update author list in license for (JAL-826)

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

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index c2b9b7f..42a09aa 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 2.5)
- * 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.
  * 
@@ -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());
       }
 
@@ -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();
 
@@ -893,8 +894,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       {
         if (av.getGlobalColourScheme() instanceof UserColourScheme)
         {
-          cs = new UserColourScheme(((UserColourScheme) av
-                  .getGlobalColourScheme()).getColours());
+          cs = new UserColourScheme(
+                  ((UserColourScheme) av.getGlobalColourScheme())
+                          .getColours());
 
         }
         else
@@ -903,9 +905,12 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
                   .getWidth(), 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,
@@ -919,8 +924,8 @@ 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);
@@ -931,9 +936,10 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       }
     }
     // 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
     }
 
   }