X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=603a80faf44ce79b5fc59267cf2731d1b99cda03;hb=0039639a8b6fa7a9bfc131c83a493b5a696f0104;hp=c45863817185173ab0dda713f701cb6ab826019c;hpb=1026b7a36483fe6fec0a3d90f1496e49dc9b00ad;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index c458638..603a80f 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -1,246 +1,478 @@
+/*
+ * 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.gui;
 
-import jalview.datamodel.*;
 import jalview.analysis.*;
-import jalview.jbgui.GTreePanel;
+
+import jalview.datamodel.*;
+
 import jalview.io.*;
-import java.awt.event.*;
-import java.util.*;
-import java.io.*;
-import jalview.util.*;
-import javax.swing.*;
-import java.awt.print.*;
-import java.awt.*;
-import java.awt.image.*;
-import org.jibble.epsgraphics.*;
-import javax.imageio.*;
 
+import jalview.jbgui.*;
 
+import org.jibble.epsgraphics.*;
 
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.image.*;
 
-public class TreePanel extends GTreePanel
-{
-  SequenceI[] seq;
-  String type;
-  String pwtype;
-  AlignViewport av;
-  int start;
-  int end;
-  TreeCanvas treeCanvas;
-  NJTree tree;
+import java.io.*;
 
-  public NJTree getTree()
-  {
-    return tree;
-  }
+import java.util.*;
 
-  public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)
-  {
-    super();
+import javax.imageio.*;
 
-    this.type = type;
-    this.pwtype = pwtype;
+import javax.swing.*;
+import java.beans.PropertyChangeEvent;
 
-    start = s;
-    end = e;
 
-    String longestName = "";
-    seq = new Sequence [seqVector.size()];
-    for (int i=0;i < seqVector.size();i++)
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class TreePanel extends GTreePanel
+{
+    SequenceI[] seq;
+    String type;
+    String pwtype;
+    int start;
+    int end;
+    TreeCanvas treeCanvas;
+    NJTree 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)
     {
-      seq[i] = (Sequence) seqVector.elementAt(i);
-      if(seq[i].getName().length()>longestName.length())
-        longestName = seq[i].getName();
-    }
+      super();
+      initTreePanel(av, seqVector, type, pwtype, s, e, null);
 
-    tree = new NJTree(seq, type, pwtype, start, end);
+      // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
+      treeCanvas.setShowDistances(true);
+    }
 
-    treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
+    /**
+     * 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);
+    }
 
-    tree.reCount(tree.getTopNode());
-    tree.findHeight(tree.getTopNode());
-    scrollPane.setViewportView(treeCanvas);
 
-  }
-  public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
-                   String type, String pwtype)
+    void initTreePanel(AlignViewport av, Vector seqVector, String type,
+                       String pwtype, int s, int e, NewickFile newTree)
     {
-      super();
-      // These are probably only  arbitrary strings reflecting source of tree
+
       this.type = type;
       this.pwtype = pwtype;
 
-      start = 0;
-      end = seqVector.size();
+      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();
-      }
-      // This constructor matches sequence names to treenodes and sets up the tree layouts.
-      tree = new NJTree(seq, newtree);
+      seq = new Sequence[seqVector.size()];
+      seqVector.toArray(seq);
 
-      tree.reCount(tree.getTopNode());
-      tree.findHeight(tree.getTopNode());
 
-      treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
-      treeCanvas.setShowBootstrap(newtree.HasBootstrap());
-      treeCanvas.setShowDistances(newtree.HasDistances());
+      treeCanvas = new TreeCanvas(av, scrollPane);
       scrollPane.setViewportView(treeCanvas);
 
-    }
+      av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
+      {
+        public void propertyChange(PropertyChangeEvent evt)
+        {
+          if (evt.getPropertyName().equals("alignment"))
+          {
+            if(tree==null)
+              System.out.println("tree is null");
+            if(evt.getNewValue()==null)
+              System.out.println("new value is null");
+
+            tree.UpdatePlaceHolders( (Vector) evt.getNewValue());
+
+            repaint();
+          }
+        }
+      });
+
+
+      TreeLoader tl = new TreeLoader(newTree);
+      tl.start();
 
-    public String getText(String format)
-    {
-      return null;
     }
 
-    public void saveAsNewick_actionPerformed(ActionEvent e)
+    class TreeLoader extends Thread
     {
+      NewickFile newtree;
 
