Merge branch 'develop' into bug/JAL-2510amendFeatures

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

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 3ae0394..458ed54 100644 (file)
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -419,11 +419,12 @@ 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;
@@ -725,7 +726,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
     if (av.hasHiddenColumns())
     {
-      width = av.getColumnSelection().findColumnPosition(width);
+      width = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(width);
     }
     if (x < 0)
     {
@@ -748,8 +750,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
     if ((hextent + x) > width)
     {
-      System.err.println("hextent was " + hextent + " and x was " + x);
-
+      // System.err.println("hextent was " + hextent + " and x was " + x);
+      //
       x = width - hextent;
     }
 
@@ -1009,7 +1011,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
       if (av.hasHiddenColumns())
       {
-        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+        maxwidth = av.getAlignment().getHiddenColumns()
+                .findColumnPosition(maxwidth) - 1;
       }
 
       int canvasWidth = seqPanel.seqCanvas