2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import jalview.analysis.NJTree;
24 import jalview.api.analysis.ScoreModelI;
25 import jalview.api.analysis.ViewBasedAnalysisI;
26 import jalview.bin.JalviewLite;
27 import jalview.datamodel.Alignment;
28 import jalview.datamodel.AlignmentView;
29 import jalview.datamodel.ColumnSelection;
30 import jalview.datamodel.SequenceI;
31 import jalview.io.NewickFile;
32 import jalview.schemes.ResidueProperties;
33 import jalview.util.MessageManager;
35 import java.awt.BorderLayout;
36 import javax.swing.JCheckBoxMenuItem;
37 import java.awt.Color;
39 import javax.swing.JFrame;
40 import javax.swing.JMenu;
41 import javax.swing.JMenuBar;
42 import javax.swing.JMenuItem;
43 import javax.swing.JScrollPane;
44 import java.awt.event.ActionEvent;
45 import java.awt.event.ActionListener;
46 import java.awt.event.ItemEvent;
47 import java.awt.event.ItemListener;
49 public class TreePanel extends EmbmenuFrame implements ActionListener,
62 TreeCanvas treeCanvas;
70 public NJTree getTree()
75 public void finalize() throws Throwable
83 * Creates a new TreePanel object.
98 public TreePanel(AlignmentPanel ap, String type, String pwtype)
103 this.setJMenuBar(jMenuBar1);
104 } catch (Exception ex)
106 ex.printStackTrace();
109 initTreePanel(ap, type, pwtype, null);
113 * Creates a new TreePanel object.
126 public TreePanel(AlignmentPanel ap, String type, String pwtype,
132 this.setJMenuBar(jMenuBar1);
133 } catch (Exception e)
138 initTreePanel(ap, type, pwtype, newtree);
141 void initTreePanel(AlignmentPanel ap, String type, String pwtype,
148 this.pwtype = pwtype;
150 treeCanvas = new TreeCanvas(ap, scrollPane);
151 TreeLoader tl = new TreeLoader(newTree);
153 embedMenuIfNeeded(treeCanvas);
154 scrollPane.add(treeCanvas, BorderLayout.CENTER);
157 void showOriginalData()
159 // decide if av alignment is sufficiently different to original data to
160 // warrant a new window to be created
161 // create new alignmnt window with hidden regions (unhiding hidden regions
162 // yields unaligned seqs)
163 // or create a selection box around columns in alignment view
164 // test Alignment(SeqCigar[])
165 if (tree.seqData != null)
170 // we try to get the associated view's gap character
171 // but this may fail if the view was closed...
172 gc = av.getGapCharacter();
173 } catch (Exception ex)
177 Object[] alAndColsel = tree.seqData
178 .getAlignmentAndColumnSelection(gc);
180 if (alAndColsel != null && alAndColsel[0] != null)
182 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
183 AlignFrame af = new AlignFrame(al, av.applet,
184 "Original Data for Tree", false);
186 af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
191 System.out.println("Original Tree Data not available");
195 class TreeLoader extends Thread
199 AlignmentView odata = null;
201 public TreeLoader(NewickFile newtree)
203 this.newtree = newtree;
212 tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
216 tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
225 boolean selview = av.getSelectionGroup() != null
226 && av.getSelectionGroup().getSize() > 1;
227 AlignmentView seqStrings = av.getAlignmentView(selview);
231 end = av.getAlignment().getWidth();
232 seqs = av.getAlignment().getSequencesArray();
236 start = av.getSelectionGroup().getStartRes();
237 end = av.getSelectionGroup().getEndRes() + 1;
238 seqs = av.getSelectionGroup().getSequencesInOrder(
241 ScoreModelI sm = ResidueProperties.getScoreModel(pwtype);
242 if (sm instanceof ViewBasedAnalysisI)
246 sm = sm.getClass().newInstance();
247 ((ViewBasedAnalysisI) sm)
248 .configureFromAlignmentView(treeCanvas.ap);
249 } catch (Exception q)
251 System.err.println("Couldn't create a scoremodel instance for "
255 tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
259 tree = new NJTree(seqs, seqStrings, type, pwtype, null, start,
264 tree.reCount(tree.getTopNode());
265 tree.findHeight(tree.getTopNode());
266 treeCanvas.setTree(tree);
269 // Set default view, paying lip service to any overriding tree view
