X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=7f30c2489ada6adc0b43fc1ea0cb955e9877c0b3;hb=4b65534cd7d7dad17375e16d38848a69f23882b4;hp=398aad9b70212e08bd65ee5713ad1d32b5759c85;hpb=6b9e5c5745220083e275a2d5e1d8c73d0dffe077;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 398aad9..7f30c24 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -31,6 +31,7 @@ public class SeqCanvas extends JPanel
     {
 	this.av         = av;
        setLayout(new BorderLayout());
+       PaintRefresher.Register(this);
 
     }
 
@@ -196,7 +197,7 @@ public class SeqCanvas extends JPanel
 
 */
 
-    if (y2 > starty && y1 < av.getEndSeq())
+   /* if (y2 > starty && y1 < av.getEndSeq())
     {
        fillBackground(g,
                    Color.red,
@@ -204,10 +205,11 @@ public class SeqCanvas extends JPanel
                    offset + AlignmentUtil.getPixelHeight(starty,y1,av.getCharHeight()),
                    (x2-x1+1)*charWidth,
                    offset + AlignmentUtil.getPixelHeight(y1,y2,av.getCharHeight()));
-    }
+    }*/
 
     SequenceI nextSeq;
     SequenceGroup group=null;
+    SequenceGroup [] groups=null;
     boolean inGroup=false; // are we in a defined group?
     boolean inRB=false; //Are we in a rubberband group?
     int sx=-1, sy=-1, ex=-1, ey=-1;
@@ -218,8 +220,9 @@ public class SeqCanvas extends JPanel
      nextSeq = av.getAlignment().getSequenceAt(i);
 
      group = av.alignment.findGroup( nextSeq );
+     groups = av.alignment.findAllGroups( nextSeq );
 
-     sr.drawSequence(g, nextSeq, group,x1,x2,
+     sr.drawSequence(g, nextSeq, groups,x1,x2,
                  (x1 - startx) * charWidth,
                  offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()),
                  charWidth,charHeight,null, i);
@@ -310,7 +313,7 @@ public class SeqCanvas extends JPanel
         if (searchSeq >= y1 && searchSeq <= y2)
         {
           SequenceRenderer ssr = (SequenceRenderer) sr;
-          ssr.drawHighlightedText(g, av.getAlignment().getSequenceAt(searchSeq),
+          ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq),
                                   searchStart,
                                   searchEnd,
                                   (searchStart - startx) * charWidth,