From 2b03990c51884ad106ec08c59f540034c09b1c78 Mon Sep 17 00:00:00 2001
From: Jenkins <jenkins@java-jenkins-research.rcsb.org>
Date: Tue, 28 Jun 2016 10:55:32 -0700
Subject: [PATCH 01/15] [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 d4d3afb89b..d90dc1eb47 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>4.2.3</version>
+		<version>4.2.4-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.3</version>
+			<version>4.2.4-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>4.2.3</version>
+			<version>4.2.4-SNAPSHOT</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index c033b8d1f0..aaced0081d 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3</version>
+		<version>4.2.4-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>4.2.3</version>
+			<version>4.2.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
@@ -74,7 +74,7 @@
   		<dependency>
   			<groupId>org.biojava</groupId>
   			<artifactId>biojava-phylo</artifactId>
-  			<version>4.2.3</version>
+  			<version>4.2.4-SNAPSHOT</version>
   		</dependency>
 	</dependencies>
 </project>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 674c0257f3..4f5a46cd4d 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3</version>
+		<version>4.2.4-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 24d410ee7c..0e28a54a0c 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3</version>
+		<version>4.2.4-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -79,13 +79,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.3</version>
+			<version>4.2.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.3</version>
+			<version>4.2.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index 61f9a178e4..6d7ba3da65 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.3</version>
+    <version>4.2.4-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -32,7 +32,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.3</version>
+    	<version>4.2.4-SNAPSHOT</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index 0c8c9b759f..f1bbd65ebe 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.3</version>
+    <version>4.2.4-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-modfinder</artifactId>
   <name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.3</version>
+    	<version>4.2.4-SNAPSHOT</version>
     	<type>jar</type>
     	<scope>compile</scope>
     </dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index b0f4378c55..fb3a6da2ae 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>4.2.3</version>
+    <version>4.2.4-SNAPSHOT</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml
index 96be175f15..1f1d09fe5b 100644
--- a/biojava-phylo/pom.xml
+++ b/biojava-phylo/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.3</version>
+    <version>4.2.4-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>4.2.3</version>
+      <version>4.2.4-SNAPSHOT</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index cd338b3b8f..89c120b49b 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>4.2.3</version>
+		<version>4.2.4-SNAPSHOT</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.3</version>
+			<version>4.2.4-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 374ea82c69..264a0798b6 100644
--- a/biojava-sequencing/pom.xml
+++ b/biojava-sequencing/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3</version>
+		<version>4.2.4-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>4.2.3</version>
+			<version>4.2.4-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 290c5a3a55..bb24a570b1 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>4.2.3</version>
+        <version>4.2.4-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>4.2.3</version>
+            <version>4.2.4-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-            <version>4.2.3</version>
+            <version>4.2.4-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index ddee49b548..d50222d410 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3</version>
+		<version>4.2.4-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>4.2.3</version>
+			<version>4.2.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.3</version>
+			<version>4.2.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 8d2875b813..cd01b059cc 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>4.2.3</version>
+        <version>4.2.4-SNAPSHOT</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index ecc74b660e..ee902d9504 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.3</version>
+		<version>4.2.4-SNAPSHOT</version>
 	</parent>	
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.3</version>
+			<version>4.2.4-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 2b575db99b..c3abff104b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>4.2.3</version>
+	<version>4.2.4-SNAPSHOT</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the
@@ -44,7 +44,7 @@
 		<developerConnection>scm:git:git@github.com:biojava/biojava.git</developerConnection>
 		<url>https://github.com/biojava/biojava</url>
 
-		<tag>biojava-4.2.3</tag>
+		<tag>biojava-4.2.1</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list 

From 15ca444a5203a3b7da52c1156471663032ca0aba Mon Sep 17 00:00:00 2001
From: Andreas Prlic <andreas.prlic@gmail.com>
Date: Wed, 29 Jun 2016 20:00:07 -0400
Subject: [PATCH 02/15] #505 switching to https for all NCBI utils traffic.

---
 .../java/org/biojava/nbio/core/sequence/ProteinSequence.java    | 2 +-
 .../nbio/core/sequence/loader/GenbankProxySequenceReader.java   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java
index 714e55b09b..e3abbea6bd 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ProteinSequence.java
@@ -153,7 +153,7 @@ public void setParentDNASequence(AbstractSequence<NucleotideCompound> parentDNAS
 	}
 
 	private DNASequence getRawParentSequence(String accessId) throws IOException {
-		String seqUrlTemplate = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=%s&rettype=fasta&retmode=text";
+		String seqUrlTemplate = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=%s&rettype=fasta&retmode=text";
 		URL url = new URL(String.format(seqUrlTemplate, accessId));
 
 		logger.trace("Getting parent DNA sequence from URL: {}", url.toString());
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
index 24b5ce1ada..045900263a 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
@@ -56,7 +56,7 @@ public class GenbankProxySequenceReader<C extends Compound> extends StringProxyS
 
 	private final static Logger logger = LoggerFactory.getLogger(GenbankProxySequenceReader.class);
 
-	private static final String eutilBaseURL = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/"; //
+	private static final String eutilBaseURL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"; //
 	private String genbankDirectoryCache = null;
 	private GenbankSequenceParser<AbstractSequence<C>, C> genbankParser;
 	private GenericGenbankHeaderParser<AbstractSequence<C>, C> headerParser;

From ebc2c973a9a0cc16064d1b0261823eb9ed2d5676 Mon Sep 17 00:00:00 2001
From: Andreas Prlic <andreas.prlic@gmail.com>
Date: Wed, 29 Jun 2016 20:08:29 -0400
Subject: [PATCH 03/15] #505 switching to https for all NCBI utils traffic.

---
 .../java/org/biojava/nbio/core/sequence/io/IUPACParser.java | 4 ++--
 .../nbio/core/search/io/blast/small-blastreport.blastxml    | 2 +-
 .../java/org/biojava/nbio/structure/align/AFPTwister.java   | 2 +-
 .../org/biojava/nbio/structure/align/fatcat/FatCat.java     | 2 +-
 .../biojava/nbio/structure/align/fatcat/FatCatFlexible.java | 2 +-
 .../biojava/nbio/structure/align/fatcat/FatCatRigid.java    | 2 +-
 .../nbio/structure/align/fatcat/calc/AFPCalculator.java     | 2 +-
 .../nbio/structure/align/fatcat/calc/AFPChainer.java        | 2 +-
 .../nbio/structure/align/fatcat/calc/AFPOptimizer.java      | 2 +-
 .../nbio/structure/align/fatcat/calc/AFPPostProcessor.java  | 2 +-
 .../nbio/structure/align/fatcat/calc/FCAlignHelper.java     | 2 +-
 .../nbio/structure/align/fatcat/calc/FatCatAligner.java     | 2 +-
 .../nbio/structure/align/fatcat/calc/FatCatParameters.java  | 2 +-
 .../biojava/nbio/structure/align/fatcat/calc/SigEva.java    | 2 +-
 .../align/fatcat/calc/StructureAlignmentOptimizer.java      | 2 +-
 .../java/org/biojava/nbio/structure/ecod/EcodDomain.java    | 2 +-
 biojava-structure/src/main/resources/ce.properties          | 6 +++---
 .../ws/alignment/qblast/BlastAlignmentParameterEnum.java    | 2 +-
 .../nbio/ws/alignment/qblast/BlastOutputParameterEnum.java  | 2 +-
 .../ws/alignment/qblast/NCBIQBlastAlignmentProperties.java  | 2 +-
 .../biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java | 4 ++--
 readme.md                                                   | 2 +-
 22 files changed, 26 insertions(+), 26 deletions(-)

diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java
index 46d058ec0f..8f1b449283 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java
@@ -57,7 +57,7 @@
  * </ul>
  *
  * Taken from <a
- * href="http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c"
+ * href="https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c"
  * >NCBI</a> with slight modification and put into the classpath resource.
  *
  * Takes in an ID, name, amino acid string and the locations of amino acids
@@ -65,7 +65,7 @@
  * position strings that correspond to the amino acid string or if you are using
  * the default IUPAC codes you can use the hardcoded ones which are consistent
  * amongst all <a
- * href="http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c"> codon
+ * href="https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c"> codon
  * tables</a>.
  *
  * The generated {@link IUPACTable} objects do not parse the data further until
diff --git a/biojava-core/src/test/resources/org/biojava/nbio/core/search/io/blast/small-blastreport.blastxml b/biojava-core/src/test/resources/org/biojava/nbio/core/search/io/blast/small-blastreport.blastxml
index 47e75cafd9..a1e441c505 100644
--- a/biojava-core/src/test/resources/org/biojava/nbio/core/search/io/blast/small-blastreport.blastxml
+++ b/biojava-core/src/test/resources/org/biojava/nbio/core/search/io/blast/small-blastreport.blastxml
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
+<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "https://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
 <BlastOutput>
   <BlastOutput_program>blastn</BlastOutput_program>
   <BlastOutput_version>BLASTN 2.2.29+</BlastOutput_version>
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java
index 96d9da57ba..43f32085c9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCat.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCat.java
index ad9dd1615d..6a5aa6dc93 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCat.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCat.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCatFlexible.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCatFlexible.java
index 3379895038..b4d6479620 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCatFlexible.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCatFlexible.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCatRigid.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCatRigid.java
index 62a5735d16..d6fc87a506 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCatRigid.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/FatCatRigid.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java
index a89500596c..51c51f8c17 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java
index 9344c9c255..3db4193ac4 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPOptimizer.java
index 8e276afa0a..ca38425aa9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPOptimizer.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPPostProcessor.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPPostProcessor.java
index 60e5a05c33..5f940ec6a1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPPostProcessor.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPPostProcessor.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FCAlignHelper.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FCAlignHelper.java
index 08a81eebb4..74c6d66ce5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FCAlignHelper.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FCAlignHelper.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FatCatAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FatCatAligner.java
index e8546908f8..b4200cd88f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FatCatAligner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FatCatAligner.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FatCatParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FatCatParameters.java
index 8e9dd2e8f9..cb5ae3628b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FatCatParameters.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/FatCatParameters.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/SigEva.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/SigEva.java
index 351d531d07..d111e55fd6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/SigEva.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/SigEva.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java
index dedeaabad8..2908f91e42 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java
@@ -3,7 +3,7 @@
  * Yuzhen Ye & Adam Godzik (2003)
  * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
  * Bioinformatics vol.19 suppl. 2. ii246-ii255.
- * http://www.ncbi.nlm.nih.gov/pubmed/14534198
+ * https://www.ncbi.nlm.nih.gov/pubmed/14534198
  * </pre>
  *
  * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this code.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDomain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDomain.java
index d0a3ec3308..1b880feef4 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDomain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDomain.java
@@ -34,7 +34,7 @@
  * chain, residue ranges and status (manual or automatic classification).
  * <p>
  * For detailed explanation about the ECOD information see the original article
- * at: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256011.
+ * at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256011.
  * <pre>
  * Cheng H, Schaeffer RD, Liao Y, et al. 
  * ECOD: An Evolutionary Classification of Protein Domains. 
diff --git a/biojava-structure/src/main/resources/ce.properties b/biojava-structure/src/main/resources/ce.properties
index 769c77ac18..d3016afc3d 100644
--- a/biojava-structure/src/main/resources/ce.properties
+++ b/biojava-structure/src/main/resources/ce.properties
@@ -11,14 +11,14 @@ ce.about=<h1>Protein Structure Comparison Tool V ${project.version}</h1> \
       Prli&#263; A, Bliven S, Rose PW, Bluhm WF, Bizon C, Godzik A, Bourne PE.<br>\
       Pre-calculated protein structure alignments at the RCSB PDB website<br>\
       Bioinformatics (2010) 26 (23): 2983-2985<br>\
-      [<a href=\"http://www.ncbi.nlm.nih.gov/pubmed/20937596\">PubMed</a>]<\
+      [<a href=\"https://www.ncbi.nlm.nih.gov/pubmed/20937596\">PubMed</a>]<\
       [<a href=\"http://bioinformatics.oxfordjournals.org/content/26/23/2983.full.pdf\">pdf</a>]<br>\
       <hr>\
       <b>CE Reference:</b><br>\
       Shindyalov IN, Bourne PE (1998)<br>\
 	  Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.<br>\
       Protein Eng 11: 739-747<br>\
-	  [<a href="http://www.ncbi.nlm.nih.gov/pubmed/9796821">PubMed</a>]\
+	  [<a href="https://www.ncbi.nlm.nih.gov/pubmed/9796821">PubMed</a>]\
 	  [<a href="http://peds.oxfordjournals.org/cgi/reprint/11/9/739">pdf</a>]<br>\
 	  <hr>\
  	  <b>FATCAT Reference:</b><br>\
@@ -35,7 +35,7 @@ ce.about=<h1>Protein Structure Comparison Tool V ${project.version}</h1> \
       BioJava: an open-source framework for bioinformatics in 2012<br>\
       Bioinformatics (2012) 28 (20): 2693-2695<br>\
       [<a href=\"http://www.biojava.org\">BioJava website</a>]\
-      [<a href=\"http://www.ncbi.nlm.nih.gov/pubmed/22877863\">PubMed</a>]\
+      [<a href=\"https://www.ncbi.nlm.nih.gov/pubmed/22877863\">PubMed</a>]\
       <hr>\
       <b>Jmol web site:</b>\
       <a href=\"http://www.jmol.org\">http://www.jmol.org</a>\
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastAlignmentParameterEnum.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastAlignmentParameterEnum.java
index 4c70b8147f..061475071a 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastAlignmentParameterEnum.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastAlignmentParameterEnum.java
@@ -27,7 +27,7 @@
  * Alignment request parameters accepted by QBlast service.<br/>
  * Not all are mandatory. Certain parameters only work with a subset of other parameters in the list.
  * <p/>
- * Taken from <a href=http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node9.html>Blast URL API</a>
+ * Taken from <a href=https://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node9.html>Blast URL API</a>
  *
  * @author Gediminas Rimsa
  */
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputParameterEnum.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputParameterEnum.java
index d0dc973f38..dfa144864d 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputParameterEnum.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputParameterEnum.java
@@ -27,7 +27,7 @@
  * Output parameters accepted by QBlast service. <br/>
  * Not all are mandatory. Certain parameters only work with a subset of other parameters in the list.
  * <p/>
- * Taken from <a href=http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node9.html>Blast URL API</a>
+ * Taken from <a href=https://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node9.html>Blast URL API</a>
  *
  * @author Gediminas Rimsa
  */
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java
index 2e4c47cbdd..3d9ad05377 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java
@@ -208,7 +208,7 @@ public int getBlastWordSize() {
 	 * <b>WARNING!!</b> At this point, the method does not verify the validity of your choice; for example, word size of
 	 * greater than 5 with blastp returns error messages from QBlast. Word size range depends on the algorithm chosen.
 	 * <p>
-	 * More at http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node74.html
+	 * More at https://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node74.html
 	 * <p>
 	 * Blastall equivalent: -W
 	 *
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java
index 12538465bf..a57d0170dd 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java
@@ -64,9 +64,9 @@ public class NCBIQBlastService implements RemotePairwiseAlignmentService {
 	public static final long WAIT_INCREMENT = 3000;
 
