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

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

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index b62a1c7..b23fbc2 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -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);
@@ -932,7 +932,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
           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.