X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=47bebbea18725d2e5cc5dbd88284e6ddc988600b;hb=8a5c39442bced20fc95272efe6d3176719ca3f15;hp=451d66361ccec419747b272e6c1ea3b7c4d4ab91;hpb=ef23c17739a6fba3a8d455b725782bce4607ac9f;p=jalview.git

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 451d663..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,
@@ -481,13 +500,29 @@ System.out.println("called here");
               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()!=null