X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=35d73dedab23aae18855c66f2db96299d7427f3c;hb=ce7259404dbb5bbeeb296d32b6a2543b30a7c924;hp=076b0a3184101004a282f6f073bb2dc700cc33af;hpb=39267ff67b3f5cabdf20ea468b9e86739223adf5;p=jalview.git

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 076b0a3..35d73de 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -131,16 +131,16 @@ public class SeqCanvas extends Panel implements ViewportListenerI
     if (av.hasHiddenColumns())
     {
       startx = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(startx);
+              .visibleToAbsoluteColumn(startx);
       endx = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(endx);
+              .visibleToAbsoluteColumn(endx);
     }
 
     int maxwidth = av.getAlignment().getWidth();
     if (av.hasHiddenColumns())
     {
       maxwidth = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(maxwidth) - 1;
+              .absoluteToVisibleColumn(maxwidth) - 1;
     }
 
     // WEST SCALE
@@ -181,7 +181,7 @@ public class SeqCanvas extends Panel implements ViewportListenerI
     if (av.hasHiddenColumns())
     {
       endx = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(endx);
+              .visibleToAbsoluteColumn(endx);
     }
 
     SequenceI seq;
@@ -455,7 +455,7 @@ public class SeqCanvas extends Panel implements ViewportListenerI
     if (av.hasHiddenColumns())
     {
       maxwidth = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(maxwidth);
+              .absoluteToVisibleColumn(maxwidth);
     }
   
     while ((ypos <= canvasHeight) && (startRes < maxwidth))
@@ -492,7 +492,7 @@ public class SeqCanvas extends Panel implements ViewportListenerI
         HiddenColumns hidden = av.getAlignment().getHiddenColumns();
         g.setColor(Color.blue);
         int res;
-        Iterator<Integer> it = hidden.getBoundedStartIterator(startRes,
+        Iterator<Integer> it = hidden.getStartRegionIterator(startRes,
                 endx + 1);
         while (it.hasNext())
         {
@@ -566,7 +566,7 @@ public class SeqCanvas extends Panel implements ViewportListenerI
 
       HiddenColumns hidden = av.getAlignment().getHiddenColumns();
       VisibleContigsIterator regions = (VisibleContigsIterator) hidden
-              .getVisContigsIterator(startRes, endRes, true);
+              .getVisContigsIterator(startRes, endRes + 1, true);
 
       while (regions.hasNext())
       {