JAL-2388 Hidden cols separated from column selection (almost complete)

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

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 2e30132..44a55ec 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;
@@ -537,7 +538,7 @@ public final class MappingUtils
               toSequences, fromGapChar);
     }
 
-    for (int[] hidden : colsel.getHiddenColumns())
+    for (int[] hidden : colsel.getListOfCols())
     {
       mapHiddenColumns(hidden, codonFrames, mappedColumns, fromSequences,
               toSequences, fromGapChar);
@@ -557,7 +558,7 @@ 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)
   {