: Yang Zhang and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004)
 	 * @param subunits subunits to be scored
 	 * @param transformation transformation matrix
-	 * @param permutations permutation that determines which subunits are superposed
+	 * @param permutation permutation that determines which subunits are superposed
 	 * @return
 	 */
 	public static QuatSymmetryScores calcScores(QuatSymmetrySubunits subunits, Matrix4d transformation, List<Integer> permutation) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Rotation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Rotation.java
index 9f1410abc6..6a9b95c3a6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Rotation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Rotation.java
@@ -147,7 +147,7 @@ public int getDirection() {
 	}
 
 	/**
-	 * @param direction the direction to set
+	 * @param axis the direction to set
 	 */
 	public void setDirection(int axis) {
 		this.direction = axis;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Stoichiometry.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Stoichiometry.java
index dc6a09053f..697ee41f82 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Stoichiometry.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Stoichiometry.java
@@ -238,7 +238,7 @@ public int numberOfComponents() {
 	}
 
 	/**
-	 * Make a combined Stoichiometry object of <i>this</> and the <i>other</>.
+	 * Make a combined Stoichiometry object of <i>this</i> and the <i>other</i>.
 	 * The combined list of clusters will be ordered by the number of subunits.
 	 * @return new {@link Stoichiometry} object.
 	 */
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Icosahedron.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Icosahedron.java
index 7de37ee842..5cb5a99458 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Icosahedron.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Icosahedron.java
@@ -67,7 +67,7 @@ public double getInscribedRadius() {
 	/**
 	 * Sets the radius of an inscribed sphere, that is tangent to each
 	 * of the icosahedron's faces
-	 * @param inscribedRadius the inscribedRadius to set
+	 * @param radius the inscribedRadius to set
 	 */
 	public void setInscribedRadius(double radius) {
 		double side = getSideLengthFromInscribedRadius(radius);
@@ -88,7 +88,7 @@ public double getMidRadius() {
 	/**
 	 * Sets the radius of radius of a sphere, that is tangent to each
 	 * of the icosahedron's edges
-	 * @param midRadius the midRadius to set
+	 * @param radius the midRadius to set
 	 */
 	public void setMidRadius(double radius) {
 		double side = getSideLengthFromMiddleRadius(radius);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Octahedron.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Octahedron.java
index 6cc5842dda..3165093908 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Octahedron.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Octahedron.java
@@ -62,7 +62,7 @@ public double getInscribedRadius() {
 	/**
 	 * Sets the radius of an inscribed sphere, that is tangent to each
 	 * of the octahedron's faces
-	 * @param inscribedRadius the inscribedRadius to set
+	 * @param radius the inscribedRadius to set
 	 */
 	public void setInscribedRadius(double radius) {
 		double side = getSideLengthFromInscribedRadius(radius);
@@ -83,7 +83,7 @@ public double getMidRadius() {
 	/**
 	 * Sets the radius of radius of a sphere, that is tangent to each
 	 * of the octahedron's edges
-	 * @param midRadius the midRadius to set
+	 * @param radius the midRadius to set
 	 */
 	public void setMidRadius(double radius) {
 		double side = getSideLengthFromMiddleRadius(radius);
@@ -92,9 +92,6 @@ public void setMidRadius(double radius) {
 
 	/**
 	 * Returns the vertices of an n-fold polygon of given radius and center
-	 * @param n
-	 * @param radius
-	 * @param center
 	 * @return
 	 */
 	@Override
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Prism.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Prism.java
index 770126b601..24166059fc 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Prism.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Prism.java
@@ -87,7 +87,7 @@ public double getInscribedRadius() {
 	/**
 	 * Sets the radius of an inscribed sphere, that is tangent to each
 	 * of the icosahedron's faces
-	 * @param inscribedRadius the inscribedRadius to set
+	 * @param radius the inscribedRadius to set
 	 */
 	public void setInscribedRadius(double radius) {
 		double side = getSideLengthFromInscribedRadius(radius, n);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/RectangularPrism.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/RectangularPrism.java
index 45d32828c3..295c6275e9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/RectangularPrism.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/RectangularPrism.java
@@ -82,9 +82,6 @@ public double getCirumscribedRadius() {
 
 	/**
 	 * Returns the vertices of an n-fold polygon of given radius and center
-	 * @param n
-	 * @param radius
-	 * @param center
 	 * @return
 	 */
 	@Override
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Tetrahedron.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Tetrahedron.java
index 7effd81cbe..a402cbef7e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Tetrahedron.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Tetrahedron.java
@@ -66,7 +66,7 @@ public double getInscribedRadius() {
 	/**
 	 * Sets the radius of an inscribed sphere, that is tangent to each
 	 * of the tetrahedron's faces
-	 * @param inscribedRadius the inscribedRadius to set
+	 * @param radius the inscribedRadius to set
 	 */
 	public void setInscribedRadius(double radius) {
 		double side = getSideLengthFromInscribedRadius(radius);
@@ -87,7 +87,7 @@ public double getMidRadius() {
 	/**
 	 * Sets the radius of radius of a sphere, that is tangent to each
 	 * of the tetrahedron's edges
-	 * @param midRadius the midRadius to set
+	 * @param radius the midRadius to set
 	 */
 	public void setMidRadius(double radius) {
 		double side = getSideLengthFromMiddleRadius(radius);
@@ -96,9 +96,6 @@ public void setMidRadius(double radius) {
 
 	/**
 	 * Returns the vertices of an n-fold polygon of given radius and center
-	 * @param n
-	 * @param radius
-	 * @param center
 	 * @return
 	 */
 	@Override
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java
index 96b41f48e9..345493ce91 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java
@@ -45,7 +45,7 @@ public class AngleOrderDetectorPlus implements OrderDetector {
 	private boolean normalizeError;
 
 	/**
-	 * @param error
+	 * @param angleError
 	 *            maximum angular error, in radians
 	 */
 	public AngleOrderDetectorPlus(double angleError) {
@@ -61,7 +61,7 @@ public AngleOrderDetectorPlus(int maxOrder) {
 	 *
 	 * @param maxOrder
 	 *            maximum order to consider
-	 * @param error
+	 * @param angleError
 	 *            maximum angular error, in radians
 	 */
 	public AngleOrderDetectorPlus(int maxOrder, double angleError) {
@@ -82,7 +82,7 @@ public AngleOrderDetectorPlus(int maxOrder, double angleError) {
 	 *
 	 * @param maxOrder
 	 *            maximum order to consider
-	 * @param error
+	 * @param angleError
 	 *            maximum angular error
 	 * @param normalize
 	 *            indicates whether error should be normalized by the order
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/ResidueGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/ResidueGroup.java
index a9e1bcdeb5..79053f55f9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/ResidueGroup.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/ResidueGroup.java
@@ -76,7 +76,7 @@ public int order() {
 	 * ResidueGroups {A,B,C}, if A is compatible with B and B is compatible with
 	 * C, then A is not necessarily compatible with C.
 	 *
-	 * @param c2
+	 * @param other
 	 *            second maximally connected component
 	 * @return true if compatible, false otherwise
 	 */
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java
index 8ea264ba67..58a8c89394 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java
@@ -107,8 +107,6 @@ public class SymmOptimizer {
 	 *
 	 * @param symmResult
 	 *            CeSymmResult with all the information
-	 * @throws RefinerFailedException
-	 * @throws StructureException
 	 */
 	public SymmOptimizer(CeSymmResult symmResult) {
 
@@ -181,11 +179,12 @@ private void initialize() throws StructureException, RefinerFailedException {
 	 * Optimization method based in a Monte-Carlo approach. Starting from the
 	 * refined alignment uses 4 types of moves:
 	 * <p>
+	 * <ul>
 	 * <li>1- Shift Row: if there are enough freePool residues available.
 	 * <li>2- Expand Block: add another alignment column.
 	 * <li>3- Shrink Block: move a block column to the freePool.
 	 * <li>4- Insert gap: insert a gap in a position of the alignment.
-	 *
+	 * </ul>
 	 * @throws StructureException
 	 * @throws RefinerFailedException
 	 *             if the alignment is not symmetric or too short.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java
index 5d58e019eb..f2a9ffb9c2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java
@@ -185,8 +185,8 @@ public static TreeMap<Integer,SpaceGroup> getAllSpaceGroups() {
 	 * A parser for the symop.lib file provided by CCP4. Note: this file is not getting re-distributed by BioJava.
 	 * It can be downloaded from:
 	 *
-	 *  http://www.ccp4.ac.uk/cvs/viewvc.cgi/libccp4/data/symop.lib?revision=1.10&view=markup
-	 *
+	 * <a href="http://www.ccp4.ac.uk/cvs/viewvc.cgi/libccp4/data/symop.lib?revision=1.10&view=markup">http://www.ccp4.ac.uk/cvs/viewvc.cgi/libccp4/data/symop.lib?revision=1.10&view=markup</a>
+	 * <p>
 	 * Note: this file is not needed by BioJava. BioJava loads equivalent information from the file spacegroups.xml
 	 *
 	 * @param symoplibIS

From 435ebe98b58bf9cc044dc37414e4ae75a08835b1 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Mon, 6 Jan 2025 16:16:59 -0800
Subject: [PATCH 18/90] Javadoc fix: many errors in struct align package

---
 .../java/org/biojava/nbio/structure/Atom.java | 62 +++++++++----------
 .../org/biojava/nbio/structure/Group.java     |  4 +-
 .../biojava/nbio/structure/StructureIO.java   |  4 +-
 .../structure/align/ce/OptimalCECPMain.java   |  9 ++-
 .../nbio/structure/align/model/AFPChain.java  |  6 +-
 .../align/util/UserConfiguration.java         |  1 -
 .../symmetry/utils/SymmetryTools.java         |  2 +-
 .../nbio/structure/xtal/SymoplibParser.java   |  2 +-
 8 files changed, 46 insertions(+), 44 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java
index 2e19acb29a..df38b06205 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java
@@ -48,7 +48,7 @@ public interface Atom extends Cloneable, PDBRecord {
 	 * @param s  a trimmed String specifying the name value
 	 * @see #getName
 	 */
-	public void   setName(String s);
+	void   setName(String s);
 
 	/**
 	 * Get atom name, e.g. "CA".
@@ -57,42 +57,42 @@ public interface Atom extends Cloneable, PDBRecord {
 	 * @return a trimmed String representing the name value
 	 * @see #setName
 	 */
-	public String getName();
+	String getName();
 
 	/**
 	 * Set element of the atom name, e.g. {@link Element#Fe}
 	 * @param e  an Element enumeration
 	 * @see #getElement
 	 */
-	public void   setElement(Element e);
+	void   setElement(Element e);
 
 	/**
 	 * Get element of the atom, e.g. {@link Element#Ca}
 	 * @return an Element enumeration
 	 * @see #setElement
 	 */
-	public Element getElement();
+	Element getElement();
 
 	/**
 	 * Set PDB atom number.
 	 * @param i  an int specifying the PDBserial value
 	 * @see #getPDBserial
 	 */
-	public void setPDBserial(int i) ;
+	void setPDBserial(int i) ;
 
 	/**
 	 * Get PDB atom number.
 	 * @return an int representing the PDBserial value
 	 * @see #setPDBserial
 	 */
-	public int  getPDBserial() ;
+	int  getPDBserial() ;
 
 	/**
 	 * Set the coordinates.
 	 * @param c  an array of doubles specifying the coords value
 	 * @see #getCoords
 	 */
-	public void    setCoords(double[] c);
+	void    setCoords(double[] c);
 
 	/**
 	 * Get the coordinates.
@@ -100,7 +100,7 @@ public interface Atom extends Cloneable, PDBRecord {
 	 * @see #setCoords
 	 * @see #getCoordsAsPoint3d()
 	 */
-	public double[] getCoords() ;
+	double[] getCoords() ;
 
 	/**
 	 * Get the coordinates.
@@ -110,56 +110,56 @@ public interface Atom extends Cloneable, PDBRecord {
 	 * @return a reference to the Point3d coordinates
 	 * @see #getCoords()
 	 */
-	public Point3d getCoordsAsPoint3d();
+	Point3d getCoordsAsPoint3d();
 
 	/**
 	 * Set the X coordinate.
 	 * @param x  a double
 	 * @see #getX()
 	 */
-	public void setX(double x);
+	void setX(double x);
 
 	/**
 	 * Set the Y coordinate.
 	 * @param y  a double
 	 * @see #getY()
 	 */
-	public void setY(double y);
+	void setY(double y);
 
 	/**
 	 * Set the Z coordinate.
 	 * @param z  a double
 	 * @see #getZ()
 	 */
-	public void setZ(double z);
+	void setZ(double z);
 
 	/**
 	 * Get coordinate X.
 	 * @return a double
 	 * @see #setX(double)
 	 */
-	public double getX() ;
+	double getX() ;
 
 	/**
 	 * Get coordinate Y.
 	 * @return a double
 	 * @see #setY(double)
 	 */
-	public double getY() ;
+	double getY() ;
 
 	/**
 	 * Get coordinate Z.
 	 * @return a double
 	 * @see #setZ(double)
 	 */
-	public double getZ() ;
+	double getZ() ;
 
 	/**
 	 * Set alternate Location.
 	 * @param c  a Character object specifying the alt loc value
 	 * @see #getAltLoc
 	 */
-	public void setAltLoc(Character c);
+	void setAltLoc(Character c);
 
 	/**
 	 * Get alternate Location.
@@ -167,41 +167,41 @@ public interface Atom extends Cloneable, PDBRecord {
 	 * is represented by ' ' (space character, ascii 32).
 	 * @see #setAltLoc
 	 */
-	public Character getAltLoc();
+	Character getAltLoc();
 
 	/**
 	 * Set occupancy.
 	 * @param occupancy  a float specifying the occupancy value
 	 * @see #getOccupancy
 	 */
-	public void setOccupancy(float occupancy) ;
+	void setOccupancy(float occupancy) ;
 
 	/**
 	 * Get occupancy.
 	 * @return a float representing the occupancy value
 	 * @see #setOccupancy
 	 */
-	public float getOccupancy();
+	float getOccupancy();
 
 	/**
 	 * Set temp factor .
 	 * @param temp  a float specifying the temp factor value
 	 * @see #getTempFactor
 	 */
-	public void   setTempFactor(float temp) ;
+	void   setTempFactor(float temp) ;
 
 	/**
 	 * Get temp factor.
 	 * @return a float representing the temp factor value
 	 * @see #setTempFactor
 	 */
-	public float getTempFactor() ;
+	float getTempFactor() ;
 
 	/**
 	 * Return an identical copy of this  object .
 	 * @return  an identical copy of this  object
 	 */
-	public Object clone();
+	Object clone();
 
 	/**
 	 * Set the back-reference to its parent Group.
@@ -209,7 +209,7 @@ public interface Atom extends Cloneable, PDBRecord {
 	 * @see #getGroup()
 	 */
 
-	public void setGroup(Group parent);
+	void setGroup(Group parent);
 
 	/**
 	 * Return the parent Group of the Atom.
@@ -217,28 +217,27 @@ public interface Atom extends Cloneable, PDBRecord {
 	 * @return Group the parent Group of the Atom, or null
 	 * @see #setGroup(Group)
 	 */
-	public Group getGroup();
+	Group getGroup();
 
 	/**
 	 * Add a bond
 	 * @param bond to be added
 	 * @see #getBonds()
 	 */
-	public void addBond(Bond bond);
+	void addBond(Bond bond);
 
 	/**
 	 * Get all {@link Bond}s this atom is part of.
 	 *
 	 * @return a list of {@link Bond}s or null if no bonds exist for this Atom
 	 */
-	public List<Bond> getBonds();
+	List<Bond> getBonds();
 
 	/**
 	 * Sets the bonds
 	 * @param bonds
 	 */
-	public void setBonds(List<Bond> bonds);
-
+	void setBonds(List<Bond> bonds);
 
 	/**
 	 * Test if another atom has a bond to this atom
@@ -246,19 +245,18 @@ public interface Atom extends Cloneable, PDBRecord {
 	 * @param other
 	 * @return
 	 */
-	public boolean hasBond(Atom other);
+	boolean hasBond(Atom other);
 
 	/**
 	 * Get the charge of this atom
 	 *
 	 * @return a the integer charge.
 	 */
-	public short getCharge();
+	short getCharge();
 
 	/**
 	 * Set the charge of this atom
 	 *
-	 * @return void.
 	 */
-	public void setCharge(short charge);
+	void setCharge(short charge);
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Group.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Group.java
index 8b7b5cb809..1ea0d1633e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Group.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Group.java
@@ -346,7 +346,7 @@ public interface Group extends Serializable {
 	 * The main group (this group) will contain the first altloc (be it the default '.' or 'A' or a mix of '.' and 'A').
 	 * <p>
 	 * This method will return the altloc groups that are not the main group, e.g.:
-	 *
+	 * <ul>
 	 * <li> if '.' (default), 'A' and 'B' altlocs are present in file, the main group will contain
 	 * the default '.' and this method will return 2 altloc groups
 	 * </li>
@@ -354,7 +354,7 @@ public interface Group extends Serializable {
 	 * <li> if 'A' and 'B' are present in file without a default '.' group, then the main group will contain the 'A'
 	 * location whilst this method will return only 1 altloc group with the 'B' location
 	 * </li>
-	 *
+	 * </ul>
 	 * <p>
 	 * Note that atoms with the default altloc (.) are included in all groups. Atoms with other altlocs (typically A, B, etc)
 	 * will be sorted into groups by altloc.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
index b08f52aba1..75e4b95194 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
@@ -149,7 +149,7 @@ public static Structure getBiologicalAssembly(String pdbId, boolean multiModel)
 	 * using multiModel={@value AtomCache#DEFAULT_BIOASSEMBLY_STYLE}
 	 * <p>
 	 * For more documentation on quaternary structures see:
-	 * {@link http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies}
+	 * <a href="http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies">http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies</a>
 	 *
 	 *
 	 * @param pdbId
@@ -165,6 +165,7 @@ public static Structure getBiologicalAssembly(String pdbId) throws IOException,
 	 * Returns the biological assembly for the given PDB id and bioassembly identifier.
 	 * <p>
 	 * The output Structure will be different depending on the multiModel parameter:
+	 * <ul>
 	 * <li>
 	 * the symmetry-expanded chains are added as new models, one per transformId. All original models but
 	 * the first one are discarded.
@@ -173,6 +174,7 @@ public static Structure getBiologicalAssembly(String pdbId) throws IOException,
 	 * as original with symmetry-expanded chains added with renamed chain ids and names (in the form
 	 * originalAsymId_transformId and originalAuthId_transformId)
 	 * </li>
+	 * </ul>
 	 * @param pdbId
 	 * @param biolAssemblyNr - the ith biological assembly that is available for a PDB ID (we start counting at 1, 0 represents the asym unit).
 	 * @param multiModel if true the output Structure will be a multi-model one with one transformId per model,
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/OptimalCECPMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/OptimalCECPMain.java
index 7fa9c4cf28..0f3e4d1283 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/OptimalCECPMain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/OptimalCECPMain.java
@@ -300,7 +300,7 @@ private static Matrix permuteMatrix(Matrix mat, int cpRows, int cpCols) {
 	/**
 	 * Modifies the {@link AFPChain#setOptAln(int[][][]) optAln} of an AFPChain
 	 * by permuting the second protein.
-	 *
+	 * <p>
 	 * Sets residue numbers in the second protein to <i>(i-cp)%len</i>
 	 *
 	 * @param afpChain
@@ -425,7 +425,7 @@ private static void assignOptAln(AFPChain afpChain, List<List<List<Integer>>> bl
 	/**
 	 * Finds the optimal alignment between two proteins allowing for a circular
 	 * permutation (CP).
-	 *
+	 * <p>
 	 * The precise algorithm is controlled by the
 	 * {@link OptimalCECPParameters parameters}. If the parameter
 	 * {@link OptimalCECPParameters#isTryAllCPs() tryAllCPs} is true, all possible
@@ -456,10 +456,9 @@ public AFPChain align(Atom[] ca1, Atom[] ca2, Object param)
 	/**
 	 * Finds the optimal alignment between two proteins allowing for a circular
 	 * permutation (CP).
-	 *
+	 * <p>
 	 * This algorithm performs a CE alignment for each possible CP site. This is
-	 * quite slow. Use {@link #alignHeuristic(Atom[], Atom[], Object)} for a
-	 * faster algorithm.
+	 * quite slow.
 	 *
 	 * @param ca1 CA atoms of the first protein
 	 * @param ca2 CA atoms of the second protein
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java
index 41cef89031..001d32d806 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java
@@ -973,6 +973,10 @@ public void setOptRmsd(double[] optRmsd)
 		this.optRmsd = optRmsd;
 	}
 
+	/**
+	 * The number of aligned residues in the final alignment.
+	 * @return
+	 */
 	public int getOptLength()
 	{
 		return optLength;
@@ -1023,7 +1027,7 @@ public void setAlnseq2(char[] alnseq2)
 
 	/**
 	 * @return The total length of the alignment, including gaps
-	 * @see #getOptLength(), the number of aligned residues in the final alignment.
+	 * @see #getOptLength()
 	 */
 	public int getAlnLength()
 	{
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/UserConfiguration.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/UserConfiguration.java
index 70e85acec3..67eba4c966 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/UserConfiguration.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/UserConfiguration.java
@@ -306,7 +306,6 @@ public XMLWriter toXML(PrintWriter pw)
 	 * @param xw the XML writer to use
 	 * @return the writer again
 	 * @throws IOException
-	 * @see org.biojava.nbio.structure.align.webstart.ConfigXMLHandler
 	 */
 
 	public XMLWriter toXML(XMLWriter xw)
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java
index 4913ac5cc5..76822af35f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java
@@ -501,7 +501,7 @@ public static Graph<Integer, DefaultEdge> buildSymmetryGraph(
 	 * @param symmetry
 	 *            CeSymmResult
 	 * @throws StructureException
-	 * @result List of structures, by repeat index sequentially
+	 * @return List of structures, by repeat index sequentially
 	 *
 	 */
 	public static List<Structure> divideStructure(CeSymmResult symmetry)
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java
index f2a9ffb9c2..0de5e33bc4 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java
@@ -185,7 +185,7 @@ public static TreeMap<Integer,SpaceGroup> getAllSpaceGroups() {
 	 * A parser for the symop.lib file provided by CCP4. Note: this file is not getting re-distributed by BioJava.
 	 * It can be downloaded from:
 	 *
-	 * <a href="http://www.ccp4.ac.uk/cvs/viewvc.cgi/libccp4/data/symop.lib?revision=1.10&view=markup">http://www.ccp4.ac.uk/cvs/viewvc.cgi/libccp4/data/symop.lib?revision=1.10&view=markup</a>
+	 * <a href="http://www.ccp4.ac.uk/cvs/viewvc.cgi/libccp4/data/symop.lib?revision=1.10&view=markup">http://www.ccp4.ac.uk/cvs/viewvc.cgi/libccp4/data/symop.lib?revision=1.10&amp;view=markup</a>
 	 * <p>
 	 * Note: this file is not needed by BioJava. BioJava loads equivalent information from the file spacegroups.xml
 	 *

From 0c7e9f5fc52f79e942cf1780baafde473b459368 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Tue, 7 Jan 2025 13:31:40 -0800
Subject: [PATCH 19/90] Javadoc fix: most other errors in structure module

---
 .../structure/align/gui/AlignmentCalc.java    |  4 +-
 .../java/demo/DemoChangeChemCompProvider.java |  5 +-
 .../java/org/biojava/nbio/structure/Bond.java | 12 +--
 .../org/biojava/nbio/structure/BondImpl.java  |  6 +-
 .../org/biojava/nbio/structure/BondType.java  |  2 +-
 .../org/biojava/nbio/structure/Structure.java | 94 ++++++-------------
 .../biojava/nbio/structure/StructureIO.java   |  2 +
 .../nbio/structure/StructureIdentifier.java   |  8 +-
 .../biojava/nbio/structure/URLIdentifier.java | 10 +-
 .../nbio/structure/align/ce/CeMain.java       |  2 +-
 .../align/util/AFPAlignmentDisplay.java       |  5 +-
 .../structure/align/util/AlignmentTools.java  | 12 +--
 .../nbio/structure/align/util/AtomCache.java  | 11 +--
 .../nbio/structure/io/LocalPDBDirectory.java  |  2 +-
 .../nbio/structure/io/PDBFileReader.java      | 15 +--
 .../nbio/structure/jama/LUDecomposition.java  |  4 +-
 .../biojava/nbio/structure/jama/Matrix.java   |  2 +-
 .../biojava/nbio/structure/package-info.java  |  7 +-
 .../nbio/structure/secstruc/BridgeType.java   |  2 +-
 .../symmetry/core/RotationGroup.java          |  2 +-
 .../symmetry/internal/CeSymmIterative.java    |  1 -
 .../symmetry/internal/SymmOptimizer.java      |  2 +-
 22 files changed, 81 insertions(+), 129 deletions(-)

diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalc.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalc.java
index 98ed76f7a4..af2f8f9d91 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalc.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalc.java
@@ -35,13 +35,13 @@
 import org.slf4j.LoggerFactory;
 
 
-/** A class that obtains two structures via DAS and aligns them
+/**
+ * A class that obtains two structures via DAS and aligns them
  *  This is done in a separate thread.
  *  It is possible to register Event listeners to get notification of when the download has finished.
  *
  * @author Andreas Prlic
  * @since 1.7
- * @version %I% %G%
  */
 public class AlignmentCalc implements AlignmentCalculationRunnable {
 
diff --git a/biojava-structure/src/main/java/demo/DemoChangeChemCompProvider.java b/biojava-structure/src/main/java/demo/DemoChangeChemCompProvider.java
index b198aeb46a..bb78c98d77 100644
--- a/biojava-structure/src/main/java/demo/DemoChangeChemCompProvider.java
+++ b/biojava-structure/src/main/java/demo/DemoChangeChemCompProvider.java
@@ -37,17 +37,18 @@
  *  componentsby using the {@link DownloadChemCompProvider}. It fetches and locally caches chemical component
  *  definitions as they are encountered during file parsing. It can be enabled by using the
  *  {@link FileParsingParameters#setLoadChemCompInfo(boolean)} method.
- *
+ * <p>
  * The {@link AllChemCompProvider} downloads and unpacks all chemcomps. It is slower and requires more memory than the
  * default {@link DownloadChemCompProvider}, but it avoids network access to the FTP site, if a new chemcomp is
  * detected, that has not been downloaded yet.
- *
+ * <p>
  * Since all chemcomps will be kept in memory, the standard memory that is available to a JVM will not be sufficient
  * in order to run this demo. Please start with -Xmx200M
  *
  * @author Andreas Prlic
  */
 public class DemoChangeChemCompProvider {
+
 	public static void main(String[] args){
 		String pdbId = "1O1G";
 		boolean loadChemComp = true;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Bond.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Bond.java
index 7af10c23e0..ae4c97f74e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Bond.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Bond.java
@@ -26,7 +26,7 @@
  * A simple bond -- it stores information about two atoms as well as information
  * about its bond order.
  *
- * @author Jules Jacobsen <jacobsen@ebi.ac.uk>
+ * @author Jules Jacobsen jacobsen@ebi.ac.uk
  * @author Ulysse Carion
  */
 public interface Bond extends Serializable {
@@ -39,7 +39,7 @@ public interface Bond extends Serializable {
 	 * @see #getAtomB()
 	 * @return one of the two atoms in this bond
 	 */
-	public Atom getAtomA();
+	Atom getAtomA();
 
 	/**
 	 * Gets atom 'B' of this bond. There is no meaning to which atom is 'A' and
@@ -49,7 +49,7 @@ public interface Bond extends Serializable {
 	 * @see #getAtomA()
 	 * @return one of the two atoms in this bond
 	 */
-	public Atom getAtomB();
+	Atom getAtomB();
 
 	/**
 	 * A utility method to get the other atom in a bond, given one of its atoms.
@@ -66,7 +66,7 @@ public interface Bond extends Serializable {
 	 *             if the passed atom is not in this bond
 	 * @return the atom in this bond that was not passed as an argument
 	 */
-	public Atom getOther(Atom exclude);
+	Atom getOther(Atom exclude);
 
 	/**
 	 * Gets the bond order of this bond. A return value of '1' corresponds to a
@@ -74,7 +74,7 @@ public interface Bond extends Serializable {
 	 *
 	 * @return this bond's bond order
 	 */
-	public int getBondOrder();
+	int getBondOrder();
 
 	/**
 	 * Gets the distance between the two atoms of this bond.
@@ -85,5 +85,5 @@ public interface Bond extends Serializable {
 	 *
 	 * @return the distance between the two atoms of this bond.
 	 */
-	public double getLength();
+	double getLength();
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java
index 78d38559f7..4deac44faa 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java
@@ -27,7 +27,7 @@
  * A simple bond -- it stores information about two atoms as well as information
  * about its bond order.
  *
- * @author Jules Jacobsen <jacobsen@ebi.ac.uk>
+ * @author Jules Jacobsen jacobsen@ebi.ac.uk
  * @author Ulysse Carion
  */
 public class BondImpl implements Bond {
@@ -44,7 +44,7 @@ public class BondImpl implements Bond {
 	 * Note that by forming a bond between atoms 'A' and 'B' with this
 	 * constructor, atoms 'A' and 'B' will be updated to have this bond in their
 	 * list of bonds. If you do not want this automatic updating, instead use
-	 * {@link Bond(Atom, Atom, int, boolean)} with the
+	 * {@link #BondImpl(Atom, Atom, int, boolean)} with the
 	 * <code>addSelfToAtoms</code> flag set to <code>false</code>.
 	 *
 	 * @param atomA one of the atoms in this bond
@@ -83,7 +83,7 @@ public BondImpl(Atom atomA, Atom atomB, int bondOrder, boolean addSelfToAtoms) {
 	 * include this bond.
 	 * <p>
 	 * If you created your Bond with the constructor
-	 * {@link Bond(Atom, Atom, int)}, this method has already been called for
+	 * {@link #BondImpl(Atom, Atom, int)}, this method has already been called for
 	 * you and should not be called again.
 	 */
 	// TODO first check if those bonds haven't been made already
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/BondType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/BondType.java
index 9b3f752092..5a8569f396 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/BondType.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/BondType.java
@@ -23,7 +23,7 @@
 
 /**
  * Work in progress - NOT final!
- * @author Jules Jacobsen <jacobsen@ebi.ac.uk>
+ * @author Jules Jacobsen jacobsen@ebi.ac.uk
  */
 public enum BondType {
 	UNDEFINED, COVALENT, IONIC, HBOND, VANDERWAALS, HYDROPHOBIC, METAL, PLANAR, ATOM_PLANE;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java
index 8521044de7..51d69234c7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java
@@ -31,9 +31,8 @@
 
 
 /**
- *
  * Interface for a structure object. Provides access to the data of a PDB file.
- *
+ * <p>
  * A structure object allows to access the PDB header information as well
  * as to the data from the ATOM records. The header information is
  * currently available through the following objects:
@@ -61,27 +60,16 @@
  *
  * <p>
  *  The tutorial for the BioJava structure modules can be found at <a href="https://github.com/biojava/biojava3-tutorial/tree/master/structure">github</a>.
- * </p>
- *
- *
  * <hr/>
  * <p>
  * Q: How can I get a Structure object from a PDB file?
- * </p>
  * <p>
  * A:
- * </p>
  * <pre>
- *  {@link Structure} loadStructure(String pathToPDBFile){
- * 		{@link PDBFileReader} pdbreader = new {@link PDBFileReader}();
- *
- * 		{@link Structure} structure = null;
- * 		try{
- * 			structure = pdbreader.getStructure(pathToPDBFile);
- * 			System.out.println(structure);
- * 		} catch (IOException e) {
- * 			e.printStackTrace();
- * 		}
+ *  Structure loadStructure(String pathToPDBFile) {
+ * 		PDBFileReader pdbreader = new PDBFileReader();
+ * 		Structure structure = pdbreader.getStructure(pathToPDBFile);
+ * 		System.out.println(structure);
  * 		return structure;
  * 	}
  *  </pre>
@@ -89,20 +77,16 @@
  * <hr>
  * <p>
  * Q: How can I calculate Phi and Psi angles of AminoAcids?
- * </p>
  * <p>
  * A:
- * </p>
- * <pre>
- *  void calcPhiPsi({@link Structure} structure){
- *
+ * <pre>{@code
+ *  void calcPhiPsi(Structure structure) {
  *
  * 		// get the first chain from the structure
- *
- * 		{@link Chain} chain  = structure.getChain(0);
+ * 		Chain chain  = structure.getChain(0);
  *
  * 		// A protein chain consists of a number of groups. These can be either
- * 		// {@link AminoAcid}, {@link HetatomImpl Hetatom} or {@link NucleotideImpl Nucleotide} groups.
+ * 		// AminoAcid, HetatomImpl or NucleotideImpl groups.
  * 		//
  * 		// Note: BioJava provides access to both the ATOM and SEQRES data in a PDB file.
  * 		// since we are interested in doing calculations here, we only request the groups
@@ -111,54 +95,35 @@
  * 		//  get the Groups of the chain that are AminoAcids.
  * 		List<Group> groups = chain.getAtomGroups(GroupType.AMINOACID);
  *
- * 		{@link AminoAcid} a;
- * 		{@link AminoAcid} b;
- * 		{@link AminoAcid} c ;
- *
- * 		for ( int i=0; i < groups.size(); i++){
- *
+ * 		AminoAcid a;
+ * 		AminoAcid b;
+ * 		AminoAcid c;
+ * 		for (int i=0; i < groups.size(); i++) {
  * 			// since we requested only groups of type AMINOACID they will always be amino acids
  * 			// Nucleotide and Hetatom groups will not be present in the groups list.
- *
- * 			b = ({@link AminoAcid})groups.get(i);
- *
- * 			double phi =360.0;
- * 			double psi =360.0;
- *
- * 			if ( i > 0) {
- * 				a = ({@link AminoAcid})groups.get(i-1) ;
- * 				try {
- *
- * 					// the Calc class provides utility methods for various calculations on
- * 					// structures, groups and atoms
- *
- * 					phi = {@link Calc}.getPhi(a,b);
- * 				} catch ({@link StructureException} e){
- * 					e.printStackTrace();
- * 					phi = 360.0 ;
- * 				}
+ * 			b = (AminoAcid)groups.get(i);
+ * 			double phi = 360.0;
+ * 			double psi = 360.0;
+ *
+ * 			if (i > 0) {
+ * 				a = (AminoAcid)groups.get(i-1) ;
+ * 				// the Calc class provides utility methods for various calculations on
+ * 				// structures, groups and atoms
+ * 				phi = Calc.getPhi(a,b);
  * 			}
- * 			if ( i < groups.size()-1) {
- * 				c = ({@link AminoAcid})groups.get(i+1) ;
- * 				try {
- * 					psi = {@link Calc}.getPsi(b,c);
- * 				}catch ({@link StructureException} e){
- * 					e.printStackTrace();
- * 					psi = 360.0 ;
- * 				}
+ * 			if (i < groups.size()-1) {
+ * 				c = (AminoAcid)groups.get(i+1) ;
+ * 				psi = Calc.getPsi(b, c);
  * 			}
- *
  * 			System.out.print(b.getPDBCode() + " " + b.getPDBName() + ":"  );
- *
  * 			System.out.println(String.format("\tphi: %+7.2f psi: %+7.2f", phi, psi));
- *
  * 		}
- * </pre>
+ * 	}
+ * }</pre>
  * <hr>
  *
  * @author Andreas Prlic
  * @since 1.4
- * @version %I% %G%
  */
 public interface Structure extends Cloneable, Serializable {
 
@@ -776,13 +741,11 @@ public interface Structure extends Cloneable, Serializable {
 	 *
 	 * @param pdb_id  a String specifying the PDBCode
 	 * @see #getPDBCode
-	 * @deprecated use {@link #setPDBCode(PdbId)}
+	 * @deprecated use {@link #setPdbId(PdbId)}
 	 */
 	@Deprecated
 	void setPDBCode (String pdb_id);
 
