X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=3fa7643b497f141e0c9e3afb11d61c99db93d3c0;hb=d5b157fc64cc6e5f633a2f7ae991a29b7c557b94;hp=9f9e32772af1ed82529773d94b96a5f9db518f58;hpb=2bce008bf6a7cdd574baa767acef76939ea1aff8;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 9f9e327..3fa7643 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -1,240 +1,550 @@
+/*
+ * 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 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
+{
+    String type;
+    String pwtype;
+    TreeCanvas treeCanvas;
+    NJTree tree;
+    AlignViewport av;
+
+    /**
+     * 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)
     {
-      seq[i] = (Sequence) seqVector.elementAt(i);
-      if(seq[i].getName().length()>longestName.length())
-        longestName = seq[i].getName();
+      super();
+      initTreePanel(av, type, pwtype, null);
+
+      // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
+      // showDistances(true);
     }
 
-    tree = new NJTree(seq, type, pwtype, start, end);
+    /**
+     * 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)
+    {
+      super();
+      initTreePanel(av, type, pwtype, newtree);
+    }
 
-    treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
+    public AlignmentI getAlignment()
+    {
+      return treeCanvas.av.getAlignment();
+    }
 
-    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, String type,  String pwtype,
+                       NewickFile newTree)
     {
-      super();
-      // These are probably only  arbitrary strings reflecting source of tree
+
       this.type = type;
       this.pwtype = pwtype;
 
-      start = 0;
-      end = seqVector.size();
+      treeCanvas = new TreeCanvas(av, scrollPane);
+      scrollPane.setViewportView(treeCanvas);
 
-      String longestName = "";
-      seq = new Sequence [seqVector.size()];
-      for (int i=0;i < seqVector.size();i++)
+      av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
       {
-        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);
-
-      tree.reCount(tree.getTopNode());
-      tree.findHeight(tree.getTopNode());
+        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");
 
-      treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
-      treeCanvas.setShowBootstrap(newtree.HasBootstrap());
-      treeCanvas.setShowDistances(newtree.HasDistances());
-      scrollPane.setViewportView(treeCanvas);
+            tree.UpdatePlaceHolders( (Vector) evt.getNewValue());
 
-    }
+            repaint();
+          }
+        }
+      });
 
+      this.av = av;
 
 
-public String getText(String format) {
-  return null;
-}
+      TreeLoader tl = new TreeLoader(newTree);
+      tl.start();
 
+    }
 
-  protected void saveMenu_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",  choice);
-      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();
+    class TreeLoader extends Thread
+    {
+      NewickFile newtree;
+      jalview.datamodel.AlignmentView odata=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());
+        }
       }
-      catch (Exception ex) {
-        ex.printStackTrace();
+
+      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);
+          }
+          if (!tree.hasOriginalSequenceData())
+            allowOriginalSeqData(false);
+        }
+        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);
+          showDistances(true);
+        }
+
+
+        tree.reCount(tree.getTopNode());
+        tree.findHeight(tree.getTopNode());
+        treeCanvas.setTree(tree);
+        treeCanvas.repaint();
+        av.setCurrentTree(tree);
+
       }
     }
-  }
 
-  protected void printMenu_actionPerformed(ActionEvent e)
-  {
-
-    //Putting in a thread avoids Swing painting problems
-    treeCanvas.startPrinting();
-  }
+    public void showDistances(boolean b)
+    {
+      treeCanvas.setShowDistances(b);
+      distanceMenu.setSelected(b);
+    }
 
-  protected void fitToWindow_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.fitToWindow = fitToWindow.isSelected();
-    repaint();
-  }
+    public void showBootstrap(boolean b)
+    {
+      treeCanvas.setShowBootstrap(b);
+      bootstrapMenu.setSelected(b);
+    }
 
+    public void showPlaceholders(boolean b)
+    {
+      placeholdersMenu.setState(b);
+      treeCanvas.setMarkPlaceholders(b);
+    }
 
