X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FMappingUtils.java;h=1f2e8dbd26633ed7baa6aa5e15544a47aca57f43;hb=373a0f23b37fdd3c40d3ebb4a3c9120f5773bb45;hp=7dd0b5c0ab30cf2e89888f9f6c3d0a5323625049;hpb=10ff37d2cb03f342ddbed679951d3e2fef0a404b;p=jalview.git

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 7dd0b5c..1f2e8db 100644
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -16,7 +16,6 @@ import jalview.datamodel.SearchResults.Match;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.gui.AlignViewport;
 
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -259,7 +258,6 @@ public final class MappingUtils
       {
         acf.markMappedRegion(seq, index, results);
       }
-      results.addResult(seq, index, index);
     }
     return results;
   }
@@ -385,8 +383,8 @@ public final class MappingUtils
     }
 
     /*
-     * Have to align the sequences before constructing the OrderCommand - which
-     * then realigns them?!?
+     * Have to sort the sequences before constructing the OrderCommand - which
+     * then resorts them?!?
      */
     final SequenceI[] mappedOrderArray = mappedOrder
             .toArray(new SequenceI[mappedOrder.size()]);
@@ -408,7 +406,7 @@ public final class MappingUtils
    * @return
    */
   public static ColumnSelection mapColumnSelection(ColumnSelection colsel,
-          AlignViewportI mapFrom, AlignViewport mapTo)
+          AlignViewportI mapFrom, AlignViewportI mapTo)
   {
     boolean targetIsNucleotide = mapTo.isNucleotide();
     AlignViewportI protein = targetIsNucleotide ? mapFrom : mapTo;
@@ -417,8 +415,15 @@ public final class MappingUtils
     ColumnSelection mappedColumns = new ColumnSelection();
     char fromGapChar = mapFrom.getAlignment().getGapCharacter();
 
-    for (int col : colsel.getSelected())
+    // FIXME allow for hidden columns
+
+    /*
+     * For each mapped column, find the range of columns that residues in that
+     * column map to.
+     */
+    for (Object obj : colsel.getSelected())
     {
+      int col = ((Integer) obj).intValue();
       int mappedToMin = Integer.MAX_VALUE;
       int mappedToMax = Integer.MIN_VALUE;
 
@@ -448,7 +453,8 @@ public final class MappingUtils
           SequenceI mappedSeq = m.getSequence();
 
           /*
-           * Locate the aligned sequence whose dataset is mappedSeq.
+           * Locate the aligned sequence whose dataset is mappedSeq. TODO a
+           * datamodel that can do this efficiently.
            */
           for (SequenceI toSeq : mapTo.getAlignment().getSequences())
           {
@@ -460,12 +466,16 @@ public final class MappingUtils
               mappedToMax = Math.max(mappedToMax, mappedEndCol);
               // System.out.println(fromSeq.getName() + " mapped to cols "
               // + mappedStartCol + ":" + mappedEndCol);
+              break;
+              // note: remove break if we ever want to map one to many sequences
             }
           }
         }
       }
       /*
-       * Add mapped columns to mapped selection (converting base 1 to base 0)
+       * Add the range of mapped columns to the mapped selection (converting
+       * base 1 to base 0). Note that this may include intron-only regions which
+       * lie between the start and end ranges of the selection.
        */
       for (int i = mappedToMin; i <= mappedToMax; i++)
       {