-
-
 	/**
 	 * Returns the PDB identifier associated with this StructureIdentifier.
 	 * @return the {@link PdbId} object
@@ -790,7 +753,6 @@ public interface Structure extends Cloneable, Serializable {
 	 */
 	PdbId getPdbId();
 	
-	
 	/**Sets the {@link PdbId} identifier associated with this structure.
 	 * @param pdbId the {@link PdbId} identifier object to set
 	 * @since 6.0.0
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
index 75e4b95194..0b802787dd 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
@@ -206,6 +206,7 @@ public static Structure getBiologicalAssembly(String pdbId, int biolAssemblyNr)
 	 * Returns all biological assemblies for the given PDB id.
 	 * <p>
 	 * The output Structure will be different depending on the multiModel parameter:
+	 * <ul>
 	 * <li>
 	 * the symmetry-expanded chains are added as new models, one per transformId. All original models but
 	 * the first one are discarded.
@@ -214,6 +215,7 @@ public static Structure getBiologicalAssembly(String pdbId, int biolAssemblyNr)
 	 * as original with symmetry-expanded chains added with renamed chain ids and names (in the form
 	 * originalAsymId_transformId and originalAuthId_transformId)
 	 * </li>
+	 * </ul>
 	 * If only one biological assembly is required use {@link #getBiologicalAssembly(String)} or {@link #getBiologicalAssembly(String, int)} instead.
 	 * @param pdbId
 	 * @param multiModel if true the output Structure will be a multi-model one with one transformId per model,
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java
index 2b8cb669cf..ba8de5d870 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java
@@ -33,12 +33,12 @@
  * An identifier that <em>uniquely</em> identifies a whole {@link Structure} or
  * arbitrary substructure. Common examples would be reducing a structure to a
  * single chain, domain, or residue range.
- *
+ * <p>
  * StructureIdentifiers are represented by unique strings. The getId() and fromId()
  * methods convert to and from the string representation.
- *
+ * <p>
  * Implementations should provide a constructor which takes a String. A static
- * <tt>fromId(String)</tt> method is also recommended.
+ * <code>fromId(String)</code> method is also recommended.
  *
  * @author dmyersturnbull
  * @author Spencer Bliven
@@ -59,7 +59,7 @@ public interface StructureIdentifier extends Serializable {
 	 * Loads a structure encompassing the structure identified.
 	 * The Structure returned should be suitable for passing as
 	 * the input to {@link #reduce(Structure)}.
-	 *
+	 * <p>
 	 * It is recommended that the most complete structure available be returned
 	 * (e.g. the full PDB) to allow processing of unselected portions where
 	 * appropriate.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java
index 016d1f592c..3505deaf02 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java
@@ -42,15 +42,15 @@
 
 /**
  * Represents a structure loaded from a URL (including a file URL)
- *
+ * <p>
  * A few custom query parameters are supported:
  *
  * <ul>
- * <li><tt>format=[pdb|cif]</tt> Specify the file format (will otherwise be
+ * <li><code>format=[pdb|cif]</code> Specify the file format (will otherwise be
  *     guessed from the extension)
- * <li><tt>pdbId=[String]</tt> Specify the PDB ID (also guessed from the filename)
- * <li><tt>chainID=[String]</tt> A single chain from the structure
- * <li><tt>residues=[String]</tt> Residue ranges, in a form understood by
+ * <li><code>pdbId=[String]</code> Specify the PDB ID (also guessed from the filename)
+ * <li><code>chainID=[String]</code> A single chain from the structure
+ * <li><code>residues=[String]</code> Residue ranges, in a form understood by
  *     {@link SubstructureIdentifier}
  * </ul>
  * @author Spencer Bliven
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java
index 70f4acb64f..e35e88fce8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java
@@ -39,7 +39,7 @@
  * The original CE paper is available from here: <a href="http://peds.oxfordjournals.org/cgi/content/short/11/9/739">http://peds.oxfordjournals.org/cgi/content/short/11/9/739</a>
  *
  * For a demo of how to use this algorithm, visit the BioJava web site:
- * <a href="">CE usage example</a>.
+ * <a href="https://github.com/biojava/biojava-tutorial/blob/master/structure/alignment.md">CE usage example</a>.
  *
  * The BioJava CE version is based on CE version 2.3 (2003 or 2004).
  *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java
index 11f36456ab..8d053a2520 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java
@@ -168,8 +168,9 @@ public static void getAlign(AFPChain afpChain,Atom[] ca1,Atom[] ca2) {
 	 * <ul>
 	 * <li>{@link AFPChain#getOptAln()} and lengths
 	 * </ul>
-	 *
-	 * <section>Known Bugs</section>
+	 * <p>
+	 * Known Bugs:
+	 * <p>
 	 * Expects the alignment to have linear topology. May give odd results
 	 * for circular permutations and other complicated topologies.
 	 *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
index f43a97392f..15d1e0712f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
@@ -470,10 +470,10 @@ public static Map<Integer, Integer> guessSequentialAlignment(
 	 * Retrieves the optimum alignment from an AFPChain and returns it as a
 	 * java collection. The result is indexed in the same way as
 	 * {@link AFPChain#getOptAln()}, but has the correct size().
-	 * <pre>
+	 * <pre>{@code
 	 * List<List<List<Integer>>> aln = getOptAlnAsList(AFPChain afpChain);
 	 * aln.get(blockNum).get(structureNum={0,1}).get(pos)
-	 * </pre>
+	 * }</pre>
 	 *
 	 * @param afpChain
 	 * @return
@@ -504,7 +504,7 @@ public static List<List<List<Integer>>> getOptAlnAsList(AFPChain afpChain) {
 
 
 	/**
-	 * A Map<K,V> can be viewed as a function from K to V. This class represents
+	 * A {@code Map<K,V>} can be viewed as a function from K to V. This class represents
 	 * the identity function. Getting a value results in the value itself.
 	 *
 	 * <p>The class is a bit inconsistent when representing its contents. On
@@ -1078,9 +1078,9 @@ public static Map<Integer, Integer> fromConciseAlignmentString(String string) {
 
 	/**
 	 * Method that calculates the number of gaps in each subunit block of an optimal AFP alignment.
-	 *
-	 * INPUT: an optimal alignment in the format int[][][].
-	 * OUTPUT: an int[] array of <order> length containing the gaps in each block as int[block].
+	 * @param optAln
+	 * 				an optimal alignment in the format int[][][]
+	 * @return an int[] array of order length containing the gaps in each block as int[block]
 	 */
 	public static int[] calculateBlockGap(int[][][] optAln){
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
index fe5bfb0f2e..e547a0cafc 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
@@ -162,7 +162,6 @@ public AtomCache(UserConfiguration config) {
 	 * @return an array of Atoms.
 	 * @throws IOException
 	 * @throws StructureException
-	 * @see
 	 */
 	public Atom[] getAtoms(String name) throws IOException, StructureException {
 		return getAtoms(new StructureName(name));
@@ -189,7 +188,6 @@ public Atom[] getAtoms(StructureIdentifier name) throws IOException, StructureEx
 	 * @return an array of Atoms.
 	 * @throws IOException
 	 * @throws StructureException
-	 * @see
 	 */
 	public Atom[] getRepresentativeAtoms(String name) throws IOException, StructureException {
 		return getRepresentativeAtoms(new StructureName(name));
@@ -223,7 +221,7 @@ public Atom[] getRepresentativeAtoms(StructureIdentifier name) throws IOExceptio
 	 * if false the outputStructure will be as the original with added chains with renamed asymIds (in the form originalAsymId_transformId and originalAuthId_transformId).
 	 * @return a structure object
 	 * @throws IOException
-	 * @throws StructureException if biassemblyId < 0 or other problems while loading structure
+	 * @throws StructureException if biassemblyId &lt; 0 or other problems while loading structure
 	 * @since 3.2
 	 */
 	public Structure getBiologicalAssembly(String pdbId, int bioAssemblyId, boolean multiModel)
@@ -247,7 +245,7 @@ public Structure getBiologicalAssembly(String pdbId, int bioAssemblyId, boolean
 	 * if false the outputStructure will be as the original with added chains with renamed asymIds (in the form originalAsymId_transformId and originalAuthId_transformId).
 	 * @return a structure object
 	 * @throws IOException
-	 * @throws StructureException if biassemblyId < 0 or other problems while loading structure
+	 * @throws StructureException if biassemblyId &lt; 0 or other problems while loading structure
 	 * @since 6.0.0
 	 */
 	public Structure getBiologicalAssembly(PdbId pdbId, int bioAssemblyId, boolean multiModel)
@@ -305,7 +303,7 @@ public Structure getBiologicalAssembly(PdbId pdbId, int bioAssemblyId, boolean m
 	 * the asymmetric unit will be returned, e.g. for NMR structures.
 	 *
 	 * <p>Biological assemblies can also be accessed using
-	 * <tt>getStructure("BIO:<i>[pdbId]</i>")</tt>
+	 * <code>getStructure("BIO:<i>[pdbId]</i>")</code>
 	 * @param pdbId the PDB id
 	 * @param multiModel if true the output Structure will be a multi-model one with one transformId per model,
 	 * if false the outputStructure will be as the original with added chains with renamed asymIds (in the form originalAsymId_transformId and originalAuthId_transformId).
@@ -791,7 +789,7 @@ protected void flagLoadingFinished(PdbId pdbId) {
 
 	/**
 	 * Loads a structure directly by PDB ID
-	 * @param pdbId
+	 * @param id
 	 * @return
 	 * @throws IOException
 	 * @throws StructureException
@@ -806,7 +804,6 @@ public Structure getStructureForPdbId(String id) throws IOException, StructureEx
 	 * @param pdbId
 	 * @return
 	 * @throws IOException
-	 * @throws StructureException
 	 */
 	public Structure getStructureForPdbId(PdbId pdbId) throws IOException {
 		if (pdbId == null)
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
index 5297443a34..51b8e91497 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
@@ -259,7 +259,7 @@ public FileParsingParameters getFileParsingParameters(){
 	 *   Load the requested ID from the PDB's obsolete repository
 	 * <li>{@link ObsoleteBehavior#FETCH_CURRENT FETCH_CURRENT}
 	 *   Load the most recent version of the requested structure
-	 *
+	 * </ul>
 	 * <p>This setting may be silently ignored by implementations which do not have
 	 * access to the server to determine whether an entry is obsolete, such as
 	 * if {@link #isAutoFetch()} is false. Note that an obsolete entry may still be
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileReader.java
index 5591fbdd84..7e12874dbc 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileReader.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileReader.java
@@ -30,27 +30,20 @@
 import java.io.InputStream;
 
 /**
- * <p>
  *  The wrapper class for parsing a PDB file.
- *  </p>
- *
  *
- *  <p>
+ * <p>
  *  Several flags can be set for this class
- *  <ul>
+ * <ul>
  *
  * <li> {@link #setAutoFetch(boolean)} - if the PDB file can not be found locally, should it be fetched
  *  from the PDB ftp servers? (default:false)</li>
- *  <li> Other parameters can be set using the {@link #setFileParsingParameters(FileParsingParameters)}</li>
- *  </ul>
- *  </p>
- *
- *
+ * <li> Other parameters can be set using the {@link #setFileParsingParameters(FileParsingParameters)}</li>
+ * </ul>
  *
  *<h2>Example</h2>
  * <p>
  * Q: How can I get a Structure object from a PDB file?
- * </p>
  * <p>
  * A:
  * <pre>
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/LUDecomposition.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/LUDecomposition.java
index 00f5d302ec..64c77c3665 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/LUDecomposition.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/LUDecomposition.java
@@ -22,10 +22,10 @@
 
 	/** LU Decomposition.
 	<P>
-	For an m-by-n matrix A with m >= n, the LU decomposition is an m-by-n
+	For an m-by-n matrix A with m &gt;= n, the LU decomposition is an m-by-n
 	unit lower triangular matrix L, an n-by-n upper triangular matrix U,
 	and a permutation vector piv of length m so that A(piv,:) = L*U.
-	If m < n, then L is m-by-m and U is m-by-n.
+	If m &lt; n, then L is m-by-m and U is m-by-n.
 	<P>
 	The LU decompostion with pivoting always exists, even if the matrix is
 	singular, so the constructor will never fail.  The primary use of the
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/Matrix.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/Matrix.java
index 2abdd1c972..fab188ce98 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/Matrix.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/Matrix.java
@@ -62,7 +62,7 @@
  * </UL>
  * <DL>
  * <DT><B>Example of use:</B></DT>
- * <P>
+ *
  * <DD>Solve a linear system A x = b and compute the residual norm, ||b - A x||.
  * <P><PRE>
  * 		double[][] vals = {{1.,2.,3},{4.,5.,6.},{7.,8.,10.}};
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/package-info.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/package-info.java
index fecc3afee6..8d5fb81573 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/package-info.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/package-info.java
@@ -19,10 +19,8 @@
  *
  */
 /**
- * <BODY>
- * <P>
  * Interfaces and classes for protein structure (PDB).
- * </P>
+ *
  * <p>
  * See also the <a href="https://github.com/biojava/biojava3-tutorial/blob/master/structure/README.md">BioJava 3 tutorial</a> for more information on the protein structure modules.
  * </p>
@@ -62,8 +60,7 @@
  * For more documentation on how to work with the Structure API please
  * see <a href="http://biojava.org/wiki/BioJava:CookBook#Protein_Structure" target="_top">
  * http://biojava.org/wiki/BioJava:CookBook#Protein_Structure</a>
- * </p>
- * </BODY>
+ *
  * @since 1.5
  */
 package org.biojava.nbio.structure;
\ No newline at end of file
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/BridgeType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/BridgeType.java
index 04e35fe14d..26b4656767 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/BridgeType.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/BridgeType.java
@@ -22,7 +22,7 @@
 
 /**
  * A bridge is formed by two non-overlapping stretches of three residues each
- * (i-1,i,i+1) and (j-1,j,j+1), where i<j.
+ * (i-1,i,i+1) and (j-1,j,j+1), where i&lt;j.
  * <p>
  * Depending on two basic patterns, a Bridge can be either of type parallel (H
  * bonds in {(i-1,j) and (j,i+1)} OR {(j-1,i) and (i,j-1)}) or antiparallel (H
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
index 9d25a7acbc..70b69afe14 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
@@ -31,7 +31,7 @@
 import java.util.List;
 
 /**
- * @see http://en.wikipedia.org/wiki/Rotation_group_SO(3)
+ * See <a href="http://en.wikipedia.org/wiki/Rotation_group_SO(3)">http://en.wikipedia.org/wiki/Rotation_group_SO(3)</a>
  * @author Peter
  */
 public class RotationGroup implements Iterable<Rotation> {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java
index 4527a7fa49..0700e34571 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java
@@ -63,7 +63,6 @@
  * <li>Repeat the last two steps until no more significant results are found.
  * <li>Map back all residues in a multiple alignment of the repeats.
  * </ul>
- * </li>
  *
  * @author Aleix Lafita
  * @since 4.1.1
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java
index 58a8c89394..d03e90080f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java
@@ -43,7 +43,7 @@
  * Optimizes a symmetry alignment by a Monte Carlo score optimization of the
  * repeat multiple alignment. The superposition of the repeats is not free
  * (felxible), because it is constrained on the symmetry axes found in the
- * structure. This is the main difference to the {@link MultipleMC} algorithm in
+ * structure. This is the main difference to the {@link org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain} algorithm in
  * biojava. Another major difference is that the free Pool is shared for all
  * repeats, so that no residue can appear to more than one repeat at a time.
  * <p>

From 2bbc82438cc8aba6dbbfbc362aef4959a0714918 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Tue, 7 Jan 2025 13:52:17 -0800
Subject: [PATCH 20/90] Javadoc fix: remaining errors in structure module.
 Mostly obsolete references

---
 .../nbio/structure/test/scop/ScopDescriptionTest.java     | 2 +-
 .../src/main/java/demo/DemoChangeChemCompProvider.java    | 5 ++---
 .../org/biojava/nbio/structure/align/model/AFPChain.java  | 2 +-
 .../biojava/nbio/structure/align/util/AlignmentTools.java | 4 +---
 .../org/biojava/nbio/structure/align/util/AtomCache.java  | 7 +++----
 .../org/biojava/nbio/structure/io/LocalPDBDirectory.java  | 7 +++----
 .../java/org/biojava/nbio/structure/io/PDBFileReader.java | 5 +----
 .../symmetry/internal/SequenceFunctionRefiner.java        | 8 ++++----
 .../java/org/biojava/nbio/structure/HetatomImplTest.java  | 2 +-
 .../java/org/biojava/nbio/structure/PDBStatusTest.java    | 2 +-
 .../org/biojava/nbio/structure/ResidueNumberTest.java     | 2 +-
 .../test/java/org/biojava/nbio/structure/SiteTest.java    | 2 +-
 .../biojava/nbio/structure/align/util/AtomCacheTest.java  | 2 +-
 13 files changed, 21 insertions(+), 29 deletions(-)

diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopDescriptionTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopDescriptionTest.java
index 39f1fdacf2..5976d635c9 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopDescriptionTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopDescriptionTest.java
@@ -30,7 +30,7 @@
 
 
 /**
- * @author Spencer Bliven <sbliven@ucsd.edu>
+ * @author Spencer Bliven sbliven@ucsd.edu
  *
  */
 public class ScopDescriptionTest {
diff --git a/biojava-structure/src/main/java/demo/DemoChangeChemCompProvider.java b/biojava-structure/src/main/java/demo/DemoChangeChemCompProvider.java
index bb78c98d77..b3c292c92d 100644
--- a/biojava-structure/src/main/java/demo/DemoChangeChemCompProvider.java
+++ b/biojava-structure/src/main/java/demo/DemoChangeChemCompProvider.java
@@ -34,9 +34,8 @@
 
 /**
  *  This demo shows how to use an alternative ChemCompProvider. The default mechanism in BioJava is to access chemical
- *  componentsby using the {@link DownloadChemCompProvider}. It fetches and locally caches chemical component
- *  definitions as they are encountered during file parsing. It can be enabled by using the
- *  {@link FileParsingParameters#setLoadChemCompInfo(boolean)} method.
+ *  components by using the {@link DownloadChemCompProvider}. It fetches and locally caches chemical component
+ *  definitions as they are encountered during file parsing.
  * <p>
  * The {@link AllChemCompProvider} downloads and unpacks all chemcomps. It is slower and requires more memory than the
  * default {@link DownloadChemCompProvider}, but it avoids network access to the FTP site, if a new chemcomp is
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java
index 001d32d806..0c4ee5ec95 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java
@@ -1312,7 +1312,7 @@ public void setSequentialAlignment(boolean sequentialAlignment) {
 	 * up to the alignment algorithm.
 	 *
 	 * <p>Note:
-	 * A {@link org.biojava.nbio.structure.gui.JMatrixPanel}, which is used in
+	 * The org.biojava.nbio.structure.gui.JMatrixPanel, used in
 	 * the structure-gui package to display distance matrices, will display the
 	 * transpose of this matrix. Be sure to take that into account when debugging
 	 * visually.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
index 15d1e0712f..c6791f4ed2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
@@ -239,8 +239,6 @@ public static <S,T> Map<S,T> applyAlignment(Map<S, T> alignmentMap, Map<T,S> ide
 			}
 		}
 
-
-
 		Map<S, T> imageMap = new HashMap<>(alignmentMap.size());
 
 		//TODO handle nulls consistently.
@@ -282,7 +280,7 @@ public static <S,T> Map<S,T> applyAlignment(Map<S, T> alignmentMap, Map<T,S> ide
 	 */
 	public static int getSymmetryOrder(Map<Integer, Integer> alignment,
 									   final int maxSymmetry, final float minimumMetricChange) {
-		return getSymmetryOrder(alignment, new IdentityMap<Integer>(), maxSymmetry, minimumMetricChange);
+		return getSymmetryOrder(alignment, new IdentityMap<>(), maxSymmetry, minimumMetricChange);
 	}
 	/**
 	 * Tries to detect symmetry in an alignment.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
index e547a0cafc..1435191c2c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
@@ -464,8 +464,7 @@ public String getPath() {
 	 * <li>If only a PDB code is provided, the whole structure will be return including ligands, but the first model
 	 * only (for NMR).
 	 * <li>Chain IDs are case sensitive, PDB ids are not. To specify a particular chain write as: 4hhb.A or 4HHB.A</li>
-	 * <li>To specify a SCOP domain write a scopId e.g. d2bq6a1. Some flexibility can be allowed in SCOP domain names,
-	 * see {@link #setStrictSCOP(boolean)}</li>
+	 * <li>To specify a SCOP domain write a scopId e.g. d2bq6a1. </li>
 	 * <li>URLs are accepted as well</li>
 	 * </ul>
 	 *
@@ -672,7 +671,7 @@ public void setFileParsingParams(FileParsingParameters params) {
 	 *
 	 * <p>This setting may be silently ignored by implementations which do not have
 	 * access to the server to determine whether an entry is obsolete, such as
-	 * if {@link #isAutoFetch()} is false. Note that an obsolete entry may still be
+	 * certain {@link FetchBehavior}s. Note that an obsolete entry may still be
 	 * returned even this is FETCH_CURRENT if the entry is found locally.
 	 *
 	 * @param behavior Whether to fetch obsolete records
@@ -685,7 +684,7 @@ public void setObsoleteBehavior(ObsoleteBehavior behavior) {
 	/**
 	 * Returns how this instance deals with obsolete entries. Note that this
 	 * setting may be ignored by some implementations or in some situations,
-	 * such as when {@link #isAutoFetch()} is false.
+	 * such as certain {@link FetchBehavior}s.
 	 *
 	 * <p>For most implementations, the default value is
 	 * {@link ObsoleteBehavior#THROW_EXCEPTION THROW_EXCEPTION}.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
index 51b8e91497..4ec4577f59 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
@@ -262,7 +262,7 @@ public FileParsingParameters getFileParsingParameters(){
 	 * </ul>
 	 * <p>This setting may be silently ignored by implementations which do not have
 	 * access to the server to determine whether an entry is obsolete, such as
-	 * if {@link #isAutoFetch()} is false. Note that an obsolete entry may still be
+	 * certain {@link FetchBehavior}s. Note that an obsolete entry may still be
 	 * returned even this is FETCH_CURRENT if the entry is found locally.
 	 *
 	 * @param behavior Whether to fetch obsolete records
@@ -276,7 +276,7 @@ public void setObsoleteBehavior(ObsoleteBehavior behavior) {
 	/**
 	 * Returns how this instance deals with obsolete entries. Note that this
 	 * setting may be ignored by some implementations or in some situations,
-	 * such as when {@link #isAutoFetch()} is false.
+	 * such as certain {@link FetchBehavior}s.
 	 *
 	 * <p>For most implementations, the default value is
 	 * {@link ObsoleteBehavior#THROW_EXCEPTION THROW_EXCEPTION}.
@@ -295,10 +295,9 @@ public ObsoleteBehavior getObsoleteBehavior() {
 	public FetchBehavior getFetchBehavior() {
 		return fetchBehavior;
 	}
+
 	/**
 	 * Set the behavior for fetching files from the server.
-	 * This replaces the {@link #setAutoFetch(boolean)} method with a more
-	 * extensive set of options.
 	 * @param fetchBehavior
 	 */
 	public void setFetchBehavior(FetchBehavior fetchBehavior) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileReader.java
index 7e12874dbc..dec97b4f61 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileReader.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileReader.java
@@ -35,10 +35,7 @@
  * <p>
  *  Several flags can be set for this class
  * <ul>
- *
- * <li> {@link #setAutoFetch(boolean)} - if the PDB file can not be found locally, should it be fetched
- *  from the PDB ftp servers? (default:false)</li>
- * <li> Other parameters can be set using the {@link #setFileParsingParameters(FileParsingParameters)}</li>
+ * <li> Parameters can be set using the {@link #setFileParsingParameters(FileParsingParameters)}</li>
  * </ul>
  *
  *<h2>Example</h2>
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java
index beeba62df2..a6ad226698 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java
@@ -61,12 +61,12 @@ public MultipleAlignment refine(AFPChain selfAlignment, Atom[] atoms,
 
 	/**
 	 * Refines a CE-Symm alignment so that it is perfectly symmetric.
-	 *
+	 * <p>
 	 * The resulting alignment will have a one-to-one correspondance between
 	 * aligned residues of each symmetric part.
 	 *
 	 * @param afpChain Input alignment from CE-Symm
-	 * @param k Symmetry order. This can be guessed by {@link CeSymm#getSymmetryOrder(AFPChain)}
+	 * @param k Symmetry order. This can be guessed by {@link AlignmentTools#getSymmetryOrder(Map, Map, int, float)}
 	 * @return The refined alignment
 	 * @throws StructureException
 	 * @throws RefinerFailedException
@@ -97,11 +97,11 @@ public static AFPChain refineSymmetry(AFPChain afpChain, Atom[] ca1, Atom[] ca2,
 
 	/**
 	 * Refines a CE-Symm alignment so that it is perfectly symmetric.
-	 *
+	 * <p>
 	 * The resulting alignment will have a one-to-one correspondance between
 	 * aligned residues of each symmetric part.
 	 * @param alignment The input alignment, as a map. This will be modified.
-	 * @param k Symmetry order. This can be guessed by {@link CeSymm#getSymmetryOrder(AFPChain)}
+	 * @param k Symmetry order. This can be guessed by {@link AlignmentTools#getSymmetryOrder(Map, Map, int, float)}
 	 * @return A modified map with the refined alignment
 	 * @throws StructureException
 	 */
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/HetatomImplTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/HetatomImplTest.java
index 74556c2434..8f9d190a71 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/HetatomImplTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/HetatomImplTest.java
@@ -29,7 +29,7 @@
 
 /**
  *
- * @author Jules Jacobsen <jacobsen@ebi.ac.uk>
+ * @author Jules Jacobsen jacobsen@ebi.ac.uk
  */
 public class HetatomImplTest {
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/PDBStatusTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/PDBStatusTest.java
index 82e26bd802..6d97b0889d 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/PDBStatusTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/PDBStatusTest.java
@@ -27,7 +27,7 @@
 import java.io.IOException;
 
 /**
- * @author Spencer Bliven <sbliven@ucsd.edu>
+ * @author Spencer Bliven sbliven@ucsd.edu
  *
  */
 public class PDBStatusTest {
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/ResidueNumberTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/ResidueNumberTest.java
index c594f0dd18..c5ebb6c028 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/ResidueNumberTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/ResidueNumberTest.java
@@ -29,7 +29,7 @@
 
 /**
  *
- * @author Jules Jacobsen <jacobsen@ebi.ac.uk>
+ * @author Jules Jacobsen jacobsen@ebi.ac.uk
  */
 public class ResidueNumberTest {
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/SiteTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/SiteTest.java
index d7a64d0017..5e39000e90 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/SiteTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/SiteTest.java
@@ -29,7 +29,7 @@
 
 /**
  * Tests functionality of Site class.
- * @author Jules Jacobsen <jacobsen@ebi.ac.uk>
+ * @author Jules Jacobsen jacobsen@ebi.ac.uk
  */
 public class SiteTest {
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java
index ec2763df9a..073a679dbb 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java
@@ -165,7 +165,7 @@ public void testGetStructureForDomain3() throws IOException, StructureException
 	}
 
 	/**
-	 * Test parsing of chain-less ranges (present in SCOP < 1.73)
+	 * Test parsing of chain-less ranges (present in SCOP &lt; 1.73)
 	 * @throws IOException
 	 * @throws StructureException
 	 */

From aefa34a52f1c208e3b43d005d5db336052cef900 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Tue, 7 Jan 2025 14:02:49 -0800
Subject: [PATCH 21/90] Javadoc fix: errors in structure-gui module

---
 .../main/java/org/biojava/nbio/ontology/io/package-info.java | 2 --
 biojava-ontology/src/main/java/package-info.java             | 2 --
 biojava-structure-gui/src/main/java/demo/AFPFromFasta.java   | 5 ++---
 .../org/biojava/nbio/structure/align/gui/DotPlotPanel.java   | 1 -
 .../org/biojava/nbio/structure/align/gui/MemoryMonitor.java  | 2 +-
 .../org/biojava/nbio/structure/align/gui/SelectPDBPanel.java | 3 ++-
 .../structure/align/gui/aligpanel/MultipleAligPanel.java     | 4 ++--
 .../nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java | 2 +-
 .../org/biojava/nbio/structure/gui/events/package-info.java  | 2 --
 .../java/org/biojava/nbio/structure/gui/package-info.java    | 2 --
 .../gui/util/color/ContinuousColorMapperTransform.java       | 2 +-
 .../biojava/nbio/structure/gui/util/color/HSVColorSpace.java | 3 +--
 .../structure/gui/util/color/LinearColorInterpolator.java    | 2 +-
 .../org/biojava/nbio/structure/gui/util/package-info.java    | 2 --
 .../biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java | 2 +-
 .../symmetry/jmolScript/JmolSymmetryScriptGenerator.java     | 2 +-
 16 files changed, 13 insertions(+), 25 deletions(-)

diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/package-info.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/package-info.java
index b6aed42304..43c5d532bc 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/package-info.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/package-info.java
@@ -19,10 +19,8 @@
  *
  */
 /**
- * <BODY>
  * <P>
  * Tools for loading and saving ontologies.
  * </P>
- * </BODY>
  */
 package org.biojava.nbio.ontology.io;
\ No newline at end of file
diff --git a/biojava-ontology/src/main/java/package-info.java b/biojava-ontology/src/main/java/package-info.java
index 56cc7e5eba..7cafa32539 100644
--- a/biojava-ontology/src/main/java/package-info.java
+++ b/biojava-ontology/src/main/java/package-info.java
@@ -19,7 +19,6 @@
  *
  */
 /**
- * <BODY>
  * <P>
  * A general-purpose API for ontologies.
  * These are directed graphs consisting of <code>Term</code> obects.  Each
@@ -30,5 +29,4 @@
  * <P>Some interfaces and implementations from this package are extended in
  * {@link org.biojavax.ontology biojavax} to better facilitate their persistence to
  * biosql.</P>
- * </BODY>
  */
\ No newline at end of file
diff --git a/biojava-structure-gui/src/main/java/demo/AFPFromFasta.java b/biojava-structure-gui/src/main/java/demo/AFPFromFasta.java
index 97f32828be..5d91f22aa8 100644
--- a/biojava-structure-gui/src/main/java/demo/AFPFromFasta.java
+++ b/biojava-structure-gui/src/main/java/demo/AFPFromFasta.java
@@ -41,10 +41,9 @@
 
 /**
  * Demo displaying a structural alignment from a FASTA file using {@link FastaAFPChainConverter}.
- *
- * @author dmyerstu
- * @see {@link DemoAlignmentFromFasta} Also demonstrates the display of {@link StructureAlignment StructureAlignments} from FASTA sequences, but does so using the more general
+ * See {@link DemoAlignmentFromFasta} Also demonstrates the display of {@link StructureAlignment StructureAlignments} from FASTA sequences, but does so using the more general
  *      {@link FastaStructureParser}
+ * @author dmyerstu
  */
 public class AFPFromFasta {
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DotPlotPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DotPlotPanel.java
index 0532d91498..b96b10a066 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DotPlotPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DotPlotPanel.java
@@ -56,7 +56,6 @@ public class DotPlotPanel extends ScaleableMatrixPanel {
 	/**
 	 *
 	 * @param alignment The alignment to plot
-	 * @param background [Optional]A matrix of 'background colors' over which to draw the alignment.
 	 *
 	 *	Originally designed as a matrix of RMSD values between AFPs, so it is colorized
 	 *	accordingly from red (0) to black (>10).
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java
index 91ca7571b4..3c60ab3275 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java
@@ -51,7 +51,7 @@
 
 
 /**
- * Tracks Memory allocated & used, displayed in graph form.
+ * Tracks Memory allocated and used, displayed in graph form.
  */
 public class MemoryMonitor extends JPanel {
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java
index 240246bb88..41eaf80b1e 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java
@@ -43,7 +43,8 @@
 import org.biojava.nbio.structure.gui.util.StructurePairSelector;
 
 
-/** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges
+/**
+ * A Panel that allows user to specify PDB and chain ID, as well as sub-ranges
  *
  * @author Andreas
  *
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java
index 483df6f2df..3614907b5b 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java
@@ -154,8 +154,8 @@ public MultipleAligPanel(AFPChain afpChain, Atom[] ca1, Atom[] ca2,
 	/**
 	 * Constructor using a MultipleAlignment.
 	 *
-	 * @param multAln
-	 * @param colors
+	 * @param msa
+	 * @param jm
 	 */
 	public MultipleAligPanel(MultipleAlignment msa, AbstractAlignmentJmol jm) {
 		this();
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java
index 4663505797..535ad182fe 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java
@@ -196,7 +196,7 @@ public Structure getStructure(){
 
 	/**
 	 * Set the title of the AlignmentJmol window.
-	 * @param label
+	 * @param title
 	 */
 	public void setTitle(String title){
 		frame.setTitle(title);
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/events/package-info.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/events/package-info.java
index 138365c88a..001686e4f6 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/events/package-info.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/events/package-info.java
@@ -19,12 +19,10 @@
  *
  */
 /**
- * <BODY>
  * <P>
  * Some event classes for the protein structure GUIs.
  * Possible start classes are one level higher at
  * org.biojava.nbio.structure.gui.BiojavaJmol, and org.biojava.nbio.structure.gui.AlignmentGui.
  * </P>
- * </BODY>
  */
 package org.biojava.nbio.structure.gui.events;
\ No newline at end of file
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/package-info.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/package-info.java
index 1a4bc6d6af..ed9ae12804 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/package-info.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/package-info.java
@@ -19,13 +19,11 @@
  *
  */
 /**
- * <BODY>
  * <P>
  * A few convenience classes to view protein structures with Jmol (if it is on the classpath),
  * to calculate a protein structure alignment and to investigate the internals of the protein structure alignment algorithm.
  * Possible start classes are BiojavaJmol, AlignmentGui.
  * Also MVC interface for structure-gui
  * </P>
- * </BODY>
  */
 package org.biojava.nbio.structure.gui;
\ No newline at end of file
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapperTransform.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapperTransform.java
index 5cd010b356..d691a5237d 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapperTransform.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapperTransform.java
@@ -60,7 +60,7 @@ public Color getColor(double value) {
 
 	/**
 	 * An arbitrary transform over reals
-	 * @param the input value
+	 * @param value the input value
 	 * @return the transformed value
 	 */
 	public abstract double transform(double value);
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/HSVColorSpace.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/HSVColorSpace.java
index 4aafce9f1e..31e3919ae5 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/HSVColorSpace.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/HSVColorSpace.java
@@ -79,9 +79,8 @@ public static void main(String[] args) {
 
 
 	}
+
 	/**
-	 * @param type
-	 * @param numcomponents
 	 */
 	public HSVColorSpace() {
 		super(ColorSpace.TYPE_HSV, 3);
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/LinearColorInterpolator.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/LinearColorInterpolator.java
index 9522ec7a15..2e6d1fc4e4 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/LinearColorInterpolator.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/LinearColorInterpolator.java
@@ -142,7 +142,7 @@ public Color interpolate(Color a, Color b, float mixing) {
 	 * InterpolationDirections.
 	 *
 	 * @param colorSpace The color space for interpolation
-	 * @param interpDirection An array of size colorSpace.getNumComponents()
+	 * @param dir An array of size colorSpace.getNumComponents()
 	 * 		giving the interpolation direction for each component.
 	 */
 	public void setColorSpace(ColorSpace colorSpace, InterpolationDirection[] dir) {
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/package-info.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/package-info.java
index 2c59281a2c..c820470c62 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/package-info.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/package-info.java
@@ -19,12 +19,10 @@
  *
  */
 /**
- * <BODY>
  * <P>
  * Some utility classes for the protein structure GUIs.
  * Possible start classes are one level higher at
  * org.biojava.nbio.structure.ngui.BiojavaJmol, and org.biojava.nbio.structure.gui.AlignmentGui.
  * </P>
- * </BODY>
  */
 package org.biojava.nbio.structure.gui.util;
\ No newline at end of file
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java
index 52df113942..ea558927a3 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java
@@ -104,7 +104,7 @@ public static MultipleAlignmentJmol displayFull(CeSymmResult symm)
 	 * Displays a single structure in a cartoon representation with each
 	 * symmetric repeat colored differently.
 	 *
-	 * @param msa
+	 * @param symmResult
 	 *            the symmetry multiple alignment obtained from CeSymm
 	 * @throws StructureException
 	 */
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGenerator.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGenerator.java
index 8a5764e1bb..507d4c727e 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGenerator.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGenerator.java
@@ -38,7 +38,7 @@ public abstract class JmolSymmetryScriptGenerator {
 	/**
 	 * Returns an instance of a JmolSymmetryScriptGenerator, based on the symmetry of a structure (factory method)
 	 * @param axisAligner
-	 * @param rotationGroup
+	 * @param name
 	 * @return instance of JmolSymmetryScriptGenerator
 	 */
 	public static JmolSymmetryScriptGenerator getInstance(AxisAligner axisAligner, String name) {

From 3580f7bac804f3305411a7a9d41bdb47cb836b4e Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Tue, 7 Jan 2025 14:10:26 -0800
Subject: [PATCH 22/90] Javadoc fix: errors in genome module

---
 .../org/biojava/nbio/genome/parsers/gff/Location.java     | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
index d0b2fc8f97..4163be2b56 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
@@ -409,9 +409,9 @@ public LocIterator iterator( int windowSize, int increment )
 	 * The part of this location before the specified position. If position is negative,
 	 * count backwards from the end.
 	 * <br><br>
-	 * For position >= 0, return Location( start, start + position ).
+	 * For position &gt;= 0, return Location( start, start + position ).
 	 * <br>
-	 * For position < 0, return Location( start, end + position ).
+	 * For position &lt; 0, return Location( start, end + position ).
 	 * <br>
 	 * @return New location from start of this location to directly before position.
 	 * @param position Where the prefix ends.
@@ -451,9 +451,9 @@ public Location prefix( int position )
 	 * The part of this location after the specified position. If position is negative, count backwards
 	 * from the end.
 	 * <br><br>
-	 * For position >= 0, return Location( start + position, end ).
+	 * For position &gt;= 0, return Location( start + position, end ).
 	 * <br>
-	 * For position < 0, return Location( end - position, end ).
+	 * For position &lt; 0, return Location( end - position, end ).
 	 * <br>
 	 * @return New location from position to end of this location.
 	 * @param position Where the suffix starts.

