X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreePanel.java;h=735a11bfd94be34941cf7809d9c559289ee194b1;hb=08598b6cbefd6e268c20f7e5ca9785dd5e243a08;hp=51ec4a0a0e27fa9e256225acf0c79e659009f88b;hpb=8a5c39442bced20fc95272efe6d3176719ca3f15;p=jalview.git

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 51ec4a0..735a11b 100755
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -1,201 +1,364 @@
-/*
- * 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 jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.jbappletgui.*;
-
-public class TreePanel
-    extends GTreePanel
-{
-  SequenceI[] seq;
-  String type;
-  String pwtype;
-  AlignmentPanel ap;
-  int start;
-  int end;
-  TreeCanvas treeCanvas;
-  NJTree tree;
-
-  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, 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;
-
-    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
-  {
-    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.repaint();
-
-    }
-  }
-
-  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, 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);
-  }
-
-  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 (Development Version 2.4.1)
+ * Copyright (C) 2009 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.awt.*;
+import java.awt.event.*;
+import java.util.Hashtable;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+
+public class TreePanel extends EmbmenuFrame 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);
+    TreeLoader tl = new TreeLoader(newTree);
+    tl.start();
+    embedMenuIfNeeded(treeCanvas);
+    scrollPane.add(treeCanvas, BorderLayout.CENTER);
+  }
+
+  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)
+    {
+      char gc = '-';
+      try
+      {
+        // we try to get the associated view's gap character
+        // but this may fail if the view was closed...
+        gc = av.getGapCharacter();
+      } catch (Exception ex)
+      {
+      }
+      ;
+      Object[] alAndColsel = tree.seqData
+              .getAlignmentAndColumnSelection(gc);
+
+      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)
+    {
+      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);
+  }
+
+}