Merge branch 'bug/JAL-3806_mappingCoversSequence_for2112' into develop

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

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 33decb4..86b7a6d 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -36,10 +36,12 @@ import jalview.commands.EditCommand.Action;
 import jalview.commands.EditCommand.Edit;
 import jalview.commands.OrderCommand;
 import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.Mapping;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
@@ -362,56 +364,55 @@ public final class MappingUtils
        */
       int startResiduePos = selected.findPosition(firstUngappedPos);
       int endResiduePos = selected.findPosition(lastUngappedPos);
-
-      for (AlignedCodonFrame acf : codonFrames)
+      for (SequenceI seq : mapTo.getAlignment().getSequences())
       {
-        SequenceI mappedSequence = targetIsNucleotide
-                ? acf.getDnaForAaSeq(selected)
-                : acf.getAaForDnaSeq(selected);
-        if (mappedSequence != null)
+        int mappedStartResidue = 0;
+        int mappedEndResidue = 0;
+        for (AlignedCodonFrame acf : codonFrames)
         {
-          for (SequenceI seq : mapTo.getAlignment().getSequences())
+          // rather than use acf.getCoveringMapping() we iterate through all
+          // mappings to make sure all CDS are selected for a protein
+          for (SequenceToSequenceMapping map: acf.getMappings())
+          {
+          if (map.covers(selected) && map.covers(seq))
           {
-            int mappedStartResidue = 0;
-            int mappedEndResidue = 0;
-            if (seq.getDatasetSequence() == mappedSequence)
+            /*
+             * Found a sequence mapping. Locate the start/end mapped residues.
+             */
+            List<AlignedCodonFrame> mapping = Arrays
+                    .asList(new AlignedCodonFrame[]
+                    { acf });
+            // locate start 
+            SearchResultsI sr = buildSearchResults(selected,
+                    startResiduePos, mapping);
+            for (SearchResultMatchI m : sr.getResults())
             {
-              /*
-               * Found a sequence mapping. Locate the start/end mapped residues.
-               */
-              List<AlignedCodonFrame> mapping = Arrays
-                      .asList(new AlignedCodonFrame[]
-                      { acf });
-              SearchResultsI sr = buildSearchResults(selected,
-                      startResiduePos, mapping);
-              for (SearchResultMatchI m : sr.getResults())
-              {
-                mappedStartResidue = m.getStart();
-                mappedEndResidue = m.getEnd();
-              }
-              sr = buildSearchResults(selected, endResiduePos, mapping);
-              for (SearchResultMatchI m : sr.getResults())
-              {
-                mappedStartResidue = Math.min(mappedStartResidue,
-                        m.getStart());
-                mappedEndResidue = Math.max(mappedEndResidue, m.getEnd());
-              }
-
-              /*
-               * Find the mapped aligned columns, save the range. Note findIndex
-               * returns a base 1 position, SequenceGroup uses base 0
-               */
-              int mappedStartCol = seq.findIndex(mappedStartResidue) - 1;
-              minStartCol = minStartCol == -1 ? mappedStartCol
-                      : Math.min(minStartCol, mappedStartCol);
-              int mappedEndCol = seq.findIndex(mappedEndResidue) - 1;
-              maxEndCol = maxEndCol == -1 ? mappedEndCol
-                      : Math.max(maxEndCol, mappedEndCol);
-              mappedGroup.addSequence(seq, false);
-              break;
+              mappedStartResidue = m.getStart();
+              mappedEndResidue = m.getEnd();
+            }
+            // locate end - allowing for adjustment of start range
+            sr = buildSearchResults(selected, endResiduePos, mapping);
+            for (SearchResultMatchI m : sr.getResults())
+            {
+              mappedStartResidue = Math.min(mappedStartResidue,
+                      m.getStart());
+              mappedEndResidue = Math.max(mappedEndResidue, m.getEnd());
             }
+
+            /*
+             * Find the mapped aligned columns, save the range. Note findIndex
+             * returns a base 1 position, SequenceGroup uses base 0
+             */
+            int mappedStartCol = seq.findIndex(mappedStartResidue) - 1;
+            minStartCol = minStartCol == -1 ? mappedStartCol
+                    : Math.min(minStartCol, mappedStartCol);
+            int mappedEndCol = seq.findIndex(mappedEndResidue) - 1;
+            maxEndCol = maxEndCol == -1 ? mappedEndCol
+                    : Math.max(maxEndCol, mappedEndCol);
+            mappedGroup.addSequence(seq, false);
+            break;
           }
-        }
+        }}
       }
     }
     mappedGroup.setStartRes(minStartCol < 0 ? 0 : minStartCol);
@@ -450,20 +451,23 @@ 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;
             }
           }
-        }
       }
     }
 
@@ -525,7 +529,7 @@ public final class MappingUtils
 
     if (colsel == null)
     {
-      return; // mappedColumns;
+      return; 
     }
 
     char fromGapChar = mapFrom.getAlignment().getGapCharacter();
@@ -549,7 +553,7 @@ public final class MappingUtils
       mapHiddenColumns(regions.next(), codonFrames, newHidden,
               fromSequences, toSequences, fromGapChar);
     }
-    return; // mappedColumns;
+    return; 
   }
 
   /**
@@ -667,7 +671,9 @@ public final class MappingUtils
          */
         for (SequenceI toSeq : toSequences)
         {
-          if (toSeq.getDatasetSequence() == mappedSeq)
+          if (toSeq.getDatasetSequence() == mappedSeq
+                  && mappedStartResidue >= toSeq.getStart()
+                  && mappedEndResidue <= toSeq.getEnd())
           {
             int mappedStartCol = toSeq.findIndex(mappedStartResidue);
             int mappedEndCol = toSeq.findIndex(mappedEndResidue);