-  protected void fontSize_actionPerformed(ActionEvent e)
-  {
-    if( treeCanvas==null )
-     return;
+    private void allowOriginalSeqData(boolean b) {
+      originalSeqData.setVisible(b);
+    }
 
-   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!
+     *
+     * @return DOCUMENT ME!
+     */
+    public NJTree getTree()
+    {
+        return tree;
+    }
 
-  }
 
-  protected void distanceMenu_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.setShowDistances(distanceMenu.isSelected());
-  }
+    /**
+     * 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);
 
-  protected void bootstrapMenu_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
-  }
+        jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+        cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));
+    }
 
+    /**
+     * 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(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());
+                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 epsTree_actionPerformed(ActionEvent e)
-  {
-    int width = treeCanvas.getWidth(), height=treeCanvas.getHeight();
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void printMenu_actionPerformed(ActionEvent e)
     {
-      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
-          "LAST_DIRECTORY"), new String[]{"eps"}, "Encapsulated Postscript");
-      chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle("Create EPS file from tree");
-      chooser.setToolTipText("Save");
+        //Putting in a thread avoids Swing painting problems
+        treeCanvas.startPrinting();
+    }
 
-      int value = chooser.showSaveDialog(this);
-      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+
+    public void originalSeqData_actionPerformed(ActionEvent e)
+    {
+      if (!tree.hasOriginalSequenceData())
+      {
+        jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
         return;
+      }
+      // 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)
+       {
+         // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
+
+         Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
+         Alignment dataset = av.getAlignment().getDataset();
+         if (dataset != null)
+         {
+           al.setDataset(dataset);
+         }
+
+         if (true)
+         {
+           // make a new frame!
+           AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1]);
+
+           //>>>This is a fix for the moment, until a better solution is found!!<<<
+           // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
+
+       //           af.addSortByOrderMenuItem(ServiceName + " Ordering",
+       //                                     msaorder);
+
+           Desktop.addInternalFrame(af, "Original Data for " + this.title,
+                                    AlignFrame.NEW_WINDOW_WIDTH,
+                                    AlignFrame.NEW_WINDOW_HEIGHT);
+         }
+       }
+    }
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
-      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
-      EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void fitToWindow_actionPerformed(ActionEvent e)
+    {
+        treeCanvas.fitToWindow = fitToWindow.isSelected();
+        repaint();
+    }
 
-      treeCanvas.draw(pg, width, height);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void font_actionPerformed(ActionEvent e)
+    {
+        if (treeCanvas == null)
+        {
+            return;
+        }
 
-        pg.flush();
-        pg.close();
+        new FontChooser(this);
     }
-    catch (Exception ex)
+
+    public Font getTreeFont()
     {
-      ex.printStackTrace();
+        return treeCanvas.font;
     }
-  }
 
-  protected void pngTree_actionPerformed(ActionEvent e)
- {
-  int width = treeCanvas.getWidth(), height = treeCanvas.getHeight();
-    try
+    public void setTreeFont(Font font)
     {
-      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
-          "LAST_DIRECTORY"), new String[]{"png"}, "Portable network graphics");
-      chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle("Create PNG image from tree");
-      chooser.setToolTipText("Save");
+      if(treeCanvas!=null)
+      treeCanvas.setFont(font);
+    }
 
-      int value = chooser.showSaveDialog(this);
-      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
-        return;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void distanceMenu_actionPerformed(ActionEvent e)
+    {
+        treeCanvas.setShowDistances(distanceMenu.isSelected());
+    }
+
+    /**
+     * 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());
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void epsTree_actionPerformed(ActionEvent e)
+    {
+      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");
+
+            int value = chooser.showSaveDialog(this);
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
-      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+            if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+            {
+                return;
+            }
 
-      BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
-      Graphics png = bi.getGraphics();
+            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                                          chooser.getSelectedFile().getParent());
 
-      treeCanvas.draw(png, width, height);
+            FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+            EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
+                                                 height);
 
-        ImageIO.write(bi, "png", out);
-        out.close();
+            pg.setAccurateTextMode(accurateText);
+
+            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();
+        }
+    }
 }