270 // parameter settings
271 boolean showDist = newtree.HasDistances()
272 && av.applet.getDefaultParameter("showTreeDistances",
273 newtree.HasDistances());
274 boolean showBoots = newtree.HasBootstrap()
275 && av.applet.getDefaultParameter("showTreeBootstraps",
276 newtree.HasBootstrap());
277 distanceMenu.setSelected(showDist);
278 bootstrapMenu.setSelected(showBoots);
279 treeCanvas.setShowBootstrap(showBoots);
280 treeCanvas.setShowDistances(showDist);
281 treeCanvas.setMarkPlaceholders(av.applet.getDefaultParameter(
282 "showUnlinkedTreeNodes", false));
285 treeCanvas.repaint();
287 av.setCurrentTree(tree);
292 public void actionPerformed(ActionEvent evt)
294 if (evt.getSource() == newickOutput)
296 newickOutput_actionPerformed();
298 else if (evt.getSource() == fontSize)
300 fontSize_actionPerformed();
302 else if (evt.getSource() == inputData)
308 public void itemStateChanged(ItemEvent evt)
310 if (evt.getSource() == fitToWindow)
312 treeCanvas.fitToWindow = fitToWindow.getState();
315 else if (evt.getSource() == distanceMenu)
317 treeCanvas.setShowDistances(distanceMenu.getState());
320 else if (evt.getSource() == bootstrapMenu)
322 treeCanvas.setShowBootstrap(bootstrapMenu.getState());
325 else if (evt.getSource() == placeholdersMenu)
327 treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
330 treeCanvas.repaint();
333 public void newickOutput_actionPerformed()
335 NewickFile fout = new NewickFile(tree.getTopNode());
336 String output = fout.print(false, true);
337 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
339 JFrame frame = new JFrame();
341 JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
344 public java.awt.Font getTreeFont()
346 return treeCanvas.font;
349 public void setTreeFont(java.awt.Font font)
351 treeCanvas.font = font;
352 treeCanvas.repaint();
355 protected void fontSize_actionPerformed()
357 if (treeCanvas == null)
362 new FontChooser(this);
365 BorderLayout borderLayout1 = new BorderLayout();
367 protected JScrollPane scrollPane = new JScrollPane();
369 JMenuBar jMenuBar1 = new JMenuBar();
371 JMenu jMenu2 = new JMenu();
373 protected JMenuItem fontSize = new JMenuItem();
375 protected JCheckBoxMenuItem bootstrapMenu = new JCheckBoxMenuItem();
377 protected JCheckBoxMenuItem distanceMenu = new JCheckBoxMenuItem();
379 protected JCheckBoxMenuItem placeholdersMenu = new JCheckBoxMenuItem();
381 protected JCheckBoxMenuItem fitToWindow = new JCheckBoxMenuItem();
383 JMenu fileMenu = new JMenu();
385 JMenuItem newickOutput = new JMenuItem();
387 JMenuItem inputData = new JMenuItem();
389 private void jbInit() throws Exception
391 setLayout(borderLayout1);
392 this.setBackground(Color.white);
393 this.setFont(new java.awt.Font("Verdana", 0, 12));
394 jMenu2.setLabel(MessageManager.getString("action.view"));
395 fontSize.setLabel(MessageManager.getString("action.font"));
396 fontSize.addActionListener(this);
397 bootstrapMenu.setLabel(MessageManager
398 .getString("label.show_bootstrap_values"));
399 bootstrapMenu.addItemListener(this);
400 distanceMenu.setLabel(MessageManager.getString("label.show_distances"));
401 distanceMenu.addItemListener(this);
402 placeholdersMenu.setLabel(MessageManager
403 .getString("label.mark_unassociated_leaves"));
404 placeholdersMenu.addItemListener(this);
405 fitToWindow.setState(true);
406 fitToWindow.setLabel(MessageManager.getString("label.fit_to_window"));
407 fitToWindow.addItemListener(this);
408 fileMenu.setLabel(MessageManager.getString("action.file"));
409 newickOutput.setLabel(MessageManager.getString("label.newick_format"));
410 newickOutput.addActionListener(this);
411 inputData.setLabel(MessageManager.getString("label.input_data"));
413 add(scrollPane, BorderLayout.CENTER);
414 jMenuBar1.add(fileMenu);
415 jMenuBar1.add(jMenu2);
416 jMenu2.add(fitToWindow);
417 jMenu2.add(fontSize);
418 jMenu2.add(distanceMenu);
419 jMenu2.add(bootstrapMenu);
420 jMenu2.add(placeholdersMenu);
421 fileMenu.add(newickOutput);
422 fileMenu.add(inputData);
423 inputData.addActionListener(this);