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diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 9483436..47bebbe 100755 (executable)
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -59,15 +59,11 @@ public class TreeCanvas
   Hashtable nameHash = new Hashtable();\r
   Hashtable nodeHash = new Hashtable();\r
 \r
-  public TreeCanvas(AlignViewport av, NJTree tree, ScrollPane scroller,\r
-                    String label)\r
+  public TreeCanvas(AlignViewport av, ScrollPane scroller)\r
   {\r
     this.av = av;\r
-    this.tree = tree;\r
     scrollPane = scroller;\r
     addMouseListener(this);\r
-    tree.findHeight(tree.getTopNode());\r
-    longestName = label;\r
     setLayout(null);\r
 \r
     PaintRefresher.Register(this, av.alignment);\r
@@ -93,6 +89,30 @@ public class TreeCanvas
   {\r
     this.tree = tree;\r
     tree.findHeight(tree.getTopNode());\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
+    longestName = "";\r
+\r
+    for (int i = 0; i < leaves.size(); i++)\r
+    {\r
+      SequenceNode lf = (SequenceNode) leaves.elementAt(i);\r
+\r
+      if (lf.isPlaceholder())\r
+      {\r
+        has_placeholders = true;\r
+      }\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
+    setMarkPlaceholders(has_placeholders);\r
   }\r
 \r
   public void drawNode(Graphics g, SequenceNode node, float chunk, float scale,\r

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 1785961..51ec4a0 100755 (executable)
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -45,87 +45,96 @@ public class TreePanel
     return tree;\r
   }\r
 \r
-  public TreePanel(AlignmentPanel ap, Vector seqVector, String type,\r
+  /**\r
+   * Creates a new TreePanel object.\r
+   *\r
+   * @param av DOCUMENT ME!\r
+   * @param seqVector DOCUMENT ME!\r
+   * @param type DOCUMENT ME!\r
+   * @param pwtype DOCUMENT ME!\r
+   * @param s DOCUMENT ME!\r
+   * @param e DOCUMENT ME!\r
+   */\r
+  public TreePanel(AlignViewport av, Vector seqVector, String type,\r
                    String pwtype, int s, int e)\r
   {\r
     super();\r
+    initTreePanel(av, seqVector, type, pwtype, s, e, null);\r
+\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
+   * Creates a new TreePanel object.\r
+   *\r
+   * @param av DOCUMENT ME!\r
+   * @param seqVector DOCUMENT ME!\r
+   * @param newtree DOCUMENT ME!\r
+   * @param type DOCUMENT ME!\r
+   * @param pwtype DOCUMENT ME!\r
+   */\r
+  public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,\r
+                   String type, String pwtype)\r
+  {\r
+    super();\r
+    initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);\r
+  }\r
+\r
+\r
+  void initTreePanel(AlignViewport av, Vector seqVector, String type,\r
+                     String pwtype, int s, int e, NewickFile newTree)\r
+  {\r
 \r
-    this.ap = ap;\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
-    for (int i = 0; i < seqVector.size(); i++)\r
-    {\r
-      seq[i] = (Sequence) seqVector.elementAt(i);\r
-      if (seq[i].getName().length() > longestName.length())\r
-      {\r
-        longestName = seq[i].getName();\r
-      }\r
-    }\r
+    for(int i=0; i<seqVector.size(); i++)\r
+      seq[i] = (SequenceI)seqVector.elementAt(i);\r
 \r
-    tree = new NJTree(seq, type, pwtype, start, end);\r
 \r
-    treeCanvas = new TreeCanvas(ap.av, tree, scrollPane, longestName);\r
-\r
-    tree.reCount(tree.getTopNode());\r
-    tree.findHeight(tree.getTopNode());\r
+    treeCanvas = new TreeCanvas(av, scrollPane);\r
     scrollPane.add(treeCanvas);\r
 \r
+    TreeLoader tl = new TreeLoader(newTree);\r
+    tl.start();\r
+\r
   }\r
 \r
-  public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,\r
-                   String type, String pwtype)\r
+  class TreeLoader extends Thread\r
   {\r
-    super();\r
-    // These are probably only  arbitrary strings reflecting source of tree\r
-    this.type = type;\r
-    this.pwtype = pwtype;\r
+    NewickFile newtree;\r
 \r
-    start = 0;\r
-    end = seqVector.size();\r
-\r
-    String longestName = "";\r
-    seq = new Sequence[seqVector.size()];\r
-    for (int i = 0; i < seqVector.size(); i++)\r
+    public TreeLoader(NewickFile newtree)\r
     {\r
-      seq[i] = (Sequence) seqVector.elementAt(i);\r
+      this.newtree = newtree;\r
     }\r
-    // This constructor matches sequence names to treenodes and sets up the tree layouts.\r
-    tree = new NJTree(seq, newtree);\r
-    // Now have to calculate longest name based on the leaves\r
-    Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());\r
 \r
-    for (int i = 0; i < leaves.size(); i++)\r
+    public void run()\r
     {\r
-      if (longestName.length() <\r
-          ( (Sequence) ( (SequenceNode) leaves.elementAt(i)).element()).getName().\r
-          length())\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
-        longestName = TreeCanvas.PLACEHOLDER +\r
-            ( (Sequence) ( (SequenceNode) leaves.elementAt(i)).element()).\r
-            getName();\r
+        treeCanvas.setShowBootstrap(newtree.HasBootstrap());\r
+        treeCanvas.setShowDistances(newtree.HasDistances());\r
       }\r
-    }\r
 \r
-    tree.reCount(tree.getTopNode());\r
-    tree.findHeight(tree.getTopNode());\r
 \r
-    treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
-    treeCanvas.setShowBootstrap(newtree.HasBootstrap());\r
-    treeCanvas.setShowDistances(newtree.HasDistances());\r
-    distanceMenu.setState(newtree.HasDistances());\r
-    bootstrapMenu.setState(newtree.HasBootstrap());\r
-    if (true) // JBPNote TODO: preference for always marking placeholders in new associated tree\r
-    {\r
-      placeholdersMenu.setState(treeCanvas.markPlaceholders);\r
-    }\r
-    scrollPane.add(treeCanvas);\r
+      treeCanvas.repaint();\r
 \r
+    }\r
   }\r
 \r
   public String getText(String format)\r