From bb073294543ce4c4096d0389ab89aad9d33675f2 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Tue, 7 Jan 2025 14:16:37 -0800
Subject: [PATCH 23/90] Javadoc fix: errors in modfinder module

---
 .../main/java/org/biojava/nbio/protmod/Component.java    | 4 ++--
 .../org/biojava/nbio/protmod/ModificationLinkage.java    | 8 ++++----
 .../nbio/protmod/ProteinModificationRegistry.java        | 2 +-
 .../biojava/nbio/protmod/structure/ModifiedCompound.java | 9 ++++-----
 .../nbio/protmod/structure/ModifiedCompoundImpl.java     | 1 -
 5 files changed, 11 insertions(+), 13 deletions(-)

diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java
index 4a35ff5218..08dafb0626 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java
@@ -30,7 +30,7 @@
  * contains information about a certain Component.
  * The Component class uses the extensible enum pattern.
  * You can't instantiate Component directly, instead
- * you have to use one of the {@link register} and {@link of} methods.
+ * you have to use one of the register and {@link #of} methods.
  *
  * @author Jianjiong Gao
  * @since 3.0
@@ -109,7 +109,7 @@ public boolean isCTerminal() {
 	/**
 	 * Get a Component that does not have to occur at terminals. If the
 	 * corresponding component has already been registered, return that one.
-	 * @param pdbccIds possible Protein Data Bank ID.
+	 * @param pdbccId possible Protein Data Bank ID.
 	 * @return a component.
 	 * @throws IllegalArgumentException if pdbccId or type is null,
 	 *  or the pdbccId has been registered as a different type.
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java
index 75ddb4c807..8bbccacce3 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java
@@ -54,10 +54,10 @@ public ModificationLinkage(
 	 *
 	 * @param components {@link Component}s involved in a modification.
 	 * @param indexOfComponent1 index of the first component.
-	 * @param labelOfAtomOnComponent1 label of the atom on the first
+	 * @param pdbNameOfAtomsOnComponent1 label of the atom on the first
 	 *  component.
 	 * @param indexOfComponent2 index of the second component.
-	 * @param labelOfAtomOnComponent2 label of the atom on the second
+	 * @param pdbNameOfAtomsOnComponent2 label of the atom on the second
 	 *  component.
 	 */
 	public ModificationLinkage(
@@ -77,10 +77,10 @@ public ModificationLinkage(
 	 *
 	 * @param components {@link Component}s involved in a modification.
 	 * @param indexOfComponent1 index of the first component.
-	 * @param labelOfAtomOnComponent1 label of the atom on the first
+	 * @param pdbNameOfPotentialAtomsOnComponent1 label of the atom on the first
 	 *  component.
 	 * @param indexOfComponent2 index of the second component.
-	 * @param labelOfAtomOnComponent2 label of the atom on the second
+	 * @param pdbNameOfPotentialAtomsOnComponent2 label of the atom on the second
 	 *  component.
 	 */
 	public ModificationLinkage(
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java
index 043aa3d779..383560ab01 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java
@@ -206,7 +206,7 @@ public static void register(final ProteinModification modification) {
 
 	/**
 	 * Remove a modification from registry.
-	 * @param mod
+	 * @param modification
 	 */
 	public static void unregister(ProteinModification modification) {
 		if (modification==null) throw new IllegalArgumentException("modification == null!");
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java
index 164c3d86d9..1a65fcdfbc 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java
@@ -47,7 +47,7 @@ public interface ModifiedCompound {
 
 	/**
 	 *
-	 * @return {@link ProteinModificationBean} occurred on the residue.
+	 * @return {@link ProteinModification} occurred on the residue.
 	 */
 	public ProteinModification getModification();
 
@@ -73,19 +73,18 @@ public interface ModifiedCompound {
 	/**
 	 *
 	 * @return a set of atom linkages.
-	 * @see #getLinkedGroupPairs
 	 * @see StructureAtomLinkage
 	 */
 	public Set<StructureAtomLinkage> getAtomLinkages();
 
-	/** Set atom linkages
+	/**
+	 * Set atom linkages
 	 *
-	 * @return
 	 */
 	public void setAtomLinkages(Set<StructureAtomLinkage> linkages);
 
 	/**
-	 * Add a linkage. Add new the involved groups first using {@link addGroup}.
+	 * Add a linkage. Add new the involved groups first using addGroup.
 	 * @param linkage an atom linkage.
 	 * @return true if this linkage was not already contained.
 	 * @see StructureAtomLinkage
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.java
index 889d3948b2..435772defd 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.java
@@ -65,7 +65,6 @@ public ModifiedCompoundImpl(){
 	 * Use this constructor for a modified residue.
 	 * @param modification {@link ProteinModification}.
 	 * @param modifiedResidue modified group.
-	 * @return a {@link ModifiedCompound}.
 	 * @throws IllegalArgumentException if either argument is null.
 	 */
 	public ModifiedCompoundImpl (

From d483bba04798f62fec44f6a83262a1c74370202e Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Tue, 7 Jan 2025 14:23:02 -0800
Subject: [PATCH 24/90] Javadoc fix: errors in ws module

---
 .../nbio/ws/alignment/qblast/MapToStringTransformer.java    | 6 +++---
 .../ws/alignment/qblast/NCBIQBlastAlignmentProperties.java  | 4 +---
 2 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/MapToStringTransformer.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/MapToStringTransformer.java
index 3fc154d009..7da35cb04b 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/MapToStringTransformer.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/MapToStringTransformer.java
@@ -41,11 +41,11 @@ public class MapToStringTransformer {
 	/**
 	 * Creates {@code MapToStringTransformer} with defaults:
 	 *
-	 * <pre>
+	 * <pre>{@code
 	 * mappingSequence = "=";
 	 * separatorSequence = "&";
 	 * nullValue = "null";
-	 * </pre>
+	 * }</pre>
 	 */
 	public MapToStringTransformer() {
 		this("=", "&", "null");
@@ -76,7 +76,7 @@ public MapToStringTransformer(String mappingSequence, String separatorSequence,
 	 * <p>
 	 * For example, if we have a map with two entries: {@code ("key1", "1")} and
 	 * {@code ("key2", "2")} this method would return {@code "key1=1&key2=2"} if
-	 * {@code mappingSequence} is "=" and separator sequence is "&";
+	 * {@code mappingSequence} is "=" and separator sequence is "&amp;";
 	 *
 	 * @param map map of arguments
 	 * @return String resulting string
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java
index 5976f9e915..ccad91b981 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java
@@ -137,11 +137,9 @@ public String getBlastDatabase() {
 	/**
 	 * Sets the database to be used with blastall
 	 * <p>
-	 * A list of available databases can be acquired by calling {@link NCBIQBlastService#printRemoteBlastInfo()}
-	 * <p>
 	 * Blastall equivalent: -d
 	 *
-	 * @param db : a valid name to a NCBI blastable database
+	 * @param database a valid name to a NCBI blastable database
 	 */
 	public void setBlastDatabase(String database) {
 		setAlignmentOption(DATABASE, database);

From 0183dc629b76a2632dfdf271462a3a90fbef085b Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Tue, 7 Jan 2025 14:26:35 -0800
Subject: [PATCH 25/90] Javadoc fix: errors in protein-disorder module

---
 .../src/main/java/org/biojava/nbio/ronn/Jronn.java               | 1 -
 1 file changed, 1 deletion(-)

diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java
index ccb85292b8..91862f0e36 100644
--- a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java
+++ b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java
@@ -270,7 +270,6 @@ public static Map<FastaSequence,Range[]> getDisorder(List<FastaSequence> sequenc
 	 * @throws FileNotFoundException if the input file cannot be found
 	 * @throws IOException of the system cannot access or read from the input file
 	 * @see #getDisorder(FastaSequence)
-	 * @see #Jronn.Range
 	 */
 	public static Map<FastaSequence,Range[]> getDisorder(String fastaFile) throws IOException {
 		final List<FastaSequence> sequences = SequenceUtil.readFasta(new FileInputStream(fastaFile));

From 24310c315b565389cae7c4d38f00908c2bedaee7 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Tue, 7 Jan 2025 14:52:26 -0800
Subject: [PATCH 26/90] Javadoc fix: errors in aaprops and survival and modules

---
 .../org/biojava/nbio/aaproperties/IPeptideProperties.java     | 2 +-
 .../biojava/nbio/aaproperties/profeat/IProfeatProperties.java | 4 ++--
 .../biojava/nbio/aaproperties/profeat/ProfeatProperties.java  | 4 ++--
 .../src/main/java/org/biojava/nbio/survival/cox/CoxR.java     | 2 +-
 .../main/java/org/biojava/nbio/survival/data/WorkSheet.java   | 2 +-
 5 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java
index 5e7ea3b6f1..5342013b61 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java
@@ -258,7 +258,7 @@ public AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMas
 	 * Returns the net charge of sequence at pH 7. The sequence argument must be
 	 * a protein sequence consisting of only non-ambiguous characters.
 	 * The net charge will be computed using the approach stated in
-	 * <a href="http://www.innovagen.se/custom-peptide-synthesis/peptide-property-calculator/peptide-property-calculator-notes.asp#NetCharge>here</a>
+	 * <a href="http://www.innovagen.se/custom-peptide-synthesis/peptide-property-calculator/peptide-property-calculator-notes.asp#NetCharge">here</a>
 	 *
 	 * pKa values used will be either
 	 * those used by Expasy which referenced "Electrophoresis 1994, 15, 529-539"
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java
index 864cb0ce78..7f39fff79e 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java
@@ -103,8 +103,8 @@ public enum DISTRIBUTION {FIRST, FIRST25, FIRST50, FIRST75, ALL};
 	 * Computes and return the position with respect to the sequence where the given distribution of the grouping can be found.<br/>
 	 * Example: "1111122222"<br/>
 	 * For the above example,<br/>
-	 * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
-	 * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
+	 * position of the GROUPING.GROUP1 &amp; DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
+	 * position of the GROUPING.GROUP1 &amp; DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
 	 *
 	 * @param sequence
 	 * 	a protein sequence consisting of non-ambiguous characters only
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java
index d8844476f4..dd0d310439 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java
@@ -119,8 +119,8 @@ public static Map<ATTRIBUTE, Map<TRANSITION, Double>> getTransition(String seque
 	 * An adaptor method which computes and return the position with respect to the sequence where the given distribution of the grouping can be found.<br/>
 	 * Example: "1111122222"<br/>
 	 * For the above example,<br/>
-	 * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
-	 * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
+	 * position of the GROUPING.GROUP1 &amp; DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
+	 * position of the GROUPING.GROUP1 &amp; DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
 	 *
 	 * @param sequence
 	 * 	a protein sequence consisting of non-ambiguous characters only
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java
index d2ac87e87a..d23ded840b 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java
@@ -75,7 +75,7 @@
  *      weights(n)   :case weights
  *      init         :initial estimate for the coefficients
  *      eps          :tolerance for convergence.  Iteration continues until
- *                      the percent change in loglikelihood is <= eps.
+ *                      the percent change in loglikelihood is &lt;= eps.
  *      chol_tol     : tolerance for the Cholesky decompostion
  *      method       : 0=Breslow, 1=Efron
  *      doscale      : 0=don't scale the X matrix, 1=scale the X matrix
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java
index 9e1f4b6fd2..542085942e 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java
@@ -1464,7 +1464,7 @@ static public WorkSheet readCSV(File f, char delimiter) throws Exception {
 	/**
 	 * Read a CSV/Tab delimited file where you pass in the delimiter
 	 *
-	 * @param f
+	 * @param is
 	 * @param delimiter
 	 * @return
 	 * @throws Exception

From b55dc80cfba061dcc9e4ca09bdc4f6c5c9137037 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Tue, 7 Jan 2025 15:07:47 -0800
Subject: [PATCH 27/90] Javadoc fix: errors in ontology module

---
 .../main/java/org/biojava/nbio/ontology/Ontology.java    | 8 --------
 .../src/main/java/org/biojava/nbio/ontology/Term.java    | 5 +----
 .../src/main/java/org/biojava/nbio/ontology/Triple.java  | 9 ++-------
 .../org/biojava/nbio/ontology/io/TabDelimParser.java     | 4 ++--
 .../org/biojava/nbio/ontology/obo/OboFileParser.java     | 5 +++--
 .../org/biojava/nbio/ontology/utils/Annotatable.java     | 1 -
 .../java/org/biojava/nbio/ontology/utils/Annotation.java | 6 +-----
 .../org/biojava/nbio/ontology/utils/EmptyAnnotation.java | 1 -
 8 files changed, 9 insertions(+), 30 deletions(-)

diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java
index b921fdd243..5463d3ccee 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java
@@ -40,7 +40,6 @@
  * @author Matthew Pocock
  *
  * @since 1.4
- * @see org.biojavax.ontology.ComparableOntology
  */
 
 public interface Ontology  {
@@ -129,7 +128,6 @@ public interface Ontology  {
 	 *         some other constraint of this implementation.
 	 * @throws AlreadyExistsException if a term of this name already exists
 	 * @return The newly created term.
-	 * @throws ChangeVetoException
 	 */
 
 	public Term createTerm(String name)
@@ -148,7 +146,6 @@ public Term createTerm(String name)
 	 *         some other constraint of this implementation.
 	 * @throws AlreadyExistsException if a term of this name already exists
 	 * @return The newly created term.
-	 * @throws ChangeVetoException
 	 */
 
 	public Term createTerm(String name, String description)
@@ -168,7 +165,6 @@ public Term createTerm(String name, String description)
 	 *         some other constraint of this implementation.
 	 * @throws AlreadyExistsException if a term of this name already exists
 	 * @return The newly created term.
-	 * @throws ChangeVetoException
 	 */
 
 	public Term createTerm(String name, String description, Object[] synonyms)
@@ -187,7 +183,6 @@ public Term createTerm(String name, String description, Object[] synonyms)
 	 *         some other constraint of this implementation.
 	 * @throws AlreadyExistsException if a term of this name already exists
 	 * @return The newly created term.
-	 * @throws ChangeVetoException
 	 */
 
 	public Variable createVariable(String name, String description)
@@ -208,7 +203,6 @@ public Variable createVariable(String name, String description)
 	 * @param t  the Term to import
 	 * @param localName  the local name to import it under, optionally null
 	 * @return a Term
-	 * @throws ChangeVetoException
 	 * @throws IllegalArgumentException
 	 */
 
@@ -228,7 +222,6 @@ public Term importTerm(Term t, String localName)
 	 * @return  a new Triple over these three terms
 	 * @throws AlreadyExistsException if a triple already exists with the same
 	 *      subject, object and predicate, regardless of the name and description
-	 * @throws ChangeVetoException
 	 * @throws NullPointerException if subject, object or predicate are null
 	 * @throws IllegalArgumentException if subject, object or predicate are not all
 	 *      from the same ontology
@@ -251,7 +244,6 @@ public Triple createTriple(Term subject, Term object, Term predicate, String nam
 	/**
 	 * Remove a term from an ontology, together with all triples which refer to it.
 	 * @param t
-	 * @throws ChangeVetoException
 	 */
 
 	public void deleteTerm(Term t) ;
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java
index 209c76414f..df26dcbcba 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java
@@ -32,7 +32,7 @@
 
 
 /**
- * A term in an ontology.  This has an {@link org.biojava.nbio.Annotation Annotation}
+ * A term in an ontology.  This has an {@link Annotation Annotation}
  * which can be used for storing additional human-displayable information.  It
  * is strongly recommended that the Annotation is not used for any machine-readable
  * data -- this should be represented by relations in the ontology instead.
@@ -51,9 +51,7 @@
  * @author Thomas Down
  * @author Matthew Pocock
  * @since 1.4
- * @see org.biojavax.ontology.ComparableTerm
  */
-
 public interface Term extends Annotatable {
 	/**
 	 * ChangeType which indicates that this term's ontology has been
@@ -113,7 +111,6 @@ public interface Term extends Annotatable {
 
 	/**
 	 * Simple in-memory implementation of an ontology term.
-	 * @see org.biojavax.ontology.SimpleComparableTerm
 	 * This can be used to implement Ontology.createTerm
 	 */
 
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java
index a265f2ff56..368bfea36e 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java
@@ -41,7 +41,6 @@
  * @author Thomas Down
  * @author Matthew Pocock
  * @since 1.4
- * @see org.biojavax.ontology.ComparableTriple
  */
 
 public interface Triple
@@ -79,7 +78,6 @@ public interface Triple
 	 * If you do not implement hashcode in this way then you have no guarantee
 	 * that your Triple objects will be found in an ontology and that they will
 	 * not be duplicated.
-	 * </p>
 	 */
 	@Override
 	public int hashCode();
@@ -90,7 +88,7 @@ public interface Triple
 	 * <p>
 	 * Two triples are equivalent if they have the same subject, object and
 	 * predicate fields.
-	 * <pre>
+	 * <pre>{@code
 	 * if (! (o instanceof Triple)) {
 	 *     return false;
 	 * }
@@ -98,11 +96,10 @@ public interface Triple
 	 * return to.getSubject() == getSubject() &&
 	 *        to.getObject() == getObject() &&
 	 *        to.getPredicate() == getPredicate();
-	 * </pre>
+	 * }</pre>
 	 * If you do not implement equals in this way then you have no guarantee
 	 * that your Triple objects will be found in an ontology and that they will
 	 * not be duplicated.
-	 * </p>
 	 */
 	@Override
 	public boolean equals(Object obj);
@@ -111,9 +108,7 @@ public interface Triple
 	 * Basic in-memory implementation of a Triple in an ontology
 	 *
 	 * This can be used to implement Ontology.createTriple
-	 * @see org.biojavax.ontology.SimpleComparableTriple
 	 */
-
 	public static final class Impl
 
 	implements Triple, java.io.Serializable {
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/TabDelimParser.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/TabDelimParser.java
index 2c0ed0a3ae..77259b0e5b 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/TabDelimParser.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/TabDelimParser.java
@@ -54,7 +54,7 @@
  * the core ontology.
  * </p>
  *
- * <code><pre>
+ * <pre>
  * ...
  * triple	is-a	any
  * triple	has-a	source
@@ -62,7 +62,7 @@
  * triple	has-a	predicate
  * (triple,has-a,any)	size	3
  * ...
- * </pre></code>
+ * </pre>
  *
  * <p>
  * The first four lines just associate triple with some type with a predicate
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java
index 96474a5385..8e8a16d174 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java
@@ -33,12 +33,13 @@
 import java.util.*;
 
 
-/** A class to parse the content of an OBO file. It delegates handling of the
+/**
+ * A class to parse the content of an OBO file. It delegates handling of the
  * content to the OBOFileEventListener implementation.
  *
  * This file contains parts of the OBO-Edit file OBOParseEngine, (particularly the encoding and decoding part)
  *
- * http://geneontology.cvs.sourceforge.net/geneontology/go-dev/java/oboedit/sources/org/geneontology/oboedit/dataadapter/OBOParseEngine.java?revision=1.10&view=markup
+ * See <a href="http://geneontology.cvs.sourceforge.net/geneontology/go-dev/java/oboedit/sources/org/geneontology/oboedit/dataadapter/OBOParseEngine.java?revision=1.10&view=markup">link</a>
  * Thanks to the OboEdit developers for giving permission to release this in BioJava.
  *
  *
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java
index 4018aa0655..c1be7a3c99 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java
@@ -75,7 +75,6 @@
  * @author  Matthew Pocock
  * @author <a href="mailto:kdj@sanger.ac.uk">Keith James</a> (docs).
  * @author  Kalle Näslund (docs)
- * @see org.biojavax.RichAnnotatable
  * @since 1.0
  */
 public interface Annotatable  {
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java
index a0cf3ce65a..e0ade9cc6b 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java
@@ -53,7 +53,6 @@
  *
  * @author Matthew Pocock
  * @author Thomas Down
- * @see org.biojavax.RichAnnotation
  *
  *
  * @since 1.0
@@ -96,8 +95,6 @@ public interface Annotation  {
 	 * @param value the new value for this key
 	 * @throws IllegalArgumentException if the property <code>key</code> is not
 	 *         legal
-	 * @throws ChangeVetoException if this annotation object can't be changed, or
-	 *         if the change was vetoed.
 	 */
 	void setProperty(Object key, Object value)
 	;
@@ -108,7 +105,6 @@ void setProperty(Object key, Object value)
 	 *
 	 * @param key the key object
 	 * @throws NoSuchElementException if the property doesn't exist
-	 * @throws ChangeVetoException if the change is vetoed
 	 * @since 1.3
 	 *
 	 */
@@ -147,7 +143,7 @@ public void removeProperty(Object key)
 	 * A really useful empty and immutable annotation object.
 	 * </p>
 	 *
-	 * Be careful when stooring Annotation arguments to
+	 * Be careful when storing Annotation arguments to
 	 *  constructors. It is possible that you have been passed EMPTY_ANNOTATION but
 	 * that code later on will access this object believing it to be
 	 * mutable. For example, the SeqIO factory code clones some
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/EmptyAnnotation.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/EmptyAnnotation.java
index 99a48861ea..985d55e911 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/EmptyAnnotation.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/EmptyAnnotation.java
@@ -35,7 +35,6 @@
  *
  * @since 1.0 as part of Annotation
  * @since 1.4 as top-level class
- * @see org.biojavax.EmptyRichAnnotation
  */
 class EmptyAnnotation
 

From c3079eaed9fb58e89a8a286f62e919cfbf6dc7de Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Tue, 7 Jan 2025 15:15:01 -0800
Subject: [PATCH 28/90] Javadoc fix: errors in integration-test module

---
 .../nbio/structure/test/util/StringManipulationTestsHelper.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/util/StringManipulationTestsHelper.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/util/StringManipulationTestsHelper.java
index 578816efb9..23664c68a3 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/util/StringManipulationTestsHelper.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/util/StringManipulationTestsHelper.java
@@ -42,7 +42,7 @@ public static void assertEqualsIgnoreEndline(String expected, String actual) {
 
 	/**
 	 * Asserts that two XML-representing strings are equal, by recursively
-	 * comparing each node's set of properties & children nodes. This method
+	 * comparing each node's set of properties and children nodes. This method
 	 * should be used when two XMLs are considered identical when all nodes are
 	 * identical regardless to their order
 	 *

From e516a40896b9b2eb57e3cfda4fdf907993ceb101 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Tue, 7 Jan 2025 15:21:38 -0800
Subject: [PATCH 29/90] Plugin updates

---
 pom.xml | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/pom.xml b/pom.xml
index 4e486ea368..21484e2943 100644
--- a/pom.xml
+++ b/pom.xml
@@ -171,11 +171,11 @@
 			<plugins>
 				<plugin>
 					<artifactId>maven-clean-plugin</artifactId>
-					<version>3.1.0</version>
+					<version>3.4.0</version>
 				</plugin>
 				<plugin>
 					<artifactId>maven-compiler-plugin</artifactId>
-					<version>3.8.1</version>
+					<version>3.13.0</version>
 					<configuration>
 						<source>${jdk.version}</source>
 						<target>${jdk.version}</target>
@@ -183,19 +183,19 @@
 				</plugin>
 				<plugin>
 					<artifactId>maven-dependency-plugin</artifactId>
-					<version>3.1.2</version>
+					<version>3.8.1</version>
 				</plugin>
 				<plugin>
 					<artifactId>maven-jar-plugin</artifactId>
-					<version>3.2.0</version>
+					<version>3.4.2</version>
 				</plugin>
 				<plugin>
 					<artifactId>maven-scm-plugin</artifactId>
-					<version>1.11.2</version>
+					<version>2.1.0</version>
 				</plugin>
 				<plugin>
 					<artifactId>maven-source-plugin</artifactId>
-					<version>3.2.1</version>
+					<version>3.3.1</version>
 				</plugin>
 				<plugin>
 					<artifactId>maven-failsafe-plugin</artifactId>
@@ -214,7 +214,7 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-release-plugin</artifactId>
-					<version>3.0.0-M1</version>
+					<version>3.1.1</version>
 					<configuration>
 						<remoteTagging>true</remoteTagging>
 						<preparationGoals>clean install</preparationGoals>
@@ -247,7 +247,7 @@
 				<plugin>
             		<groupId>org.apache.maven.plugins</groupId>
             		<artifactId>maven-surefire-plugin</artifactId>
-            		<version>3.0.0-M5</version>
+            		<version>3.5.2</version>
              	</plugin>
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
@@ -256,7 +256,7 @@
 				</plugin>
 				<plugin>
 					<artifactId>maven-assembly-plugin</artifactId>
-					<version>3.3.0</version>
+					<version>3.7.1</version>
 					<configuration>
 						<descriptors>
 							<descriptor>src/main/assembly/assembly.xml</descriptor>
@@ -296,7 +296,7 @@
 
 				<plugin>
 					<artifactId>maven-enforcer-plugin</artifactId>
-					<version>3.0.0-M3</version>
+					<version>3.5.0</version>
 					<executions>
 						<execution>
 							<id>enforce-java</id>
@@ -316,7 +316,7 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-install-plugin</artifactId>
-					<version>3.0.0-M1</version>
+					<version>3.1.3</version>
 				</plugin>
 
 				<plugin>
@@ -334,7 +334,7 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-deploy-plugin</artifactId>
-					<version>3.0.0-M1</version>
+					<version>3.1.3</version>
 				</plugin>
 
 			</plugins>

From 93fe015ab9c6151997c6f353e5e1f1a2ba0a9e68 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Tue, 7 Jan 2025 16:03:04 -0800
Subject: [PATCH 30/90] Adding pom metadata required for mvn site:stage. Adding
 release instructions to readme

---
 README.md | 10 ++++++++++
 pom.xml   |  7 +++++++
 2 files changed, 17 insertions(+)

