X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreePanel.java;h=65f3d9156a22cf76fb34df2f4fa5eb0b48648c92;hb=ad20cd92225f2ee8c251d39b00b90555d382a616;hp=99d032859f9756524d4f476b2cb0e104070c333c;hpb=c3db82330376f20423dc617cfa92d131dc40e515;p=jalview.git

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
old mode 100755
new mode 100644
index 99d0328..65f3d91
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -1,158 +1,384 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *  
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ */
 package jalview.appletgui;
 
-import jalview.datamodel.*;
-import jalview.io.NewickFile;
-import jalview.analysis.*;
-import jalview.jbappletgui.GTreePanel;
+import java.awt.*;
 import java.awt.event.*;
-import java.util.*;
-import jalview.io.NewickFile;
 
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.io.*;
 
-public class TreePanel extends GTreePanel
+public class TreePanel extends EmbmenuFrame implements ActionListener,
+        ItemListener
 {
   SequenceI[] seq;
+
   String type;
+
   String pwtype;
-  AlignViewport av;
+
   int start;
+
   int end;
+
   TreeCanvas treeCanvas;
+
   NJTree tree;
 
+  AlignmentPanel ap;
+
+  AlignViewport av;
+
   public NJTree getTree()
   {
     return tree;
   }
 
-  public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)
+  public void finalize() throws Throwable
   {
-    super();
+    ap = null;
+    av = null;
+    super.finalize();
+  }
 
-    this.type = type;
-    this.pwtype = pwtype;
+  /**
+   * 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(AlignmentPanel ap, String type, String pwtype)
+  {
+    try
+    {
+      jbInit();
+      this.setMenuBar(jMenuBar1);
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
 
-    start = s;
-    end = e;
+    initTreePanel(ap, type, pwtype, null);
+  }
 
-    String longestName = "";
-    seq = new Sequence [seqVector.size()];
-    for (int i=0;i < seqVector.size();i++)
+  /**
+   * 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(AlignmentPanel ap, String type, String pwtype,
+          NewickFile newtree)
+  {
+    try
+    {
+      jbInit();
+      this.setMenuBar(jMenuBar1);
+    } catch (Exception e)
     {
-      seq[i] = (Sequence) seqVector.elementAt(i);
-      if(seq[i].getName().length()>longestName.length())
-        longestName = seq[i].getName();
+      e.printStackTrace();
     }
 
-    tree = new NJTree(seq, type, pwtype, start, end);
+    initTreePanel(ap, type, pwtype, newtree);
+  }
 
-    treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
+  void initTreePanel(AlignmentPanel ap, String type, String pwtype,
+          NewickFile newTree)
+  {
 
-    tree.reCount(tree.getTopNode());
-    tree.findHeight(tree.getTopNode());
-    scrollPane.add(treeCanvas);
+    this.ap = ap;
+    this.av = ap.av;
+    this.type = type;
+    this.pwtype = pwtype;
 
+    treeCanvas = new TreeCanvas(ap, scrollPane);
+    TreeLoader tl = new TreeLoader(newTree);
+    tl.start();
+    embedMenuIfNeeded(treeCanvas);
+    scrollPane.add(treeCanvas, BorderLayout.CENTER);
   }
-  public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
-                   String type, String pwtype)
+
+  void showOriginalData()
+  {
+    // 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[])
+    if (tree.seqData != null)
+    {
+      char gc = '-';
+      try
+      {
+        // we try to get the associated view's gap character
+        // but this may fail if the view was closed...
+        gc = av.getGapCharacter();
+      } catch (Exception ex)
+      {
+      }
+      ;
+      Object[] alAndColsel = tree.seqData
+              .getAlignmentAndColumnSelection(gc);
+
+      if (alAndColsel != null && alAndColsel[0] != null)
+      {
+        Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
+        AlignFrame af = new AlignFrame(al, av.applet,
+                "Original Data for Tree", false);
+
+        af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
+      }
+    }
+    else
     {
-      super();
-      // These are probably only  arbitrary strings reflecting source of tree
-      this.type = type;
-      this.pwtype = pwtype;
+      System.out.println("Original Tree Data not available");
+    }
+  }
+
+  class TreeLoader extends Thread
+  {
+    NewickFile newtree;
+
+    jalview.datamodel.AlignmentView odata = null;
 
