From 714649cb0cb0c2d6f5c519efd4d6afe3e48daa4a Mon Sep 17 00:00:00 2001
From: Jenkins <jenkins@java-jenkins-research.rcsb.org>
Date: Tue, 7 Mar 2017 16:29:05 -0800
Subject: [PATCH 01/13] [maven-release-plugin]prepare for next development
 iteration

---
 biojava-aa-prop/pom.xml          | 6 +++---
 biojava-alignment/pom.xml        | 6 +++---
 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-phylo/pom.xml            | 4 ++--
 biojava-protein-disorder/pom.xml | 4 ++--
 biojava-sequencing/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 ++--
 15 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index 1a449c7ef8..b5cc3c5bea 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>4.2.7</version>
+		<version>4.2.8-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>4.2.7</version>
+			<version>4.2.8-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>4.2.7</version>
+			<version>4.2.8-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 7dfe24c010..6faea5b5c2 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.7</version>
+		<version>4.2.8-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -46,7 +46,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.7</version>
+			<version>4.2.8-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
@@ -74,7 +74,7 @@
   		<dependency>
   			<groupId>org.biojava</groupId>
   			<artifactId>biojava-phylo</artifactId>
-  			<version>4.2.7</version>
+  			<version>4.2.8-SNAPSHOT</version>
   		</dependency>
 	</dependencies>
 </project>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 90e465d2dc..3530fbb568 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.7</version>
+		<version>4.2.8-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 c82fade42d..98d334f9de 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.7</version>
+		<version>4.2.8-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -85,13 +85,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.7</version>
+			<version>4.2.8-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.7</version>
+			<version>4.2.8-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index c52783d2a1..eef43d9c3a 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.7</version>
+    <version>4.2.8-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -32,7 +32,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.7</version>
+    	<version>4.2.8-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 0ca1247f39..296a38bd63 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.7</version>
+    <version>4.2.8-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>4.2.7</version>
+    	<version>4.2.8-SNAPSHOT</version>
     	<type>jar</type>
     	<scope>compile</scope>
     </dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 03b1c00b76..cbfec2ba46 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>4.2.7</version>
+    <version>4.2.8-SNAPSHOT</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml
index d374a993fd..59f4080f6a 100644
--- a/biojava-phylo/pom.xml
+++ b/biojava-phylo/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.7</version>
+    <version>4.2.8-SNAPSHOT</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>biojava-phylo</artifactId>
@@ -44,7 +44,7 @@
     <dependency>
       <groupId>org.biojava</groupId>
       <artifactId>biojava-core</artifactId>
-      <version>4.2.7</version>
+      <version>4.2.8-SNAPSHOT</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 73c642d3e1..67415f4fe4 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>4.2.7</version>
+		<version>4.2.8-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>4.2.7</version>
+			<version>4.2.8-SNAPSHOT</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or 
 			scopes here) -->
diff --git a/biojava-sequencing/pom.xml b/biojava-sequencing/pom.xml
index 0b4d66e069..cc6fd99460 100644
--- a/biojava-sequencing/pom.xml
+++ b/biojava-sequencing/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.7</version>
+		<version>4.2.8-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-sequencing</artifactId>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.7</version>
+			<version>4.2.8-SNAPSHOT</version>
 			<scope>compile</scope>
 		</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 cfd684d103..5ba8f8353c 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>4.2.7</version>
+        <version>4.2.8-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -25,13 +25,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-            <version>4.2.7</version>
+            <version>4.2.8-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-            <version>4.2.7</version>
+            <version>4.2.8-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index db1c41a4f1..64316bf8e6 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.7</version>
+		<version>4.2.8-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -22,13 +22,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.7</version>
+			<version>4.2.8-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.7</version>
+			<version>4.2.8-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index e6c0294b34..09925ab0df 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>4.2.7</version>
+        <version>4.2.8-SNAPSHOT</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index 0f2e83e414..b5990c0ea7 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.7</version>
+		<version>4.2.8-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>4.2.7</version>
+			<version>4.2.8-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 6513c4cb61..e594cba972 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>4.2.7</version>
+	<version>4.2.8-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
@@ -44,7 +44,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>biojava-4.2.7</tag>
+		<tag>biojava-4.2.1</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list 

From a3edf549cf4353fd52f72b0b3ceffe977a32f1ce Mon Sep 17 00:00:00 2001
From: valasatava <yana.valasatava@gmail.com>
Date: Wed, 12 Apr 2017 20:06:16 -0700
Subject: [PATCH 02/13] Cherry-pick the c5fa135 commit

