JAL-2591 simplifying hidden columns usage

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

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index f35339c..f75286a 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;
@@ -107,7 +108,7 @@ public final class MappingUtils
      * Cache a copy of the target sequences so we can mimic successive edits on
      * them. This lets us compute mappings for all edits in the set.
      */
-    Map<SequenceI, SequenceI> targetCopies = new HashMap<SequenceI, SequenceI>();
+    Map<SequenceI, SequenceI> targetCopies = new HashMap<>();
     for (SequenceI seq : mapTo.getSequences())
     {
       SequenceI ds = seq.getDatasetSequence();
@@ -320,7 +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;
@@ -432,7 +433,7 @@ public final class MappingUtils
           boolean undo, AlignmentI mapTo, List<AlignedCodonFrame> mappings)
   {
     SequenceI[] sortOrder = command.getSequenceOrder(undo);
-    List<SequenceI> mappedOrder = new ArrayList<SequenceI>();
+    List<SequenceI> mappedOrder = new ArrayList<>();
     int j = 0;
 
     /*
@@ -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)
     {
-      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)
   {
@@ -693,7 +696,7 @@ public final class MappingUtils
   public static List<char[]> findCodonsFor(SequenceI seq, int col,
           List<AlignedCodonFrame> mappings)
   {
-    List<char[]> result = new ArrayList<char[]>();
+    List<char[]> result = new ArrayList<>();
     int dsPos = seq.findPosition(col);
     for (AlignedCodonFrame mapping : mappings)
     {
@@ -772,7 +775,7 @@ public final class MappingUtils
           SequenceI sequence, List<AlignedCodonFrame> mappings,
           List<SequenceI> filterList)
   {
-    List<AlignedCodonFrame> result = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> result = new ArrayList<>();
     if (sequence == null || mappings == null)
     {
       return result;