From 2888f8f1af844c4f343f4ca691a626338de97d9f Mon Sep 17 00:00:00 2001
From: Jenkins <jenkins@java-jenkins-research.rcsb.org>
Date: Fri, 17 Feb 2017 18:36:53 -0800
Subject: [PATCH 1/7] [maven-release-plugin]prepare for next development
 iteration

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

diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
index 89ef2154ef..766390590f 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>4.2.6</version>
+		<version>4.2.7-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>4.2.6</version>
+			<version>4.2.7-SNAPSHOT</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>4.2.6</version>
+			<version>4.2.7-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 41389cdd4e..1d4051dec0 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.6</version>
+		<version>4.2.7-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>4.2.6</version>
+			<version>4.2.7-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
@@ -74,7 +74,7 @@
   		<dependency>
   			<groupId>org.biojava</groupId>
   			<artifactId>biojava-phylo</artifactId>
-  			<version>4.2.6</version>
+  			<version>4.2.7-SNAPSHOT</version>
   		</dependency>
 	</dependencies>
 </project>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index e3b0e9a7a1..358cae9ab3 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.6</version>
+		<version>4.2.7-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 b382489846..b53bd2df99 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.6</version>
+		<version>4.2.7-SNAPSHOT</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -85,13 +85,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.6</version>
+			<version>4.2.7-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.6</version>
+			<version>4.2.7-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index dca85357b3..930ed7a555 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.6</version>
+    <version>4.2.7-SNAPSHOT</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -32,7 +32,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.6</version>
+    	<version>4.2.7-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 e969b11f09..03ac151f18 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.6</version>
+    <version>4.2.7-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>4.2.6</version>
+    	<version>4.2.7-SNAPSHOT</version>
     	<type>jar</type>
     	<scope>compile</scope>
     </dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 305039b548..79e2415534 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>4.2.6</version>
+    <version>4.2.7-SNAPSHOT</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml
index bc55ac6307..7ef7750049 100644
--- a/biojava-phylo/pom.xml
+++ b/biojava-phylo/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.6</version>
+    <version>4.2.7-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>4.2.6</version>
+      <version>4.2.7-SNAPSHOT</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index b95632bc2c..3b1b7789b1 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>4.2.6</version>
+		<version>4.2.7-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>4.2.6</version>
+			<version>4.2.7-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 0990a8e9b2..fa0030a998 100644
--- a/biojava-sequencing/pom.xml
+++ b/biojava-sequencing/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.6</version>
+		<version>4.2.7-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>4.2.6</version>
+			<version>4.2.7-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 f96aad2a97..8110e5ff82 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>4.2.6</version>
+        <version>4.2.7-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>4.2.6</version>
+            <version>4.2.7-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-            <version>4.2.6</version>
+            <version>4.2.7-SNAPSHOT</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index ac6de4757a..916f1acb74 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.6</version>
+		<version>4.2.7-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>4.2.6</version>
+			<version>4.2.7-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.6</version>
+			<version>4.2.7-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 1f03bad9be..5787cb90f4 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>4.2.6</version>
+        <version>4.2.7-SNAPSHOT</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index 646bd14a0b..d0dba4c0d6 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.6</version>
+		<version>4.2.7-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>4.2.6</version>
+			<version>4.2.7-SNAPSHOT</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 3993929e35..4bad7b322d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>4.2.6</version>
+	<version>4.2.7-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-4.2.6</tag>
+		<tag>biojava-4.2.1</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list 

From eee49af30cf27316f69d4b604f08e900466f718f Mon Sep 17 00:00:00 2001
From: Jose Manuel Duarte <jose.m.duarte@gmail.com>
Date: Thu, 2 Mar 2017 12:11:19 -0800
Subject: [PATCH 2/7] Bugfix: header was wrongly specified. Better error
 handling

---
 .../nbio/ws/hmmer/RemoteHmmerScan.java        | 41 +++++++------------
 1 file changed, 15 insertions(+), 26 deletions(-)

diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
index 4e83b61ec8..586aad785f 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
@@ -23,6 +23,8 @@
 import net.sf.json.JSONArray;
 import net.sf.json.JSONObject;
 import org.biojava.nbio.core.sequence.ProteinSequence;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.io.*;
 import java.net.HttpURLConnection;
@@ -31,14 +33,17 @@
 import java.util.TreeSet;
 
 
-/** Makes remote calls to the HMMER web service at the EBI web site and returns Pfam domain annotations for an input protein sequence.
+/** 
+ * Makes remote calls to the HMMER web service at the EBI web site and returns Pfam domain annotations for an input protein sequence.
  *
  * @author Andreas Prlic
  * @since 3.0.3
  */
 public class RemoteHmmerScan implements HmmerScan {
 
-	public static String HMMER_SERVICE = "http://www.ebi.ac.uk/Tools/hmmer/search/hmmscan";
+	private static final Logger LOGGER = LoggerFactory.getLogger(RemoteHmmerScan.class);
+	
+	public static final String HMMER_SERVICE = "http://www.ebi.ac.uk/Tools/hmmer/search/hmmscan";
 
 	public RemoteHmmerScan(){
 
@@ -54,7 +59,8 @@ public  SortedSet<HmmerResult> scan(ProteinSequence sequence) throws IOException
 
 	}
 
-	/** Scans a protein sequence for Pfam profile matches.
+	/** 
+	 * Scans a protein sequence for Pfam profile matches.
 	 *
 	 * @param sequence
 	 * @param serviceLocation
@@ -68,7 +74,7 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
 		postContent.append("hmmdb=pfam");
 
 
-		// by default hmmscan runs with the HMMER3 cut_ga parameter enabled, the "gathering freshold", which depends on
+		// by default hmmscan runs with the HMMER3 cut_ga parameter enabled, the "gathering threshold", which depends on
 		// the cutoffs defined in the underlying HMM files.
 		// to request a different cutoff by e-value this could be enabled:
 		//postContent.append("&E=1");
@@ -86,7 +92,7 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
 		connection.setRequestMethod("POST");
 		connection.setRequestProperty("Content-Type", "application/x-www-form-urlencoded");
 
-		connection.setRequestProperty("Accept:","application/json");
+		connection.setRequestProperty("Accept","application/json");
 
 		connection.setRequestProperty("Content-Length", "" +
 				Integer.toString(postContent.toString().getBytes().length));
@@ -99,13 +105,12 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
 		wr.close ();
 
