Merge branch 'features/JAL-2360colourSchemeApplicability' into

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

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index da83338..2e30132 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -31,8 +31,9 @@ import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResults;
-import jalview.datamodel.SearchResults.Match;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -194,7 +195,7 @@ public final class MappingUtils
       /*
        * Determine all mappings from this position to mapped sequences.
        */
-      SearchResults sr = buildSearchResults(seq, seqpos, mappings);
+      SearchResultsI sr = buildSearchResults(seq, seqpos, mappings);
 
       if (!sr.isEmpty())
       {
@@ -266,10 +267,10 @@ public final class MappingUtils
    * @param seqmappings
    * @return
    */
-  public static SearchResults buildSearchResults(SequenceI seq, int index,
+  public static SearchResultsI buildSearchResults(SequenceI seq, int index,
           List<AlignedCodonFrame> seqmappings)
   {
-    SearchResults results = new SearchResults();
+    SearchResultsI results = new SearchResults();
     addSearchResults(results, seq, index, seqmappings);
     return results;
   }
@@ -283,7 +284,7 @@ public final class MappingUtils
    * @param index
    * @param seqmappings
    */
-  public static void addSearchResults(SearchResults results, SequenceI seq,
+  public static void addSearchResults(SearchResultsI results, SequenceI seq,
           int index, List<AlignedCodonFrame> seqmappings)
   {
     if (index >= seq.getStart() && index <= seq.getEnd())
@@ -319,7 +320,7 @@ public final class MappingUtils
      * Copy group name, colours etc, but not sequences or sequence colour scheme
      */
     SequenceGroup mappedGroup = new SequenceGroup(sg);
-    mappedGroup.cs = mapTo.getGlobalColourScheme();
+    mappedGroup.setColourScheme(mapTo.getGlobalColourScheme());
     mappedGroup.clear();
 
     int minStartCol = -1;
@@ -374,16 +375,17 @@ 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,
+              List<AlignedCodonFrame> mapping = Arrays
+                      .asList(new AlignedCodonFrame[] { acf });
+              SearchResultsI sr = buildSearchResults(selected,
                       startResiduePos, mapping);
-              for (Match m : sr.getResults())
+              for (SearchResultMatchI m : sr.getResults())
               {
                 mappedStartResidue = m.getStart();
                 mappedEndResidue = m.getEnd();
               }
               sr = buildSearchResults(selected, endResiduePos, mapping);
-              for (Match m : sr.getResults())
+              for (SearchResultMatchI m : sr.getResults())
               {
                 mappedStartResidue = Math.min(mappedStartResidue,
                         m.getStart());
@@ -555,9 +557,9 @@ 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 +591,9 @@ 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);
@@ -646,9 +648,8 @@ public final class MappingUtils
        * Get the residue position and find the mapped position.
        */
       int residuePos = fromSeq.findPosition(col);
-      SearchResults sr = buildSearchResults(fromSeq, residuePos,
-              mappings);
-      for (Match m : sr.getResults())
+      SearchResultsI sr = buildSearchResults(fromSeq, residuePos, mappings);
+      for (SearchResultMatchI m : sr.getResults())
       {
         int mappedStartResidue = m.getStart();
         int mappedEndResidue = m.getEnd();
@@ -893,7 +894,7 @@ public final class MappingUtils
     {
       return ranges;
     }
-  
+
     int[] copy = Arrays.copyOf(ranges, ranges.length);
     int sxpos = -1;
     int cdspos = 0;
@@ -921,7 +922,7 @@ public final class MappingUtils
         break;
       }
     }
-  
+
     if (sxpos > 0)
     {
       /*