JAL-2490 refactored test for 'hasFeatures'

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

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 1fe452d..926ccc7 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -31,8 +31,10 @@ import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+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 +196,7 @@ 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 +268,10 @@ 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 +285,7 @@ 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 +321,7 @@ 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;
@@ -376,15 +378,15 @@ public final class MappingUtils
                */
               List<AlignedCodonFrame> mapping = Arrays
                       .asList(new AlignedCodonFrame[] { acf });
-              SearchResults sr = buildSearchResults(selected,
+              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());
@@ -507,18 +509,20 @@ public final class MappingUtils
    * @param mapTo
    * @return
    */
-  public static ColumnSelection mapColumnSelection(ColumnSelection colsel,
-          AlignViewportI mapFrom, AlignViewportI mapTo)
+  public static void mapColumnSelection(ColumnSelection colsel,
+          HiddenColumns hiddencols, AlignViewportI mapFrom,
+          AlignViewportI mapTo, ColumnSelection newColSel,
+          HiddenColumns newHidden)
   {
     boolean targetIsNucleotide = mapTo.isNucleotide();
     AlignViewportI protein = targetIsNucleotide ? mapFrom : mapTo;
     List<AlignedCodonFrame> codonFrames = protein.getAlignment()
             .getCodonFrames();
-    ColumnSelection mappedColumns = new ColumnSelection();
+    // ColumnSelection mappedColumns = new ColumnSelection();
 
     if (colsel == null)
     {
-      return mappedColumns;
+      return; // mappedColumns;
     }
 
     char fromGapChar = mapFrom.getAlignment().getGapCharacter();
@@ -532,16 +536,16 @@ public final class MappingUtils
 
     for (Integer sel : colsel.getSelected())
     {
-      mapColumn(sel.intValue(), codonFrames, mappedColumns, fromSequences,
+      mapColumn(sel.intValue(), codonFrames, newColSel, fromSequences,
               toSequences, fromGapChar);
     }
 
-    for (int[] hidden : colsel.getHiddenColumns())
+    for (int[] hidden : hiddencols.getHiddenRegions())
     {
-      mapHiddenColumns(hidden, codonFrames, mappedColumns, fromSequences,
+      mapHiddenColumns(hidden, codonFrames, newHidden, fromSequences,
               toSequences, fromGapChar);
     }
-    return mappedColumns;
+    return; // mappedColumns;
   }
 
   /**
@@ -556,7 +560,7 @@ public final class MappingUtils
    * @param fromGapChar
    */
   protected static void mapHiddenColumns(int[] hidden,
-          List<AlignedCodonFrame> mappings, ColumnSelection mappedColumns,
+          List<AlignedCodonFrame> mappings, HiddenColumns mappedColumns,
           List<SequenceI> fromSequences, List<SequenceI> toSequences,
           char fromGapChar)
   {
@@ -647,8 +651,8 @@ 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();