From d45321592ecc619abe5d591b79dfd09911e95c5a Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Thu, 19 Oct 2017 11:19:23 -0700
Subject: [PATCH 1/7] [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 6461800d58..c326e4b205 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</version>
+		<version>4.2.10-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</version>
+			<version>4.2.10-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>4.2.9</version>
+			<version>4.2.10-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 bbd3516da4..e2e2b775c6 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</version>
+		<version>4.2.10-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</version>
+			<version>4.2.10-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
@@ -74,7 +74,7 @@
   		<dependency>
   			<groupId>org.biojava</groupId>
   			<artifactId>biojava-phylo</artifactId>
-  			<version>4.2.9</version>
+  			<version>4.2.10-SNAPSHOT</version>
   		</dependency>
 	</dependencies>
 </project>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 7807aaefeb..cdeab00acb 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</version>
+		<version>4.2.10-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 e3c8bc66e0..2373d6a17f 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</version>
+		<version>4.2.10-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</version>
+			<version>4.2.10-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.9</version>
+			<version>4.2.10-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index d024d95f5c..8da81d33da 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</version>
+    <version>4.2.10-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</version>
+    	<version>4.2.10-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 95f8367ac7..e91e62bd4c 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</version>
+    <version>4.2.10-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</version>
+    	<version>4.2.10-SNAPSHOT</version>
     	<type>jar</type>
     	<scope>compile</scope>
     </dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index e104b8caf8..6a8de2f64c 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</version>
+    <version>4.2.10-SNAPSHOT</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml
index ef52ff66d9..7e5a8c44cf 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</version>
+    <version>4.2.10-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</version>
+      <version>4.2.10-SNAPSHOT</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index c1be8471f4..8153a4028b 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</version>
+		<version>4.2.10-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</version>
+			<version>4.2.10-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 271a3b0a74..05ba0abbbe 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</version>
+		<version>4.2.10-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</version>
+			<version>4.2.10-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 7ee5f84970..0c0b9bc1d8 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</version>
+        <version>4.2.10-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</version>
+            <version>4.2.10-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-            <version>4.2.9</version>
+            <version>4.2.10-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 3942a08a66..12252e4cd2 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</version>
+		<version>4.2.10-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</version>
+			<version>4.2.10-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.9</version>
+			<version>4.2.10-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 56312cb608..d83fbc37db 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</version>
+        <version>4.2.10-SNAPSHOT</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index b41fac0e17..8f4fe21858 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</version>
+		<version>4.2.10-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</version>
+			<version>4.2.10-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 02983fdba1..b2242ca22d 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</version>
+	<version>4.2.10-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-4.2.9</tag>
+		<tag>biojava-4.2.1</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list 

From 56b9d07c9c24c6cdb807fff12a48a0eb7b8c20b3 Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Thu, 16 Nov 2017 09:00:27 -0800
Subject: [PATCH 2/7] Backporting bugfix from 5.0 branch

---
 .../io/mmcif/SimpleMMcifConsumer.java         | 20 +++++++++++--------
 1 file changed, 12 insertions(+), 8 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java
index 096bd77797..1b34f1238b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java
@@ -1603,13 +1603,9 @@ private StructRef getStructRef(String ref_id){
 	 */
 	@Override
 	public void newStructRefSeq(StructRefSeq sref) {
-		//if (DEBUG)
-		//	System.out.println(sref);
 		DBRef r = new DBRef();
 
 
-		//if (DEBUG)
-		//	System.out.println( " " + sref.getPdbx_PDB_id_code() + " " + sref.getPdbx_db_accession());
 		r.setIdCode(sref.getPdbx_PDB_id_code());
 		r.setDbAccession(sref.getPdbx_db_accession());
 		r.setDbIdCode(sref.getPdbx_db_accession());
@@ -1617,15 +1613,23 @@ public void newStructRefSeq(StructRefSeq sref) {
 		r.setChainId(sref.getPdbx_strand_id());
 		StructRef structRef = getStructRef(sref.getRef_id());
 		if (structRef == null){
-			logger.warn("could not find StructRef " + sref.getRef_id() + " for StructRefSeq " + sref);
+			logger.info("could not find StructRef " + sref.getRef_id() + " for StructRefSeq " + sref);
 		} else {
 			r.setDatabase(structRef.getDb_name());
 			r.setDbIdCode(structRef.getDb_code());
 		}
+		
+		int seqbegin;
+		int seqend;
+		try{
+			seqbegin = Integer.parseInt(sref.getPdbx_auth_seq_align_beg());
+			seqend   = Integer.parseInt(sref.getPdbx_auth_seq_align_end());
+		}
+		catch(NumberFormatException e){
+			logger.warn("Couldn't parse sequence alignment positions: {}", e.getMessage());
+			return;
+		}
 
