X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=5c6223432f3f6c6a705bed3ae97948a6f4a5fad6;hb=ca5bf8c6364a63b98d37e2e76c13ce19a3b54897;hp=4c56e694ac192bc771c50695dc373571439a819b;hpb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;p=jalview.git

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 4c56e69..5c62234 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -1,13 +1,13 @@
 /*
- * 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)
+ * 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 
@@ -64,7 +64,8 @@ public class TreeCanvas extends Panel implements MouseListener,
 
   SequenceNode highlightNode;
 
-  AlignmentPanel ap; 
+  AlignmentPanel ap;
+
   public TreeCanvas(AlignmentPanel ap, ScrollPane scroller)
   {
     this.ap = ap;
@@ -143,7 +144,7 @@ public class TreeCanvas extends Panel implements MouseListener,
 
       if (node.element() instanceof SequenceI)
       {
-        SequenceI seq = (SequenceI) ((SequenceNode) node).element();
+        SequenceI seq = (SequenceI) node.element();
 
         if (av.getSequenceColour(seq) == Color.white)
         {
@@ -194,13 +195,12 @@ public class TreeCanvas extends Panel implements MouseListener,
       Rectangle rect = new Rectangle(xend + 10, ypos - charHeight,
               charWidth, charHeight);
 
-      nameHash.put((SequenceI) node.element(), rect);
+      nameHash.put(node.element(), rect);
 
       // Colour selected leaves differently
       SequenceGroup selected = av.getSelectionGroup();
       if (selected != null
-              && selected.getSequences(null).contains(
-                      (SequenceI) node.element()))
+              && selected.getSequences(null).contains(node.element()))
       {
         g.setColor(Color.gray);
 
@@ -224,7 +224,7 @@ public class TreeCanvas extends Panel implements MouseListener,
       int xend = (int) (height * scale) + offx;
       int ypos = (int) (node.ycount * chunk) + offy;
 
-      g.setColor(((SequenceNode) node).color.darker());
+      g.setColor(node.color.darker());
 
       // Draw horizontal line
       g.drawLine(xstart, ypos, xend, ypos);
@@ -390,11 +390,13 @@ public class TreeCanvas extends Panel implements MouseListener,
     }
   }
 
+  @Override
   public void update(Graphics g)
   {
     paint(g);
   }
 
+  @Override
   public void paint(Graphics g)
   {
     if (tree == null)
@@ -440,8 +442,7 @@ public class TreeCanvas extends Panel implements MouseListener,
     // for
     // scrollbar
 
-    float wscale = (float) (width - labelLength - offx * 2)
-            / tree.getMaxHeight();
+    float wscale = (width - labelLength - offx * 2) / tree.getMaxHeight();
 
     SequenceNode top = tree.getTopNode();
 
@@ -465,26 +466,29 @@ public class TreeCanvas extends Panel implements MouseListener,
         g.setColor(Color.gray);
       }
 
-      int x = (int) (threshold
-              * (float) (getSize().width - labelLength - 2 * offx) + offx);
+      int x = (int) (threshold * (getSize().width - labelLength - 2 * offx) + offx);
 
       g.drawLine(x, 0, x, getSize().height);
     }
 
   }
 
+  @Override
   public void mouseReleased(MouseEvent e)
   {
   }
 
+  @Override
   public void mouseEntered(MouseEvent e)
   {
   }
 
+  @Override
   public void mouseExited(MouseEvent e)
   {
   }
 
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
     if (highlightNode != null)
@@ -514,10 +518,12 @@ public class TreeCanvas extends Panel implements MouseListener,
     }
   }
 
+  @Override
   public void mouseDragged(MouseEvent ect)
   {
   }
 
+  @Override
   public void mouseMoved(MouseEvent evt)
   {
     av.setCurrentTree(tree);
@@ -539,6 +545,7 @@ public class TreeCanvas extends Panel implements MouseListener,
     }
   }
 
+  @Override
   public void mousePressed(MouseEvent e)
   {
     av.setCurrentTree(tree);
@@ -622,19 +629,20 @@ 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);
@@ -657,7 +665,7 @@ public class TreeCanvas extends Panel implements MouseListener,
 
     }
     ap.updateAnnotation();
-    
+
   }
 
   public void setShowDistances(boolean state)