---
 .../core/alignment/SimpleAlignedSequence.java | 126 +++++++++++++-----
 .../alignment/template/AlignedSequence.java   |  12 ++
 2 files changed, 107 insertions(+), 31 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 ede117fc88..b369c50fa9 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
@@ -31,6 +31,7 @@
 import org.biojava.nbio.core.sequence.location.template.Location;
 import org.biojava.nbio.core.sequence.location.template.Point;
 import org.biojava.nbio.core.sequence.template.*;
+import org.biojava.nbio.core.util.Equals;
 
 import java.io.Serializable;
 import java.util.ArrayList;
@@ -59,7 +60,10 @@ public class SimpleAlignedSequence<S extends Sequence<C>, C extends Compound> im
 
 	// cached (lazily initialized)
 	private int numGaps = -1;
-	private int[] alignmentFromSequence, sequenceFromAlignment;
+	private int numGapPositions = -1;
+
+	private int[] alignmentFromSequence;
+	private int[] sequenceFromAlignment;
 
 	/**
 	 * Creates an {@link AlignedSequence} for the given {@link Sequence} in a global alignment.
@@ -131,25 +135,35 @@ public void clearCache() {
 		sequenceFromAlignment = null;
 	}
 
-	@Override
-	public int getAlignmentIndexAt(int sequenceIndex) {
-		if (alignmentFromSequence == null) {
-			alignmentFromSequence = new int[original.getLength()];
-			int s = 1, a = 1;
-			for (int i = 0; i < numBefore; i++, s++) {
-				alignmentFromSequence[s - 1] = a;
-			}
-			for (; s <= alignmentFromSequence.length && a <= length; s++, a++) {
-				while (a <= length && isGap(a)) {
-					a++;
-				}
-				alignmentFromSequence[s - 1] = a;
-			}
-			a--;
-			for (int i = 0; i < numAfter; i++, s++) {
-				alignmentFromSequence[s - 1] = a;
+	private void setAlignmentFromSequence() {
+		alignmentFromSequence = new int[original.getLength()];
+		int s = 1, a = 1;
+		for (int i = 0; i < numBefore; i++, s++) {
+			alignmentFromSequence[s - 1] = a;
+		}
+		for (; s <= alignmentFromSequence.length && a <= length; s++, a++) {
+			while (a <= length && isGap(a)) {
+				a++;
 			}
+			alignmentFromSequence[s - 1] = a;
+		}
+		a--;
+		for (int i = 0; i < numAfter; i++, s++) {
+			alignmentFromSequence[s - 1] = a;
 		}
+	}
+
+	@Override
+	public int[] getAlignmentFromSequence() {
+		if (alignmentFromSequence == null)
+			setAlignmentFromSequence();
+		return alignmentFromSequence;
+	}
+
+	@Override
+	public int getAlignmentIndexAt(int sequenceIndex) {
+		if (alignmentFromSequence == null)
+			setAlignmentFromSequence();
 		return alignmentFromSequence[sequenceIndex - 1];
 	}
 
@@ -167,6 +181,7 @@ public Location getLocationInAlignment() {
 	public int getNumGaps() {
 		if (numGaps == -1) {
 			numGaps = 0;
+			numGapPositions = 0;
 			C cGap = getCompoundSet().getCompoundForString(gap);
 			boolean inGap = false;
 			for (C compound : getAsList()) {
@@ -175,6 +190,7 @@ public int getNumGaps() {
 						numGaps++;
 						inGap = true;
 					}
+					numGapPositions++;
 				} else {
 					inGap = false;
 				}
@@ -194,21 +210,31 @@ public int getOverlapCount() {
 		return 1;
 	}
 
-	@Override
-	public int getSequenceIndexAt(int alignmentIndex) {
-		if (sequenceFromAlignment == null) {
-			sequenceFromAlignment = new int[length];
-			int a = 1, s = numBefore + 1;
-			for (int i = 0; i < getStart().getPosition(); i++, a++) {
-				sequenceFromAlignment[a - 1] = s;
-			}
-			for (; a <= length; a++) {
-				if (!isGap(a)) {
-					s++;
-				}
-				sequenceFromAlignment[a - 1] = s;
+	private void setSequenceFromAlignment() {
+		sequenceFromAlignment = new int[length];
+		int a = 1, s = numBefore + 1;
+		for (int i = 0; i < getStart().getPosition(); i++, a++) {
+			sequenceFromAlignment[a - 1] = s;
+		}
+		for (; a <= length; a++) {
+			if (!isGap(a)) {
+				s++;
 			}
+			sequenceFromAlignment[a - 1] = s;
 		}
+	}
+
+	@Override
+	public int[] getSequenceFromAlignment() {
+		if (sequenceFromAlignment == null)
+			setSequenceFromAlignment();
+		return sequenceFromAlignment;
+	}
+
+	@Override
+	public int getSequenceIndexAt(int alignmentIndex) {
+		if (sequenceFromAlignment == null)
+			setSequenceFromAlignment();
 		return sequenceFromAlignment[alignmentIndex - 1];
 	}
 
