X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=bd619a3436cd94095386df9e2c00f9a945129bee;hb=32ce9ddb7ce1a68add53dd81785ae428ca136a83;hp=f723fdc2673743c4ecb7517729cf72af3f5eebdd;hpb=764f4139569c1135e41348b24943c3e6d22f74ef;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index f723fdc..bd619a3 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -1,311 +1,402 @@
+/*
+ * 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.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 jalview.datamodel.*;
 
-public class TreePanel extends GTreePanel
-{
-  SequenceI[] seq;
-  String type;
-  String pwtype;
-  AlignViewport av;
-  int start;
-  int end;
-  TreeCanvas treeCanvas;
-  NJTree tree;
+import jalview.io.*;
 
-  FileProperties       fp;
-  PostscriptProperties pp;
+import jalview.jbgui.*;
 
-  PrintWriter bw;
-  PrintStream ps;
-  boolean makeString = false;
-  StringBuffer out;
 
+import java.awt.*;
+import java.awt.event.*;
 
+import java.io.*;
 
-  public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)
-  {
-    super();
+import java.util.*;
 
-    this.type = type;
-    this.pwtype = pwtype;
+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();
-    }
-
-    tree = new NJTree(seq, type, pwtype, start, end);
-    av.setCurrentTree(tree);
-
-    propertiesInit();
-
-    treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
-
-    tree.reCount(tree.getTopNode());
-    tree.findHeight(tree.getTopNode());
-    scrollPane.setViewportView(treeCanvas);
-
-  }
-
+      super();
+      initTreePanel(av, seqVector, type, pwtype, s, e, null);
 
-public void drawPostscript(PostscriptProperties pp) {
-  try {
-    int width = 0;
-    int height = 0;
-
-    printout("%!\n");
-
-    printout("/" + pp.font + " findfont\n");
-    printout(pp.fsize + " scalefont setfont\n");
-
-    int offx = pp.xoffset;
-    int offy = pp.yoffset;
-
-    if (pp.orientation == PostscriptProperties.PORTRAIT) {
-      width = PostscriptProperties.SHORTSIDE;
-      height = PostscriptProperties.LONGSIDE;
-    } else {
-      height = PostscriptProperties.SHORTSIDE;
-      width = PostscriptProperties.LONGSIDE;
-      printout(height + " 0 translate\n90 rotate\n");
+      // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
+      showDistances(true);
     }
-    float wscale = (float)(width*.8-offx*2)/tree.getMaxHeight();
-    SequenceNode top = tree.getTopNode();
 
-    if (top.count == 0) {
-        top.count = ((SequenceNode)top.left()).count + ((SequenceNode)top.right()).count ;
+    /**
+     * 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);
     }
 
-    float chunk = (float)(height-offy*2)/(((SequenceNode)top).count+1);
-
-    drawPostscriptNode(top,chunk,wscale,width,offx,offy);
-
-    printout("showpage\n");
-  } catch (java.io.IOException e) {
-    System.out.println("Exception " + e);
-  }
-}
+    public AlignmentI getAlignment()
+    {
+      return treeCanvas.av.getAlignment();
+    }
 
-public void drawPostscriptNode(SequenceNode node, float chunk, float scale, int width, int offx, int offy) throws java.io.IOException {
-  if (node == null) {
-    return;
-  }
 
-  if (node.left() == null && node.right() == null) {
-    // Drawing leaf node
+    void initTreePanel(AlignViewport av, Vector seqVector, String type,
+                       String pwtype, int s, int e, NewickFile newTree)
+    {
 
-    float height = node.height;
-    float dist = node.dist;
+      this.type = type;
+      this.pwtype = pwtype;
 
-    int xstart = (int)((height-dist)*scale) + offx;
-    int xend =   (int)(height*scale) + offx;
+      start = s;
+      end = e;
 
-    int ypos = (int)(node.ycount * chunk) + offy;
+      seq = new Sequence[seqVector.size()];
+      seqVector.toArray(seq);
 
-    // g.setColor(Color.black);
-    printout("\n" + new Format("%5.3f").form((double)node.color.getRed()/255) + " " +
-             new Format("%5.3f").form((double)node.color.getGreen()/255) + " " +
-             new Format("%5.3f").form((double)node.color.getBlue()/255) + " setrgbcolor\n");
 
-    // Draw horizontal line
-    //  g.drawLine(xstart,ypos,xend,ypos);
-    printout(xstart + " " + ypos + " moveto " + xend + " " + ypos + " lineto stroke \n");
+      treeCanvas = new TreeCanvas(av, scrollPane);
+      scrollPane.setViewportView(treeCanvas);
 