-
-		int seqbegin = Integer.parseInt(sref.getPdbx_auth_seq_align_beg());
-		int seqend   = Integer.parseInt(sref.getPdbx_auth_seq_align_end());
 		Character begin_ins_code = new Character(sref.getPdbx_seq_align_beg_ins_code().charAt(0));
 		Character end_ins_code   = new Character(sref.getPdbx_seq_align_end_ins_code().charAt(0));
 

From fe8c7167393d6baebddb40c07be971c8b390e135 Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Thu, 7 Dec 2017 15:09:16 -0800
Subject: [PATCH 3/7] Fix and unit test for #715

---
 .../java/org/biojava/nbio/structure/Calc.java |  5 ++
 .../org/biojava/nbio/structure/TestCalc.java  | 47 +++++++++++++++++++
 2 files changed, 52 insertions(+)

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 d09252f16c..0f7b6faf70 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
@@ -521,6 +521,11 @@ public static final void transform (Chain chain, Matrix4d m) {
 			for (Atom atom: g.getAtoms()) {
 				transform(atom,m);
 			}
+			for (Group altG : g.getAltLocs()) {
+				for (Atom atom : altG.getAtoms()) {
+					transform(atom, m);
+				}				
+			}
 		}
 	}
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java
index c84c1e30e4..b6d38d4907 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java
@@ -156,6 +156,53 @@ public void testVecmathTransformation() {
 
 		assertEquals(expected, actual);
 	}
+	
+	/**
+	 * Issue https://github.com/biojava/biojava/issues/715
+	 */
+	@Test
+	public void testChainTransform() {
+		Group g = new AminoAcidImpl();
+		Atom a = new AtomImpl();
+		a.setName("CA");
+		a.setX(1);
+		a.setY(1);
+		a.setZ(1);
+		g.addAtom(a);
+		Group altLocG = new AminoAcidImpl();
+		Atom a2 = new AtomImpl();
+		a2.setName("CA");
+		a2.setX(2);
+		a2.setY(2);
+		a2.setZ(2);
+		altLocG.addAtom(a2);
+		
+		g.addAltLoc(altLocG);
+		
+		Chain c = new ChainImpl();
+		c.addGroup(g);
+		
+		Matrix4d m = new Matrix4d(1,0,0,1, 0,1,0,0, 0,0,1,0, 0,0,0,1); // shift of 1 in x axis
+ 		Calc.transform(c, m);
+ 		
+ 		Group thegroup = c.getAtomGroup(0);
+ 		Group thealtlocgroup = thegroup.getAltLocs().get(0);
+ 		
+ 		Atom atom1 = thegroup.getAtom("CA");
+ 		Atom atom2 = thealtlocgroup.getAtom("CA");
+ 		
+ 		// x should be shitfted by 1
+ 		assertEquals(2, atom1.getX(), 0.00001);
+ 		assertEquals(1, atom1.getY(), 0.00001);
+ 		assertEquals(1, atom1.getZ(), 0.00001);
+ 		
+ 		// x should be shitfted by 1
+ 		assertEquals(3, atom2.getX(), 0.00001);
+ 		assertEquals(2, atom2.getY(), 0.00001);
+ 		assertEquals(2, atom2.getZ(), 0.00001);
+
+ 		
+	}
 
 	private static Atom getAtom(double x, double y, double z) {
 		Atom a = new AtomImpl();

From 8f5d03d2a87ef6a88dc232671ca3629408ae714d Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Thu, 7 Dec 2017 17:44:32 -0800
Subject: [PATCH 4/7] Back porting fix and test for #716

---
 .../java/org/biojava/nbio/structure/Calc.java | 41 ++++-----
 .../org/biojava/nbio/structure/TestCalc.java  | 83 ++++++++++++++++++-
 2 files changed, 99 insertions(+), 25 deletions(-)

