X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=d1003e551d7e290085b1e9b9ca9f7c78722e3abe;hb=87ea83af3e209a8c3a4b19f9530a9c05b4541148;hp=9022182f137f626f2007cf0363d5723f321ba111;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 9022182..d1003e5 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -1,13 +1,13 @@
 /*
- * 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 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -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();
@@ -889,6 +889,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       }
 
       ColourSchemeI cs = null;
+      SequenceGroup sg = new SequenceGroup(sequences, null, cs, true, true,
+              false, 0, av.getAlignment().getWidth() - 1);
 
       if (av.getGlobalColourScheme() != null)
       {
@@ -901,18 +903,18 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         }
         else
         {
-          cs = ColourSchemeProperty.getColour(sequences, av.alignment
-                  .getWidth(), ColourSchemeProperty.getColourName(av
-                  .getGlobalColourScheme()));
+          cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty
+                  .getColourName(av.getGlobalColourScheme()));
+        }
+        // cs is null if shading is an annotationColourGradient
+        if (cs != null)
+        {
+          cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
+                  av.getIgnoreGapsConsensus());
         }
-
-        cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
-                av.getIgnoreGapsConsensus());
       }
-
-      SequenceGroup sg = new SequenceGroup(sequences, null, cs, true, true,
-              false, 0, av.alignment.getWidth() - 1);
-
+      sg.cs = cs;
+      // sg.recalcConservation();
       sg.setName("JTreeGroup:" + sg.hashCode());
       sg.setIdColour(col);
       for (int a = 0; a < aps.length; a++)
@@ -925,17 +927,19 @@ 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(new SequenceGroup(sg));
       }
     }
     // notify the panel to redo any group specific stuff.
     for (int a = 0; a < aps.length; a++)
     {
       aps[a].updateAnnotation();
+      // TODO: JAL-868 - need to ensure view colour change message is broadcast
+      // to any Jmols listening in
     }
 
   }