@@ -266,6 +292,30 @@ public List<C> getAsList() {
 		return compounds;
 	}
 
+	@Override
+	public boolean equals(Object o){
+
+		if(! Equals.classEqual(this, o)) {
+			return false;
+		}
+
+		Sequence<C> other = (Sequence<C>)o;
+		if ( original.getAsList().size() != other.getAsList().size())
+			return false;
+
+		for ( int i = 0 ; i< original.getAsList().size() ; i++){
+			if ( ! original.getAsList().get(i).equalsIgnoreCase(other.getAsList().get(i)))
+				return false;
+		}
+		return true;
+	}
+
+	@Override
+	public int hashCode(){
+		String s = getSequenceAsString();
+		return s.hashCode();
+	}
+
 	@Override
 	public C getCompoundAt(int alignmentIndex) {
 		return alignmentIndex >= 1 && alignmentIndex <= length && isGap(alignmentIndex) ?
@@ -382,4 +432,18 @@ private void setLocation(List<Step> steps) {
 	public SequenceView<C> getInverse() {
 		throw new UnsupportedOperationException("Not supported yet.");
 	}
+
+	@Override
+	public int getNumGapPositions() {
+		if (numGapPositions == -1)
+			getNumGaps();
+		return numGapPositions;
+	}
+
+	@Override
+	public double getCoverage() {
+		
+		double coverage = getLength() - getNumGapPositions();
+		return coverage / getOriginalSequence().getLength();
+	}
 }
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 5ddcde13a1..98ec5c9794 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
@@ -47,6 +47,18 @@ enum Step { COMPOUND, GAP }
 	 */
 	void clearCache();
 
+	/** Returns the alignment.
+	 *
+	 * @return the alignment
+	 */
+	int[] getAlignmentFromSequence();
+
+	/** Returns the sequence positions at each alignment index
+	 *
+	 * @return array of the sequence positions
+	 */
+	int[] getSequenceFromAlignment();
+
 	/**
 	 * Returns the column index within an alignment corresponding to the given index in the original {@link Sequence}.
 	 * Both indices are 1-indexed and inclusive.

From 450b43c7ce0fc3e31da1485583aaf90d00e1c35e Mon Sep 17 00:00:00 2001
From: valasatava <yana.valasatava@gmail.com>
Date: Wed, 5 Jul 2017 15:06:49 -0700
Subject: [PATCH 03/13] Adding missing methods to the interface

---
 .../core/alignment/template/AlignedSequence.java | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

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 98ec5c9794..76a1fe1c8b 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
@@ -142,4 +142,20 @@ enum Step { COMPOUND, GAP }
 	 */
 	boolean isGap(int alignmentIndex);
 
+	/**
+	 * Returns number of gap positions (gap openings and extensions) in the sequence. This could be determined from the {@link Location}
+	 * information or from gap {@link Compound}s, which may not necessarily result in the same number.
+	 *
+	 * @return number of gap positions in the sequence
+	 */
+	int getNumGapPositions();
+
+	/**
+	 * Returns the coverage, as a fraction between 0 and 1, of this {@link AlignedSequence} with respect to the original sequence.
+	 * This is equivalent to ({@link #getLength()} - {@link #getNumGapPositions()}) / getOriginalSequence().getLength().
+	 *
+	 * @return coverage of the original sequence by the aligned sequence
+	 */
+	double getCoverage();
+
 }

From 4bdd304dbb8e90596982c1885be5a989a4350828 Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Wed, 5 Jul 2017 16:40:58 -0700
Subject: [PATCH 04/13] Updating dssp urls to latest RCSB convention

---
 .../org/biojava/nbio/structure/secstruc/DSSPParser.java   | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/DSSPParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/DSSPParser.java
index aa5de5a35a..eb762b9f25 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/DSSPParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/DSSPParser.java
@@ -31,6 +31,7 @@
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.zip.GZIPInputStream;
 
 import org.biojava.nbio.structure.Group;
 import org.biojava.nbio.structure.ResidueNumber;
@@ -95,8 +96,11 @@ public static List<SecStrucState> fetch(String pdb,
 			Structure structure, boolean assign)
 					throws IOException, StructureException {
 
-		InputStream in = new URL("http://www.rcsb.org/pdb/files/"+
-				pdb+".dssp").openStream();
+		URL url = new URL("http://files.rcsb.org/dssp/" + 
+				pdb.toLowerCase().substring(1, 3) + "/" + 
+				pdb.toLowerCase() + "/" +
+				pdb + ".dssp.gz");
+		InputStream in = new GZIPInputStream(url.openStream());
 		Reader read = new InputStreamReader(in);
 		BufferedReader reader = new BufferedReader(read);
 		return generalParse(reader, structure, assign);

