X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreePanel.java;h=42be37b1624c65f99aefa7a8e5401e719b88d9cd;hb=80a1a1f98f80f52fbd536f5e83ebab4354e74d5e;hp=c33975b28f60003f6a3ec461c3e8f4e3e2e3327e;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index c33975b..42be37b 100755
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -1,39 +1,40 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 
 package jalview.appletgui;
 
-import jalview.datamodel.*;
-import jalview.io.NewickFile;
-import jalview.analysis.*;
-import jalview.jbappletgui.GTreePanel;
-import java.awt.event.*;
 import java.util.*;
-import jalview.io.NewickFile;
 
+import java.awt.event.*;
 
-public class TreePanel extends GTreePanel
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.jbappletgui.*;
+
+public class TreePanel
+    extends GTreePanel
 {
   SequenceI[] seq;
   String type;
   String pwtype;
-  AlignViewport av;
+  AlignmentPanel ap;
   int start;
   int end;
   TreeCanvas treeCanvas;
@@ -44,9 +45,46 @@ public class TreePanel extends GTreePanel
     return tree;
   }
 
-  public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)
+  /**
+   * 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.type = type;
     this.pwtype = pwtype;
@@ -54,67 +92,55 @@ public class TreePanel extends GTreePanel
     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();
-    }
+    seq = new Sequence[seqVector.size()];
+    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(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)
-    {
-      super();
-      // These are probably only  arbitrary strings reflecting source of tree
-      this.type = type;
-      this.pwtype = pwtype;
 
-      start = 0;
-      end = seqVector.size();
+  class TreeLoader extends Thread
+  {
+    NewickFile newtree;
 
-      String longestName = "";
-      seq = new Sequence [seqVector.size()];
-      for (int i=0;i < seqVector.size();i++)
-      {
-        seq[i] = (Sequence) seqVector.elementAt(i);
-      }
-      // 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());
+    public TreeLoader(NewickFile newtree)
+    {
+      this.newtree = newtree;
+    }
 
-      for (int i=0;i < leaves.size();i++)
-        if (longestName.length()<((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName().length())
-          longestName = TreeCanvas.PLACEHOLDER+((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName();
+    public void run()
+    {
+      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());
-      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) {
-  return null;
-}
+  public String getText(String format)
+  {
+    return null;
+  }
 
   protected void fitToWindow_actionPerformed(ActionEvent e)
   {
@@ -126,37 +152,35 @@ public String getText(String format) {
   {
     jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
     String output = fout.print(false, true);
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame.applet);
     cap.setText(output);
     java.awt.Frame frame = new java.awt.Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, type+" "+pwtype, 500,100);
+    jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
   }
 
-
-
   protected void fontSize_actionPerformed(ActionEvent e)
   {
- /*   if( treeCanvas==null )
-     return;
-
-   String size = fontSize.getLabel().substring( fontSize.getLabel().indexOf("-")+1);
-
-   Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,
-                               "Select font size",
-                               "Font size",
-                               JOptionPane.QUESTION_MESSAGE,
-                               null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
-                               ,"Font Size - "+size);
-   if(selection!=null)
-   {
-     fontSize.setText("Font Size - " + selection);
-
-     int i = Integer.parseInt(selection.toString());
-     treeCanvas.setFontSize(i);
-   }
-    scrollPane.setViewportView(treeCanvas);
-*/
+    /*   if( treeCanvas==null )
+        return;
+
+      String size = fontSize.getLabel().substring( fontSize.getLabel().indexOf("-")+1);
+
+      Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,
+                                  "Select font size",
+                                  "Font size",
+                                  JOptionPane.QUESTION_MESSAGE,
+     null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
+                                  ,"Font Size - "+size);
+      if(selection!=null)
+      {
+        fontSize.setText("Font Size - " + selection);
+
+        int i = Integer.parseInt(selection.toString());
+        treeCanvas.setFontSize(i);
+      }
+       scrollPane.setViewportView(treeCanvas);
+     */
   }
 
   protected void distanceMenu_actionPerformed(ActionEvent e)
@@ -171,7 +195,7 @@ public String getText(String format) {
 
   protected void placeholdersMenu_actionPerformed(ActionEvent e)
   {
-      treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
+    treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
   }
 
 }