SequenceGroup is now an array

[jalview.git] / src / jalview / gui / SeqCanvas.java

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