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 0f7b6faf70..426d6c8a17 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
@@ -450,7 +450,8 @@ public static final void rotate(Structure structure, Matrix m){
 	 * @param t transformation Matrix4d
 	 */
 	public static void transform(Atom[] ca, Matrix4d t) {
-		for (Atom atom : ca) Calc.transform(atom, t);
+		for (Atom atom : ca)
+			Calc.transform(atom, t);
 	}
 
 	/**
@@ -479,13 +480,14 @@ public static final void transform (Atom atom, Matrix4d m) {
 	 * @param group
 	 * @param m
 	 */
-	public static final void transform (Group group, Matrix4d m) {
-		AtomIterator iter = new AtomIterator(group) ;
-
-		while (iter.hasNext()) {
-			Atom atom = iter.next() ;
-			transform(atom,m);
-
+	public static final void transform(Group group, Matrix4d m) {
+		for (Atom atom : group.getAtoms()) {
+			transform(atom, m);
+		}
+		for (Group altG : group.getAltLocs()) {
+			for (Atom atom : altG.getAtoms()) {
+				transform(atom, m);
+			}				
 		}
 	}
 
@@ -497,13 +499,11 @@ public static final void transform (Group group, Matrix4d m) {
 	 * @param structure
 	 * @param m
 	 */
-	public static final void transform (Structure structure, Matrix4d m) {
-		AtomIterator iter = new AtomIterator(structure) ;
-
-		while (iter.hasNext()) {
-			Atom atom = iter.next() ;
-			transform(atom,m);
-
+	public static final void transform(Structure structure, Matrix4d m) {
+		for (int n=0; n<structure.nrModels();n++) {
+			for (Chain c : structure.getChains(n)) {
+				transform(c, m);
+			}
 		}
 	}
 
@@ -517,15 +517,8 @@ public static final void transform (Structure structure, Matrix4d m) {
 	 */
 	public static final void transform (Chain chain, Matrix4d m) {
 
-		for (Group g:chain.getAtomGroups()) {
-			for (Atom atom: g.getAtoms()) {
-				transform(atom,m);
-			}
-			for (Group altG : g.getAltLocs()) {
-				for (Atom atom : altG.getAtoms()) {
-					transform(atom, m);
-				}				
-			}
+		for (Group g : chain.getAtomGroups()) {
+			transform(g, m);
 		}
 	}
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java
index b6d38d4907..be2a2b11f3 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java
@@ -204,13 +204,94 @@ public void testChainTransform() {
  		
 	}
 
-	private static Atom getAtom(double x, double y, double z) {
+	/**
+	 * Issue https://github.com/biojava/biojava/issues/715
+	 */
+	@Test
+	public void testStructureTransform() throws StructureException {
+		Group g = new AminoAcidImpl();
+		Atom a = getAtom("CA", 1, 1, 1);
+		g.addAtom(a);
+		Group altLocG = new AminoAcidImpl();
+		Atom a2 = getAtom("CA", 2, 2, 2);
+		altLocG.addAtom(a2);
+		
+		g.addAltLoc(altLocG);
+		
+		Chain c1 = new ChainImpl();
+		c1.addGroup(g);
+		c1.setChainID("A");
+		
+		Group gc2 = new AminoAcidImpl();
+		Atom ac2 = getAtom("CA", 3, 3, 3);
+		gc2.addAtom(ac2);
+		Group altLocGc2 = new AminoAcidImpl();
+		Atom ac22 = getAtom("CA", 4, 4, 4);
+		altLocGc2.addAtom(ac22);
+		
+		gc2.addAltLoc(altLocGc2);
+		
+		Chain c2 = new ChainImpl();
+		c2.addGroup(gc2);
+		c2.setChainID("B");
+		
+		Structure s = new StructureImpl();
+		s.addChain(c1);
+		s.addChain(c2);
+		
+		
+		Matrix4d m = new Matrix4d(1,0,0,1, 0,1,0,0, 0,0,1,0, 0,0,0,1); // shift of 1 in x axis
+ 		Calc.transform(s, m);
+ 		
+ 		// testing 1st chain
+ 		Group thegroup = s.getChainByPDB("A").getAtomGroup(0);
+ 		Group thealtlocgroup = thegroup.getAltLocs().get(0);
+ 		
+ 		Atom atom1 = thegroup.getAtom("CA");
+ 		Atom atom2 = thealtlocgroup.getAtom("CA");
+ 		
+ 		// x should be shitfted by 1
+ 		assertEquals(2, atom1.getX(), 0.00001);
+ 		assertEquals(1, atom1.getY(), 0.00001);
+ 		assertEquals(1, atom1.getZ(), 0.00001);
+ 		
+ 		// x should be shitfted by 1
+ 		assertEquals(3, atom2.getX(), 0.00001);
+ 		assertEquals(2, atom2.getY(), 0.00001);
+ 		assertEquals(2, atom2.getZ(), 0.00001);
+
+ 		// testing 2nd chain
+ 		thegroup = s.getChainByPDB("B").getAtomGroup(0);
+ 		thealtlocgroup = thegroup.getAltLocs().get(0);
+ 		
+ 		atom1 = thegroup.getAtom("CA");
+ 		atom2 = thealtlocgroup.getAtom("CA");
+ 		
+ 		// x should be shitfted by 1
+ 		assertEquals(4, atom1.getX(), 0.00001);
+ 		assertEquals(3, atom1.getY(), 0.00001);
+ 		assertEquals(3, atom1.getZ(), 0.00001);
+ 		
+ 		// x should be shitfted by 1
+ 		assertEquals(5, atom2.getX(), 0.00001);
+ 		assertEquals(4, atom2.getY(), 0.00001);
+ 		assertEquals(4, atom2.getZ(), 0.00001);
+
+ 		
+	}
+
+	private static Atom getAtom(String name, double x, double y, double z) {
 		Atom a = new AtomImpl();
 		a.setX(x);
 		a.setY(y);
 		a.setZ(z);
+		a.setName(name);
 		return a;
 	}
+	
+	private static Atom getAtom(double x, double y, double z) {
+		return getAtom(null, x, y, z);
+	}
 
