1 package jalview.appletgui;
3 import jalview.datamodel.*;
4 import jalview.io.NewickFile;
5 import jalview.analysis.*;
6 import jalview.jbappletgui.GTreePanel;
7 import java.awt.event.*;
9 import jalview.io.NewickFile;
12 public class TreePanel extends GTreePanel
20 TreeCanvas treeCanvas;
23 public NJTree getTree()
28 public TreePanel(AlignViewport av, Vector seqVector, String type, String pwtype, int s, int e)
38 String longestName = "";
39 seq = new Sequence [seqVector.size()];
40 for (int i=0;i < seqVector.size();i++)
42 seq[i] = (Sequence) seqVector.elementAt(i);
43 if(seq[i].getName().length()>longestName.length())
44 longestName = seq[i].getName();
47 tree = new NJTree(seq, type, pwtype, start, end);
49 treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
51 tree.reCount(tree.getTopNode());
52 tree.findHeight(tree.getTopNode());
53 scrollPane.add(treeCanvas);
56 public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
57 String type, String pwtype)
60 // These are probably only arbitrary strings reflecting source of tree
65 end = seqVector.size();
67 String longestName = "";
68 seq = new Sequence [seqVector.size()];
69 for (int i=0;i < seqVector.size();i++)
71 seq[i] = (Sequence) seqVector.elementAt(i);
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());
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();
82 tree.reCount(tree.getTopNode());
83 tree.findHeight(tree.getTopNode());
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);
96 public String getText(String format) {
100 protected void fitToWindow_actionPerformed(ActionEvent e)
102 treeCanvas.fitToWindow = fitToWindow.getState();
106 public void newickOutput_actionPerformed(ActionEvent actionEvent)
108 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
109 String output = fout.print(false, true);
110 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
112 java.awt.Frame frame = new java.awt.Frame();
114 jalview.bin.JalviewLite.addFrame(frame, type+" "+pwtype, 500,500);
119 protected void fontSize_actionPerformed(ActionEvent e)
121 /* if( treeCanvas==null )
124 String size = fontSize.getLabel().substring( fontSize.getLabel().indexOf("-")+1);
126 Object selection = JOptionPane.showInternalInputDialog(Desktop.desktop,
129 JOptionPane.QUESTION_MESSAGE,
130 null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}
131 ,"Font Size - "+size);
134 fontSize.setText("Font Size - " + selection);
136 int i = Integer.parseInt(selection.toString());
137 treeCanvas.setFontSize(i);
139 scrollPane.setViewportView(treeCanvas);
143 protected void distanceMenu_actionPerformed(ActionEvent e)
145 treeCanvas.setShowDistances(distanceMenu.getState());
148 protected void bootstrapMenu_actionPerformed(ActionEvent e)
150 treeCanvas.setShowBootstrap(bootstrapMenu.getState());
153 protected void placeholdersMenu_actionPerformed(ActionEvent e)
155 treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());