X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=ca78bdac0adb7e304535549d6f78fb762dcbe914;hb=d6509fcf3a8cc90616e18cb22cec97f85c722bb8;hp=9a4c82c39822715e1da1f04d57790cc52befea71;hpb=d053a3c980cf4318b9a19a255f9fc870e74de989;p=jalview.git

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 9a4c82c..ca78bda 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -1,18 +1,18 @@
 /*
  * 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.
- * 
+ *
  * 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/>.
  */
 package jalview.appletgui;
@@ -64,7 +64,7 @@ public class TreeCanvas extends Panel implements MouseListener,
 
   SequenceNode highlightNode;
 
-  AlignmentPanel ap; 
+  AlignmentPanel ap;
   public TreeCanvas(AlignmentPanel ap, ScrollPane scroller)
   {
     this.ap = ap;
@@ -143,7 +143,7 @@ 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 +194,13 @@ 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()))
+                      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)
@@ -440,7 +442,7 @@ public class TreeCanvas extends Panel implements MouseListener,
     // for
     // scrollbar
 
-    float wscale = (float) (width - labelLength - offx * 2)
+    float wscale = (width - labelLength - offx * 2)
             / tree.getMaxHeight();
 
     SequenceNode top = tree.getTopNode();
@@ -466,25 +468,29 @@ public class TreeCanvas extends Panel implements MouseListener,
       }
 
       int x = (int) (threshold
-              * (float) (getSize().width - labelLength - 2 * offx) + offx);
+              * (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 +520,12 @@ public class TreeCanvas extends Panel implements MouseListener,
     }
   }
 
+  @Override
   public void mouseDragged(MouseEvent ect)
   {
   }
 
+  @Override
   public void mouseMoved(MouseEvent evt)
   {
     av.setCurrentTree(tree);
@@ -539,6 +547,7 @@ public class TreeCanvas extends Panel implements MouseListener,
     }
   }
 
+  @Override
   public void mousePressed(MouseEvent e)
   {
     av.setCurrentTree(tree);
@@ -608,6 +617,9 @@ public class TreeCanvas extends Panel implements MouseListener,
 
       ColourSchemeI cs = null;
 
+      SequenceGroup sg = new SequenceGroup(sequences, "", cs, true, true,
+              false, 0, av.getAlignment().getWidth() - 1);
+
       if (av.getGlobalColourScheme() != null)
       {
         if (av.getGlobalColourScheme() instanceof UserColourScheme)
@@ -619,8 +631,7 @@ public class TreeCanvas extends Panel implements MouseListener,
         }
         else
         {
-          cs = ColourSchemeProperty.getColour(sequences, av.getAlignment()
-                  .getWidth(), ColourSchemeProperty.getColourName(av
+          cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty.getColourName(av
                   .getGlobalColourScheme()));
         }
         // cs is null if shading is an annotationColourGradient
@@ -630,9 +641,9 @@ public class TreeCanvas extends Panel implements MouseListener,
                   av.getIgnoreGapsConsensus());
         }
       }
-
-      SequenceGroup sg = new SequenceGroup(sequences, "", cs, true, true,
-              false, 0, av.getAlignment().getWidth() - 1);
+      // 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.setName("JTreeGroup:" + sg.hashCode());
       sg.setIdColour(col);
@@ -655,7 +666,7 @@ public class TreeCanvas extends Panel implements MouseListener,
 
     }
     ap.updateAnnotation();
-    
+
   }
 
   public void setShowDistances(boolean state)