 	private static final MapToStringTransformer MAP_TO_STRING_TRANSFORMER = new MapToStringTransformer();
-	private static final String SERVICE_URL = "http://blast.ncbi.nlm.nih.gov/Blast.cgi";
+	private static final String SERVICE_URL = "https://blast.ncbi.nlm.nih.gov/Blast.cgi";
 	private static final String DEFAULT_EMAIL = "anonymous@biojava.org";
-	private static final String DEFAULT_TOOL = "biojava3";
+	private static final String DEFAULT_TOOL = "biojava5";
 
 	private URL serviceUrl;
 	private String email = DEFAULT_EMAIL;
diff --git a/readme.md b/readme.md
index b9b4ce4b2c..986b3dec6a 100644
--- a/readme.md
+++ b/readme.md
@@ -72,4 +72,4 @@ This list is intended for more technical discussions about API design, bugs in g
 **BioJava: an open-source framework for bioinformatics in 2012**<br/>
 *Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L. Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis* <br/>
 [Bioinformatics (2012) 28 (20): 2693-2695.](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) <br/>
-[![doi](http://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbts494-blue.svg?style=flat)](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) [![pubmed](http://img.shields.io/badge/pubmed-22877863-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/22877863)
+[![doi](http://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbts494-blue.svg?style=flat)](http://bioinformatics.oxfordjournals.org/content/28/20/2693.abstract) [![pubmed](http://img.shields.io/badge/pubmed-22877863-blue.svg?style=flat)](https://www.ncbi.nlm.nih.gov/pubmed/22877863)

From 2785fdf14ec1e1961c8632510d5807bff547cb0e Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Wed, 13 Jul 2016 08:27:59 -0700
Subject: [PATCH 04/15] Fixing #533

---
 .../structure/io/mmcif/MMCIFFileTools.java    |   2 +-
 .../nbio/structure/io/TestMMCIFWriting.java   | 252 +++++++-----------
 2 files changed, 97 insertions(+), 157 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java
index e5ecbb2455..f483cb23d5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java
@@ -511,7 +511,7 @@ public static List<AtomSite> convertStructureToAtomSites(Structure s) {
 		List<AtomSite> list = new ArrayList<AtomSite>();
 
 		for (int m=0;m<s.nrModels();m++) {
-			for (Chain c:s.getChains()) {
+			for (Chain c:s.getChains(m)) {
 				list.addAll(convertChainToAtomSites(c, m+1, c.getChainID(), c.getInternalChainID()));
 			}
 		}
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMCIFWriting.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMCIFWriting.java
index 5fda97a2af..c500bba1c0 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMCIFWriting.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestMMCIFWriting.java
@@ -28,10 +28,12 @@
 import java.io.FileWriter;
 import java.io.IOException;
 
+import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Chain;
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
+import org.biojava.nbio.structure.StructureTools;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.mmcif.MMCIFFileTools;
 import org.biojava.nbio.structure.io.mmcif.MMcifParser;
@@ -45,59 +47,8 @@ public class TestMMCIFWriting {
 
 	@Test
 	public void test1SMT() throws IOException, StructureException {
-		AtomCache cache = new AtomCache();
-
-		StructureIO.setAtomCache(cache);
-
-		cache.setUseMmCif(true);
-
-		FileParsingParameters params = new FileParsingParameters();
-		params.setAlignSeqRes(true);
-		cache.setFileParsingParams(params);
-
-		Structure originalStruct = StructureIO.getStructure("1SMT");
-
-		File outputFile = File.createTempFile("biojava_testing_", ".cif");
-		outputFile.deleteOnExit();
-
-		FileWriter fw = new FileWriter(outputFile);
-		fw.write(originalStruct.toMMCIF());
-		fw.close();
-
-
-		MMcifParser parser = new SimpleMMcifParser();
-
-		SimpleMMcifConsumer consumer = new SimpleMMcifConsumer();
-
-		FileParsingParameters fileParsingParams = new FileParsingParameters();
-		fileParsingParams.setAlignSeqRes(true);
-
-		consumer.setFileParsingParameters(fileParsingParams);
-
-		parser.addMMcifConsumer(consumer);
-
-		//parser.parse(new BufferedReader(new FileReader(new File("/home/duarte_j/test.cif"))));
-		parser.parse(new BufferedReader(new FileReader(outputFile)));
-
-		Structure readStruct = consumer.getStructure();
-
-		assertNotNull(readStruct);
-
-		assertEquals(originalStruct.getChains().size(), readStruct.getChains().size());
-
-		for (int i=0;i<originalStruct.getChains().size();i++) {
-			assertEquals(originalStruct.getChains().get(i).getAtomGroups().size(),
-							readStruct.getChains().get(i).getAtomGroups().size());
-
-			Chain origChain = originalStruct.getChains().get(i);
-			Chain readChain = readStruct.getChains().get(i);
-
-			assertEquals(origChain.getAtomGroups().size(), readChain.getAtomGroups().size());
-			//assertEquals(origChain.getSeqResGroups().size(), readChain.getSeqResGroups().size());
-		}
-
-		// Test cell and symmetry
-		assertEquals(originalStruct.getCrystallographicInfo().getSpaceGroup(),readStruct.getCrystallographicInfo().getSpaceGroup());
+		// an x-ray structure
+		testRoundTrip("1SMT");
 	}
 
 	/**
@@ -107,71 +58,57 @@ public void test1SMT() throws IOException, StructureException {
 	 */
 	@Test
 	public void test2N3J() throws IOException, StructureException {
-		AtomCache cache = new AtomCache();
-
-		StructureIO.setAtomCache(cache);
-
-		cache.setUseMmCif(true);
-
-		FileParsingParameters params = new FileParsingParameters();
-		params.setAlignSeqRes(true);
-		cache.setFileParsingParams(params);
-
-		Structure originalStruct = StructureIO.getStructure("2N3J");
-
-		File outputFile = File.createTempFile("biojava_testing_", ".cif");
-		outputFile.deleteOnExit();
-
-
-		FileWriter fw = new FileWriter(outputFile);
-		fw.write(originalStruct.toMMCIF());
-		fw.close();
-
-
-		MMcifParser parser = new SimpleMMcifParser();
-
-		SimpleMMcifConsumer consumer = new SimpleMMcifConsumer();
-
-		FileParsingParameters fileParsingParams = new FileParsingParameters();
-		fileParsingParams.setAlignSeqRes(true);
-
-		consumer.setFileParsingParameters(fileParsingParams);
-
-		parser.addMMcifConsumer(consumer);
-
-		//parser.parse(new BufferedReader(new FileReader(new File("/home/duarte_j/test.cif"))));
-		parser.parse(new BufferedReader(new FileReader(outputFile)));
-
-		Structure readStruct = consumer.getStructure();
-
-		assertNotNull(readStruct);
-
-		assertEquals(originalStruct.getChains().size(), readStruct.getChains().size());
-
-		assertEquals(originalStruct.nrModels(), readStruct.nrModels());
+		// an NMR structure (multimodel) with 2 chains
+		testRoundTrip("2N3J");
+	}
+	
+	@Test
+	public void test1A2C() throws IOException, StructureException {
+		// a structure with insertion codes
+		testRoundTrip("1A2C");	
+	}
+	
+	private static class DemoBean {
+		@IgnoreField
+		String not_a_field;
+		
+		@SuppressWarnings("unused")//used by reflection
+		String default_field;
+		
+		@CIFLabel(label="custom_label")
+		String custom_field;
 
-		for (int i=0; i<originalStruct.nrModels();i++) {
-			assertEquals(originalStruct.getModel(i).size(), readStruct.getModel(i).size());
+		public void setNot_a_field(String not_a_field) {
+			this.not_a_field = not_a_field;
 		}
-
-		for (int i=0;i<originalStruct.getChains().size();i++) {
-			assertEquals(originalStruct.getChains().get(i).getAtomGroups().size(),
-							readStruct.getChains().get(i).getAtomGroups().size());
-
-			Chain origChain = originalStruct.getChains().get(i);
-			Chain readChain = readStruct.getChains().get(i);
-
-			assertEquals(origChain.getAtomGroups().size(), readChain.getAtomGroups().size());
-			//assertEquals(origChain.getSeqResGroups().size(), readChain.getSeqResGroups().size());
+		public void setDefault_field(String default_field) {
+			this.default_field = default_field;
+		}
+		public void setCustom_field(String custom_field) {
+			this.custom_field = custom_field;
 		}
-
 	}
-	
+
 	@Test
-	public void test1A2C() throws IOException, StructureException {
+	public void testBeanAnnotations() {
+		DemoBean bean = new DemoBean();
+		bean.setCustom_field("custom_field");
+		bean.setDefault_field(null);
+		bean.setNot_a_field("not_a_field");
 		
-		// a structure with insertion codes
 		
+		// Test (1) should have custom_label (@CIFLabel)
+		//      (2) shouldn't have not_a_field (@IgnoreField)
+		String newline = System.getProperty("line.separator");
+		String mmcif = MMCIFFileTools.toMMCIF("_demo", bean);
+		String expected = 
+				  "_demo.default_field   ?" + newline
+				+ "_demo.custom_label    custom_field" + newline
+				+ "#" + newline;
+		assertEquals(expected, mmcif);
+	}
+	
+	private static void testRoundTrip(String pdbId) throws IOException, StructureException {
 		AtomCache cache = new AtomCache();
 
 		StructureIO.setAtomCache(cache);
@@ -182,7 +119,7 @@ public void test1A2C() throws IOException, StructureException {
 		params.setAlignSeqRes(true);
 		cache.setFileParsingParams(params);
 
-		Structure originalStruct = StructureIO.getStructure("1A2C");
+		Structure originalStruct = StructureIO.getStructure(pdbId);
 
 		File outputFile = File.createTempFile("biojava_testing_", ".cif");
 		outputFile.deleteOnExit();
@@ -204,7 +141,6 @@ public void test1A2C() throws IOException, StructureException {
 
 		parser.addMMcifConsumer(consumer);
 
-		//parser.parse(new BufferedReader(new FileReader(new File("/home/duarte_j/test.cif"))));
 		parser.parse(new BufferedReader(new FileReader(outputFile)));
 
 		Structure readStruct = consumer.getStructure();
@@ -213,56 +149,60 @@ public void test1A2C() throws IOException, StructureException {
 
 		assertEquals(originalStruct.getChains().size(), readStruct.getChains().size());
 
-		for (int i=0;i<originalStruct.getChains().size();i++) {
-			assertEquals(originalStruct.getChains().get(i).getAtomGroups().size(),
-							readStruct.getChains().get(i).getAtomGroups().size());
-
-			Chain origChain = originalStruct.getChains().get(i);
-			Chain readChain = readStruct.getChains().get(i);
+		assertEquals(originalStruct.nrModels(), readStruct.nrModels());
 
-			assertEquals(origChain.getAtomGroups().size(), readChain.getAtomGroups().size());
-			//assertEquals(origChain.getSeqResGroups().size(), readChain.getSeqResGroups().size());
+		for (int i=0; i<originalStruct.nrModels();i++) {
+			assertEquals(originalStruct.getModel(i).size(), readStruct.getModel(i).size());
 		}
 
-	}
-	
-	private static class DemoBean {
-		@IgnoreField
-		String not_a_field;
 		
-		@SuppressWarnings("unused")//used by reflection
-		String default_field;
 		
