X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;fp=src%2Fjalview%2Fgui%2FTreePanel.java;h=8d13e93c2c591dd1f453c4b9c671e5e202e6c3ad;hb=8a5c39442bced20fc95272efe6d3176719ca3f15;hp=ff02d49ec487eef6189d2acba088ca4b4267e9bf;hpb=5ac7843efbf08ac78859912b6b3df19cb2b99279;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index ff02d49..8d13e93 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -68,37 +68,13 @@ public class TreePanel extends GTreePanel
      * @param e DOCUMENT ME!
      */
     public TreePanel(AlignViewport av, Vector seqVector, String type,
-        String pwtype, int s, int e)
+                     String pwtype, int s, int e)
     {
-        super();
+      super();
+      initTreePanel(av, seqVector, type, pwtype, s, e, null);
 
-        this.type = type;
-        this.pwtype = pwtype;
-
-        start = s;
-        end = e;
-
-        String longestName = "";
-        seq = new Sequence[seqVector.size()];
-
-        for (int i = 0; i < seqVector.size(); i++)
-        {
-            seq[i] = (Sequence) seqVector.elementAt(i);
-
-            if (seq[i].getName().length() > longestName.length())
-            {
-                longestName = seq[i].getName();
-            }
-        }
-
-        tree = new NJTree(seq, type, pwtype, start, end);
-
-        treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
-        treeCanvas.setShowDistances(true); // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
-        setViewStateFromTreeCanvas(treeCanvas);
-        tree.reCount(tree.getTopNode());
-        tree.findHeight(tree.getTopNode());
-        scrollPane.setViewportView(treeCanvas);
+      // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
+      treeCanvas.setShowDistances(true);
     }
 
     /**
@@ -111,62 +87,69 @@ public class TreePanel extends GTreePanel
      * @param pwtype DOCUMENT ME!
      */
     public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
-        String type, String pwtype)
+                     String type, String pwtype)
     {
-        super();
+      super();
+      initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);
+    }
 
-        // These are probably only  arbitrary strings reflecting source of tree
-        this.type = type;
-        this.pwtype = pwtype;
 
-        start = 0;
-        end = seqVector.size();
+    void initTreePanel(AlignViewport av, Vector seqVector, String type,
+                       String pwtype, int s, int e, NewickFile newTree)
+    {
 
-        String longestName = "";
-        seq = new Sequence[seqVector.size()];
+      this.type = type;
+      this.pwtype = pwtype;
 
-        for (int i = 0; i < seqVector.size(); i++)
-        {
-            seq[i] = (Sequence) seqVector.elementAt(i);
-        }
+      start = s;
+      end = e;
 
-        // This constructor matches sequence names to treenodes and sets up the tree layouts.
-        tree = new NJTree(seq, newtree);
+      seq = new Sequence[seqVector.size()];
+      seqVector.toArray(seq);
 
-        // Now have to calculate longest name based on the leaves
-        Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
-        boolean has_placeholders = false;
 
-        for (int i = 0; i < leaves.size(); i++)
-        {
-            SequenceNode lf = (SequenceNode) leaves.elementAt(i);
+      treeCanvas = new TreeCanvas(av, scrollPane);
+      scrollPane.setViewportView(treeCanvas);
 
-            if (lf.isPlaceholder())
-            {
-                has_placeholders = true;
-            }
+      TreeLoader tl = new TreeLoader(newTree);
+      tl.start();
 
-            if (longestName.length() < ((Sequence) lf.element()).getName()
-                                            .length())
-            {
-                longestName = TreeCanvas.PLACEHOLDER +
-                    ((Sequence) lf.element()).getName();
-            }
-        }
+    }
+
+    class TreeLoader extends Thread
+    {
+      NewickFile newtree;
+
+      public TreeLoader(NewickFile newtree)
+      {
+        this.newtree = newtree;
+      }
+
+      public void run()
+      {
+        NJTree tree;
+        if(newtree!=null)
+          tree = new NJTree(seq, newtree);
+        else
+          tree = new NJTree(seq, type, pwtype, start, end);
 
         tree.reCount(tree.getTopNode());
         tree.findHeight(tree.getTopNode());
+        treeCanvas.setTree(tree);
+        if(newtree!=null)
+        {
+          treeCanvas.setShowBootstrap(newtree.HasBootstrap());
+          treeCanvas.setShowDistances(newtree.HasDistances());
+        }
 
-        treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
-        treeCanvas.setShowBootstrap(newtree.HasBootstrap());
-        treeCanvas.setShowDistances(newtree.HasDistances());
-        scrollPane.setViewportView(treeCanvas);
-        treeCanvas.setMarkPlaceholders(has_placeholders);
         setViewStateFromTreeCanvas(treeCanvas);
 
-        // JBPNote TODO: preference for always marking placeholders in new associated tree
+        treeCanvas.repaint();
+
+      }
     }
 
+
     /**
      * DOCUMENT ME!
      *