X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FTreePanel.java;h=6bb96f1472321efd3beb1b47f72411b99b25e153;hb=3c7a633b4868a7a95ed1cfe19be6dd44c22ac473;hp=6d17918049bc34bbbd73735a6082a5eab1133478;hpb=9bbb5a6c6054d67fb98dba12566e7c2059ced62f;p=jalview.git

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 6d17918..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
@@ -19,16 +19,15 @@
 
 package jalview.appletgui;
 
-import java.util.*;
-
-import java.awt.event.*;
 import java.awt.*;
+import java.awt.event.*;
 
 import jalview.analysis.*;
 import jalview.datamodel.*;
 import jalview.io.*;
 
-public class TreePanel extends Frame implements ActionListener, ItemListener
+public class TreePanel
+    extends Frame implements ActionListener, ItemListener
 {
   SequenceI[] seq;
   String type;
@@ -54,8 +53,7 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
    * @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)
   {
     try
     {
@@ -67,7 +65,7 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
       ex.printStackTrace();
     }
 
-    initTreePanel(av, seqVector, type, pwtype, s, e, null);
+    initTreePanel(av, type, pwtype, null);
   }
 
   /**
@@ -79,8 +77,10 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
    * @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)
   {
     try
     {
@@ -92,38 +92,60 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
       e.printStackTrace();
     }
 
-    initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);
+    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)
     {
@@ -132,15 +154,44 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
 
     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());
@@ -148,7 +199,6 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
         treeCanvas.setShowDistances(newtree.HasDistances());
       }
 
-
       treeCanvas.repaint();
 
       av.setCurrentTree(tree);
@@ -158,30 +208,45 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
 
   public void actionPerformed(ActionEvent evt)
   {
-    if(evt.getSource()==newickOutput)
+    if (evt.getSource() == newickOutput)
+    {
       newickOutput_actionPerformed();
-    else if(evt.getSource()==fontSize)
+    }
+    else if (evt.getSource() == fontSize)
+    {
       fontSize_actionPerformed();
+    }
+    else if (evt.getSource() == inputData)
+    {
+      showOriginalData();
+    }
   }
 
   public void itemStateChanged(ItemEvent evt)
   {
-    if(evt.getSource()==fitToWindow)
+    if (evt.getSource() == fitToWindow)
+    {
       treeCanvas.fitToWindow = fitToWindow.getState();
+    }
 
-    else if(evt.getSource()==distanceMenu)
+    else if (evt.getSource() == distanceMenu)
+    {
       treeCanvas.setShowDistances(distanceMenu.getState());
+    }
 
-    else if(evt.getSource()==bootstrapMenu)
+    else if (evt.getSource() == bootstrapMenu)
+    {
       treeCanvas.setShowBootstrap(bootstrapMenu.getState());
+    }
 
-    else if(evt.getSource()==placeholdersMenu)
+    else if (evt.getSource() == placeholdersMenu)
+    {
       treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
+    }
 
     treeCanvas.repaint();
   }
 
-
   public void newickOutput_actionPerformed()
   {
     jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
@@ -206,13 +271,14 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
 
   protected void fontSize_actionPerformed()
   {
-     if( treeCanvas==null )
-        return;
+    if (treeCanvas == null)
+    {
+      return;
+    }
 
     new FontChooser(this);
   }
 
-
   BorderLayout borderLayout1 = new BorderLayout();
   protected ScrollPane scrollPane = new ScrollPane();
   MenuBar jMenuBar1 = new MenuBar();
@@ -224,36 +290,42 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
   protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();
   Menu fileMenu = new Menu();
   MenuItem newickOutput = new MenuItem();
+  MenuItem inputData = new MenuItem();
 
-  private void jbInit() throws Exception {
-      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);
+  private void jbInit()
+      throws Exception
+  {
+    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);
+    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);
   }
 
 }