X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=c39e407909461306d244e8595a46bf399087dd44;hb=a8bb0960ee2534ea27fd24586fdc0fb9a9a9715e;hp=1a11630dce8ffbd7f98297ae24db26df8d641621;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 1a11630..c39e407 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -4,11 +4,11 @@ package jalview.gui;
 import jalview.analysis.*;
 import jalview.datamodel.*;
 import jalview.util.*;
+import jalview.schemes.*;
 import javax.swing.*;
 import java.awt.*;
 import java.awt.event.*;
 import java.util.*;
-import java.io.*;
 
 public class TreeCanvas extends JPanel implements MouseListener
 {
@@ -91,11 +91,20 @@ public class TreeCanvas extends JPanel implements MouseListener
 
       int ypos = (int)(node.ycount * chunk) + offy;
 
-      if (node.element() instanceof SequenceI) {
-          g.setColor(((SequenceI)((SequenceNode)node).element()).getColor().darker());
-      } else {
-          g.setColor(Color.black);
+      if (node.element() instanceof SequenceI)
+      {
+       if ( ( (SequenceI) ( (SequenceNode) node).element()).getColor() == Color.white)
+       {
+         g.setColor(Color.black);
+       }
+       else
+        g.setColor( ( (SequenceI) ( (SequenceNode) node).element()).getColor().
+                   darker());
+
       }
+      else
+          g.setColor(Color.black);
+
 
       // Draw horizontal line
       g.drawLine(xstart,ypos,xend,ypos);
@@ -238,18 +247,19 @@ public class TreeCanvas extends JPanel implements MouseListener
     }
   }
 
-  public void setColor(SequenceNode node, Color c) {
-    if (node == null) {
+  public void setColor(SequenceNode node, Color c)
+  {
+    if (node == null)
       return;
-    }
 
-    if (node.left() == null && node.right() == null) {
+    if (node.left() == null && node.right() == null)
+    {
       node.color = c;
 
-      if (node.element() instanceof SequenceI) {
+      if (node.element() instanceof SequenceI)
           ((SequenceI)node.element()).setColor(c);
-      }
-    } else {
+    } else
+    {
       node.color = c;
       setColor((SequenceNode)node.left(),c);
       setColor((SequenceNode)node.right(),c);
@@ -348,22 +358,53 @@ public class TreeCanvas extends JPanel implements MouseListener
               tree.groupNodes(tree.getTopNode(),fthreshold);
               setColor(tree.getTopNode(),Color.black);
 
-              for (int i=0; i < tree.getGroups().size(); i++) {
+              av.sel.clear();
+              av.alignment.deleteAllGroups();
+
+              for (int i=0; i < tree.getGroups().size(); i++)
+              {
 
-                  int tmp = i%(7);
                   Color col = new Color((int)(Math.random()*255),
                                         (int)(Math.random()*255),
                                         (int)(Math.random()*255));
-
                   setColor((SequenceNode)tree.getGroups().elementAt(i),col.brighter());
 
-                  // l is vector of Objects
                   Vector l = tree.findLeaves((SequenceNode)tree.getGroups().elementAt(i),new Vector());
+                  SequenceGroup sg = null;
+                  for (int j = 0; j < l.size(); j++)
+                  {
+                    SequenceNode sn = (SequenceNode) l.elementAt(j);
+                    if(sg==null)
+                       sg  = new SequenceGroup("TreeGroup", av.getGlobalColourScheme(), true, true,false,0,av.alignment.getWidth());
+
+                    sg.addSequence( (Sequence) sn.element());
+                  }
+
+                  if (av.getGlobalColourScheme() instanceof ConservationColourScheme)
+                  {
+                    ConservationColourScheme ccs = (ConservationColourScheme) av.getGlobalColourScheme();
+                    Conservation c = new Conservation("Group",
+                                                      ResidueProperties.propHash, 3,
+                                                      sg.sequences, sg.getStartRes(),
+                                                      sg.getEndRes());
+
+                    c.calculate();
+                    c.verdict(false, 100);
+                    ccs = new ConservationColourScheme(c, ccs.cs);
+
+                    sg.cs = ccs;
+
+                  }
+
+
+
+                  av.alignment.addGroup(sg);
 
               }
           }
       }
 
+      PaintRefresher.Refresh(this);
       repaint();
 
   }