src/jalview/appletgui/TreePanel.java

   1 package jalview.appletgui;
   2
   3 import jalview.datamodel.*;
   4 import jalview.io.NewickFile;
   5 import jalview.analysis.*;
   6 import jalview.jbappletgui.GTreePanel;
   7 import java.awt.event.*;
   8 import java.util.*;
   9 import jalview.io.NewickFile;
  10
  11
  12 public class TreePanel extends GTreePanel
  13 {
  14   SequenceI[] seq;
  15   String type;
  16   String pwtype;
  17   AlignViewport av;
  18   int start;
  19   int end;
  20   TreeCanvas treeCanvas;
  21   NJTree tree;
  22
  23   public NJTree getTree()
  24   {
  25     return tree;
  26   }
  27
  28   public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)
  29   {
  30     super();
  31
  32     this.type = type;
  33     this.pwtype = pwtype;
  34
  35     start = s;
  36     end = e;
  37
  38     String longestName = "";
  39     seq = new Sequence [seqVector.size()];
  40     for (int i=0;i < seqVector.size();i++)
  41     {
  42       seq[i] = (Sequence) seqVector.elementAt(i);
  43       if(seq[i].getName().length()>longestName.length())
  44         longestName = seq[i].getName();
  45     }
  46
  47     tree = new NJTree(seq, type, pwtype, start, end);
  48
  49     treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
  50
  51     tree.reCount(tree.getTopNode());
  52     tree.findHeight(tree.getTopNode());
  53     scrollPane.add(treeCanvas);
  54
  55   }
  56   public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
  57                    String type, String pwtype)
  58     {
  59       super();
  60       // These are probably only  arbitrary strings reflecting source of tree
  61       this.type = type;
  62       this.pwtype = pwtype;
  63
  64       start = 0;
  65       end = seqVector.size();
  66
  67       String longestName = "";
  68       seq = new Sequence [seqVector.size()];
  69       for (int i=0;i < seqVector.size();i++)
  70       {
  71         seq[i] = (Sequence) seqVector.elementAt(i);
  72       }
  73       // This constructor matches sequence names to treenodes and sets up the tree layouts.
  74       tree = new NJTree(seq, newtree);
  75       // Now have to calculate longest name based on the leaves
  76       Vector leaves = tree.findLeaves(tree.getTopNode(),new Vector());
  77
  78       for (int i=0;i < leaves.size();i++)
  79         if (longestName.length()<((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName().length())
  80           longestName = TreeCanvas.PLACEHOLDER+((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName();
  81
  82       tree.reCount(tree.getTopNode());
  83       tree.findHeight(tree.getTopNode());
  84
  85       treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
  86       treeCanvas.setShowBootstrap(newtree.HasBootstrap());
  87       treeCanvas.setShowDistances(newtree.HasDistances());
  88       distanceMenu.setState(newtree.HasDistances());
  89       bootstrapMenu.setState(newtree.HasBootstrap());
  90       if (true) // JBPNote TODO: preference for always marking placeholders in new associated tree
  91         placeholdersMenu.setState(treeCanvas.markPlaceholders);
  92       scrollPane.add(treeCanvas);
  93
  94     }
  95
  96 public String getText(String format) {
  97   return null;
  98 }
  99
 100   protected void fitToWindow_actionPerformed(ActionEvent e)
 101   {
 102     treeCanvas.fitToWindow = fitToWindow.getState();
 103     repaint();
 104   }
 105
 106   public void newickOutput_actionPerformed(ActionEvent actionEvent)
 107   {
 108     jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
 109     String output = fout.print(false, true);
 110     CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
 111     cap.setText(output);
 112     java.awt.Frame frame = new java.awt.Frame();
 113     frame.add(cap);
 114     jalview.bin.JalviewLite.addFrame(frame, type+" "+pwtype, 500,500);
 115   }
 116
 117
 118
 119   protected void fontSize_actionPerformed(ActionEvent e)
 120   {
 121  /*   if( treeCanvas==null )
 122      return;
 123
 124    String size = fontSize.getLabel().substring( fontSize.getLabel().indexOf("-")+1);
 125
 126    Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,
 127                                "Select font size",
 128                                "Font size",
 129                                JOptionPane.QUESTION_MESSAGE,
 130                                null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
 131                                ,"Font Size - "+size);
 132    if(selection!=null)
 133    {
 134      fontSize.setText("Font Size - " + selection);
 135
 136      int i = Integer.parseInt(selection.toString());
 137      treeCanvas.setFontSize(i);
 138    }
 139     scrollPane.setViewportView(treeCanvas);
 140 */
 141   }
 142
 143   protected void distanceMenu_actionPerformed(ActionEvent e)
 144   {
 145     treeCanvas.setShowDistances(distanceMenu.getState());
 146   }
 147
 148   protected void bootstrapMenu_actionPerformed(ActionEvent e)
 149   {
 150     treeCanvas.setShowBootstrap(bootstrapMenu.getState());
 151   }
 152
 153   protected void placeholdersMenu_actionPerformed(ActionEvent e)
 154   {
 155       treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
 156   }
 157
 158 }