 
-//		//Now get the redirect URL
+		//Now get the redirect URL
 		URL respUrl = new URL( connection.getHeaderField( "Location" ));
 
 		int responseCode = connection.getResponseCode();
 		if ( responseCode == 500){
-			System.err.println("something went wrong!" + serviceLocation);
-			System.err.println(connection.getResponseMessage());
+			LOGGER.warn("Got 500 response code for URL {}. Response message: {}.", serviceLocation, connection.getResponseMessage());	
 		}
 
 		HttpURLConnection connection2 = (HttpURLConnection) respUrl.openConnection();
@@ -122,7 +127,6 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
 
 		StringBuffer result = new StringBuffer();
 		while ((inputLine = in.readLine()) != null) {
-			//System.out.println(inputLine);
 			result.append(inputLine);
 		}
 
@@ -141,7 +145,6 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
 
 			for(int i =0 ; i < hits.size() ; i++){
 				JSONObject hit = hits.getJSONObject(i);
-				//System.out.println("hit: "+ hit);
 
 				HmmerResult hmmResult = new HmmerResult();
 
@@ -170,13 +173,8 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
 				SortedSet<HmmerDomain> domains = new TreeSet<HmmerDomain>();
 				for ( int j= 0 ; j < hmmdomains.size() ; j++){
 					JSONObject d = hmmdomains.getJSONObject(j);
-					//System.out.println(d);
 					Integer is_included = getInteger(d.get("is_included"));
 					if ( is_included == 0) {
-//						System.out.println("  excluding: " + d.get("alihmmdesc") + " " + d.get("alihmmname") + " " +
-//								hit.get("evalue") + " " +
-//								d.get("alisqfrom") + " " +
-//								d.get("alisqto"));
 						continue;
 					}
 
@@ -184,21 +182,12 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
 					// this filters out multiple hits to the same clan
 					Integer outcompeted = getInteger(d.get("outcompeted"));
 					if ( outcompeted != null && outcompeted == 1) {
-//						System.out.println("  outcompeted: " + d.get("alihmmdesc") + " " + d.get("alihmmname")+ " " +
-//								hit.get("evalue") + " " +
-//								d.get("alisqfrom") + " " +
-//								d.get("alisqto")
-//						);
 						continue;
 					}
 
 					Integer significant = getInteger(d.get("significant"));
 
 					if (  significant != 1) {
-//						System.out.println("  not significant: " + d.get("alihmmdesc") + " " + d.get("alihmmname")+ " " +
-//								hit.get("evalue") + " " +
-//								d.get("alisqfrom") + " " +
-//								d.get("alisqto"));
 						continue;
 					}
 
@@ -224,8 +213,8 @@ public SortedSet<HmmerResult> scan(ProteinSequence sequence, URL serviceLocation
 
 				results.add(hmmResult);
 			}
-		} catch (Exception e){
-			e.printStackTrace();
+		} catch (NumberFormatException e){
+			LOGGER.warn("Could not parse number in Hmmer web service json response: {}", e.getMessage());
 		}
 
 		return results;

From 331ac2609e2c9c31f9ef06d4afb8c0c52b57be1a Mon Sep 17 00:00:00 2001
From: Yana Valasatava <yana.valasatava@rcsb.org>
Date: Wed, 22 Feb 2017 16:55:04 -0800
Subject: [PATCH 3/7] Bugfix: chromosome mapping tool returns -1 if position
 falls outside coding region on the forward strand

---
 .../genome/util/ChromosomeMappingTools.java   | 17 ++++++---
 .../nbio/genome/TestGenomeMapping.java        | 35 ++++++++++++++++---
 2 files changed, 44 insertions(+), 8 deletions(-)

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 07ace5278b..4c6dc4c162 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
@@ -924,7 +924,7 @@ private static List<Range<Integer>> getCDSExonRangesForward(GeneChromosomePositi
     public static int getCDSPosForChromosomeCoordinate(int coordinate, GeneChromosomePosition chromosomePosition) {
 
         if ( chromosomePosition.getOrientation() == '+')
-            return getCDSPosForward(coordinate,
+        	return getCDSPosForward(coordinate,
                     chromosomePosition.getExonStarts(),
                     chromosomePosition.getExonEnds(),
                     chromosomePosition.getCdsStart(),
@@ -935,7 +935,6 @@ public static int getCDSPosForChromosomeCoordinate(int coordinate, GeneChromosom
                 chromosomePosition.getExonEnds(),
                 chromosomePosition.getCdsStart(),
                 chromosomePosition.getCdsEnd());
-
     }
 
 
@@ -1145,10 +1144,20 @@ public static int getCDSPosForward(int chromPos, List<Integer> exonStarts, List<
         boolean inCoding = false;
         int codingLength = 0;
 
-
         logger.debug("looking for CDS position for " +chromPos);
+        
+        if ( chromPos <  cdsStart+1 ) {
+            logger.debug(chromPos + " < " + cdsStart+1 );
+            return -1; // this is not in a coding region!
+        }
 
+        if ( chromPos >  cdsEnd+1 ) {
+            logger.debug(chromPos + " > " + cdsEnd+1 );
+            return -1; // this is not in a coding region!
+        }
+        
         int lengthExons = 0;
+        
         // map forward
         for (int i = 0; i < exonStarts.size(); i++) {
 
@@ -1223,7 +1232,7 @@ public static int getCDSPosForward(int chromPos, List<Integer> exonStarts, List<
 
         }
 
-        //logger.debug("length exons: " + lengthExons);
+        logger.debug("length exons: " + lengthExons);
         //return codingLength - 3;
 
         // could not map!
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
index b4615b9db2..cff4faf89d 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java
@@ -16,7 +16,7 @@
 /**
  * Created by andreas on 7/19/16.
  */
-public class TestGenomeMapping extends TestCase{
+public class TestGenomeMapping extends TestCase {
 
     private static final String geneChromosomeFile = "http://cdn.rcsb.org/gene/hg38/geneChromosome38.tsf.gz";
 
@@ -27,11 +27,8 @@ 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";
@@ -148,4 +145,34 @@ private void validateExon(int exonNr, int start, int stop, List<Range<Integer>>
         assertTrue("Exon " + exonNr + " boundary " + exon.upperEndpoint() + " does not match " + stop, exon.upperEndpoint().equals(stop));
 
