From 8a5c39442bced20fc95272efe6d3176719ca3f15 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 8 Sep 2005 15:47:23 +0000
Subject: [PATCH] Load in a thread

---
 src/jalview/appletgui/TreeCanvas.java |   30 +++++++--
 src/jalview/appletgui/TreePanel.java  |  115 +++++++++++++++++---------------
 src/jalview/gui/TreeCanvas.java       |   75 ++++++++++++++-------
 src/jalview/gui/TreePanel.java        |  117 ++++++++++++++-------------------
 4 files changed, 189 insertions(+), 148 deletions(-)

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 9483436..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);
@@ -93,6 +89,30 @@ public class TreeCanvas
   {
     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,
diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 1785961..51ec4a0 100755
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -45,87 +45,96 @@ public class TreePanel
     return tree;
   }
 
-  public TreePanel(AlignmentPanel ap, Vector seqVector, String type,
+  /**
+   * Creates a new TreePanel object.
+   *
+   * @param av DOCUMENT ME!
+   * @param seqVector DOCUMENT ME!
+   * @param type DOCUMENT ME!
+   * @param pwtype DOCUMENT ME!
+   * @param s DOCUMENT ME!
+   * @param e DOCUMENT ME!
+   */
+  public TreePanel(AlignViewport av, Vector seqVector, String type,
                    String pwtype, int s, int e)
   {
     super();
+    initTreePanel(av, seqVector, type, pwtype, s, e, null);
+
+    // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
+    treeCanvas.setShowDistances(true);
+  }
+
+  /**
+   * Creates a new TreePanel object.
+   *
+   * @param av DOCUMENT ME!
+   * @param seqVector DOCUMENT ME!
+   * @param newtree DOCUMENT ME!
+   * @param type DOCUMENT ME!
+   * @param pwtype DOCUMENT ME!
+   */
+  public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
+                   String type, String pwtype)
+  {
+    super();
+    initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);
+  }
+
+
+  void initTreePanel(AlignViewport av, Vector seqVector, String type,
+                     String pwtype, int s, int e, NewickFile newTree)
+  {
 
-    this.ap = ap;
     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();
-      }
-    }
+    for(int i=0; i<seqVector.size(); i++)
+      seq[i] = (SequenceI)seqVector.elementAt(i);
 
-    tree = new NJTree(seq, type, pwtype, start, end);
 
-    treeCanvas = new TreeCanvas(ap.av, tree, scrollPane, longestName);
-
-    tree.reCount(tree.getTopNode());
-    tree.findHeight(tree.getTopNode());
+    treeCanvas = new TreeCanvas(av, scrollPane);
     scrollPane.add(treeCanvas);
 
+    TreeLoader tl = new TreeLoader(newTree);
+    tl.start();
+
   }
 
-  public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
-                   String type, String pwtype)
+  class TreeLoader extends Thread
   {
-    super();
-    // These are probably only  arbitrary strings reflecting source of tree
-    this.type = type;
-    this.pwtype = pwtype;
+    NewickFile newtree;
 
-    start = 0;
-    end = seqVector.size();
-
-    String longestName = "";
-    seq = new Sequence[seqVector.size()];
-    for (int i = 0; i < seqVector.size(); i++)
+    public TreeLoader(NewickFile newtree)
     {
-      seq[i] = (Sequence) seqVector.elementAt(i);
+      this.newtree = newtree;
     }
-    // This constructor matches sequence names to treenodes and sets up the tree layouts.
-    tree = new NJTree(seq, newtree);
-    // Now have to calculate longest name based on the leaves
-    Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
 
-    for (int i = 0; i < leaves.size(); i++)
+    public void run()
     {
-      if (longestName.length() <
-          ( (Sequence) ( (SequenceNode) leaves.elementAt(i)).element()).getName().
-          length())
+      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)
       {
-        longestName = TreeCanvas.PLACEHOLDER +
-            ( (Sequence) ( (SequenceNode) leaves.elementAt(i)).element()).
-            getName();
+        treeCanvas.setShowBootstrap(newtree.HasBootstrap());
+        treeCanvas.setShowDistances(newtree.HasDistances());
       }
-    }
 
-    tree.reCount(tree.getTopNode());
-    tree.findHeight(tree.getTopNode());
 
-    treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
-    treeCanvas.setShowBootstrap(newtree.HasBootstrap());
-    treeCanvas.setShowDistances(newtree.HasDistances());
-    distanceMenu.setState(newtree.HasDistances());
-    bootstrapMenu.setState(newtree.HasBootstrap());
-    if (true) // JBPNote TODO: preference for always marking placeholders in new associated tree
-    {
-      placeholdersMenu.setState(treeCanvas.markPlaceholders);
-    }
-    scrollPane.add(treeCanvas);
+      treeCanvas.repaint();
 
+    }
   }
 
   public String getText(String format)
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 2f5ddf4..672d200 100755
--- 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!
      * @param label DOCUMENT ME!
      */
-    public TreeCanvas(AlignViewport av, NJTree tree, JScrollPane scroller,
-        String label)
+    public TreeCanvas(AlignViewport av, JScrollPane scroller)
     {
         this.av = av;
-        this.tree = tree;
         scrollPane = scroller;
         addMouseListener(this);
-        tree.findHeight(tree.getTopNode());
-        longestName = label;
-
         PaintRefresher.Register(this, av.alignment);
     }
 
+
     /**
      * DOCUMENT ME!
      *
@@ -118,6 +114,30 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     {
         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);
     }
 
     /**
@@ -503,32 +523,41 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     public void paintComponent(Graphics g)
     {
         super.paintComponent(g);
-        font = new Font("Verdana", Font.PLAIN, fontSize);
-        g.setFont(font);
+        if(tree==null)
+        {
+          g.setFont(new Font("Verdana", Font.PLAIN, 18));
+          g.drawString("Calculating tree....", 20, getHeight()/2);
+        }
+        else
+        {
 
-        FontMetrics fm = g.getFontMetrics(font);
+          font = new Font("Verdana", Font.PLAIN, fontSize);
+          g.setFont(font);
 
-        if (nameHash.size() == 0)
-        {
+          FontMetrics fm = g.getFontMetrics(font);
+
+          if (nameHash.size() == 0)
+          {
             repaint();
-        }
+          }
 
-        if (fitToWindow ||
-                (!fitToWindow &&
-                (scrollPane.getHeight() > ((fm.getHeight() * nameHash.size()) +
-                offy))))
-        {
+          if (fitToWindow ||
+              (!fitToWindow &&
+               (scrollPane.getHeight() > ( (fm.getHeight() * nameHash.size()) +
+                                          offy))))
+          {
             draw(g, scrollPane.getWidth(), scrollPane.getHeight());
             setPreferredSize(null);
-        }
-        else
-        {
+          }
+          else
+          {
             setPreferredSize(new Dimension(scrollPane.getWidth(),
-                    fm.getHeight() * nameHash.size()));
+                                           fm.getHeight() * nameHash.size()));
             draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size());
-        }
+          }
 
-        scrollPane.revalidate();
+          scrollPane.revalidate();
+        }
     }
 
     /**
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!
      *
-- 
1.7.10.2