From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 11 Aug 2020 11:10:14 +0000 (+0100)
Subject: JAL-3706 handle e.g. mapped exon feature extending beyond mapped range
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=62c6e630bd24574d279417dd6b4ee921b5537131;p=jalview.git

JAL-3706 handle e.g. mapped exon feature extending beyond mapped range
---

diff --git a/src/jalview/datamodel/MappedFeatures.java b/src/jalview/datamodel/MappedFeatures.java
index 1f672be..2bc82bc 100644
--- a/src/jalview/datamodel/MappedFeatures.java
+++ b/src/jalview/datamodel/MappedFeatures.java
@@ -296,21 +296,30 @@ public class MappedFeatures
   {
     int[] result = null;
     MapList map = mapping.getMap();
+    
+    /*
+     * mapping may be in either direction, so handle either case;
+     * limit feature extent to the range of the mapping if it is greater
+     * (e.g. an overlapping exon); if that still fails, try reducing by
+     * 3 positions (to omit a mapped stop codon)
+     */
     if (mapping.to == featureSequence)
     {
+      begin = Math.max(begin, map.getToLowest());
+      end = Math.min(end,  map.getToHighest());
       result = map.locateInFrom(begin, end);
       if (result == null)
       {
-        // fudge for feature (e.g. CDS) extending to a mapped stop codon
         result = map.locateInFrom(begin, end-3);
       }
     }
     else
     {
+      begin = Math.max(begin, map.getFromLowest());
+      end = Math.min(end,  map.getFromHighest());
       result = map.locateInTo(begin, end);
       if (result == null)
       {
-        // fudge for feature (e.g. CDS) extending to a mapped stop codon
         result = map.locateInTo(begin, end-3);
       }
     }
diff --git a/test/jalview/datamodel/MappedFeaturesTest.java b/test/jalview/datamodel/MappedFeaturesTest.java
index 5d00089..06fb303 100644
--- a/test/jalview/datamodel/MappedFeaturesTest.java
+++ b/test/jalview/datamodel/MappedFeaturesTest.java
@@ -143,13 +143,20 @@ public class MappedFeaturesTest
     assertEquals(pepPos[1], 2);
     
     /*
-     * scenario: exon feature on CDS including stop codon;
+     * scenario: CDS feature on CDS including stop codon;
      */
     pepPos = mf.getMappedPositions(10, 21);
     assertEquals(pepPos[0], 1);
     assertEquals(pepPos[1], 3);
     
     /*
+     * scenario: exon feature on CDS extending beyond start and stop codons
+     */
+    pepPos = mf.getMappedPositions(2, 222);
+    assertEquals(pepPos[0], 1);
+    assertEquals(pepPos[1], 3);
+    
+    /*
      * now with the mapping from protein to CDS
      */
     mapping = new Mapping(cds, map.getInverse());