From 541b61c28b6ca0fd57112f036b4c98040b6301f2 Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Wed, 5 Jul 2017 16:43:33 -0700
Subject: [PATCH 05/13] Updating to latest RCSB URL

---
 .../test/java/org/biojava/nbio/structure/TestURLIdentifier.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestURLIdentifier.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestURLIdentifier.java
index 141cb9e034..3d55a3e286 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestURLIdentifier.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestURLIdentifier.java
@@ -101,7 +101,7 @@ public void testURLParameters() throws StructureException, IOException {
 		assertEquals("wrong length for chainId=A", 94, StructureTools.getRepresentativeAtomArray(reduced).length);
 
 		try {
-			url = new URL("http://www.rcsb.org/pdb/files/1B8G.pdb.gz");
+			url = new URL("http://files.rcsb.org/download/1B8G.pdb.gz");
 			id = new URLIdentifier(url);
 
 			full = id.loadStructure(cache);

From 42d628d2dc3d07582782ecdf983e9ab57e9991ab Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Wed, 5 Jul 2017 16:59:10 -0700
Subject: [PATCH 06/13] Fixing test after remediation

---
 .../test/java/org/biojava/nbio/structure/Test2JA5.java | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/Test2JA5.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/Test2JA5.java
index 2dbdda4c93..4835800e70 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/Test2JA5.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/Test2JA5.java
@@ -20,9 +20,9 @@
  */
 package org.biojava.nbio.structure;
 
-import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.assertEquals;
 
 import java.io.IOException;
 
@@ -55,7 +55,7 @@ public void test2JA5() throws IOException, StructureException {
 		// assertTrue(StructureTools.getNrAtoms(s1) == 0);
 
 		// SeqRes contains 15 chains, but since we cannot align Chain N to AtomGroups => 14.
-		assertTrue(s1.getChains().size() == 14);
+		assertEquals(14, s1.getChains().size());
 
 		Chain nChain = null;
 		try {
@@ -84,8 +84,8 @@ public void test2JA5noHeader() throws IOException, StructureException {
 		// This is not applicable anymore, we need to parse atoms to have chains to match.
 		assertTrue(StructureTools.getNrAtoms(s1) == 0);
 
-		// All 15 seqres chains will be store.
-		assertTrue(s1.getChains().size() == 15);
+		// 2ja5 has been remediated on March 2017, now it has 14 chains in seqres matching the 14 chains in atoms (chain N has been removed)
+		assertEquals(14, s1.getChains().size());
 
 		Chain nChain = null;
 		try {
@@ -93,6 +93,6 @@ public void test2JA5noHeader() throws IOException, StructureException {
 		} catch (StructureException e){
 			// this is expected here, since there is no chain N
 		}
-		assertNotNull(nChain);
+		assertNull(nChain);
 	}
 }

From dc7f3ead20034ccda5ce0933b548a96f81209f3b Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Wed, 5 Jul 2017 17:28:12 -0700
Subject: [PATCH 07/13] Updating ligand URLs to latest RCSB convention

---
 .../nbio/structure/io/mmcif/DownloadChemCompProvider.java       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java
index d41e116971..174ad3389e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java
@@ -67,7 +67,7 @@ public class DownloadChemCompProvider implements ChemCompProvider {
 
 	public static final String CHEM_COMP_CACHE_DIRECTORY = "chemcomp";
 
-	public static final String SERVER_LOCATION = "http://www.rcsb.org/pdb/files/ligand/";
+	public static final String SERVER_LOCATION = "https://files.rcsb.org/ligands/download/";
 
 
 	private static File path;

From a38c8c8babdc68a75711b2e607ba5d9317b749d7 Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Thu, 6 Jul 2017 12:49:05 -0700
Subject: [PATCH 08/13] Better http than https

---
 .../nbio/structure/io/mmcif/DownloadChemCompProvider.java       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java
index 174ad3389e..fac2a86cbb 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java
@@ -67,7 +67,7 @@ public class DownloadChemCompProvider implements ChemCompProvider {
 
 	public static final String CHEM_COMP_CACHE_DIRECTORY = "chemcomp";
 
-	public static final String SERVER_LOCATION = "https://files.rcsb.org/ligands/download/";
+	public static final String SERVER_LOCATION = "http://files.rcsb.org/ligands/download/";
 
 
 	private static File path;

From 9fb8fccc055785c58307475a74e5d4c11a495ac2 Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Thu, 6 Jul 2017 14:23:32 -0700
Subject: [PATCH 09/13] [maven-release-plugin] prepare release biojava-4.2.8

