From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 4 Feb 2022 13:13:02 +0000 (+0000)
Subject: JAL-3806 require mapping extent covers both sequence’s dataset sequence to avoid... 
X-Git-Tag: Release_2_11_2_0~13^2~4^2~1
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=f19db76149ae51db15f904890fb56b4c9aa25d8d

JAL-3806 require mapping extent covers both sequence’s dataset sequence to avoid spurious  mappings from overlapping CDS
---

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 3c33063..eda1a13 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -445,7 +445,9 @@ public class AlignedCodonFrame
     SequenceI ds = seq.getDatasetSequence();
     for (SequenceToSequenceMapping ssm : mappings)
     {
-      if (ssm.fromSeq == seq || ssm.fromSeq == ds)
+      if (ssm.covers(seq,true,true))
+      {
+      if ((ssm.fromSeq == seq || ssm.fromSeq == ds))
       {
         codon = ssm.mapping.map.locateInTo(index, index);
         if (codon != null)
@@ -456,7 +458,7 @@ public class AlignedCodonFrame
           }
         }
       }
-      else if (ssm.mapping.to == seq || ssm.mapping.to == ds)
+      else if ((ssm.mapping.to == seq || ssm.mapping.to == ds))
       {
         {
           codon = ssm.mapping.map.locateInFrom(index, index);
@@ -468,7 +470,7 @@ public class AlignedCodonFrame
             }
           }
         }
-      }
+      }}
     }
   }
 
diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 03a32c9..c66fe00 100644
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -380,6 +380,7 @@ public final class MappingUtils
             List<AlignedCodonFrame> mapping = Arrays
                     .asList(new AlignedCodonFrame[]
                     { acf });
+            // locate start 
             SearchResultsI sr = buildSearchResults(selected,
                     startResiduePos, mapping);
             for (SearchResultMatchI m : sr.getResults())
@@ -387,6 +388,7 @@ public final class MappingUtils
               mappedStartResidue = m.getStart();
               mappedEndResidue = m.getEnd();
             }
+            // locate end - allowing for adjustment of start range
             sr = buildSearchResults(selected, endResiduePos, mapping);
             for (SearchResultMatchI m : sr.getResults())
             {