     }
+    
+    @Test
+	/** Test to make sure the reverse mapping of a genomic coordinate handles border cases
+	 * 
+	 * @author Yana Valasatava
+	 */
+    public void testReverseMappingForExonBoundaries() {
+    	
+    	String geneName = "BCL11B"; // gene on the reverse DNA strand 
+    	String genebankId = "NM_138576"; // GeneBank ID for the transcript used for testing (ENST00000357195)
+    	
+    	int posExonStart = 99174151; // starting position of the first base in a coding region (1st exon)
+    	int posExonEnd = 99176195; // ending position of the first base in a coding region (1st exon)
+    	
+    	for (GeneChromosomePosition gcp : gcps) {
+    		
+    		if ( !gcp.getGeneName().equals(geneName) )
+    			continue;
+    		if ( !gcp.getGenebankId().equals(genebankId) )
+    			continue;
+    		
+    		int cdsSE = ChromosomeMappingTools.getCDSPosForChromosomeCoordinate(posExonStart-1, gcp);
+    		assertEquals(cdsSE, -1);
+    		
+    		int cdsEE = ChromosomeMappingTools.getCDSPosForChromosomeCoordinate(posExonEnd+1, gcp);
+    		assertEquals(cdsEE, -1);
+    		
+    		break;
+		}	
+    }
 }

From 4e292b4bb51c3ab3f989d3899cb6de4ee209070f Mon Sep 17 00:00:00 2001
From: Yana Valasatava <yana.valasatava@rcsb.org>
Date: Thu, 23 Feb 2017 16:15:12 -0800
Subject: [PATCH 4/7] Chromosome mapping tool patch for converting a genomic
 position to the position on mRNA for the genes leaving on the forward strand

---
 .../genome/util/ChromosomeMappingTools.java   | 392 +++++-------------
 1 file changed, 112 insertions(+), 280 deletions(-)

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 4c6dc4c162..ea9538f333 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
@@ -13,8 +13,11 @@
 import java.util.List;
 
 /**
- *  A class that take care of the painful mapping
+ *  A class that can map chromosomal positions to mRNA (coding sequence) positions.
+ *
+ *  @author Andreas Prlic
  */
+
 public class ChromosomeMappingTools {
 
     private static final Logger logger = LoggerFactory.getLogger(ChromosomeMappingTools.class);
@@ -915,7 +918,7 @@ private static List<Range<Integer>> getCDSExonRangesForward(GeneChromosomePositi
 //
 
     /**
-     * I have a genomic coordinate, where is it in the Gene?
+     * I have a genomic coordinate, where is it on the mRNA
      *
      * @param coordinate
      * @param chromosomePosition
@@ -937,308 +940,137 @@ public static int getCDSPosForChromosomeCoordinate(int coordinate, GeneChromosom
                 chromosomePosition.getCdsEnd());
     }
 
+	/** Converts the genetic coordinate to the position of the nucleotide on the mRNA sequence for a gene
+	 * living on the forward DNA strand.
+	 *
+	 * @param chromPos The genetic coordinate on a chromosome
+     * @param exonStarts The list holding the genetic coordinates pointing to the start positions of the exons (including UTR regions)
+     * @param exonEnds The list holding the genetic coordinates pointing to the end positions of the exons (including UTR regions)
+     * @param cdsStart The start position of a coding region
+     * @param cdsEnd The end position of a coding region
+     *
+     * @return the position of the nucleotide base on the mRNA sequence corresponding to the input genetic coordinate (base 1)
+	 *
+	 * @author Yana Valasatava
+	 */
+    public static int getCDSPosForward(int chromPos, List<Integer> exonStarts, List<Integer> exonEnds,
+            int cdsStart, int cdsEnd) {
 
-    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 );
+    	// the genetic coordinate is not in a coding region
+        if ( (chromPos < (cdsStart+1) ) || ( chromPos > (cdsEnd+1) ) ) {
+        	logger.debug("The "+format(chromPos)+" position is not in a coding region");
             return -1;
         }
 
-        if ( chromPos >  cdsEnd+1 ) {
-            // this is not in a coding region!
+        logger.debug("looking for CDS position for " +format(chromPos));
 
-            logger.debug(chromPos + " > " + cdsEnd+1 );
-            return -1;
+        // remove exons that are fully landed in UTRs
+        List<Integer> tmpS = new ArrayList<Integer>(exonStarts);
+        List<Integer> tmpE = new ArrayList<Integer>(exonEnds);
+
+        int j=0;
+        for (int i = 0; i < tmpS.size(); i++) {
+        	if ( ( tmpE.get(i) < cdsStart) || ( tmpS.get(i) > cdsEnd) ) {
+        		exonStarts.remove(j);
+        		exonEnds.remove(j);
+        	}
+        	else {
+        		j++;
+        	}
         }
 
-        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);
-                    }
-
+        // remove untranslated regions from exons
+        int nExons = exonStarts.size();
+        exonStarts.remove(0);
+        exonStarts.add(0, cdsStart);
+        exonEnds.remove(nExons-1);
+        exonEnds.add(cdsEnd);
 
-                    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);
-
-            }
+        int codingLength = 0;
+        int lengthExon = 0;
 
-            //if ( inCoding )
-            //	logger.debug("     exon phase at end:" + ((codingLength) % 3));
+        // map the genetic coordinate on a stretch of a reverse strand
+        for (int i = 0; i < nExons; i++) {
 
-            logger.debug("     coding length: " + codingLength + "(phase:" + (codingLength % 3) + ") CDS POS trying to map:" + chromPos);
+		    int start = exonStarts.get(i);
+		    int end = exonEnds.get(i);
 
+		    lengthExon = end - start;
 
