X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreePanel.java;h=6bb96f1472321efd3beb1b47f72411b99b25e153;hb=ae45339b760492fc71cadf5a52b0b386942a4bd4;hp=3e26a4b0e31c939b2f2c6f01218b2cad83ecf803;hpb=ee53965807b83bf93a21cbc341cee9a9e005b2cb;p=jalview.git

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 3e26a4b..6bb96f1 100755
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 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
@@ -19,26 +19,24 @@
 
 package jalview.appletgui;
 
-import java.util.*;
-
+import java.awt.*;
 import java.awt.event.*;
 
 import jalview.analysis.*;
 import jalview.datamodel.*;
 import jalview.io.*;
-import jalview.jbappletgui.*;
 
 public class TreePanel
-    extends GTreePanel
+    extends Frame implements ActionListener, ItemListener
 {
   SequenceI[] seq;
   String type;
   String pwtype;
-  AlignmentPanel ap;
   int start;
   int end;
   TreeCanvas treeCanvas;
   NJTree tree;
+  AlignViewport av;
 
   public NJTree getTree()
   {
@@ -55,11 +53,19 @@ public class TreePanel
    * @param s DOCUMENT ME!
    * @param e DOCUMENT ME!
    */
-  public TreePanel(AlignViewport av, Vector seqVector, String type,
-                   String pwtype, int s, int e)
+  public TreePanel(AlignViewport av, String type, String pwtype)
   {
-    super();
-    initTreePanel(av, seqVector, type, pwtype, s, e, null);
+    try
+    {
+      jbInit();
+      this.setMenuBar(jMenuBar1);
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+
+    initTreePanel(av, type, pwtype, null);
   }
 
   /**
@@ -71,41 +77,75 @@ public class TreePanel
    * @param type DOCUMENT ME!
    * @param pwtype DOCUMENT ME!
    */
-  public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
-                   String type, String pwtype)
+  public TreePanel(AlignViewport av,
+                   String type,
+                   String pwtype,
+                   NewickFile newtree)
   {
-    super();
-    initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);
-  }
+    try
+    {
+      jbInit();
+      this.setMenuBar(jMenuBar1);
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
 
+    initTreePanel(av, type, pwtype, newtree);
+  }
 
-  void initTreePanel(AlignViewport av, Vector seqVector, String type,
-                     String pwtype, int s, int e, NewickFile newTree)
+  void initTreePanel(AlignViewport av,
+                     String type,
+                     String pwtype,
+                     NewickFile newTree)
   {
 
+    this.av = av;
     this.type = type;
     this.pwtype = pwtype;
 
-    start = s;
-    end = e;
-
-    seq = new Sequence[seqVector.size()];
-    for(int i=0; i<seqVector.size(); i++)
-      seq[i] = (SequenceI)seqVector.elementAt(i);
-
-
     treeCanvas = new TreeCanvas(av, scrollPane);
     scrollPane.add(treeCanvas);
 
-
     TreeLoader tl = new TreeLoader(newTree);
     tl.start();
 
   }
 
-  class TreeLoader extends Thread
+  void showOriginalData()
+  {
+    // decide if av alignment is sufficiently different to original data to warrant a new window to be created
+    // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
+    // or create a selection box around columns in alignment view
+    // test Alignment(SeqCigar[])
+    if (tree.seqData != null)
+    {
+      Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.
+          getGapCharacter());
+
+      if (alAndColsel != null && alAndColsel[0] != null)
+      {
+        Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);
+        AlignFrame af = new AlignFrame(al,
+                                       av.applet,
+                                       "Original Data for Tree",
+                                       false);
+
+        af.viewport.setHiddenColumns( (ColumnSelection) alAndColsel[1]);
+      }
+    }
+    else
+    {
+      System.out.println("Original Tree Data not available");
+    }
+  }
+
+  class TreeLoader
+      extends Thread
   {
     NewickFile newtree;
+    jalview.datamodel.AlignmentView odata = null;
 
     public TreeLoader(NewickFile newtree)
     {
@@ -114,15 +154,44 @@ public class TreePanel
 
     public void run()
     {
-      if(newtree!=null)
-        tree = new NJTree(seq, newtree);
+      if (newtree != null)
+      {
+        if (odata == null)
+        {
+          tree = new NJTree(av.alignment.getSequencesArray(),
+                            newtree);
+        }
+        else
+        {
+          tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
+        }
+
+      }
       else
-        tree = new NJTree(seq, type, pwtype, start, end);
+      {
+        int start, end;
+        SequenceI[] seqs;
+        AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup() != null);
+        if (av.getSelectionGroup() == null)
+        {
+          start = 0;
+          end = av.alignment.getWidth();
+          seqs = av.alignment.getSequencesArray();
+        }
+        else
+        {
+          start = av.getSelectionGroup().getStartRes();
+          end = av.getSelectionGroup().getEndRes() + 1;
+          seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+        }
+
+        tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+      }
 
       tree.reCount(tree.getTopNode());
       tree.findHeight(tree.getTopNode());
       treeCanvas.setTree(tree);
-      if(newtree!=null)
+      if (newtree != null)
       {
         distanceMenu.setState(newtree.HasDistances());
         bootstrapMenu.setState(newtree.HasBootstrap());
@@ -130,28 +199,59 @@ public class TreePanel
         treeCanvas.setShowDistances(newtree.HasDistances());
       }
 
