X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=47bebbea18725d2e5cc5dbd88284e6ddc988600b;hb=a6cd54c46366acd8bc3350a79374b18f9eb0b240;hp=136be529298649cd2ca432758121e9b21e25c6ee;hpb=6e71f42b0a3713ddbc3054e7ea9d8f5088130ec9;p=jalview.git

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 136be52..47bebbe 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -59,15 +59,11 @@ public class TreeCanvas
   Hashtable nameHash = new Hashtable();
   Hashtable nodeHash = new Hashtable();
 
-  public TreeCanvas(AlignViewport av, NJTree tree, ScrollPane scroller,
-                    String label)
+  public TreeCanvas(AlignViewport av, ScrollPane scroller)
   {
     this.av = av;
-    this.tree = tree;
     scrollPane = scroller;
     addMouseListener(this);
-    tree.findHeight(tree.getTopNode());
-    longestName = label;
     setLayout(null);
 
     PaintRefresher.Register(this, av.alignment);
@@ -82,10 +78,9 @@ public class TreeCanvas
       av.setSelectionGroup(selected);
     }
 
-    selected.setEndRes(av.alignment.getWidth());
+    selected.setEndRes(av.alignment.getWidth()-1);
     selected.addOrRemove(sequence, true);
 
-System.out.println("called here");
     PaintRefresher.Refresh(this, av.alignment);
     repaint();
   }
@@ -94,6 +89,30 @@ System.out.println("called here");
   {
     this.tree = tree;
     tree.findHeight(tree.getTopNode());
+
+    // Now have to calculate longest name based on the leaves
+    Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
+    boolean has_placeholders = false;
+    longestName = "";
+
+    for (int i = 0; i < leaves.size(); i++)
+    {
+      SequenceNode lf = (SequenceNode) leaves.elementAt(i);
+
+      if (lf.isPlaceholder())
+      {
+        has_placeholders = true;
+      }
+
+      if (longestName.length() < ( (Sequence) lf.element()).getName()
+          .length())
+      {
+        longestName = TreeCanvas.PLACEHOLDER +
+            ( (Sequence) lf.element()).getName();
+      }
+    }
+
+    setMarkPlaceholders(has_placeholders);
   }
 
   public void drawNode(Graphics g, SequenceNode node, float chunk, float scale,
@@ -476,22 +495,39 @@ System.out.println("called here");
           Vector sequences = new Vector();
           for (int j = 0; j < l.size(); j++)
           {
-            sequences.addElement( (Sequence) ( (SequenceNode) l.elementAt(j)).element());
+            SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element();
+            if(!sequences.contains(s1))
+              sequences.addElement(s1);
           }
 
-          ColourSchemeI cs = ColourSchemeProperty.getColour(sequences, av.alignment.getWidth(),
-              ColourSchemeProperty.getColourName(av.getGlobalColourScheme()));
+          ColourSchemeI cs = null;
 
+          if (av.getGlobalColourScheme() != null)
+          {
+            if (av.getGlobalColourScheme() instanceof UserColourScheme)
+            {
+              cs = new UserColourScheme(
+                  ( (UserColourScheme) av.getGlobalColourScheme()).getColours());
+
+            }
+            else
+              cs = ColourSchemeProperty.getColour(sequences,
+                                                  av.alignment.getWidth(),
+                                                  ColourSchemeProperty.getColourName(
+                                                      av.getGlobalColourScheme()));
+
+              cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
+                                                   av.getIgnoreGapsConsensus());
+          }
 
           SequenceGroup sg = new SequenceGroup(sequences, "TreeGroup",
                                                cs, true, true,
-                                               false, 0, av.alignment.getWidth());
+                                               false, 0, av.alignment.getWidth()-1);
 
 
-          if (av.getGlobalColourScheme() instanceof ConservationColourScheme)
-          {
-            ConservationColourScheme ccs = (ConservationColourScheme) av.
-                getGlobalColourScheme();
+          if (  av.getGlobalColourScheme()!=null
+             && av.getGlobalColourScheme().conservationApplied())
+            {
             Conservation c = new Conservation("Group",
                                               ResidueProperties.propHash, 3,
                                               sg.sequences, sg.getStartRes(),
@@ -499,9 +535,9 @@ System.out.println("called here");
 
             c.calculate();
             c.verdict(false, av.ConsPercGaps);
-            ccs = new ConservationColourScheme(c, ccs.cs);
+            cs.setConservation(c);
 
-            sg.cs = ccs;
+            sg.cs = cs;
 
           }