+		    if (start+1 <= chromPos && end >= chromPos ) {
+		    	return codingLength + (chromPos-start);
+		    }
+	        else {
+	        	codingLength += lengthExon;
+	        }
         }
-
-        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)
+	/** Converts the genetic coordinate to the position of the nucleotide on the mRNA sequence for a gene
+	 * living on the reverse DNA strand.
+	 *
+	 * @param chromPos The genetic coordinate on a chromosome
+     * @param exonStarts The list holding the genetic coordinates pointing to the start positions of the exons (including UTR regions)
+     * @param exonEnds The list holding the genetic coordinates pointing to the end positions of the exons (including UTR regions)
+     * @param cdsStart The start position of a coding region
+     * @param cdsEnd The end position of a coding region
      *
-     * @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);
-        
-        if ( chromPos <  cdsStart+1 ) {
-            logger.debug(chromPos + " < " + cdsStart+1 );
-            return -1; // this is not in a coding region!
-        }
+     * @return the position of the nucleotide base on the mRNA sequence corresponding to the input genetic coordinate (base 1)
+	 *
+	 * @author Yana Valasatava
+	 */
+    public static int getCDSPosReverse(int chromPos, List<Integer> exonStarts, List<Integer> exonEnds,
+            int cdsStart, int cdsEnd) {
 
-        if ( chromPos >  cdsEnd+1 ) {
-            logger.debug(chromPos + " > " + cdsEnd+1 );
-            return -1; // this is not in a coding region!
+    	// the genetic coordinate is not in a coding region
+        if ( (chromPos < (cdsStart+1)) || ( chromPos > (cdsEnd+1) ) ) {
+        	logger.debug("The "+format(chromPos)+" position is not in a coding region");
+            return -1;
         }
-        
-        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("looking for CDS position for " +format(chromPos));
 
+        // remove exons that are fully landed in UTRs
+        List<Integer> tmpS = new ArrayList<Integer>(exonStarts);
+        List<Integer> tmpE = new ArrayList<Integer>(exonEnds);
+
+        int j=0;
+        for (int i = tmpS.size() - 1; i >= 0; i--) {
+        	if ( ( tmpE.get(i) < cdsStart) || ( tmpS.get(i) > cdsEnd) ) {
+        		exonStarts.remove(j);
+        		exonEnds.remove(j);
+        	}
+        	else {
+        		j++;
+        	}
         }
 
-        logger.debug("length exons: " + lengthExons);
-        //return codingLength - 3;
-
-        // could not map!
+        // remove untranslated regions from exons
+        int nExons = exonStarts.size();
+        exonStarts.remove(0);
+        exonStarts.add(0, cdsStart);
+        exonEnds.remove(nExons-1);
+        exonEnds.add(cdsEnd);
 
+        int codingLength = 0;
+        int lengthExon = 0;
+        
+        // map the genetic coordinate on a stretch of a reverse strand
+        for (int i = nExons - 1; i >= 0; i--) {
+
+		    int start = exonStarts.get(i);
+		    int end = exonEnds.get(i);
+
+		    lengthExon = end - start;
+		    // +1 offset to be a base 1
+		    if (start+1 <= chromPos && end >= chromPos ) {
+		    	return codingLength + (end-chromPos+1);
+		    }
+	        else {
+	        	codingLength += lengthExon;
+	        }
+        }
         return -1;
     }
-
-
 }

From 73b56c3b6ddbb6a7e29f8d72cccd9762a90cfdc8 Mon Sep 17 00:00:00 2001
From: Yana Valasatava <yana.valasatava@rcsb.org>
Date: Thu, 23 Feb 2017 16:15:33 -0800
Subject: [PATCH 5/7] Unit tests for converting a genomic position to the
 position on mRNA for the genes leaving on the forward strand

---
 .../nbio/genome/TestGenomeMapping.java        | 362 ++++++++++++------
 1 file changed, 250 insertions(+), 112 deletions(-)

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
index cff4faf89d..24b75ee2c1 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java
@@ -10,6 +10,7 @@
 
 import java.io.InputStream;
 import java.net.URL;
+import java.util.Arrays;
 import java.util.List;
 import java.util.zip.GZIPInputStream;
 
@@ -18,161 +19,298 @@
  */
 public class TestGenomeMapping extends TestCase {
 
-    private static final String geneChromosomeFile = "http://cdn.rcsb.org/gene/hg38/geneChromosome38.tsf.gz";
+	private static final String geneChromosomeFile = "http://cdn.rcsb.org/gene/hg38/geneChromosome38.tsf.gz";
 
-    private List<GeneChromosomePosition> gcps = null;
+	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);
-    }
+	@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";
+	@Test
+	public void testAK1() {
+		String geneName = "AK1";
 
-        assertNotNull(gcps);
-        assertTrue("Problems with downloading refFlat file from UCSC browser ", gcps.size() > 100);
+		assertNotNull(gcps);
+		assertTrue("Problems with downloading refFlat file from UCSC browser ", gcps.size() > 100);
 
-        int uniProtLength = 194;
+		int uniProtLength = 194;
 
-        try {
+		try {
 
-            for (GeneChromosomePosition pos : gcps) {
+			for (GeneChromosomePosition pos : gcps) {
 
-                //System.out.println(pos.getGeneName());
-                if (!pos.getGeneName().equals(geneName))
-                    continue;
+				//System.out.println(pos.getGeneName());
+				if (!pos.getGeneName().equals(geneName))
+					continue;
 
-                /// there are three alternative transcripts for AK1.
-                // we are just testing one here:
+				/// there are three alternative transcripts for AK1.
+				// we are just testing one here:
 
-                if ( ! pos.getGenebankId().equals("NM_000476"))
-                    continue;
+				if ( ! pos.getGenebankId().equals("NM_000476"))
+					continue;
 
-                assertTrue(pos.getGeneName().equals(geneName));
-                assertTrue(pos.getOrientation().equals('-'));
-                assertTrue(pos.getChromosome().equals("chr9"));
+				assertTrue(pos.getGeneName().equals(geneName));
+				assertTrue(pos.getOrientation().equals('-'));
+				assertTrue(pos.getChromosome().equals("chr9"));
 
-                List<Range<Integer>> cdsranges = ChromosomeMappingTools.getCDSExonRanges(pos);
+				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  );
+				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);
+				int cdslength = ChromosomeMappingTools.getCDSLength(pos);
 
-                assertTrue("CDS length should be 582, but is " + cdslength, cdslength == (uniProtLength *3));
+				assertTrue("CDS length should be 582, but is " + cdslength, cdslength == (uniProtLength *3));
 
-                List<Range<Integer>> chromranges = ChromosomeMappingTools.getChromosomalRangesForCDS(pos);
+				List<Range<Integer>> chromranges = ChromosomeMappingTools.getChromosomalRangesForCDS(pos);
 