 	private static Matrix4d getSampleTransform(){
 

From 1bd46063710fa7076b8ca9c9b8b8bee539b1fe82 Mon Sep 17 00:00:00 2001
From: Dak Rojnuckarin <atipatr@amgen.com>
Date: Fri, 7 Jul 2017 22:57:38 -0400
Subject: [PATCH 5/7] Attempt to fix issue #659 - Error parsing FASTA in
 multiple passes

---
 .../nbio/core/sequence/io/FastaReader.java    |  39 ++---
 .../nbio/core/fasta/TestFASTAReader.java      | 150 ++++++++++++++++++
 .../org/biojava/nbio/core/fasta/P02768.fasta  |  12 ++
 .../nbio/core/fasta/P02768_blank_lines.fasta  |  21 +++
 .../nbio/core/fasta/TwoSequences.fasta        |  16 ++
 .../core/fasta/TwoSequences_blank_lines.fasta |  21 +++
 6 files changed, 237 insertions(+), 22 deletions(-)
 create mode 100644 biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java
 create mode 100644 biojava-core/src/test/resources/org/biojava/nbio/core/fasta/P02768.fasta
 create mode 100644 biojava-core/src/test/resources/org/biojava/nbio/core/fasta/P02768_blank_lines.fasta
 create mode 100644 biojava-core/src/test/resources/org/biojava/nbio/core/fasta/TwoSequences.fasta
 create mode 100644 biojava-core/src/test/resources/org/biojava/nbio/core/fasta/TwoSequences_blank_lines.fasta

diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java
index 09eea5716c..8fddae0693 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java
@@ -122,6 +122,8 @@ public LinkedHashMap<String,S> process() throws IOException {
 	 * <ul>
 	 * <li>This method can't be called after calling its NO-ARGUMENT twin.</li>
 	 * <li>remember to close the underlying resource when you are done.</li>
+	 * <li>This method always return non-null hash map. When end-of-file is reached,
+	 * the number of sequences returned will be smaller than the number requested.</li>
 	 * </ul>
 	 * @see #process()
 	 * @author Amr AL-Hossary
@@ -188,37 +190,30 @@ public LinkedHashMap<String,S> process(int max) throws IOException {
 			line = br.readLine();
 