-
       treeCanvas.repaint();
 
+      av.setCurrentTree(tree);
+
     }
   }
 
-  public String getText(String format)
+  public void actionPerformed(ActionEvent evt)
   {
-    return null;
+    if (evt.getSource() == newickOutput)
+    {
+      newickOutput_actionPerformed();
+    }
+    else if (evt.getSource() == fontSize)
+    {
+      fontSize_actionPerformed();
+    }
+    else if (evt.getSource() == inputData)
+    {
+      showOriginalData();
+    }
   }
 
-  protected void fitToWindow_actionPerformed(ActionEvent e)
+  public void itemStateChanged(ItemEvent evt)
   {
-    treeCanvas.fitToWindow = fitToWindow.getState();
+    if (evt.getSource() == fitToWindow)
+    {
+      treeCanvas.fitToWindow = fitToWindow.getState();
+    }
+
+    else if (evt.getSource() == distanceMenu)
+    {
+      treeCanvas.setShowDistances(distanceMenu.getState());
+    }
+
+    else if (evt.getSource() == bootstrapMenu)
+    {
+      treeCanvas.setShowBootstrap(bootstrapMenu.getState());
+    }
+
+    else if (evt.getSource() == placeholdersMenu)
+    {
+      treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
+    }
+
     treeCanvas.repaint();
   }
 
-  public void newickOutput_actionPerformed(ActionEvent actionEvent)
+  public void newickOutput_actionPerformed()
   {
     jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
     String output = fout.print(false, true);
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame.applet);
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
     cap.setText(output);
     java.awt.Frame frame = new java.awt.Frame();
     frame.add(cap);
@@ -169,27 +269,63 @@ public class TreePanel
     treeCanvas.repaint();
   }
 
-  protected void fontSize_actionPerformed(ActionEvent e)
+  protected void fontSize_actionPerformed()
   {
-     if( treeCanvas==null )
-        return;
+    if (treeCanvas == null)
+    {
+      return;
+    }
 
     new FontChooser(this);
   }
 
-  protected void distanceMenu_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.setShowDistances(distanceMenu.getState());
-  }
-
-  protected void bootstrapMenu_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.setShowBootstrap(bootstrapMenu.getState());
-  }
-
-  protected void placeholdersMenu_actionPerformed(ActionEvent e)
+  BorderLayout borderLayout1 = new BorderLayout();
+  protected ScrollPane scrollPane = new ScrollPane();
+  MenuBar jMenuBar1 = new MenuBar();
+  Menu jMenu2 = new Menu();
+  protected MenuItem fontSize = new MenuItem();
+  protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();
+  protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();
+  protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();
+  protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();
+  Menu fileMenu = new Menu();
+  MenuItem newickOutput = new MenuItem();
+  MenuItem inputData = new MenuItem();
+
+  private void jbInit()
+      throws Exception
   {
-    treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
+    setLayout(borderLayout1);
+    this.setBackground(Color.white);
+    this.setFont(new java.awt.Font("Verdana", 0, 12));
+    jMenu2.setLabel("View");
+    fontSize.setLabel("Font...");
+    fontSize.addActionListener(this);
+    bootstrapMenu.setLabel("Show Bootstrap Values");
+    bootstrapMenu.addItemListener(this);
+    distanceMenu.setLabel("Show Distances");
+    distanceMenu.addItemListener(this);
+    placeholdersMenu.setLabel("Mark Unassociated Leaves");
+    placeholdersMenu.addItemListener(this);
+    fitToWindow.setState(true);
+    fitToWindow.setLabel("Fit To Window");
+    fitToWindow.addItemListener(this);
+    fileMenu.setLabel("File");
+    newickOutput.setLabel("Newick Format");
+    newickOutput.addActionListener(this);
+    inputData.setLabel("Input Data...");
+
+    add(scrollPane, BorderLayout.CENTER);
+    jMenuBar1.add(fileMenu);
+    jMenuBar1.add(jMenu2);
+    jMenu2.add(fitToWindow);
+    jMenu2.add(fontSize);
+    jMenu2.add(distanceMenu);
+    jMenu2.add(bootstrapMenu);
+    jMenu2.add(placeholdersMenu);
+    fileMenu.add(newickOutput);
+    fileMenu.add(inputData);
+    inputData.addActionListener(this);
   }
 
 }