-      start = 0;
-      end = seqVector.size();
+    public TreeLoader(NewickFile newtree)
+    {
+      this.newtree = newtree;
+    }
 
-      String longestName = "";
-      seq = new Sequence [seqVector.size()];
-      for (int i=0;i < seqVector.size();i++)
+    public void run()
+    {
+      if (newtree != null)
       {
-        seq[i] = (Sequence) seqVector.elementAt(i);
+        if (odata == null)
+        {
+          tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
+        }
+        else
+        {
+          tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
+                  newtree);
+        }
+
       }
-      // 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());
+      else
+      {
+        int start, end;
+        SequenceI[] seqs;
+        boolean selview = (av.getSelectionGroup() != null)
+                && (av.getSelectionGroup().getSize() > 1);
+        AlignmentView seqStrings = av.getAlignmentView(selview);
+        if (!selview)
+        {
+          start = 0;
+          end = av.getAlignment().getWidth();
+          seqs = av.getAlignment().getSequencesArray();
+        }
+        else
+        {
+          start = av.getSelectionGroup().getStartRes();
+          end = av.getSelectionGroup().getEndRes() + 1;
+          seqs = av.getSelectionGroup().getSequencesInOrder(
+                  av.getAlignment());
+        }
 
-      for (int i=0;i < leaves.size();i++)
-        if (longestName.length()<((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName().length())
-          longestName = TreeCanvas.PLACEHOLDER+((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName();
+        tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+      }
 
       tree.reCount(tree.getTopNode());
       tree.findHeight(tree.getTopNode());
+      treeCanvas.setTree(tree);
+      if (newtree != null)
+      {
+        // Set default view, paying lip service to any overriding tree view
+        // parameter settings
+        boolean showDist = newtree.HasDistances()
+                && av.applet.getDefaultParameter("showTreeDistances",
+                        newtree.HasDistances());
+        boolean showBoots = newtree.HasBootstrap()
+                && av.applet.getDefaultParameter("showTreeBootstraps",
+                        newtree.HasBootstrap());
+        distanceMenu.setState(showDist);
+        bootstrapMenu.setState(showBoots);
+        treeCanvas.setShowBootstrap(showBoots);
+        treeCanvas.setShowDistances(showDist);
+        treeCanvas.setMarkPlaceholders(av.applet.getDefaultParameter(
+                "showUnlinkedTreeNodes", false));
+      }
+
+      treeCanvas.repaint();
 
-      treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
-      treeCanvas.setShowBootstrap(newtree.HasBootstrap());
-      treeCanvas.setShowDistances(newtree.HasDistances());
-      distanceMenu.setState(newtree.HasDistances());
-      bootstrapMenu.setState(newtree.HasBootstrap());
-      if (true) // JBPNote TODO: preference for always marking placeholders in new associated tree
-        placeholdersMenu.setState(treeCanvas.markPlaceholders);
-      scrollPane.add(treeCanvas);
+      av.setCurrentTree(tree);
 
     }
+  }
 
-public String getText(String format) {
-  return null;
-}
+  public void actionPerformed(ActionEvent evt)
+  {
+    if (evt.getSource() == newickOutput)
+    {
+      newickOutput_actionPerformed();
+    }
+    else if (evt.getSource() == fontSize)
+    {
+      fontSize_actionPerformed();
+    }
+    else if (evt.getSource() == inputData)
+    {
+      showOriginalData();
+    }
+  }
 
