X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=b4ef770883b7d6947dd810d688dd4d1666219b12;hb=c20e9d4ae9c98b093e74a10bf965e6d20d80fadf;hp=8623872ff550697490b6fcfc3e791e57ce448e5f;hpb=628a29c56cc280f434f3568f3bf79555e1c77726;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 8623872..b4ef770 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -600,10 +600,11 @@ public class SeqCanvas extends JComponent
           if(av.getShowHiddenMarkers())
           {
             g1.setColor(Color.blue);
+
             g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1,
-                        startSeq + offset,
+                        0+offset,
                         (blockEnd - blockStart + 1) * av.charWidth - 1,
-                        startSeq + (endSeq - startSeq) * av.charHeight + offset);
+                        (endSeq - startSeq) * av.charHeight + offset);
           }
 
           g1.translate( -screenY * av.charWidth, 0);
@@ -698,6 +699,7 @@ public class SeqCanvas extends JComponent
         int sy = -1;
         int ex = -1;
         int groupIndex = -1;
+        int visWidth = (endRes - startRes +1) * av.charWidth;
 
         if ((group == null) && (av.alignment.getGroups().size() > 0))
         {
@@ -705,6 +707,7 @@ public class SeqCanvas extends JComponent
             groupIndex = 0;
         }
 
+
         if (group != null)
         {
             do
@@ -722,7 +725,7 @@ public class SeqCanvas extends JComponent
                     ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -
                         1;
 
-                    if(sx+ex<0 || sx>imgWidth)
+                    if(sx+ex<0 || sx>visWidth)
                     {
                       continue;
                     }
@@ -769,10 +772,10 @@ public class SeqCanvas extends JComponent
                     {
                       if (inGroup)
                       {
-                        if (sx >= 0 && sx < imgWidth)
+                        if (sx >= 0 && sx < visWidth)
                           g.drawLine(sx, oldY, sx, sy);
 
-                        if (sx + ex < imgWidth)
+                        if (sx + ex < visWidth)
                           g.drawLine(sx + ex, oldY, sx + ex, sy);
 
                         if (sx < 0)
@@ -781,8 +784,8 @@ public class SeqCanvas extends JComponent
                           sx = 0;
                         }
 
-                        if (sx + ex > imgWidth)
-                          ex = imgWidth;
+                        if (sx + ex > visWidth)
+                          ex = visWidth;
 
                         else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
                           ex = (endRes - startRes + 1) * av.charWidth;
@@ -807,10 +810,10 @@ public class SeqCanvas extends JComponent
                 if (inGroup)
                 {
                   sy = offset + ( (i - startSeq) * av.charHeight);
-                  if (sx >= 0 && sx < imgWidth)
+                  if (sx >= 0 && sx < visWidth)
                     g.drawLine(sx, oldY, sx, sy);
 
-                  if (sx + ex < imgWidth)
+                  if (sx + ex < visWidth)
                     g.drawLine(sx + ex, oldY, sx + ex, sy);
 
                   if (sx < 0)
@@ -819,8 +822,8 @@ public class SeqCanvas extends JComponent
                     sx = 0;
                   }
 
-                  if (sx + ex > imgWidth)
-                    ex = imgWidth;
+                  if (sx + ex > visWidth)
+                    ex = visWidth;
                   else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
                     ex = (endRes - startRes + 1) * av.charWidth;
 
@@ -841,6 +844,8 @@ public class SeqCanvas extends JComponent
 
                 groupIndex++;
 
+                g.setStroke(new BasicStroke());
+
                 if (groupIndex >= av.alignment.getGroups().size())
                 {
                     break;
@@ -848,7 +853,7 @@ public class SeqCanvas extends JComponent
 
                 group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);
 
-                g.setStroke(new BasicStroke());
+
             }
             while (groupIndex < av.alignment.getGroups().size());