 			if (line == null) {
-
-
-				// Fix for #282
-				if ( sequences.size() == 0 && max != -1) {
-					return null;
-				}
-
 				//i.e. EOF
-				String seq = sb.toString();
-				if ( seq.length() == 0) {
+				if ( sb.length() == 0 && header.length() != 0 ) {
 					logger.warn("Can't parse sequence {}. Got sequence of length 0!", sequenceIndex);
 					logger.warn("header: {}", header);
-				}
-				//logger.info("Sequence index=" + sequenceIndex + " " + fileIndex );
-				try {
-					@SuppressWarnings("unchecked")
-					S sequence = (S)sequenceCreator.getSequence(seq, sequenceIndex);
-					headerParser.parseHeader(header, sequence);
-					sequences.put(sequence.getAccession().getID(),sequence);
-					processedSequences++;
-				} catch (CompoundNotFoundException e) {
-					logger.warn("Sequence with header '{}' has unrecognised compounds ({}), it will be ignored",
-							header, e.getMessage());
+					header = null;
+				} else if ( sb.length() > 0 ) {
+					//logger.info("Sequence index=" + sequenceIndex + " " + fileIndex );
+					try {
+						@SuppressWarnings("unchecked")
+						S sequence = (S)sequenceCreator.getSequence(sb.toString(), sequenceIndex);
+						headerParser.parseHeader(header, sequence);
+						sequences.put(sequence.getAccession().getID(),sequence);
+						processedSequences++;
+						header = null;
+					} catch (CompoundNotFoundException e) {
+						logger.warn("Sequence with header '{}' has unrecognised compounds ({}), it will be ignored",
+								header, e.getMessage());
+					}
 				}
 				keepGoing = false;
 			}
 			if (max > -1 && processedSequences>=max) {
 				keepGoing=false;
 			}
-			if ( this.line == null)
-				keepGoing = false;
 		} while (keepGoing);
 
