X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=b23fbc278b2ee6a1459617d7df39c749d9344ada;hb=7b414ed4f2cd0a458ec2cc60a181b1aadd24c73e;hp=17830fea8c74f88b3972b0db95184b1702042fa2;hpb=4789b0c6467eee2928113c97fe03e887ea4032d4;p=jalview.git

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 17830fe..b23fbc2 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -125,7 +125,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         aps[a].av.setSelectionGroup(selected);
       }
 
-      selected.setEndRes(aps[a].av.alignment.getWidth() - 1);
+      selected.setEndRes(aps[a].av.getAlignment().getWidth() - 1);
       selected.addOrRemove(sequence, true);
     }
   }
@@ -851,7 +851,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         for (int a = 0; a < aps.length; a++)
         {
           aps[a].av.setSelectionGroup(null);
-          aps[a].av.alignment.deleteAllGroups();
+          aps[a].av.getAlignment().deleteAllGroups();
           aps[a].av.sequenceColours = null;
         }
         colourGroups();
@@ -901,7 +901,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         }
         else
         {
-          cs = ColourSchemeProperty.getColour(sequences, av.alignment
+          cs = ColourSchemeProperty.getColour(sequences, av.getAlignment()
                   .getWidth(), ColourSchemeProperty.getColourName(av
                   .getGlobalColourScheme()));
         }
@@ -914,7 +914,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       }
 
       SequenceGroup sg = new SequenceGroup(sequences, null, cs, true, true,
-              false, 0, av.alignment.getWidth() - 1);
+              false, 0, av.getAlignment().getWidth() - 1);
 
       sg.setName("JTreeGroup:" + sg.hashCode());
       sg.setIdColour(col);
@@ -928,11 +928,11 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
                   sg.getStartRes(), sg.getEndRes());
 
           c.calculate();
-          c.verdict(false, aps[a].av.ConsPercGaps);
+          c.verdict(false, aps[a].av.getConsPercGaps());
           sg.cs.setConservation(c);
         }
 
-        aps[a].av.alignment.addGroup(sg);
+        aps[a].av.getAlignment().addGroup(sg);
       }
     }
     // notify the panel to redo any group specific stuff.