-                // we are reverse strand. reverse the order
-                chromranges = Lists.reverse(chromranges);
+				// we are reverse strand. reverse the order
+				chromranges = Lists.reverse(chromranges);
 
-                assertTrue(chromranges.size() == 6);
+				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  );
+				// 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());
-        }
-    }
+			}
+		} catch (Exception e) {
+			fail(e.getMessage());
+		}
+	}
 
-    @Test
-    public void testHBA(){
+	@Test
+	public void testHBA(){
 
-        String geneName = "HBA1";
-        assertNotNull(gcps);
+		String geneName = "HBA1";
+		assertNotNull(gcps);
 
-        assertTrue("Problems with downloading refFlat file from UCSC browser ", gcps.size() > 100);
+		assertTrue("Problems with downloading refFlat file from UCSC browser ", gcps.size() > 100);
 
-        try {
+		try {
 
-            for ( GeneChromosomePosition pos : gcps){
+			for ( GeneChromosomePosition pos : gcps){
 
-                //System.out.println(pos.getGeneName());
-                if ( ! pos.getGeneName().equals(geneName))
-                    continue;
+				//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('+'));
+				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);
+				List<Range<Integer>> cdsranges = ChromosomeMappingTools.getCDSExonRanges(pos);
 
-                assertTrue(cdsranges.size() == 3);
+				assertTrue(cdsranges.size() == 3);
 
-                validateExon(0,0,95,cdsranges);
-                validateExon(1,95,300,cdsranges);
-                validateExon(2,300,429,cdsranges);
+				validateExon(0,0,95,cdsranges);
+				validateExon(1,95,300,cdsranges);
+				validateExon(2,300,429,cdsranges);
 
 
-                List<Range<Integer>> chromranges = ChromosomeMappingTools.getChromosomalRangesForCDS(pos);
+				List<Range<Integer>> chromranges = ChromosomeMappingTools.getChromosomalRangesForCDS(pos);
 
-                validateExon(0,176716,176811, chromranges  );
-                validateExon(1,176928,177133, chromranges  );
-                validateExon(2,177282,177411, chromranges  );
+				validateExon(0,176716,176811, chromranges  );
+				validateExon(1,176928,177133, chromranges  );
+				validateExon(2,177282,177411, chromranges  );
 
 
-            }
-        } catch (Exception e){
-            fail(e.getMessage());
-        }
+			}
+		} catch (Exception e){
+			fail(e.getMessage());
+		}
 
 
-    }
+	}
 
-    private void validateExon(int exonNr, int start, int stop, List<Range<Integer>> cdsranges) {
+	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));
+		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));
 
