X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=ff02d49ec487eef6189d2acba088ca4b4267e9bf;hb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;hp=3ba9cdd5b0b51cc13b56964877acfb37ef88658a;hpb=9257b8510c7354cbd7e43a3fc2817978cc8e4ae9;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 3ba9cdd..ff02d49 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -18,350 +18,439 @@
  */
 package jalview.gui;
 
-import java.io.*;
-import java.util.*;
-import javax.imageio.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-import javax.swing.*;
-
-import org.jibble.epsgraphics.*;
 import jalview.analysis.*;
+
 import jalview.datamodel.*;
+
 import jalview.io.*;
+
 import jalview.jbgui.*;
 
-public class TreePanel
-    extends GTreePanel
-{
-  SequenceI[] seq;
-  String type;
-  String pwtype;
-  int start;
-  int end;
-  TreeCanvas treeCanvas;
-  NJTree tree;
+import org.jibble.epsgraphics.*;
 
-  public TreePanel(AlignViewport av, Vector seqVector, String type,
-                   String pwtype, int s, int e)
-  {
-    super();
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.image.*;
 
-    this.type = type;
-    this.pwtype = pwtype;
+import java.io.*;
 
-    start = s;
-    end = e;
+import java.util.*;
 
-    String longestName = "";
-    seq = new Sequence[seqVector.size()];
+import javax.imageio.*;
+
+import javax.swing.*;
 
-    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);
+        super();
 
-      if (seq[i].getName().length() > longestName.length())
-      {
-        longestName = seq[i].getName();
-      }
-    }
+        this.type = type;
+        this.pwtype = pwtype;
 
-    tree = new NJTree(seq, type, pwtype, start, end);
+        start = s;
+        end = e;
 
-    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);
-  }
+        String longestName = "";
+        seq = new Sequence[seqVector.size()];
 
-  public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
-                   String type, String pwtype)
-  {
-    super();
+        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();
+            }
+        }
+
+        tree = new NJTree(seq, type, pwtype, start, end);
+
+        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);
+    }
 
-    // These are probably only  arbitrary strings reflecting source of tree
-    this.type = type;
-    this.pwtype = pwtype;
+    /**
+     * 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();
 
-    start = 0;
-    end = seqVector.size();
+        // These are probably only  arbitrary strings reflecting source of tree
+        this.type = type;
+        this.pwtype = pwtype;
 
-    String longestName = "";
-    seq = new Sequence[seqVector.size()];
+        start = 0;
+        end = seqVector.size();
 
-    for (int i = 0; i < seqVector.size(); i++)
-    {
-      seq[i] = (Sequence) seqVector.elementAt(i);
-    }
+        String longestName = "";
+        seq = new Sequence[seqVector.size()];
 
-    // This constructor matches sequence names to treenodes and sets up the tree layouts.
-    tree = new NJTree(seq, newtree);
+        for (int i = 0; i < seqVector.size(); i++)
+        {
+            seq[i] = (Sequence) seqVector.elementAt(i);
+        }
 
-    // Now have to calculate longest name based on the leaves
-    Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
-    boolean has_placeholders = false;
+        // This constructor matches sequence names to treenodes and sets up the tree layouts.
+        tree = new NJTree(seq, newtree);
 
-    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();
-      }
-    }
+        // Now have to calculate longest name based on the leaves
+        Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
+        boolean has_placeholders = false;
 
-    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
-  }
-
-  public NJTree getTree()
-  {
-    return tree;
-  }
-
-  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);
-  }
-
-  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();
-  }
-
-  public void textbox_actionPerformed(ActionEvent e)
-  {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer();
-
-    StringBuffer buffer = new StringBuffer();
-
-    if (type.equals("AV"))
-    {
-      buffer.append("Average distance tree using ");
+        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
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public NJTree getTree()
     {
-      buffer.append("Neighbour joining tree using ");
+        return tree;
     }
 
-    if (pwtype.equals("BL"))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param tree DOCUMENT ME!
+     */
+    private void setViewStateFromTreeCanvas(TreeCanvas tree)
     {
-      buffer.append("BLOSUM62");
+        // update view menu state from treeCanvas render state
+        distanceMenu.setSelected(tree.showDistances);
+        bootstrapMenu.setSelected(tree.showBootstrap);
+        placeholdersMenu.setSelected(tree.markPlaceholders);
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param tree DOCUMENT ME!
+     */
+    private void setTreeCanvasFromViewState(TreeCanvas tree)
     {
-      buffer.append("PID");
+        // update view menu state from treeCanvas render state
+        tree.showDistances = distanceMenu.isSelected();
+        tree.showBootstrap = bootstrapMenu.isSelected();
+        tree.markPlaceholders = placeholdersMenu.isSelected();
     }
 
-    Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void textbox_actionPerformed(ActionEvent e)
+    {
+        CutAndPasteTransfer cap = new CutAndPasteTransfer();
 
-    jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
-    cap.setText(fout.print(false, true));
-  }
+        StringBuffer buffer = new StringBuffer();
 
-  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");
+        if (type.equals("AV"))
+        {
+            buffer.append("Average distance tree using ");
+        }
+        else
+        {
+            buffer.append("Neighbour joining tree using ");
+        }
 
