JAL-653 AlignedCodonFrame collections changed from Set to List

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

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 11597eb..22714b8 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -38,12 +38,11 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 
 import java.util.ArrayList;
-import java.util.Collections;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
-import java.util.Set;
 
 /**
  * Helper methods for manipulations involving sequence mappings.
@@ -69,7 +68,7 @@ public final class MappingUtils
    */
   protected static void mapCutOrPaste(Edit edit, boolean undo,
           List<SequenceI> targetSeqs, EditCommand result,
-          Set<AlignedCodonFrame> mappings)
+          List<AlignedCodonFrame> mappings)
   {
     Action action = edit.getAction();
     if (undo)
@@ -93,7 +92,7 @@ public final class MappingUtils
    */
   public static EditCommand mapEditCommand(EditCommand command,
           boolean undo, final AlignmentI mapTo, char gapChar,
-          Set<AlignedCodonFrame> mappings)
+          List<AlignedCodonFrame> mappings)
   {
     /*
      * For now, only support mapping from protein edits to cDna
@@ -165,7 +164,7 @@ public final class MappingUtils
           Map<SequenceI, SequenceI> originalSequences,
           final List<SequenceI> targetSeqs,
           Map<SequenceI, SequenceI> targetCopies, char gapChar,
-          EditCommand result, Set<AlignedCodonFrame> mappings)
+          EditCommand result, List<AlignedCodonFrame> mappings)
   {
     Action action = edit.getAction();
 
@@ -268,7 +267,7 @@ public final class MappingUtils
    * @return
    */
   public static SearchResults buildSearchResults(SequenceI seq, int index,
-          Set<AlignedCodonFrame> seqmappings)
+          List<AlignedCodonFrame> seqmappings)
   {
     SearchResults results = new SearchResults();
     addSearchResults(results, seq, index, seqmappings);
@@ -285,7 +284,7 @@ public final class MappingUtils
    * @param seqmappings
    */
   public static void addSearchResults(SearchResults results, SequenceI seq,
-          int index, Set<AlignedCodonFrame> seqmappings)
+          int index, List<AlignedCodonFrame> seqmappings)
   {
     if (index >= seq.getStart() && index <= seq.getEnd())
     {
@@ -314,7 +313,7 @@ public final class MappingUtils
      */
     boolean targetIsNucleotide = mapTo.isNucleotide();
     AlignViewportI protein = targetIsNucleotide ? mapFrom : mapTo;
-    Set<AlignedCodonFrame> codonFrames = protein.getAlignment()
+    List<AlignedCodonFrame> codonFrames = protein.getAlignment()
             .getCodonFrames();
     /*
      * Copy group name, colours etc, but not sequences or sequence colour scheme
@@ -375,15 +374,15 @@ public final class MappingUtils
               /*
                * Found a sequence mapping. Locate the start/end mapped residues.
                */
+              List<AlignedCodonFrame> mapping = Arrays.asList(new AlignedCodonFrame[] { acf });
               SearchResults sr = buildSearchResults(selected,
-                      startResiduePos, Collections.singleton(acf));
+                      startResiduePos, mapping);
               for (Match m : sr.getResults())
               {
                 mappedStartResidue = m.getStart();
                 mappedEndResidue = m.getEnd();
               }
-              sr = buildSearchResults(selected, endResiduePos,
-                      Collections.singleton(acf));
+              sr = buildSearchResults(selected, endResiduePos, mapping);
               for (Match m : sr.getResults())
               {
                 mappedStartResidue = Math.min(mappedStartResidue,
@@ -428,7 +427,7 @@ public final class MappingUtils
    * @return
    */
   public static CommandI mapOrderCommand(OrderCommand command,
-          boolean undo, AlignmentI mapTo, Set<AlignedCodonFrame> mappings)
+          boolean undo, AlignmentI mapTo, List<AlignedCodonFrame> mappings)
   {
     SequenceI[] sortOrder = command.getSequenceOrder(undo);
     List<SequenceI> mappedOrder = new ArrayList<SequenceI>();
@@ -512,7 +511,7 @@ public final class MappingUtils
   {
     boolean targetIsNucleotide = mapTo.isNucleotide();
     AlignViewportI protein = targetIsNucleotide ? mapFrom : mapTo;
-    Set<AlignedCodonFrame> codonFrames = protein.getAlignment()
+    List<AlignedCodonFrame> codonFrames = protein.getAlignment()
             .getCodonFrames();
     ColumnSelection mappedColumns = new ColumnSelection();
 
@@ -594,8 +593,8 @@ public final class MappingUtils
   }
 
   /**
-   * Returns the mapped codon for a given aligned sequence column position (base
-   * 0).
+   * Returns the mapped codon or codons for a given aligned sequence column
+   * position (base 0).
    * 
    * @param seq
    *          an aligned peptide sequence
@@ -603,21 +602,27 @@ public final class MappingUtils
    *          an aligned column position (base 0)
    * @param mappings
    *          a set of codon mappings
-   * @return the bases of the mapped codon in the cDNA dataset sequence, or null
-   *         if not found
+   * @return the bases of the mapped codon(s) in the cDNA dataset sequence(s),
+   *         or an empty list if none found
    */
-  public static char[] findCodonFor(SequenceI seq, int col,
-          Set<AlignedCodonFrame> mappings)
+  public static List<char[]> findCodonsFor(SequenceI seq, int col,
+          List<AlignedCodonFrame> mappings)
   {
+    List<char[]> result = new ArrayList<char[]>();
     int dsPos = seq.findPosition(col);
     for (AlignedCodonFrame mapping : mappings)
     {
       if (mapping.involvesSequence(seq))
       {
-        return mapping.getMappedCodon(seq.getDatasetSequence(), dsPos);
+        List<char[]> codons = mapping.getMappedCodons(
+                seq.getDatasetSequence(), dsPos);
+        if (codons != null)
+        {
+          result.addAll(codons);
+        }
       }
     }
-    return null;
+    return result;
   }
 
   /**
@@ -663,7 +668,7 @@ public final class MappingUtils
    * @return
    */
   public static List<AlignedCodonFrame> findMappingsForSequence(
-          SequenceI sequence, Set<AlignedCodonFrame> mappings)
+          SequenceI sequence, List<AlignedCodonFrame> mappings)
   {
     List<AlignedCodonFrame> result = new ArrayList<AlignedCodonFrame>();
     if (sequence == null || mappings == null)