---
 biojava-aa-prop/pom.xml          | 6 +++---
 biojava-alignment/pom.xml        | 6 +++---
 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-phylo/pom.xml            | 4 ++--
 biojava-protein-disorder/pom.xml | 4 ++--
 biojava-sequencing/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 ++--
 15 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index b5cc3c5bea..72d5044e69 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>4.2.8-SNAPSHOT</version>
+		<version>4.2.8</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>4.2.8-SNAPSHOT</version>
+			<version>4.2.8</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>4.2.8-SNAPSHOT</version>
+			<version>4.2.8</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 6faea5b5c2..d1ebe860f9 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.8-SNAPSHOT</version>
+		<version>4.2.8</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -46,7 +46,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.8-SNAPSHOT</version>
+			<version>4.2.8</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
@@ -74,7 +74,7 @@
   		<dependency>
   			<groupId>org.biojava</groupId>
   			<artifactId>biojava-phylo</artifactId>
-  			<version>4.2.8-SNAPSHOT</version>
+  			<version>4.2.8</version>
   		</dependency>
 	</dependencies>
 </project>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 3530fbb568..20b75fcb33 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.8-SNAPSHOT</version>
+		<version>4.2.8</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 98d334f9de..452b909abd 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.8-SNAPSHOT</version>
+		<version>4.2.8</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -85,13 +85,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.8-SNAPSHOT</version>
+			<version>4.2.8</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.8-SNAPSHOT</version>
+			<version>4.2.8</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index eef43d9c3a..7fbc1deff2 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.8-SNAPSHOT</version>
+    <version>4.2.8</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -32,7 +32,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.8-SNAPSHOT</version>
+    	<version>4.2.8</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 296a38bd63..fded08c306 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.8-SNAPSHOT</version>
+    <version>4.2.8</version>
   </parent>
   <artifactId>biojava-modfinder</artifactId>
   <name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.8-SNAPSHOT</version>
+    	<version>4.2.8</version>
     	<type>jar</type>
     	<scope>compile</scope>
     </dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index cbfec2ba46..cf6af99b55 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>4.2.8-SNAPSHOT</version>
+    <version>4.2.8</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml
index 59f4080f6a..8f4fae1576 100644
--- a/biojava-phylo/pom.xml
+++ b/biojava-phylo/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.8-SNAPSHOT</version>
+    <version>4.2.8</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>biojava-phylo</artifactId>
@@ -44,7 +44,7 @@
     <dependency>
       <groupId>org.biojava</groupId>
       <artifactId>biojava-core</artifactId>
-      <version>4.2.8-SNAPSHOT</version>
+      <version>4.2.8</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 67415f4fe4..cdbd04df3b 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>4.2.8-SNAPSHOT</version>
+		<version>4.2.8</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.8-SNAPSHOT</version>
+			<version>4.2.8</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or 
 			scopes here) -->
diff --git a/biojava-sequencing/pom.xml b/biojava-sequencing/pom.xml
index cc6fd99460..2e5f4af250 100644
--- a/biojava-sequencing/pom.xml
+++ b/biojava-sequencing/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.8-SNAPSHOT</version>
+		<version>4.2.8</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-sequencing</artifactId>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.8-SNAPSHOT</version>
+			<version>4.2.8</version>
 			<scope>compile</scope>
 		</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 5ba8f8353c..d9ea4db9f5 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>4.2.8-SNAPSHOT</version>
+        <version>4.2.8</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -25,13 +25,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-            <version>4.2.8-SNAPSHOT</version>
+            <version>4.2.8</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-            <version>4.2.8-SNAPSHOT</version>
+            <version>4.2.8</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 64316bf8e6..0577749f78 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.8-SNAPSHOT</version>
+		<version>4.2.8</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -22,13 +22,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.8-SNAPSHOT</version>
+			<version>4.2.8</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.8-SNAPSHOT</version>
+			<version>4.2.8</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 09925ab0df..784fe909ab 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>4.2.8-SNAPSHOT</version>
+        <version>4.2.8</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index b5990c0ea7..fa83379487 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.8-SNAPSHOT</version>
+		<version>4.2.8</version>
 	</parent>	
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.8-SNAPSHOT</version>
+			<version>4.2.8</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index e594cba972..6b4be3f56d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>4.2.8-SNAPSHOT</version>
+	<version>4.2.8</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
@@ -44,7 +44,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>biojava-4.2.1</tag>
+		<tag>biojava-4.2.8</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list 

From f7f5eec88e181941d1e05528c4e68718803c9959 Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Thu, 6 Jul 2017 14:23:40 -0700
Subject: [PATCH 10/13] [maven-release-plugin] prepare for next development
 iteration