-  protected void fitToWindow_actionPerformed(ActionEvent e)
+  public void itemStateChanged(ItemEvent evt)
   {
-    treeCanvas.fitToWindow = fitToWindow.getState();
-    repaint();
+    if (evt.getSource() == fitToWindow)
+    {
+      treeCanvas.fitToWindow = fitToWindow.getState();
+    }
+
+    else if (evt.getSource() == distanceMenu)
+    {
+      treeCanvas.setShowDistances(distanceMenu.getState());
+    }
+
+    else if (evt.getSource() == bootstrapMenu)
+    {
+      treeCanvas.setShowBootstrap(bootstrapMenu.getState());
+    }
+
+    else if (evt.getSource() == placeholdersMenu)
+    {
+      treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
+    }
+
+    treeCanvas.repaint();
   }
 
-  public void newickOutput_actionPerformed(ActionEvent actionEvent)
+  public void newickOutput_actionPerformed()
   {
-    jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
+    jalview.io.NewickFile fout = new jalview.io.NewickFile(
+            tree.getTopNode());
     String output = fout.print(false, true);
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
     cap.setText(output);
     java.awt.Frame frame = new java.awt.Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, type+" "+pwtype, 500,500);
+    jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
   }
 
-
-
-  protected void fontSize_actionPerformed(ActionEvent e)
+  public java.awt.Font getTreeFont()
   {
- /*   if( treeCanvas==null )
-     return;
-
-   String size = fontSize.getLabel().substring( fontSize.getLabel().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);
-*/
+    return treeCanvas.font;
   }
 
-  protected void distanceMenu_actionPerformed(ActionEvent e)
+  public void setTreeFont(java.awt.Font font)
   {
-    treeCanvas.setShowDistances(distanceMenu.getState());
+    treeCanvas.font = font;
+    treeCanvas.repaint();
   }
 
-  protected void bootstrapMenu_actionPerformed(ActionEvent e)
+  protected void fontSize_actionPerformed()
   {
-    treeCanvas.setShowBootstrap(bootstrapMenu.getState());
+    if (treeCanvas == null)
+    {
+      return;
+    }
+
+    new FontChooser(this);
   }
 
-  protected void placeholdersMenu_actionPerformed(ActionEvent e)
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  protected ScrollPane scrollPane = new ScrollPane();
+
+  MenuBar jMenuBar1 = new MenuBar();
+
+  Menu jMenu2 = new Menu();
+
+  protected MenuItem fontSize = new MenuItem();
+
+  protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();
+
+  protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();
+
+  protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();
+
+  protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();
+
+  Menu fileMenu = new Menu();
+
+  MenuItem newickOutput = new MenuItem();
+
+  MenuItem inputData = new MenuItem();
+
+  private void jbInit() throws Exception
   {
-      treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
+    setLayout(borderLayout1);
+    this.setBackground(Color.white);
+    this.setFont(new java.awt.Font("Verdana", 0, 12));
+    jMenu2.setLabel("View");
+    fontSize.setLabel("Font...");
+    fontSize.addActionListener(this);
+    bootstrapMenu.setLabel("Show Bootstrap Values");
+    bootstrapMenu.addItemListener(this);
+    distanceMenu.setLabel("Show Distances");
+    distanceMenu.addItemListener(this);
+    placeholdersMenu.setLabel("Mark Unassociated Leaves");
+    placeholdersMenu.addItemListener(this);
+    fitToWindow.setState(true);
+    fitToWindow.setLabel("Fit To Window");
+    fitToWindow.addItemListener(this);
+    fileMenu.setLabel("File");
+    newickOutput.setLabel("Newick Format");
+    newickOutput.addActionListener(this);
+    inputData.setLabel("Input Data...");
+
+    add(scrollPane, BorderLayout.CENTER);
+    jMenuBar1.add(fileMenu);
+    jMenuBar1.add(jMenu2);
+    jMenu2.add(fitToWindow);
+    jMenu2.add(fontSize);
+    jMenu2.add(distanceMenu);
+    jMenu2.add(bootstrapMenu);
+    jMenu2.add(placeholdersMenu);
+    fileMenu.add(newickOutput);
+    fileMenu.add(inputData);
+    inputData.addActionListener(this);
   }
 
 }