X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=7f30c2489ada6adc0b43fc1ea0cb955e9877c0b3;hb=f5700411d71ab46a54d9e7dd46223b59fd1565b8;hp=8fcca782189c29145ee9fe9f2277cf9e320957da;hpb=353236b63bd005adee3fb297984228e26bc9d66c;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 8fcca78..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,
@@ -204,24 +205,24 @@ 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;
-    boolean newGroup=false;
+    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;
     int oldStartX=0,oldEndX=0,oldY=0;
+    int oldRStartX=0,oldREndX=0,oldRY=0;
     for (int i = y1 ; i < y2 ;i++)
     {
      nextSeq = av.getAlignment().getSequenceAt(i);
-     if(group==null || group!=av.alignment.findGroup( nextSeq ))
-        newGroup = true;
-     else
-        newGroup = false;
 
-    group = av.alignment.findGroup( nextSeq );
+     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);
@@ -238,10 +239,10 @@ public class SeqCanvas extends JPanel
         ey = offset + AlignmentUtil.getPixelHeight(starty, i+1, av.getCharHeight());
 
 
-        if (newGroup)
+        if (!inGroup)
         {
-          g.drawLine(oldStartX, oldY, oldEndX, oldY); // Horizontal, bottom of old box
           g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box
+          inGroup=true;
         }
 
         g.drawLine(sx, sy, sx, ey ); // vertical line, left hand side
@@ -254,17 +255,18 @@ public class SeqCanvas extends JPanel
         oldY = ey;
 
      }
-     else if(sx>-1)
+     else if(inGroup)
      {
        g.setColor(Color.lightGray);
-       g.drawLine(sx, ey, ex, ey); // Horizontal, bottom of old box
+       g.drawLine(oldStartX, oldY, oldEndX, oldY); // Horizontal, bottom of old box
      }
+     else
+       inGroup = false;
 
      group = av.getRubberbandGroup();
-     if( group !=null &&  group.sequences.contains(nextSeq) )
+     if( group != null && group.sequences.contains(nextSeq) )
      {
-         g.setColor(Color.red);
-
+         g.setColor(Color.RED.brighter());
          sx = (group.getStartRes() - startx) * charWidth;
          sy = offset +
              AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight());
@@ -272,10 +274,11 @@ public class SeqCanvas extends JPanel
          ey = offset +
              AlignmentUtil.getPixelHeight(starty, i + 1, av.getCharHeight());
 
-         if (newGroup)
+         if (!inRB)
          {
-           g.drawLine(oldStartX, oldY, oldEndX, oldY); // Horizontal, bottom of old box
+
            g.drawLine(sx, sy, ex, sy); // Horizontal, top of new box
+           inRB = true;
          }
 
          g.drawLine(sx, sy, sx, ey); // vertical line, left hand side
@@ -283,11 +286,18 @@ public class SeqCanvas extends JPanel
          if (i == y2 - 1) // last line of alignment, seal the box
            g.drawLine(sx, ey, ex, ey); // Horizontal, bottom of old box
 
-      //   oldStartX = sx;
-        // oldEndX = ex;
-        // oldY = ey;
-
+          oldRStartX = sx;
+          oldREndX = ex;
+          oldRY = ey;
      }
+     else if(inRB)
+     {
+       g.setColor(Color.RED.brighter());
+       g.drawLine(oldRStartX, oldRY, oldREndX, oldRY); // Horizontal, bottom of old box
+       inRB = false;
+     }
+     else
+       inRB = false;
 
     }
 
@@ -303,7 +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,