X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=c2a2ccbdab4bbf429c20c7c78e8720db4daa0e09;hb=56d68286221ccea4f894ef480df4173a880152b2;hp=64e5fdc10df1f05c9f469e8edcfe69292d3f2f22;hpb=f5d913e184c4bd83448d0c20093e079ae7af107a;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 64e5fdc..c2a2ccb 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -165,14 +166,17 @@ public class SeqCanvas extends JComponent
 
     if (av.hasHiddenColumns())
     {
-      startx = av.getColumnSelection().adjustForHiddenColumns(startx);
-      endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+      startx = av.getAlignment().getHiddenColumns()
+              .adjustForHiddenColumns(startx);
+      endx = av.getAlignment().getHiddenColumns()
+              .adjustForHiddenColumns(endx);
     }
 
     int maxwidth = av.getAlignment().getWidth();
     if (av.hasHiddenColumns())
     {
-      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      maxwidth = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(maxwidth) - 1;
     }
 
     // WEST SCALE
@@ -224,7 +228,8 @@ public class SeqCanvas extends JComponent
 
     if (av.hasHiddenColumns())
     {
-      endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+      endx = av.getAlignment().getHiddenColumns()
+              .adjustForHiddenColumns(endx);
     }
 
     SequenceI seq;
@@ -515,7 +520,8 @@ public class SeqCanvas extends JComponent
 
     if (av.hasHiddenColumns())
     {
-      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      maxwidth = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(maxwidth) - 1;
     }
 
     while ((ypos <= canvasHeight) && (startRes < maxwidth))
@@ -553,11 +559,10 @@ public class SeqCanvas extends JComponent
       {
         g.setColor(Color.blue);
         int res;
-        for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
-                .size(); i++)
+        HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+        for (int i = 0; i < hidden.getHiddenRegions().size(); i++)
         {
-          res = av.getColumnSelection().findHiddenRegionPosition(i)
-                  - startRes;
+          res = hidden.findHiddenRegionPosition(i) - startRes;
 
           if (res < 0 || res > endx - startRes)
           {
@@ -654,7 +659,8 @@ public class SeqCanvas extends JComponent
     }
     else
     {
-      List<int[]> regions = av.getColumnSelection().getHiddenColumns();
+      List<int[]> regions = av.getAlignment().getHiddenColumns()
+              .getHiddenRegions();
 
       int screenY = 0;
       int blockStart = startRes;