JAL-3700 fix for propagation of sort commands

[jalview.git] / src / jalview / util / MappingUtils.java

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index cf90bf9..499fc6b 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -22,6 +22,7 @@ package jalview.util;
 
 import jalview.analysis.AlignmentSorter;
 import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
@@ -79,7 +80,7 @@ public final class MappingUtils
       action = action.getUndoAction();
     }
     // TODO write this
-    System.err.println("MappingUtils.mapCutOrPaste not yet implemented");
+    Cache.log.error("MappingUtils.mapCutOrPaste not yet implemented");
   }
 
   /**
@@ -443,20 +444,23 @@ public final class MappingUtils
     {
       for (AlignedCodonFrame acf : mappings)
       {
-        SequenceI mappedSeq = mappingToNucleotide ? acf.getDnaForAaSeq(seq)
-                : acf.getAaForDnaSeq(seq);
-        if (mappedSeq != null)
-        {
           for (SequenceI seq2 : mapTo.getSequences())
           {
-            if (seq2.getDatasetSequence() == mappedSeq)
+            /*
+             * the corresponding peptide / CDS is the one for which there is
+             * a complete ('covering') mapping to 'seq'
+             */
+            SequenceI peptide = mappingToNucleotide ? seq2 : seq;
+            SequenceI cds = mappingToNucleotide ? seq : seq2;
+            SequenceToSequenceMapping s2s = acf.getCoveringMapping(cds,
+                    peptide);
+            if (s2s != null)
             {
               mappedOrder.add(seq2);
               j++;
               break;
             }
           }
-        }
       }
     }