X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=0df43221d887ea52b81726be920d580b8dfe54b2;hb=2ac5b6423fe366e093c8f12b0935aefc9aafbe5f;hp=f6ef5779f0e3433e508c8d38b14370e3301c15e9;hpb=f7d45a21db810c5f8f7ca668d1a28f1403defe32;p=jalview.git

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index f6ef577..0df4322 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -141,7 +141,7 @@ public class SeqCanvas
           continue;
         }
 
-        value = av.alignment.getSequenceAt(i).findPosition(index);
+        value = seq.findPosition(index);
         break;
       }
       if (value != -1)
@@ -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());
@@ -366,7 +365,7 @@ public class SeqCanvas
 
     while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
     {
-      endx = startRes + cWidth;
+      endx = startRes + cWidth -1;
 
       if (endx > al.getWidth())
       {
@@ -407,7 +406,7 @@ public class SeqCanvas
           if(annotations==null)
             annotations = new AnnotationPanel(av);
 
-          annotations.drawComponent( g, startRes, endx );
+          annotations.drawComponent( g, startRes, endx+1 );
           g.translate(0, -cHeight - ypos-4);
         }
         g.translate(-LABEL_WEST, 0);
@@ -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++)
           {
@@ -519,21 +519,21 @@ 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)
+                if ( (bottom == -1) &&
+                    (i >= alHeight ||
+                     !group.getSequences(false).contains(
+                         av.alignment.getSequenceAt(i + 1))))
                 {
-                 if(i == endSeq-1 || // Dont check for i+1 if on the bottom row
-                  !group.sequences.contains(av.alignment.getSequenceAt(i+1 )))
-
                     bottom = sy + av.charHeight;
                 }
 
                   if (!inGroup)
                   {
                       if (((top == -1) && (i == 0)) ||
-                              !group.sequences.contains(
+                              !group.getSequences(false).contains(
                                   av.alignment.getSequenceAt(i - 1)))
                       {
                           top = sy;