JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 515ff51..1fe452d 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -374,7 +374,8 @@ public final class MappingUtils
               /*
                * Found a sequence mapping. Locate the start/end mapped residues.
                */
-              List<AlignedCodonFrame> mapping = Arrays.asList(new AlignedCodonFrame[] { acf });
+              List<AlignedCodonFrame> mapping = Arrays
+                      .asList(new AlignedCodonFrame[] { acf });
               SearchResults sr = buildSearchResults(selected,
                       startResiduePos, mapping);
               for (Match m : sr.getResults())
@@ -555,9 +556,9 @@ public final class MappingUtils
    * @param fromGapChar
    */
   protected static void mapHiddenColumns(int[] hidden,
-          List<AlignedCodonFrame> mappings,
-          ColumnSelection mappedColumns, List<SequenceI> fromSequences,
-          List<SequenceI> toSequences, char fromGapChar)
+          List<AlignedCodonFrame> mappings, ColumnSelection mappedColumns,
+          List<SequenceI> fromSequences, List<SequenceI> toSequences,
+          char fromGapChar)
   {
     for (int col = hidden[0]; col <= hidden[1]; col++)
     {
@@ -589,9 +590,9 @@ public final class MappingUtils
    * @param fromGapChar
    */
   protected static void mapColumn(int col,
-          List<AlignedCodonFrame> mappings,
-          ColumnSelection mappedColumns, List<SequenceI> fromSequences,
-          List<SequenceI> toSequences, char fromGapChar)
+          List<AlignedCodonFrame> mappings, ColumnSelection mappedColumns,
+          List<SequenceI> fromSequences, List<SequenceI> toSequences,
+          char fromGapChar)
   {
     int[] mappedTo = findMappedColumns(col, mappings, fromSequences,
             toSequences, fromGapChar);
@@ -646,8 +647,7 @@ public final class MappingUtils
        * Get the residue position and find the mapped position.
        */
       int residuePos = fromSeq.findPosition(col);
-      SearchResults sr = buildSearchResults(fromSeq, residuePos,
-              mappings);
+      SearchResults sr = buildSearchResults(fromSeq, residuePos, mappings);
       for (Match m : sr.getResults())
       {
         int mappedStartResidue = m.getStart();
@@ -757,9 +757,19 @@ public final class MappingUtils
     return findMappingsForSequenceAndOthers(sequence, mappings, null);
   }
 
+  /**
+   * Returns a list of any mappings that are from or to the given (aligned or
+   * dataset) sequence, optionally limited to mappings involving one of a given
+   * list of sequences.
+   * 
+   * @param sequence
+   * @param mappings
+   * @param filterList
+   * @return
+   */
   public static List<AlignedCodonFrame> findMappingsForSequenceAndOthers(
           SequenceI sequence, List<AlignedCodonFrame> mappings,
-          AlignmentI alignment)
+          List<SequenceI> filterList)
   {
     List<AlignedCodonFrame> result = new ArrayList<AlignedCodonFrame>();
     if (sequence == null || mappings == null)
@@ -770,14 +780,14 @@ public final class MappingUtils
     {
       if (mapping.involvesSequence(sequence))
       {
-        if (alignment != null)
+        if (filterList != null)
         {
-          for (SequenceI otherseq : alignment.getSequences())
+          for (SequenceI otherseq : filterList)
           {
+            SequenceI otherDataset = otherseq.getDatasetSequence();
             if (otherseq == sequence
-                    || (otherseq.getDatasetSequence() != null && (otherseq
-                            .getDatasetSequence() == sequence || otherseq
-                            .getDatasetSequence() == sequence
+                    || otherseq == sequence.getDatasetSequence()
+                    || (otherDataset != null && (otherDataset == sequence || otherDataset == sequence
                             .getDatasetSequence())))
             {
               // skip sequences in subset which directly relate to sequence
@@ -883,7 +893,7 @@ public final class MappingUtils
     {
       return ranges;
     }
-  
+
     int[] copy = Arrays.copyOf(ranges, ranges.length);
     int sxpos = -1;
     int cdspos = 0;
@@ -911,7 +921,7 @@ public final class MappingUtils
         break;
       }
     }
-  
+
     if (sxpos > 0)
     {
       /*