From 40460cd7a6f6d80c6a8c2f86c5bc55d941445975 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 8 Sep 2010 14:10:29 +0000
Subject: [PATCH] trap NPE possiblity for trees that have no associated
 alignment panels (usually because they've been closed)

---
 src/jalview/gui/TreeCanvas.java |   38 ++++++++++++++++++++------------------
 1 file changed, 20 insertions(+), 18 deletions(-)

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index c2b9b7f..a66f251 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -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
@@ -904,8 +906,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
                   .getGlobalColourScheme()));
         }
 
-        cs.setThreshold(av.getGlobalColourScheme().getThreshold(), av
-                .getIgnoreGapsConsensus());
+        cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
+                av.getIgnoreGapsConsensus());
       }
 
       SequenceGroup sg = new SequenceGroup(sequences, null, cs, true, true,
@@ -919,8 +921,8 @@ 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);
@@ -931,7 +933,7 @@ 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();
     }
-- 
1.7.10.2