 		this.line  = line;
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java b/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java
new file mode 100644
index 0000000000..e4a9653cf5
--- /dev/null
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java
@@ -0,0 +1,150 @@
+package org.biojava.nbio.core.fasta;
+
+import java.io.InputStream;
+import java.util.LinkedHashMap;
+
+import static org.junit.Assert.* ;
+import static org.hamcrest.CoreMatchers.* ;
+
+import org.biojava.nbio.core.sequence.ProteinSequence;
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
+import org.biojava.nbio.core.sequence.io.FastaReader;
+import org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser;
+import org.biojava.nbio.core.sequence.io.ProteinSequenceCreator;
+import org.biojava.nbio.core.sequence.io.util.ClasspathResource;
+import org.junit.Test;
+
+
+public class TestFASTAReader {
+
+	private void testProcessAll(String path) throws Exception {
+        ClasspathResource r = new ClasspathResource(path);
+        FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = null ;
+        try( InputStream inStream = r.getInputStream() ) {
+            fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
+                    inStream,
+                    new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
+                    new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+            LinkedHashMap<String, ProteinSequence> sequences = fastaReader.process();
+            assertThat(sequences,is(notNullValue()));
+            assertThat(sequences.size(),is(1));
+            assertThat(sequences.containsKey("P02768"),is(true));
+            assertThat(sequences.get("P02768").getLength(),is(609));
+        } finally {
+            if(fastaReader != null) fastaReader.close();
+        }
+	}
+	
+	/**
+	 * Test file contains one sequence (P02768 from swissprot). Read the whole
+	 * file all at once by calling {@link FastaReader#process()} and verify that
+	 * one sequence is read.
+	 *
+	 * @throws Exception
+	 */
+    @Test
+    public void testProcessAll() throws Exception {
+    	testProcessAll("org/biojava/nbio/core/fasta/P02768.fasta");
+    }
+    
+    /**
+     * Same as {@link #testProcessAll()} but input files contains blank lines
+     * 
+     * @throws Exception
+     */
+    @Test
+    public void testProcessAllWithBlankLines() throws Exception {
+    	testProcessAll("org/biojava/nbio/core/fasta/P02768_blank_lines.fasta");
+    }
+    
+    private void testProcess1(String path) throws Exception {
+        ClasspathResource r = new ClasspathResource(path);
+        FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = null ;
+        try( InputStream inStream = r.getInputStream() ) {
+            fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
+                    inStream,
+                    new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
+                    new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+            LinkedHashMap<String,ProteinSequence> out1 = fastaReader.process(1);
+            assertThat(out1,is(notNullValue()));
+            assertThat(out1.size(),is(1));
+            assertThat(out1.containsKey("P02768"),is(true));
+            assertThat(out1.get("P02768").getLength(),is(609));
+            LinkedHashMap<String,ProteinSequence> out2 = fastaReader.process(1);
+            assertThat(out2,is(notNullValue()));
+            assertThat(out2.size(),is(0));
+        } finally {
+            if(fastaReader != null) fastaReader.close();
+        }
+    }
+    
+	/**
+	 * Test file contains one sequence (P02768 from swissprot). Read one
+	 * sequence at a time by calling {@link FastaReader#process(int)} and verify
+	 * that the first call get one sequence and the second call get none.
+	 * 
+	 * @throws Exception
+	 */
+    @Test
+    public void testProcess1() throws Exception {
+    	testProcess1("org/biojava/nbio/core/fasta/P02768.fasta");
+    }
+    
+    /**
+     * Same as {@link #testProcess1()}, but input contains blank lines.
+     * 
+     * @throws Exception
+     */
+    @Test
+    public void testProcess1WithBlankLines() throws Exception {
+    	testProcess1("org/biojava/nbio/core/fasta/P02768_blank_lines.fasta");
+    }
+    
+    private void testProcess2(String path) throws Exception {
+        ClasspathResource r = new ClasspathResource(path);
+        FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = null ;
+        try( InputStream inStream = r.getInputStream() ) {
+            fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>(
+                    inStream,
+                    new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
+                    new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
+            LinkedHashMap<String,ProteinSequence> out1 = fastaReader.process(1);
+            assertThat(out1,is(notNullValue()));
+            assertThat(out1.size(),is(1));
+            assertThat(out1.containsKey("P02768"),is(true));
+            assertThat(out1.get("P02768").getLength(),is(609));
+            LinkedHashMap<String,ProteinSequence> out2 = fastaReader.process(1);
+            assertThat(out2,is(notNullValue()));
+            assertThat(out2.size(),is(1));
+            assertThat(out2.containsKey("P00698"),is(true));
+            assertThat(out2.get("P00698").getLength(),is(147));
+            LinkedHashMap<String,ProteinSequence> out3 = fastaReader.process(1);
+            assertThat(out3,is(notNullValue()));
+            assertThat(out3.size(),is(0));
+        } finally {
+            if(fastaReader != null) fastaReader.close();
+        }
+    }
+    
+	/**
+	 * Test file contains two sequences. Read one sequence at a time by calling
+	 * {@link FastaReader#process(int)} and verify that the first and second
+	 * call get one sequence each and the third call get none.
+	 * 
+	 * @throws Exception
+	 */
+    @Test
+    public void testProcess2() throws Exception {
+    	testProcess2("org/biojava/nbio/core/fasta/TwoSequences.fasta");
+    }
+
+    /**
+     * Sane as {@link #testProcess2()} but input file contain blank lines
+     * @throws Exception
+     */
+    @Test
+    public void testProcess2WithBlankLines() throws Exception {
+    	testProcess2("org/biojava/nbio/core/fasta/TwoSequences_blank_lines.fasta");
+    }
+}
diff --git a/biojava-core/src/test/resources/org/biojava/nbio/core/fasta/P02768.fasta b/biojava-core/src/test/resources/org/biojava/nbio/core/fasta/P02768.fasta
new file mode 100644
index 0000000000..a435ae5a76
--- /dev/null
+++ b/biojava-core/src/test/resources/org/biojava/nbio/core/fasta/P02768.fasta
@@ -0,0 +1,12 @@
+>sp|P02768|ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2
+MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF
+EDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP
+ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF
+FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV
+ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLK
+ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYAR
+RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFE
+QLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV
+LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTL
+SEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLV
+AASQAALGL
\ No newline at end of file
diff --git a/biojava-core/src/test/resources/org/biojava/nbio/core/fasta/P02768_blank_lines.fasta b/biojava-core/src/test/resources/org/biojava/nbio/core/fasta/P02768_blank_lines.fasta
new file mode 100644
index 0000000000..2d56071f34
--- /dev/null
+++ b/biojava-core/src/test/resources/org/biojava/nbio/core/fasta/P02768_blank_lines.fasta
@@ -0,0 +1,21 @@
+>sp|P02768|ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2
+MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF
+EDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP
+ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF
+FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV
+
+ 
+
+ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLK
+ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYAR
+RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFE
+QLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV
+LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTL
+SEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLV
+AASQAALGL
+
+
+
+
+
+
diff --git a/biojava-core/src/test/resources/org/biojava/nbio/core/fasta/TwoSequences.fasta b/biojava-core/src/test/resources/org/biojava/nbio/core/fasta/TwoSequences.fasta
new file mode 100644
index 0000000000..2fde8a3f43
--- /dev/null
+++ b/biojava-core/src/test/resources/org/biojava/nbio/core/fasta/TwoSequences.fasta
@@ -0,0 +1,16 @@
+>sp|P02768|ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2
+MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF
+EDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP
+ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF
+FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV
+ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLK
+ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYAR
+RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFE
+QLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV
+LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTL
+SEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLV
+AASQAALGL
+>sp|P00698|LYSC_CHICK Lysozyme C OS=Gallus gallus GN=LYZ PE=1 SV=1
+MRSLLILVLCFLPLAALGKVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQA
+TNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDG
+NGMNAWVAWRNRCKGTDVQAWIRGCRL
\ No newline at end of file
diff --git a/biojava-core/src/test/resources/org/biojava/nbio/core/fasta/TwoSequences_blank_lines.fasta b/biojava-core/src/test/resources/org/biojava/nbio/core/fasta/TwoSequences_blank_lines.fasta
new file mode 100644
index 0000000000..78006dd898
--- /dev/null
+++ b/biojava-core/src/test/resources/org/biojava/nbio/core/fasta/TwoSequences_blank_lines.fasta
@@ -0,0 +1,21 @@
+>sp|P02768|ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2
+MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF
+EDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP
+ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF
+
+
+FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV
+ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLK
+ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYAR
+RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFE
+QLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV
+LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTL
+SEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLV
+AASQAALGL
+ 
+ 
+>sp|P00698|LYSC_CHICK Lysozyme C OS=Gallus gallus GN=LYZ PE=1 SV=1
+MRSLLILVLCFLPLAALGKVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQA
+
+TNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDG
+NGMNAWVAWRNRCKGTDVQAWIRGCRL
\ No newline at end of file