-		@CIFLabel(label="custom_label")
-		String custom_field;
+		for (int modelIdx=0;modelIdx<originalStruct.nrModels();modelIdx++) {
+			
+			for (int i=0;i<originalStruct.getModel(modelIdx).size();i++) {
+				assertEquals(originalStruct.getChains().get(i).getAtomGroups().size(),
+								readStruct.getChains().get(i).getAtomGroups().size());
+
+				Chain origChain = originalStruct.getModel(modelIdx).get(i);
+				Chain readChain = readStruct.getModel(modelIdx).get(i);
+
+				assertEquals(origChain.getAtomGroups().size(), readChain.getAtomGroups().size());
+				//assertEquals(origChain.getSeqResGroups().size(), readChain.getSeqResGroups().size());
+				assertEquals(origChain.getChainID(), readChain.getChainID());
+				
+				Atom[] origAtoms = StructureTools.getAllAtomArray(origChain);
+				Atom[] readAtoms = StructureTools.getAllAtomArray(readChain);
+				
+				assertEquals(origAtoms.length, readAtoms.length);
+				
+				for (int atomIdx=0;atomIdx<origAtoms.length;atomIdx++) {
+					
+					assertEquals("atom serials don't match for atom "+origAtoms[atomIdx].toString(),
+							origAtoms[atomIdx].getPDBserial(), readAtoms[atomIdx].getPDBserial());
+					
+					assertEquals("atom names don't match for atom "+origAtoms[atomIdx].toString(),
+							origAtoms[atomIdx].getName(), readAtoms[atomIdx].getName());
+					
+					assertEquals("atom elements don't match for atom "+origAtoms[atomIdx].toString(),
+							origAtoms[atomIdx].getElement(), readAtoms[atomIdx].getElement());
+					
+					assertEquals("x values don't match for atom "+origAtoms[atomIdx].toString(),
+							origAtoms[atomIdx].getX(), readAtoms[atomIdx].getX(),0.0001);
+					
+					assertEquals("y values don't match for atom "+origAtoms[atomIdx].toString(),
+							origAtoms[atomIdx].getY(), readAtoms[atomIdx].getY(),0.0001);
+
+					assertEquals("z values don't match for atom "+origAtoms[atomIdx].toString(),
+							origAtoms[atomIdx].getZ(), readAtoms[atomIdx].getZ(),0.0001);
+				}
+			}
 
-		public void setNot_a_field(String not_a_field) {
-			this.not_a_field = not_a_field;
-		}
-		public void setDefault_field(String default_field) {
-			this.default_field = default_field;
-		}
-		public void setCustom_field(String custom_field) {
-			this.custom_field = custom_field;
 		}
-	}
 
-	@Test
-	public void testBeanAnnotations() {
-		DemoBean bean = new DemoBean();
-		bean.setCustom_field("custom_field");
-		bean.setDefault_field(null);
-		bean.setNot_a_field("not_a_field");
-		
-		
-		// Test (1) should have custom_label (@CIFLabel)
-		//      (2) shouldn't have not_a_field (@IgnoreField)
-		String newline = System.getProperty("line.separator");
-		String mmcif = MMCIFFileTools.toMMCIF("_demo", bean);
-		String expected = 
-				  "_demo.default_field   ?" + newline
-				+ "_demo.custom_label    custom_field" + newline
-				+ "#" + newline;
-		assertEquals(expected, mmcif);
+		// Test cell and symmetry
+		assertEquals(originalStruct.getCrystallographicInfo().getSpaceGroup(),
+				readStruct.getCrystallographicInfo().getSpaceGroup());
+
+
 	}
 }

From 234d0daa109c54e8c70549fd006c70d938bda174 Mon Sep 17 00:00:00 2001
From: Andreas Prlic <andreas.prlic@gmail.com>
Date: Wed, 27 Jul 2016 13:55:00 -0700
Subject: [PATCH 05/15] #542 changing default SCOP download location to
 Berkeley- SCOP.

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

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java
index 63cfae34d9..e144e8da85 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java
@@ -73,7 +73,7 @@ public class ScopInstallation implements LocalScopDatabase {
 	public static final String comFileName = "dir.com.scop.txt_";
 
 	// Download locations
-	public static final String SCOP_DOWNLOAD = "http://scop.mrc-lmb.cam.ac.uk/scop/parse/";
+	public static final String SCOP_DOWNLOAD = "http://scop.berkeley.edu/downloads/parse/";
 	public static final String SCOP_DOWNLOAD_ALTERNATE = "http://scop.berkeley.edu/downloads/parse/";
 
 	public static final String NEWLINE;

From 46b30b35f409f2b5b705190f523cf47542537a91 Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Wed, 27 Jul 2016 17:46:48 -0700
Subject: [PATCH 06/15] Back-porting cloning fix (see #541) into bugfixes-4.2

---
 .../biojava/nbio/structure/AminoAcidImpl.java |  4 +++
 .../biojava/nbio/structure/HetatomImpl.java   |  5 ++-
 .../nbio/structure/NucleotideImpl.java        | 33 +++----------------
 3 files changed, 12 insertions(+), 30 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/AminoAcidImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/AminoAcidImpl.java
index 5e20e9be4a..ab9c576210 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/AminoAcidImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/AminoAcidImpl.java
@@ -183,6 +183,10 @@ public Object clone() {
 				n.addAltLoc(nAltLocGroup);
 			}
 		}
+		
+		if (chemComp!=null)
+			n.setChemComp(chemComp);
+
 
 		return n;
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/HetatomImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/HetatomImpl.java
index 076bd86f0d..6039cb8f32 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/HetatomImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/HetatomImpl.java
@@ -88,7 +88,7 @@ public static enum PerformanceBehavior {
 
 	private Map<String,Atom> atomNameLookup;
 
-	private ChemComp chemComp ;
+	protected ChemComp chemComp ;
 
 	private List<Group> altLocs;
 
@@ -402,6 +402,9 @@ public Object clone() {
 				n.addAltLoc(nAltLocGroup);
 			}
 		}
+		
+		if (chemComp!=null)
+			n.setChemComp(chemComp);
 
 		return n;
 	}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/NucleotideImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/NucleotideImpl.java
index 1616de1ef0..7cc5a9400b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/NucleotideImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/NucleotideImpl.java
@@ -27,10 +27,9 @@
 
 
 /**
- *
- *  A nucleotide group is almost the same as a Hetatm group.
- *  @see HetatomImpl
- *  @see AminoAcidImpl
+ * A nucleotide group is almost the same as a Hetatm group.
+ * @see HetatomImpl
+ * @see AminoAcidImpl
  * @author Andreas Prlic
  * @since 1.4
  * @version %I% %G%
@@ -94,29 +93,5 @@ public Atom getP() {
 
 	}
 
-	@Override
-	public Object clone(){
-		NucleotideImpl n = new NucleotideImpl();
-
-		n.setPDBFlag(has3D());
-		n.setResidueNumber(getResidueNumber());
-
-		n.setPDBName(getPDBName());
-
-		// copy the atoms
-		for (Atom atom1 : atoms) {
-			Atom atom = (Atom) atom1.clone();
-			n.addAtom(atom);
-			atom.setGroup(n);
-		}
-
-		// copying the alt loc groups if present, otherwise they stay null
-		if (getAltLocs()!=null && !getAltLocs().isEmpty()) {
-			for (Group altLocGroup:this.getAltLocs()) {
-				Group nAltLocGroup = (Group)altLocGroup.clone();
-				n.addAltLoc(nAltLocGroup);
-			}
-		}
-		return n;
-	}
+	// no need to implement clone here, it's already in super class
 }

From 7453eeef5186630dfbbdf81774783a8942d922e2 Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Thu, 28 Jul 2016 10:26:26 -0700
Subject: [PATCH 07/15] Some work towards fixing #544

---
 .../nbio/structure/cath/CathFactory.java      |  3 +-
 .../nbio/structure/cath/CathInstallation.java | 40 +++++++++----------
 2 files changed, 22 insertions(+), 21 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathFactory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathFactory.java
index d80664affa..c84873b86d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathFactory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathFactory.java
@@ -37,7 +37,8 @@ public class CathFactory {
 
 	public static final String VERSION_3_5_0 = "3.5.0";
 	public static final String VERSION_4_0_0 = "4.0.0";
-	public static final String LATEST_VERSION = VERSION_4_0_0;
+	public static final String VERSION_4_1_0 = "4_1_0";
+	public static final String LATEST_VERSION = VERSION_4_1_0;
 
 	public static String DEFAULT_VERSION = LATEST_VERSION;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
index 77346f0cc6..52988fcc21 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
@@ -45,37 +45,37 @@ public class CathInstallation implements CathDatabase{
 
 	String cathVersion;
 
-	public static final String domainListFileName = "CathDomainList";
+	public static final String domainListFileName = "cath-domain-list-v4_1_0.txt";
 	public static final String domainDescriptionFileName = "CathDomainDescriptionFile";
 	public static final String nodeListFileName = "CathNames";
 	public static final String domallFileName = "CathDomall";
+	
+	//http://download.cathdb.info/cath/releases/latest-release/v4_1_0/cath-classification-data/cath-domain-list-v4_1_0.txt
 
-	public static final String CATH_DOWNLOAD = "http://release.cathdb.info/";
+	public static final String CATH_DOWNLOAD = "http://download.cathdb.info/cath/releases/latest-release/";
+	public static final String CATH_DOWNLOAD_SUFFIX = "cath-classification-data";
 
-	String cathDownloadUrl;
+	private String cathDownloadUrl;
 
-	public static final String NEWLINE;
-	public static final String FILESPLIT ;
+	public static final String NEWLINE = System.getProperty("line.separator");;
+	public static final String FILESPLIT = System.getProperty("file.separator");;
 
-	static {
-		NEWLINE     = System.getProperty("line.separator");
-		FILESPLIT   = System.getProperty("file.separator");
-	}
+	
 
 	private String cacheLocation ;
 
-	AtomicBoolean installedDomainList;
-	AtomicBoolean installedDomainDescription;
-	AtomicBoolean installedNodeList;
-	AtomicBoolean installedDomall;
+	private AtomicBoolean installedDomainList;
+	private AtomicBoolean installedDomainDescription;
+	private AtomicBoolean installedNodeList;
+	private AtomicBoolean installedDomall;
 
-	final boolean useCathDomainDescriptionFile;
-	final boolean parseCathFragments;
+	private final boolean useCathDomainDescriptionFile;
+	private final boolean parseCathFragments;
 
-	Map<String, List<CathDomain>> pdbMap;
-	Map<String, CathDomain> domainMap;
-	Map<String, CathNode> cathTree;
-	Map<String, List<CathFragment>> fragmentMap;
+	private Map<String, List<CathDomain>> pdbMap;
+	private Map<String, CathDomain> domainMap;
+	private Map<String, CathNode> cathTree;
+	private Map<String, List<CathFragment>> fragmentMap;
 
 
 
@@ -682,7 +682,7 @@ private boolean domallFileAvailable() {
 
 	protected void downloadDomainListFile() throws FileNotFoundException, IOException{
 		String remoteFilename = domainListFileName;
-		URL url = new URL(cathDownloadUrl + "v" + cathVersion + "/" + remoteFilename);
+		URL url = new URL(cathDownloadUrl + "v" + cathVersion + "/" + CATH_DOWNLOAD_SUFFIX + "/" + remoteFilename);
 		String localFileName = getDomainListFileName();
 		File localFile = new File(localFileName);
 		downloadFileFromRemote(url, localFile);

From a9db14880792be598f2a98ccfce3a31e791aafc4 Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Thu, 28 Jul 2016 11:29:26 -0700
Subject: [PATCH 08/15] Fixing #544 and improving logging

---
 .../nbio/structure/cath/CathFactory.java      |  6 +-
 .../nbio/structure/cath/CathInstallation.java | 84 +++++++++++--------
 2 files changed, 54 insertions(+), 36 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathFactory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathFactory.java
index c84873b86d..1b185fc01b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathFactory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathFactory.java
@@ -35,12 +35,12 @@
  */
 public class CathFactory {
 
-	public static final String VERSION_3_5_0 = "3.5.0";
-	public static final String VERSION_4_0_0 = "4.0.0";
+	public static final String VERSION_3_5_0 = "3_5_0";
+	public static final String VERSION_4_0_0 = "4_0_0";
 	public static final String VERSION_4_1_0 = "4_1_0";
 	public static final String LATEST_VERSION = VERSION_4_1_0;
 
-	public static String DEFAULT_VERSION = LATEST_VERSION;
+	public static final String DEFAULT_VERSION = LATEST_VERSION;
 
 	private static CathDatabase cath;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
index 52988fcc21..ff5db84d83 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
@@ -25,6 +25,8 @@
 
 import org.biojava.nbio.structure.align.util.UserConfiguration;
 import org.biojava.nbio.structure.io.util.FileDownloadUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.biojava.nbio.core.util.InputStreamProvider;
 
 import java.io.*;
@@ -41,27 +43,29 @@
  */
 public class CathInstallation implements CathDatabase{
 
+	private static final Logger LOGGER = LoggerFactory.getLogger(CathInstallation.class);
+	
 	public static final String DEFAULT_VERSION = CathFactory.DEFAULT_VERSION;
 
-	String cathVersion;
-
-	public static final String domainListFileName = "cath-domain-list-v4_1_0.txt";
+	public static final String domainListFileName = "cath-domain-list-v%s.txt";
+	// TODO I don't know what are the new file nams for domainDescriptionFileName and nodeListFileName in the new CATH 4.1.0 servers, must find out! - JD 2016-07-28 
 	public static final String domainDescriptionFileName = "CathDomainDescriptionFile";
 	public static final String nodeListFileName = "CathNames";
-	public static final String domallFileName = "CathDomall";
+	public static final String domallFileName = "cath-domain-boundaries-v%s.txt";
 	
-	//http://download.cathdb.info/cath/releases/latest-release/v4_1_0/cath-classification-data/cath-domain-list-v4_1_0.txt
-
-	public static final String CATH_DOWNLOAD = "http://download.cathdb.info/cath/releases/latest-release/";
-	public static final String CATH_DOWNLOAD_SUFFIX = "cath-classification-data";
-
-	private String cathDownloadUrl;
+	public static final String CATH_DOWNLOAD_URL                     = "http://download.cathdb.info/cath/releases/";
+	public static final String CATH_DOWNLOAD_LATEST_RELEASE_DIR      = "latest-release";
+	public static final String CATH_DOWNLOAD_PREV_RELEASE_DIR        = "previous-releases";
+	public static final String CATH_DOWNLOAD_CLASSIFICATION_DATA_DIR = "cath-classification-data";
 
 	public static final String NEWLINE = System.getProperty("line.separator");;
 	public static final String FILESPLIT = System.getProperty("file.separator");;
 