-    }
-    
-    @Test
-	/** Test to make sure the reverse mapping of a genomic coordinate handles border cases
+	}
+
+	@Test
+	/** Test to make sure the mapping tool correctly retrieves the mRNA position for a gene 
+	 * living on the forward DNA strand for different chromosome positions. 
+	 * 
+	 * @author Yana Valasatava
+	 */
+	public void testForwardMappingPositions() {
+
+		String geneName = "HORMAD2"; // gene on the forward DNA strand 
+		String genebankId = "NM_152510"; // GeneBank ID for the transcript used for testing (ENST00000336726)
+		
+		List<String> scenarios = Arrays.asList("first1exon", "last1exon", "last3exon");
+		
+		int cds;
+		int posExonStart;
+		int posInmRNA;
+		for (String scenario : scenarios) {
+			
+			switch (scenario) {
+				
+				case "first1exon":
+			    	posExonStart = 30093953; // ending position of the last exon coding region (on forward strand)
+			    	posInmRNA = 1; // base 1 position in mRNA sequence
+					cds = getPositionInmRNA(geneName, genebankId, posExonStart);
+					assertEquals(cds, posInmRNA);
+					break;
+					
+				case "last1exon":
+			    	posExonStart = 30094003; // starting position of the last exon coding region (on forward strand)
+			    	posInmRNA = 51; // position in mRNA sequence equals to the length of the exon
+					cds = getPositionInmRNA(geneName, genebankId, posExonStart);
+					assertEquals(cds, posInmRNA);		
+					break;
+				
+				case "last3exon":
+					posExonStart = 30103500; // starting position of the first base in a coding region (3rd exon)
+					posInmRNA = 257; // position in mRNA sequence equals to the sum length of the 3 last exons 
+					cds = getPositionInmRNA(geneName, genebankId, posExonStart);
+					assertEquals(cds, posInmRNA);
+					break;
+			}
+		}
+	}
+	
+	@Test
+	/** Test to make sure the mapping tool correctly retrieves the mRNA position for a gene 
+	 * living on the reverse DNA strand for different chromosome positions. 
 	 * 
 	 * @author Yana Valasatava
 	 */
-    public void testReverseMappingForExonBoundaries() {
-    	
-    	String geneName = "BCL11B"; // gene on the reverse DNA strand 
-    	String genebankId = "NM_138576"; // GeneBank ID for the transcript used for testing (ENST00000357195)
-    	
-    	int posExonStart = 99174151; // starting position of the first base in a coding region (1st exon)
-    	int posExonEnd = 99176195; // ending position of the first base in a coding region (1st exon)
-    	
-    	for (GeneChromosomePosition gcp : gcps) {
-    		
-    		if ( !gcp.getGeneName().equals(geneName) )
-    			continue;
-    		if ( !gcp.getGenebankId().equals(genebankId) )
-    			continue;
-    		
-    		int cdsSE = ChromosomeMappingTools.getCDSPosForChromosomeCoordinate(posExonStart-1, gcp);
-    		assertEquals(cdsSE, -1);
-    		
-    		int cdsEE = ChromosomeMappingTools.getCDSPosForChromosomeCoordinate(posExonEnd+1, gcp);
-    		assertEquals(cdsEE, -1);
-    		
-    		break;
+	public void testReverseMappingPositions() {
+
+		String geneName = "BCL11B"; // gene on the reverse DNA strand 
+		String genebankId = "NM_138576"; // GeneBank ID for the transcript used for testing (ENST00000357195)
+		
+		List<String> scenarios = Arrays.asList("first1exon", "last1exon", "last3exon");
+		
+		int cds;
+		int posExonStart;
+		int posInmRNA;
+		for (String scenario : scenarios) {
+			
+			switch (scenario) {
+				
+				case "first1exon":
+			    	posExonStart = 99271218; // ending position of the last exon coding region (on forward strand)
+			    	posInmRNA = 1; // base 1 position in mRNA sequence
+					cds = getPositionInmRNA(geneName, genebankId, posExonStart);
+					assertEquals(cds, posInmRNA);
+					break;
+					
+				case "last1exon":
+			    	posExonStart = 99271161; // starting position of the last exon coding region (on forward strand)
+			    	posInmRNA = 58; // position in mRNA sequence equals to the length of the exon
+					cds = getPositionInmRNA(geneName, genebankId, posExonStart);
+					assertEquals(cds, posInmRNA);		
+					break;
+				
+				case "last3exon":
+					posExonStart = 99231345; // starting position of the first base in a coding region (3rd exon)
+					posInmRNA = 640; // position in mRNA sequence equals to the sum length of the 3 last exons 
+					cds = getPositionInmRNA(geneName, genebankId, posExonStart);
+					assertEquals(cds, posInmRNA);
+					break;
+			}
+		}
+	}
+
+	@Test
+	/** Test to make sure the mapping tool correctly identify that position falls outside the coding region 
+	 * for a gene living on the forward DNA strand.
+	 * 
+	 * @author Yana Valasatava
+	 */
+	public void testForwardMappingForExonBoundaries() {
+
+		String geneName = "HBA1"; // gene on the reverse DNA strand 
+		String genebankId = "NM_000558"; // GeneBank ID for the transcript used for testing (ENST00000320868)
+
+		int posExonStart = 176717; // starting position of the first base in a coding region (1st exon)
+		int posExonEnd = 176811; // ending position of the first base in a coding region (1st exon)
+
+		for (GeneChromosomePosition gcp : gcps) {
+
+			if ( !gcp.getGeneName().equals(geneName) )
+				continue;
+			if ( !gcp.getGenebankId().equals(genebankId) )
+				continue;
+
+			int cdsSE = ChromosomeMappingTools.getCDSPosForChromosomeCoordinate(posExonStart-1, gcp);
+			assertEquals(cdsSE, -1);
+
+			int cdsEE = ChromosomeMappingTools.getCDSPosForChromosomeCoordinate(posExonEnd+1, gcp);
+			assertEquals(cdsEE, -1);
+
+			break;
 		}	
-    }
+	}
+	
+	@Test
+	/** Test to make sure the mapping tool correctly identify that position falls outside the coding region 
+	 * for a gene living on the reverse DNA strand.
+	 * 
+	 * @author Yana Valasatava
+	 */
+	public void testReverseMappingForExonBoundaries() {
+
+		String geneName = "BCL11B"; // gene on the reverse DNA strand 
+		String genebankId = "NM_138576"; // GeneBank ID for the transcript used for testing (ENST00000357195)
+
+		int posExonStart = 99174151; // starting position of the first base in a coding region (1st exon)
+		int posExonEnd = 99176195; // ending position of the first base in a coding region (1st exon)
+
+		for (GeneChromosomePosition gcp : gcps) {
+
+			if ( !gcp.getGeneName().equals(geneName) )
+				continue;
+			if ( !gcp.getGenebankId().equals(genebankId) )
+				continue;
+
+			int cdsSE = ChromosomeMappingTools.getCDSPosForChromosomeCoordinate(posExonStart-1, gcp);
+			assertEquals(cdsSE, -1);
+
+			int cdsEE = ChromosomeMappingTools.getCDSPosForChromosomeCoordinate(posExonEnd+1, gcp);
+			assertEquals(cdsEE, -1);
+
+			break;
+		}	
+	}
+	
+	/** Get the position of the nucleotide base corresponding to the position of that base on the mRNA sequence 
+	 * for a gene living on the reverse DNA strand. 
+	 * 
+	 * @author Yana Valasatava
+	 */
+	private int getPositionInmRNA(String geneName, String genebankId, int posChrom) {
+		for (GeneChromosomePosition gcp : gcps) {	
+			if ( !gcp.getGeneName().equals(geneName) )
+				continue;
+			if ( !gcp.getGenebankId().equals(genebankId) )
+				continue;       		
+			return ChromosomeMappingTools.getCDSPosForChromosomeCoordinate(posChrom, gcp);
+		}
+		return -1;
+	}
 }
+

From 55639ac81c55b34fa59c8324931f5cd7f7ffb70f Mon Sep 17 00:00:00 2001
From: Yana Valasatava <yana.valasatava@rcsb.org>
Date: Thu, 23 Feb 2017 18:34:17 -0800
Subject: [PATCH 6/7] Chromosome mapping tool: unit test to check handling
 multiple UTRs preceding the coding region

---
 .../nbio/genome/TestGenomeMapping.java        | 99 +++++++++----------
 1 file changed, 49 insertions(+), 50 deletions(-)

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
index 24b75ee2c1..7f9ded778a 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/TestGenomeMapping.java
@@ -141,18 +141,34 @@ public void testHBA(){
 
 	private void validateExon(int exonNr, int start, int stop, List<Range<Integer>> cdsranges) {
 
-		Range exon = cdsranges.get(exonNr);
+		Range<Integer> 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));
 
 	}
 
-	@Test
-	/** Test to make sure the mapping tool correctly retrieves the mRNA position for a gene 
+	/** Get the position of the nucleotide base corresponding to the position of that base on the mRNA sequence 
+	 * for a gene living on the reverse DNA strand. 
+	 * 
+	 * @author Yana Valasatava
+	 */
+	private int getPositionInmRNA(String geneName, String genebankId, int posChrom) {
+		for (GeneChromosomePosition gcp : gcps) {	
+			if ( gcp.getGeneName().equals(geneName) ) {
+				if ( gcp.getGenebankId().equals(genebankId) ) {
+					return ChromosomeMappingTools.getCDSPosForChromosomeCoordinate(posChrom, gcp);
+				}
+			}	
+		}
+		return -1;
+	}
+	
+	/** Make sure the mapping tool correctly retrieves the mRNA position for a gene 
 	 * living on the forward DNA strand for different chromosome positions. 
 	 * 
 	 * @author Yana Valasatava
 	 */
+	@Test
 	public void testForwardMappingPositions() {
 
