Merge branch 'develop' into bug/JAL-2510amendFeatures

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

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 2e30132..926ccc7 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -31,6 +31,7 @@ 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.SearchResultsI;
@@ -508,18 +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();
@@ -533,16 +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;
   }
 
   /**
@@ -557,7 +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)
   {