(JAL-969) refactored alignmentViewport base class to own package and pulled up most...

[jalview.git] / src / jalview / appletgui / TreeCanvas.java

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 2ab7bf7..9a4c82c 100755 (executable)
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -87,7 +87,7 @@ public class TreeCanvas extends Panel implements MouseListener,
       av.setSelectionGroup(selected);
     }
 
-    selected.setEndRes(av.alignment.getWidth() - 1);
+    selected.setEndRes(av.getAlignment().getWidth() - 1);
     selected.addOrRemove(sequence, true);
   }
 
@@ -570,7 +570,7 @@ public class TreeCanvas extends Panel implements MouseListener,
         setColor(tree.getTopNode(), Color.black);
 
         av.setSelectionGroup(null);
-        av.alignment.deleteAllGroups();
+        av.getAlignment().deleteAllGroups();
         av.sequenceColours = null;
 
         colourGroups();
@@ -619,7 +619,7 @@ public class TreeCanvas extends Panel implements MouseListener,
         }
         else
         {
-          cs = ColourSchemeProperty.getColour(sequences, av.alignment
+          cs = ColourSchemeProperty.getColour(sequences, av.getAlignment()
                   .getWidth(), ColourSchemeProperty.getColourName(av
                   .getGlobalColourScheme()));
         }
@@ -632,7 +632,7 @@ public class TreeCanvas extends Panel implements MouseListener,
       }
 
       SequenceGroup sg = new SequenceGroup(sequences, "", cs, true, true,
-              false, 0, av.alignment.getWidth() - 1);
+              false, 0, av.getAlignment().getWidth() - 1);
 
       sg.setName("JTreeGroup:" + sg.hashCode());
       sg.setIdColour(col);
@@ -651,7 +651,7 @@ public class TreeCanvas extends Panel implements MouseListener,
 
       }
 
-      av.alignment.addGroup(sg);
+      av.getAlignment().addGroup(sg);
 
     }
     ap.updateAnnotation();