diff --git a/README.md b/README.md
index 92473664be..6ddbaa89d1 100644
--- a/README.md
+++ b/README.md
@@ -35,6 +35,16 @@ If you are using Maven you can add the BioJava repository by adding the followin
     </dependencies>
 ```
 
+### For developers
+
+Release biojava to maven central:
+- `mvn -Prelease release:prepare`
+- `mvn -Prelease release:perform`
+Publish new javadocs:
+- `mvn site` this will write `target/site`, but that's not enough for a multimodule project. See [docs](https://maven.apache.org/plugins/maven-site-plugin/examples/multimodule.html)
+- `mvn site:stage` this will write the full html directory tree to `target/staging`
+- Push the contents of `target/staging` to the [biojava.github.io repo](https://github.com/biojava/biojava.github.io) under directory `docs/api` for it to be published in biojava.org
+
 ### Mailing Lists
 
 BioJava has one main mailing list. In order to avoid SPAM the list only accepts postings from list members. Anybody can become a list member, so please subscribe before you post. If you send without being subscribed your mail might get stuck in the moderation loop, which can cause several weeks of delay (no fun to read through all that spam).
diff --git a/pom.xml b/pom.xml
index 21484e2943..81c89ea5bd 100644
--- a/pom.xml
+++ b/pom.xml
@@ -534,6 +534,13 @@
 			<id>ossrh</id>
 			<url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
 		</repository>
+		<site>
+			<!-- Needed for site plugin, to do mvn site:stage (without which a multimodule project won't have all the correct directory structure)
+			     Note that the values here are not actually used for deployment (for that we'd need some sort of proper git+ssh url I guess) - JD 2024-01-07 -->
+			<id>deploy</id>
+			<name>biojava.org</name>
+			<url>git:github.com:biojava/biojava.github.io.git</url>
+		</site>
 	</distributionManagement>
 
 	<profiles>

From bac14fdc7e35558e23bb73eb3c1ec5addd880a31 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Tue, 7 Jan 2025 16:03:49 -0800
Subject: [PATCH 31/90] Format fix

---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 6ddbaa89d1..19a41e0dbb 100644
--- a/README.md
+++ b/README.md
@@ -40,6 +40,7 @@ If you are using Maven you can add the BioJava repository by adding the followin
 Release biojava to maven central:
 - `mvn -Prelease release:prepare`
 - `mvn -Prelease release:perform`
+
 Publish new javadocs:
 - `mvn site` this will write `target/site`, but that's not enough for a multimodule project. See [docs](https://maven.apache.org/plugins/maven-site-plugin/examples/multimodule.html)
 - `mvn site:stage` this will write the full html directory tree to `target/staging`

From de1598c0e2728d29966c86a0d556bdc2d404278c Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Tue, 7 Jan 2025 16:29:08 -0800
Subject: [PATCH 32/90] [maven-release-plugin] prepare release biojava-7.1.4

---
 biojava-aa-prop/pom.xml                 |  6 +++---
 biojava-alignment/pom.xml               |  4 ++--
 biojava-core/pom.xml                    |  2 +-
 biojava-genome/pom.xml                  |  6 +++---
 biojava-integrationtest/pom.xml         |  4 ++--
 biojava-modfinder/pom.xml               |  4 ++--
 biojava-ontology/pom.xml                |  2 +-
 biojava-protein-comparison-tool/pom.xml | 10 +++++-----
 biojava-protein-disorder/pom.xml        |  4 ++--
 biojava-structure-gui/pom.xml           |  6 +++---
 biojava-structure/pom.xml               |  6 +++---
 biojava-survival/pom.xml                |  2 +-
 biojava-ws/pom.xml                      |  4 ++--
 pom.xml                                 |  4 ++--
 14 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index 474d4e32cf..fbf05525e8 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index d0024aaf6f..c439bed2b2 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 9b8af63ea1..3ceee1bb10 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 5de6f9ec8a..048092115a 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -70,13 +70,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index f0be361c82..61fd787570 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>7.1.4-SNAPSHOT</version>
+    <version>7.1.4</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -40,7 +40,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>7.1.4-SNAPSHOT</version>
+    	<version>7.1.4</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index 2a8b240f62..168865e2e8 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<artifactId>biojava-modfinder</artifactId>
 	<name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<type>jar</type>
 			<scope>compile</scope>
 		</dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 43e55d9d11..46ff9673b0 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>7.1.4-SNAPSHOT</version>
+    <version>7.1.4</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml
index d5815b33b3..656ebb46b0 100644
--- a/biojava-protein-comparison-tool/pom.xml
+++ b/biojava-protein-comparison-tool/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 
 	<artifactId>biojava-protein-comparison-tool</artifactId>
@@ -36,23 +36,23 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure-gui</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 		</dependency>
 		<dependency>
 			<groupId>net.sourceforge.jmol</groupId>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 2c31c5b87f..b0d678ec6f 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or
 			scopes here) -->
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index d60945af3d..3a77ed2003 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -27,13 +27,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 7572967f73..790bcc3db8 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -51,13 +51,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 8827137d94..ab77567b9b 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>7.1.4-SNAPSHOT</version>
+        <version>7.1.4</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index e02301197a..abe0573f87 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 81c89ea5bd..696ee974ba 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>7.1.4-SNAPSHOT</version>
+	<version>7.1.4</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the
@@ -51,7 +51,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>HEAD</tag>
+		<tag>biojava-7.1.4</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list

From cdf14076d84037ea690cc354ef1dcf674417b6d4 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Tue, 7 Jan 2025 16:29:11 -0800
Subject: [PATCH 33/90] [maven-release-plugin] prepare for next development
 iteration

---
 biojava-aa-prop/pom.xml                 |  6 +++---
 biojava-alignment/pom.xml               |  4 ++--
 biojava-core/pom.xml                    |  2 +-
 biojava-genome/pom.xml                  |  6 +++---
 biojava-integrationtest/pom.xml         |  4 ++--
 biojava-modfinder/pom.xml               |  4 ++--
 biojava-ontology/pom.xml                |  2 +-
 biojava-protein-comparison-tool/pom.xml | 10 +++++-----
 biojava-protein-disorder/pom.xml        |  4 ++--
 biojava-structure-gui/pom.xml           |  6 +++---
 biojava-structure/pom.xml               |  6 +++---
 biojava-survival/pom.xml                |  2 +-
 biojava-ws/pom.xml                      |  4 ++--
 pom.xml                                 |  4 ++--
 14 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index fbf05525e8..30b6642ae6 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index c439bed2b2..b1c7eb9a94 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 3ceee1bb10..2b3994284c 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 048092115a..86b0d8c93f 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -70,13 +70,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index 61fd787570..a9e79f3d1b 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>7.1.4</version>
+    <version>7.1.5-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -40,7 +40,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>7.1.4</version>
+    	<version>7.1.5-SNAPSHOT</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index 168865e2e8..abb9cab35d 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-modfinder</artifactId>
 	<name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<type>jar</type>
 			<scope>compile</scope>
 		</dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 46ff9673b0..0813129079 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>7.1.4</version>
+    <version>7.1.5-SNAPSHOT</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml
index 656ebb46b0..73b06a6159 100644
--- a/biojava-protein-comparison-tool/pom.xml
+++ b/biojava-protein-comparison-tool/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>biojava-protein-comparison-tool</artifactId>
@@ -36,23 +36,23 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure-gui</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>net.sourceforge.jmol</groupId>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index b0d678ec6f..e612fe824f 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or
 			scopes here) -->
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index 3a77ed2003..9d80f82e80 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -27,13 +27,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 790bcc3db8..4c14aee143 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -51,13 +51,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index ab77567b9b..d469386344 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>7.1.4</version>
+        <version>7.1.5-SNAPSHOT</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index abe0573f87..2b0b0f56cd 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 696ee974ba..b2cd37268c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>7.1.4</version>
+	<version>7.1.5-SNAPSHOT</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the
@@ -51,7 +51,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>biojava-7.1.4</tag>
+		<tag>HEAD</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list

From 6387a2ed9029c3b1b254fb4d28424a2182b0a106 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Tue, 7 Jan 2025 16:53:32 -0800
Subject: [PATCH 34/90] [maven-release-plugin] rollback the release of
 biojava-7.1.4

---
 biojava-aa-prop/pom.xml                 |  6 +++---
 biojava-alignment/pom.xml               |  4 ++--
 biojava-core/pom.xml                    |  2 +-
 biojava-genome/pom.xml                  |  6 +++---
 biojava-integrationtest/pom.xml         |  4 ++--
 biojava-modfinder/pom.xml               |  4 ++--
 biojava-ontology/pom.xml                |  2 +-
 biojava-protein-comparison-tool/pom.xml | 10 +++++-----
 biojava-protein-disorder/pom.xml        |  4 ++--
 biojava-structure-gui/pom.xml           |  6 +++---
 biojava-structure/pom.xml               |  6 +++---
 biojava-survival/pom.xml                |  2 +-
 biojava-ws/pom.xml                      |  4 ++--
 pom.xml                                 |  2 +-
 14 files changed, 31 insertions(+), 31 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index 30b6642ae6..474d4e32cf 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index b1c7eb9a94..d0024aaf6f 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 2b3994284c..9b8af63ea1 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 86b0d8c93f..5de6f9ec8a 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -70,13 +70,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index a9e79f3d1b..f0be361c82 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>7.1.5-SNAPSHOT</version>
+    <version>7.1.4-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -40,7 +40,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>7.1.5-SNAPSHOT</version>
+    	<version>7.1.4-SNAPSHOT</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index abb9cab35d..2a8b240f62 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-modfinder</artifactId>
 	<name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<type>jar</type>
 			<scope>compile</scope>
 		</dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 0813129079..43e55d9d11 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>7.1.5-SNAPSHOT</version>
+    <version>7.1.4-SNAPSHOT</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml
index 73b06a6159..d5815b33b3 100644
--- a/biojava-protein-comparison-tool/pom.xml
+++ b/biojava-protein-comparison-tool/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>biojava-protein-comparison-tool</artifactId>
@@ -36,23 +36,23 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure-gui</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>net.sourceforge.jmol</groupId>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index e612fe824f..2c31c5b87f 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or
 			scopes here) -->
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index 9d80f82e80..d60945af3d 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -27,13 +27,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 4c14aee143..7572967f73 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -51,13 +51,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index d469386344..8827137d94 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>7.1.5-SNAPSHOT</version>
+        <version>7.1.4-SNAPSHOT</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index 2b0b0f56cd..e02301197a 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index b2cd37268c..81c89ea5bd 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>7.1.5-SNAPSHOT</version>
+	<version>7.1.4-SNAPSHOT</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the

From 5ad2964afb154ea78bf7325262017e8efbd55abe Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Wed, 8 Jan 2025 10:52:53 -0800
Subject: [PATCH 35/90] Reports plugin update

---
 pom.xml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 81c89ea5bd..45fd5022ec 100644
--- a/pom.xml
+++ b/pom.xml
@@ -254,6 +254,11 @@
 					<artifactId>maven-shade-plugin</artifactId>
 					<version>3.2.4</version>
 				</plugin>
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-project-info-reports-plugin</artifactId>
+					<version>3.8.0</version>
+				</plugin>
 				<plugin>
 					<artifactId>maven-assembly-plugin</artifactId>
 					<version>3.7.1</version>
@@ -492,8 +497,8 @@
 				</configuration>
 			</plugin>
 			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-project-info-reports-plugin</artifactId>
-				<version>2.9</version>
 				<reportSets>
 					<reportSet>
 						<reports>

From 7286c3fe75257f5c41c6fd673bd62ec2ef3c238d Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Wed, 8 Jan 2025 11:01:31 -0800
Subject: [PATCH 36/90] [maven-release-plugin] prepare release biojava-7.1.4

---
 biojava-aa-prop/pom.xml                 |  6 +++---
 biojava-alignment/pom.xml               |  4 ++--
 biojava-core/pom.xml                    |  2 +-
 biojava-genome/pom.xml                  |  6 +++---
 biojava-integrationtest/pom.xml         |  4 ++--
 biojava-modfinder/pom.xml               |  4 ++--
 biojava-ontology/pom.xml                |  2 +-
 biojava-protein-comparison-tool/pom.xml | 10 +++++-----
 biojava-protein-disorder/pom.xml        |  4 ++--
 biojava-structure-gui/pom.xml           |  6 +++---
 biojava-structure/pom.xml               |  6 +++---
 biojava-survival/pom.xml                |  2 +-
 biojava-ws/pom.xml                      |  4 ++--
 pom.xml                                 |  4 ++--
 14 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index 474d4e32cf..fbf05525e8 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index d0024aaf6f..c439bed2b2 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 9b8af63ea1..3ceee1bb10 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 5de6f9ec8a..048092115a 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -70,13 +70,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index f0be361c82..61fd787570 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>7.1.4-SNAPSHOT</version>
+    <version>7.1.4</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -40,7 +40,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>7.1.4-SNAPSHOT</version>
+    	<version>7.1.4</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index 2a8b240f62..168865e2e8 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<artifactId>biojava-modfinder</artifactId>
 	<name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<type>jar</type>
 			<scope>compile</scope>
 		</dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 43e55d9d11..46ff9673b0 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>7.1.4-SNAPSHOT</version>
+    <version>7.1.4</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml
index d5815b33b3..656ebb46b0 100644
--- a/biojava-protein-comparison-tool/pom.xml
+++ b/biojava-protein-comparison-tool/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 
 	<artifactId>biojava-protein-comparison-tool</artifactId>
@@ -36,23 +36,23 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure-gui</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 		</dependency>
 		<dependency>
 			<groupId>net.sourceforge.jmol</groupId>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 2c31c5b87f..b0d678ec6f 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or
 			scopes here) -->
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index d60945af3d..3a77ed2003 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -27,13 +27,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 7572967f73..790bcc3db8 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -51,13 +51,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 8827137d94..ab77567b9b 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>7.1.4-SNAPSHOT</version>
+        <version>7.1.4</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index e02301197a..abe0573f87 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 45fd5022ec..e75cd7317c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>7.1.4-SNAPSHOT</version>
+	<version>7.1.4</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the
@@ -51,7 +51,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>HEAD</tag>
+		<tag>biojava-7.1.4</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list

From 3ec109c93b38ac5da65af9925fd66bb97ee6b638 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Wed, 8 Jan 2025 11:01:35 -0800
Subject: [PATCH 37/90] [maven-release-plugin] prepare for next development
 iteration

---
 biojava-aa-prop/pom.xml                 |  6 +++---
 biojava-alignment/pom.xml               |  4 ++--
 biojava-core/pom.xml                    |  2 +-
 biojava-genome/pom.xml                  |  6 +++---
 biojava-integrationtest/pom.xml         |  4 ++--
 biojava-modfinder/pom.xml               |  4 ++--
 biojava-ontology/pom.xml                |  2 +-
 biojava-protein-comparison-tool/pom.xml | 10 +++++-----
 biojava-protein-disorder/pom.xml        |  4 ++--
 biojava-structure-gui/pom.xml           |  6 +++---
 biojava-structure/pom.xml               |  6 +++---
 biojava-survival/pom.xml                |  2 +-
 biojava-ws/pom.xml                      |  4 ++--
 pom.xml                                 |  4 ++--
 14 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index fbf05525e8..30b6642ae6 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index c439bed2b2..b1c7eb9a94 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 3ceee1bb10..2b3994284c 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 048092115a..86b0d8c93f 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -70,13 +70,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index 61fd787570..a9e79f3d1b 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>7.1.4</version>
+    <version>7.1.5-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -40,7 +40,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>7.1.4</version>
+    	<version>7.1.5-SNAPSHOT</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index 168865e2e8..abb9cab35d 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-modfinder</artifactId>
 	<name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<type>jar</type>
 			<scope>compile</scope>
 		</dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 46ff9673b0..0813129079 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>7.1.4</version>
+    <version>7.1.5-SNAPSHOT</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml
index 656ebb46b0..73b06a6159 100644
--- a/biojava-protein-comparison-tool/pom.xml
+++ b/biojava-protein-comparison-tool/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>biojava-protein-comparison-tool</artifactId>
@@ -36,23 +36,23 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure-gui</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>net.sourceforge.jmol</groupId>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index b0d678ec6f..e612fe824f 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or
 			scopes here) -->
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index 3a77ed2003..9d80f82e80 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -27,13 +27,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 790bcc3db8..4c14aee143 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -51,13 +51,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index ab77567b9b..d469386344 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>7.1.4</version>
+        <version>7.1.5-SNAPSHOT</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index abe0573f87..2b0b0f56cd 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index e75cd7317c..032fafdf2d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>7.1.4</version>
+	<version>7.1.5-SNAPSHOT</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the
@@ -51,7 +51,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>biojava-7.1.4</tag>
+		<tag>HEAD</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list

From 9ef2c30072d64c7b07e00cf2137821ee20cdd1bc Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Wed, 8 Jan 2025 11:20:35 -0800
Subject: [PATCH 38/90] [maven-release-plugin] rollback the release of
 biojava-7.1.4

---
 biojava-aa-prop/pom.xml                 |  6 +++---
 biojava-alignment/pom.xml               |  4 ++--
 biojava-core/pom.xml                    |  2 +-
 biojava-genome/pom.xml                  |  6 +++---
 biojava-integrationtest/pom.xml         |  4 ++--
 biojava-modfinder/pom.xml               |  4 ++--
 biojava-ontology/pom.xml                |  2 +-
 biojava-protein-comparison-tool/pom.xml | 10 +++++-----
 biojava-protein-disorder/pom.xml        |  4 ++--
 biojava-structure-gui/pom.xml           |  6 +++---
 biojava-structure/pom.xml               |  6 +++---
 biojava-survival/pom.xml                |  2 +-
 biojava-ws/pom.xml                      |  4 ++--
 pom.xml                                 |  2 +-
 14 files changed, 31 insertions(+), 31 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index 30b6642ae6..474d4e32cf 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index b1c7eb9a94..d0024aaf6f 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 2b3994284c..9b8af63ea1 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 86b0d8c93f..5de6f9ec8a 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -70,13 +70,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index a9e79f3d1b..f0be361c82 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>7.1.5-SNAPSHOT</version>
+    <version>7.1.4-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -40,7 +40,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>7.1.5-SNAPSHOT</version>
+    	<version>7.1.4-SNAPSHOT</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index abb9cab35d..2a8b240f62 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-modfinder</artifactId>
 	<name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<type>jar</type>
 			<scope>compile</scope>
 		</dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 0813129079..43e55d9d11 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>7.1.5-SNAPSHOT</version>
+    <version>7.1.4-SNAPSHOT</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml
index 73b06a6159..d5815b33b3 100644
--- a/biojava-protein-comparison-tool/pom.xml
+++ b/biojava-protein-comparison-tool/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>biojava-protein-comparison-tool</artifactId>
@@ -36,23 +36,23 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure-gui</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>net.sourceforge.jmol</groupId>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index e612fe824f..2c31c5b87f 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or
 			scopes here) -->
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index 9d80f82e80..d60945af3d 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -27,13 +27,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 4c14aee143..7572967f73 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -51,13 +51,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index d469386344..8827137d94 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>7.1.5-SNAPSHOT</version>
+        <version>7.1.4-SNAPSHOT</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index 2b0b0f56cd..e02301197a 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 032fafdf2d..45fd5022ec 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>7.1.5-SNAPSHOT</version>
+	<version>7.1.4-SNAPSHOT</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the

From d2ce0893668942b55d751ad1a22494040bf21c84 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Wed, 8 Jan 2025 14:04:25 -0800
Subject: [PATCH 39/90] Adding explicit plugin versions to profile "release".
 Somehow the profile doesn't seem to inherit from pluginManagement

---
 pom.xml | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 45fd5022ec..55b4221758 100644
--- a/pom.xml
+++ b/pom.xml
@@ -300,6 +300,7 @@
 				</plugin>
 
 				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-enforcer-plugin</artifactId>
 					<version>3.5.0</version>
 					<executions>
@@ -598,7 +599,7 @@
 					<plugin>
 						<groupId>org.apache.maven.plugins</groupId>
 						<artifactId>maven-source-plugin</artifactId>
-						<version>3.2.0</version>
+						<version>3.3.1</version>
 						<executions>
 							<execution>
 								<id>attach-sources</id>
@@ -613,6 +614,7 @@
 					<plugin>
 						<groupId>org.apache.maven.plugins</groupId>
 						<artifactId>maven-javadoc-plugin</artifactId>
+						<version>3.11.2</version>
 						<executions>
 							<execution>
 								<id>attach-javadocs</id>
@@ -623,6 +625,12 @@
 						</executions>
 					</plugin>
 
+					<plugin>
+						<groupId>org.apache.maven.plugins</groupId>
+						<artifactId>maven-enforcer-plugin</artifactId>
+						<version>3.5.0</version>
+					</plugin>
+
 				</plugins>
 			</build>
 		</profile>

From f29a52137eccc09c873bad0be792160c362b6f22 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Wed, 8 Jan 2025 14:13:59 -0800
Subject: [PATCH 40/90] [maven-release-plugin] prepare release biojava-7.1.4

---
 biojava-aa-prop/pom.xml                 |  6 +++---
 biojava-alignment/pom.xml               |  4 ++--
 biojava-core/pom.xml                    |  2 +-
 biojava-genome/pom.xml                  |  6 +++---
 biojava-integrationtest/pom.xml         |  4 ++--
 biojava-modfinder/pom.xml               |  4 ++--
 biojava-ontology/pom.xml                |  2 +-
 biojava-protein-comparison-tool/pom.xml | 10 +++++-----
 biojava-protein-disorder/pom.xml        |  4 ++--
 biojava-structure-gui/pom.xml           |  6 +++---
 biojava-structure/pom.xml               |  6 +++---
 biojava-survival/pom.xml                |  2 +-
 biojava-ws/pom.xml                      |  4 ++--
 pom.xml                                 |  4 ++--
 14 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index 474d4e32cf..fbf05525e8 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index d0024aaf6f..c439bed2b2 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 9b8af63ea1..3ceee1bb10 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 5de6f9ec8a..048092115a 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -70,13 +70,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index f0be361c82..61fd787570 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>7.1.4-SNAPSHOT</version>
+    <version>7.1.4</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -40,7 +40,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>7.1.4-SNAPSHOT</version>
+    	<version>7.1.4</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index 2a8b240f62..168865e2e8 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<artifactId>biojava-modfinder</artifactId>
 	<name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<type>jar</type>
 			<scope>compile</scope>
 		</dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 43e55d9d11..46ff9673b0 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>7.1.4-SNAPSHOT</version>
+    <version>7.1.4</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml
index d5815b33b3..656ebb46b0 100644
--- a/biojava-protein-comparison-tool/pom.xml
+++ b/biojava-protein-comparison-tool/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 
 	<artifactId>biojava-protein-comparison-tool</artifactId>
@@ -36,23 +36,23 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure-gui</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 		</dependency>
 		<dependency>
 			<groupId>net.sourceforge.jmol</groupId>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 2c31c5b87f..b0d678ec6f 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or
 			scopes here) -->
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index d60945af3d..3a77ed2003 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -27,13 +27,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 7572967f73..790bcc3db8 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -51,13 +51,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 8827137d94..ab77567b9b 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>7.1.4-SNAPSHOT</version>
+        <version>7.1.4</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index e02301197a..abe0573f87 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 55b4221758..7cd4e79bb0 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>7.1.4-SNAPSHOT</version>
+	<version>7.1.4</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the
@@ -51,7 +51,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>HEAD</tag>
+		<tag>biojava-7.1.4</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list

From 76dfee8ca339d66fd05485d1fe12310778949053 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Wed, 8 Jan 2025 14:14:03 -0800
Subject: [PATCH 41/90] [maven-release-plugin] prepare for next development
 iteration

---
 biojava-aa-prop/pom.xml                 |  6 +++---
 biojava-alignment/pom.xml               |  4 ++--
 biojava-core/pom.xml                    |  2 +-
 biojava-genome/pom.xml                  |  6 +++---
 biojava-integrationtest/pom.xml         |  4 ++--
 biojava-modfinder/pom.xml               |  4 ++--
 biojava-ontology/pom.xml                |  2 +-
 biojava-protein-comparison-tool/pom.xml | 10 +++++-----
 biojava-protein-disorder/pom.xml        |  4 ++--
 biojava-structure-gui/pom.xml           |  6 +++---
 biojava-structure/pom.xml               |  6 +++---
 biojava-survival/pom.xml                |  2 +-
 biojava-ws/pom.xml                      |  4 ++--
 pom.xml                                 |  4 ++--
 14 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index fbf05525e8..30b6642ae6 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index c439bed2b2..b1c7eb9a94 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 3ceee1bb10..2b3994284c 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 048092115a..86b0d8c93f 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -70,13 +70,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index 61fd787570..a9e79f3d1b 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>7.1.4</version>
+    <version>7.1.5-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -40,7 +40,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>7.1.4</version>
+    	<version>7.1.5-SNAPSHOT</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index 168865e2e8..abb9cab35d 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-modfinder</artifactId>
 	<name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<type>jar</type>
 			<scope>compile</scope>
 		</dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 46ff9673b0..0813129079 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>7.1.4</version>
+    <version>7.1.5-SNAPSHOT</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml
index 656ebb46b0..73b06a6159 100644
--- a/biojava-protein-comparison-tool/pom.xml
+++ b/biojava-protein-comparison-tool/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>biojava-protein-comparison-tool</artifactId>
@@ -36,23 +36,23 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure-gui</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>net.sourceforge.jmol</groupId>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index b0d678ec6f..e612fe824f 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or
 			scopes here) -->
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index 3a77ed2003..9d80f82e80 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -27,13 +27,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 790bcc3db8..4c14aee143 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -51,13 +51,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index ab77567b9b..d469386344 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>7.1.4</version>
+        <version>7.1.5-SNAPSHOT</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index abe0573f87..2b0b0f56cd 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 7cd4e79bb0..588e582265 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>7.1.4</version>
+	<version>7.1.5-SNAPSHOT</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the
@@ -51,7 +51,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>biojava-7.1.4</tag>
+		<tag>HEAD</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list

From 3a312186188d3f8234407e5c8940b86d26002700 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Wed, 8 Jan 2025 14:15:51 -0800
Subject: [PATCH 42/90] [maven-release-plugin] rollback the release of
 biojava-7.1.4

---
 biojava-aa-prop/pom.xml                 |  6 +++---
 biojava-alignment/pom.xml               |  4 ++--
 biojava-core/pom.xml                    |  2 +-
 biojava-genome/pom.xml                  |  6 +++---
 biojava-integrationtest/pom.xml         |  4 ++--
 biojava-modfinder/pom.xml               |  4 ++--
 biojava-ontology/pom.xml                |  2 +-
 biojava-protein-comparison-tool/pom.xml | 10 +++++-----
 biojava-protein-disorder/pom.xml        |  4 ++--
 biojava-structure-gui/pom.xml           |  6 +++---
 biojava-structure/pom.xml               |  6 +++---
 biojava-survival/pom.xml                |  2 +-
 biojava-ws/pom.xml                      |  4 ++--
 pom.xml                                 |  2 +-
 14 files changed, 31 insertions(+), 31 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index 30b6642ae6..474d4e32cf 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index b1c7eb9a94..d0024aaf6f 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 2b3994284c..9b8af63ea1 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 86b0d8c93f..5de6f9ec8a 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -70,13 +70,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index a9e79f3d1b..f0be361c82 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>7.1.5-SNAPSHOT</version>
+    <version>7.1.4-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -40,7 +40,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>7.1.5-SNAPSHOT</version>
+    	<version>7.1.4-SNAPSHOT</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index abb9cab35d..2a8b240f62 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-modfinder</artifactId>
 	<name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<type>jar</type>
 			<scope>compile</scope>
 		</dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 0813129079..43e55d9d11 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>7.1.5-SNAPSHOT</version>
+    <version>7.1.4-SNAPSHOT</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml
index 73b06a6159..d5815b33b3 100644
--- a/biojava-protein-comparison-tool/pom.xml
+++ b/biojava-protein-comparison-tool/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>biojava-protein-comparison-tool</artifactId>
@@ -36,23 +36,23 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure-gui</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>net.sourceforge.jmol</groupId>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index e612fe824f..2c31c5b87f 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or
 			scopes here) -->
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index 9d80f82e80..d60945af3d 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -27,13 +27,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 4c14aee143..7572967f73 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -51,13 +51,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index d469386344..8827137d94 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>7.1.5-SNAPSHOT</version>
+        <version>7.1.4-SNAPSHOT</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index 2b0b0f56cd..e02301197a 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.1.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.1.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 588e582265..55b4221758 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>7.1.5-SNAPSHOT</version>
+	<version>7.1.4-SNAPSHOT</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the

From 54fd26ad239866590eaae79f150f1ee3e526f2b0 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Wed, 8 Jan 2025 15:02:46 -0800
Subject: [PATCH 43/90] Hopefully fixing issue with site:deploy which was
 failing (as part of release:perform)

---
 pom.xml | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/pom.xml b/pom.xml
index 55b4221758..c22715d396 100644
--- a/pom.xml
+++ b/pom.xml
@@ -543,8 +543,9 @@
 		<site>
 			<!-- Needed for site plugin, to do mvn site:stage (without which a multimodule project won't have all the correct directory structure)
 			     Note that the values here are not actually used for deployment (for that we'd need some sort of proper git+ssh url I guess) - JD 2024-01-07 -->
-			<id>deploy</id>
-			<name>biojava.org</name>
+			<id>biojava.org</id>
+			<name>The biojava.org site</name>
+			<!-- NOTE this is not a proper URL supported by mvn site:deploy . That's why in site configuration for release profile we disable deployment with skipDeploy -->
 			<url>git:github.com:biojava/biojava.github.io.git</url>
 		</site>
 	</distributionManagement>
@@ -631,6 +632,16 @@
 						<version>3.5.0</version>
 					</plugin>
 
+					<plugin>
+						<groupId>org.apache.maven.plugins</groupId>
+						<artifactId>maven-site-plugin</artifactId>
+						<version>3.21.0</version>
+						<configuration>
+							<!-- In distributionManagement we have a site setting with a fake url (needed for mvn site:stage to work). This is here to skip the deployment that would fail for the fake url -->
+							<skipDeploy>true</skipDeploy>
+						</configuration>
+					</plugin>
+
 				</plugins>
 			</build>
 		</profile>

From c1c8c506edf652ef404c4c501666b36c431b7aea Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Wed, 8 Jan 2025 15:12:00 -0800
Subject: [PATCH 44/90] [maven-release-plugin] prepare release biojava-7.1.4

---
 biojava-aa-prop/pom.xml                 |  6 +++---
 biojava-alignment/pom.xml               |  4 ++--
 biojava-core/pom.xml                    |  2 +-
 biojava-genome/pom.xml                  |  6 +++---
 biojava-integrationtest/pom.xml         |  4 ++--
 biojava-modfinder/pom.xml               |  4 ++--
 biojava-ontology/pom.xml                |  2 +-
 biojava-protein-comparison-tool/pom.xml | 10 +++++-----
 biojava-protein-disorder/pom.xml        |  4 ++--
 biojava-structure-gui/pom.xml           |  6 +++---
 biojava-structure/pom.xml               |  6 +++---
 biojava-survival/pom.xml                |  2 +-
 biojava-ws/pom.xml                      |  4 ++--
 pom.xml                                 |  4 ++--
 14 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index 474d4e32cf..fbf05525e8 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index d0024aaf6f..c439bed2b2 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 9b8af63ea1..3ceee1bb10 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 5de6f9ec8a..048092115a 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -70,13 +70,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index f0be361c82..61fd787570 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>7.1.4-SNAPSHOT</version>
+    <version>7.1.4</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -40,7 +40,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>7.1.4-SNAPSHOT</version>
+    	<version>7.1.4</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index 2a8b240f62..168865e2e8 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<artifactId>biojava-modfinder</artifactId>
 	<name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<type>jar</type>
 			<scope>compile</scope>
 		</dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 43e55d9d11..46ff9673b0 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>7.1.4-SNAPSHOT</version>
+    <version>7.1.4</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml
index d5815b33b3..656ebb46b0 100644
--- a/biojava-protein-comparison-tool/pom.xml
+++ b/biojava-protein-comparison-tool/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 
 	<artifactId>biojava-protein-comparison-tool</artifactId>
@@ -36,23 +36,23 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure-gui</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 		</dependency>
 		<dependency>
 			<groupId>net.sourceforge.jmol</groupId>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 2c31c5b87f..b0d678ec6f 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or
 			scopes here) -->
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index d60945af3d..3a77ed2003 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -27,13 +27,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 7572967f73..790bcc3db8 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -51,13 +51,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 8827137d94..ab77567b9b 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>7.1.4-SNAPSHOT</version>
+        <version>7.1.4</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index e02301197a..abe0573f87 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4-SNAPSHOT</version>
+		<version>7.1.4</version>
 	</parent>
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4-SNAPSHOT</version>
+			<version>7.1.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index c22715d396..39c29a4b48 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>7.1.4-SNAPSHOT</version>
+	<version>7.1.4</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the
