X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreePanel.java;h=b3fc3b341b27a0592507e2b26d5627428dae5701;hb=6dd523c9bd707b197e7311fba62387777286debb;hp=99d032859f9756524d4f476b2cb0e104070c333c;hpb=c3db82330376f20423dc617cfa92d131dc40e515;p=jalview.git

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 99d0328..b3fc3b3 100755
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -1,158 +1,309 @@
-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;
-
-
-public class TreePanel extends GTreePanel
-{
-  SequenceI[] seq;
-  String type;
-  String pwtype;
-  AlignViewport av;
-  int start;
-  int end;
-  TreeCanvas treeCanvas;
-  NJTree tree;
-
-  public NJTree getTree()
-  {
-    return tree;
-  }
-
-  public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)
-  {
-    super();
-
-    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);
-
-    tree.reCount(tree.getTopNode());
-    tree.findHeight(tree.getTopNode());
-    scrollPane.add(treeCanvas);
-
-  }
-  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();
-
-      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());
-
-      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();
-
-      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);
-
-    }
-
-public String getText(String format) {
-  return null;
-}
-
-  protected void fitToWindow_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.fitToWindow = fitToWindow.getState();
-    repaint();
-  }
-
-  public void newickOutput_actionPerformed(ActionEvent actionEvent)
-  {
-    jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
-    String output = fout.print(false, true);
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
-    cap.setText(output);
-    java.awt.Frame frame = new java.awt.Frame();
-    frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, type+" "+pwtype, 500,500);
-  }
-
-
-
-  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);
-*/
-  }
-
-  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)
-  {
-      treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
-  }
-
-}
+/*
+ * 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 java.util.*;
+
+import java.awt.event.*;
+import java.awt.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+
+public class TreePanel extends Frame implements ActionListener, ItemListener
+{
+  SequenceI[] seq;
+  String type;
+  String pwtype;
+  int start;
+  int end;
+  TreeCanvas treeCanvas;
+  NJTree tree;
+  AlignViewport av;
+
+  public NJTree getTree()
+  {
+    return tree;
+  }
+
+  /**
+   * 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, String type, String pwtype)
+  {
+    try
+    {
+      jbInit();
+      this.setMenuBar(jMenuBar1);
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+
+    initTreePanel(av, type, pwtype, null);
+  }
+
+  /**
+   * 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,
+                   String type,
+                   String pwtype,
+                   NewickFile newtree)
+  {
+    try
+    {
+      jbInit();
+      this.setMenuBar(jMenuBar1);
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+    initTreePanel(av, type, pwtype, newtree);
+  }
+
+
+  void initTreePanel(AlignViewport av,
+                     String type,
+                     String pwtype,
+                     NewickFile newTree)
+  {
+
+    this.av = av;
+    this.type = type;
+    this.pwtype = pwtype;
+
+    treeCanvas = new TreeCanvas(av, scrollPane);
+    scrollPane.add(treeCanvas);
+
+
+    TreeLoader tl = new TreeLoader(newTree);
+    tl.start();
+
+  }
+
+  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[])
+    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] );
+     }
+  }
+
+  class TreeLoader extends Thread
+  {
+    NewickFile newtree;
+    jalview.datamodel.AlignmentView odata=null;
+
+    public TreeLoader(NewickFile newtree)
+    {
+      this.newtree = newtree;
+    }
+
+    public void run()
+    {
+      if(newtree!=null)
+      {
+        if (odata == null)
+          tree = new NJTree(av.alignment.getSequencesArray(),
+                            newtree);
+        else
+          tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
+
+        }
+        else
+        {
+          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)
+      {
+        distanceMenu.setState(newtree.HasDistances());
+        bootstrapMenu.setState(newtree.HasBootstrap());
+        treeCanvas.setShowBootstrap(newtree.HasBootstrap());
+        treeCanvas.setShowDistances(newtree.HasDistances());
+      }
+
+
+      treeCanvas.repaint();
+
+      av.setCurrentTree(tree);
+
+    }
+  }
+
+  public void actionPerformed(ActionEvent evt)
+  {
+    if(evt.getSource()==newickOutput)
+      newickOutput_actionPerformed();
+    else if(evt.getSource()==fontSize)
+      fontSize_actionPerformed();
+    else if(evt.getSource()==inputData)
+      showOriginalData();
+  }
+
+  public void itemStateChanged(ItemEvent evt)
+  {
+    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()
+  {
+    jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+    String output = fout.print(false, true);
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
+    cap.setText(output);
+    java.awt.Frame frame = new java.awt.Frame();
+    frame.add(cap);
+    jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
+  }
+
+  public java.awt.Font getTreeFont()
+  {
+    return treeCanvas.font;
+  }
+
+  public void setTreeFont(java.awt.Font font)
+  {
+    treeCanvas.font = font;
+    treeCanvas.repaint();
+  }
+
+  protected void fontSize_actionPerformed()
+  {
+     if( treeCanvas==null )
+        return;
+
+    new FontChooser(this);
+  }
+
+
+
+
+  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 {
+      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);
+  }
+
+}