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

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

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index db7aa36..282e826 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;
@@ -232,7 +233,8 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (av.hasHiddenColumns())
     {
-      res = av.getColumnSelection().adjustForHiddenColumns(res);
+      res = av.getAlignment().getHiddenColumns()
+              .adjustForHiddenColumns(res);
     }
 
     return res;
@@ -338,20 +340,23 @@ 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;
       }
@@ -397,16 +402,17 @@ 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))
           {
@@ -1143,8 +1149,10 @@ 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))
@@ -1219,8 +1227,8 @@ 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;
@@ -1948,6 +1956,7 @@ public class SeqPanel extends JPanel implements MouseListener,
    */
   @Override
   public void selection(SequenceGroup seqsel, ColumnSelection colsel,
+          HiddenColumns hidden,
           SelectionSource source)
   {
     // TODO: fix this hack - source of messages is align viewport, but SeqPanel
@@ -2045,8 +2054,8 @@ 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");
     }