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 2f5ddf4..672d200 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -74,19 +74,15 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
      * @param scroller DOCUMENT ME!\r
      * @param label DOCUMENT ME!\r
      */\r
-    public TreeCanvas(AlignViewport av, NJTree tree, JScrollPane scroller,\r
-        String label)\r
+    public TreeCanvas(AlignViewport av, JScrollPane scroller)\r
     {\r
         this.av = av;\r
-        this.tree = tree;\r
         scrollPane = scroller;\r
         addMouseListener(this);\r
-        tree.findHeight(tree.getTopNode());\r
-        longestName = label;\r
-\r
         PaintRefresher.Register(this, av.alignment);\r
     }\r
 \r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -118,6 +114,30 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     {\r
         this.tree = tree;\r
         tree.findHeight(tree.getTopNode());\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
+        longestName = "";\r
+\r
+        for (int i = 0; i < leaves.size(); i++)\r
+        {\r
+          SequenceNode lf = (SequenceNode) leaves.elementAt(i);\r
+\r
+          if (lf.isPlaceholder())\r
+          {\r
+            has_placeholders = true;\r
+          }\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
+        setMarkPlaceholders(has_placeholders);\r
     }\r
 \r
     /**\r
@@ -503,32 +523,41 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     public void paintComponent(Graphics g)\r
     {\r
         super.paintComponent(g);\r
-        font = new Font("Verdana", Font.PLAIN, fontSize);\r
-        g.setFont(font);\r
+        if(tree==null)\r
+        {\r
+          g.setFont(new Font("Verdana", Font.PLAIN, 18));\r
+          g.drawString("Calculating tree....", 20, getHeight()/2);\r
+        }\r
+        else\r
+        {\r
 \r
-        FontMetrics fm = g.getFontMetrics(font);\r
+          font = new Font("Verdana", Font.PLAIN, fontSize);\r
+          g.setFont(font);\r
 \r
-        if (nameHash.size() == 0)\r
-        {\r
+          FontMetrics fm = g.getFontMetrics(font);\r
+\r
+          if (nameHash.size() == 0)\r
+          {\r
             repaint();\r
-        }\r
+          }\r
 \r
-        if (fitToWindow ||\r
-                (!fitToWindow &&\r
-                (scrollPane.getHeight() > ((fm.getHeight() * nameHash.size()) +\r
-                offy))))\r
-        {\r
+          if (fitToWindow ||\r
+              (!fitToWindow &&\r
+               (scrollPane.getHeight() > ( (fm.getHeight() * nameHash.size()) +\r
+                                          offy))))\r
+          {\r
             draw(g, scrollPane.getWidth(), scrollPane.getHeight());\r
             setPreferredSize(null);\r
-        }\r
-        else\r
-        {\r
+          }\r
+          else\r
+          {\r
             setPreferredSize(new Dimension(scrollPane.getWidth(),\r
-                    fm.getHeight() * nameHash.size()));\r
+                                           fm.getHeight() * nameHash.size()));\r
             draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size());\r
-        }\r
+          }\r
 \r
-        scrollPane.revalidate();\r
+          scrollPane.revalidate();\r
+        }\r
     }\r
 \r
     /**\r

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