---
 biojava-aa-prop/pom.xml          | 6 +++---
 biojava-alignment/pom.xml        | 6 +++---
 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-phylo/pom.xml            | 4 ++--
 biojava-protein-disorder/pom.xml | 4 ++--
 biojava-sequencing/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 ++--
 15 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index 72d5044e69..80754119a3 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>4.2.8</version>
+		<version>4.2.9-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>4.2.8</version>
+			<version>4.2.9-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>4.2.8</version>
+			<version>4.2.9-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 d1ebe860f9..a0303b0dae 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.8</version>
+		<version>4.2.9-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -46,7 +46,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.8</version>
+			<version>4.2.9-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
@@ -74,7 +74,7 @@
   		<dependency>
   			<groupId>org.biojava</groupId>
   			<artifactId>biojava-phylo</artifactId>
-  			<version>4.2.8</version>
+  			<version>4.2.9-SNAPSHOT</version>
   		</dependency>
 	</dependencies>
 </project>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 20b75fcb33..0f629b0f23 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.8</version>
+		<version>4.2.9-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 452b909abd..d0d9df8990 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.8</version>
+		<version>4.2.9-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -85,13 +85,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.8</version>
+			<version>4.2.9-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.8</version>
+			<version>4.2.9-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index 7fbc1deff2..b65c612ea0 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.8</version>
+    <version>4.2.9-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -32,7 +32,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.8</version>
+    	<version>4.2.9-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 fded08c306..8ded38b053 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.8</version>
+    <version>4.2.9-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>4.2.8</version>
+    	<version>4.2.9-SNAPSHOT</version>
     	<type>jar</type>
     	<scope>compile</scope>
     </dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index cf6af99b55..3cbfe076b7 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>4.2.8</version>
+    <version>4.2.9-SNAPSHOT</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml
index 8f4fae1576..6f4e0477e5 100644
--- a/biojava-phylo/pom.xml
+++ b/biojava-phylo/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.8</version>
+    <version>4.2.9-SNAPSHOT</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>biojava-phylo</artifactId>
@@ -44,7 +44,7 @@
     <dependency>
       <groupId>org.biojava</groupId>
       <artifactId>biojava-core</artifactId>
-      <version>4.2.8</version>
+      <version>4.2.9-SNAPSHOT</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index cdbd04df3b..6d2dc6ff41 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>4.2.8</version>
+		<version>4.2.9-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>4.2.8</version>
+			<version>4.2.9-SNAPSHOT</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or 
 			scopes here) -->
diff --git a/biojava-sequencing/pom.xml b/biojava-sequencing/pom.xml
index 2e5f4af250..2cc15beadd 100644
--- a/biojava-sequencing/pom.xml
+++ b/biojava-sequencing/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.8</version>
+		<version>4.2.9-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-sequencing</artifactId>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.8</version>
+			<version>4.2.9-SNAPSHOT</version>
 			<scope>compile</scope>
 		</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 d9ea4db9f5..dcc92b9372 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>4.2.8</version>
+        <version>4.2.9-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -25,13 +25,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-            <version>4.2.8</version>
+            <version>4.2.9-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-            <version>4.2.8</version>
+            <version>4.2.9-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 0577749f78..85feaccc3b 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.8</version>
+		<version>4.2.9-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -22,13 +22,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.8</version>
+			<version>4.2.9-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.8</version>
+			<version>4.2.9-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 784fe909ab..75854051ee 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>4.2.8</version>
+        <version>4.2.9-SNAPSHOT</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index fa83379487..97f9d915b9 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.8</version>
+		<version>4.2.9-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>4.2.8</version>
+			<version>4.2.9-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 6b4be3f56d..ed284f9e1c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>4.2.8</version>
+	<version>4.2.9-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
@@ -44,7 +44,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>biojava-4.2.8</tag>
+		<tag>biojava-4.2.1</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list 

From 7c802e082b936fed37e998ca22e730cf0191a8cb Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Thu, 6 Jul 2017 14:30:08 -0700
Subject: [PATCH 11/13] [maven-release-plugin] rollback the release of
 biojava-4.2.8

