X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=0df43221d887ea52b81726be920d580b8dfe54b2;hb=d8c6e303402455460fb1d987b4c18a2d75e6a3c9;hp=3e47139930bad4fe91581ffd79ea1474d9eb8d2c;hpb=7d451923bf2ad5a358109eed435f354fc935f6ab;p=jalview.git

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 3e47139..0df4322 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -294,6 +294,8 @@ public class SeqCanvas
   int LABEL_WEST, LABEL_EAST;
   public int getWrappedCanvasWidth(int cwidth)
   {
+      cwidth -= cwidth % av.charWidth;
+
       FontMetrics fm = getFontMetrics(av.getFont());
 
       LABEL_EAST = 0;
@@ -334,15 +336,12 @@ public class SeqCanvas
 
     FontMetrics fm = getFontMetrics(av.getFont());
 
-    int LABEL_EAST = 0;
 
     if (av.scaleRightWrapped)
     {
         LABEL_EAST = fm.stringWidth(getMask());
     }
 
-    int LABEL_WEST = 0;
-
     if (av.scaleLeftWrapped)
     {
         LABEL_WEST = fm.stringWidth(getMask());
@@ -496,7 +495,7 @@ public class SeqCanvas
       groupIndex = 0;
   }
 
-  if ( group != null)
+  if ( group != null )
   {
       do
       {
@@ -505,6 +504,7 @@ public class SeqCanvas
           boolean inGroup = false;
           int top = -1;
           int bottom = -1;
+          int alHeight = av.alignment.getHeight()-1;
 
           for (i = startSeq; i < endSeq; i++)
           {
@@ -519,12 +519,13 @@ public class SeqCanvas
               }
 
               if ( (sx <= (endRes-startRes)*av.charWidth) &&
-                      group.sequences.contains(av.alignment.getSequenceAt(
+                      group.getSequences(false).contains(av.alignment.getSequenceAt(
                               i)))
               {
-                if ((bottom == -1) &&
-                        !group.sequences.contains(
-                            av.alignment.getSequenceAt(i + 1)))
+                if ( (bottom == -1) &&
+                    (i >= alHeight ||
+                     !group.getSequences(false).contains(
+                         av.alignment.getSequenceAt(i + 1))))
                 {
                     bottom = sy + av.charHeight;
                 }
@@ -532,7 +533,7 @@ public class SeqCanvas
                   if (!inGroup)
                   {
                       if (((top == -1) && (i == 0)) ||
-                              !group.sequences.contains(
+                              !group.getSequences(false).contains(
                                   av.alignment.getSequenceAt(i - 1)))
                       {
                           top = sy;