-  JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty("LAST_DIRECTORY"));
-    chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Save tree as newick file");
-    chooser.setToolTipText("Save");
-    int value = chooser.showSaveDialog(null);
-    if (value == JalviewFileChooser.APPROVE_OPTION) {
-      String choice =  chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",  chooser.getSelectedFile().getParent());
-      try{
-        jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
-        String output = fout.print(false,true); // distances only
-        java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );
-        out.println(output);
-        out.close();
-      }
-      catch (Exception ex) {
-        ex.printStackTrace();
+      public TreeLoader(NewickFile newtree)
+      {
+        this.newtree = newtree;
       }
-    }
-  }
 
-  protected void printMenu_actionPerformed(ActionEvent e)
-  {
+      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());
+        }
+
+        setViewStateFromTreeCanvas(treeCanvas);
 
-    //Putting in a thread avoids Swing painting problems
-    treeCanvas.startPrinting();
-  }
+        treeCanvas.repaint();
 
-  protected void fitToWindow_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.fitToWindow = fitToWindow.isSelected();
-    repaint();
-  }
+      }
+    }
 
 
-  protected void fontSize_actionPerformed(ActionEvent e)
-  {
-    if( treeCanvas==null )
-     return;
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public NJTree getTree()
+    {
+        return tree;
+    }
 
-   String size = fontSize.getText().substring( fontSize.getText().indexOf("-")+1);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param tree DOCUMENT ME!
+     */
+    private void setViewStateFromTreeCanvas(TreeCanvas tree)
+    {
+        // update view menu state from treeCanvas render state
+        distanceMenu.setSelected(tree.showDistances);
+        bootstrapMenu.setSelected(tree.showBootstrap);
+        placeholdersMenu.setSelected(tree.markPlaceholders);
+    }
 
-   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);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param tree DOCUMENT ME!
+     */
+    private void setTreeCanvasFromViewState(TreeCanvas tree)
+    {
+        // update view menu state from treeCanvas render state
+        tree.showDistances = distanceMenu.isSelected();
+        tree.showBootstrap = bootstrapMenu.isSelected();
+        tree.markPlaceholders = placeholdersMenu.isSelected();
+    }
 
-     int i = Integer.parseInt(selection.toString());
-     treeCanvas.setFontSize(i);
-   }
-    scrollPane.setViewportView(treeCanvas);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void textbox_actionPerformed(ActionEvent e)
+    {
+        CutAndPasteTransfer cap = new CutAndPasteTransfer();
+
+        StringBuffer buffer = new StringBuffer();
+
+        if (type.equals("AV"))
+        {
+            buffer.append("Average distance tree using ");
+        }
+        else
+        {
+            buffer.append("Neighbour joining tree using ");
+        }
+
+        if (pwtype.equals("BL"))
+        {
+            buffer.append("BLOSUM62");
+        }
+        else
+        {
+            buffer.append("PID");
+        }
+
+        Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
 
-  }
+        jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+        cap.setText(fout.print(false, true));
+    }
 
-  protected void distanceMenu_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.setShowDistances(distanceMenu.isSelected());
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void saveAsNewick_actionPerformed(ActionEvent e)
+    {
+        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+                    "LAST_DIRECTORY"));
+        chooser.setFileView(new JalviewFileView());
+        chooser.setDialogTitle("Save tree as newick file");
+        chooser.setToolTipText("Save");
+
+        int value = chooser.showSaveDialog(null);
+
+        if (value == JalviewFileChooser.APPROVE_OPTION)
+        {
+            String choice = chooser.getSelectedFile().getPath();
+            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                chooser.getSelectedFile().getParent());
+
+            try
+            {
+                jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+                String output = fout.print(false, true); // distances only
+                java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
+                            choice));
+                out.println(output);
+                out.close();
+            }
+            catch (Exception ex)
+            {
+                ex.printStackTrace();
+            }
+        }
+    }
 
-  protected void bootstrapMenu_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void printMenu_actionPerformed(ActionEvent e)
+    {
+        //Putting in a thread avoids Swing painting problems
+        treeCanvas.startPrinting();
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void fitToWindow_actionPerformed(ActionEvent e)
+    {
+        treeCanvas.fitToWindow = fitToWindow.isSelected();
+        repaint();
+    }
 
-  protected void epsTree_actionPerformed(ActionEvent e)
-  {
-    int width = treeCanvas.getWidth(), height=treeCanvas.getHeight();
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void font_actionPerformed(ActionEvent e)
     {
-      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
-          "LAST_DIRECTORY"),
-              new String[]{"eps"},
-              new String[]{"Encapsulated Postscript"},
-              "Encapsulated Postscript");
-      chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle("Create EPS file from tree");
-      chooser.setToolTipText("Save");
+        if (treeCanvas == null)
+        {
+            return;
+        }
 
