From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 27 Aug 2020 14:40:22 +0000 (+0100)
Subject: JAL-3725 exclude stop codon from CDS-to-protein mapping
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=874fe73aa58e600466aab1609b258e14d5eacdf8;p=jalview.git

JAL-3725 exclude stop codon from CDS-to-protein mapping
---

diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index 19366e0..5457114 100644
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -20,6 +20,25 @@
  */
 package jalview.ws.dbsources;
 
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.InputStream;
+import java.text.ParseException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.JAXBException;
+import javax.xml.stream.FactoryConfigurationError;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
+
 import jalview.analysis.SequenceIdMatcher;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
@@ -40,29 +59,9 @@ import jalview.ws.ebi.EBIFetchClient;
 import jalview.xml.binding.embl.EntryType;
 import jalview.xml.binding.embl.EntryType.Feature;
 import jalview.xml.binding.embl.EntryType.Feature.Qualifier;
-import jalview.xml.binding.jalview.JalviewModel;
 import jalview.xml.binding.embl.ROOT;
 import jalview.xml.binding.embl.XrefType;
 
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.InputStream;
-import java.text.ParseException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.JAXBException;
-import javax.xml.stream.FactoryConfigurationError;
-import javax.xml.stream.XMLInputFactory;
-import javax.xml.stream.XMLStreamException;
-import javax.xml.stream.XMLStreamReader;
-
 public abstract class EmblXmlSource extends EbiFileRetrievedProxy
 {
   /*
@@ -443,9 +442,9 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
         else
         {
           // final product length truncation check
-          int[] cdsRanges = adjustForProteinLength(translationLength,
+          int [] exons2 = adjustForProteinLength(translationLength,
                   exons);
-          dnaToProteinMapping = new Mapping(product, cdsRanges,
+          dnaToProteinMapping = new Mapping(product, exons2,
                   new int[]
                   { 1, translationLength }, 3, 1);
           if (product != null)
@@ -713,8 +712,7 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
 
   /**
    * Truncates (if necessary) the exon intervals to match 3 times the length of
-   * the protein; also accepts 3 bases longer (for stop codon not included in
-   * protein)
+   * the protein (including truncation for stop codon included in exon)
    * 
    * @param proteinLength
    * @param exon
@@ -731,11 +729,9 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     int exonLength = MappingUtils.getLength(Arrays.asList(exon));
   
     /*
-     * if exon length matches protein, or is shorter, or longer by the 
-     * length of a stop codon (3 bases), then leave it unchanged
+     * if exon length matches protein, or is shorter, then leave it unchanged
      */
-    if (expectedCdsLength >= exonLength
-            || expectedCdsLength == exonLength - 3)
+    if (expectedCdsLength >= exonLength)
     {
       return exon;
     }
diff --git a/test/jalview/ws/dbsources/EmblSourceTest.java b/test/jalview/ws/dbsources/EmblSourceTest.java
index 5bf215c..93e8e51 100644
--- a/test/jalview/ws/dbsources/EmblSourceTest.java
+++ b/test/jalview/ws/dbsources/EmblSourceTest.java
@@ -26,6 +26,13 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import java.io.ByteArrayInputStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.testng.annotations.Test;
+
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
@@ -35,13 +42,6 @@ import jalview.xml.binding.embl.EntryType.Feature;
 import jalview.xml.binding.embl.EntryType.Feature.Qualifier;
 import jalview.xml.binding.embl.XrefType;
 
-import java.io.ByteArrayInputStream;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import org.testng.annotations.Test;
-
 public class EmblSourceTest
 {
 
@@ -315,11 +315,12 @@ public class EmblSourceTest
     // exact length match:
     assertSame(exons, EmblXmlSource.adjustForProteinLength(6, exons));
 
-    // match if we assume exons include stop codon not in protein:
-    assertSame(exons, EmblXmlSource.adjustForProteinLength(5, exons));
+    // truncate last exon by 3bp (e.g. stop codon)
+    int[] truncated = EmblXmlSource.adjustForProteinLength(5, exons);
+    assertEquals("[11, 15, 21, 25, 31, 35]", Arrays.toString(truncated));
 
     // truncate last exon by 6bp
-    int[] truncated = EmblXmlSource.adjustForProteinLength(4, exons);
+    truncated = EmblXmlSource.adjustForProteinLength(4, exons);
     assertEquals("[11, 15, 21, 25, 31, 32]", Arrays.toString(truncated));
 
     // remove last exon and truncate preceding by 1bp