From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 14 Jul 2016 13:53:33 +0000 (+0100)
Subject: fix for JAL-2147
X-Git-Tag: Release_2_10_0~140^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6cedd15f7decf9a291f380f9bb57c939a1082aef;hp=81dc9ebd9bd93355897a9c5c87733c0bdb3e5f3b;p=jalview.git

fix for JAL-2147
- scope search for codonmappings to local alignment
- efficiency - use discovered mappings directly rather than letting highlight search results do the work again
---

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index eab4aa5..d3df56c 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -2700,6 +2700,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
      * all gapped visible regions
      */
     int lastSeq = alignment.getHeight() - 1;
+    List<AlignedCodonFrame> seqMappings = null;
     for (int seqNo = getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
     {
       sequence = getAlignment().getSequenceAt(seqNo);
@@ -2711,15 +2712,16 @@ public abstract class AlignmentViewport implements AlignViewportI,
       {
         continue;
       }
-      List<AlignedCodonFrame> seqMappings = MappingUtils
-              .findMappingsForSequence(sequence, mappings);
+      seqMappings = MappingUtils
+              .findMappingsForSequenceAndOthers(sequence, mappings,
+                      getCodingComplement().getAlignment());
       if (!seqMappings.isEmpty())
       {
         break;
       }
     }
 
-    if (sequence == null)
+    if (sequence == null || seqMappings == null || seqMappings.isEmpty())
     {
       /*
        * No ungapped mapped sequence in middle column - do nothing
@@ -2727,7 +2729,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
       return 0;
     }
     MappingUtils.addSearchResults(sr, sequence,
-            sequence.findPosition(middleColumn), mappings);
+            sequence.findPosition(middleColumn), seqMappings);
     return seqOffset;
   }