X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=3af9fb939edc8b3476e5f144a6172f718437d824;hb=b61f2d9b571c4e4ab3285257c6ddbd39da61fa05;hp=e947f7ab0a49bf80a21c75f800b7ab6b6d0b080e;hpb=5cd5b6e7864fe435ceb3f5c2f339a436ea0aac93;p=jalview.git

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index e947f7a..3af9fb9 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/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
@@ -49,7 +49,7 @@ public class SeqCanvas
     this.av = av;
     fr = new FeatureRenderer(av);
     sr = new SequenceRenderer(av);
-    PaintRefresher.Register(this, av.alignment);
+    PaintRefresher.Register(this, av.getSequenceSetId());
   }
 
   public AlignViewport getViewport()
@@ -355,13 +355,22 @@ public class SeqCanvas
    */
   String getMask()
   {
-    String mask = "00";
-    for (int i = av.alignment.getWidth(); i > 0; i /= 10)
+    String mask = "0";
+    int maxWidth = 0;
+    int tmp;
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      tmp = av.alignment.getSequenceAt(i).getEnd();
+      if (tmp > maxWidth)
+        maxWidth = tmp;
+    }
+
+    for (int i = maxWidth; i > 0; i /= 10)
     {
       mask += "0";
     }
     return mask;
-    }
+  }
 
   public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
                                int startRes)
@@ -532,9 +541,9 @@ public class SeqCanvas
           {
             g1.setColor(Color.blue);
             g1.drawLine( (blockEnd - blockStart + 1) * av.charWidth - 1,
-                        startSeq + offset,
-                        (blockEnd - blockStart + 1) * av.charWidth - 1,
-                        startSeq + (endSeq - startSeq) * av.charHeight + offset);
+                         0 + offset,
+                         (blockEnd - blockStart + 1) * av.charWidth - 1,
+                         (endSeq - startSeq) * av.charHeight + offset);
           }
 
           g1.translate( -screenY * av.charWidth, 0);
@@ -575,6 +584,9 @@ public class SeqCanvas
         {
             nextSeq = av.alignment.getSequenceAt(i);
 
+            if(nextSeq==null)
+              continue;
+
             sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq),
                             startRes, endRes,
                             offset + ( (i - startSeq) * av.charHeight));
@@ -629,7 +641,7 @@ public class SeqCanvas
      int ex = -1;
      int groupIndex = -1;
 
-     if ( (group == null) && (group.getSize(false) > 0))
+     if ( (group == null) && (av.alignment.getGroups().size() > 0))
      {
        group = (SequenceGroup) av.alignment.getGroups().elementAt(0);
        groupIndex = 0;
@@ -659,12 +671,12 @@ public class SeqCanvas
            }
 
            if ( (sx <= (endRes - startRes) * av.charWidth) &&
-               group.getSequences(false).
+               group.getSequences(null).
                contains(av.alignment.getSequenceAt(i)))
            {
              if ( (bottom == -1) &&
              (i >= alHeight ||
-                 !group.getSequences(false).contains(
+                 !group.getSequences(null).contains(
                      av.alignment.getSequenceAt(i + 1))))
              {
                bottom = sy + av.charHeight;
@@ -673,7 +685,7 @@ public class SeqCanvas
              if (!inGroup)
              {
                if ( ( (top == -1) && (i == 0)) ||
-                   !group.getSequences(false).contains(
+                   !group.getSequences(null).contains(
                        av.alignment.getSequenceAt(i - 1)))
                {
                  top = sy;