@@ -51,7 +51,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>HEAD</tag>
+		<tag>biojava-7.1.4</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list

From a1bb15f92d9b01953d239bd3e0ff65822f79858a Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Wed, 8 Jan 2025 15:12:04 -0800
Subject: [PATCH 45/90] [maven-release-plugin] prepare for next development
 iteration

---
 biojava-aa-prop/pom.xml                 |  6 +++---
 biojava-alignment/pom.xml               |  4 ++--
 biojava-core/pom.xml                    |  2 +-
 biojava-genome/pom.xml                  |  6 +++---
 biojava-integrationtest/pom.xml         |  4 ++--
 biojava-modfinder/pom.xml               |  4 ++--
 biojava-ontology/pom.xml                |  2 +-
 biojava-protein-comparison-tool/pom.xml | 10 +++++-----
 biojava-protein-disorder/pom.xml        |  4 ++--
 biojava-structure-gui/pom.xml           |  6 +++---
 biojava-structure/pom.xml               |  6 +++---
 biojava-survival/pom.xml                |  2 +-
 biojava-ws/pom.xml                      |  4 ++--
 pom.xml                                 |  4 ++--
 14 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index fbf05525e8..30b6642ae6 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index c439bed2b2..b1c7eb9a94 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 3ceee1bb10..2b3994284c 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 048092115a..86b0d8c93f 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -70,13 +70,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index 61fd787570..a9e79f3d1b 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>7.1.4</version>
+    <version>7.1.5-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -40,7 +40,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>7.1.4</version>
+    	<version>7.1.5-SNAPSHOT</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index 168865e2e8..abb9cab35d 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-modfinder</artifactId>
 	<name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<type>jar</type>
 			<scope>compile</scope>
 		</dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 46ff9673b0..0813129079 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>7.1.4</version>
+    <version>7.1.5-SNAPSHOT</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml
index 656ebb46b0..73b06a6159 100644
--- a/biojava-protein-comparison-tool/pom.xml
+++ b/biojava-protein-comparison-tool/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>biojava-protein-comparison-tool</artifactId>
@@ -36,23 +36,23 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure-gui</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>net.sourceforge.jmol</groupId>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index b0d678ec6f..e612fe824f 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or
 			scopes here) -->
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index 3a77ed2003..9d80f82e80 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -27,13 +27,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 790bcc3db8..4c14aee143 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -51,13 +51,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index ab77567b9b..d469386344 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>7.1.4</version>
+        <version>7.1.5-SNAPSHOT</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index abe0573f87..2b0b0f56cd 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.4</version>
+		<version>7.1.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.4</version>
+			<version>7.1.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 39c29a4b48..7908304f2c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>7.1.4</version>
+	<version>7.1.5-SNAPSHOT</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the
@@ -51,7 +51,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>biojava-7.1.4</tag>
+		<tag>HEAD</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list

From 0cd5bd77112336d4814a0e836a36556c8ed48668 Mon Sep 17 00:00:00 2001
From: Jose Duarte <jose.m.duarte@gmail.com>
Date: Wed, 8 Jan 2025 15:29:03 -0800
Subject: [PATCH 46/90] Updating after release

---
 CHANGELOG.md | 7 +++++++
 README.md    | 4 ++--
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 14fb2b0610..589a894f06 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,13 @@
 BioJava Changelog
 -----------------
 
+BioJava 7.1.4
+==============================
+### Fixed
+* More lenient mmCIF parsing, now can read files produced by [Gemmi](https://gemmi.readthedocs.io/en/latest/) #1103
+* Javadocs: all javadoc lint errors fixed
+* Plugin updates and fixed issues in maven release process
+
 BioJava 7.1.3
 ==============================
 ### Fixed
diff --git a/README.md b/README.md
index 19a41e0dbb..b2f19a7a07 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 # Welcome to <img src="logo-full.png" height="35"/>
 
 ![Build](https://github.com/biojava/biojava/actions/workflows/master.yml/badge.svg)
-[![Version](http://img.shields.io/badge/version-7.1.3-blue.svg?style=flat)](https://github.com/biojava/biojava/releases/tag/biojava-7.1.3) [![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/biojava/biojava/blob/master/LICENSE) [![Join the chat at https://gitter.im/biojava/biojava](https://badges.gitter.im/biojava/biojava.svg)](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+[![Version](http://img.shields.io/badge/version-7.1.4-blue.svg?style=flat)](https://github.com/biojava/biojava/releases/tag/biojava-7.1.4) [![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/biojava/biojava/blob/master/LICENSE) [![Join the chat at https://gitter.im/biojava/biojava](https://badges.gitter.im/biojava/biojava.svg)](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 
 
 BioJava is an open-source project dedicated to providing a Java framework for **processing biological data**. It provides analytical and statistical routines, parsers for common file formats, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.
@@ -29,7 +29,7 @@ If you are using Maven you can add the BioJava repository by adding the followin
       <dependency>
         <groupId>org.biojava</groupId>
         <artifactId>biojava-core</artifactId>
-        <version>7.1.3</version>
+        <version>7.1.4</version>
       </dependency>
       <!-- other biojava modules as needed -->
     </dependencies>

From d4242d269237dcb6f2eb062ed8947c5c8c5acae1 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Wed, 8 Jan 2025 16:40:28 -0800
Subject: [PATCH 47/90] Hopefully good final solution for generating apidocs
 site

---
 README.md |  5 ++---
 pom.xml   | 19 ++++++++++++++++---
 2 files changed, 18 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index b2f19a7a07..bb36b69de1 100644
--- a/README.md
+++ b/README.md
@@ -42,9 +42,8 @@ Release biojava to maven central:
 - `mvn -Prelease release:perform`
 
 Publish new javadocs:
-- `mvn site` this will write `target/site`, but that's not enough for a multimodule project. See [docs](https://maven.apache.org/plugins/maven-site-plugin/examples/multimodule.html)
-- `mvn site:stage` this will write the full html directory tree to `target/staging`
-- Push the contents of `target/staging` to the [biojava.github.io repo](https://github.com/biojava/biojava.github.io) under directory `docs/api` for it to be published in biojava.org
+- `mvn -Prelease site` this will write `target/site`
+- Push the contents of `target/site/apidocs` to the [biojava.github.io repo](https://github.com/biojava/biojava.github.io) under directory `docs/apiM.m.p` (e.g. docs/api7.1.4) and then link `docs/api` to `docs/apiM.m.p`, for it to be published in biojava.org
 
 ### Mailing Lists
 
diff --git a/pom.xml b/pom.xml
index 7908304f2c..0e137edb3c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -487,6 +487,18 @@
 		<plugins>
 			<plugin>
 				<artifactId>maven-javadoc-plugin</artifactId>
+				<!-- Make a single javadoc site at target/site/apidocs subdir with all sub-modules, see:
+				 https://stackoverflow.com/questions/5927590/maven-multi-module-project-site-with-javadocs (main solution)
+				 https://stackoverflow.com/questions/39489567/intellij-maven-site-plugin-reportplugins-showing-error-havent-even-done-anyt (to make intellij happy) -->
+				<reportSets>
+					<reportSet>
+						<id>aggregate</id>
+						<reports>
+							<report>aggregate</report>
+						</reports>
+					</reportSet>
+				</reportSets>
+
 				<configuration>
 					<goal>javadoc:aggregate</goal>
 					<breakiterator>true</breakiterator>
@@ -541,12 +553,13 @@
 			<url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
 		</repository>
 		<site>
-			<!-- Needed for site plugin, to do mvn site:stage (without which a multimodule project won't have all the correct directory structure)
-			     Note that the values here are not actually used for deployment (for that we'd need some sort of proper git+ssh url I guess) - JD 2024-01-07 -->
+			<!-- Needed for site plugin, to do mvn site:stage (without which a multimodule project won't have all the correct directory structure) -->
+			<!-- Also seems to be needed at mvn release:perform time, where a mvn site:deploy runs and complains if this is not present -->
 			<id>biojava.org</id>
 			<name>The biojava.org site</name>
 			<!-- NOTE this is not a proper URL supported by mvn site:deploy . That's why in site configuration for release profile we disable deployment with skipDeploy -->
-			<url>git:github.com:biojava/biojava.github.io.git</url>
+			<!-- NOTE we don't actually deploy the "site" but just the "apidocs" part of it to /docs/api -->
+			<url>https://biojava.org/docs/site</url>
 		</site>
 	</distributionManagement>
 

From ac2084b9081600cb993a84f335576601945e8646 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Thu, 9 Jan 2025 10:11:31 -0800
Subject: [PATCH 48/90] Forcing enforcer plugin upgrade: somehow version wasn't
 being taken from pluginManagement. Hopefully this fixes issue in CI building
 with java 17

---
 pom.xml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/pom.xml b/pom.xml
index 0e137edb3c..ff16373e0a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -392,6 +392,13 @@
 				</configuration>
 			</plugin>
 
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-enforcer-plugin</artifactId>
+				<version>3.5.0</version>
+			</plugin>
+
+
 		</plugins>
 
 		<extensions>

From f271214e76f2772a5364aed9d203087af648f992 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Thu, 9 Jan 2025 14:33:23 -0800
Subject: [PATCH 49/90] Docs

---
 pom.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pom.xml b/pom.xml
index ff16373e0a..a77a23a43a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -392,6 +392,7 @@
 				</configuration>
 			</plugin>
 
+			<!-- Forcing the enforcer-plugin version: somehow the one declared in pluginManagement doesn't go through without this. No idea why. Other plugins do respect the version in pluginManagement -->
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-enforcer-plugin</artifactId>

From e170fc9dc84f9a97482af781fa6c57e23b36c6ba Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Thu, 9 Jan 2025 14:37:33 -0800
Subject: [PATCH 50/90] Avoiding a (harmless) error in mvn site by upgrading
 javadoc plugin

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index a77a23a43a..691dedc831 100644
--- a/pom.xml
+++ b/pom.xml
@@ -229,7 +229,7 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-javadoc-plugin</artifactId>
-					<version>3.3.1</version>
+					<version>3.11.2</version>
 					<configuration>
 					    <additionalJOptions>-Xdoclint:none</additionalJOptions>
 					    <!-- we need to allow script in comments or otherwise we can't use google analytics js in footer below - JD 2017-03-30 -->

From be55381c8b9656d146209083121199e335c936b8 Mon Sep 17 00:00:00 2001
From: Michael L Heuer <heuermh@acm.org>
Date: Thu, 13 Feb 2025 10:27:15 -0600
Subject: [PATCH 51/90] Update guava dependency version to 33.4.0-jre

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 691dedc831..1381eb8041 100644
--- a/pom.xml
+++ b/pom.xml
@@ -486,7 +486,7 @@
 			<dependency>
 				<groupId>com.google.guava</groupId>
 				<artifactId>guava</artifactId>
-				<version>33.3.0-jre</version>
+				<version>33.4.0-jre</version>
 			</dependency>
 		</dependencies>
 	</dependencyManagement>

From 93c1c8f9d4c1fa3d12d2c7f7d250532ed6b62098 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Fri, 21 Feb 2025 11:01:55 -0800
Subject: [PATCH 52/90] Handle more missing fields in struct_ref_seq

---
 .../io/cif/CifStructureConsumerImpl.java      | 55 ++++++++++---------
 1 file changed, 30 insertions(+), 25 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
index b204687762..45fd8fc417 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
@@ -975,7 +975,7 @@ public void consumeStructRefSeq(StructRefSeq structRefSeq) {
             dbRef.setIdCode(structRefSeq.getPdbxPDBIdCode().isDefined()? structRefSeq.getPdbxPDBIdCode().get(rowIndex):null);
             dbRef.setDbAccession(structRefSeq.getPdbxDbAccession().isDefined()? structRefSeq.getPdbxDbAccession().get(rowIndex):null);
             dbRef.setDbIdCode(structRefSeq.getPdbxDbAccession().isDefined()? structRefSeq.getPdbxDbAccession().get(rowIndex):null);
-            dbRef.setChainName(structRefSeq.getPdbxStrandId().get(rowIndex));
+            dbRef.setChainName(structRefSeq.getPdbxStrandId().isDefined()? structRefSeq.getPdbxStrandId().get(rowIndex):null);
 
             OptionalInt structRefRowIndex = IntStream.range(0, structRef.getRowCount())
                     .filter(i -> structRef.getId().get(i).equals(refId))
@@ -990,34 +990,39 @@ public void consumeStructRefSeq(StructRefSeq structRefSeq) {
 
             int seqBegin;
             int seqEnd;
+            char beginInsCode = ' ';
+            char endInsCode = ' ';
 
-            try {
-                seqBegin = Integer.parseInt(structRefSeq.getPdbxAuthSeqAlignBeg().get(rowIndex));
-                seqEnd = Integer.parseInt(structRefSeq.getPdbxAuthSeqAlignEnd().get(rowIndex));
-            } catch (NumberFormatException e) {
-                // this happens in a few entries, annotation error? e.g. 6eoj
-                logger.warn("Couldn't parse pdbx_auth_seq_align_beg/end in _struct_ref_seq. Will not store dbref " +
-                        "alignment info for accession {}. Error: {}", dbRef.getDbAccession(), e.getMessage());
-                return;
-            }
+            if (structRefSeq.getPdbxAuthSeqAlignBeg().isDefined() && structRefSeq.getPdbxAuthSeqAlignEnd().isDefined()) {
+                try {
+                    seqBegin = Integer.parseInt(structRefSeq.getPdbxAuthSeqAlignBeg().get(rowIndex));
+                    seqEnd = Integer.parseInt(structRefSeq.getPdbxAuthSeqAlignEnd().get(rowIndex));
+                } catch (NumberFormatException e) {
+                    // this happens in a few entries, annotation error? e.g. 6eoj
+                    logger.warn("Couldn't parse pdbx_auth_seq_align_beg/end in _struct_ref_seq. Will not store dbref " +
+                            "alignment info for accession {}. Error: {}", dbRef.getDbAccession(), e.getMessage());
+                    return;
+                }
 
-            char beginInsCode = ' ';
-            String pdbxSeqAlignBegInsCode = structRefSeq.getPdbxSeqAlignBegInsCode().get(rowIndex);
-            if (pdbxSeqAlignBegInsCode.length() > 0) {
-                beginInsCode = pdbxSeqAlignBegInsCode.charAt(0);
-            }
+                String pdbxSeqAlignBegInsCode = structRefSeq.getPdbxSeqAlignBegInsCode().get(rowIndex);
+                if (pdbxSeqAlignBegInsCode.length() > 0) {
+                    beginInsCode = pdbxSeqAlignBegInsCode.charAt(0);
+                }
 
-            char endInsCode = ' ';
-            String pdbxSeqAlignEndInsCode = structRefSeq.getPdbxSeqAlignEndInsCode().get(rowIndex);
-            if (pdbxSeqAlignEndInsCode.length() > 0) {
-                endInsCode = pdbxSeqAlignEndInsCode.charAt(0);
-            }
+                String pdbxSeqAlignEndInsCode = structRefSeq.getPdbxSeqAlignEndInsCode().get(rowIndex);
+                if (pdbxSeqAlignEndInsCode.length() > 0) {
+                    endInsCode = pdbxSeqAlignEndInsCode.charAt(0);
+                }
 
-            if (beginInsCode == '?') {
-                beginInsCode = ' ';
-            }
-            if (endInsCode == '?') {
-                endInsCode = ' ';
+                if (beginInsCode == '?') {
+                    beginInsCode = ' ';
+                }
+                if (endInsCode == '?') {
+                    endInsCode = ' ';
+                }
+            } else {
+                seqBegin = structRefSeq.getSeqAlignBeg().get(rowIndex);
+                seqEnd = structRefSeq.getSeqAlignEnd().get(rowIndex);
             }
 
             dbRef.setSeqBegin(seqBegin);

From 65d3dcde9a49b3b3f36750815c2c2b3e0d501d5a Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Fri, 21 Feb 2025 11:24:49 -0800
Subject: [PATCH 53/90] Lenient to missing atom_site.occupancy

---
 .../biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
index 45fd8fc417..1dccf8ae30 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
@@ -333,7 +333,7 @@ public void consumeAtomSite(AtomSite atomSite) {
             atom.setY(cartnY.get(atomIndex));
             atom.setZ(cartnZ.get(atomIndex));
 
-            atom.setOccupancy((float) occupancy.get(atomIndex));
+            atom.setOccupancy((float) (occupancy.isDefined()? occupancy.get(atomIndex) : 1.0));
             atom.setTempFactor((float) bIsoOrEquiv.get(atomIndex));
 
             if (altLocation == null || altLocation.isEmpty() || ".".equals(altLocation)) {

From 12dcb2ce3c1a03d67798311ca7cf6fd26e12563f Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Fri, 21 Feb 2025 15:29:44 -0800
Subject: [PATCH 54/90] Another safeguard, that applies to some PDB-IHM entries

---
 .../nbio/structure/io/cif/CifStructureConsumerImpl.java       | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
index 1dccf8ae30..c610c05f2b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
@@ -1819,6 +1819,10 @@ private void initMaps() {
 
             String[] chainNames = entityPoly.getPdbxStrandId().get(rowIndex).split(",");
             List<String> asymIds = entityId2asymId.get(entityPoly.getEntityId().get(rowIndex));
+            if (asymIds == null) {
+                logger.warn("No asym ids found for entity {} in _struct_asym. Can't provide a mapping from asym ids to author chain ids for this entity", entityPoly.getEntityId().get(rowIndex));
+                break;
+            }
             if (chainNames.length != asymIds.size()) {
                 logger.warn("The list of asym ids (from _struct_asym) and the list of author ids (from _entity_poly) " +
                         "for entity {} have different lengths! Can't provide a mapping from asym ids to author chain " +

From c45c3dd05beaed3f214b991526f713d9090b5e1f Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Fri, 21 Feb 2025 15:39:16 -0800
Subject: [PATCH 55/90] Bugfix: ASA calculation was by default using all
 models. Now it will use model 1 by default. Added new constructor to choose
 model.

---
 .../nbio/structure/asa/AsaCalculator.java     | 34 +++++++++++++++++--
 1 file changed, 32 insertions(+), 2 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
index 84effc3e44..21d6935eb3 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
@@ -126,7 +126,37 @@ static class IndexAndDistance {
 	 * Constructs a new AsaCalculator. Subsequently call {@link #calculateAsas()}
 	 * or {@link #getGroupAsas()} to calculate the ASAs
 	 * Only non-Hydrogen atoms are considered in the calculation.
-	 * @param structure the structure, all non-H atoms will be used
+	 * @param structure the structure, all non-H atoms of given model number will be used
+	 * @param probe the probe size
+	 * @param nSpherePoints the number of points to be used in generating the spherical
+	 *                         dot-density, the more points the more accurate (and slower) calculation
+	 * @param nThreads the number of parallel threads to use for the calculation
+	 * @param hetAtoms if true HET residues are considered, if false they aren't, equivalent to
+	 * @param modelNr the model number from which we want atoms extracted
+	 * NACCESS' -h option
+	 */
+	public AsaCalculator(Structure structure, double probe, int nSpherePoints, int nThreads, boolean hetAtoms, int modelNr) {
+		this.atoms = StructureTools.getAllNonHAtomArray(structure, hetAtoms, modelNr);
+		this.atomCoords = Calc.atomsToPoints(atoms);
+		this.probe = probe;
+		this.nThreads = nThreads;
+
+		this.useSpatialHashingForNeighbors = DEFAULT_USE_SPATIAL_HASHING;
+
+		// initialising the radii by looking them up through AtomRadii
+		radii = new double[atomCoords.length];
+		for (int i=0;i<atomCoords.length;i++) {
+			radii[i] = getRadius(atoms[i]);
+		}
+
+		initSpherePoints(nSpherePoints);
+	}
+
+	/**
+	 * Constructs a new AsaCalculator. Subsequently call {@link #calculateAsas()}
+	 * or {@link #getGroupAsas()} to calculate the ASAs
+	 * Only non-Hydrogen atoms are considered in the calculation.
+	 * @param structure the structure, all non-H atoms of model 1 will be used
 	 * @param probe the probe size
 	 * @param nSpherePoints the number of points to be used in generating the spherical
 	 *                         dot-density, the more points the more accurate (and slower) calculation
@@ -135,7 +165,7 @@ static class IndexAndDistance {
 	 * NACCESS' -h option
 	 */
 	public AsaCalculator(Structure structure, double probe, int nSpherePoints, int nThreads, boolean hetAtoms) {
-		this.atoms = StructureTools.getAllNonHAtomArray(structure, hetAtoms);
+		this.atoms = StructureTools.getAllNonHAtomArray(structure, hetAtoms, 1);
 		this.atomCoords = Calc.atomsToPoints(atoms);
 		this.probe = probe;
 		this.nThreads = nThreads;

From 324319e20d5c2ffcbe8b2d10189e369b590a34aa Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Fri, 21 Feb 2025 16:33:57 -0800
Subject: [PATCH 56/90] Fix: first model is model index 0

---
 .../main/java/org/biojava/nbio/structure/asa/AsaCalculator.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
index 21d6935eb3..a47c67db72 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
@@ -165,7 +165,7 @@ public AsaCalculator(Structure structure, double probe, int nSpherePoints, int n
 	 * NACCESS' -h option
 	 */
 	public AsaCalculator(Structure structure, double probe, int nSpherePoints, int nThreads, boolean hetAtoms) {
-		this.atoms = StructureTools.getAllNonHAtomArray(structure, hetAtoms, 1);
+		this.atoms = StructureTools.getAllNonHAtomArray(structure, hetAtoms, 0);
 		this.atomCoords = Calc.atomsToPoints(atoms);
 		this.probe = probe;
 		this.nThreads = nThreads;

From a5b46ab0bb748317516dbdb95f18bb8ab30fb2ca Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Fri, 21 Feb 2025 16:36:08 -0800
Subject: [PATCH 57/90] Review comment

---
 .../biojava/nbio/structure/asa/AsaCalculator.java | 15 +--------------
 1 file changed, 1 insertion(+), 14 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
index a47c67db72..0f46b7f416 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
@@ -165,20 +165,7 @@ public AsaCalculator(Structure structure, double probe, int nSpherePoints, int n
 	 * NACCESS' -h option
 	 */
 	public AsaCalculator(Structure structure, double probe, int nSpherePoints, int nThreads, boolean hetAtoms) {
-		this.atoms = StructureTools.getAllNonHAtomArray(structure, hetAtoms, 0);
-		this.atomCoords = Calc.atomsToPoints(atoms);
-		this.probe = probe;
-		this.nThreads = nThreads;
-
-		this.useSpatialHashingForNeighbors = DEFAULT_USE_SPATIAL_HASHING;
-
-		// initialising the radii by looking them up through AtomRadii
-		radii = new double[atomCoords.length];
-		for (int i=0;i<atomCoords.length;i++) {
-			radii[i] = getRadius(atoms[i]);
-		}
-
-		initSpherePoints(nSpherePoints);
+		this(structure, probe, nSpherePoints, nThreads, hetAtoms, 0);
 	}
 
 	/**

From 48992a6b126fc6c0ba4ecda15e49c089cea0ebaf Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Thu, 27 Feb 2025 10:18:17 -0800
Subject: [PATCH 58/90] [maven-release-plugin] prepare release biojava-7.2.0

---
 biojava-aa-prop/pom.xml                 |  6 +++---
 biojava-alignment/pom.xml               |  4 ++--
 biojava-core/pom.xml                    |  2 +-
 biojava-genome/pom.xml                  |  6 +++---
 biojava-integrationtest/pom.xml         |  4 ++--
 biojava-modfinder/pom.xml               |  4 ++--
 biojava-ontology/pom.xml                |  2 +-
 biojava-protein-comparison-tool/pom.xml | 10 +++++-----
 biojava-protein-disorder/pom.xml        |  4 ++--
 biojava-structure-gui/pom.xml           |  6 +++---
 biojava-structure/pom.xml               |  6 +++---
 biojava-survival/pom.xml                |  2 +-
 biojava-ws/pom.xml                      |  4 ++--
 pom.xml                                 |  4 ++--
 14 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index 30b6642ae6..6b06141174 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.2.0</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.2.0</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.2.0</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index b1c7eb9a94..1d860b9ea0 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.2.0</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.2.0</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 2b3994284c..776112a6ed 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.2.0</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 86b0d8c93f..8d8ee15617 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.2.0</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -70,13 +70,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.2.0</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.2.0</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index a9e79f3d1b..01d398e4e3 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>7.1.5-SNAPSHOT</version>
+    <version>7.2.0</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -40,7 +40,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>7.1.5-SNAPSHOT</version>
+    	<version>7.2.0</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index abb9cab35d..e8a940627a 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.2.0</version>
 	</parent>
 	<artifactId>biojava-modfinder</artifactId>
 	<name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.2.0</version>
 			<type>jar</type>
 			<scope>compile</scope>
 		</dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 0813129079..ee76a29c39 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>7.1.5-SNAPSHOT</version>
+    <version>7.2.0</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml
index 73b06a6159..2ab628e46f 100644
--- a/biojava-protein-comparison-tool/pom.xml
+++ b/biojava-protein-comparison-tool/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.2.0</version>
 	</parent>
 
 	<artifactId>biojava-protein-comparison-tool</artifactId>
@@ -36,23 +36,23 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.2.0</version>
 
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.2.0</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.2.0</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure-gui</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.2.0</version>
 		</dependency>
 		<dependency>
 			<groupId>net.sourceforge.jmol</groupId>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index e612fe824f..90719b4aca 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.2.0</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.2.0</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or
 			scopes here) -->
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index 9d80f82e80..35763e930c 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.2.0</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -27,13 +27,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.2.0</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.2.0</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 4c14aee143..de8df79dd8 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.2.0</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -51,13 +51,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.2.0</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.2.0</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index d469386344..8eee2ee49d 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>7.1.5-SNAPSHOT</version>
+        <version>7.2.0</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index 2b0b0f56cd..a242020712 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.1.5-SNAPSHOT</version>
+		<version>7.2.0</version>
 	</parent>
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.1.5-SNAPSHOT</version>
+			<version>7.2.0</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 1381eb8041..84774f7281 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>7.1.5-SNAPSHOT</version>
+	<version>7.2.0</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the
@@ -51,7 +51,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>HEAD</tag>
+		<tag>biojava-7.2.0</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list

From 6da7fd904f77d3c84bbb326671ea43d9c2a305d3 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Thu, 27 Feb 2025 10:18:20 -0800
Subject: [PATCH 59/90] [maven-release-plugin] prepare for next development
 iteration

---
 biojava-aa-prop/pom.xml                 |  6 +++---
 biojava-alignment/pom.xml               |  4 ++--
 biojava-core/pom.xml                    |  2 +-
 biojava-genome/pom.xml                  |  6 +++---
 biojava-integrationtest/pom.xml         |  4 ++--
 biojava-modfinder/pom.xml               |  4 ++--
 biojava-ontology/pom.xml                |  2 +-
 biojava-protein-comparison-tool/pom.xml | 10 +++++-----
 biojava-protein-disorder/pom.xml        |  4 ++--
 biojava-structure-gui/pom.xml           |  6 +++---
 biojava-structure/pom.xml               |  6 +++---
 biojava-survival/pom.xml                |  2 +-
 biojava-ws/pom.xml                      |  4 ++--
 pom.xml                                 |  4 ++--
 14 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index 6b06141174..b417f96f4d 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.0</version>
+		<version>7.2.1-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.0</version>
+			<version>7.2.1-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.0</version>
+			<version>7.2.1-SNAPSHOT</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index 1d860b9ea0..4d6be17cc5 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.0</version>
+		<version>7.2.1-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.0</version>
+			<version>7.2.1-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 776112a6ed..60334dd098 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.0</version>
+		<version>7.2.1-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 8d8ee15617..ef5598c959 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.0</version>
+		<version>7.2.1-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -70,13 +70,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.0</version>
+			<version>7.2.1-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.0</version>
+			<version>7.2.1-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index 01d398e4e3..e492366488 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>7.2.0</version>
+    <version>7.2.1-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -40,7 +40,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>7.2.0</version>
+    	<version>7.2.1-SNAPSHOT</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index e8a940627a..1f7def0959 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.0</version>
+		<version>7.2.1-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-modfinder</artifactId>
 	<name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.0</version>
+			<version>7.2.1-SNAPSHOT</version>
 			<type>jar</type>
 			<scope>compile</scope>
 		</dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index ee76a29c39..013d82a5a6 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>7.2.0</version>
+    <version>7.2.1-SNAPSHOT</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml
index 2ab628e46f..068801a027 100644
--- a/biojava-protein-comparison-tool/pom.xml
+++ b/biojava-protein-comparison-tool/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.0</version>
+		<version>7.2.1-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>biojava-protein-comparison-tool</artifactId>
@@ -36,23 +36,23 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.0</version>
+			<version>7.2.1-SNAPSHOT</version>
 
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.0</version>
+			<version>7.2.1-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.0</version>
+			<version>7.2.1-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure-gui</artifactId>
-			<version>7.2.0</version>
+			<version>7.2.1-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>net.sourceforge.jmol</groupId>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 90719b4aca..e643485899 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.0</version>
+		<version>7.2.1-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.0</version>
+			<version>7.2.1-SNAPSHOT</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or
 			scopes here) -->
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index 35763e930c..589fc60734 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-		<version>7.2.0</version>
+		<version>7.2.1-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -27,13 +27,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-			<version>7.2.0</version>
+			<version>7.2.1-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-			<version>7.2.0</version>
+			<version>7.2.1-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index de8df79dd8..5492c03468 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.0</version>
+		<version>7.2.1-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -51,13 +51,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.0</version>
+			<version>7.2.1-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.0</version>
+			<version>7.2.1-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 8eee2ee49d..9f103b485a 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>7.2.0</version>
+        <version>7.2.1-SNAPSHOT</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index a242020712..656570d8a4 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.0</version>
+		<version>7.2.1-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.0</version>
+			<version>7.2.1-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 84774f7281..064503177e 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>7.2.0</version>
+	<version>7.2.1-SNAPSHOT</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the
@@ -51,7 +51,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>biojava-7.2.0</tag>
+		<tag>HEAD</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list

From b03fb3f578638c650f503adee4d11155df52a09f Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Thu, 27 Feb 2025 11:35:38 -0800
Subject: [PATCH 60/90] Updates after release

---
 CHANGELOG.md | 9 +++++++++
 README.md    | 4 ++--
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 589a894f06..3da4829ae4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,15 @@
 BioJava Changelog
 -----------------
 
+BioJava 7.2.0
+==============================
+### Fixed
+* More lenient mmCIF parsing to be able to parse [PDB-IHM](https://pdb-ihm.org/) entries #1106
+* Now AsaCalculator main constructor will use first model only instead of all #1107 
+
+### Added
+* New constructor for AsaCalculator to provide Structure and model #1107
+
 BioJava 7.1.4
 ==============================
 ### Fixed
diff --git a/README.md b/README.md
index bb36b69de1..5492e38913 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 # Welcome to <img src="logo-full.png" height="35"/>
 
 ![Build](https://github.com/biojava/biojava/actions/workflows/master.yml/badge.svg)
-[![Version](http://img.shields.io/badge/version-7.1.4-blue.svg?style=flat)](https://github.com/biojava/biojava/releases/tag/biojava-7.1.4) [![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/biojava/biojava/blob/master/LICENSE) [![Join the chat at https://gitter.im/biojava/biojava](https://badges.gitter.im/biojava/biojava.svg)](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+[![Version](http://img.shields.io/badge/version-7.2.0-blue.svg?style=flat)](https://github.com/biojava/biojava/releases/tag/biojava-7.2.0) [![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/biojava/biojava/blob/master/LICENSE) [![Join the chat at https://gitter.im/biojava/biojava](https://badges.gitter.im/biojava/biojava.svg)](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 
 
 BioJava is an open-source project dedicated to providing a Java framework for **processing biological data**. It provides analytical and statistical routines, parsers for common file formats, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.
@@ -29,7 +29,7 @@ If you are using Maven you can add the BioJava repository by adding the followin
       <dependency>
         <groupId>org.biojava</groupId>
         <artifactId>biojava-core</artifactId>
-        <version>7.1.4</version>
+        <version>7.2.0</version>
       </dependency>
       <!-- other biojava modules as needed -->
     </dependencies>

From a6723d42a22166de949bed6a6c4f4f1f29a87ee7 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Fri, 28 Feb 2025 11:12:52 -0800
Subject: [PATCH 61/90] Deal with some missing fields in IHM

---
 .../structure/io/cif/CifStructureConsumerImpl.java    | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
index c610c05f2b..c9ab103037 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
@@ -1297,15 +1297,18 @@ public void finish() {
             SeqMisMatch seqMisMatch = new SeqMisMatchImpl();
             seqMisMatch.setDetails(structRefSeqDif.getDetails().get(rowIndex));
 
-            String insCode = structRefSeqDif.getPdbxPdbInsCode().get(rowIndex);
+            String insCode = null;
+            if (structRefSeqDif.getPdbxPdbInsCode().isDefined()) {
+                insCode = structRefSeqDif.getPdbxPdbInsCode().get(rowIndex);
                 if ("?".equals(insCode)) {
-                insCode = null;
+                    insCode = null;
+                }
             }
             seqMisMatch.setInsCode(insCode);
             seqMisMatch.setOrigGroup(structRefSeqDif.getDbMonId().get(rowIndex));
             seqMisMatch.setPdbGroup(structRefSeqDif.getMonId().get(rowIndex));
-            seqMisMatch.setPdbResNum(structRefSeqDif.getPdbxAuthSeqNum().get(rowIndex));
-            seqMisMatch.setUniProtId(structRefSeqDif.getPdbxSeqDbAccessionCode().get(rowIndex));
+            seqMisMatch.setPdbResNum(structRefSeqDif.getPdbxAuthSeqNum().isDefined()? structRefSeqDif.getPdbxAuthSeqNum().get(rowIndex):null);
+            seqMisMatch.setUniProtId(structRefSeqDif.getPdbxSeqDbAccessionCode().isDefined()? structRefSeqDif.getPdbxSeqDbAccessionCode().get(rowIndex):null);
             seqMisMatch.setSeqNum(structRefSeqDif.getSeqNum().get(rowIndex));
 
             String strandId = structRefSeqDif.getPdbxPdbStrandId().get(rowIndex);

From 8286260589643583c6d631a989b708b4d8c7b956 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Fri, 28 Feb 2025 11:15:03 -0800
Subject: [PATCH 62/90] Dealing with struct_ref_seq_dif strand_id by
 referencing through struct_ref_seq and struct_ref

---
 .../io/cif/CifStructureConsumerImpl.java      | 81 ++++++++++++++-----
 1 file changed, 63 insertions(+), 18 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
index c9ab103037..23ab32f3bf 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
@@ -144,6 +144,7 @@ public class CifStructureConsumerImpl implements CifStructureConsumer {
     private StructNcsOper structNcsOper;
     private PdbxStructOperList structOpers;
     private StructRef structRef;
+    private StructRefSeq structRefSeq;
     private StructRefSeqDif structRefSeqDif;
     private StructSiteGen structSiteGen;
 
@@ -689,7 +690,7 @@ public void consumeEntitySrcSyn(PdbxEntitySrcSyn entitySrcSyn) {
     @Override
     public void consumeEntityPolySeq(EntityPolySeq entityPolySeq) {
         for (int rowIndex = 0; rowIndex < entityPolySeq.getRowCount(); rowIndex++) {
-            Chain entityChain = getEntityChain(entityPolySeq.getEntityId().get(rowIndex));
+            Chain entityChain = getEntityChain(entityPolySeq.getEntityId().get(rowIndex), true);
 
             // first we check through the chemcomp provider, if it fails we do some heuristics to guess the type of group
             // TODO some of this code is analogous to getNewGroup() and we should try to unify them - JD 2016-03-08
@@ -728,19 +729,27 @@ public void consumeEntityPolySeq(EntityPolySeq entityPolySeq) {
         }
     }
 
-    private Chain getEntityChain(String entityId) {
+    /**
+     * Get a chain from the temporary list holding them. If createNewChains is true, a new chain
+     * will be added is none are found with the given entityId
+     * @param entityId the entity id
+     * @param createNewChains whether to add new chains if not found or not. If false, null will be returned if chain not found
+     * @return the chain
+     */
+    private Chain getEntityChain(String entityId, boolean createNewChains) {
         for (Chain chain : entityChains) {
             if (chain.getId().equals(entityId)) {
                 return chain;
             }
         }
-
-        // does not exist yet, so create...
-        Chain chain = new ChainImpl();
-        chain.setId(entityId);
-        entityChains.add(chain);
-
-        return chain;
+        if (createNewChains) {
+            // does not exist yet, so create...
+            Chain chain = new ChainImpl();
+            chain.setId(entityId);
+            entityChains.add(chain);
+            return chain;
+        }
+        return null;
     }
 
     @Override
@@ -967,6 +976,7 @@ public void consumeStructRef(StructRef structRef) {
 
     @Override
     public void consumeStructRefSeq(StructRefSeq structRefSeq) {
+        this.structRefSeq = structRefSeq;
         for (int rowIndex = 0; rowIndex < structRefSeq.getRowCount(); rowIndex++) {
             String refId = structRefSeq.getRefId().get(rowIndex);
 
@@ -1173,7 +1183,7 @@ public void finish() {
             String entityId = structAsym.getEntityId().get(rowIndex);
             logger.debug("Entity {} matches asym_id: {}", entityId, id);
 
-            Chain chain = getEntityChain(entityId);
+            Chain chain = getEntityChain(entityId, true);
             Chain seqRes = (Chain) chain.clone();
             // to solve issue #160 (e.g. 3u7t)
             seqRes = removeSeqResHeterogeneity(seqRes);
@@ -1292,7 +1302,8 @@ public void finish() {
         setStructNcsOps();
         setCrystallographicInfoMetadata();
 
-        Map<String, List<SeqMisMatch>> misMatchMap = new HashMap<>();
+        // entity id to list of SeqMisMatch
