From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 16 Sep 2020 16:37:15 +0000 (+0100)
Subject: JAL-3700 JAL-3748 use AlignedCodonFrame.covers(seq,true) to select the protein that... 
X-Git-Tag: Release_2_11_1_3~5^2~31
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=da3b58afa56be8d7177ff824a3490509dbcf984d

JAL-3700 JAL-3748 use AlignedCodonFrame.covers(seq,true) to select the protein that matches a CDS sequence
---

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 9fa11cc..fbc8a61 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -464,8 +464,7 @@ public class AlignedCodonFrame
       {
         for (SequenceI sourceAligned : al.getSequences())
         {
-          if (ssm.mapping.to == sourceAligned.getDatasetSequence()
-                  || ssm.mapping.to == sourceAligned)
+          if (ssm.covers(sourceAligned,true))
           {
             return sourceAligned;
           }
@@ -483,7 +482,7 @@ public class AlignedCodonFrame
       {
         for (SequenceI sourceAligned : al.getSequences())
         {
-          if (ssm.fromSeq == sourceAligned.getDatasetSequence())
+          if (ssm.covers(sourceAligned,true))
           {
             return sourceAligned;
           }