Add support RNAML format

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

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index ea78d0f..9f65511 100755 (executable)
--- 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();
@@ -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
+          cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty.getColourName(av
                   .getGlobalColourScheme()));
         }
-
-        cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
-                av.getIgnoreGapsConsensus());
+        // cs is null if shading is an annotationColourGradient
+        if (cs!=null)
+        {
+          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++)
@@ -925,11 +927,11 @@ 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.