X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=ff02d49ec487eef6189d2acba088ca4b4267e9bf;hb=f2d10e204281911d5da924b7aa4cdb93102a4e24;hp=4b605bf3379de18248c612a35c76724c51ed06d2;hpb=af94a4ec352bed730ba82f9e3bdcc7a34656b1e4;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 4b605bf..ff02d49 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -1,304 +1,456 @@
+/*
+ * 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.*;
 
+import jalview.io.*;
 
-public class TreePanel extends GTreePanel
-{
-  SequenceI[] seq;
-  String type;
-  String pwtype;
-  AlignViewport av;
-  int start;
-  int end;
-  TreeCanvas treeCanvas;
-  NJTree tree;
+import jalview.jbgui.*;
 
-  FileProperties       fp;
-  PostscriptProperties pp;
+import org.jibble.epsgraphics.*;
 
-  PrintWriter bw;
-  PrintStream ps;
-  boolean makeString = false;
-  StringBuffer out;
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.image.*;
 
+import java.io.*;
 
+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.*;
 
-    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();
+        super();
 
-    treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
+        this.type = type;
+        this.pwtype = pwtype;
 
-    tree.reCount(tree.getTopNode());
-    tree.findHeight(tree.getTopNode());
-    scrollPane.setViewportView(treeCanvas);
+        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);
 
-public void drawPostscript(PostscriptProperties pp) {
-  try {
-    int width = 0;
-    int height = 0;
+            if (seq[i].getName().length() > longestName.length())
+            {
+                longestName = seq[i].getName();
+            }
+        }
 
-    printout("%!\n");
+        tree = new NJTree(seq, type, pwtype, start, end);
 
-    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");
+        treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
+        treeCanvas.setShowDistances(true); // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
+        setViewStateFromTreeCanvas(treeCanvas);
+        tree.reCount(tree.getTopNode());
+        tree.findHeight(tree.getTopNode());
+        scrollPane.setViewportView(treeCanvas);
     }
-    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();
+
+        // 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());
+        boolean has_placeholders = false;
+
+        for (int i = 0; i < leaves.size(); i++)
+        {
+            SequenceNode lf = (SequenceNode) leaves.elementAt(i);
+
+            if (lf.isPlaceholder())
+            {
+                has_placeholders = true;
+            }
+
+            if (longestName.length() < ((Sequence) lf.element()).getName()
+                                            .length())
+            {
+                longestName = TreeCanvas.PLACEHOLDER +
+                    ((Sequence) lf.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());
+        scrollPane.setViewportView(treeCanvas);
+        treeCanvas.setMarkPlaceholders(has_placeholders);
+        setViewStateFromTreeCanvas(treeCanvas);
+
+        // JBPNote TODO: preference for always marking placeholders in new associated tree
     }
 
-    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 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
-
-    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;
-
-    // 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");
-
-    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");
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public NJTree getTree()
+    {
+        return tree;
     }
-  }
-}
-
-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);
-  }
-}
-
-
-public PostscriptProperties getPostscriptProperties() {
-  return pp;
-}
-
-public FileProperties getFileProperties() {
-  return fp;
-}
-
-public void setPostscriptProperties(PostscriptProperties pp) {
-  this.pp = pp;
-}
-
-public void setFileProperties(FileProperties fp) {
-  this.fp = fp;
-}
-
-public String getText(String format) {
-  return null;
-}
-
-public void getPostscript(PrintWriter bw) {
-  this.bw = bw;
-  drawPostscript(pp);
-
-}
-
-public void getPostscript(PrintStream bw) {
-  this.ps = bw;
-  drawPostscript(pp);
-  bw.flush();
-}
-
-public StringBuffer getPostscript() {
-  makeString = true;
-  out = new StringBuffer();
-  drawPostscript(pp);
-  return out;
-}
-
-public void propertiesInit() {
-  this.pp = new PostscriptProperties();
-  this.fp = new FileProperties();
-}
 
+    /**
+     * 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);
+    }
 
-  public void saveButton_actionPerformed(ActionEvent e)
-  {
+    /**
+     * 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();
+    }
 
-    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);
+    /**
+     * 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));
+    }
 
-        bw = new PrintWriter(new FileWriter(choice));
-        getPostscript(bw);
-        bw.close();
+    /**
+     * 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();
+    }
 
-    }catch(Exception ex){ex.printStackTrace();}
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void fitToWindow_actionPerformed(ActionEvent e)
+    {
+        treeCanvas.fitToWindow = fitToWindow.isSelected();
+        repaint();
+    }
 
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void fontSize_actionPerformed(ActionEvent e)
+    {
+        if (treeCanvas == null)
+        {
+            return;
+        }
+
+        String size = fontSize.getText().substring(fontSize.getText().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);
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void distanceMenu_actionPerformed(ActionEvent e)
+    {
+        treeCanvas.setShowDistances(distanceMenu.isSelected());
+    }
 
-  protected void saveMenu_actionPerformed(ActionEvent e)
-  {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void bootstrapMenu_actionPerformed(ActionEvent e)
+    {
+        treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
+    }
 
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void placeholdersMenu_actionPerformed(ActionEvent e)
+    {
+        treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
+    }
 
-  protected void printMenu_actionPerformed(ActionEvent e)
-  {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void epsTree_actionPerformed(ActionEvent e)
+    {
+        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");
+
+            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());
+            EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
+                    height);
+
+            treeCanvas.draw(pg, width, height);
+
+            pg.flush();
+            pg.close();
+        }
+        catch (Exception ex)
+        {
+            ex.printStackTrace();
+        }
+    }
 
-    //Putting in a thread avoids Swing painting problems
-    treeCanvas.startPrinting();
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void pngTree_actionPerformed(ActionEvent e)
+    {
+        int width = treeCanvas.getWidth();
+        int height = treeCanvas.getHeight();
 
-  protected void fontSize_actionPerformed(ActionEvent e)
-  {
-    if( treeCanvas==null )
-     return;
+        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");
 
-   String size = fontSize.getText().substring( fontSize.getText().indexOf("-")+1);
+            chooser.setFileView(new jalview.io.JalviewFileView());
+            chooser.setDialogTitle("Create PNG image from tree");
+            chooser.setToolTipText("Save");
 
-   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 value = chooser.showSaveDialog(this);
 
-     int i = Integer.parseInt(selection.toString());
-     treeCanvas.setFontSize(i);
-   }
-    scrollPane.setViewportView(treeCanvas);
+            if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+            {
+                return;
+            }
 
-  }
+            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                chooser.getSelectedFile().getParent());
 
-  protected void distanceMenu_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.setShowDistances(distanceMenu.isSelected());
-  }
+            FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
 
-  protected void bootstrapMenu_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
-  }
+            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();
+        }
+    }
 }