 		String geneName = "HORMAD2"; // gene on the forward DNA strand 
@@ -190,13 +206,13 @@ public void testForwardMappingPositions() {
 			}
 		}
 	}
-	
-	@Test
-	/** Test to make sure the mapping tool correctly retrieves the mRNA position for a gene 
+		
+	/** Make sure the mapping tool correctly retrieves the mRNA position for a gene 
 	 * living on the reverse DNA strand for different chromosome positions. 
 	 * 
 	 * @author Yana Valasatava
 	 */
+	@Test
 	public void testReverseMappingPositions() {
 
 		String geneName = "BCL11B"; // gene on the reverse DNA strand 
@@ -235,12 +251,12 @@ public void testReverseMappingPositions() {
 		}
 	}
 
-	@Test
 	/** Test to make sure the mapping tool correctly identify that position falls outside the coding region 
 	 * for a gene living on the forward DNA strand.
 	 * 
 	 * @author Yana Valasatava
 	 */
+	@Test
 	public void testForwardMappingForExonBoundaries() {
 
 		String geneName = "HBA1"; // gene on the reverse DNA strand 
@@ -249,29 +265,19 @@ public void testForwardMappingForExonBoundaries() {
 		int posExonStart = 176717; // starting position of the first base in a coding region (1st exon)
 		int posExonEnd = 176811; // ending position of the first base in a coding region (1st exon)
 
-		for (GeneChromosomePosition gcp : gcps) {
-
-			if ( !gcp.getGeneName().equals(geneName) )
-				continue;
-			if ( !gcp.getGenebankId().equals(genebankId) )
-				continue;
-
-			int cdsSE = ChromosomeMappingTools.getCDSPosForChromosomeCoordinate(posExonStart-1, gcp);
-			assertEquals(cdsSE, -1);
-
-			int cdsEE = ChromosomeMappingTools.getCDSPosForChromosomeCoordinate(posExonEnd+1, gcp);
-			assertEquals(cdsEE, -1);
+		int cdsSE = getPositionInmRNA(geneName, genebankId, posExonStart-1);
+		assertEquals(cdsSE, -1);
 
-			break;
-		}	
+		int cdsEE = getPositionInmRNA(geneName, genebankId, posExonEnd+1);
+		assertEquals(cdsEE, -1);
 	}
-	
-	@Test
+		
 	/** Test to make sure the mapping tool correctly identify that position falls outside the coding region 
 	 * for a gene living on the reverse DNA strand.
 	 * 
 	 * @author Yana Valasatava
 	 */
+	@Test
 	public void testReverseMappingForExonBoundaries() {
 
 		String geneName = "BCL11B"; // gene on the reverse DNA strand 
@@ -279,38 +285,31 @@ public void testReverseMappingForExonBoundaries() {
 
 		int posExonStart = 99174151; // starting position of the first base in a coding region (1st exon)
 		int posExonEnd = 99176195; // ending position of the first base in a coding region (1st exon)
-
-		for (GeneChromosomePosition gcp : gcps) {
-
-			if ( !gcp.getGeneName().equals(geneName) )
-				continue;
-			if ( !gcp.getGenebankId().equals(genebankId) )
-				continue;
-
-			int cdsSE = ChromosomeMappingTools.getCDSPosForChromosomeCoordinate(posExonStart-1, gcp);
-			assertEquals(cdsSE, -1);
-
-			int cdsEE = ChromosomeMappingTools.getCDSPosForChromosomeCoordinate(posExonEnd+1, gcp);
-			assertEquals(cdsEE, -1);
-
-			break;
-		}	
+		
+		int cdsSE = getPositionInmRNA(geneName, genebankId, posExonStart-1);
+		assertEquals(cdsSE, -1);
+		
+		int cdsEE = getPositionInmRNA(geneName, genebankId, posExonEnd+1);
+		assertEquals(cdsEE, -1);	
 	}
 	
-	/** Get the position of the nucleotide base corresponding to the position of that base on the mRNA sequence 
-	 * for a gene living on the reverse DNA strand. 
+	/** Test to make sure the mapping tool correctly converts the genetic position to a position on mRNA 
+	 * when multiple UTR regions are consecutive.
 	 * 
 	 * @author Yana Valasatava
 	 */
-	private int getPositionInmRNA(String geneName, String genebankId, int posChrom) {
-		for (GeneChromosomePosition gcp : gcps) {	
-			if ( !gcp.getGeneName().equals(geneName) )
-				continue;
-			if ( !gcp.getGenebankId().equals(genebankId) )
-				continue;       		
-			return ChromosomeMappingTools.getCDSPosForChromosomeCoordinate(posChrom, gcp);
-		}
-		return -1;
+	@Test
+	public void testMappingCromosomePosTomRNAMultiUTRs() {
+
+		String geneName = "ILK"; // gene on the reverse DNA strand 
+		String genebankId = "NM_001278442"; // GeneBank ID for the transcript used for testing (ENST00000532063)
+
+		int chromPos = 6608760;
+		int mRNAPos = 16;
+				
+		int cds = getPositionInmRNA(geneName, genebankId, chromPos);
+		assertEquals(cds, mRNAPos);
+		
 	}
 }
 

From b369f5fd05cbaa479b05d8272dfbf593f2728d14 Mon Sep 17 00:00:00 2001
From: Jenkins <jenkins@java-jenkins-research.rcsb.org>
Date: Tue, 7 Mar 2017 16:28:58 -0800
Subject: [PATCH 7/7] [maven-release-plugin]prepare release biojava-4.2.7

