X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=d1003e551d7e290085b1e9b9ca9f7c78722e3abe;hb=59d682209891099d46b960509907c79e3fb276fe;hp=c2b9b7fbe26e31c2f9e00912fcdc390f01021eb6;hpb=a28784f8c598dbb91e41df691c86b282fe7174c4;p=jalview.git

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index c2b9b7f..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 2.5)
- * 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);
     }
   }
@@ -247,8 +247,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       }
 
       String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node
-              .getName())
-              : node.getName();
+              .getName()) : node.getName();
 
       int charWidth = fm.stringWidth(name) + 3;
       int charHeight = font.getSize();
@@ -487,9 +486,12 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       if (node.element() instanceof SequenceI)
       {
         AlignmentPanel[] aps = getAssociatedPanels();
-        for (int a = 0; a < aps.length; a++)
+        if (aps != null)
         {
-          aps[a].av.setSequenceColour((SequenceI) node.element(), c);
+          for (int a = 0; a < aps.length; a++)
+          {
+            aps[a].av.setSequenceColour((SequenceI) node.element(), c);
+          }
         }
       }
     }
@@ -626,9 +628,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       }
       else
       {
-        setPreferredSize(new Dimension(scrollPane.getWidth(), fm
-                .getHeight()
-                * nameHash.size()));
+        setPreferredSize(new Dimension(scrollPane.getWidth(),
+                fm.getHeight() * nameHash.size()));
         draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size());
       }
 
@@ -850,7 +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();
@@ -867,12 +868,12 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     AlignmentPanel[] aps = getAssociatedPanels();
     for (int i = 0; i < tree.getGroups().size(); i++)
     {
-      Color col = new Color((int) (Math.random() * 255), (int) (Math
-              .random() * 255), (int) (Math.random() * 255));
+      Color col = new Color((int) (Math.random() * 255),
+              (int) (Math.random() * 255), (int) (Math.random() * 255));
       setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter());
 
-      Vector l = tree.findLeaves((SequenceNode) tree.getGroups().elementAt(
-              i), new Vector());
+      Vector l = tree.findLeaves(
+              (SequenceNode) tree.getGroups().elementAt(i), new Vector());
 
       Vector sequences = new Vector();
 
@@ -888,29 +889,32 @@ 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)
       {
         if (av.getGlobalColourScheme() instanceof UserColourScheme)
         {
-          cs = new UserColourScheme(((UserColourScheme) av
-                  .getGlobalColourScheme()).getColours());
+          cs = new UserColourScheme(
+                  ((UserColourScheme) av.getGlobalColourScheme())
+                          .getColours());
 
         }
         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++)
@@ -919,21 +923,23 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
                 && aps[a].av.getGlobalColourScheme().conservationApplied())
         {
           Conservation c = new Conservation("Group",
-                  ResidueProperties.propHash, 3, sg.getSequences(null), sg
-                          .getStartRes(), sg.getEndRes());
+                  ResidueProperties.propHash, 3, sg.getSequences(null),
+                  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++)
+    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
     }
 
   }