+        Map<Integer, List<SeqMisMatch>> misMatchMap = new HashMap<>();
         for (int rowIndex = 0; rowIndex < structRefSeqDif.getRowCount(); rowIndex++) {
             SeqMisMatch seqMisMatch = new SeqMisMatchImpl();
             seqMisMatch.setDetails(structRefSeqDif.getDetails().get(rowIndex));
@@ -1311,20 +1322,54 @@ public void finish() {
             seqMisMatch.setUniProtId(structRefSeqDif.getPdbxSeqDbAccessionCode().isDefined()? structRefSeqDif.getPdbxSeqDbAccessionCode().get(rowIndex):null);
             seqMisMatch.setSeqNum(structRefSeqDif.getSeqNum().get(rowIndex));
 
-            String strandId = structRefSeqDif.getPdbxPdbStrandId().get(rowIndex);
-            List<SeqMisMatch> seqMisMatches = misMatchMap.computeIfAbsent(strandId, k -> new ArrayList<>());
-            seqMisMatches.add(seqMisMatch);
+            // try to trace the reference entity_id to struct_ref_seq -> struct_ref
+            String alignId = findRefIdInStructRefSeq(structRefSeqDif.getAlignId().get(rowIndex));
+            if (alignId!=null) {
+                int entityId = findEntityIdInStructRef(alignId);
+                if (entityId > 0) {
+                    List<SeqMisMatch> seqMisMatches = misMatchMap.computeIfAbsent(entityId, k -> new ArrayList<>());
+                    seqMisMatches.add(seqMisMatch);
+                }
+            }
         }
 
-        for (String chainId : misMatchMap.keySet()){
-            Chain chain = structure.getPolyChainByPDB(chainId);
+        for (int entityId : misMatchMap.keySet()){
+            Chain chain = getEntityChain(String.valueOf(entityId), false);
             if (chain == null) {
-                logger.warn("Could not set mismatches for chain with author id {}", chainId);
+                logger.warn("Could not set mismatches for chain with entity id {}", entityId);
                 continue;
             }
+            chain.setSeqMisMatches(misMatchMap.get(entityId));
+        }
+    }
 
-            chain.setSeqMisMatches(misMatchMap.get(chainId));
+    private String findRefIdInStructRefSeq(String alignId) {
+        for (int rowIndex = 0; rowIndex < structRefSeq.getRowCount(); rowIndex++) {
+            String currentAlignId = structRefSeq.getAlignId().get(rowIndex);
+            if (alignId.equals(currentAlignId)) {
+                return structRefSeq.getRefId().isDefined()? structRefSeq.getRefId().get(rowIndex) : null;
+            }
+        }
+        return null;
+    }
+
+    private int findEntityIdInStructRef(String refId) {
+        String entityIdStr = null;
+        for (int rowIndex = 0; rowIndex < structRef.getRowCount(); rowIndex++) {
+            String currentId = structRef.getId().get(rowIndex);
+            if (refId.equals(currentId)) {
+                entityIdStr = structRef.getEntityId().isDefined()? structRef.getEntityId().get(rowIndex) : null;
+            }
+        }
+        int entityId = -1;
+        if (entityIdStr != null) {
+            try {
+                entityId = Integer.parseInt(entityIdStr);
+            } catch (NumberFormatException e) {
+                logger.warn("Could not parse entity id from '{}'", entityIdStr);
+            }
         }
+        return entityId;
     }
 
     private String getEntityType(String entityId) {

From 58136fe36f4c0c25d3227580e9e3d0b7f869dc7d Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Fri, 28 Feb 2025 13:13:47 -0800
Subject: [PATCH 63/90] Logging

---
 .../biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
index 23ab32f3bf..1de00f7e4c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
@@ -1171,7 +1171,7 @@ public void finish() {
                 currentModel.add(currentChain);
             }
         } else if (!params.isHeaderOnly()) {
-            logger.warn("current chain is null at end of document.");
+            logger.warn("No chains were instantiated after parsing the whole CIF document. This could be due to the atom_site category being absent");
         }
 
         allModels.add(currentModel);

From fdf98644c046416531cb53da0f67e8b7fc6a44cf Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Fri, 28 Feb 2025 13:22:51 -0800
Subject: [PATCH 64/90] Revert "Dealing with struct_ref_seq_dif strand_id by
 referencing through struct_ref_seq and struct_ref"

This reverts commit 8286260589643583c6d631a989b708b4d8c7b956.
---
 .../io/cif/CifStructureConsumerImpl.java      | 81 +++++--------------
 1 file changed, 18 insertions(+), 63 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
index 1de00f7e4c..b90b085609 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
@@ -144,7 +144,6 @@ public class CifStructureConsumerImpl implements CifStructureConsumer {
     private StructNcsOper structNcsOper;
     private PdbxStructOperList structOpers;
     private StructRef structRef;
-    private StructRefSeq structRefSeq;
     private StructRefSeqDif structRefSeqDif;
     private StructSiteGen structSiteGen;
 
@@ -690,7 +689,7 @@ public void consumeEntitySrcSyn(PdbxEntitySrcSyn entitySrcSyn) {
     @Override
     public void consumeEntityPolySeq(EntityPolySeq entityPolySeq) {
         for (int rowIndex = 0; rowIndex < entityPolySeq.getRowCount(); rowIndex++) {
-            Chain entityChain = getEntityChain(entityPolySeq.getEntityId().get(rowIndex), true);
+            Chain entityChain = getEntityChain(entityPolySeq.getEntityId().get(rowIndex));
 
             // first we check through the chemcomp provider, if it fails we do some heuristics to guess the type of group
             // TODO some of this code is analogous to getNewGroup() and we should try to unify them - JD 2016-03-08
@@ -729,27 +728,19 @@ public void consumeEntityPolySeq(EntityPolySeq entityPolySeq) {
         }
     }
 
-    /**
-     * Get a chain from the temporary list holding them. If createNewChains is true, a new chain
-     * will be added is none are found with the given entityId
-     * @param entityId the entity id
-     * @param createNewChains whether to add new chains if not found or not. If false, null will be returned if chain not found
-     * @return the chain
-     */
-    private Chain getEntityChain(String entityId, boolean createNewChains) {
+    private Chain getEntityChain(String entityId) {
         for (Chain chain : entityChains) {
             if (chain.getId().equals(entityId)) {
                 return chain;
             }
         }
-        if (createNewChains) {
-            // does not exist yet, so create...
-            Chain chain = new ChainImpl();
-            chain.setId(entityId);
-            entityChains.add(chain);
-            return chain;
-        }
-        return null;
+
+        // does not exist yet, so create...
+        Chain chain = new ChainImpl();
+        chain.setId(entityId);
+        entityChains.add(chain);
+
+        return chain;
     }
 
     @Override
@@ -976,7 +967,6 @@ public void consumeStructRef(StructRef structRef) {
 
     @Override
     public void consumeStructRefSeq(StructRefSeq structRefSeq) {
-        this.structRefSeq = structRefSeq;
         for (int rowIndex = 0; rowIndex < structRefSeq.getRowCount(); rowIndex++) {
             String refId = structRefSeq.getRefId().get(rowIndex);
 
@@ -1183,7 +1173,7 @@ public void finish() {
             String entityId = structAsym.getEntityId().get(rowIndex);
             logger.debug("Entity {} matches asym_id: {}", entityId, id);
 
-            Chain chain = getEntityChain(entityId, true);
+            Chain chain = getEntityChain(entityId);
             Chain seqRes = (Chain) chain.clone();
             // to solve issue #160 (e.g. 3u7t)
             seqRes = removeSeqResHeterogeneity(seqRes);
@@ -1302,8 +1292,7 @@ public void finish() {
         setStructNcsOps();
         setCrystallographicInfoMetadata();
 
-        // entity id to list of SeqMisMatch
-        Map<Integer, List<SeqMisMatch>> misMatchMap = new HashMap<>();
+        Map<String, List<SeqMisMatch>> misMatchMap = new HashMap<>();
         for (int rowIndex = 0; rowIndex < structRefSeqDif.getRowCount(); rowIndex++) {
             SeqMisMatch seqMisMatch = new SeqMisMatchImpl();
             seqMisMatch.setDetails(structRefSeqDif.getDetails().get(rowIndex));
@@ -1322,54 +1311,20 @@ public void finish() {
             seqMisMatch.setUniProtId(structRefSeqDif.getPdbxSeqDbAccessionCode().isDefined()? structRefSeqDif.getPdbxSeqDbAccessionCode().get(rowIndex):null);
             seqMisMatch.setSeqNum(structRefSeqDif.getSeqNum().get(rowIndex));
 
-            // try to trace the reference entity_id to struct_ref_seq -> struct_ref
-            String alignId = findRefIdInStructRefSeq(structRefSeqDif.getAlignId().get(rowIndex));
-            if (alignId!=null) {
-                int entityId = findEntityIdInStructRef(alignId);
-                if (entityId > 0) {
-                    List<SeqMisMatch> seqMisMatches = misMatchMap.computeIfAbsent(entityId, k -> new ArrayList<>());
-                    seqMisMatches.add(seqMisMatch);
-                }
-            }
+            String strandId = structRefSeqDif.getPdbxPdbStrandId().get(rowIndex);
+            List<SeqMisMatch> seqMisMatches = misMatchMap.computeIfAbsent(strandId, k -> new ArrayList<>());
+            seqMisMatches.add(seqMisMatch);
         }
 
-        for (int entityId : misMatchMap.keySet()){
-            Chain chain = getEntityChain(String.valueOf(entityId), false);
+        for (String chainId : misMatchMap.keySet()){
+            Chain chain = structure.getPolyChainByPDB(chainId);
             if (chain == null) {
-                logger.warn("Could not set mismatches for chain with entity id {}", entityId);
+                logger.warn("Could not set mismatches for chain with author id {}", chainId);
                 continue;
             }
-            chain.setSeqMisMatches(misMatchMap.get(entityId));
-        }
-    }
 
-    private String findRefIdInStructRefSeq(String alignId) {
-        for (int rowIndex = 0; rowIndex < structRefSeq.getRowCount(); rowIndex++) {
-            String currentAlignId = structRefSeq.getAlignId().get(rowIndex);
-            if (alignId.equals(currentAlignId)) {
-                return structRefSeq.getRefId().isDefined()? structRefSeq.getRefId().get(rowIndex) : null;
-            }
-        }
-        return null;
-    }
-
-    private int findEntityIdInStructRef(String refId) {
-        String entityIdStr = null;
-        for (int rowIndex = 0; rowIndex < structRef.getRowCount(); rowIndex++) {
-            String currentId = structRef.getId().get(rowIndex);
-            if (refId.equals(currentId)) {
-                entityIdStr = structRef.getEntityId().isDefined()? structRef.getEntityId().get(rowIndex) : null;
-            }
-        }
-        int entityId = -1;
-        if (entityIdStr != null) {
-            try {
-                entityId = Integer.parseInt(entityIdStr);
-            } catch (NumberFormatException e) {
-                logger.warn("Could not parse entity id from '{}'", entityIdStr);
-            }
+            chain.setSeqMisMatches(misMatchMap.get(chainId));
         }
-        return entityId;
     }
 
     private String getEntityType(String entityId) {

From 2841770e794679818e8eab458b387d157b97f9ec Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Fri, 28 Feb 2025 13:24:40 -0800
Subject: [PATCH 65/90] Deal with missing strand_id

---
 .../nbio/structure/io/cif/CifStructureConsumerImpl.java        | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
index b90b085609..8451d7b8fb 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
@@ -1311,7 +1311,8 @@ public void finish() {
             seqMisMatch.setUniProtId(structRefSeqDif.getPdbxSeqDbAccessionCode().isDefined()? structRefSeqDif.getPdbxSeqDbAccessionCode().get(rowIndex):null);
             seqMisMatch.setSeqNum(structRefSeqDif.getSeqNum().get(rowIndex));
 
-            String strandId = structRefSeqDif.getPdbxPdbStrandId().get(rowIndex);
+            String strandId = structRefSeqDif.getPdbxPdbStrandId().isDefined()? structRefSeqDif.getPdbxPdbStrandId().get(rowIndex) : null;
+            if (strandId == null) continue;
             List<SeqMisMatch> seqMisMatches = misMatchMap.computeIfAbsent(strandId, k -> new ArrayList<>());
             seqMisMatches.add(seqMisMatch);
         }

From 48cb462e137a17d5161f390bbf265a11bc4f48ee Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Tue, 4 Mar 2025 13:52:57 -0800
Subject: [PATCH 66/90] Update
 biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java

Co-authored-by: Sebastian Bittrich <sebastian.bittrich@rcsb.org>
---
 .../nbio/structure/io/cif/CifStructureConsumerImpl.java       | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
index 8451d7b8fb..67514edd84 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
@@ -1311,8 +1311,8 @@ public void finish() {
             seqMisMatch.setUniProtId(structRefSeqDif.getPdbxSeqDbAccessionCode().isDefined()? structRefSeqDif.getPdbxSeqDbAccessionCode().get(rowIndex):null);
             seqMisMatch.setSeqNum(structRefSeqDif.getSeqNum().get(rowIndex));
 
-            String strandId = structRefSeqDif.getPdbxPdbStrandId().isDefined()? structRefSeqDif.getPdbxPdbStrandId().get(rowIndex) : null;
-            if (strandId == null) continue;
+            if (!structRefSeqDif.getPdbxPdbStrandId().isDefined()) continue;
+            String strandId = structRefSeqDif.getPdbxPdbStrandId().get(rowIndex);
             List<SeqMisMatch> seqMisMatches = misMatchMap.computeIfAbsent(strandId, k -> new ArrayList<>());
             seqMisMatches.add(seqMisMatch);
         }

From 5589e1eed3c92170c71fa5da80a3f528b37413a3 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Wed, 5 Mar 2025 11:58:40 -0800
Subject: [PATCH 67/90] [maven-release-plugin] prepare release biojava-7.2.1

---
 biojava-aa-prop/pom.xml                 |  6 +++---
 biojava-alignment/pom.xml               |  4 ++--
 biojava-core/pom.xml                    |  2 +-
 biojava-genome/pom.xml                  |  6 +++---
 biojava-integrationtest/pom.xml         |  4 ++--
 biojava-modfinder/pom.xml               |  4 ++--
 biojava-ontology/pom.xml                |  2 +-
 biojava-protein-comparison-tool/pom.xml | 10 +++++-----
 biojava-protein-disorder/pom.xml        |  4 ++--
 biojava-structure-gui/pom.xml           |  6 +++---
 biojava-structure/pom.xml               |  6 +++---
 biojava-survival/pom.xml                |  2 +-
 biojava-ws/pom.xml                      |  4 ++--
 pom.xml                                 |  4 ++--
 14 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index b417f96f4d..4642728024 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.1-SNAPSHOT</version>
+		<version>7.2.1</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.1-SNAPSHOT</version>
+			<version>7.2.1</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.1-SNAPSHOT</version>
+			<version>7.2.1</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index 4d6be17cc5..ad562e3ef9 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.1-SNAPSHOT</version>
+		<version>7.2.1</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.1-SNAPSHOT</version>
+			<version>7.2.1</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 60334dd098..8a26fa5fef 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.1-SNAPSHOT</version>
+		<version>7.2.1</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index ef5598c959..1875291310 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.1-SNAPSHOT</version>
+		<version>7.2.1</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -70,13 +70,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.1-SNAPSHOT</version>
+			<version>7.2.1</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.1-SNAPSHOT</version>
+			<version>7.2.1</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index e492366488..2b169e7212 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>7.2.1-SNAPSHOT</version>
+    <version>7.2.1</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -40,7 +40,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>7.2.1-SNAPSHOT</version>
+    	<version>7.2.1</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index 1f7def0959..e99c843aa9 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.1-SNAPSHOT</version>
+		<version>7.2.1</version>
 	</parent>
 	<artifactId>biojava-modfinder</artifactId>
 	<name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.1-SNAPSHOT</version>
+			<version>7.2.1</version>
 			<type>jar</type>
 			<scope>compile</scope>
 		</dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 013d82a5a6..befd1e208e 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>7.2.1-SNAPSHOT</version>
+    <version>7.2.1</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml
index 068801a027..82f5c7507d 100644
--- a/biojava-protein-comparison-tool/pom.xml
+++ b/biojava-protein-comparison-tool/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.1-SNAPSHOT</version>
+		<version>7.2.1</version>
 	</parent>
 
 	<artifactId>biojava-protein-comparison-tool</artifactId>
@@ -36,23 +36,23 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.1-SNAPSHOT</version>
+			<version>7.2.1</version>
 
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.1-SNAPSHOT</version>
+			<version>7.2.1</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.1-SNAPSHOT</version>
+			<version>7.2.1</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure-gui</artifactId>
-			<version>7.2.1-SNAPSHOT</version>
+			<version>7.2.1</version>
 		</dependency>
 		<dependency>
 			<groupId>net.sourceforge.jmol</groupId>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index e643485899..72705a2ec5 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.1-SNAPSHOT</version>
+		<version>7.2.1</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.1-SNAPSHOT</version>
+			<version>7.2.1</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or
 			scopes here) -->
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index 589fc60734..27061b3c5c 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-		<version>7.2.1-SNAPSHOT</version>
+		<version>7.2.1</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -27,13 +27,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-			<version>7.2.1-SNAPSHOT</version>
+			<version>7.2.1</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-			<version>7.2.1-SNAPSHOT</version>
+			<version>7.2.1</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 5492c03468..72b76cbed9 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.1-SNAPSHOT</version>
+		<version>7.2.1</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -51,13 +51,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.1-SNAPSHOT</version>
+			<version>7.2.1</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.1-SNAPSHOT</version>
+			<version>7.2.1</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 9f103b485a..6f73371344 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>7.2.1-SNAPSHOT</version>
+        <version>7.2.1</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index 656570d8a4..e68c318de9 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.1-SNAPSHOT</version>
+		<version>7.2.1</version>
 	</parent>
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.1-SNAPSHOT</version>
+			<version>7.2.1</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 064503177e..7ae8b07016 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>7.2.1-SNAPSHOT</version>
+	<version>7.2.1</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the
@@ -51,7 +51,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>HEAD</tag>
+		<tag>biojava-7.2.1</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list

From 8289418368990fc2510be96a11999511953991ed Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Wed, 5 Mar 2025 11:58:43 -0800
Subject: [PATCH 68/90] [maven-release-plugin] prepare for next development
 iteration

---
 biojava-aa-prop/pom.xml                 |  6 +++---
 biojava-alignment/pom.xml               |  4 ++--
 biojava-core/pom.xml                    |  2 +-
 biojava-genome/pom.xml                  |  6 +++---
 biojava-integrationtest/pom.xml         |  4 ++--
 biojava-modfinder/pom.xml               |  4 ++--
 biojava-ontology/pom.xml                |  2 +-
 biojava-protein-comparison-tool/pom.xml | 10 +++++-----
 biojava-protein-disorder/pom.xml        |  4 ++--
 biojava-structure-gui/pom.xml           |  6 +++---
 biojava-structure/pom.xml               |  6 +++---
 biojava-survival/pom.xml                |  2 +-
 biojava-ws/pom.xml                      |  4 ++--
 pom.xml                                 |  4 ++--
 14 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index 4642728024..4de0856cdb 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.1</version>
+		<version>7.2.2-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.1</version>
+			<version>7.2.2-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.1</version>
+			<version>7.2.2-SNAPSHOT</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index ad562e3ef9..2c6b2b1ce6 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.1</version>
+		<version>7.2.2-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.1</version>
+			<version>7.2.2-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 8a26fa5fef..e3b7b4cc95 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.1</version>
+		<version>7.2.2-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 1875291310..4d8696959a 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.1</version>
+		<version>7.2.2-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -70,13 +70,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.1</version>
+			<version>7.2.2-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.1</version>
+			<version>7.2.2-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index 2b169e7212..d20cf89df6 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>7.2.1</version>
+    <version>7.2.2-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -40,7 +40,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>7.2.1</version>
+    	<version>7.2.2-SNAPSHOT</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index e99c843aa9..981c499e0a 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.1</version>
+		<version>7.2.2-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-modfinder</artifactId>
 	<name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.1</version>
+			<version>7.2.2-SNAPSHOT</version>
 			<type>jar</type>
 			<scope>compile</scope>
 		</dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index befd1e208e..9044de341f 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>7.2.1</version>
+    <version>7.2.2-SNAPSHOT</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml
index 82f5c7507d..29be159250 100644
--- a/biojava-protein-comparison-tool/pom.xml
+++ b/biojava-protein-comparison-tool/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.1</version>
+		<version>7.2.2-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>biojava-protein-comparison-tool</artifactId>
@@ -36,23 +36,23 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.1</version>
+			<version>7.2.2-SNAPSHOT</version>
 
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.1</version>
+			<version>7.2.2-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.1</version>
+			<version>7.2.2-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure-gui</artifactId>
-			<version>7.2.1</version>
+			<version>7.2.2-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>net.sourceforge.jmol</groupId>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 72705a2ec5..3c70be5d34 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.1</version>
+		<version>7.2.2-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.1</version>
+			<version>7.2.2-SNAPSHOT</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or
 			scopes here) -->
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index 27061b3c5c..3b8112acfa 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-		<version>7.2.1</version>
+		<version>7.2.2-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -27,13 +27,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-			<version>7.2.1</version>
+			<version>7.2.2-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-			<version>7.2.1</version>
+			<version>7.2.2-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 72b76cbed9..39baa731dd 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.1</version>
+		<version>7.2.2-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -51,13 +51,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.1</version>
+			<version>7.2.2-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.1</version>
+			<version>7.2.2-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 6f73371344..d5ac6b03ab 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>7.2.1</version>
+        <version>7.2.2-SNAPSHOT</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index e68c318de9..e28c7823a3 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.1</version>
+		<version>7.2.2-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.1</version>
+			<version>7.2.2-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 7ae8b07016..899abc3d64 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>7.2.1</version>
+	<version>7.2.2-SNAPSHOT</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the
@@ -51,7 +51,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>biojava-7.2.1</tag>
+		<tag>HEAD</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list

From 602b4d52b0fe10f4a9d880d9c79a2f9f76f48146 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Wed, 5 Mar 2025 13:08:51 -0800
Subject: [PATCH 69/90] Updating after release

---
 CHANGELOG.md | 5 +++++
 README.md    | 4 ++--
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3da4829ae4..d9a873e718 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,11 @@
 BioJava Changelog
 -----------------
 
+BioJava 7.2.1
+==============================
+### Fixed
+* More lenient mmCIF parsing to be able to parse [PDB-IHM](https://pdb-ihm.org/) entries, some more edge cases #1108
+
 BioJava 7.2.0
 ==============================
 ### Fixed
diff --git a/README.md b/README.md
index 5492e38913..2235ae8d35 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 # Welcome to <img src="logo-full.png" height="35"/>
 
 ![Build](https://github.com/biojava/biojava/actions/workflows/master.yml/badge.svg)
-[![Version](http://img.shields.io/badge/version-7.2.0-blue.svg?style=flat)](https://github.com/biojava/biojava/releases/tag/biojava-7.2.0) [![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/biojava/biojava/blob/master/LICENSE) [![Join the chat at https://gitter.im/biojava/biojava](https://badges.gitter.im/biojava/biojava.svg)](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+[![Version](http://img.shields.io/badge/version-7.2.1-blue.svg?style=flat)](https://github.com/biojava/biojava/releases/tag/biojava-7.2.1) [![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/biojava/biojava/blob/master/LICENSE) [![Join the chat at https://gitter.im/biojava/biojava](https://badges.gitter.im/biojava/biojava.svg)](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 
 
 BioJava is an open-source project dedicated to providing a Java framework for **processing biological data**. It provides analytical and statistical routines, parsers for common file formats, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.
@@ -29,7 +29,7 @@ If you are using Maven you can add the BioJava repository by adding the followin
       <dependency>
         <groupId>org.biojava</groupId>
         <artifactId>biojava-core</artifactId>
-        <version>7.2.0</version>
+        <version>7.2.1</version>
       </dependency>
       <!-- other biojava modules as needed -->
     </dependencies>

From 501a09e2590965318d0a85c52d1759291060f450 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Mon, 17 Mar 2025 15:08:43 -0700
Subject: [PATCH 70/90] Make entity type case insensitive. Also improved docs

---
 .../biojava/nbio/structure/EntityType.java    | 23 +++++++------------
 1 file changed, 8 insertions(+), 15 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java
index de8b5ca4d1..f41930681a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java
@@ -21,8 +21,7 @@
 package org.biojava.nbio.structure;
 
 /**
- *
- * The type of entity (polymer, non-polymer, water, macrolide)
+ * The type of entity (polymer, non-polymer, water, macrolide, branched)
  * as defined in the mmCIF dictionary: <a href="http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_entity.type.html"></a>
  * <p>
  * Entities are of four types:  polymer, non-polymer, macrolide and water.
@@ -76,10 +75,8 @@ public enum EntityType {
 	/**
 	 * @param entType the type of the Entity
 	 */
-	private EntityType(String entType) {
-
+	EntityType(String entType) {
 		this.setEntityType(entType);
-
 	}
 
 	/**
@@ -101,19 +98,15 @@ private void setEntityType(String entityType) {
 	 * Returns null if entityType is null or not one of the supported
 	 * standard types.
 	 *
-	 * @param entityType String value , should be one of "polymer","non-polymer","water","macrolide"
-	 * @return an EntityType object
+	 * @param entityType should be one of "polymer", "non-polymer", "water", "macrolide", "branched" (case insensitive)
+	 * @return an EntityType object or null if the input string doesn't correspond to a known entity
 	 */
-	public static EntityType entityTypeFromString(String entityType)
-	{
-
-		if ( entityType == null)
+	public static EntityType entityTypeFromString(String entityType) {
+		if (entityType == null)
 			return null;
 
-		for(EntityType et : EntityType.values())
-		{
-			if(entityType.equals(et.entityType))
-			{
+		for(EntityType et : EntityType.values()) {
+			if (entityType.toLowerCase().equals(et.entityType)) {
 				return et;
 			}
 		}

From aa0d5767badb81bc672127343ae8a1ce3ea84ad9 Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Tue, 18 Mar 2025 10:59:54 -0700
Subject: [PATCH 71/90] Update
 biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java

Co-authored-by: Sebastian Bittrich <jonstargaryen90@gmail.com>
---
 .../src/main/java/org/biojava/nbio/structure/EntityType.java    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java
index f41930681a..b4978fc582 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java
@@ -106,7 +106,7 @@ public static EntityType entityTypeFromString(String entityType) {
 			return null;
 
 		for(EntityType et : EntityType.values()) {
-			if (entityType.toLowerCase().equals(et.entityType)) {
+			if (entityType.equalsIgnoreCase(et.entityType)) {
 				return et;
 			}
 		}

From a24b6f601b4bae2c58b96bc5cf760724e06a1801 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Tue, 18 Mar 2025 13:24:36 -0700
Subject: [PATCH 72/90] Latest ciftools: should fix performance for some bcif
 edgecases

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 899abc3d64..10b10b029c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -44,7 +44,7 @@
 		<log4j.version>2.23.1</log4j.version>
 		<junit-jupiter.version>5.10.1</junit-jupiter.version>
 		<ciftools.artifact>ciftools-java</ciftools.artifact>
-		<ciftools.version>5.0.1</ciftools.version>
+		<ciftools.version>7.0.1</ciftools.version>
 	</properties>
 	<scm>
 		<connection>scm:git:git://github.com/biojava/biojava.git</connection>

From 381fedd40e6b105fa1b806b1d28b02533fb48436 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Wed, 19 Mar 2025 10:44:51 -0700
Subject: [PATCH 73/90] Formatting and docs cleanup

---
 .../org/biojava/nbio/structure/Structure.java |  24 ++--
 .../biojava/nbio/structure/StructureImpl.java | 115 +++++-------------
 2 files changed, 42 insertions(+), 97 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java
index 51d69234c7..605a717577 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java
@@ -232,10 +232,10 @@ public interface Structure extends Cloneable, Serializable {
 	 * Retrieve all Chains belonging to a model .
 	 * @see #getChains(int modelnr)
 	 *
-	 * @param modelnr  an int
+	 * @param modelIdx the model index
 	 * @return a List object containing the Chains of Model nr. modelnr
 	 */
-	List<Chain> getModel(int modelnr);
+	List<Chain> getModel(int modelIdx);
 
 	/**
 	 * Retrieve all chains for the first model.
@@ -261,17 +261,17 @@ public interface Structure extends Cloneable, Serializable {
 	 * Retrieve all chains of a model.
 	 * @see #getModel
 	 *
-	 * @param modelnr  an int
+	 * @param modelIdx the model index
 	 * @return a List object containing the Chains of Model nr. modelnr
 	 */
-	List<Chain> getChains(int modelnr);
+	List<Chain> getChains(int modelIdx);
 
 	/**
 	 * Set the chains for a model
 	 * @param chains the chains for a model
 	 * @param modelnr the number of the model
 	 */
-	void setChains( int modelnr, List<Chain> chains);
+	void setChains(int modelnr, List<Chain> chains);
 
 	/**
 	 * Return all polymeric chains for the first model
@@ -315,7 +315,7 @@ public interface Structure extends Cloneable, Serializable {
 
 	/**
 	 * Return all water chains for the given model index
-	 * @param modelIdx
+	 * @param modelIdx the model index
 	 * @return
 	 * @since 5.0
 	 */
@@ -332,9 +332,9 @@ public interface Structure extends Cloneable, Serializable {
 	 * Add a new chain to the model specified by the given index
 	 *
 	 * @param chain    a Chain object
-	 * @param modelnr  an int specifying to which model the Chain should be added
+	 * @param modelIdx  an int specifying to which model the Chain should be added
 	 */
-	void addChain(Chain chain, int modelnr);
+	void addChain(Chain chain, int modelIdx);
 
 	/**
 	 * Retrieve a chain by its index within the Structure .
@@ -348,10 +348,10 @@ public interface Structure extends Cloneable, Serializable {
 	 * Retrieve a chain by its indices within the Structure and model.
 	 *
 	 * @param chainIndex the index of the desired chain in the structure
-	 * @param modelnr the model the desired chain is in
+	 * @param modelIdx the model index
 	 * @return a Chain object
 	 */
-	Chain getChainByIndex(int modelnr, int chainIndex);
+	Chain getChainByIndex(int modelIdx, int chainIndex);
 
 	/**
 	 * Check if a chain with the chainId aymId is contained in this structure.
@@ -394,11 +394,11 @@ public interface Structure extends Cloneable, Serializable {
 	 * considers only model nr X. count starts with 0.
 	 * @param authId the chain name of the chain to use
 	 * @param pdbResnum the PDB residue number of the requested group
-	 * @param modelnr the number of the model to use
+	 * @param modelIdx the model index
 	 * @return Group the requested Group
 	 * @throws StructureException
 	 */
-	Group findGroup(String authId, String pdbResnum, int modelnr) throws StructureException;
+	Group findGroup(String authId, String pdbResnum, int modelIdx) throws StructureException;
 
 	/**
 	 * Retrieve a Chain (polymeric, non-polymeric or water) based on
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
index ae00c8f7f3..1f5e371e56 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
@@ -123,20 +123,15 @@ public Structure clone() {
 		n.setDBRefs(this.getDBRefs());
 		n.setSites(getSites());
 
-
 		// go through each chain and clone chain
 		for (int i=0;i<nrModels();i++){
 			List<Chain> cloned_model = new ArrayList<>();
 
 			for (int j=0;j<size(i);j++){
-
 				Chain cloned_chain  = (Chain) getChainByIndex(i,j).clone();
-
 				// setting the parent: can only be done from the parent
 				cloned_chain.setStructure(n);
-
 				cloned_model.add(cloned_chain);
-
 			}
 			n.addModel(cloned_model);
 
@@ -170,36 +165,30 @@ public Structure clone() {
 
 	/** {@inheritDoc} */
 	@Override
-	public Group findGroup(String chainName, String pdbResnum, int modelnr)
+	public Group findGroup(String chainName, String pdbResnum, int modelIdx)
 			throws StructureException {
 
-
 		// if structure is xray there will be only one "model".
-		if ( modelnr > models.size())
-			throw new StructureException(" no model nr " + modelnr +
+		if ( modelIdx > models.size())
+			throw new StructureException(" no model nr " + modelIdx +
 					" in this structure. (contains "+models.size()+")");
 
-
 		// first we need to gather all groups with the author id chainName: polymers, non-polymers and waters
-		Chain polyChain = getPolyChainByPDB(chainName, modelnr);
+		Chain polyChain = getPolyChainByPDB(chainName, modelIdx);
 		if(polyChain != null) {
-			List<Group> groups = new ArrayList<>();
-
-			groups.addAll(polyChain.getAtomGroups());
 
+            List<Group> groups = new ArrayList<>(polyChain.getAtomGroups());
 
 			// there can be more than one non-poly chain for a given author id
-			for (Chain chain: getNonPolyChainsByPDB(chainName, modelnr)) {
+			for (Chain chain: getNonPolyChainsByPDB(chainName, modelIdx)) {
 				groups.addAll(chain.getAtomGroups());
 			}
 
-			Chain water = getWaterChainByPDB(chainName, modelnr);
+			Chain water = getWaterChainByPDB(chainName, modelIdx);
 
 			if (water!=null)
 				groups.addAll(water.getAtomGroups());
 
-
-
 			// now iterate over all groups
 			// in order to find the amino acid that has this pdbRenum.
 
@@ -260,7 +249,7 @@ public void addChain(Chain chain) {
 
 	/** {@inheritDoc} */
 	@Override
-	public void addChain(Chain chain, int modelnr) {
+	public void addChain(Chain chain, int modelIdx) {
 		// if model has not been initialized, init it!
 		chain.setStructure(this);
 		if (models.isEmpty()) {
@@ -271,16 +260,11 @@ public void addChain(Chain chain, int modelnr) {
 			models.add(model);
 
 		} else {
-			Model model = models.get(modelnr);
+			Model model = models.get(modelIdx);
 			model.addChain(chain);
 		}
-
-
-
 	}
 
-
-
 	/** {@inheritDoc} */
 	@Override
 	public Chain getChainByIndex(int number) {
@@ -293,9 +277,9 @@ public Chain getChainByIndex(int number) {
 
 	/** {@inheritDoc} */
 	@Override
-	public Chain getChainByIndex(int modelnr,int number) {
+	public Chain getChainByIndex(int modelIdx, int number) {
 
-		Model model = models.get(modelnr);
+		Model model = models.get(modelIdx);
 
 		return model.getChains().get(number);
 	}
@@ -333,8 +317,6 @@ public void setModel(int position, List<Chain> modelChains){
 			c.setStructure(this);
 
 		//System.out.println("model size:" + models.size());
-
-
 		Model model = new Model();
 		model.setChains(modelChains);
 
@@ -350,7 +332,7 @@ public void setModel(int position, List<Chain> modelChains){
 	 */
 	@Override
 	public String toString(){
-		String newline = System.getProperty("line.separator");
+		String newline = System.lineSeparator();
 		StringBuilder str = new StringBuilder();
 		str.append("structure ");
 		str.append(name);
@@ -384,16 +366,12 @@ public String toString(){
 				List<Group> hgr = cha.getAtomGroups(GroupType.HETATM);
 				List<Group> ngr = cha.getAtomGroups(GroupType.NUCLEOTIDE);
 
-
-
-
 				str.append("chain ")
 						.append(j).append(": asymId:")
 						.append(cha.getId())
 						.append(" authId:")
 						.append(cha.getName()).append(" ");
 
-
 				if ( cha.getEntityInfo() != null){
 					EntityInfo comp = cha.getEntityInfo();
 					String molName = comp.getDescription();
@@ -406,7 +384,6 @@ public String toString(){
 							.append(")");
 				}
 
-
 				str.append(newline);
 				str.append(" length SEQRES: ").append(cha.getSeqResLength());
 				str.append(" length ATOM: ").append(cha.getAtomLength());
@@ -425,7 +402,6 @@ public String toString(){
 			str.append(mol).append(newline);
 		}
 
-
 		return str.toString() ;
 	}
 
@@ -566,8 +542,6 @@ public List<Chain> getWaterChains(int modelIdx) {
 		return models.get(modelIdx).getWaterChains();
 	}
 
-
-
 	/** {@inheritDoc} */
 	@Override
 	public void setChains(int modelnr, List<Chain> chains){
@@ -584,37 +558,32 @@ public void setChains(int modelnr, List<Chain> chains){
 
 	}
 
-	/** Retrieve all Chains belonging to a model .
-	 *
-	 * @param modelnr  an int
-	 * @return a List object
+	/**
+	 * {@inheritDoc}
 	 */
 	@Override
-	public List<Chain> getModel(int modelnr) {
+	public List<Chain> getModel(int modelIdx) {
 
-		return models.get(modelnr).getChains();
+		return models.get(modelIdx).getChains();
 	}
 
 	/** {@inheritDoc} */
 	@Override
-	public Chain getChain(String asymId, int modelnr) {
+	public Chain getChain(String asymId, int modelIdx) {
 
-		List<Chain> chains = getChains(modelnr);
+		List<Chain> chains = getChains(modelIdx);
 		for (Chain c : chains) {
 			if (c.getId().equals(asymId)) {
 				return c;
 			}
 		}
 		return null;
-
 	}
 
 	/** {@inheritDoc} */
 	@Override
 	public Chain getChain(String asymId) {
-
 		return getChain(asymId,0);
-
 	}
 
 	@Override
@@ -693,7 +662,6 @@ public List<Chain> getNonPolyChainsByPDB(String authId, int modelIdx) {
 			return chains;
 		}
 
-
 		List<Chain> nonpolyChains = model.getNonPolyChains();
 		for (Chain c : nonpolyChains){
 			if (c.getName().equals(authId))
@@ -745,8 +713,6 @@ public Chain getWaterChainByPDB(String authId, int modelIdx) {
 		return null;
 	}
 
-
-
 	/** {@inheritDoc} */
 	@Override
 	public String toPDB() {
@@ -835,7 +801,6 @@ public EntityInfo getEntityById(int entityId) {
 		return null;
 	}
 
-
 	/** {@inheritDoc} */
 	@Override
 	public List<DBRef> getDBRefs() {
@@ -872,7 +837,6 @@ public void setPDBHeader(PDBHeader pdbHeader){
 	@Override
 	public List<Bond> getSSBonds(){
 		return ssbonds;
-
 	}
 
 	/** {@inheritDoc} */
@@ -882,9 +846,7 @@ public void setSSBonds(List<Bond> ssbonds){
 	}
 
 	/**
-	 * Adds a single disulfide Bond to this structure
-	 *
-	 * @param ssbond the SSBond.
+	 * {@inheritDoc}
 	 */
 	@Override
 	public void addSSBond(Bond ssbond){
@@ -892,10 +854,7 @@ public void addSSBond(Bond ssbond){
 	}
 
 	/**
-	 * Return whether or not the entry has an associated journal article
-	 * or publication. The JRNL section is not mandatory and thus may not be
-	 * present.
-	 * @return flag if a JournalArticle could be found.
+	 * R{@inheritDoc}
 	 */
 	@Override
 	public boolean hasJournalArticle() {
@@ -903,9 +862,7 @@ public boolean hasJournalArticle() {
 	}
 
 	/**
-	 * get the associated publication as defined by the JRNL records in a PDB
-	 * file.
-	 * @return a JournalArticle
+	 * {@inheritDoc}
 	 */
 	@Override
 	public JournalArticle getJournalArticle() {
@@ -913,9 +870,7 @@ public JournalArticle getJournalArticle() {
 	}
 
 	/**
-	 * set the associated publication as defined by the JRNL records in a PDB
-	 * file.
-	 * @param journalArticle the article
+	 * {@inheritDoc}
 	 */
 	@Override
 	public void setJournalArticle(JournalArticle journalArticle) {
@@ -923,29 +878,21 @@ public void setJournalArticle(JournalArticle journalArticle) {
 	}
 
 	/**
-	 * @return the sites contained in this structure
+	 * {@inheritDoc}
 	 */
-
 	@Override
 	public List<Site> getSites() {
 		return sites;
 	}
 
 	/**
-	 * @param sites the sites to set in the structure
+	 * {@inheritDoc}
 	 */
-
 	@Override
 	public void setSites(List<Site> sites) {
 		this.sites = sites;
 	}
 
-	/** Caution: we should probably remove this to avoid confusion. Currently this is always an empty list!
-	 *
-	 * @return a list of Groups listed in the HET records - this will not
-	 * include any waters.
-	 */
-
 	/**
 	 * Sets a flag to indicate if this structure is a biological assembly
