2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.appletgui;
21 import java.awt.event.*;
23 import jalview.analysis.*;
24 import jalview.datamodel.*;
26 import jalview.util.MessageManager;
28 public class TreePanel extends EmbmenuFrame implements ActionListener,
41 TreeCanvas treeCanvas;
49 public NJTree getTree()
54 public void finalize() throws Throwable
62 * Creates a new TreePanel object.
77 public TreePanel(AlignmentPanel ap, String type, String pwtype)
82 this.setMenuBar(jMenuBar1);
83 } catch (Exception ex)
88 initTreePanel(ap, type, pwtype, null);
92 * Creates a new TreePanel object.
105 public TreePanel(AlignmentPanel ap, String type, String pwtype,
111 this.setMenuBar(jMenuBar1);
112 } catch (Exception e)
117 initTreePanel(ap, type, pwtype, newtree);
120 void initTreePanel(AlignmentPanel ap, String type, String pwtype,
127 this.pwtype = pwtype;
129 treeCanvas = new TreeCanvas(ap, scrollPane);
130 TreeLoader tl = new TreeLoader(newTree);
132 embedMenuIfNeeded(treeCanvas);
133 scrollPane.add(treeCanvas, BorderLayout.CENTER);
136 void showOriginalData()
138 // decide if av alignment is sufficiently different to original data to
139 // warrant a new window to be created
140 // create new alignmnt window with hidden regions (unhiding hidden regions
141 // yields unaligned seqs)
142 // or create a selection box around columns in alignment view
143 // test Alignment(SeqCigar[])
144 if (tree.seqData != null)
149 // we try to get the associated view's gap character
150 // but this may fail if the view was closed...
151 gc = av.getGapCharacter();
152 } catch (Exception ex)
156 Object[] alAndColsel = tree.seqData
157 .getAlignmentAndColumnSelection(gc);
159 if (alAndColsel != null && alAndColsel[0] != null)
161 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
162 AlignFrame af = new AlignFrame(al, av.applet,
163 "Original Data for Tree", false);
165 af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
170 System.out.println("Original Tree Data not available");
174 class TreeLoader extends Thread
178 jalview.datamodel.AlignmentView odata = null;
180 public TreeLoader(NewickFile newtree)
182 this.newtree = newtree;
191 tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
195 tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
204 boolean selview = (av.getSelectionGroup() != null)
205 && (av.getSelectionGroup().getSize() > 1);
206 AlignmentView seqStrings = av.getAlignmentView(selview);
210 end = av.getAlignment().getWidth();
211 seqs = av.getAlignment().getSequencesArray();
215 start = av.getSelectionGroup().getStartRes();
216 end = av.getSelectionGroup().getEndRes() + 1;
217 seqs = av.getSelectionGroup().getSequencesInOrder(
221 tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
224 tree.reCount(tree.getTopNode());
225 tree.findHeight(tree.getTopNode());
226 treeCanvas.setTree(tree);
229 // Set default view, paying lip service to any overriding tree view
230 // parameter settings
231 boolean showDist = newtree.HasDistances()
232 && av.applet.getDefaultParameter("showTreeDistances",
233 newtree.HasDistances());
234 boolean showBoots = newtree.HasBootstrap()
235 && av.applet.getDefaultParameter("showTreeBootstraps",
236 newtree.HasBootstrap());
237 distanceMenu.setState(showDist);
238 bootstrapMenu.setState(showBoots);
239 treeCanvas.setShowBootstrap(showBoots);
240 treeCanvas.setShowDistances(showDist);
241 treeCanvas.setMarkPlaceholders(av.applet.getDefaultParameter(
242 "showUnlinkedTreeNodes", false));
245 treeCanvas.repaint();
247 av.setCurrentTree(tree);
252 public void actionPerformed(ActionEvent evt)
254 if (evt.getSource() == newickOutput)
256 newickOutput_actionPerformed();
258 else if (evt.getSource() == fontSize)
260 fontSize_actionPerformed();
262 else if (evt.getSource() == inputData)
268 public void itemStateChanged(ItemEvent evt)
270 if (evt.getSource() == fitToWindow)
272 treeCanvas.fitToWindow = fitToWindow.getState();
275 else if (evt.getSource() == distanceMenu)
277 treeCanvas.setShowDistances(distanceMenu.getState());
280 else if (evt.getSource() == bootstrapMenu)
282 treeCanvas.setShowBootstrap(bootstrapMenu.getState());
285 else if (evt.getSource() == placeholdersMenu)
287 treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
290 treeCanvas.repaint();
293 public void newickOutput_actionPerformed()
295 jalview.io.NewickFile fout = new jalview.io.NewickFile(
297 String output = fout.print(false, true);
298 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
300 java.awt.Frame frame = new java.awt.Frame();
302 jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
305 public java.awt.Font getTreeFont()
307 return treeCanvas.font;
310 public void setTreeFont(java.awt.Font font)
312 treeCanvas.font = font;
313 treeCanvas.repaint();
316 protected void fontSize_actionPerformed()
318 if (treeCanvas == null)
323 new FontChooser(this);
326 BorderLayout borderLayout1 = new BorderLayout();
328 protected ScrollPane scrollPane = new ScrollPane();
330 MenuBar jMenuBar1 = new MenuBar();
332 Menu jMenu2 = new Menu();
334 protected MenuItem fontSize = new MenuItem();
336 protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();
338 protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();
340 protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();
342 protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();
344 Menu fileMenu = new Menu();
346 MenuItem newickOutput = new MenuItem();
348 MenuItem inputData = new MenuItem();
350 private void jbInit() throws Exception
352 setLayout(borderLayout1);
353 this.setBackground(Color.white);
354 this.setFont(new java.awt.Font("Verdana", 0, 12));
355 jMenu2.setLabel(MessageManager.getString("action.view"));
356 fontSize.setLabel(MessageManager.getString("action.font"));
357 fontSize.addActionListener(this);
358 bootstrapMenu.setLabel(MessageManager.getString("label.show_bootstrap_values"));
359 bootstrapMenu.addItemListener(this);
360 distanceMenu.setLabel(MessageManager.getString("label.show_distances"));
361 distanceMenu.addItemListener(this);
362 placeholdersMenu.setLabel(MessageManager.getString("label.mark_unassociated_leaves"));
363 placeholdersMenu.addItemListener(this);
364 fitToWindow.setState(true);
365 fitToWindow.setLabel(MessageManager.getString("label.fit_to_window"));
366 fitToWindow.addItemListener(this);
367 fileMenu.setLabel(MessageManager.getString("action.file"));
368 newickOutput.setLabel(MessageManager.getString("label.newick_format"));
369 newickOutput.addActionListener(this);
370 inputData.setLabel(MessageManager.getString("label.input_data"));
372 add(scrollPane, BorderLayout.CENTER);
373 jMenuBar1.add(fileMenu);
374 jMenuBar1.add(jMenu2);
375 jMenu2.add(fitToWindow);
376 jMenu2.add(fontSize);
377 jMenu2.add(distanceMenu);
378 jMenu2.add(bootstrapMenu);
379 jMenu2.add(placeholdersMenu);
380 fileMenu.add(newickOutput);
381 fileMenu.add(inputData);
382 inputData.addActionListener(this);