 	
+	private String cathVersion;
 
+	private String cathDownloadUrl;
+	
 	private String cacheLocation ;
 
 	private AtomicBoolean installedDomainList;
@@ -91,7 +95,7 @@ public CathInstallation(String cacheLocation, boolean usingCDDF, boolean parseCF
 		installedDomall = new AtomicBoolean(false);
 
 		cathVersion = DEFAULT_VERSION;
-		cathDownloadUrl = CATH_DOWNLOAD;
+		cathDownloadUrl = CATH_DOWNLOAD_URL;
 
 		pdbMap = new HashMap<String, List<CathDomain>>();
 		domainMap = new HashMap<String ,CathDomain>();
@@ -110,19 +114,32 @@ public CathInstallation() {
 	}
 
 	public String getDomainListFileName() {
-		return cacheLocation + domainListFileName + ".v" + cathVersion;
+		return cacheLocation + buildFileName(domainListFileName);
 	}
 
 	public String getDomainDescriptionFileName() {
-		return cacheLocation + domainDescriptionFileName + ".v" + cathVersion;
+		return cacheLocation + buildFileName(domainDescriptionFileName);
 	}
 
 	public String getNodeListFileName() {
-		return cacheLocation + nodeListFileName + ".v" + cathVersion;
+		return cacheLocation + buildFileName(nodeListFileName);
 	}
 
 	public String getDomallFileName() {
-		return cacheLocation + domallFileName + ".v" + cathVersion;
+		return cacheLocation + buildFileName(domallFileName);
+	}
+	
+	private String buildFileName(String fileNameTemplate) {
+		return String.format(fileNameTemplate, cathVersion);
+	}
+	
+	private String buildUrl(String remoteFileName) {
+		String remoteFileNameWithVer =  buildFileName(remoteFileName);
+		String releasesDir = CATH_DOWNLOAD_LATEST_RELEASE_DIR;
+		if (!cathVersion.equals(CathFactory.LATEST_VERSION)) {
+			releasesDir = CATH_DOWNLOAD_PREV_RELEASE_DIR;
+		}
+		return cathDownloadUrl + releasesDir + "/v" + cathVersion + "/" + CATH_DOWNLOAD_CLASSIFICATION_DATA_DIR + "/" + remoteFileNameWithVer;
 	}
 
 	public String getCathDownloadUrl() {
@@ -418,7 +435,7 @@ private void parseCathDomainDescriptionFile(BufferedReader bufferedReader) throw
 				try {
 					cathDescription.setDate( dateFormat.parse( line.substring(10) ) );
 				} catch (ParseException e) {
-					e.printStackTrace();
+					LOGGER.error(e.getMessage(), e);
 				}
 			} else if ( line.startsWith("NAME") ) {
 				name.append( line.substring(10) );
@@ -622,7 +639,7 @@ private void parseCathDomall(BufferedReader bufferedReader) throws IOException{
 		}
 	}
 
-	protected void downloadFileFromRemote(URL remoteURL, File localFile) throws FileNotFoundException, IOException{
+	protected void downloadFileFromRemote(URL remoteURL, File localFile) throws IOException{
 //        System.out.println("downloading " + remoteURL + " to: " + localFile);
 
 		long timeS = System.currentTimeMillis();
@@ -653,7 +670,7 @@ protected void downloadFileFromRemote(URL remoteURL, File localFile) throws File
 			disp = disp / 1024.0;
 		}
 		long timeE = System.currentTimeMillis();
-		System.out.println("downloaded " + String.format("%.1f",disp) + unit  + " in " + (timeE - timeS)/1000 + " sec.");
+		LOGGER.info("Downloaded file {} ({}) to local file {} in {} sec.", remoteURL, String.format("%.1f",disp) + unit, localFile, (timeE - timeS)/1000);
 	}
 
 	private boolean domainDescriptionFileAvailable(){
@@ -680,25 +697,25 @@ private boolean domallFileAvailable() {
 		return f.exists();
 	}
 
-	protected void downloadDomainListFile() throws FileNotFoundException, IOException{
+	protected void downloadDomainListFile() throws IOException{
 		String remoteFilename = domainListFileName;
-		URL url = new URL(cathDownloadUrl + "v" + cathVersion + "/" + CATH_DOWNLOAD_SUFFIX + "/" + remoteFilename);
+		URL url = new URL(buildUrl(remoteFilename)); 
 		String localFileName = getDomainListFileName();
 		File localFile = new File(localFileName);
 		downloadFileFromRemote(url, localFile);
 	}
 
-	protected void downloadDomainDescriptionFile() throws FileNotFoundException, IOException{
+	protected void downloadDomainDescriptionFile() throws IOException{
 		String remoteFilename = domainDescriptionFileName;
-		URL url = new URL(cathDownloadUrl + "v" + cathVersion + "/" + remoteFilename);
+		URL url = new URL(buildUrl(remoteFilename));
 		String localFileName = getDomainDescriptionFileName();
 		File localFile = new File(localFileName);
 		downloadFileFromRemote(url, localFile);
 	}
 
-	protected void downloadNodeListFile() throws FileNotFoundException, IOException{
+	protected void downloadNodeListFile() throws IOException{
 		String remoteFilename = nodeListFileName;
-		URL url = new URL(cathDownloadUrl + "v" + cathVersion + "/" + remoteFilename);
+		URL url = new URL(buildUrl(remoteFilename));
 		String localFileName = getNodeListFileName();
 		File localFile = new File(localFileName);
 		downloadFileFromRemote(url, localFile);
@@ -706,7 +723,7 @@ protected void downloadNodeListFile() throws FileNotFoundException, IOException{
 
 	protected void downloadDomallFile() throws IOException {
 		String remoteFileName = domallFileName;
-		URL url = new URL(cathDownloadUrl + "v" + cathVersion + "/" + remoteFileName);
+		URL url = new URL(buildUrl(remoteFileName));
 		String localFileName = getDomallFileName();
 		File localFile = new File(localFileName);
 		downloadFileFromRemote(url, localFile);
@@ -719,7 +736,7 @@ public void ensureDomainListInstalled(){
 			try {
 				downloadDomainListFile();
 			} catch (Exception e){
-				e.printStackTrace();
+				LOGGER.error("Could not download CATH domain list file. Error: {}", e.getMessage());
 				installedDomainList.set(false);
 				return;
 			}
@@ -728,7 +745,7 @@ public void ensureDomainListInstalled(){
 		try {
 			parseCathDomainList();
 		} catch (Exception e){
-			e.printStackTrace();
+			LOGGER.error(e.getMessage(), e);
 			installedDomainList.set(false);
 			return;
 		}
@@ -742,7 +759,7 @@ public void ensureDomainDescriptionInstalled(){
 			try {
 				downloadDomainDescriptionFile();
 			} catch (Exception e){
-				e.printStackTrace();
+				LOGGER.error("Could not download CATH domain description file. Error: {}", e.getMessage());
 				installedDomainDescription.set(false);
 				return;
 			}
@@ -751,7 +768,7 @@ public void ensureDomainDescriptionInstalled(){
 		try {
 			parseCathDomainDescriptionFile();
 		} catch (Exception e){
-			e.printStackTrace();
+			LOGGER.error(e.getMessage(), e);
 			installedDomainDescription.set(false);
 			return;
 		}
@@ -765,7 +782,7 @@ public void ensureNodeListInstalled(){
 			try {
 				downloadNodeListFile();
 			} catch (Exception e){
-				e.printStackTrace();
+				LOGGER.error("Could not download CATH node list file. Error: {}", e.getMessage());
 				installedNodeList.set(false);
 				return;
 			}
@@ -774,7 +791,7 @@ public void ensureNodeListInstalled(){
 		try {
 			parseCathNames();
 		} catch (Exception e){
-			e.printStackTrace();
+			LOGGER.error(e.getMessage(), e);
 			installedNodeList.set(false);
 			return;
 		}
@@ -795,7 +812,7 @@ public void ensureDomallInstalled() {
 			try {
 				downloadDomallFile();
 			} catch (Exception e) {
-				e.printStackTrace();
+				LOGGER.error("Could not download CATH domain all file. Error: {}", e.getMessage());
 				installedDomall.set(false);
 				return;
 			}
@@ -804,7 +821,7 @@ public void ensureDomallInstalled() {
 		try {
 			parseCathDomall();
 		} catch (Exception e) {
-			e.printStackTrace();
+			LOGGER.error(e.getMessage(), e);
 			installedDomall.set(false);
 			return;
 		}
@@ -814,5 +831,6 @@ public void ensureDomallInstalled() {
 	public void setCathVersion(String cathVersion) {
 		this.cathVersion = cathVersion;
 	}
+	
 
 }

From 3bc719af6196b6e9a32938f69cfa162a662e8044 Mon Sep 17 00:00:00 2001
From: lafita <aleixlafita@gmail.com>
Date: Fri, 29 Jul 2016 10:33:33 +0200
Subject: [PATCH 09/15] Complete new CATH file names #546 and #544

CathNames and CathDomainDescriptionFile
---
 .../org/biojava/nbio/structure/cath/CathInstallation.java  | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
index ff5db84d83..41ae6b014f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
@@ -47,10 +47,9 @@ public class CathInstallation implements CathDatabase{
 	
 	public static final String DEFAULT_VERSION = CathFactory.DEFAULT_VERSION;
 
-	public static final String domainListFileName = "cath-domain-list-v%s.txt";
-	// TODO I don't know what are the new file nams for domainDescriptionFileName and nodeListFileName in the new CATH 4.1.0 servers, must find out! - JD 2016-07-28 
-	public static final String domainDescriptionFileName = "CathDomainDescriptionFile";
-	public static final String nodeListFileName = "CathNames";
+	public static final String domainListFileName = "cath-domain-list-v%s.txt"; 
+	public static final String domainDescriptionFileName = "cath-domain-description-file-v%s.txt";
+	public static final String nodeListFileName = "cath-names-v%s.txt";
 	public static final String domallFileName = "cath-domain-boundaries-v%s.txt";
 	
 	public static final String CATH_DOWNLOAD_URL                     = "http://download.cathdb.info/cath/releases/";

From bceab293eb75df4dbbb8157f16c08891de1ae827 Mon Sep 17 00:00:00 2001
From: Andreas Prlic <andreas.prlic@gmail.com>
Date: Fri, 29 Jul 2016 10:37:32 -0700
Subject: [PATCH 10/15] Adding test for genome mapping

---
 .../nbio/genome/TestGenomeMapping.java        | 151 ++++++++++++++++++
 1 file changed, 151 insertions(+)
 create mode 100644 biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java

diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java
new file mode 100644
index 0000000000..b4615b9db2
--- /dev/null
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java
@@ -0,0 +1,151 @@
+package org.biojava.nbio.genome;
+
+import com.google.common.collect.Lists;
+import com.google.common.collect.Range;
+import junit.framework.TestCase;
+import org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition;
+import org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser;
+import org.biojava.nbio.genome.util.ChromosomeMappingTools;
+import org.junit.Test;
+
+import java.io.InputStream;
+import java.net.URL;
+import java.util.List;
+import java.util.zip.GZIPInputStream;
+
+/**
+ * Created by andreas on 7/19/16.
+ */
+public class TestGenomeMapping extends TestCase{
+
+    private static final String geneChromosomeFile = "http://cdn.rcsb.org/gene/hg38/geneChromosome38.tsf.gz";
+
+    private List<GeneChromosomePosition> gcps = null;
+
+    @Override
+    protected void setUp() throws Exception {
+        super.setUp();
+        InputStream input = new GZIPInputStream(new URL(geneChromosomeFile).openStream());
+        gcps = GeneChromosomePositionParser.getChromosomeMappings(input);
+
+
+    }
+
+
+    @Test
+    public void testAK1() {
+        String geneName = "AK1";
+
+        assertNotNull(gcps);
+        assertTrue("Problems with downloading refFlat file from UCSC browser ", gcps.size() > 100);
+
+        int uniProtLength = 194;
+
+        try {
+
+            for (GeneChromosomePosition pos : gcps) {
+
+                //System.out.println(pos.getGeneName());
+                if (!pos.getGeneName().equals(geneName))
+                    continue;
+
+                /// there are three alternative transcripts for AK1.
+                // we are just testing one here:
+
+                if ( ! pos.getGenebankId().equals("NM_000476"))
+                    continue;
+
+                assertTrue(pos.getGeneName().equals(geneName));
+                assertTrue(pos.getOrientation().equals('-'));
+                assertTrue(pos.getChromosome().equals("chr9"));
+
+                List<Range<Integer>> cdsranges = ChromosomeMappingTools.getCDSExonRanges(pos);
+
+                validateExon(0,0,7, cdsranges  );
+                validateExon(1,7,43, cdsranges  );
+                validateExon(2,43,207, cdsranges  );
+                validateExon(3,207,324, cdsranges  );
+                validateExon(4,324,516, cdsranges  );
+                validateExon(5,516,585, cdsranges  );
+
+
+                int cdslength = ChromosomeMappingTools.getCDSLength(pos);
+
+                assertTrue("CDS length should be 582, but is " + cdslength, cdslength == (uniProtLength *3));
+
+                List<Range<Integer>> chromranges = ChromosomeMappingTools.getChromosomalRangesForCDS(pos);
+
+                // we are reverse strand. reverse the order
+                chromranges = Lists.reverse(chromranges);
+
+                assertTrue(chromranges.size() == 6);
+
+                // compare with https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=CCDS6881
+                validateExon(0,127868008,127868076, chromranges  );
+                validateExon(1,127868320,127868512, chromranges  );
+                validateExon(2,127871822,127871939, chromranges  );
+                validateExon(3,127872689,127872853, chromranges  );
+                validateExon(4,127873025,127873061, chromranges  );
+                validateExon(5,127874610,127874617, chromranges  );
+
+            }
+        } catch (Exception e) {
+            fail(e.getMessage());
+        }
+    }
+
+    @Test
+    public void testHBA(){
+
+        String geneName = "HBA1";
+        assertNotNull(gcps);
+
+        assertTrue("Problems with downloading refFlat file from UCSC browser ", gcps.size() > 100);
+
+        try {
+
+            for ( GeneChromosomePosition pos : gcps){
+
+                //System.out.println(pos.getGeneName());
+                if ( ! pos.getGeneName().equals(geneName))
+                    continue;
+
+                assertTrue(pos.getGeneName().equals("HBA1"));
+                assertTrue(pos.getGenebankId().equals("NM_000558"));
+                assertTrue(pos.getChromosome().equals("chr16"));
+                assertTrue(pos.getTranscriptionStart().equals(176650));
+                assertTrue(pos.getTranscriptionEnd().equals(177522));
+                assertTrue(pos.getOrientation().equals('+'));
+
+                List<Range<Integer>> cdsranges = ChromosomeMappingTools.getCDSExonRanges(pos);
+
+                assertTrue(cdsranges.size() == 3);
+
+                validateExon(0,0,95,cdsranges);
+                validateExon(1,95,300,cdsranges);
+                validateExon(2,300,429,cdsranges);
+
+
+                List<Range<Integer>> chromranges = ChromosomeMappingTools.getChromosomalRangesForCDS(pos);
+
+                validateExon(0,176716,176811, chromranges  );
+                validateExon(1,176928,177133, chromranges  );
+                validateExon(2,177282,177411, chromranges  );
+
+
+            }
+        } catch (Exception e){
+            fail(e.getMessage());
+        }
+
+
+    }
+
+    private void validateExon(int exonNr, int start, int stop, List<Range<Integer>> cdsranges) {
+
+        Range exon = cdsranges.get(exonNr);
+        assertTrue("Exon " + exonNr + " boundary "+ exon.lowerEndpoint()  + " does not match " +start , exon.lowerEndpoint().equals(start));
+        assertTrue("Exon " + exonNr + " boundary " + exon.upperEndpoint() + " does not match " + stop, exon.upperEndpoint().equals(stop));
+
+    }
+}

