X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=a2626e74587aee98628796f371d40fd1ac732194;hb=84684213f7f7c7b31d3c33dc49ca3b377a295438;hp=ca78bdac0adb7e304535549d6f78fb762dcbe914;hpb=c78ae20a67370e2566d204e3f4c55749ad9bad27;p=jalview.git

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index ca78bda..a2626e7 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -1,19 +1,20 @@
 /*
- * 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
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
  * 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
+ * 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
+ *  
+ * 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 
  * PURPOSE.  See the GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
@@ -65,6 +66,7 @@ public class TreeCanvas extends Panel implements MouseListener,
   SequenceNode highlightNode;
 
   AlignmentPanel ap;
+
   public TreeCanvas(AlignmentPanel ap, ScrollPane scroller)
   {
     this.ap = ap;
@@ -199,8 +201,7 @@ public class TreeCanvas extends Panel implements MouseListener,
       // Colour selected leaves differently
       SequenceGroup selected = av.getSelectionGroup();
       if (selected != null
-              && selected.getSequences(null).contains(
-                      node.element()))
+              && selected.getSequences(null).contains(node.element()))
       {
         g.setColor(Color.gray);
 
@@ -442,8 +443,7 @@ public class TreeCanvas extends Panel implements MouseListener,
     // for
     // scrollbar
 
-    float wscale = (width - labelLength - offx * 2)
-            / tree.getMaxHeight();
+    float wscale = (width - labelLength - offx * 2) / tree.getMaxHeight();
 
     SequenceNode top = tree.getTopNode();
 
@@ -467,8 +467,7 @@ public class TreeCanvas extends Panel implements MouseListener,
         g.setColor(Color.gray);
       }
 
-      int x = (int) (threshold
-              * (getSize().width - labelLength - 2 * offx) + offx);
+      int x = (int) (threshold * (getSize().width - labelLength - 2 * offx) + offx);
 
       g.drawLine(x, 0, x, getSize().height);
     }
@@ -580,7 +579,7 @@ public class TreeCanvas extends Panel implements MouseListener,
 
         av.setSelectionGroup(null);
         av.getAlignment().deleteAllGroups();
-        av.sequenceColours = null;
+        av.clearSequenceColours();
 
         colourGroups();
 
@@ -631,19 +630,20 @@ public class TreeCanvas extends Panel implements MouseListener,
         }
         else
         {
-          cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty.getColourName(av
-                  .getGlobalColourScheme()));
+          cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty
+                  .getColourName(av.getGlobalColourScheme()));
         }
         // cs is null if shading is an annotationColourGradient
-        if (cs!=null)
+        if (cs != null)
         {
           cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
                   av.getIgnoreGapsConsensus());
         }
       }
-      // TODO: cs used to be initialized with a sequence collection and recalcConservation called automatically
+      // TODO: cs used to be initialized with a sequence collection and
+      // recalcConservation called automatically
       // instead we set it manually - recalc called after updateAnnotation
-      sg.cs=cs;
+      sg.cs = cs;
 
       sg.setName("JTreeGroup:" + sg.hashCode());
       sg.setIdColour(col);