-      int value = chooser.showSaveDialog(this);
-      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
-        return;
+        FontChooser fontchooser = new FontChooser(this);
+    }
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent());
-      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
-      EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
+    public Font getFont()
+    {
+      return treeCanvas.font;
+    }
 
+    public void setFont(Font font)
+    {
+      if(treeCanvas!=null)
+      treeCanvas.setFont(font);
+    }
 
-      treeCanvas.draw(pg, width, height);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void distanceMenu_actionPerformed(ActionEvent e)
+    {
+        treeCanvas.setShowDistances(distanceMenu.isSelected());
+    }
 
-        pg.flush();
-        pg.close();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void bootstrapMenu_actionPerformed(ActionEvent e)
+    {
+        treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
     }
-    catch (Exception ex)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void placeholdersMenu_actionPerformed(ActionEvent e)
     {
-      ex.printStackTrace();
+        treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
     }
-  }
 
-  protected void pngTree_actionPerformed(ActionEvent e)
- {
-  int width = treeCanvas.getWidth(), height = treeCanvas.getHeight();
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void epsTree_actionPerformed(ActionEvent e)
     {
-      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
-          jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-          new String[] {"png"},
-          new String[] {"Portable network graphics"},
-          "Portable network graphics");
+      boolean accurateText = true;
+
+      String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
+          "Prompt each time");
+
+    // If we need to prompt, and if the GUI is visible then
+    // Prompt for EPS rendering style
+      if (renderStyle.equalsIgnoreCase("Prompt each time")
+          && !
+          (System.getProperty("java.awt.headless") != null
+           && System.getProperty("java.awt.headless").equals("true")))
+      {
+        EPSOptions eps = new EPSOptions();
+        renderStyle = eps.getValue();
+
+        if (renderStyle==null || eps.cancelled)
+          return;
+
+
+      }
+
+      if (renderStyle.equalsIgnoreCase("text"))
+      {
+        accurateText = false;
+      }
+
+        int width = treeCanvas.getWidth();
+        int height = treeCanvas.getHeight();
+
+        try
+        {
+            jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
+                        "LAST_DIRECTORY"), new String[] { "eps" },
+                    new String[] { "Encapsulated Postscript" },
+                    "Encapsulated Postscript");
+            chooser.setFileView(new jalview.io.JalviewFileView());
+            chooser.setDialogTitle("Create EPS file from tree");
+            chooser.setToolTipText("Save");
 
-      chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle("Create PNG image from tree");
-      chooser.setToolTipText("Save");
+            int value = chooser.showSaveDialog(this);
 
-      int value = chooser.showSaveDialog(this);
-      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
-        return;
+            if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+            {
+                return;
+            }
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getParent());
-      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                                          chooser.getSelectedFile().getParent());
 
-      BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
-      Graphics png = bi.getGraphics();
+            FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+            EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
+                                                 height);
 
-      treeCanvas.draw(png, width, height);
+            pg.setAccurateTextMode(accurateText);
 
-        ImageIO.write(bi, "png", out);
-        out.close();
+            treeCanvas.draw(pg, width, height);
+
+            pg.flush();
+            pg.close();
+        }
+        catch (Exception ex)
+        {
+            ex.printStackTrace();
+        }
     }
-    catch (Exception ex)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void pngTree_actionPerformed(ActionEvent e)
     {
-      ex.printStackTrace();
-    }
-  }
+        int width = treeCanvas.getWidth();
+        int height = treeCanvas.getHeight();
+
+        try
+        {
+            jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
+                        "LAST_DIRECTORY"), new String[] { "png" },
+                    new String[] { "Portable network graphics" },
+                    "Portable network graphics");
+
+            chooser.setFileView(new jalview.io.JalviewFileView());
+            chooser.setDialogTitle("Create PNG image from tree");
+            chooser.setToolTipText("Save");
+
+            int value = chooser.showSaveDialog(this);
 
+            if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+            {
+                return;
+            }
+
+            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                chooser.getSelectedFile().getParent());
+
+            FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+
+            BufferedImage bi = new BufferedImage(width, height,
+                    BufferedImage.TYPE_INT_RGB);
+            Graphics png = bi.getGraphics();
+
+            treeCanvas.draw(png, width, height);
+
+            ImageIO.write(bi, "png", out);
+            out.close();
+        }
+        catch (Exception ex)
+        {
+            ex.printStackTrace();
+        }
+    }
 }