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[jalview.git] / src / jalview / gui / TreePanel.java

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