-    if (treeCanvas.showDistances && node.dist > 0) {
-      //	g.drawString(new Format("%5.2f").form(node.dist),xstart,ypos - 5);
-      printout("(" + new Format("%5.2f").form(node.dist) + ") " + xstart + " " + (ypos+5) + " moveto show\n");
-    }
-    //g.drawString((String)node.element(),xend+20,ypos);
-    printout("(" + (((SequenceI)node.element()).getName()) + ") " + (xend+20) + " " + (ypos) + " moveto show\n");
-  } else {
-    drawPostscriptNode((SequenceNode)node.left(),chunk,scale,width,offx,offy);
-    drawPostscriptNode((SequenceNode)node.right(),chunk,scale,width,offx,offy);
-
-
-    float height = node.height;
-    float dist = node.dist;
-
-    int xstart = (int)((height-dist)*scale) + offx;
-    int xend =   (int)(height*scale) + offx;
-    int ypos = (int)(node.ycount * chunk) + offy;
-
-    printout("\n" + new Format("%5.3f").form((double)node.color.getRed()/255) + " " +
-             new Format("%5.3f").form((double)node.color.getGreen()/255) + " " +
-             new Format("%5.3f").form((double)node.color.getBlue()/255) + " setrgbcolor\n");
-    //      g.setColor(Color.black);
-    //      bw.append("\nblack setrgbcolor\n");
-    // Draw horizontal line
-    //      g.drawLine(xstart,ypos,xend,ypos);
-    printout(xstart + " " + ypos + " moveto " + xend + " " + ypos + " lineto stroke\n");
-    int ystart = (int)(((SequenceNode)node.left()).ycount * chunk) + offy;
-    int yend = (int)(((SequenceNode)node.right()).ycount * chunk) + offy;
-
-    //      g.drawLine((int)(height*scale) + offx, ystart,
-    //		 (int)(height*scale) + offx, yend);
-    printout
-    (((int)(height*scale) + offx) + " " + ystart + " moveto " +  ((int)(height*scale) + offx) + " " +
-     yend + " lineto stroke\n");
-    if (treeCanvas.showDistances && node.dist > 0) {
-      //	g.drawString(new Format("%5.2f").form(node.dist),xstart,ypos - 5);
-      printout("(" +new Format("%5.2f").form(node.dist) + ") " + (xstart) + " " + (ypos+5) + " moveto show\n");
-    }
-  }
-}
+      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");
 
-public void printout(String s) throws IOException {
-  if (bw != null) {
-    bw.write(s);
-  }
-  if (ps != null) {
-    ps.print(s);
-  }
-  if (makeString == true) {
-    out.append(s);
-  }
-}
+            tree.UpdatePlaceHolders( (Vector) evt.getNewValue());
 
+            repaint();
+          }
+        }
+      });
 
-public PostscriptProperties getPostscriptProperties() {
-  return pp;
-}
 
-public FileProperties getFileProperties() {
-  return fp;
-}
+      TreeLoader tl = new TreeLoader(newTree);
+      tl.start();
 
-public void setPostscriptProperties(PostscriptProperties pp) {
-  this.pp = pp;
-}
+    }
 
-public void setFileProperties(FileProperties fp) {
-  this.fp = fp;
-}
+    class TreeLoader extends Thread
+    {
+      NewickFile newtree;
 
-public String getText(String format) {
-  return null;
-}
+      public TreeLoader(NewickFile newtree)
+      {
+        this.newtree = newtree;
+        if (newtree != null)
+        {
+          // Must be outside run(), as Jalview2XML tries to
+          // update distance/bootstrap visibility at the same time
+          showBootstrap(newtree.HasBootstrap());
+          showDistances(newtree.HasDistances());
+          showPlaceholders(true);
+        }
+      }
 
-public void getPostscript(PrintWriter bw) {
-  this.bw = bw;
-  drawPostscript(pp);
+      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);
 
-public void getPostscript(PrintStream bw) {
-  this.ps = bw;
-  drawPostscript(pp);
-  bw.flush();
-}
+        treeCanvas.repaint();
+      }
 
-public StringBuffer getPostscript() {
-  makeString = true;
-  out = new StringBuffer();
-  drawPostscript(pp);
-  return out;
-}
+    }
 