From f2f4143c8adc9057f893c086337d5444e633c3f2 Mon Sep 17 00:00:00 2001
From: Andreas Prlic <andreas.prlic@gmail.com>
Date: Fri, 29 Jul 2016 10:38:44 -0700
Subject: [PATCH 11/15] new utility class for chromosome mappings.

---
 .../biojava/nbio/genome/util/ChromosomeMappingTools.java   | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java

diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java
new file mode 100644
index 0000000000..41eea76808
--- /dev/null
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java
@@ -0,0 +1,7 @@
+package org.biojava.nbio.genome.util;
+
+/**
+ * Created by andreas on 7/29/16.
+ */
+public class ChromosomeMappingTools {
+}

From 04b8f4a4ac8ef4cf5f2fd0d29f2764d27d66b1b3 Mon Sep 17 00:00:00 2001
From: Andreas Prlic <andreas.prlic@gmail.com>
Date: Fri, 29 Jul 2016 10:39:24 -0700
Subject: [PATCH 12/15] new utility class for chromosome mappings.

---
 .../genome/util/ChromosomeMappingTools.java   | 1230 ++++++++++++++++-
 1 file changed, 1229 insertions(+), 1 deletion(-)

diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java
index 41eea76808..07ace5278b 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/ChromosomeMappingTools.java
@@ -1,7 +1,1235 @@
 package org.biojava.nbio.genome.util;
 