 	 * @param biologicalAssembly true if biological assembly, otherwise false
@@ -1026,19 +973,17 @@ public void setPDBCode(String pdb_id){
 			pdbId = new PdbId(pdb_id);
 		}
 	}
-	
-
 
-	/** {@inheritDoc} 
-	 * @since 6.0.0
-	 * */
+	/**
+	 * {@inheritDoc}
+	 **/
 	public PdbId getPdbId() {
 		return this.pdbId;
 	}
 	
-	/** {@inheritDoc}
-	 * @since 6.0.0
-	 *  */
+	/**
+	 * {@inheritDoc}
+	 **/
 	public void setPdbId(PdbId pdbId) {
 		this.pdbId = pdbId;
 	}

From 743a9fdc23eaadd4f60a93e57618a33bb2857c49 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Wed, 19 Mar 2025 10:53:06 -0700
Subject: [PATCH 74/90] More cleanup

---
 .../org/biojava/nbio/structure/Structure.java |  8 ++--
 .../biojava/nbio/structure/StructureImpl.java | 45 +++++--------------
 2 files changed, 14 insertions(+), 39 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java
index 605a717577..05bd0ba859 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java
@@ -178,10 +178,10 @@ public interface Structure extends Cloneable, Serializable {
 	/**
 	 * Return number of chains of model.
 	 *
-	 * @param modelnr  an int specifying the number of the Model that should be used
+	 * @param modelIdx  an int specifying the index of the Model that should be used
 	 * @return an int representing the number of Chains in this Model
 	 */
-	int size(int modelnr);
+	int size(int modelIdx);
 
 	/**
 	 * Return the number of models .
@@ -269,9 +269,9 @@ public interface Structure extends Cloneable, Serializable {
 	/**
 	 * Set the chains for a model
 	 * @param chains the chains for a model
-	 * @param modelnr the number of the model
+	 * @param modelIdx the model index
 	 */
-	void setChains(int modelnr, List<Chain> chains);
+	void setChains(int modelIdx, List<Chain> chains);
 
 	/**
 	 * Return all polymeric chains for the first model
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
index 1f5e371e56..f91f8aff23 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
@@ -268,24 +268,17 @@ public void addChain(Chain chain, int modelIdx) {
 	/** {@inheritDoc} */
 	@Override
 	public Chain getChainByIndex(int number) {
-
-		int modelnr = 0 ;
-
-		return getChainByIndex(modelnr,number);
+		return getChainByIndex(0, number);
 	}
 
 
 	/** {@inheritDoc} */
 	@Override
 	public Chain getChainByIndex(int modelIdx, int number) {
-
 		Model model = models.get(modelIdx);
-
 		return model.getChains().get(number);
 	}
 
-
-
 	/** {@inheritDoc} */
 	@Override
 	public void addModel(List<Chain> modelChains){
@@ -297,7 +290,6 @@ public void addModel(List<Chain> modelChains){
 		models.add(model);
 	}
 
-
 	/** {@inheritDoc} */
 	@Override
 	public void setChains(List<Chain> chains){
@@ -305,8 +297,6 @@ public void setChains(List<Chain> chains){
 		setModel(0,chains);
 	}
 
-
-
 	/** {@inheritDoc} */
 	@Override
 	public void setModel(int position, List<Chain> modelChains){
@@ -327,9 +317,6 @@ public void setModel(int position, List<Chain> modelChains){
 		}
 	}
 
-	/** String representation.
-	 *
-	 */
 	@Override
 	public String toString(){
 		String newline = System.lineSeparator();
@@ -418,15 +405,11 @@ public int size() {
 
 	}
 
-	/** return number of chains  of model.
-	 *
-	 */
 	@Override
-	public int size(int modelnr) { return models.get(modelnr).size(); }
+	public int size(int modelIdx) { return models.get(modelIdx).size(); }
 
 	// some NMR stuff :
 
-	/** return number of models. */
 	@Override
 	public int nrModels() {
 		return models.size() ;
@@ -496,16 +479,15 @@ public List<Chain> getChains(int modelIdx){
 	/** {@inheritDoc} */
 	@Override
 	public List<Chain> getChains(){
-		if (models.size()==0) {
+		if (models.isEmpty()) {
 			return new ArrayList<>(0);
 		}
 		return getChains(0);
-
 	}
 
 	@Override
 	public List<Chain> getPolyChains() {
-		if (models.size()==0) {
+		if (models.isEmpty()) {
 			return new ArrayList<>(0);
 		}
 		return getPolyChains(0);
@@ -518,7 +500,7 @@ public List<Chain> getPolyChains(int modelIdx) {
 
 	@Override
 	public List<Chain> getNonPolyChains() {
-		if (models.size()==0) {
+		if (models.isEmpty()) {
 			return new ArrayList<>(0);
 		}
 		return  getNonPolyChains(0);
@@ -531,7 +513,7 @@ public List<Chain> getNonPolyChains(int modelIdx) {
 
 	@Override
 	public List<Chain> getWaterChains() {
-		if (models.size()==0) {
+		if (models.isEmpty()) {
 			return new ArrayList<>(0);
 		}
 		return getWaterChains(0);
@@ -544,18 +526,17 @@ public List<Chain> getWaterChains(int modelIdx) {
 
 	/** {@inheritDoc} */
 	@Override
-	public void setChains(int modelnr, List<Chain> chains){
+	public void setChains(int modelIdx, List<Chain> chains){
 		for (Chain c: chains){
 			c.setStructure(this);
 		}
-		if (models.size()>modelnr) {
-			models.remove(modelnr);
+		if (models.size()> modelIdx) {
+			models.remove(modelIdx);
 		}
 
 		Model model = new Model();
 		model.setChains(chains);
-		models.add(modelnr, model);
-
+		models.add(modelIdx, model);
 	}
 
 	/**
@@ -563,7 +544,6 @@ public void setChains(int modelnr, List<Chain> chains){
 	 */
 	@Override
 	public List<Chain> getModel(int modelIdx) {
-
 		return models.get(modelIdx).getChains();
 	}
 
@@ -606,7 +586,6 @@ public Chain getPolyChain(String asymId, int modelIdx) {
 		return null;
 	}
 
-
 	@Override
 	public Chain getNonPolyChain(String asymId) {
 		return getNonPolyChain(asymId, 0);
@@ -624,7 +603,6 @@ public Chain getNonPolyChain(String asymId, int modelIdx) {
 			if (c.getId().equals(asymId))
 				return c;
 		}
-
 		return null;
 	}
 
@@ -676,7 +654,6 @@ public Chain getWaterChain(String asymId) {
 		return getWaterChain(asymId, 0);
 	}
 
-
 	@Override
 	public Chain getWaterChain(String asymId, int modelIdx) {
 		Model model = models.get(modelIdx);
@@ -697,7 +674,6 @@ public Chain getWaterChainByPDB(String authId) {
 		return getWaterChainByPDB(authId, 0);
 	}
 
-
 	@Override
 	public Chain getWaterChainByPDB(String authId, int modelIdx) {
 		Model model = models.get(modelIdx);
@@ -820,7 +796,6 @@ public void setDBRefs(List<DBRef> dbrefs) {
 		this.dbrefs = dbrefs;
 	}
 
-
 	/** {@inheritDoc} */
 	@Override
 	public PDBHeader getPDBHeader() {

From c33627f85311f35b5efc947c94cd7439b0db82c5 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Wed, 19 Mar 2025 11:03:04 -0700
Subject: [PATCH 75/90] More cleanup

---
 .../biojava/nbio/structure/StructureImpl.java  | 18 +++++-------------
 1 file changed, 5 insertions(+), 13 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
index f91f8aff23..b0165ec3a7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
@@ -243,8 +243,7 @@ public void setStructureIdentifier(StructureIdentifier structureIdentifier) {
 	/** {@inheritDoc} */
 	@Override
 	public void addChain(Chain chain) {
-		int modelnr = 0 ;
-		addChain(chain,modelnr);
+		addChain(chain, 0);
 	}
 
 	/** {@inheritDoc} */
@@ -293,8 +292,7 @@ public void addModel(List<Chain> modelChains){
 	/** {@inheritDoc} */
 	@Override
 	public void setChains(List<Chain> chains){
-
-		setModel(0,chains);
+		setModel(0, chains);
 	}
 
 	/** {@inheritDoc} */
@@ -359,7 +357,7 @@ public String toString(){
 						.append(" authId:")
 						.append(cha.getName()).append(" ");
 
-				if ( cha.getEntityInfo() != null){
+				if (cha.getEntityInfo() != null){
 					EntityInfo comp = cha.getEntityInfo();
 					String molName = comp.getDescription();
 					if ( molName != null){
@@ -394,22 +392,16 @@ public String toString(){
 
 	@Override
 	public int size() {
-		int modelnr = 0 ;
-
 		if (!models.isEmpty()) {
-			return models.get(modelnr).getPolyChains().size();
-		}
-		else {
+			return models.get(0).getPolyChains().size();
+		} else {
 			return 0 ;
 		}
-
 	}
 
 	@Override
 	public int size(int modelIdx) { return models.get(modelIdx).size(); }
 
-	// some NMR stuff :
-
 	@Override
 	public int nrModels() {
 		return models.size() ;

From 7217ee82acf8098206d67b67feb54c0ed5170b6a Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Wed, 19 Mar 2025 12:58:42 -0700
Subject: [PATCH 76/90] Safeguards

---
 .../main/java/org/biojava/nbio/structure/StructureImpl.java   | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
index b0165ec3a7..0a697e2d7b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
@@ -536,13 +536,13 @@ public void setChains(int modelIdx, List<Chain> chains){
 	 */
 	@Override
 	public List<Chain> getModel(int modelIdx) {
+		if (models.isEmpty()) return new ArrayList<>();
 		return models.get(modelIdx).getChains();
 	}
 
 	/** {@inheritDoc} */
 	@Override
 	public Chain getChain(String asymId, int modelIdx) {
-
 		List<Chain> chains = getChains(modelIdx);
 		for (Chain c : chains) {
 			if (c.getId().equals(asymId)) {
@@ -566,6 +566,8 @@ public Chain getPolyChain(String asymId) {
 
 	@Override
 	public Chain getPolyChain(String asymId, int modelIdx) {
+		if (models.isEmpty()) return null;
+
 		Model model = models.get(modelIdx);
 		if (model==null) {
 			return null;

From 6e7891b630262ff75f70430ac27629932e6740c5 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Thu, 20 Mar 2025 12:19:40 -0700
Subject: [PATCH 77/90] [maven-release-plugin] prepare release biojava-7.2.2

---
 biojava-aa-prop/pom.xml                 |  6 +++---
 biojava-alignment/pom.xml               |  4 ++--
 biojava-core/pom.xml                    |  2 +-
 biojava-genome/pom.xml                  |  6 +++---
 biojava-integrationtest/pom.xml         |  4 ++--
 biojava-modfinder/pom.xml               |  4 ++--
 biojava-ontology/pom.xml                |  2 +-
 biojava-protein-comparison-tool/pom.xml | 10 +++++-----
 biojava-protein-disorder/pom.xml        |  4 ++--
 biojava-structure-gui/pom.xml           |  6 +++---
 biojava-structure/pom.xml               |  6 +++---
 biojava-survival/pom.xml                |  2 +-
 biojava-ws/pom.xml                      |  4 ++--
 pom.xml                                 |  4 ++--
 14 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index 4de0856cdb..e53c796e3d 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.2-SNAPSHOT</version>
+		<version>7.2.2</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.2-SNAPSHOT</version>
+			<version>7.2.2</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.2-SNAPSHOT</version>
+			<version>7.2.2</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index 2c6b2b1ce6..4d64a820ce 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.2-SNAPSHOT</version>
+		<version>7.2.2</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.2-SNAPSHOT</version>
+			<version>7.2.2</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index e3b7b4cc95..7662ec2488 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.2-SNAPSHOT</version>
+		<version>7.2.2</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 4d8696959a..4ce37b1110 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.2-SNAPSHOT</version>
+		<version>7.2.2</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -70,13 +70,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.2-SNAPSHOT</version>
+			<version>7.2.2</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.2-SNAPSHOT</version>
+			<version>7.2.2</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index d20cf89df6..12bb171142 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>7.2.2-SNAPSHOT</version>
+    <version>7.2.2</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -40,7 +40,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>7.2.2-SNAPSHOT</version>
+    	<version>7.2.2</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index 981c499e0a..baf5f746ce 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.2-SNAPSHOT</version>
+		<version>7.2.2</version>
 	</parent>
 	<artifactId>biojava-modfinder</artifactId>
 	<name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.2-SNAPSHOT</version>
+			<version>7.2.2</version>
 			<type>jar</type>
 			<scope>compile</scope>
 		</dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 9044de341f..4fa75588f4 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>7.2.2-SNAPSHOT</version>
+    <version>7.2.2</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml
index 29be159250..e8c0c8da22 100644
--- a/biojava-protein-comparison-tool/pom.xml
+++ b/biojava-protein-comparison-tool/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.2-SNAPSHOT</version>
+		<version>7.2.2</version>
 	</parent>
 
 	<artifactId>biojava-protein-comparison-tool</artifactId>
@@ -36,23 +36,23 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.2-SNAPSHOT</version>
+			<version>7.2.2</version>
 
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.2-SNAPSHOT</version>
+			<version>7.2.2</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.2-SNAPSHOT</version>
+			<version>7.2.2</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure-gui</artifactId>
-			<version>7.2.2-SNAPSHOT</version>
+			<version>7.2.2</version>
 		</dependency>
 		<dependency>
 			<groupId>net.sourceforge.jmol</groupId>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 3c70be5d34..bb8885d2d8 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.2-SNAPSHOT</version>
+		<version>7.2.2</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.2-SNAPSHOT</version>
+			<version>7.2.2</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or
 			scopes here) -->
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index 3b8112acfa..569a2b4d43 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-		<version>7.2.2-SNAPSHOT</version>
+		<version>7.2.2</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -27,13 +27,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-			<version>7.2.2-SNAPSHOT</version>
+			<version>7.2.2</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-			<version>7.2.2-SNAPSHOT</version>
+			<version>7.2.2</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 39baa731dd..7a9e8da139 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.2-SNAPSHOT</version>
+		<version>7.2.2</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -51,13 +51,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.2-SNAPSHOT</version>
+			<version>7.2.2</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.2-SNAPSHOT</version>
+			<version>7.2.2</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index d5ac6b03ab..8deffb1d69 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>7.2.2-SNAPSHOT</version>
+        <version>7.2.2</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index e28c7823a3..2a649166a1 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.2-SNAPSHOT</version>
+		<version>7.2.2</version>
 	</parent>
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.2-SNAPSHOT</version>
+			<version>7.2.2</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 10b10b029c..a7ba4e4e52 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>7.2.2-SNAPSHOT</version>
+	<version>7.2.2</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the
@@ -51,7 +51,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>HEAD</tag>
+		<tag>biojava-7.2.2</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list

From b9c4cd0afee6ea10e30eb7489178755c25c0662d Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Thu, 20 Mar 2025 12:19:43 -0700
Subject: [PATCH 78/90] [maven-release-plugin] prepare for next development
 iteration

---
 biojava-aa-prop/pom.xml                 |  6 +++---
 biojava-alignment/pom.xml               |  4 ++--
 biojava-core/pom.xml                    |  2 +-
 biojava-genome/pom.xml                  |  6 +++---
 biojava-integrationtest/pom.xml         |  4 ++--
 biojava-modfinder/pom.xml               |  4 ++--
 biojava-ontology/pom.xml                |  2 +-
 biojava-protein-comparison-tool/pom.xml | 10 +++++-----
 biojava-protein-disorder/pom.xml        |  4 ++--
 biojava-structure-gui/pom.xml           |  6 +++---
 biojava-structure/pom.xml               |  6 +++---
 biojava-survival/pom.xml                |  2 +-
 biojava-ws/pom.xml                      |  4 ++--
 pom.xml                                 |  4 ++--
 14 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index e53c796e3d..b2b642b661 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.2</version>
+		<version>7.2.3-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.2</version>
+			<version>7.2.3-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.2</version>
+			<version>7.2.3-SNAPSHOT</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index 4d64a820ce..fe75c181c7 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.2</version>
+		<version>7.2.3-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.2</version>
+			<version>7.2.3-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 7662ec2488..0836ffe54c 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.2</version>
+		<version>7.2.3-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 4ce37b1110..7729a6e9e3 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.2</version>
+		<version>7.2.3-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -70,13 +70,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.2</version>
+			<version>7.2.3-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.2</version>
+			<version>7.2.3-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index 12bb171142..2c44988004 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>7.2.2</version>
+    <version>7.2.3-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -40,7 +40,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>7.2.2</version>
+    	<version>7.2.3-SNAPSHOT</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index baf5f746ce..0b8cb53791 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.2</version>
+		<version>7.2.3-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-modfinder</artifactId>
 	<name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.2</version>
+			<version>7.2.3-SNAPSHOT</version>
 			<type>jar</type>
 			<scope>compile</scope>
 		</dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 4fa75588f4..001e3e52f1 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>7.2.2</version>
+    <version>7.2.3-SNAPSHOT</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml
index e8c0c8da22..12e4941d55 100644
--- a/biojava-protein-comparison-tool/pom.xml
+++ b/biojava-protein-comparison-tool/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.2</version>
+		<version>7.2.3-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>biojava-protein-comparison-tool</artifactId>
@@ -36,23 +36,23 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.2</version>
+			<version>7.2.3-SNAPSHOT</version>
 
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.2</version>
+			<version>7.2.3-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.2</version>
+			<version>7.2.3-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure-gui</artifactId>
-			<version>7.2.2</version>
+			<version>7.2.3-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>net.sourceforge.jmol</groupId>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index bb8885d2d8..82107e8058 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.2</version>
+		<version>7.2.3-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.2</version>
+			<version>7.2.3-SNAPSHOT</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or
 			scopes here) -->
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index 569a2b4d43..24644c8ffe 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-		<version>7.2.2</version>
+		<version>7.2.3-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -27,13 +27,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-			<version>7.2.2</version>
+			<version>7.2.3-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-			<version>7.2.2</version>
+			<version>7.2.3-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 7a9e8da139..5392798310 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.2</version>
+		<version>7.2.3-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -51,13 +51,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.2</version>
+			<version>7.2.3-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.2</version>
+			<version>7.2.3-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 8deffb1d69..4f3e00f56b 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>7.2.2</version>
+        <version>7.2.3-SNAPSHOT</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index 2a649166a1..7a4fa63589 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.2</version>
+		<version>7.2.3-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.2</version>
+			<version>7.2.3-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index a7ba4e4e52..f17d3c2d67 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>7.2.2</version>
+	<version>7.2.3-SNAPSHOT</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the
@@ -51,7 +51,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>biojava-7.2.2</tag>
+		<tag>HEAD</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list

From 5a699eb6465509b853463ae34ec04c4d90bc2a54 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Thu, 20 Mar 2025 13:30:44 -0700
Subject: [PATCH 79/90] Updating after release

---
 CHANGELOG.md | 7 +++++++
 README.md    | 4 ++--
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d9a873e718..74b52303b0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,13 @@
 BioJava Changelog
 -----------------
 
+BioJava 7.2.2
+==============================
+### Fixed
+* mmCIF parsing: entity type should be case insensitive #1109
+* Upgraded to latest version of ciftools-java, fixes mmCIF parsing performance issues in some edge cases https://github.com/rcsb/ciftools-java/issues/13
+* Added safeguards for `Structure.get*Chain*()` methods #1111
+
 BioJava 7.2.1
 ==============================
 ### Fixed
diff --git a/README.md b/README.md
index 2235ae8d35..af128cd92c 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 # Welcome to <img src="logo-full.png" height="35"/>
 
 ![Build](https://github.com/biojava/biojava/actions/workflows/master.yml/badge.svg)
-[![Version](http://img.shields.io/badge/version-7.2.1-blue.svg?style=flat)](https://github.com/biojava/biojava/releases/tag/biojava-7.2.1) [![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/biojava/biojava/blob/master/LICENSE) [![Join the chat at https://gitter.im/biojava/biojava](https://badges.gitter.im/biojava/biojava.svg)](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+[![Version](http://img.shields.io/badge/version-7.2.2-blue.svg?style=flat)](https://github.com/biojava/biojava/releases/tag/biojava-7.2.2) [![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/biojava/biojava/blob/master/LICENSE) [![Join the chat at https://gitter.im/biojava/biojava](https://badges.gitter.im/biojava/biojava.svg)](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 
 
 BioJava is an open-source project dedicated to providing a Java framework for **processing biological data**. It provides analytical and statistical routines, parsers for common file formats, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.
@@ -29,7 +29,7 @@ If you are using Maven you can add the BioJava repository by adding the followin
       <dependency>
         <groupId>org.biojava</groupId>
         <artifactId>biojava-core</artifactId>
-        <version>7.2.1</version>
+        <version>7.2.2</version>
       </dependency>
       <!-- other biojava modules as needed -->
     </dependencies>

From 7b82b27b15c76899a9042386ea955882feaa070e Mon Sep 17 00:00:00 2001
From: Jose Duarte <jose.m.duarte@gmail.com>
Date: Fri, 18 Jul 2025 08:18:34 -0700
Subject: [PATCH 80/90] Using new mvn central plugin

---
 pom.xml | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/pom.xml b/pom.xml
index f17d3c2d67..c2a70eb02e 100644
--- a/pom.xml
+++ b/pom.xml
@@ -580,17 +580,20 @@
 			<id>release</id>
 			<build>
 				<plugins>
-					<!-- for deployment on OSS Sonatype -->
-					<!-- handles propagating the build to the staging repository -->
+					<!-- handles uploading the build to the maven central repository -->
 					<plugin>
-						<groupId>org.sonatype.plugins</groupId>
-						<artifactId>nexus-staging-maven-plugin</artifactId>
-						<version>1.6.13</version>
+						<groupId>org.sonatype.central</groupId>
+						<artifactId>central-publishing-maven-plugin</artifactId>
+						<version>0.8.0</version>
 						<extensions>true</extensions>
 						<configuration>
-							<serverId>ossrh</serverId>
-							<nexusUrl>https://oss.sonatype.org/</nexusUrl>
-							<autoReleaseAfterClose>true</autoReleaseAfterClose>
+							<!-- Note your maven settings.xml needs a server section with <id> that matches this one and valid credentials for maven central -->
+							<publishingServerId>central</publishingServerId>
+							<!-- If this is set to false, the artifact is only staged and then needs pushing manually via the web interface at https://central.sonatype.com/publishing/deployments -->
+							<!-- With true it publishes automatically -->
+							<autoPublish>true</autoPublish>
+							<!-- NOTE this is to wait for the new release to be validated and publicly available. Not essential but nice that when build is done, we know the artifacts are available publicly -->
+							<waitUntil>published</waitUntil>
 						</configuration>
 					</plugin>
 

From 274a36abf39908eb0eb27c3da6d8e47ae875a83d Mon Sep 17 00:00:00 2001
From: Jose Duarte <jose.m.duarte@gmail.com>
Date: Fri, 7 Nov 2025 21:53:06 -0800
Subject: [PATCH 81/90] Fix for #1116

---
 CHANGELOG.md                                               | 5 +++++
 .../nbio/structure/io/cif/AbstractCifFileSupplier.java     | 7 ++++++-
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 74b52303b0..07be3a5172 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,11 @@
 BioJava Changelog
 -----------------
 
+BioJava 7.2.3 - future release
+==============================
+### Fixed
+* Don't use label_seq_id in mmCIF output for non-polymers #1116
+
 BioJava 7.2.2
 ==============================
 ### Fixed
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.java
index 826d9588ef..7e9d8ad7ac 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.java
@@ -308,7 +308,12 @@ public void accept(WrappedAtom wrappedAtom) {
                 }
             }
             labelEntityId.add(entityId);
-            labelSeqId.add(seqId);
+            // see https://github.com/biojava/biojava/issues/1116
+            if (chain.getEntityInfo().getType() == EntityType.POLYMER) {
+                labelSeqId.add(seqId);
+            } else {
+                labelSeqId.markNextNotPresent();
+            }
             String insCode = "";
             if (group.getResidueNumber().getInsCode() != null) {
                 insCode = Character.toString(group.getResidueNumber().getInsCode());

From 611fcadeaa9f7dee203de34ae5d8d448df03ea8c Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Wed, 12 Nov 2025 16:55:57 -0800
Subject: [PATCH 82/90] [maven-release-plugin] prepare release biojava-7.2.3

---
 biojava-aa-prop/pom.xml                 |  6 +++---
 biojava-alignment/pom.xml               |  4 ++--
 biojava-core/pom.xml                    |  2 +-
 biojava-genome/pom.xml                  |  6 +++---
 biojava-integrationtest/pom.xml         |  4 ++--
 biojava-modfinder/pom.xml               |  4 ++--
 biojava-ontology/pom.xml                |  2 +-
 biojava-protein-comparison-tool/pom.xml | 10 +++++-----
 biojava-protein-disorder/pom.xml        |  4 ++--
 biojava-structure-gui/pom.xml           |  6 +++---
 biojava-structure/pom.xml               |  6 +++---
 biojava-survival/pom.xml                |  2 +-
 biojava-ws/pom.xml                      |  4 ++--
 pom.xml                                 |  4 ++--
 14 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index b2b642b661..0c1016c3b6 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.3-SNAPSHOT</version>
+		<version>7.2.3</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.3-SNAPSHOT</version>
+			<version>7.2.3</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.3-SNAPSHOT</version>
+			<version>7.2.3</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index fe75c181c7..7bb6e3b2ee 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.3-SNAPSHOT</version>
+		<version>7.2.3</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.3-SNAPSHOT</version>
+			<version>7.2.3</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 0836ffe54c..890ce360bc 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.3-SNAPSHOT</version>
+		<version>7.2.3</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 7729a6e9e3..79608afaf4 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.3-SNAPSHOT</version>
+		<version>7.2.3</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -70,13 +70,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.3-SNAPSHOT</version>
+			<version>7.2.3</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.3-SNAPSHOT</version>
+			<version>7.2.3</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index 2c44988004..41d9be230c 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>7.2.3-SNAPSHOT</version>
+    <version>7.2.3</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -40,7 +40,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>7.2.3-SNAPSHOT</version>
+    	<version>7.2.3</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index 0b8cb53791..876203f207 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.3-SNAPSHOT</version>
+		<version>7.2.3</version>
 	</parent>
 	<artifactId>biojava-modfinder</artifactId>
 	<name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.3-SNAPSHOT</version>
+			<version>7.2.3</version>
 			<type>jar</type>
 			<scope>compile</scope>
 		</dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 001e3e52f1..02e4a894d2 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>7.2.3-SNAPSHOT</version>
+    <version>7.2.3</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml
index 12e4941d55..b4de1b1e8a 100644
--- a/biojava-protein-comparison-tool/pom.xml
+++ b/biojava-protein-comparison-tool/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.3-SNAPSHOT</version>
+		<version>7.2.3</version>
 	</parent>
 
 	<artifactId>biojava-protein-comparison-tool</artifactId>
@@ -36,23 +36,23 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.3-SNAPSHOT</version>
+			<version>7.2.3</version>
 
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.3-SNAPSHOT</version>
+			<version>7.2.3</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.3-SNAPSHOT</version>
+			<version>7.2.3</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure-gui</artifactId>
-			<version>7.2.3-SNAPSHOT</version>
+			<version>7.2.3</version>
 		</dependency>
 		<dependency>
 			<groupId>net.sourceforge.jmol</groupId>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 82107e8058..d5e216b60d 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.3-SNAPSHOT</version>
+		<version>7.2.3</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.3-SNAPSHOT</version>
+			<version>7.2.3</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or
 			scopes here) -->
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index 24644c8ffe..62db686d60 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-		<version>7.2.3-SNAPSHOT</version>
+		<version>7.2.3</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -27,13 +27,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-			<version>7.2.3-SNAPSHOT</version>
+			<version>7.2.3</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-			<version>7.2.3-SNAPSHOT</version>
+			<version>7.2.3</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 5392798310..aeff7465c0 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.3-SNAPSHOT</version>
+		<version>7.2.3</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -51,13 +51,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.3-SNAPSHOT</version>
+			<version>7.2.3</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.3-SNAPSHOT</version>
+			<version>7.2.3</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 4f3e00f56b..a1facab532 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>7.2.3-SNAPSHOT</version>
+        <version>7.2.3</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index 7a4fa63589..23866ccbb1 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.3-SNAPSHOT</version>
+		<version>7.2.3</version>
 	</parent>
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.3-SNAPSHOT</version>
+			<version>7.2.3</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index c2a70eb02e..c4dfdd3b74 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>7.2.3-SNAPSHOT</version>
+	<version>7.2.3</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the
@@ -51,7 +51,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>HEAD</tag>
+		<tag>biojava-7.2.3</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list

From 515c623529daf9c7fb643a94fa6e55a374ed7ad4 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Wed, 12 Nov 2025 16:56:00 -0800
Subject: [PATCH 83/90] [maven-release-plugin] prepare for next development
 iteration

---
 biojava-aa-prop/pom.xml                 |  6 +++---
 biojava-alignment/pom.xml               |  4 ++--
 biojava-core/pom.xml                    |  2 +-
 biojava-genome/pom.xml                  |  6 +++---
 biojava-integrationtest/pom.xml         |  4 ++--
 biojava-modfinder/pom.xml               |  4 ++--
 biojava-ontology/pom.xml                |  2 +-
 biojava-protein-comparison-tool/pom.xml | 10 +++++-----
 biojava-protein-disorder/pom.xml        |  4 ++--
 biojava-structure-gui/pom.xml           |  6 +++---
 biojava-structure/pom.xml               |  6 +++---
 biojava-survival/pom.xml                |  2 +-
 biojava-ws/pom.xml                      |  4 ++--
 pom.xml                                 |  4 ++--
 14 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index 0c1016c3b6..fd7bfcd086 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.3</version>
+		<version>7.2.4-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.3</version>
+			<version>7.2.4-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.3</version>
+			<version>7.2.4-SNAPSHOT</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index 7bb6e3b2ee..3886b68bd1 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.3</version>
+		<version>7.2.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.3</version>
+			<version>7.2.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 890ce360bc..6b3eb9d8ae 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.3</version>
+		<version>7.2.4-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 79608afaf4..29479bcfdf 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.3</version>
+		<version>7.2.4-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -70,13 +70,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.3</version>
+			<version>7.2.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.3</version>
+			<version>7.2.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index 41d9be230c..4646e96277 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>7.2.3</version>
+    <version>7.2.4-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -40,7 +40,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>7.2.3</version>
+    	<version>7.2.4-SNAPSHOT</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index 876203f207..953feeed09 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.3</version>
+		<version>7.2.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-modfinder</artifactId>
 	<name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.3</version>
+			<version>7.2.4-SNAPSHOT</version>
 			<type>jar</type>
 			<scope>compile</scope>
 		</dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 02e4a894d2..a6475ce2d7 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>7.2.3</version>
+    <version>7.2.4-SNAPSHOT</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml
index b4de1b1e8a..9b06a29f3b 100644
--- a/biojava-protein-comparison-tool/pom.xml
+++ b/biojava-protein-comparison-tool/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.3</version>
+		<version>7.2.4-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>biojava-protein-comparison-tool</artifactId>
@@ -36,23 +36,23 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.3</version>
+			<version>7.2.4-SNAPSHOT</version>
 
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.3</version>
+			<version>7.2.4-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.3</version>
+			<version>7.2.4-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure-gui</artifactId>
-			<version>7.2.3</version>
+			<version>7.2.4-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>net.sourceforge.jmol</groupId>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index d5e216b60d..eba96d6f87 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.3</version>
+		<version>7.2.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.3</version>
+			<version>7.2.4-SNAPSHOT</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or
 			scopes here) -->
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index 62db686d60..caa5e31782 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-		<version>7.2.3</version>
+		<version>7.2.4-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -27,13 +27,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-			<version>7.2.3</version>
+			<version>7.2.4-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-			<version>7.2.3</version>
+			<version>7.2.4-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index aeff7465c0..3cc048a81a 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.3</version>
+		<version>7.2.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -51,13 +51,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.3</version>
+			<version>7.2.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.3</version>
+			<version>7.2.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index a1facab532..e2ca04fe41 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>7.2.3</version>
+        <version>7.2.4-SNAPSHOT</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index 23866ccbb1..532034b29f 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.3</version>
+		<version>7.2.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.3</version>
+			<version>7.2.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index c4dfdd3b74..faa29d48ad 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>7.2.3</version>
+	<version>7.2.4-SNAPSHOT</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the
@@ -51,7 +51,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>biojava-7.2.3</tag>
+		<tag>HEAD</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list

From 94c6ebcab5c2f78144fab1d7a2c85c6d6af18475 Mon Sep 17 00:00:00 2001
From: Jose Duarte <jose.m.duarte@gmail.com>
Date: Wed, 12 Nov 2025 17:25:22 -0800
Subject: [PATCH 84/90] Updating after release

---
 CHANGELOG.md | 2 +-
 README.md    | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 07be3a5172..1c4033c826 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,7 +1,7 @@
 BioJava Changelog
 -----------------
 
-BioJava 7.2.3 - future release
+BioJava 7.2.3
 ==============================
 ### Fixed
 * Don't use label_seq_id in mmCIF output for non-polymers #1116
diff --git a/README.md b/README.md
index af128cd92c..da352ee3f2 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 # Welcome to <img src="logo-full.png" height="35"/>
 
 ![Build](https://github.com/biojava/biojava/actions/workflows/master.yml/badge.svg)
-[![Version](http://img.shields.io/badge/version-7.2.2-blue.svg?style=flat)](https://github.com/biojava/biojava/releases/tag/biojava-7.2.2) [![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/biojava/biojava/blob/master/LICENSE) [![Join the chat at https://gitter.im/biojava/biojava](https://badges.gitter.im/biojava/biojava.svg)](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+[![Version](http://img.shields.io/badge/version-7.2.3-blue.svg?style=flat)](https://github.com/biojava/biojava/releases/tag/biojava-7.2.3) [![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/biojava/biojava/blob/master/LICENSE) [![Join the chat at https://gitter.im/biojava/biojava](https://badges.gitter.im/biojava/biojava.svg)](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 
 
 BioJava is an open-source project dedicated to providing a Java framework for **processing biological data**. It provides analytical and statistical routines, parsers for common file formats, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.
@@ -29,7 +29,7 @@ If you are using Maven you can add the BioJava repository by adding the followin
       <dependency>
         <groupId>org.biojava</groupId>
         <artifactId>biojava-core</artifactId>
-        <version>7.2.2</version>
+        <version>7.2.3</version>
       </dependency>
       <!-- other biojava modules as needed -->
     </dependencies>

From 0af196ffd522f98aa093dd569659438f1ab81ebf Mon Sep 17 00:00:00 2001
From: JasonKamsu <silhakaj@3il.fr>
Date: Fri, 21 Nov 2025 08:24:39 +0100
Subject: [PATCH 85/90] Fix RSPEC-1940 boolean checks

---
 .../nbio/core/sequence/location/InsdcParser.java |  4 +++-
 .../java/org/biojava/nbio/core/util/Equals.java  | 16 ++++++++++++++--
 .../nbio/genome/parsers/gff/Location.java        |  4 ++--
 .../java/org/biojava/nbio/structure/Author.java  |  2 +-
 .../java/org/biojava/nbio/structure/Element.java |  2 +-
 .../nbio/structure/align/ce/CECalculator.java    |  2 +-
 .../structure/align/ce/CeCalculatorEnhanced.java |  2 +-
 .../structure/quaternary/BioAssemblyTools.java   |  2 +-
 .../nbio/structure/secstruc/SecStrucTools.java   |  2 +-
 9 files changed, 25 insertions(+), 11 deletions(-)

diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java
index e49bd22216..2d43a481bf 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/InsdcParser.java
@@ -260,7 +260,9 @@ private List<Location> parseLocationString(String string, int versus) {
 					l.setPartialOn3prime(true);
 				}
 
-				if (!(accession == null || "".equals(accession))) l.setAccession(new AccessionID(accession));
+				if (accession != null && !"".equals(accession)) {
+					l.setAccession(new AccessionID(accession));
+				}
 
 				boundedLocationsCollection.add(l);
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java
index e8f78243ed..7e2c7128c9 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/Equals.java
@@ -49,7 +49,13 @@ public static boolean equal(boolean one, boolean two) {
 	 * @see #classEqual(Object, Object)
 	 */
 	public static boolean equal(Object one, Object two) {
-		return one == null && two == null || !(one == null || two == null) && (one == two || one.equals(two));
+		if (one == two) {
+			return true;
+		}
+		if (one == null || two == null) {
+			return false;
+		}
+		return one.equals(two);
 	}
 
 	/**
@@ -84,6 +90,12 @@ public static boolean equal(Object one, Object two) {
 	 *         equal at the class level
 	 */
 	public static boolean classEqual(Object one, Object two) {
-		return one == two || !(one == null || two == null) && one.getClass() == two.getClass();
+		if (one == two) {
+			return true;
+		}
+		if (one == null || two == null) {
+			return false;
+		}
+		return one.getClass() == two.getClass();
 	}
 }
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