From 9f6ed0392ebcf6cc8024622fac0ff8cf9aaf8ea7 Mon Sep 17 00:00:00 2001
From: Dak Rojnuckarin <atipatr@amgen.com>
Date: Sat, 8 Jul 2017 00:01:51 -0400
Subject: [PATCH 6/7] Revert to old behavior where process(int) return null on
 end-of-file.

---
 .../java/org/biojava/nbio/core/sequence/io/FastaReader.java | 4 +---
 .../java/org/biojava/nbio/core/fasta/TestFASTAReader.java   | 6 ++----
 2 files changed, 3 insertions(+), 7 deletions(-)

diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java
index 8fddae0693..4ad7dbeb9c 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReader.java
@@ -122,8 +122,6 @@ public LinkedHashMap<String,S> process() throws IOException {
 	 * <ul>
 	 * <li>This method can't be called after calling its NO-ARGUMENT twin.</li>
 	 * <li>remember to close the underlying resource when you are done.</li>
-	 * <li>This method always return non-null hash map. When end-of-file is reached,
-	 * the number of sequences returned will be smaller than the number requested.</li>
 	 * </ul>
 	 * @see #process()
 	 * @author Amr AL-Hossary
@@ -219,7 +217,7 @@ public LinkedHashMap<String,S> process(int max) throws IOException {
 		this.line  = line;
 		this.header= header;
 
-		return sequences;
+		return max > -1 && sequences.isEmpty() ? null :  sequences;
 	}
 
 	public void close() throws IOException {
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java b/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java
index e4a9653cf5..2458fd5f1f 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/fasta/TestFASTAReader.java
@@ -72,8 +72,7 @@ private void testProcess1(String path) throws Exception {
             assertThat(out1.containsKey("P02768"),is(true));
             assertThat(out1.get("P02768").getLength(),is(609));
             LinkedHashMap<String,ProteinSequence> out2 = fastaReader.process(1);
-            assertThat(out2,is(notNullValue()));
-            assertThat(out2.size(),is(0));
+            assertThat(out2,is(nullValue()));
         } finally {
             if(fastaReader != null) fastaReader.close();
         }
@@ -120,8 +119,7 @@ private void testProcess2(String path) throws Exception {
             assertThat(out2.containsKey("P00698"),is(true));
             assertThat(out2.get("P00698").getLength(),is(147));
             LinkedHashMap<String,ProteinSequence> out3 = fastaReader.process(1);
-            assertThat(out3,is(notNullValue()));
-            assertThat(out3.size(),is(0));
+            assertThat(out3,is(nullValue()));
         } finally {
             if(fastaReader != null) fastaReader.close();
         }