+import com.google.common.collect.Range;
+
+import org.biojava.nbio.genome.parsers.genename.ChromPos;
+import org.biojava.nbio.genome.parsers.genename.GeneChromosomePosition;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+
+import java.io.StringWriter;
+import java.util.ArrayList;
+import java.util.List;
+
 /**
- * Created by andreas on 7/29/16.
+ *  A class that take care of the painful mapping
  */
 public class ChromosomeMappingTools {
+
+    private static final Logger logger = LoggerFactory.getLogger(ChromosomeMappingTools.class);
+
+
+    private static final String newline = System.getProperty("line.separator");
+
+
+    public static final String CHROMOSOME = "CHROMOSOME";
+    public static final String CDS = "CDS";
+
+
+    /** Pretty print the details of a GeneChromosomePosition to a String
+     *
+     * @param chromosomePosition
+     * @return
+     */
+    public static String formatExonStructure(GeneChromosomePosition chromosomePosition ){
+        if ( chromosomePosition.getOrientation() == '+')
+            return formatExonStructureForward(chromosomePosition);
+
+        return formatExonStructureReverse(chromosomePosition);
+
+    }
+
+
+    private static String formatExonStructureForward(GeneChromosomePosition chromPos) {
+
+        StringWriter s = new StringWriter();
+
+        List<Integer> exonStarts = chromPos.getExonStarts();
+        List<Integer> exonEnds   = chromPos.getExonEnds();
+
+        int cdsStart = chromPos.getCdsStart();
+        int cdsEnd   = chromPos.getCdsEnd();
+
+        boolean inCoding = false;
+        int codingLength = 0;
+
+        for (int i = 0; i < exonStarts.size(); i++) {
+
+            int start = exonStarts.get(i);
+            int end = exonEnds.get(i);
+
+            if (start <= cdsStart +1 && end >= cdsStart+1) {
+
+                inCoding = true;
+                codingLength += (end - cdsStart);
+                s.append("     UTR         : ").append(format(start)).append(" - ").append(format(cdsStart));
+                s.append(newline);
+                s.append(" ->  Exon        : ").append(format(cdsStart + 1)).append(" - ").append(format(end)).append(" | ").append(Integer.toString(end - cdsStart)).append(" | ").append(Integer.toString(codingLength)).append(" | ").append(Integer.toString(codingLength % 3));
+                s.append(newline);
+
+            } else if (start <= cdsEnd && end >= cdsEnd) {
+                //logger.debug(" <-- CDS end at: " + cdsEnd );
+                inCoding = false;
+                codingLength += (cdsEnd - start);
+
+                s.append(" <-  Exon        : ").append(format(start + 1)).append(" - ").append(format(cdsEnd)).append(" | ").append(Integer.toString(cdsEnd - start)).append(" | ").append(Integer.toString(codingLength)).append(" | ").append(Integer.toString(codingLength % 3));
+                s.append(newline);
+                s.append("     UTR         : " + (cdsEnd +1) + " - " + format(end));
+                s.append(newline);
+
+
+            } else if (inCoding) {
+                // full exon is coding
+                codingLength += (end - start);
+
+                s.append("     Exon        : ").append(format(start + 1)).append(" - ").append(format(end)).append(" | ").append(Integer.toString(end - start)).append(" | ").append(Integer.toString(codingLength)).append(" | ").append(Integer.toString(codingLength % 3));
+                s.append(newline);
+            }
+
+        }
+        s.append("Coding Length: ");
+        s.append((codingLength-3)+"");
+        s.append(newline);
+        return s.toString();
+    }
+
+
+
+    private static String showGenePosLink(GeneChromosomePosition chromPos, Integer pos ) {
+
+        String spos = format(pos);
+
+        StringBuffer buf = new StringBuffer();
+        buf.append("<a href=\"/pdb/gene/");
+        buf.append(chromPos.getGeneName());
+        buf.append("?chromosome=");
+        buf.append(chromPos.getChromosome());
+        buf.append("&range=");
+        buf.append(pos);
+        buf.append("\">");
+        buf.append(spos);
+        buf.append("</a>");
+
+        return buf.toString();
+    }
+
+
+    private static String formatExonStructureReverse(GeneChromosomePosition chromPos) {
+        StringWriter s = new StringWriter();
+
+        List<Integer> exonStarts = chromPos.getExonStarts();
+        List<Integer> exonEnds   = chromPos.getExonEnds();
+
+
+        int cdsStart = chromPos.getCdsStart();
+        int cdsEnd   = chromPos.getCdsEnd();
+
+        // logger.debug("CDS START:" +format(cdsStart) + " - " + format(cdsEnd));
+
+        boolean inCoding = false;
+        int codingLength = 0;
+
+        if (cdsEnd < cdsStart) {
+            int tmp = cdsEnd;
+            cdsEnd = cdsStart;
+            cdsStart = tmp;
+        }
+
+        // map reverse
+        for (int i = exonStarts.size() - 1; i >= 0; i--) {
+
+            int end = exonStarts.get(i);
+            int start = exonEnds.get(i);
+
+            if (end < start) {
+                int tmp = end;
+                end = start;
+                start = tmp;
+            }
+
+            if (start <= cdsEnd && end >= cdsEnd) {
+                inCoding = true;
+
+                int tmpstart = start;
+                if (start < cdsStart) {
+                    tmpstart = cdsStart;
+                }
+                codingLength += (cdsEnd - tmpstart);
+
+                s.append("     UTR         :" + format(cdsEnd + 1) + " | " + format(end));
+                s.append(newline);
+                if (tmpstart == start)
+                    s.append(" ->  ");
+                else
+                    s.append(" <-> ");
+                s.append("Exon        :").append(format(tmpstart + 1)).append(" - ").append(format(cdsEnd)).append(" | ").append(Integer.toString(cdsEnd - tmpstart)).append(" | ").append(Integer.toString(codingLength)).append(" | ").append(Integer.toString(codingLength % 3));
+                s.append(newline);
+                // single exon with UTR on both ends
+                if (tmpstart != start)
+                    s.append("     UTR         :" + format(cdsStart ) + " - " + format(start + 1));
+                s.append(newline);
+
+            } else if (start <= cdsStart && end >= cdsStart) {
+                inCoding = false;
+                codingLength += (end - cdsStart);
+
+                s.append(" <-  Exon        : " + format(cdsStart+1) + " - " + format(end) + " | " + (end - cdsStart) + " | " + codingLength + " | " + (codingLength % 3));
+                s.append(newline);
+                s.append("     UTR         : " + format(start+1) + " - " + format(cdsStart ));
+                s.append(newline);
+
+
+            } else if (inCoding) {
+                // full exon is coding
+                codingLength += (end - start);
+
+                s.append("     Exon        : " + format(start+1) + " - " + format(end) + " | " + (end - start) + " | " + codingLength + " | " + (codingLength % 3));
+                s.append(newline);
+            } else {
+                // e.g. see UBQLN3
+                s.append(" no translation! UTR: ").append(format(start)).append(" - ").append(format(end));
+                s.append(newline);
+            }
+        }
+
+        s.append("CDS length: ").append(Integer.toString(codingLength - 3));
+        s.append(newline);
+
+        return s.toString();
+    }
+
+    /**
+     * Get the length of the CDS in nucleotides.
+     *
+     * @param chromPos
+     * @return length of the CDS in nucleotides.
+     */
+    public static int getCDSLength(GeneChromosomePosition chromPos) {
+
+        logger.debug(chromPos.toString());
+
+        logger.debug("chromosomal information: ");
+
+        logger.debug("Gene:" + chromPos.getGeneName());
+        logger.debug("  Transcription (including UTRs): " + chromPos.getTranscriptionStart() + " - " + chromPos.getTranscriptionEnd() + " (length:" + (chromPos.getTranscriptionEnd() - chromPos.getTranscriptionStart()) + ")");
+        logger.debug("  Orientation: " + chromPos.getOrientation());
+        logger.debug("  CDS: " + (chromPos.getCdsStart()) + " - " + chromPos.getCdsEnd() + " (length: " + (chromPos.getCdsEnd() - chromPos.getCdsStart()) + ")");
+
+
+        List<Integer> exonStarts = chromPos.getExonStarts();
+        List<Integer> exonEnds = chromPos.getExonEnds();
+
+        logger.debug("Exons:" + exonStarts.size());
+
+        int cdsStart = chromPos.getCdsStart();
+        int cdsEnd = chromPos.getCdsEnd();
+
+
+        int codingLength;
+        if (chromPos.getOrientation().equals('+'))
+            codingLength = ChromosomeMappingTools.getCDSLengthForward(exonStarts, exonEnds, cdsStart, cdsEnd);
+        else
+            codingLength = ChromosomeMappingTools.getCDSLengthReverse(exonStarts, exonEnds, cdsStart, cdsEnd);
+        return codingLength;
+    }
+
+
+    /**
+     * maps the position of a CDS nucleotide back to the genome
+     *
+     * @param cdsNucleotidePosition
+     * @return a ChromPos object
+     */
+    public static ChromPos getChromosomePosForCDScoordinate(int cdsNucleotidePosition, GeneChromosomePosition chromPos) {
+
+        logger.debug(" ? Checking chromosome position for CDS position " + cdsNucleotidePosition);
+
+        List<Integer> exonStarts = chromPos.getExonStarts();
+        List<Integer> exonEnds = chromPos.getExonEnds();
+
+        logger.debug(" Exons:" + exonStarts.size());
+
+        int cdsStart = chromPos.getCdsStart();
+        int cdsEnd = chromPos.getCdsEnd();
+
+
+        ChromPos chromosomePos = null;
+
+        if (chromPos.getOrientation().equals('+'))
+
+            chromosomePos = ChromosomeMappingTools.getChromPosForward(cdsNucleotidePosition, exonStarts, exonEnds, cdsStart, cdsEnd);
+        else
+            chromosomePos = ChromosomeMappingTools.getChromPosReverse(cdsNucleotidePosition, exonStarts, exonEnds, cdsStart, cdsEnd);
+
+        logger.debug("=> CDS pos " + cdsNucleotidePosition + " for " + chromPos.getGeneName() + " is on chromosome at  " + chromosomePos);
+        return chromosomePos;
+
+    }
+
+    /** returns a nicely formatted representation of the position
+     *
+     * @param chromosomePosition
+     * @return
+     */
+    private static String format(int chromosomePosition){
+
+
+        return String.format("%,d", chromosomePosition);
+    }
+
+    /**
+     * Get the CDS position mapped on the chromosome position
+     *
+     * @param exonStarts
+     * @param exonEnds
+     * @param cdsStart
+     * @param cdsEnd
+     * @return
+     */
+    public static ChromPos getChromPosReverse(int cdsPos, List<Integer> exonStarts,
+                                              List<Integer> exonEnds, int cdsStart, int cdsEnd) {
+
+        boolean inCoding = false;
+        int codingLength = 0;
+
+        if (cdsEnd < cdsStart) {
+            int tmp = cdsEnd;
+            cdsEnd = cdsStart;
+            cdsStart = tmp;
+        }
+
+        int lengthExons = 0;
+
+        // map reverse
+        for (int i = exonStarts.size() - 1; i >= 0; i--) {
+
+            logger.debug("Exon #" + (i+1) + "/" + exonStarts.size());
+            int end = exonStarts.get(i);
+            int start = exonEnds.get(i);
+
+            if (end < start) {
+                int tmp = end;
+                end = start;
+                start = tmp;
+            }
+            lengthExons += end - start;
+
+            logger.debug("     is " + cdsPos + " part of Reverse exon? " + format(start+1) + " - " + format(end) + " | " + (end - start+1));
+            logger.debug("     CDS start: " + format(cdsStart+1) + "-" + format(cdsEnd) + " coding length counter:" + codingLength);
+
+            if (start+1 <= cdsEnd && end >= cdsEnd) {
+
+
+                // FIRST EXON
+                inCoding = true;
+
+
+                int tmpstart = start;
+                if (start < cdsStart) {
+                    tmpstart = cdsStart;
+                }
+
+                // here one of the few places where we don't say start+1
+                int check = codingLength + cdsEnd - tmpstart ;
+
+                logger.debug("First Exon    | " + (check) + " | " + format(start+1) + " " + format(end) + " | " + (cdsEnd - tmpstart) + " | " + cdsPos );
+
+
+                if ( ( check > cdsPos)  )
+                {
+
+                    int tmp = cdsPos - codingLength ;
+
+
+                    logger.debug(" -> found position in UTR exon:  " + format(cdsPos) + " " + format(tmpstart+1) + " tmp:" + format(tmp) + " cs:" + format(cdsStart+1) + " ce:" + format(cdsEnd) + " cl:" + codingLength);
+
+                    return new ChromPos((cdsEnd - tmp), -1) ;
+                }
+
+
+                // don't add 1 here
+                codingLength += (cdsEnd - tmpstart );
+
+                boolean debug = logger.isDebugEnabled();
+
+
+                if ( debug ) {
+
+                    StringBuffer b = new StringBuffer();
+
+                    b.append("     UTR         :" + format(cdsEnd + 1) + " - " + format(end) + newline);
+                    if (tmpstart == start)
+                        b.append(" ->  ");
+                    else
+                        b.append(" <-> ");
+                    b.append("Exon        :" + format(tmpstart + 1) + " - " + (cdsEnd) + " | " + format(cdsEnd - tmpstart + 1) + " - " + codingLength + " | " + (codingLength % 3) + newline);
+
+                    // single exon with UTR on both ends
+                    if (tmpstart != start)
+                        b.append("     UTR         :" + format(cdsStart) + " - " + format(start + 1) + newline);
+
+                    logger.debug(b.toString());
+                }
+            } else if (start <= cdsStart && end >= cdsStart) {
+
+                // LAST EXON
+                inCoding = false;
+
+                if (codingLength + end - cdsStart >= cdsPos) {
+
+                    // how many remaining coding nucleotides?
+                    int tmp = codingLength + end - cdsStart - cdsPos ;
+
+                    logger.debug("cdl: " +codingLength + " tmp:" + tmp + " cdsStart: " + format(cdsStart));
+
+                    logger.debug(" -> XXX found position noncoding exon:  cdsPos:" + cdsPos + " s:" + format(start + 1) + " tmp:" + format(tmp) + " cdsStart:" + (cdsStart + 1) + " codingLength:" + codingLength + " cdsEnd:" + format(cdsEnd));
+
+                    return new ChromPos((cdsStart + tmp),-1);
+                }
+
+                codingLength += (end - cdsStart);
+
+                logger.debug(" <-  Exon        : " + format(cdsStart+1) + " - " + format(end) + " | " + format(end - cdsStart+1) + " | " + codingLength + " | " + (codingLength % 3));
+                logger.debug("     UTR         : " + format(start+1) + " - " + format(cdsStart ));
+
+            } else if (inCoding) {
+
+
+                if (codingLength + end - start -1  >= cdsPos) {
+
+                    int tmp = cdsPos - codingLength ;
+
+                    if ( tmp > (end - start ) ) {
+
+                        tmp = (end - start );
+
+                        logger.debug("changing tmp to " + tmp);
+
+                    }
+
+                    logger.debug("     " + cdsPos + " " + codingLength + " | " + (cdsPos - codingLength) + " | " + (end -start) + " | " + tmp);
+                    logger.debug("     Exon        : " + format(start+1) + " - " + format(end) + " | " + format(end - start) + " | " + codingLength + " | " + (codingLength % 3));
+                    logger.debug(" ->  RRR found position coding exon:  " + cdsPos + " " + format(start+1) + " " + format(end) + " " + tmp + " " + format(cdsStart+1) + " " + codingLength);
+
+                    return new ChromPos((end - tmp),cdsPos %3);
+                }
+
+                // full exon is coding
+                codingLength += (end - start) ;
+
+                logger.debug("     Exon        : " + format(start+1) + " - " + format(end) + " | " + format(end - start+1) + " | " + codingLength + " | " + (codingLength % 3));
+            } else {
+                // e.g. see UBQLN3
+
+                logger.debug(" no translation!");
+            }
+
+
+            logger.debug("     coding length: " + codingLength + "(phase:" + (codingLength % 3) + ") CDS POS trying to map:" + cdsPos);
+
+
+        }
+
+        logger.debug("length exons: " + lengthExons);
+        // could not map, or map over the full length??
+        return new ChromPos(-1,-1);
+
+
+    }
+
+    /**
+     * Get the CDS position mapped onto the chromosome position
+     *
+     * @param exonStarts
+     * @param exonEnds
+     * @param cdsStart
+     * @param cdsEnd
+     * @return
+     */
+    public static ChromPos getChromPosForward(int cdsPos, List<Integer> exonStarts, List<Integer> exonEnds,
+                                              int cdsStart, int cdsEnd) {
+        boolean inCoding = false;
+        int codingLength = 0;
+
+        int lengthExons = 0;
+        // map forward
+        for (int i = 0; i < exonStarts.size(); i++) {
+
+
+            // start can include UTR
+            int start = exonStarts.get(i);
+            int end = exonEnds.get(i);
+
+            lengthExons += end - start;
+
+
+            if (start <= cdsStart +1 && end >= cdsStart+1) {
+                // first exon with UTR
+                if (codingLength + (end - cdsStart-1) >= cdsPos) {
+                    // we are reaching our target position
+                    int tmp = cdsPos - codingLength;
+
+
+                    logger.debug(cdsStart + " | " + codingLength + " | " + tmp);
+                    logger.debug(" -> found position in UTR exon:  #"+(i+1)+ " cdsPos:" + cdsPos +
+                            " return:"+(cdsStart +1 + tmp) +" start:" + format(start + 1) + " " + format(tmp) + " " + cdsStart + " " + codingLength);
+
+                    // we start 1 after cdsStart...
+                    return new ChromPos((cdsStart +1 + tmp),-1);
+                }
+                inCoding = true;
+                codingLength += (end - cdsStart);
+
+                logger.debug("     UTR         : " + format(start+1) + " - " + (cdsStart ));
+                logger.debug(" ->  Exon        : " + format(cdsStart+1) + " - " + format(end) + " | " + format(end - cdsStart) + " | " + codingLength + " | " + (codingLength % 3));
+
+            } else if (start+1 <= cdsEnd && end >= cdsEnd) {
+                // LAST EXON with UTR
+                //logger.debug(" <-- CDS end at: " + cdsEnd );
+                inCoding = false;
+                if (codingLength + (cdsEnd - start-1) >= cdsPos) {
+                    int tmp = cdsPos - codingLength;
+
+
+                    logger.debug(" <-  Exon        : " + format(start+1) + " - " + format(cdsEnd) + " | " + format(cdsEnd - start) + " | " + codingLength + " | " + (codingLength % 3));
+                    logger.debug("     UTR         : " + format(cdsEnd + 1) + " - " + format(end));
+                    logger.debug( codingLength + " | " + tmp + " | " + format(start+1));
+                    logger.debug(" -> chromPosForward found position in non coding exon:  " + cdsPos + " " + format(start+1) + " " + format(tmp) + " " + format(cdsStart) + " " + codingLength);
+
+                    return new ChromPos((start +1 + tmp),cdsPos%3);
+                }
+                codingLength += (cdsEnd - start-1);
+
+                logger.debug(" <-  Exon        : " + format(start+1) + " - " + format(cdsEnd) + " | " + format(cdsEnd - start) + " | " + codingLength + " | " + (codingLength % 3));
+                logger.debug("     UTR         : " + format(cdsEnd + 1) + " - " + format(end));
+
+
+            } else if (inCoding) {
+                // A standard coding Exon
+                // tests for the maximum length of this coding exon
+                if (codingLength + (end - start -1)  >= cdsPos) {
+
+                    // we are within the range of this exon
+                    int tmp = cdsPos - codingLength ;
+
+
+                    logger.debug("     Exon        : " + format(start+1) + " - " + format(end) + " | " + format(end - start) + " | " + tmp + " | " + codingLength);
+                    logger.debug(" -> found chr position in coding exon #" + (i+1) + ":  cdsPos:" + format(cdsPos) + " s:" + format(start) + "-" + format(end) + " tmp:" + format(tmp) + " cdsStart:" + format(cdsStart) + " codingLength:" + codingLength);
+
+                    return new ChromPos((start +1 + tmp),cdsPos%3);
+                }
+                // full exon is coding
+                codingLength += (end - start );
+
+                logger.debug("     Exon        : " + format(start+1) + " - " + format(end) + " | " + format(end - start) + " | " + codingLength + " | " + (codingLength % 3));
+            }
+            //			if ( inCoding )
+            //				logger.debug("exon phase at end:" + (codingLength % 3));
+            //
+            //			logger.debug("   coding length: " + codingLength);
+
+
+        }
+
+        //logger.debug("length exons: " + lengthExons);
+        //return codingLength - 3;
+
+        // could not map!
+
+        return new ChromPos(-1,-1);
+    }
+
+
+    /**
+     * Get the length of the coding sequence
+     *
+     * @param exonStarts
+     * @param exonEnds
+     * @param cdsStart
+     * @param cdsEnd
+     * @return
+     */
+    public static int getCDSLengthReverse(List<Integer> exonStarts,
+                                          List<Integer> exonEnds, int cdsStart, int cdsEnd) {
+
+        boolean inCoding = false;
+        int codingLength = 0;
+
+        if (cdsEnd < cdsStart) {
+            int tmp = cdsEnd;
+            cdsEnd = cdsStart;
+            cdsStart = tmp;
+        }
+
+        int lengthExons = 0;
+
+        // map reverse
+        for (int i = exonStarts.size() - 1; i >= 0; i--) {
+
+            int end = exonStarts.get(i);
+            int start = exonEnds.get(i);
+
+            if (end < start) {
+                int tmp = end;
+                end = start;
+                start = tmp;
+            }
+            lengthExons += end - start;
+
+            if (start <= cdsEnd && end >= cdsEnd) {
+                inCoding = true;
+
+
+                int tmpstart = start;
+                if (start < cdsStart) {
+                    tmpstart = cdsStart;
+                }
+                codingLength += (cdsEnd - tmpstart);
+
+                boolean debug = logger.isDebugEnabled();
+
+                if ( debug) {
+
+                    StringBuffer b = new StringBuffer();
+
+                    b.append("     UTR         :" + (cdsEnd + 1) + " - " + (end) + newline);
+                    if (tmpstart == start)
+                        b.append(" ->  ");
+                    else
+                        b.append(" <-> ");
+                    b.append("Exon        :" + tmpstart + " - " + cdsEnd + " | " + (cdsEnd - tmpstart) + " | " + codingLength + " | " + (codingLength % 3) + newline);
+                    // single exon with UTR on both ends
+                    if (tmpstart != start)
+                        b.append("     UTR         :" + (cdsStart - 1) + " - " + start  + newline);