---
 biojava-aa-prop/pom.xml          | 6 +++---
 biojava-alignment/pom.xml        | 6 +++---
 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-phylo/pom.xml            | 4 ++--
 biojava-protein-disorder/pom.xml | 4 ++--
 biojava-sequencing/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 +-
 15 files changed, 31 insertions(+), 31 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index 80754119a3..b5cc3c5bea 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>4.2.9-SNAPSHOT</version>
+		<version>4.2.8-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>4.2.9-SNAPSHOT</version>
+			<version>4.2.8-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>4.2.9-SNAPSHOT</version>
+			<version>4.2.8-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 a0303b0dae..6faea5b5c2 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.9-SNAPSHOT</version>
+		<version>4.2.8-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -46,7 +46,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.9-SNAPSHOT</version>
+			<version>4.2.8-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
@@ -74,7 +74,7 @@
   		<dependency>
   			<groupId>org.biojava</groupId>
   			<artifactId>biojava-phylo</artifactId>
-  			<version>4.2.9-SNAPSHOT</version>
+  			<version>4.2.8-SNAPSHOT</version>
   		</dependency>
 	</dependencies>
 </project>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 0f629b0f23..3530fbb568 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.9-SNAPSHOT</version>
+		<version>4.2.8-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 d0d9df8990..98d334f9de 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.9-SNAPSHOT</version>
+		<version>4.2.8-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -85,13 +85,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.9-SNAPSHOT</version>
+			<version>4.2.8-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.9-SNAPSHOT</version>
+			<version>4.2.8-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index b65c612ea0..eef43d9c3a 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.9-SNAPSHOT</version>
+    <version>4.2.8-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -32,7 +32,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.9-SNAPSHOT</version>
+    	<version>4.2.8-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 8ded38b053..296a38bd63 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.9-SNAPSHOT</version>
+    <version>4.2.8-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>4.2.9-SNAPSHOT</version>
+    	<version>4.2.8-SNAPSHOT</version>
     	<type>jar</type>
     	<scope>compile</scope>
     </dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 3cbfe076b7..cbfec2ba46 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>4.2.9-SNAPSHOT</version>
+    <version>4.2.8-SNAPSHOT</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml
index 6f4e0477e5..59f4080f6a 100644
--- a/biojava-phylo/pom.xml
+++ b/biojava-phylo/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.9-SNAPSHOT</version>
+    <version>4.2.8-SNAPSHOT</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>biojava-phylo</artifactId>
@@ -44,7 +44,7 @@
     <dependency>
       <groupId>org.biojava</groupId>
       <artifactId>biojava-core</artifactId>
-      <version>4.2.9-SNAPSHOT</version>
+      <version>4.2.8-SNAPSHOT</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 6d2dc6ff41..67415f4fe4 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>4.2.9-SNAPSHOT</version>
+		<version>4.2.8-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>4.2.9-SNAPSHOT</version>
+			<version>4.2.8-SNAPSHOT</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or 
 			scopes here) -->
diff --git a/biojava-sequencing/pom.xml b/biojava-sequencing/pom.xml
index 2cc15beadd..cc6fd99460 100644
--- a/biojava-sequencing/pom.xml
+++ b/biojava-sequencing/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.9-SNAPSHOT</version>
+		<version>4.2.8-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-sequencing</artifactId>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.9-SNAPSHOT</version>
+			<version>4.2.8-SNAPSHOT</version>
 			<scope>compile</scope>
 		</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 dcc92b9372..5ba8f8353c 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>4.2.9-SNAPSHOT</version>
+        <version>4.2.8-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -25,13 +25,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-            <version>4.2.9-SNAPSHOT</version>
+            <version>4.2.8-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-            <version>4.2.9-SNAPSHOT</version>
+            <version>4.2.8-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 85feaccc3b..64316bf8e6 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.9-SNAPSHOT</version>
+		<version>4.2.8-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -22,13 +22,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.9-SNAPSHOT</version>
+			<version>4.2.8-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.9-SNAPSHOT</version>
+			<version>4.2.8-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 75854051ee..09925ab0df 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>4.2.9-SNAPSHOT</version>
+        <version>4.2.8-SNAPSHOT</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index 97f9d915b9..b5990c0ea7 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.9-SNAPSHOT</version>
+		<version>4.2.8-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>4.2.9-SNAPSHOT</version>
+			<version>4.2.8-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index ed284f9e1c..e594cba972 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>4.2.9-SNAPSHOT</version>
+	<version>4.2.8-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 d7d7a28d29cbe5bc6dcaaeaf5899862207408c48 Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Thu, 6 Jul 2017 14:34:01 -0700
Subject: [PATCH 12/13] Fix for pom needed for release to be performed

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

diff --git a/pom.xml b/pom.xml
index e594cba972..09e6e0a4dd 100644
--- a/pom.xml
+++ b/pom.xml
@@ -211,6 +211,8 @@
 					<artifactId>maven-javadoc-plugin</artifactId>
 					<version>2.10.3</version>
 					<configuration>
+						<!-- we need to allow script in comments or otherwise we can't use google analytics js in footer below - JD 2017-06-06 -->
+						<additionalparam>--allow-script-in-comments</additionalparam>
 						<maxmemory>256m</maxmemory>
 						<footer>&lt;script src="http://www.google-analytics.com/urchin.js"
 							type="text/javascript"&gt;&lt;/script&gt;&lt;script