-public void propertiesInit() {
-  this.pp = new PostscriptProperties();
-  this.fp = new FileProperties();
-}
+    public void showDistances(boolean b)
+    {
+      treeCanvas.setShowDistances(b);
+      distanceMenu.setSelected(b);
+    }
 
+    public void showBootstrap(boolean b)
+    {
+      treeCanvas.setShowBootstrap(b);
+      bootstrapMenu.setSelected(b);
+    }
 
-  public void saveButton_actionPerformed(ActionEvent e)
-  {
+    public void showPlaceholders(boolean b)
+    {
+      placeholdersMenu.setState(b);
+      treeCanvas.setMarkPlaceholders(b);
+    }
 
-    try{
-      JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-      chooser.setDialogTitle("Save Tree as postscript file");
-      chooser.setToolTipText("Save");
-      int value = chooser.showSaveDialog(this);
-      if (value == JFileChooser.APPROVE_OPTION)
-      {
-        String choice = chooser.getSelectedFile().getPath();
-        jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
 
-        bw = new PrintWriter(new FileWriter(choice));
-        getPostscript(bw);
-        bw.close();
 
-      }
 
-    }catch(Exception ex){ex.printStackTrace();}
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public NJTree getTree()
+    {
+        return tree;
+    }
 
-  }
 
+    /**
+     * 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 saveMenu_actionPerformed(ActionEvent e)
-  {
+    /**
+     * 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();
+            }
+        }
+    }
 
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void printMenu_actionPerformed(ActionEvent e)
+    {
+        //Putting in a thread avoids Swing painting problems
+        treeCanvas.startPrinting();
+    }
 
-  protected void printMenu_actionPerformed(ActionEvent e)
-  {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void fitToWindow_actionPerformed(ActionEvent e)
+    {
+        treeCanvas.fitToWindow = fitToWindow.isSelected();
+        repaint();
+    }
 
-    //Putting in a thread avoids Swing painting problems
-    treeCanvas.startPrinting();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void font_actionPerformed(ActionEvent e)
+    {
+        if (treeCanvas == null)
+        {
+            return;
+        }
 
-  protected void fitToWindow_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.fitToWindow = fitToWindow.isSelected();
-    repaint();
-  }
+        new FontChooser(this);
+    }
 
+    public Font getTreeFont()
+    {
+        return treeCanvas.font;
+    }
 
-  protected void fontSize_actionPerformed(ActionEvent e)
-  {
-    if( treeCanvas==null )
-     return;
+    public void setTreeFont(Font font)
+    {
+      if(treeCanvas!=null)
+      treeCanvas.setFont(font);
+    }
 
-   String size = fontSize.getText().substring( fontSize.getText().indexOf("-")+1);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void distanceMenu_actionPerformed(ActionEvent e)
+    {
+        treeCanvas.setShowDistances(distanceMenu.isSelected());
+    }
 
-   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 e DOCUMENT ME!
+     */
+    public void bootstrapMenu_actionPerformed(ActionEvent e)
+    {
+        treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
+    }
 
-     int i = Integer.parseInt(selection.toString());
-     treeCanvas.setFontSize(i);
-   }
-    scrollPane.setViewportView(treeCanvas);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void placeholdersMenu_actionPerformed(ActionEvent e)
+    {
+        treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
+    }
 
-  }
 
-  protected void distanceMenu_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.setShowDistances(distanceMenu.isSelected());
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void epsTree_actionPerformed(ActionEvent e)
+    {
+      makeTreeImage(jalview.util.ImageMaker.EPS);
+    }
 
-  protected void bootstrapMenu_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void pngTree_actionPerformed(ActionEvent e)
+    {
+       makeTreeImage(jalview.util.ImageMaker.PNG);
+    }
 
+    void makeTreeImage(int type)
+    {
+      int width = treeCanvas.getWidth();
+      int height = treeCanvas.getHeight();
+
+      jalview.util.ImageMaker im;
+
+      if(type == jalview.util.ImageMaker.PNG)
+        im = new jalview.util.ImageMaker(this,
+                                         jalview.util.ImageMaker.PNG,
+                                         "Make PNG image from tree",
+                                         width, height,
+                                         null, null);
+        else
+          im = new jalview.util.ImageMaker(this,
+                                 jalview.util.ImageMaker.EPS,
+                                 "Make EPS file from tree",
+                                 width, height,
+                                 null, this.getTitle());
+
+      if(im.getGraphics()!=null)
+      {
+        treeCanvas.draw(im.getGraphics(), width, height);
+        im.writeImage();
+      }
+    }
 
 }