+                    logger.debug(b.toString());
+
+                }
+            } else if (start <= cdsStart && end >= cdsStart) {
+                inCoding = false;
+                codingLength += (end - cdsStart);
+
+
+                logger.debug(" <-  Exon        : " + (cdsStart+1) + " - " + end + " | " + (end - cdsStart) + " | " + (codingLength-3)  + " | " + (codingLength % 3));
+                logger.debug("     UTR         : " + start + " - " + (cdsStart ));
+
+
+
+            } else if (inCoding) {
+                // full exon is coding
+                codingLength += (end - start);
+
+                logger.debug("     Exon        : " + start + " - " + end + " | " + (end - start) + " | " + codingLength + " | " + (codingLength % 3));
+            } else {
+                // e.g. see UBQLN3
+
+                logger.debug(" no translation!");
+            }
+
+        }
+
+        logger.debug("length exons: " + lengthExons + " codin length: " + (codingLength - 3));
+        return codingLength - 3;
+    }
+
+    /**
+     * Get the length of the coding sequence
+     *
+     * @param exonStarts
+     * @param exonEnds
+     * @param cdsStart
+     * @param cdsEnd
+     * @return
+     */
+    public static int getCDSLengthForward(List<Integer> exonStarts, List<Integer> exonEnds,
+                                          int cdsStart, int cdsEnd) {
+        boolean inCoding = false;
+        int codingLength = 0;
+
+        int lengthExons = 0;
+        // map forward
+        for (int i = 0; i < exonStarts.size(); i++) {
+
+            int start = exonStarts.get(i);
+            int end = exonEnds.get(i);
+            lengthExons += end - start;
+
+
+            logger.debug("forward exon: " + (start+1) + " - " + end + " | " + (end - start));
+
+            if (start+1 <= cdsStart +1 && end >= cdsStart+1) {
+
+                inCoding = true;
+                codingLength += (end - cdsStart);
+
+                logger.debug("     UTR         : " + start + " - " + (cdsStart ));
+                logger.debug(" ->  Exon        : " + (cdsStart+1) + " - " + end + " | " + (end - cdsStart+1) + " | " + codingLength + " | " + (codingLength % 3));
+
+            } else if (start+1 <= cdsEnd && end >= cdsEnd) {
+
+                inCoding = false;
+                codingLength += (cdsEnd - start);
+
+                logger.debug(" <-  Exon        : " + (start +1)+ " - " + cdsEnd + " | " + (cdsEnd - start+1) + " | " + codingLength + " | " + (codingLength % 3));
+                logger.debug("     UTR         : " + cdsEnd + 1 + " - " + end);
+
+
+            } else if (inCoding) {
+                // full exon is coding
+                codingLength += (end - start);
+
+                logger.debug("     Exon        :" + (start+1) + " - " + end + " | " + (end - start+1) + " | " + codingLength + " | " + (codingLength % 3));
+            }
+
+
+        }
+
+        logger.debug("length exons: " + Integer.toString(lengthExons));
+        logger.debug("CDS length:" + Integer.toString((codingLength-3)));
+
+        return codingLength-3 ;
+    }
+
+
+
+    /** Extracts the exon boundaries in CDS coordinates. (needs to be divided by 3 to get AA positions)
+     *
+     * @param chromPos
+     * @return
+     */
+    public static List<Range<Integer>> getCDSExonRanges(GeneChromosomePosition chromPos){
+        if ( chromPos.getOrientation() == '+')
+
+            return getCDSExonRangesForward(chromPos,CDS);
+
+        return getCDSExonRangesReverse(chromPos,CDS);
+    }
+
+
+    /** Extracts the boundaries of the coding regions in chromosomal coordinates
+     *
+     * @param chromPos
+     * @return
+     */
+    public static List<Range<Integer>> getChromosomalRangesForCDS(GeneChromosomePosition chromPos){
+        if ( chromPos.getOrientation() == '+')
+            return getCDSExonRangesForward(chromPos,CHROMOSOME);
+
+        return getCDSExonRangesReverse(chromPos,CHROMOSOME);
+    }
+
+    private static List<Range<Integer>> getCDSExonRangesReverse(GeneChromosomePosition chromPos,
+                                                                String responseType) {
+
+        List<Integer> exonStarts = chromPos.getExonStarts();
+        List<Integer> exonEnds   = chromPos.getExonEnds();
+
+        List<Range<Integer>> data = new ArrayList<>();
+        int cdsStart = chromPos.getCdsStart();
+        int cdsEnd   = chromPos.getCdsEnd();
+
+        boolean inCoding = false;
+        int codingLength = 0;
+
+        if (cdsEnd < cdsStart) {
+            int tmp = cdsEnd;
+            cdsEnd = cdsStart;
+            cdsStart = tmp;
+        }
+
+        java.lang.StringBuffer s =null;
+
+        boolean debug = logger.isDebugEnabled();
+
+
+        if ( debug)
+            s = new StringBuffer();
+
+        int lengthExons = 0;
+
+        // map reverse
+        for (int i = exonStarts.size() - 1; i >= 0; i--) {
+
+            int end = exonStarts.get(i);
+            int start = exonEnds.get(i);
+
+            if (end < start) {
+                int tmp = end;
+                end = start;
+                start = tmp;
+            }
+            lengthExons += end - start;
+            //s.append("Reverse exon: " + end + " - " + start + " | " + (end - start));
+            //s.append(newline);
+
+            if (start <= cdsEnd && end >= cdsEnd) {
+                inCoding = true;
+
+
+                int tmpstart = start;
+                if (start < cdsStart) {
+                    tmpstart = cdsStart;
+                }
+                codingLength += (cdsEnd - tmpstart);
+                if ( debug ) {
+                    s.append("     UTR         :").append(format(cdsEnd + 1)).append(" | ").append(format(end));
+                    s.append(newline);
+                    if (tmpstart == start)
+                        s.append(" ->  ");
+                    else
+                        s.append(" <-> ");
+                    s.append("Exon        :").append(format(tmpstart + 1)).append(" - ").append(format(cdsEnd)).append(" | ").append(cdsEnd - tmpstart).append(" | ").append(codingLength).append(" | ").append(codingLength % 3);
+                    s.append(newline);
+                    // single exon with UTR on both ends
+                    if (tmpstart != start)
+                        s.append("     UTR         :").append(format(cdsStart)).append(" - ").append(format(start + 1));
+                    s.append(newline);
+                }
+
+
+                Range r ;
+                if ( responseType.equals(CDS))
+                    r = Range.closed(0,codingLength);
+                else
+                    r = Range.closed(tmpstart,cdsEnd);
+
+                data.add(r);
+
+            } else if (start <= cdsStart && end >= cdsStart) {
+                inCoding = false;
+
+                Range r;
+                if ( responseType.equals(CDS))
+                    r = Range.closed(codingLength,codingLength+(end-cdsStart));
+                else
+                    r = Range.closed(cdsStart+1,end);
+
+                data.add(r);
+
+                codingLength += (end - cdsStart);
+                if  (debug) {
+                    s.append(" <-  Exon        : " + format(cdsStart + 1) + " - " + format(end) + " | " + (end - cdsStart) + " | " + codingLength + " | " + (codingLength % 3));
+                    s.append(newline);
+                    s.append("     UTR         : ").append(format(start + 1)).append(" - ").append(format(cdsStart));
+                    s.append(newline);
+                }
+
+
+            } else if (inCoding) {
+                // full exon is coding
+
+                Range r;
+                if ( responseType.equals(CDS))
+                    r = Range.closed(codingLength,codingLength+(end-start));
+                else
+                    r = Range.closed(start,end);
+                data.add(r);
+
+                codingLength += (end - start);
+                if  (debug) {
+                    s.append("     Exon        : " + format(start + 1) + " - " + format(end) + " | " + (end - start) + " | " + codingLength + " | " + (codingLength % 3));
+                    s.append(newline);
+                }
+            } else {
+                // e.g. see UBQLN3
+                if ( debug ) {
+                    s.append(" no translation! UTR: " + format(start) + " - " + format(end));
+                    s.append(newline);
+                }
+            }
+        }
+        if ( debug ) {
+            s.append("CDS length: ").append(Integer.toString(codingLength - 3));
+            s.append(newline);
+            logger.debug(s.toString());
+        }
+
+        return data;
+    }
+
+
+
+    private static List<Range<Integer>> getCDSExonRangesForward(GeneChromosomePosition chromPos,
+                                                                String responseType) {
+
+        List<Range<Integer>> data = new ArrayList<>();
+        List<Integer> exonStarts = chromPos.getExonStarts();
+        List<Integer> exonEnds   = chromPos.getExonEnds();
+
+
+        int cdsStart = chromPos.getCdsStart();
+        int cdsEnd   = chromPos.getCdsEnd();
+
+        boolean inCoding = false;
+        int codingLength = 0;
+
+        for (int i = 0; i < exonStarts.size(); i++) {
+
+            int start = exonStarts.get(i);
+            int end = exonEnds.get(i);
+
+            if (start <= cdsStart && end >= cdsStart) {
+
+                inCoding = true;
+                codingLength += (end - cdsStart);
+//
+
+
+                Range r;
+                if ( responseType.equals(CDS))
+                    r = Range.closed(0,codingLength);
+                else
+                    r = Range.closed(cdsStart,end);
+                data.add(r);
+
+            } else if (start <= cdsEnd && end >= cdsEnd) {
+                //logger.debug(" <-- CDS end at: " + cdsEnd );
+                inCoding = false;
+
+
+                Range r;
+                if ( responseType.equals(CDS))
+                    r = Range.closed(codingLength,codingLength+(cdsEnd-start));
+                else
+                    r = Range.closed(start,cdsEnd);
+                data.add(r);
+                codingLength += (cdsEnd - start);
+
+            } else if (inCoding) {
+                // full exon is coding
+
+                Range r;
+                if ( responseType.equals(CDS))
+                    r = Range.closed(codingLength,codingLength+(end-start));
+                else
+                    r = Range.closed(start,end);
+                data.add(r);
+                codingLength += (end - start);
+
+            }
+
+        }
+
+        return data;
+    }
+//
+
+    /**
+     * I have a genomic coordinate, where is it in the Gene?
+     *
+     * @param coordinate
+     * @param chromosomePosition
+     * @return
+     */
+    public static int getCDSPosForChromosomeCoordinate(int coordinate, GeneChromosomePosition chromosomePosition) {
+
+        if ( chromosomePosition.getOrientation() == '+')
+            return getCDSPosForward(coordinate,
+                    chromosomePosition.getExonStarts(),
+                    chromosomePosition.getExonEnds(),
+                    chromosomePosition.getCdsStart(),
+                    chromosomePosition.getCdsEnd());
+
+        return getCDSPosReverse(coordinate,
+                chromosomePosition.getExonStarts(),
+                chromosomePosition.getExonEnds(),
+                chromosomePosition.getCdsStart(),
+                chromosomePosition.getCdsEnd());
+
+    }
+
+
+    public static int getCDSPosReverse(int chromPos, List<Integer> exonStarts, List<Integer> exonEnds,
+                                       int cdsStart, int cdsEnd) {
+        boolean inCoding = false;
+        int codingLength = 0;
+
+        if (cdsEnd < cdsStart) {
+            int tmp = cdsEnd;
+            cdsEnd = cdsStart;
+            cdsStart = tmp;
+        }
+
+        logger.debug("looking for CDS position for " +format(chromPos));
+
+
+        if ( chromPos <  cdsStart+1 ) {
+            // this is not in a coding region!
+
+            logger.debug(chromPos + " < " + cdsStart+1 );
+            return -1;
+        }
+
+        if ( chromPos >  cdsEnd+1 ) {
+            // this is not in a coding region!
+
+            logger.debug(chromPos + " > " + cdsEnd+1 );
+            return -1;
+        }
+
+        int lengthExons = 0;
+
+        // map reverse
+        for (int i = exonStarts.size() - 1; i >= 0; i--) {
+
+            logger.debug("Reverse Exon #" + (i+1) + "/" + exonStarts.size());
+            int end = exonStarts.get(i);
+            int start = exonEnds.get(i);
+
+            if (end < start) {
+                int tmp = end;
+                end = start;
+                start = tmp;
+            }
+            lengthExons += end - start;
+
+
+            logger.debug("     is " + format(chromPos) + " part of Reverse exon? s:" + format(start+1) + " - e:" + format(end) + " | " + (end - start+1));
+            logger.debug("     CDS start: " + format(cdsStart+1) + "-" + format(cdsEnd) + " coding length counter:" + codingLength);
+
+
+
+            if (start+1 <= cdsEnd && end >= cdsEnd ) {
+
+                // first exon with UTR
+
+                inCoding = true;
+
+                int tmpstart = start;
+                if (start < cdsStart) {
+                    tmpstart = cdsStart;
+                }
+
+
+                logger.debug(" --- codingLength " + codingLength +
+                        " s:" +
+                        format(tmpstart+1) +
+                        " e:" +
+                        format(cdsEnd) +
+                        " p:" +
+                        format(chromPos) + " tmp: " + (chromPos - cdsStart));
+
+                logger.debug("check: " + (codingLength + cdsEnd - tmpstart+1) + " ==?? " + format(chromPos));
+
+                int tmp = cdsEnd - chromPos ;
+                // if (codingLength + cdsEnd - tmpstart >= chromPos) {
+                //if (end >= chromPos && start + (end-start) >= chromPos) {
+                // if (codingLength + cdsEnd - tmpstart >= chromPos) {
+                if ( chromPos >= start +1 && chromPos <= end){
+
+
+                    logger.debug(" -> found position in UTR exon:  P: " + format(chromPos) + " s:" + format(tmpstart+1) + " l:" + format(tmp) + " cdsS:" + format(cdsStart+1) + " cdsE:" + format(cdsEnd)  + " codingL:" + codingLength);
+                    return codingLength + tmp;
+                }
+
+
+                logger.debug("     codinglength " + codingLength + " + " + (cdsEnd - tmpstart ) );
+
+                // do not add 1 here
+                codingLength += (cdsEnd - tmpstart );
+
+                boolean debug = logger.isDebugEnabled();
+
+                if (debug) {
+                    StringBuffer b = new StringBuffer();
+                    b.append("     UTR         :" + format(cdsEnd + 1) + " - " + format(end) + newline);
+                    if (tmpstart == start)
+                        b.append(" ->  ");
+                    else
+                        b.append(" <-> ");
+                    b.append("Reverse Exon        :" + format(tmpstart+1) + " - " + (cdsEnd) + " | " + format(cdsEnd - tmpstart) + " - " + codingLength + " | " + (codingLength % 3) + newline);
+
+                    logger.debug(b.toString());
+
+                    // single exon with UTR on both ends
+                    if (tmpstart != start)
+                        logger.debug("     UTR         :" + format(cdsStart - 1) + " - " + format(start));
+                }
+            } else if (start <= cdsStart && end >= cdsStart) {
+
+                // terminal exon with UTR
+                inCoding = false;
+
+
+                logger.debug(format(start  + codingLength + end - cdsStart) + " ?? " + format(chromPos));
+                // (start  + codingLength + end - cdsStart >= chromPos &&
+                if (( start+1 <= chromPos) && ( end >= chromPos)) {
+
+                    //int tmp =  end - cdsStart ;
+//                    int tmp =  chromPos - cdsStart ;
+//                    int l = end - cdsStart;
+                    int tmp = end-chromPos ;
+                    if  ( tmp > end -cdsStart) {
+                        tmp = end-cdsStart ;
+
+                        logger.debug("Adjust tmp to " + tmp);
+                    }
+
+
+
+                    logger.debug(  codingLength + " | " + (end -chromPos) + " | " + (end - cdsStart) );
+                    logger.debug(" <-  Exon        : " + format(cdsStart) + " - " + format(end) + " | " + format(end - cdsStart +1) + " | ");
+                    logger.debug("     UTR         : " + format(start+1) + " - " + format(cdsStart ));
+                    logger.debug(" <- YYY found position noncoding exon:  #" + (i+1) + " "  + format(chromPos) + " s:" + format(start) + " tmp: " + format(tmp) + " cdsStart" + format(cdsStart) + " cdl:" + codingLength + " " + format(cdsEnd));
+
+                    return codingLength + tmp;
+                }
+
+
+                logger.debug("     codinglength " + codingLength + " + " + (end - cdsStart) );
+                codingLength += (end - cdsStart+1);
+
+                logger.debug(" <-  Exon        : " + format(cdsStart+1) + " - " + format(end) + " | " + format(end - cdsStart) + " | " + codingLength + " | " + (codingLength % 3));
+                logger.debug("     UTR         : " + format(start+1) + " - " + format(cdsStart ));
+
+            } else if (inCoding) {
+                // standard coding exon
+                // if (codingLength + end - start >= chromPos) {
+                if ( chromPos >= start+1 && chromPos <= end) {
+
+                    int tmp = end -chromPos  ;
+                    if ( tmp > (end-start+1)) {
+
+                        tmp = (end - start+1);
+
+                        logger.debug("Adjusting tmp to " + tmp);
+                    }
+
+
+                    logger.debug(" -> found position in reverse coding exon:  #" + (i+1) + " chromPos:"  + format(chromPos) + " start:" + format(start+1) + " end:" + format(end) + " tmp:" + tmp + " cdsStart:" + cdsStart + " codingLength:" + codingLength);
+
+                    return codingLength+tmp;
+                }
+
+                // full exon is coding
+
+                logger.debug("     codinglength " + codingLength + " + " + (end - start) );
+                // don't add 1
+                codingLength += (end - start);
+
+                logger.debug("     Exon        : " + format(start+1) + " - " + format(end) + " | " + format(end - start) + " | " + codingLength + " | " + (codingLength % 3));
+            } else {
+                // e.g. see UBQLN3
+
+                logger.debug(" no translation! cdl:" + codingLength);
+
+            }
+
+            //if ( inCoding )
+            //	logger.debug("     exon phase at end:" + ((codingLength) % 3));
+
+            logger.debug("     coding length: " + codingLength + "(phase:" + (codingLength % 3) + ") CDS POS trying to map:" + chromPos);
+
+
+        }
+
+        logger.debug("length exons: " + lengthExons);
+        // could not map, or map over the full length??
+
+
+        return -1;
+
+    }
+
+    /**
+     * Get the chromosome position mapped onto the mrna CDS transcript position (needs to be divided by 3 to get protein coordinate)
+     *
+     * @param exonStarts
+     * @param exonEnds
+     * @param cdsStart
+     * @param cdsEnd
+     * @return
+     */
+    public static int getCDSPosForward(int chromPos, List<Integer> exonStarts, List<Integer> exonEnds,
+                                       int cdsStart, int cdsEnd) {
+        boolean inCoding = false;
+        int codingLength = 0;
+
+
+        logger.debug("looking for CDS position for " +chromPos);
+
+        int lengthExons = 0;
+        // map forward
+        for (int i = 0; i < exonStarts.size(); i++) {
+
+
+            // start can include UTR
+            int start = exonStarts.get(i);
+            int end = exonEnds.get(i);
+
+            lengthExons += end - start;
+
+
+            logger.debug("forward exon: " + (start+1) + " - " + end + " | " + (end - start) + " ? overlaps with " + format(chromPos));
+
+            if (start +1 <= cdsStart +1 && end >= cdsStart+1) {
+
+                if (end >= chromPos) {
+                    // we are reaching our target position
+                    // -1 is important  here...
+                    int tmp = chromPos - cdsStart -1;
+
+
+                    logger.debug("cdl:" + codingLength + " | " + tmp);
+                    logger.debug(" -> found position in UTR exon:  " + chromPos + " " + format(start) + " " + format(tmp) + " " + cdsStart + " " + codingLength);
+
+                    return codingLength + tmp;
+                }
+                inCoding = true;
+                codingLength += (end - cdsStart);
+
+                logger.debug("     UTR         : " + format(start) + " - " + (cdsStart ));
+                logger.debug(" ->  Exon        : " + format(cdsStart+1) + " - " + format(end) + " | " + format(end - cdsStart) + " | " + codingLength + " | " + (codingLength % 3));
+
+            } else if (start <= cdsEnd && end >= cdsEnd) {
+                //logger.debug(" <-- CDS end at: " + cdsEnd );
+                inCoding = false;
+                if (cdsEnd >= chromPos && (start +1 <= chromPos)) {
+                    int tmp =  chromPos - start -1 ;
+
+
+                    logger.debug(" -> cdsForward found position in non coding exon#"+i+":  " + chromPos + " " + format(start+1) + " " + format(tmp) + " " + cdsStart   + " " + codingLength);
+                    return codingLength + tmp ;
+                }
+                codingLength += (cdsEnd - start);
+
+                logger.debug(" <-  Exon        : " + format(start+1) + " - " + format(cdsEnd) + " | " + format(cdsEnd - start+1) + " | " + codingLength + " | " + (codingLength % 3));
+                logger.debug("     UTR         : " + format(cdsEnd + 1) + " - " + format(end));
+
+
+            } else if (inCoding) {
+
+                if (end >= chromPos && (start +1 <=chromPos)) {
+
+                    int tmp = chromPos-start-1 ;
+
+
+                    logger.debug(codingLength + " | " + tmp);
+                    logger.debug(" -> found position in coding exon #" + (i + 1) + ":  " + format(chromPos) + " " + format(start + 1) + " " + format(tmp) + " " + cdsStart + " " + codingLength);
+
+
+                    return codingLength + tmp ;
+                }
+                // full exon is coding
+                codingLength += (end - start);
+
+                logger.debug("     Exon        :" + format(start) + " - " + format(end) + " | " + format(end - start) + " | " + codingLength + " | " + (codingLength % 3));
+            }
+            //			if ( inCoding )
+            //				logger.debug("exon phase at end:" + (codingLength % 3));
+            //
+            //			logger.debug("   coding length: " + codingLength);
+
+
+        }
+
+        //logger.debug("length exons: " + lengthExons);
+        //return codingLength - 3;
+
+        // could not map!
+
+        return -1;
+    }
+
+
 }