From dee8b41939be97e31a9bd657c5057bd2f16942b9 Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Thu, 6 Jul 2017 14:41:05 -0700
Subject: [PATCH 13/13] [maven-release-plugin] prepare release biojava-4.2.8

---
 biojava-aa-prop/pom.xml          | 6 +++---
 biojava-alignment/pom.xml        | 6 +++---
 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-phylo/pom.xml            | 4 ++--
 biojava-protein-disorder/pom.xml | 4 ++--
 biojava-sequencing/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 ++--
 15 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index b5cc3c5bea..72d5044e69 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>4.2.8-SNAPSHOT</version>
+		<version>4.2.8</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>4.2.8-SNAPSHOT</version>
+			<version>4.2.8</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>4.2.8-SNAPSHOT</version>
+			<version>4.2.8</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 6faea5b5c2..d1ebe860f9 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.8-SNAPSHOT</version>
+		<version>4.2.8</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -46,7 +46,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.8-SNAPSHOT</version>
+			<version>4.2.8</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
@@ -74,7 +74,7 @@
   		<dependency>
   			<groupId>org.biojava</groupId>
   			<artifactId>biojava-phylo</artifactId>
-  			<version>4.2.8-SNAPSHOT</version>
+  			<version>4.2.8</version>
   		</dependency>
 	</dependencies>
 </project>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 3530fbb568..20b75fcb33 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.8-SNAPSHOT</version>
+		<version>4.2.8</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 98d334f9de..452b909abd 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.8-SNAPSHOT</version>
+		<version>4.2.8</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -85,13 +85,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.8-SNAPSHOT</version>
+			<version>4.2.8</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.8-SNAPSHOT</version>
+			<version>4.2.8</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index eef43d9c3a..7fbc1deff2 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.8-SNAPSHOT</version>
+    <version>4.2.8</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -32,7 +32,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.8-SNAPSHOT</version>
+    	<version>4.2.8</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 296a38bd63..fded08c306 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.8-SNAPSHOT</version>
+    <version>4.2.8</version>
   </parent>
   <artifactId>biojava-modfinder</artifactId>
   <name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.8-SNAPSHOT</version>
+    	<version>4.2.8</version>
     	<type>jar</type>
     	<scope>compile</scope>
     </dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index cbfec2ba46..cf6af99b55 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>4.2.8-SNAPSHOT</version>
+    <version>4.2.8</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml
index 59f4080f6a..8f4fae1576 100644
--- a/biojava-phylo/pom.xml
+++ b/biojava-phylo/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.8-SNAPSHOT</version>
+    <version>4.2.8</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>biojava-phylo</artifactId>
@@ -44,7 +44,7 @@
     <dependency>
       <groupId>org.biojava</groupId>
       <artifactId>biojava-core</artifactId>
-      <version>4.2.8-SNAPSHOT</version>
+      <version>4.2.8</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 67415f4fe4..cdbd04df3b 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>4.2.8-SNAPSHOT</version>
+		<version>4.2.8</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.8-SNAPSHOT</version>
+			<version>4.2.8</version>
 		</dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or 
 			scopes here) -->
diff --git a/biojava-sequencing/pom.xml b/biojava-sequencing/pom.xml
index cc6fd99460..2e5f4af250 100644
--- a/biojava-sequencing/pom.xml
+++ b/biojava-sequencing/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.8-SNAPSHOT</version>
+		<version>4.2.8</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-sequencing</artifactId>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.8-SNAPSHOT</version>
+			<version>4.2.8</version>
 			<scope>compile</scope>
 		</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 5ba8f8353c..d9ea4db9f5 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>4.2.8-SNAPSHOT</version>
+        <version>4.2.8</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -25,13 +25,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-            <version>4.2.8-SNAPSHOT</version>
+            <version>4.2.8</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-            <version>4.2.8-SNAPSHOT</version>
+            <version>4.2.8</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 64316bf8e6..0577749f78 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.8-SNAPSHOT</version>
+		<version>4.2.8</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -22,13 +22,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.8-SNAPSHOT</version>
+			<version>4.2.8</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.8-SNAPSHOT</version>
+			<version>4.2.8</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 09925ab0df..784fe909ab 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>4.2.8-SNAPSHOT</version>
+        <version>4.2.8</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index b5990c0ea7..fa83379487 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.8-SNAPSHOT</version>
+		<version>4.2.8</version>
 	</parent>	
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.8-SNAPSHOT</version>
+			<version>4.2.8</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 09e6e0a4dd..8085813a81 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>4.2.8-SNAPSHOT</version>
+	<version>4.2.8</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
@@ -44,7 +44,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>biojava-4.2.1</tag>
+		<tag>biojava-4.2.8</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list