From f6870a20d93b96dfec99bff8bc677c96b597c045 Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Mon, 11 Dec 2017 16:18:35 -0800
Subject: [PATCH 7/7] [maven-release-plugin] prepare release biojava-4.2.10

---
 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 c326e4b205..aee8bc50cc 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>4.2.10-SNAPSHOT</version>
+		<version>4.2.10</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>4.2.10-SNAPSHOT</version>
+			<version>4.2.10</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>4.2.10-SNAPSHOT</version>
+			<version>4.2.10</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 e2e2b775c6..272bbe77a2 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.10-SNAPSHOT</version>
+		<version>4.2.10</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -46,7 +46,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.10-SNAPSHOT</version>
+			<version>4.2.10</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
@@ -74,7 +74,7 @@
   		<dependency>
   			<groupId>org.biojava</groupId>
   			<artifactId>biojava-phylo</artifactId>
-  			<version>4.2.10-SNAPSHOT</version>
+  			<version>4.2.10</version>
   		</dependency>
 	</dependencies>
 </project>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index cdeab00acb..31e9217495 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.10-SNAPSHOT</version>
+		<version>4.2.10</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 2373d6a17f..2f865c9f1c 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.10-SNAPSHOT</version>
+		<version>4.2.10</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>4.2.10-SNAPSHOT</version>
+			<version>4.2.10</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.10-SNAPSHOT</version>
+			<version>4.2.10</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index 8da81d33da..a2c489c21c 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.10-SNAPSHOT</version>
+    <version>4.2.10</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -32,7 +32,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.10-SNAPSHOT</version>
+    	<version>4.2.10</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 e91e62bd4c..5b180290a5 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.10-SNAPSHOT</version>
+    <version>4.2.10</version>
   </parent>
   <artifactId>biojava-modfinder</artifactId>
   <name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.10-SNAPSHOT</version>
+    	<version>4.2.10</version>
     	<type>jar</type>
     	<scope>compile</scope>
     </dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 6a8de2f64c..6ef151037f 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>4.2.10-SNAPSHOT</version>
+    <version>4.2.10</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml
index 7e5a8c44cf..adc2a88a14 100644
--- a/biojava-phylo/pom.xml
+++ b/biojava-phylo/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.10-SNAPSHOT</version>
+    <version>4.2.10</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>4.2.10-SNAPSHOT</version>
+      <version>4.2.10</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 8153a4028b..b9ce3e69ea 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>4.2.10-SNAPSHOT</version>
+		<version>4.2.10</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.10-SNAPSHOT</version>
+			<version>4.2.10</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 05ba0abbbe..092c50284c 100644
--- a/biojava-sequencing/pom.xml
+++ b/biojava-sequencing/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.10-SNAPSHOT</version>
+		<version>4.2.10</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>4.2.10-SNAPSHOT</version>
+			<version>4.2.10</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 0c0b9bc1d8..061398727b 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>4.2.10-SNAPSHOT</version>
+        <version>4.2.10</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>4.2.10-SNAPSHOT</version>
+            <version>4.2.10</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-            <version>4.2.10-SNAPSHOT</version>
+            <version>4.2.10</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 12252e4cd2..3c165e33d3 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.10-SNAPSHOT</version>
+		<version>4.2.10</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -22,13 +22,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.10-SNAPSHOT</version>
+			<version>4.2.10</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.10-SNAPSHOT</version>
+			<version>4.2.10</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index d83fbc37db..058e18519f 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>4.2.10-SNAPSHOT</version>
+        <version>4.2.10</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index 8f4fe21858..dd810a38bd 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.10-SNAPSHOT</version>
+		<version>4.2.10</version>
 	</parent>	
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.10-SNAPSHOT</version>
+			<version>4.2.10</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index b2242ca22d..b6dca9f797 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>4.2.10-SNAPSHOT</version>
+	<version>4.2.10</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-4.2.10</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list