From f63309dbba32add3f05425f684239b87df57e940 Mon Sep 17 00:00:00 2001
From: Andreas Prlic <andreas.prlic@gmail.com>
Date: Fri, 29 Jul 2016 10:40:09 -0700
Subject: [PATCH 13/15] adding new dependency on guava

---
 biojava-genome/pom.xml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index 0e28a54a0c..bed7db065a 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -71,6 +71,12 @@
 		</plugins>
 	</build>
 	<dependencies>
+		<dependency>
+			<groupId>com.google.guava</groupId>
+			<artifactId>guava</artifactId>
+			<scope>compile</scope>
+			<version>19.0</version>
+		</dependency>
 		<dependency>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>

From 795be8f04e461e7f4f9f67399567b27dfa7b153b Mon Sep 17 00:00:00 2001
From: Andreas Prlic <andreas.prlic@gmail.com>
Date: Fri, 29 Jul 2016 10:41:48 -0700
Subject: [PATCH 14/15] new utility class for chromosome mappings.

---
 .../genome/parsers/genename/ChromPos.java     | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/ChromPos.java

diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/ChromPos.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/ChromPos.java
new file mode 100644
index 0000000000..3d343d2f1a
--- /dev/null
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/ChromPos.java
@@ -0,0 +1,31 @@
+package org.biojava.nbio.genome.parsers.genename;
+
+/**
+ * Created by ap3 on 27/10/2014.
+ */
+public class ChromPos {
+
+    int pos;
+    int phase;
+
+    public int getPhase() {
+        return phase;
+    }
+
+    public void setPhase(int phase) {
+        this.phase = phase;
+    }
+
+    public int getPos() {
+        return pos;
+    }
+
+    public void setPos(int pos) {
+        this.pos = pos;
+    }
+
+    public ChromPos(int pos, int phase){
+        this.pos = pos;
+        this.phase = phase;
+    }
+}
\ No newline at end of file

From 79f57d7bd97d0001f82659c2046662b5c1fb02c0 Mon Sep 17 00:00:00 2001
From: Jenkins <jenkins@java-jenkins-research.rcsb.org>
Date: Fri, 29 Jul 2016 15:07:20 -0700
Subject: [PATCH 15/15] [maven-release-plugin]prepare release biojava-4.2.4

---
 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 d90dc1eb47..d20dfbb6ce 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>4.2.4-SNAPSHOT</version>
+		<version>4.2.4</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.4-SNAPSHOT</version>
+			<version>4.2.4</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>4.2.4-SNAPSHOT</version>
+			<version>4.2.4</version>
 		</dependency>
 
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index aaced0081d..f6dae05256 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.4-SNAPSHOT</version>
+		<version>4.2.4</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -46,7 +46,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.4-SNAPSHOT</version>
+			<version>4.2.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
@@ -74,7 +74,7 @@
   		<dependency>
   			<groupId>org.biojava</groupId>
   			<artifactId>biojava-phylo</artifactId>
-  			<version>4.2.4-SNAPSHOT</version>
+  			<version>4.2.4</version>
   		</dependency>
 	</dependencies>
 </project>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 4f5a46cd4d..38b1f1ba0c 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.4-SNAPSHOT</version>
+		<version>4.2.4</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index bed7db065a..bb8d08147c 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.4-SNAPSHOT</version>
+		<version>4.2.4</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>4.2.4-SNAPSHOT</version>
+			<version>4.2.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.4-SNAPSHOT</version>
+			<version>4.2.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index 6d7ba3da65..c10746a76e 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.4-SNAPSHOT</version>
+    <version>4.2.4</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -32,7 +32,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.4-SNAPSHOT</version>
+    	<version>4.2.4</version>
     </dependency>
 		<!-- logging dependencies (managed by parent pom, don't set versions or scopes here) -->
 		<dependency>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
index f1bbd65ebe..4551514d9a 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.4-SNAPSHOT</version>
+    <version>4.2.4</version>
   </parent>
   <artifactId>biojava-modfinder</artifactId>
   <name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.4-SNAPSHOT</version>
+    	<version>4.2.4</version>
     	<type>jar</type>
     	<scope>compile</scope>
     </dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index fb3a6da2ae..8e0ccad72f 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>4.2.4-SNAPSHOT</version>
+    <version>4.2.4</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml
index 1f1d09fe5b..e7758ae1ec 100644
--- a/biojava-phylo/pom.xml
+++ b/biojava-phylo/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.4-SNAPSHOT</version>
+    <version>4.2.4</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>4.2.4-SNAPSHOT</version>
+      <version>4.2.4</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 89c120b49b..535e7095ff 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>4.2.4-SNAPSHOT</version>
+		<version>4.2.4</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.4-SNAPSHOT</version>
+			<version>4.2.4</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 264a0798b6..461bddf663 100644
--- a/biojava-sequencing/pom.xml
+++ b/biojava-sequencing/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.4-SNAPSHOT</version>
+		<version>4.2.4</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>4.2.4-SNAPSHOT</version>
+			<version>4.2.4</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 bb24a570b1..df3eb75ffe 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>4.2.4-SNAPSHOT</version>
+        <version>4.2.4</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>4.2.4-SNAPSHOT</version>
+            <version>4.2.4</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-            <version>4.2.4-SNAPSHOT</version>
+            <version>4.2.4</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index d50222d410..c59b4e1068 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.4-SNAPSHOT</version>
+		<version>4.2.4</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -22,13 +22,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.4-SNAPSHOT</version>
+			<version>4.2.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.4-SNAPSHOT</version>
+			<version>4.2.4</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index cd01b059cc..5c87ef8b70 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>4.2.4-SNAPSHOT</version>
+        <version>4.2.4</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index ee902d9504..f6ef1afbfa 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.4-SNAPSHOT</version>
+		<version>4.2.4</version>
 	</parent>	
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.4-SNAPSHOT</version>
+			<version>4.2.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index c3abff104b..3aa5456d2e 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>4.2.4-SNAPSHOT</version>
+	<version>4.2.4</version>
 	<name>biojava</name>
 	<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
         data. It provides analytical and statistical routines, parsers for common file formats and allows the
@@ -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-4.2.4</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list