index 4163be2b56..a28f1019fb 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
@@ -135,7 +135,7 @@ public static Location fromBio( int start, int end, char strand )
 		int s= start - 1;
 		int e= end;
 
-		if( !( strand == '-' || strand == '+' || strand == '.' ))
+		if( strand != '-' && strand != '+' && strand != '.' )
 		{
 			throw new IllegalArgumentException( "Strand must be '+', '-', or '.'" );
 		}
@@ -166,7 +166,7 @@ public static Location fromBioExt( int start, int length, char strand, int total
 		int s= start;
 		int e= s + length;
 
-		if( !( strand == '-' || strand == '+' || strand == '.' ))
+		if( strand != '-' && strand != '+' && strand != '.' )
 		{
 			throw new IllegalArgumentException( "Strand must be '+', '-', or '.'" );
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java
index b0d7253507..bd5a01b885 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java
@@ -62,7 +62,7 @@ public boolean equals(Object obj) {
 		if ((this.surname == null) ? (other.surname != null) : !this.surname.equals(other.surname)) {
 			return false;
 		}
-		return !((this.initials == null) ? (other.initials != null) : !this.initials.equals(other.initials));
+		return (this.initials == null) ? other.initials == null : this.initials.equals(other.initials);
 	}
 
 	@Override
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java
index 2f534b2828..4e2d3e340a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java
@@ -424,7 +424,7 @@ public boolean isHeavyAtom() {
 	 * @return <CODE>true</CODE> if Element is not Hydrogen and not Carbon.
 	 */
 	public boolean isHeteroAtom() {
-		return !(this == C || this == H);
+		return this != C && this != H;
 	}
 
 	/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
index 6c045ba48e..83f16b7982 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
@@ -1450,7 +1450,7 @@ private int optimizeSuperposition(AFPChain afpChain, int nse1, int nse2, int str
 			//afpChain.setTotalRmsdOpt(rmsd);
 			//System.out.println("rmsd: " + rmsd);
 
-			if(!(nAtom<strLen*0.95) && (!isRmsdLenAssigned)) {
+			if(nAtom >= strLen * 0.95 && !isRmsdLenAssigned) {
 				rmsdLen=rmsd;
 				isRmsdLenAssigned=true;
 			}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
index 4f57161268..cab98b0113 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
@@ -1455,7 +1455,7 @@ private int optimizeSuperposition(AFPChain afpChain, int nse1, int nse2, int str
 			//afpChain.setTotalRmsdOpt(rmsd);
 			//System.out.println("rmsd: " + rmsd);
 
-			if(!(nAtom<strLen*0.95) && (!isRmsdLenAssigned)) {
+			if(nAtom >= strLen * 0.95 && !isRmsdLenAssigned) {
 				rmsdLen=rmsd;
 				isRmsdLenAssigned=true;
 			}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
index 7c359121de..f65f4617fe 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
@@ -55,7 +55,7 @@ public static boolean isUnaryExpression(String expression) {
 		if (first < 0 || last < 0) {
 			return true;
 		}
-		return ! (first == 0 && last > first);
+		return first != 0 || last <= first;
 	}
 
 	public static List<String> parseUnaryOperatorExpression(String operatorExpression) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
index 7732c04b80..42191d682d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
@@ -57,7 +57,7 @@ public static List<SecStrucInfo> getSecStrucInfo(Structure s) {
 			Group g = iter.next();
 			if (g.hasAminoAtoms()) {
 				Object p = g.getProperty(Group.SEC_STRUC);
-				if (!(p == null)) {
+				if (p != null) {
 					SecStrucInfo ss = (SecStrucInfo) p;
 					listSSI.add(ss);
 				}

From 3f039fd3f5128e3f97981873f9855f45949848a0 Mon Sep 17 00:00:00 2001
From: Pasjonat90D <20847880+Pasjonat90D@users.noreply.github.com>
Date: Sun, 30 Nov 2025 20:44:39 +0100
Subject: [PATCH 86/90] Fix #1079: Use isEmpty() instead of size() == 0

---
 .../nbio/core/alignment/SimpleAlignedSequence.java   |  2 +-
 .../org/biojava/nbio/core/sequence/GeneSequence.java |  2 +-
 .../sequence/storage/SequenceAsStringHelper.java     |  2 +-
 .../org/biojava/nbio/core/util/PrettyXMLWriter.java  |  2 +-
 .../nbio/structure/gui/util/SequenceScalePanel.java  |  2 +-
 .../nbio/structure/align/ClusterAltAligs.java        |  2 +-
 .../nbio/structure/align/multiple/BlockImpl.java     |  2 +-
 .../nbio/structure/align/multiple/BlockSetImpl.java  |  6 +++---
 .../align/multiple/MultipleAlignmentImpl.java        |  4 ++--
 .../align/multiple/mc/MultipleMcOptimizer.java       |  2 +-
 .../structure/align/quaternary/QsAlignResult.java    |  2 +-
 .../biojava/nbio/structure/align/util/AtomCache.java | 12 ++++++------
 .../nbio/structure/chem/ZipChemCompProvider.java     |  2 +-
 .../nbio/structure/cluster/SubunitCluster.java       |  2 +-
 .../nbio/structure/cluster/SubunitClusterer.java     |  2 +-
 .../nbio/structure/geometry/MomentsOfInertia.java    |  2 +-
 .../org/biojava/nbio/structure/io/PDBFileParser.java |  4 ++--
 .../nbio/structure/io/mmtf/MmtfStructureReader.java  |  2 +-
 .../nbio/structure/quaternary/BioAssemblyTools.java  |  2 +-
 .../quaternary/BiologicalAssemblyBuilder.java        |  2 +-
 .../structure/symmetry/core/HelicalRepeatUnit.java   |  2 +-
 .../nbio/structure/symmetry/core/RotationGroup.java  |  2 +-
 .../nbio/structure/symmetry/core/RotationSolver.java |  2 +-
 .../structure/symmetry/core/SystematicSolver.java    |  2 +-
 .../structure/symmetry/geometry/DistanceBox.java     |  2 +-
 .../org/biojava/nbio/structure/xtal/SpaceGroup.java  |  4 ++--
 .../kaplanmeier/figure/NumbersAtRiskPanel.java       |  2 +-
 .../java/org/biojava/nbio/ws/hmmer/HmmerResult.java  |  2 +-
 28 files changed, 38 insertions(+), 38 deletions(-)

diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java
index 331480bbef..99b70c036d 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java
@@ -411,7 +411,7 @@ private void setLocation(List<Step> steps) {
 		}
 
 		// combine sublocations into 1 Location
-		if (sublocations.size() == 0) {
+		if (sublocations.isEmpty()) {
 			location = null;
 		} else if (sublocations.size() == 1) {
 			location = sublocations.get(0);
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java
index f0f2662fea..638e4e68d9 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java
@@ -119,7 +119,7 @@ public void addIntronsUsingExons() throws Exception {
 		if (intronAdded) { //going to assume introns are correct
 			return;
 		}
-		if (exonSequenceList.size() == 0) {
+		if (exonSequenceList.isEmpty()) {
 			return;
 		}
 		ExonComparator exonComparator = new ExonComparator();
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SequenceAsStringHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SequenceAsStringHelper.java
index c2b02debee..4acd8969f1 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SequenceAsStringHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SequenceAsStringHelper.java
@@ -44,7 +44,7 @@ public class SequenceAsStringHelper<C extends Compound> {
 	 */
 	public String getSequenceAsString(List<C> parsedCompounds, CompoundSet<C> compoundSet, Integer bioBegin, Integer bioEnd, Strand strand) {
 		// TODO Optimise/cache.
-		if(parsedCompounds.size() == 0)
+		if(parsedCompounds.isEmpty())
 			return "";
 		StringBuilder builder = new StringBuilder();
 		if (strand.equals(Strand.NEGATIVE)) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java
index 437085866f..6e4a7db77c 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/PrettyXMLWriter.java
@@ -72,7 +72,7 @@ public void declareNamespace(String nsURI, String prefixHint)
 	private void handleDeclaredNamespaces()
 		throws IOException
 	{
-		if (namespacesDeclared.size() == 0) {
+		if (namespacesDeclared.isEmpty()) {
 			for (Iterator<String> nsi = namespacesDeclared.iterator(); nsi.hasNext(); ) {
 				String nsURI = nsi.next();
 				if (!namespacePrefixes.containsKey(nsURI)) {
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceScalePanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceScalePanel.java
index 06542e5271..75da6c8e28 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceScalePanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceScalePanel.java
@@ -126,7 +126,7 @@ private void setPrefSize() {
 	public void setAligMap(List<AlignedPosition> apos){
 		this.apos = apos;
 
-		if ( apos.size() == 0)
+		if (apos.isEmpty())
 			return;
 
 		AlignedPosition last = apos.get(apos.size()-1);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ClusterAltAligs.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ClusterAltAligs.java
index 373bcf1611..0933198d7b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ClusterAltAligs.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ClusterAltAligs.java
@@ -102,7 +102,7 @@ public static void cluster(AlternativeAlignment[] aligs, int cutoff){
 
 			}
 			clusters.add(currentCluster);
-			if ( remainList.size() == 0) {
+			if ( remainList.isEmpty()) {
 				break;
 			}
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java
index e0423b6f8f..43da1d7c06 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java
@@ -127,7 +127,7 @@ public void setAlignRes(List<List<Integer>> alignRes) {
 	public int length() {
 		if (alignRes == null)
 			return 0;
-		if (alignRes.size() == 0)
+		if (alignRes.isEmpty())
 			return 0;
 		return alignRes.get(0).size();
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java
index cbbb3ae895..344ee3c239 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java
@@ -179,7 +179,7 @@ public int size() {
 		// Get the size from the variables that can contain the information
 		if (parent != null)
 			return parent.size();
-		else if (getBlocks().size() == 0) {
+		else if (getBlocks().isEmpty()) {
 			throw new IndexOutOfBoundsException(
 					"Empty BlockSet: number of Blocks == 0.");
 		} else
@@ -194,7 +194,7 @@ public int getCoreLength() {
 	}
 
 	protected void updateLength() {
-		if (getBlocks().size() == 0) {
+		if (getBlocks().isEmpty()) {
 			throw new IndexOutOfBoundsException(
 					"Empty BlockSet: number of Blocks == 0.");
 		}
@@ -207,7 +207,7 @@ protected void updateLength() {
 	}
 
 	protected void updateCoreLength() {
-		if (getBlocks().size() == 0) {
+		if (getBlocks().isEmpty()) {
 			throw new IndexOutOfBoundsException(
 					"Empty BlockSet: number of Blocks == 0.");
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java
index 738eee30c5..06c93a4403 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java
@@ -207,7 +207,7 @@ public int getCoreLength() {
 	 * lengths.
 	 */
 	protected void updateLength() {
-		if (getBlockSets().size() == 0) {
+		if (getBlockSets().isEmpty()) {
 			throw new IndexOutOfBoundsException(
 					"Empty MultipleAlignment: blockSets size == 0.");
 		} // Otherwise try to calculate it from the BlockSet information
@@ -223,7 +223,7 @@ protected void updateLength() {
 	 * BlockSet core lengths.
 	 */
 	protected void updateCoreLength() {
-		if (getBlockSets().size() == 0) {
+		if (getBlockSets().isEmpty()) {
 			throw new IndexOutOfBoundsException(
 					"Empty MultipleAlignment: blockSets size == 0.");
 		} // Otherwise try to calculate it from the BlockSet information
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
index 052f147fc6..29c7012801 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
@@ -153,7 +153,7 @@ public MultipleMcOptimizer(MultipleAlignment seedAln,
 		for (Block b : toDelete) {
 			for (BlockSet bs : msa.getBlockSets()) {
 				bs.getBlocks().remove(b);
-				if (bs.getBlocks().size() == 0)
+				if (bs.getBlocks().isEmpty())
 					emptyBs.add(bs);
 			}
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java
index 7ac77a602e..fe1c9c411b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java
@@ -117,7 +117,7 @@ public void setSubunitMap(Map<Integer, Integer> subunitMap) {
 					"Subunit Map index higher than Subunit List size.");
 
 		// Update the relation enum
-		if (subunitMap.size() == 0) {
+		if (subunitMap.isEmpty()) {
 			relation = QsRelation.DIFFERENT;
 		} else if (subunitMap.keySet().size() == subunits1.size()) {
 			if (subunitMap.values().size() == subunits2.size()) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
index 1435191c2c..71b8a3da22 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
@@ -228,7 +228,7 @@ public Structure getBiologicalAssembly(String pdbId, int bioAssemblyId, boolean
 			throws StructureException, IOException {
 		return getBiologicalAssembly(new PdbId(pdbId), bioAssemblyId, multiModel);
 	}
-	
+
 	/**
 	 * Returns the biological assembly for a given PDB ID and bioAssemblyId, by building the
 	 * assembly from the biounit annotations found in {@link Structure#getPDBHeader()}
@@ -284,7 +284,7 @@ public Structure getBiologicalAssembly(PdbId pdbId, int bioAssemblyId, boolean m
 				asymUnit.getPDBHeader().getBioAssemblies().get(bioAssemblyId).getTransforms();
 
 
-		if (transformations == null || transformations.size() == 0) {
+		if (transformations == null || transformations.isEmpty()) {
 			throw new StructureException("Could not load transformations to recreate biological assembly id " + bioAssemblyId + " of " + pdbId);
 		}
 
@@ -339,7 +339,7 @@ public Structure getBiologicalAssembly(String pdbId, boolean multiModel) throws
 				asymUnit.getPDBHeader().getBioAssemblies().get(bioAssemblyId).getTransforms();
 
 
-		if (transformations == null || transformations.size() == 0) {
+		if (transformations == null || transformations.isEmpty()) {
 			throw new StructureException("Could not load transformations to recreate biological assembly id " + bioAssemblyId + " of " + pdbId);
 		}
 
@@ -385,7 +385,7 @@ public List<Structure> getBiologicalAssemblies(String pdbId, boolean multiModel)
 			List<BiologicalAssemblyTransformation> transformations =
 					asymUnit.getPDBHeader().getBioAssemblies().get(bioAssemblyId).getTransforms();
 
-			if (transformations == null || transformations.size() == 0) {
+			if (transformations == null || transformations.isEmpty()) {
 				logger.info("Could not load transformations to recreate biological assembly id {} of {}. Assembly " +
 						"id will be missing in biological assemblies.", bioAssemblyId, pdbId);
 				continue;
@@ -807,7 +807,7 @@ public Structure getStructureForPdbId(String id) throws IOException, StructureEx
 	public Structure getStructureForPdbId(PdbId pdbId) throws IOException {
 		if (pdbId == null)
 			return null;
-		
+
 		while (checkLoading(pdbId)) {
 			// waiting for loading to be finished...
 			try {
@@ -833,7 +833,7 @@ public Structure getStructureForPdbId(PdbId pdbId) throws IOException {
 	protected Structure loadStructureFromCifByPdbId(String pdbId) throws IOException {
 		return loadStructureFromCifByPdbId(new PdbId(pdbId));
 	}
-	
+
 	protected Structure loadStructureFromCifByPdbId(PdbId pdbId) throws IOException {
 		logger.debug("Loading structure {} from mmCIF file {}.", pdbId, path);
 		Structure s;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/ZipChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/ZipChemCompProvider.java
index 4fe19aca58..a68019efb7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/ZipChemCompProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/ZipChemCompProvider.java
@@ -120,7 +120,7 @@ public ChemComp getChemComp(String recordName) {
         }
 
         // If a null record or an empty chemcomp, return a default ChemComp and blacklist.
-        if (cc == null || (null == cc.getName() && cc.getAtoms().size() == 0)) {
+        if (cc == null || (null == cc.getName() && cc.getAtoms().isEmpty())) {
             s_logger.info("Unable to find or download {} - excluding from future searches.", recordName);
             unavailable.add(recordName);
             return getEmptyChemComp(recordName);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
index 9a87e92f88..b8ef74c8f1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
@@ -331,7 +331,7 @@ public boolean mergeIdenticalByEntityId(SubunitCluster other) {
 			}
 		}
 
-		if (thisAligned.size() == 0 && otherAligned.size() == 0) {
+		if (thisAligned.isEmpty() && otherAligned.isEmpty()) {
 			logger.warn("No equivalent aligned atoms found between SubunitClusters {}-{} via entity SEQRES alignment. Is FileParsingParameters.setAlignSeqRes() set?", thisName, otherName);
 		}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java
index 6295f8fdf0..964a0aaba3 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java
@@ -58,7 +58,7 @@ public static Stoichiometry cluster(Structure structure,
 
 	public static Stoichiometry cluster(List<Subunit> subunits, SubunitClustererParameters params) {
 		List<SubunitCluster> clusters = new ArrayList<>();
-		if (subunits.size() == 0)
+		if (subunits.isEmpty())
 			return new Stoichiometry(clusters);
 
 		// First generate a new cluster for each Subunit
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java
index 8cfd032daa..5a6e69c4cf 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java
@@ -72,7 +72,7 @@ public void addPoint(Point3d point, double mass) {
 
 	public Point3d getCenterOfMass() {
 
-		if (points.size() == 0) {
+		if (points.isEmpty()) {
 			throw new IllegalStateException(
 					"MomentsOfInertia: no points defined");
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
index 176459bbf2..58e4ee6625 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
@@ -1970,7 +1970,7 @@ private Group getCorrectAltLocGroup( Character altLoc,
 		// build it up.
 
 		if ( groupCode3.equals(currentGroup.getPDBName())) {
-			if ( currentGroup.getAtoms().size() == 0) {
+			if ( currentGroup.getAtoms().isEmpty()) {
 				//System.out.println("current group is empty " + current_group + " " + altLoc);
 				return currentGroup;
 			}
@@ -2762,7 +2762,7 @@ private void makeCompounds(List<String> compoundList,
 		}
 		//		System.out.println("[makeCompounds] adding sources to compounds from sourceLines");
 		// since we're starting again from the first compound, reset it here
-		if ( entities.size() == 0){
+		if ( entities.isEmpty()){
 			current_compound = new EntityInfo();
 		} else {
 			current_compound = entities.get(0);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
index c2830c1685..21ef8bb64c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
@@ -396,7 +396,7 @@ private Group getCorrectAltLocGroup(Character altLoc) {
 		}
 		// no matching altLoc group found.
 		// build it up.
-		if (group.getAtoms().size() == 0) {
+		if (group.getAtoms().isEmpty()) {
 			return group;
 		}
 		Group altLocG = (Group) group.clone();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
index 7c359121de..786ce7646f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
@@ -279,7 +279,7 @@ public static double[] getBiologicalMoleculeCentroid( final Structure asymUnit,
 			return centroid;
 		}
 
-		if ( transformations.size() == 0) {
+		if ( transformations.isEmpty()) {
 			return Calc.getCentroid(atoms).getCoords();
 
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java
index c6ec6bc8ff..9edb8f404c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java
@@ -205,7 +205,7 @@ private void addChainMultiModel(Structure s, Chain newChain, String transformId)
 
 		// multi-model bioassembly
 
-		if ( modelIndex.size() == 0)
+		if (modelIndex.isEmpty())
 			modelIndex.add("PLACEHOLDER FOR ASYM UNIT");
 
 		int modelCount = modelIndex.indexOf(transformId);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java
index ff9c77cf13..cd16aa5f87 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java
@@ -64,7 +64,7 @@ public Map<Integer[], Integer> getInteractingRepeatUnits() {
 
 private void run() {
 	this.repeatUnitCenters = calcRepeatUnitCenters();
-	if (this.repeatUnitCenters.size() == 0) {
+	if (this.repeatUnitCenters.isEmpty()) {
 		return;
 	}
 	this.repeatUnits = calcRepeatUnits();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
index 70b69afe14..1490d27036 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
@@ -98,7 +98,7 @@ public void complete() {
 
 	public String getPointGroup() {
 		if (modified) {
-			if (rotations.size() == 0) {
+			if (rotations.isEmpty()) {
 				return "C1";
 			}
 			complete();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
index 37a44be7ac..b1566a6d2f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
@@ -305,7 +305,7 @@ private boolean isSpherical() {
 	 * @return null if invalid, or a rotation if valid
 	 */
 	private Rotation isValidPermutation(List<Integer> permutation) {
-		if (permutation.size() == 0) {
+		if (permutation.isEmpty()) {
 			return null;
 		}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
index d13fa4db16..a449771b58 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
@@ -145,7 +145,7 @@ private void completeRotationGroup() {
 	}
 
 	private boolean isValidPermutation(List<Integer> permutation) {
-		if (permutation.size() == 0) {
+		if (permutation.isEmpty()) {
 			return false;
 		}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java
index 2d9b1d6dca..25d37693fb 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java
@@ -166,7 +166,7 @@ private List<T> getBoxTwo(long location) {
 		}
 		// ensure that boxTwo has no empty element by copying from tempBox of defined size
 		List<T> boxTwo = null;
-		if (tempBox.size() == 0) {
+		if (tempBox.isEmpty()) {
 			boxTwo = Collections.emptyList();
 		} else if (tempBox.size() == 1) {
 			boxTwo = Collections.singletonList(tempBox.get(0));
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java
index cff84c70f8..852d213bb9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java
@@ -645,10 +645,10 @@ public List<String> getTransfAlgebraic() {
 
 	public void setTransfAlgebraic(List<String> transfAlgebraic) {
 		//System.out.println("setting transfAlgebraic " + transfAlgebraic);
-		if ( transformations == null || transformations.size() == 0)
+		if ( transformations == null || transformations.isEmpty())
 			transformations = new ArrayList<Matrix4d>(transfAlgebraic.size());
 
-		if ( this.transfAlgebraic == null || this.transfAlgebraic.size() == 0)
+		if ( this.transfAlgebraic == null || this.transfAlgebraic.isEmpty())
 			this.transfAlgebraic = new ArrayList<>(transfAlgebraic.size());
 
 		for ( String transf : transfAlgebraic){
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java
index c4578f1c8b..144942a809 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java
@@ -76,7 +76,7 @@ private void paintTable(Graphics g) {
 			sfiHashMap = sfi.getStrataInfoHashMap();
 		}
 
-		if(sfiHashMap.size() == 0)
+		if(sfiHashMap.isEmpty())
 			return;
 		//int height = this.getHeight();
 
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java
index 3304e78d4f..373b78cd0a 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java
@@ -140,7 +140,7 @@ public int compareTo(HmmerResult o) {
 		return(me.getSqFrom().compareTo(other.getSqFrom()));
 	}
 	private boolean emptyDomains(HmmerResult o) {
-		if ( o.getDomains() == null || o.getDomains().size() == 0)
+		if ( o.getDomains() == null || o.getDomains().isEmpty())
 			return true;
 		return false;
 	}

From 423cd86fbc2355f9943a3bbd81597c3d0c231627 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Mon, 8 Dec 2025 15:22:01 -0800
Subject: [PATCH 87/90] Bugfix: edge-case with no equiv residues in alignment
 wasn't dealt with and led to IllegalArgumentException. Also: improved logging

---
 .../structure/cluster/SubunitCluster.java     | 43 ++++++++-----------
 .../structure/cluster/SubunitClusterer.java   | 11 ++---
 2 files changed, 23 insertions(+), 31 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
index 9a87e92f88..2bbad10f1f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
@@ -507,27 +507,24 @@ public boolean mergeStructure(SubunitCluster other, SubunitClustererParameters p
 			}
 		}
 
-		AFPChain afp = aligner.align(this.subunits.get(this.representative)
-				.getRepresentativeAtoms(),
-				other.subunits.get(other.representative)
-						.getRepresentativeAtoms());
+		AFPChain afp = aligner.align(this.subunits.get(this.representative).getRepresentativeAtoms(),
+				other.subunits.get(other.representative).getRepresentativeAtoms());
 
+        String pairName = this.subunits.get(this.representative).getName() + "-" + other.subunits.get(other.representative).getName();
 		if (afp.getOptLength() < 1) {
 			// alignment failed (eg if chains were too short)
 			throw new StructureException(
-					String.format("Subunits failed to align using %s", params.getSuperpositionAlgorithm()));
+					String.format("Subunits %s failed to align using %s", pairName, params.getSuperpositionAlgorithm()));
 		}
 
 		// Convert AFPChain to MultipleAlignment for convenience
 		MultipleAlignment msa = new MultipleAlignmentEnsembleImpl(
 				afp,
 				this.subunits.get(this.representative).getRepresentativeAtoms(),
-				other.subunits.get(other.representative)
-						.getRepresentativeAtoms(), false)
-				.getMultipleAlignment(0);
+				other.subunits.get(other.representative).getRepresentativeAtoms(),
+                false).getMultipleAlignment(0);
 
-		double structureCoverage = Math.min(msa.getCoverages().get(0), msa
-				.getCoverages().get(1));
+		double structureCoverage = Math.min(msa.getCoverages().get(0), msa.getCoverages().get(1));
 
 		if(params.isUseStructureCoverage() && structureCoverage < params.getStructureCoverageThreshold()) {
 			return false;
@@ -543,8 +540,7 @@ public boolean mergeStructure(SubunitCluster other, SubunitClustererParameters p
 			return false;
 		}
 
-		logger.info(String.format("SubunitClusters are structurally similar with "
-				+ "%.2f RMSD %.2f coverage", rmsd, structureCoverage));
+		logger.info("SubunitClusters {} are structurally similar with [ {} ] RMSD and [ {} ] coverage", pairName, String.format("%.2f", rmsd), String.format("%.2f", structureCoverage));
 
 		// Merge clusters
 		List<List<Integer>> alignedRes = msa.getBlock(0).getAlignRes();
@@ -565,13 +561,18 @@ public boolean mergeStructure(SubunitCluster other, SubunitClustererParameters p
 
 			// Only consider residues that are part of the SubunitCluster
 			if (this.subunitEQR.get(this.representative).contains(thisIndex)
-					&& other.subunitEQR.get(other.representative).contains(
-							otherIndex)) {
+					&& other.subunitEQR.get(other.representative).contains(otherIndex)) {
 				thisAligned.add(thisIndex);
 				otherAligned.add(otherIndex);
 			}
 		}
 
+        // this can happen in very rare cases, e.g. 9y9z when merging E_1 into the cluster D_1, OM_1, Y_1
+        if (thisAligned.isEmpty() && otherAligned.isEmpty()) {
+            logger.warn("No equivalent aligned atoms found between SubunitClusters {} via structure alignment. Will not merge the second one into the first.", pairName);
+            return false;
+        }
+
 		updateEquivResidues(other, thisAligned, otherAligned);
 
 		this.method = SubunitClustererMethod.STRUCTURE;
@@ -602,18 +603,12 @@ private void updateEquivResidues(SubunitCluster other, List<Integer> thisAligned
 		Collections.sort(otherRemove);
 		Collections.reverse(otherRemove);
 
-		for (int t = 0; t < thisRemove.size(); t++) {
-			for (List<Integer> eqr : this.subunitEQR) {
-				int column = thisRemove.get(t);
-				eqr.remove(column);
-			}
+		for (int column : thisRemove) {
+            this.subunitEQR.forEach(eqr -> eqr.remove(column));
 		}
 
-		for (int t = 0; t < otherRemove.size(); t++) {
-			for (List<Integer> eqr : other.subunitEQR) {
-				int column = otherRemove.get(t);
-				eqr.remove(column);
-			}
+		for (int column : otherRemove) {
+            other.subunitEQR.forEach(eqr -> eqr.remove(column));
 		}
 
 		// The representative is the longest sequence
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java
index 6295f8fdf0..70da0b56db 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java
@@ -83,8 +83,7 @@ public static Stoichiometry cluster(List<Subunit> subunits, SubunitClustererPara
 						}
 
 					} catch (CompoundNotFoundException e) {
-						logger.warn("Could not merge by Sequence. {}",
-								e.getMessage());
+						logger.info("Could not merge by Sequence. {}", e.getMessage());
 					}
 				}
 			}
@@ -100,7 +99,7 @@ public static Stoichiometry cluster(List<Subunit> subunits, SubunitClustererPara
 							clusters.remove(c2);
 						}
 					} catch (StructureException e) {
-						logger.warn("Could not merge by Structure. {}", e.getMessage());
+						logger.info("Could not merge by Structure. {}", e.getMessage());
 					}
 				}
 			}
@@ -112,8 +111,7 @@ public static Stoichiometry cluster(List<Subunit> subunits, SubunitClustererPara
 				try {
 					clusters.get(c).divideInternally(params);
 				} catch (StructureException e) {
-					logger.warn("Error analyzing internal symmetry. {}",
-							e.getMessage());
+					logger.info("Error analyzing internal symmetry. {}", e.getMessage());
 				}
 			}
 
@@ -125,8 +123,7 @@ public static Stoichiometry cluster(List<Subunit> subunits, SubunitClustererPara
 						if (clusters.get(c1).mergeStructure(clusters.get(c2), params))
 							clusters.remove(c2);
 					} catch (StructureException e) {
-						logger.warn("Could not merge by Structure. {}",
-								e.getMessage());
+						logger.info("Could not merge by Structure. {}", e.getMessage());
 					}
 				}
 			}

From f55940c0612a61e4f347d8cec502797f34cf8c1f Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Wed, 10 Dec 2025 13:55:30 -0800
Subject: [PATCH 88/90] [maven-release-plugin] prepare release biojava-7.2.4

---
 biojava-aa-prop/pom.xml                 |  6 +++---
 biojava-alignment/pom.xml               |  4 ++--
 biojava-core/pom.xml                    |  2 +-
 biojava-genome/pom.xml                  |  6 +++---
 biojava-integrationtest/pom.xml         |  4 ++--
 biojava-modfinder/pom.xml               |  4 ++--
 biojava-ontology/pom.xml                |  2 +-
 biojava-protein-comparison-tool/pom.xml | 10 +++++-----
 biojava-protein-disorder/pom.xml        |  4 ++--
 biojava-structure-gui/pom.xml           |  6 +++---
 biojava-structure/pom.xml               |  6 +++---
 biojava-survival/pom.xml                |  2 +-
 biojava-ws/pom.xml                      |  4 ++--
 pom.xml                                 |  4 ++--
 14 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index fd7bfcd086..b1efc6c661 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.4-SNAPSHOT</version>
+		<version>7.2.4</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.4-SNAPSHOT</version>
+			<version>7.2.4</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.4-SNAPSHOT</version>
+			<version>7.2.4</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index 3886b68bd1..a03519aeca 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.4-SNAPSHOT</version>
+		<version>7.2.4</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.4-SNAPSHOT</version>
+			<version>7.2.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 6b3eb9d8ae..e7f36a646d 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.4-SNAPSHOT</version>
+		<version>7.2.4</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 29479bcfdf..b4e2a0e791 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.4-SNAPSHOT</version>
+		<version>7.2.4</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -70,13 +70,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.4-SNAPSHOT</version>
+			<version>7.2.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.4-SNAPSHOT</version>
+			<version>7.2.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index 4646e96277..a5b307c637 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>7.2.4-SNAPSHOT</version>
+    <version>7.2.4</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -40,7 +40,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>7.2.4-SNAPSHOT</version>
+    	<version>7.2.4</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index 953feeed09..4545d15f2f 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.4-SNAPSHOT</version>
+		<version>7.2.4</version>
 	</parent>
 	<artifactId>biojava-modfinder</artifactId>
 	<name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.4-SNAPSHOT</version>
+			<version>7.2.4</version>
 			<type>jar</type>
 			<scope>compile</scope>
 		</dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index a6475ce2d7..82ccc0ed59 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>7.2.4-SNAPSHOT</version>
+    <version>7.2.4</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml
index 9b06a29f3b..3425644447 100644
--- a/biojava-protein-comparison-tool/pom.xml
+++ b/biojava-protein-comparison-tool/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.4-SNAPSHOT</version>
+		<version>7.2.4</version>
 	</parent>
 
 	<artifactId>biojava-protein-comparison-tool</artifactId>
@@ -36,23 +36,23 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.4-SNAPSHOT</version>
+			<version>7.2.4</version>
 
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.4-SNAPSHOT</version>
+			<version>7.2.4</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.4-SNAPSHOT</version>
+			<version>7.2.4</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure-gui</artifactId>
-			<version>7.2.4-SNAPSHOT</version>
+			<version>7.2.4</version>
 		</dependency>
 		<dependency>
 			<groupId>net.sourceforge.jmol</groupId>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index eba96d6f87..30c263b398 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.4-SNAPSHOT</version>
+		<version>7.2.4</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.4-SNAPSHOT</version>
+			<version>7.2.4</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or
 			scopes here) -->
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index caa5e31782..133f64781c 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-		<version>7.2.4-SNAPSHOT</version>
+		<version>7.2.4</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -27,13 +27,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-			<version>7.2.4-SNAPSHOT</version>
+			<version>7.2.4</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-			<version>7.2.4-SNAPSHOT</version>
+			<version>7.2.4</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 3cc048a81a..b58fda9a96 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.4-SNAPSHOT</version>
+		<version>7.2.4</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -51,13 +51,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.4-SNAPSHOT</version>
+			<version>7.2.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.4-SNAPSHOT</version>
+			<version>7.2.4</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index e2ca04fe41..993b9aa1fe 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>7.2.4-SNAPSHOT</version>
+        <version>7.2.4</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index 532034b29f..32a8af0fb4 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.4-SNAPSHOT</version>
+		<version>7.2.4</version>
 	</parent>
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.4-SNAPSHOT</version>
+			<version>7.2.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index faa29d48ad..0cd4634a92 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>7.2.4-SNAPSHOT</version>
+	<version>7.2.4</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the
@@ -51,7 +51,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>HEAD</tag>
+		<tag>biojava-7.2.4</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list

From 006e5eff4e3f779f9ac8b42c6d82bbad873bc171 Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Wed, 10 Dec 2025 13:55:34 -0800
Subject: [PATCH 89/90] [maven-release-plugin] prepare for next development
 iteration

---
 biojava-aa-prop/pom.xml                 |  6 +++---
 biojava-alignment/pom.xml               |  4 ++--
 biojava-core/pom.xml                    |  2 +-
 biojava-genome/pom.xml                  |  6 +++---
 biojava-integrationtest/pom.xml         |  4 ++--
 biojava-modfinder/pom.xml               |  4 ++--
 biojava-ontology/pom.xml                |  2 +-
 biojava-protein-comparison-tool/pom.xml | 10 +++++-----
 biojava-protein-disorder/pom.xml        |  4 ++--
 biojava-structure-gui/pom.xml           |  6 +++---
 biojava-structure/pom.xml               |  6 +++---
 biojava-survival/pom.xml                |  2 +-
 biojava-ws/pom.xml                      |  4 ++--
 pom.xml                                 |  4 ++--
 14 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index b1efc6c661..cbc82fff7b 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.4</version>
+		<version>7.2.5-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.4</version>
+			<version>7.2.5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.4</version>
+			<version>7.2.5-SNAPSHOT</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index a03519aeca..b1d0bd9097 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.4</version>
+		<version>7.2.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.4</version>
+			<version>7.2.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index e7f36a646d..909f46f088 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.4</version>
+		<version>7.2.5-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index b4e2a0e791..68575bbb9b 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.4</version>
+		<version>7.2.5-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -70,13 +70,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.4</version>
+			<version>7.2.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.4</version>
+			<version>7.2.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index a5b307c637..1c21373bd1 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>7.2.4</version>
+    <version>7.2.5-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -40,7 +40,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>7.2.4</version>
+    	<version>7.2.5-SNAPSHOT</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index 4545d15f2f..e8de9e38d9 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.4</version>
+		<version>7.2.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-modfinder</artifactId>
 	<name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.4</version>
+			<version>7.2.5-SNAPSHOT</version>
 			<type>jar</type>
 			<scope>compile</scope>
 		</dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 82ccc0ed59..6a3fd5cbc4 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>7.2.4</version>
+    <version>7.2.5-SNAPSHOT</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml
index 3425644447..cf8cd570a7 100644
--- a/biojava-protein-comparison-tool/pom.xml
+++ b/biojava-protein-comparison-tool/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.4</version>
+		<version>7.2.5-SNAPSHOT</version>
 	</parent>
 
 	<artifactId>biojava-protein-comparison-tool</artifactId>
@@ -36,23 +36,23 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.4</version>
+			<version>7.2.5-SNAPSHOT</version>
 
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.4</version>
+			<version>7.2.5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>7.2.4</version>
+			<version>7.2.5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure-gui</artifactId>
-			<version>7.2.4</version>
+			<version>7.2.5-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>net.sourceforge.jmol</groupId>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 30c263b398..7273bbff8f 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.4</version>
+		<version>7.2.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.4</version>
+			<version>7.2.5-SNAPSHOT</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or
 			scopes here) -->
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
index 133f64781c..581b8a53cc 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-		<version>7.2.4</version>
+		<version>7.2.5-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -27,13 +27,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-			<version>7.2.4</version>
+			<version>7.2.5-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-			<version>7.2.4</version>
+			<version>7.2.5-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index b58fda9a96..7fbc64a3c1 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.4</version>
+		<version>7.2.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -51,13 +51,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>7.2.4</version>
+			<version>7.2.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.4</version>
+			<version>7.2.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 993b9aa1fe..88f901cdea 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>7.2.4</version>
+        <version>7.2.5-SNAPSHOT</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index 32a8af0fb4..7e960b4445 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>7.2.4</version>
+		<version>7.2.5-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>7.2.4</version>
+			<version>7.2.5-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 0cd4634a92..e9f246202b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>7.2.4</version>
+	<version>7.2.5-SNAPSHOT</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the
@@ -51,7 +51,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>biojava-7.2.4</tag>
+		<tag>HEAD</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list

From 51f48cd517e21fdc6552381777f6747226c6711a Mon Sep 17 00:00:00 2001
From: josemduarte <jose.m.duarte@gmail.com>
Date: Wed, 10 Dec 2025 14:16:36 -0800
Subject: [PATCH 90/90] Updating after release

---
 CHANGELOG.md | 5 +++++
 README.md    | 4 ++--
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1c4033c826..9610b211df 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,11 @@
 BioJava Changelog
 -----------------
 
+BioJava 7.2.4
+==============================
+### Fixed
+* Edge case in quaternary symmetry calculation #1120
+
 BioJava 7.2.3
 ==============================
 ### Fixed
diff --git a/README.md b/README.md
index da352ee3f2..eddeb65379 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 # Welcome to <img src="logo-full.png" height="35"/>
 
 ![Build](https://github.com/biojava/biojava/actions/workflows/master.yml/badge.svg)
-[![Version](http://img.shields.io/badge/version-7.2.3-blue.svg?style=flat)](https://github.com/biojava/biojava/releases/tag/biojava-7.2.3) [![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/biojava/biojava/blob/master/LICENSE) [![Join the chat at https://gitter.im/biojava/biojava](https://badges.gitter.im/biojava/biojava.svg)](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+[![Version](http://img.shields.io/badge/version-7.2.4-blue.svg?style=flat)](https://github.com/biojava/biojava/releases/tag/biojava-7.2.4) [![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/biojava/biojava/blob/master/LICENSE) [![Join the chat at https://gitter.im/biojava/biojava](https://badges.gitter.im/biojava/biojava.svg)](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 
 
 BioJava is an open-source project dedicated to providing a Java framework for **processing biological data**. It provides analytical and statistical routines, parsers for common file formats, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.
@@ -29,7 +29,7 @@ If you are using Maven you can add the BioJava repository by adding the followin
       <dependency>
         <groupId>org.biojava</groupId>
         <artifactId>biojava-core</artifactId>
-        <version>7.2.3</version>
+        <version>7.2.4</version>
       </dependency>
       <!-- other biojava modules as needed -->
     </dependencies>