-    int value = chooser.showSaveDialog(null);
+        if (pwtype.equals("BL"))
+        {
+            buffer.append("BLOSUM62");
+        }
+        else
+        {
+            buffer.append("PID");
+        }
 
-    if (value == JalviewFileChooser.APPROVE_OPTION)
-    {
-      String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                                    chooser.getSelectedFile().getParent());
+        Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
 
-      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();
-      }
+        cap.setText(fout.print(false, true));
     }
-  }
-
-  public void printMenu_actionPerformed(ActionEvent e)
-  {
-    //Putting in a thread avoids Swing painting problems
-    treeCanvas.startPrinting();
-  }
-
-  public void fitToWindow_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.fitToWindow = fitToWindow.isSelected();
-    repaint();
-  }
-
-  public void fontSize_actionPerformed(ActionEvent e)
-  {
-    if (treeCanvas == null)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void saveAsNewick_actionPerformed(ActionEvent e)
     {
-      return;
-    }
+        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+                    "LAST_DIRECTORY"));
+        chooser.setFileView(new JalviewFileView());
+        chooser.setDialogTitle("Save tree as newick file");
+        chooser.setToolTipText("Save");
 
-    String size = fontSize.getText().substring(fontSize.getText().indexOf("-") +
-                                               1);
+        int value = chooser.showSaveDialog(null);
 
-    Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,
-        "Select font size", "Font size", JOptionPane.QUESTION_MESSAGE,
-        null,
-        new String[]
+        if (value == JalviewFileChooser.APPROVE_OPTION)
         {
-        "1", "2", "4", "6", "8", "10", "12", "14", "16", "18", "20"
-    }, "Font Size - " + size);
+            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();
+            }
+        }
+    }
 
-    if (selection != null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void printMenu_actionPerformed(ActionEvent e)
     {
-      fontSize.setText("Font Size - " + selection);
+        //Putting in a thread avoids Swing painting problems
+        treeCanvas.startPrinting();
+    }
 
-      int i = Integer.parseInt(selection.toString());
-      treeCanvas.setFontSize(i);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void fitToWindow_actionPerformed(ActionEvent e)
+    {
+        treeCanvas.fitToWindow = fitToWindow.isSelected();
+        repaint();
     }
 
-    scrollPane.setViewportView(treeCanvas);
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void fontSize_actionPerformed(ActionEvent e)
+    {
+        if (treeCanvas == null)
+        {
+            return;
+        }
 
-  public void distanceMenu_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.setShowDistances(distanceMenu.isSelected());
-  }
+        String size = fontSize.getText().substring(fontSize.getText().indexOf("-") +
+                1);
 
-  public void bootstrapMenu_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.setShowBootstrap(bootstrapMenu.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);
 
-  public void placeholdersMenu_actionPerformed(ActionEvent e)
-  {
-    treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
-  }
+        if (selection != null)
+        {
+            fontSize.setText("Font Size - " + selection);
+
+            int i = Integer.parseInt(selection.toString());
+            treeCanvas.setFontSize(i);
+        }
 
-  public void epsTree_actionPerformed(ActionEvent e)
-  {
-    int width = treeCanvas.getWidth();
-    int height = treeCanvas.getHeight();
+        scrollPane.setViewportView(treeCanvas);
+    }
 
-    try
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void distanceMenu_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");
-
-      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();
+        treeCanvas.setShowDistances(distanceMenu.isSelected());
     }
-    catch (Exception ex)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void bootstrapMenu_actionPerformed(ActionEvent e)
     {
-      ex.printStackTrace();
+        treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
     }
-  }
 
-  public void pngTree_actionPerformed(ActionEvent e)
-  {
-    int width = treeCanvas.getWidth();
-    int height = treeCanvas.getHeight();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void placeholdersMenu_actionPerformed(ActionEvent e)
+    {
+        treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
+    }
 
-    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");
+        int width = treeCanvas.getWidth();
+        int height = treeCanvas.getHeight();
 
-      chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle("Create PNG image from tree");
-      chooser.setToolTipText("Save");
+        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();
+        }
+    }
 
-      int value = chooser.showSaveDialog(this);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void pngTree_actionPerformed(ActionEvent e)
+    {
+        int width = treeCanvas.getWidth();
+        int height = treeCanvas.getHeight();
 
-      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
-      {
-        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");
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                                    chooser.getSelectedFile().getParent());
+            chooser.setFileView(new jalview.io.JalviewFileView());
+            chooser.setDialogTitle("Create PNG image from tree");
+            chooser.setToolTipText("Save");
 
-      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+            int value = chooser.showSaveDialog(this);
 
-      BufferedImage bi = new BufferedImage(width, height,
-                                           BufferedImage.TYPE_INT_RGB);
-      Graphics png = bi.getGraphics();
+            if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+            {
+                return;
+            }
 
-      treeCanvas.draw(png, width, height);
+            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                chooser.getSelectedFile().getParent());
 
-      ImageIO.write(bi, "png", out);
-      out.close();
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
+            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();
+        }
     }
-  }
 }