Merge remote-tracking branch 'origin/develop' into

[jalview.git] / src / jalview / gui / SeqPanel.java

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 1432fcb..749b390 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -27,6 +27,7 @@ import jalview.commands.EditCommand.Action;
 import jalview.commands.EditCommand.Edit;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
@@ -233,7 +234,8 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (av.hasHiddenColumns())
     {
-      res = av.getColumnSelection().adjustForHiddenColumns(res);
+      res = av.getAlignment().getHiddenColumns()
+              .adjustForHiddenColumns(res);
     }
 
     return res;
@@ -339,20 +341,23 @@ public class SeqPanel extends JPanel implements MouseListener,
   {
     seqCanvas.cursorX += dx;
     seqCanvas.cursorY += dy;
+
+    HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+
     if (av.hasHiddenColumns()
-            && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
+ && !hidden.isVisible(seqCanvas.cursorX))
     {
       int original = seqCanvas.cursorX - dx;
       int maxWidth = av.getAlignment().getWidth();
 
-      while (!av.getColumnSelection().isVisible(seqCanvas.cursorX)
+      while (!hidden.isVisible(seqCanvas.cursorX)
               && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
       {
         seqCanvas.cursorX += dx;
       }
 
       if (seqCanvas.cursorX >= maxWidth
-              || !av.getColumnSelection().isVisible(seqCanvas.cursorX))
+              || !hidden.isVisible(seqCanvas.cursorX))
       {
         seqCanvas.cursorX = original;
       }
@@ -398,16 +403,17 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
       if (!av.getWrapAlignment())
       {
-        while (seqCanvas.cursorX < av.getColumnSelection()
-                .adjustForHiddenColumns(av.getRanges().getStartRes()))
+        HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+        while (seqCanvas.cursorX < hidden.adjustForHiddenColumns(av
+                .getRanges().getStartRes()))
         {
           if (!ap.scrollRight(false))
           {
             break;
           }
         }
-        while (seqCanvas.cursorX > av.getColumnSelection()
-                .adjustForHiddenColumns(av.getRanges().getEndRes()))
+        while (seqCanvas.cursorX > hidden.adjustForHiddenColumns(av
+                .getRanges().getEndRes()))
         {
           if (!ap.scrollRight(true))
           {
@@ -1144,8 +1150,10 @@ public class SeqPanel extends JPanel implements MouseListener,
     if (av.hasHiddenColumns())
     {
       fixedColumns = true;
-      int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
-      int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
+      int y1 = av.getAlignment().getHiddenColumns()
+              .getHiddenBoundaryLeft(startres);
+      int y2 = av.getAlignment().getHiddenColumns()
+              .getHiddenBoundaryRight(startres);
 
       if ((insertGap && startres > y1 && lastres < y1)
               || (!insertGap && startres < y2 && lastres > y2))
@@ -1220,8 +1228,8 @@ public class SeqPanel extends JPanel implements MouseListener,
         {
           if (sg.getSize() == av.getAlignment().getHeight())
           {
-            if ((av.hasHiddenColumns() && startres < av
-                    .getColumnSelection().getHiddenBoundaryRight(startres)))
+            if ((av.hasHiddenColumns() && startres < av.getAlignment()
+                    .getHiddenColumns().getHiddenBoundaryRight(startres)))
             {
               endEditing();
               return;
@@ -1957,7 +1965,7 @@ public class SeqPanel extends JPanel implements MouseListener,
    */
   @Override
   public void selection(SequenceGroup seqsel, ColumnSelection colsel,
-          SelectionSource source)
+          HiddenColumns hidden, SelectionSource source)
   {
     // TODO: fix this hack - source of messages is align viewport, but SeqPanel
     // handles selection messages...
@@ -1993,7 +2001,7 @@ public class SeqPanel extends JPanel implements MouseListener,
      * Check for selection in a view of which this one is a dna/protein
      * complement.
      */
-    if (selectionFromTranslation(seqsel, colsel, source))
+    if (selectionFromTranslation(seqsel, colsel, hidden, source))
     {
       return;
     }
@@ -2056,7 +2064,8 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
         else
         {
-          av.getColumnSelection().setElementsFrom(colsel);
+          av.getColumnSelection().setElementsFrom(colsel,
+                  av.getAlignment().getHiddenColumns());
         }
       }
       av.isColSelChanged(true);
@@ -2065,8 +2074,8 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (copycolsel
             && av.hasHiddenColumns()
-            && (av.getColumnSelection() == null || av.getColumnSelection()
-                    .getHiddenColumns() == null))
+            && (av.getAlignment().getHiddenColumns() == null || av
+                    .getAlignment().getHiddenColumns().getListOfCols() == null))
     {
       System.err.println("Bad things");
     }
@@ -2095,7 +2104,8 @@ public class SeqPanel extends JPanel implements MouseListener,
    * @param source
    */
   protected boolean selectionFromTranslation(SequenceGroup seqsel,
-          ColumnSelection colsel, SelectionSource source)
+          ColumnSelection colsel, HiddenColumns hidden,
+          SelectionSource source)
   {
     if (!(source instanceof AlignViewportI))
     {
@@ -2118,9 +2128,13 @@ public class SeqPanel extends JPanel implements MouseListener,
     /*
      * Map column selection
      */
-    ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
-            av);
+    // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
+    // av);
+    ColumnSelection cs = new ColumnSelection();
+    HiddenColumns hs = new HiddenColumns();
+    MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
     av.setColumnSelection(cs);
+    av.getAlignment().setHiddenColumns(hs);
 
     // lastly, update any dependent dialogs
     if (ap.getCalculationDialog() != null)