From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 23 Sep 2020 16:34:32 +0000 (+0100)
Subject: JAL-3748 not testing for sequence’s containment in mapped range breaks CDS reconstruc... 
X-Git-Tag: Release_2_11_1_3~5^2~17
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=48f5f04700dcb49463b20303c2075292f9d4d1d3

JAL-3748 not testing for sequence’s containment in mapped range breaks CDS reconstruction but allows  testAlignProteinAsDna_incompleteStartCodon to pass
---

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 84a74b6..25f1c27 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -504,7 +504,9 @@ public class AlignedCodonFrame
     {
       int mStart=ssm.getMapping().getMap().getFromLowest(),mEnd=ssm.getMapping().map.getFromHighest();
       if ((ssm.fromSeq == seq || ssm.fromSeq == seq.getDatasetSequence())
-              && seq.getStart()>=mStart && seq.getEnd()<=mEnd)
+              // here AlignmentUtilsTest. testAlignProteinAsDna_incompleteStartCodon fails because mStart/mEnd is contained by seq
+              // without this filter, we don't get the correct mapping, however
+           )//   && seq.getStart()>=mStart && seq.getEnd()<=mEnd)
       {
         for (SequenceI sourceAligned : al.getSequences())
         {