---
 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 766390590f..1a449c7ef8 100644
--- a/biojava-aa-prop/pom.xml
+++ b/biojava-aa-prop/pom.xml
@@ -2,7 +2,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.7-SNAPSHOT</version>
+		<version>4.2.7</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-aa-prop</artifactId>
@@ -70,12 +70,12 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.7-SNAPSHOT</version>
+			<version>4.2.7</version>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-structure</artifactId>
-			<version>4.2.7-SNAPSHOT</version>
+			<version>4.2.7</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 1d4051dec0..7dfe24c010 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.7-SNAPSHOT</version>
+		<version>4.2.7</version>
 	</parent>
 	<artifactId>biojava-alignment</artifactId>
 	<name>biojava-alignment</name>
@@ -46,7 +46,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.7-SNAPSHOT</version>
+			<version>4.2.7</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
@@ -74,7 +74,7 @@
   		<dependency>
   			<groupId>org.biojava</groupId>
   			<artifactId>biojava-phylo</artifactId>
-  			<version>4.2.7-SNAPSHOT</version>
+  			<version>4.2.7</version>
   		</dependency>
 	</dependencies>
 </project>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
index 358cae9ab3..90e465d2dc 100644
--- a/biojava-core/pom.xml
+++ b/biojava-core/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.7-SNAPSHOT</version>
+		<version>4.2.7</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-core</artifactId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
index b53bd2df99..c82fade42d 100644
--- a/biojava-genome/pom.xml
+++ b/biojava-genome/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.7-SNAPSHOT</version>
+		<version>4.2.7</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-genome</artifactId>
@@ -85,13 +85,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.7-SNAPSHOT</version>
+			<version>4.2.7</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.7-SNAPSHOT</version>
+			<version>4.2.7</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
index 930ed7a555..c52783d2a1 100644
--- a/biojava-integrationtest/pom.xml
+++ b/biojava-integrationtest/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.7-SNAPSHOT</version>
+    <version>4.2.7</version>
   </parent>
   <artifactId>biojava-integrationtest</artifactId>
   <packaging>jar</packaging>
@@ -32,7 +32,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.7-SNAPSHOT</version>
+    	<version>4.2.7</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 03ac151f18..0ca1247f39 100644
--- a/biojava-modfinder/pom.xml
+++ b/biojava-modfinder/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.7-SNAPSHOT</version>
+    <version>4.2.7</version>
   </parent>
   <artifactId>biojava-modfinder</artifactId>
   <name>biojava-modfinder</name>
@@ -31,7 +31,7 @@
     <dependency>
     	<groupId>org.biojava</groupId>
     	<artifactId>biojava-structure</artifactId>
-    	<version>4.2.7-SNAPSHOT</version>
+    	<version>4.2.7</version>
     	<type>jar</type>
     	<scope>compile</scope>
     </dependency>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
index 79e2415534..03b1c00b76 100644
--- a/biojava-ontology/pom.xml
+++ b/biojava-ontology/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.biojava</groupId>
     <artifactId>biojava</artifactId>
-    <version>4.2.7-SNAPSHOT</version>
+    <version>4.2.7</version>
   </parent>
 
   <artifactId>biojava-ontology</artifactId>
diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml
index 7ef7750049..d374a993fd 100644
--- a/biojava-phylo/pom.xml
+++ b/biojava-phylo/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>biojava</artifactId>
     <groupId>org.biojava</groupId>
-    <version>4.2.7-SNAPSHOT</version>
+    <version>4.2.7</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>biojava-phylo</artifactId>
@@ -44,7 +44,7 @@
     <dependency>
       <groupId>org.biojava</groupId>
       <artifactId>biojava-core</artifactId>
-      <version>4.2.7-SNAPSHOT</version>
+      <version>4.2.7</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
index 3b1b7789b1..73c642d3e1 100644
--- a/biojava-protein-disorder/pom.xml
+++ b/biojava-protein-disorder/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.7-SNAPSHOT</version>
+		<version>4.2.7</version>
 	</parent>
 	<artifactId>biojava-protein-disorder</artifactId>
 	<packaging>jar</packaging>
@@ -63,7 +63,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.7-SNAPSHOT</version>
+			<version>4.2.7</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 fa0030a998..0b4d66e069 100644
--- a/biojava-sequencing/pom.xml
+++ b/biojava-sequencing/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.7-SNAPSHOT</version>
+		<version>4.2.7</version>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
 	<artifactId>biojava-sequencing</artifactId>
@@ -47,7 +47,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.7-SNAPSHOT</version>
+			<version>4.2.7</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 8110e5ff82..cfd684d103 100644
--- a/biojava-structure-gui/pom.xml
+++ b/biojava-structure-gui/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <artifactId>biojava</artifactId>
         <groupId>org.biojava</groupId>
-        <version>4.2.7-SNAPSHOT</version>
+        <version>4.2.7</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>biojava-structure-gui</artifactId>
@@ -25,13 +25,13 @@
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-structure</artifactId>
-            <version>4.2.7-SNAPSHOT</version>
+            <version>4.2.7</version>
             <scope>compile</scope>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
             <artifactId>biojava-core</artifactId>
-            <version>4.2.7-SNAPSHOT</version>
+            <version>4.2.7</version>
             <scope>compile</scope>
         </dependency>
 
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index 916f1acb74..db1c41a4f1 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.7-SNAPSHOT</version>
+		<version>4.2.7</version>
 	</parent>
 	<artifactId>biojava-structure</artifactId>
 	<name>biojava-structure</name>
@@ -22,13 +22,13 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-alignment</artifactId>
-			<version>4.2.7-SNAPSHOT</version>
+			<version>4.2.7</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.7-SNAPSHOT</version>
+			<version>4.2.7</version>
 			<scope>compile</scope>
 		</dependency>
 
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 5787cb90f4..e6c0294b34 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>org.biojava</groupId>
         <artifactId>biojava</artifactId>
-        <version>4.2.7-SNAPSHOT</version>
+        <version>4.2.7</version>
     </parent>
 
     <artifactId>biojava-survival</artifactId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index d0dba4c0d6..0f2e83e414 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
 	<parent>
 		<artifactId>biojava</artifactId>
 		<groupId>org.biojava</groupId>
-		<version>4.2.7-SNAPSHOT</version>
+		<version>4.2.7</version>
 	</parent>	
 	<artifactId>biojava-ws</artifactId>
 	<name>biojava-ws</name>
@@ -19,7 +19,7 @@
 		<dependency>
 			<groupId>org.biojava</groupId>
 			<artifactId>biojava-core</artifactId>
-			<version>4.2.7-SNAPSHOT</version>
+			<version>4.2.7</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
diff --git a/pom.xml b/pom.xml
index 4bad7b322d..6513c4cb61 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
 	<groupId>org.biojava</groupId>
 	<artifactId>biojava</artifactId>
 	<packaging>pom</packaging>
-	<version>4.2.7-SNAPSHOT</version>
+	<version>4.2.7</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-4.2.7</tag>
 	</scm>
 
 	<!-- This section required for release at Maven Central. For a full list