X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=e402b9b3606a9d998745a88db13cf707c08f768b;hb=5e8ec77d921ff2d604811e5e4ba7e9211b0f48de;hp=975345376cd81a0435b3dc016a4e5cce3a1ad037;hpb=733b32eba6687bc7d4194c0d6d90a9efe7c5855e;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 9753453..e402b9b 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -407,7 +407,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       {
         int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1;
         start = Math.max(start - offset, 0);
-        end = Math.min(end + offset, seq.getEnd() - 1);
+        end = end + offset - 1;
+        // end = Math.min(end + offset, seq.getEnd() - 1);
       }
 
       if (start < 0)
@@ -436,11 +437,12 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     int start = -1;
     if (av.hasHiddenColumns())
     {
-      start = av.getColumnSelection().findColumnPosition(ostart);
-      end = av.getColumnSelection().findColumnPosition(end);
+      AlignmentI al = av.getAlignment();
+      start = al.getHiddenColumns().findColumnPosition(ostart);
+      end = al.getHiddenColumns().findColumnPosition(end);
       if (start == end)
       {
-        if (!scrollToNearest && !av.getColumnSelection().isVisible(ostart))
+        if (!scrollToNearest && !al.getHiddenColumns().isVisible(ostart))
         {
           // don't scroll - position isn't visible
           return false;
@@ -689,7 +691,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
       if (av.hasHiddenColumns())
       {
-        width = av.getColumnSelection().findColumnPosition(width);
+        width = av.getAlignment().getHiddenColumns()
+                .findColumnPosition(width);
       }
       if (x < 0)
       {
@@ -990,7 +993,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     int maxwidth = av.getAlignment().getWidth();
     if (av.hasHiddenColumns())
     {
-      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      maxwidth = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(maxwidth) - 1;
     }
 
     // get the width of the canvas in residues