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

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 8ade5d6..dc5f7cc 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -25,6 +25,7 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
@@ -395,11 +396,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
       if (av.hasHiddenColumns())
       {
-        start = av.getColumnSelection().findColumnPosition(start);
-        end = av.getColumnSelection().findColumnPosition(end);
+        HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+        start = hidden.findColumnPosition(start);
+        end = hidden.findColumnPosition(end);
         if (start == end)
         {
-          if (!av.getColumnSelection().isVisible(r[0]))
+          if (!hidden.isVisible(r[0]))
           {
             // don't scroll - position isn't visible
             return false;
@@ -704,7 +706,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (av.hasHiddenColumns())
     {
       // reset the width to exclude hidden columns
-      width = av.getColumnSelection().findColumnPosition(width);
+      width = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(width);
     }
 
     hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
@@ -917,7 +920,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
       if (av.hasHiddenColumns())
       {
-        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+        maxwidth = av.getAlignment().getHiddenColumns()
+                .findColumnPosition(maxwidth) - 1;
       }
 
       int canvasWidth = getSeqPanel().seqCanvas
@@ -1205,7 +1209,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int maxwidth = av.getAlignment().getWidth();
     if (av.hasHiddenColumns())
     {
-      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      maxwidth = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(maxwidth) - 1;
     }
 
     int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth
@@ -1399,7 +1404,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int maxwidth = av.getAlignment().getWidth();
     if (av.hasHiddenColumns())
     {
-      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
+      maxwidth = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(maxwidth);
     }
 
     int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
@@ -1629,7 +1635,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int maxwidth = av.getAlignment().getWidth();
     if (av.hasHiddenColumns())
     {
-      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      maxwidth = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(maxwidth) - 1;
     }
 
     int height = ((maxwidth / chunkWidth) + 1) * cHeight;