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.datamodel.Alignment;
27 import jalview.datamodel.AlignmentView;
28 import jalview.datamodel.HiddenColumns;
29 import jalview.datamodel.SequenceI;
30 import jalview.io.NewickFile;
31 import jalview.schemes.ResidueProperties;
32 import jalview.util.MessageManager;
34 import java.awt.BorderLayout;
35 import java.awt.CheckboxMenuItem;
36 import java.awt.Color;
38 import java.awt.MenuBar;
39 import java.awt.MenuItem;
40 import java.awt.ScrollPane;
41 import java.awt.event.ActionEvent;
42 import java.awt.event.ActionListener;
43 import java.awt.event.ItemEvent;
44 import java.awt.event.ItemListener;
46 public class TreePanel extends EmbmenuFrame implements ActionListener,
59 TreeCanvas treeCanvas;
67 public NJTree getTree()
73 public void finalize() throws Throwable
81 * Creates a new TreePanel object.
96 public TreePanel(AlignmentPanel ap, String type, String pwtype)
101 this.setMenuBar(jMenuBar1);
102 } catch (Exception ex)
104 ex.printStackTrace();
107 initTreePanel(ap, type, pwtype, null);
111 * Creates a new TreePanel object.
124 public TreePanel(AlignmentPanel ap, String type, String pwtype,
130 this.setMenuBar(jMenuBar1);
131 } catch (Exception e)
136 initTreePanel(ap, type, pwtype, newtree);
139 void initTreePanel(AlignmentPanel ap, String type, String pwtype,
146 this.pwtype = pwtype;
148 treeCanvas = new TreeCanvas(ap, scrollPane);
149 TreeLoader tl = new TreeLoader(newTree);
151 embedMenuIfNeeded(treeCanvas);
152 scrollPane.add(treeCanvas, BorderLayout.CENTER);
155 void showOriginalData()
157 // decide if av alignment is sufficiently different to original data to
158 // warrant a new window to be created
159 // create new alignmnt window with hidden regions (unhiding hidden regions
160 // yields unaligned seqs)
161 // or create a selection box around columns in alignment view
162 // test Alignment(SeqCigar[])
163 if (tree.seqData != null)
168 // we try to get the associated view's gap character
169 // but this may fail if the view was closed...
170 gc = av.getGapCharacter();
171 } catch (Exception ex)
175 Object[] alAndColsel = tree.seqData
176 .getAlignmentAndHiddenColumns(gc);
178 if (alAndColsel != null && alAndColsel[0] != null)
180 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
181 AlignFrame af = new AlignFrame(al, av.applet,
182 "Original Data for Tree", false);
184 af.viewport.getAlignment().setHiddenColumns(
185 (HiddenColumns) alAndColsel[1]);
190 System.out.println("Original Tree Data not available");
194 class TreeLoader extends Thread
198 jalview.datamodel.AlignmentView odata = null;
200 public TreeLoader(NewickFile newtree)
202 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.setState(showDist);
278 bootstrapMenu.setState(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);
293 public void actionPerformed(ActionEvent evt)
295 if (evt.getSource() == newickOutput)
297 newickOutput_actionPerformed();
299 else if (evt.getSource() == fontSize)
301 fontSize_actionPerformed();
303 else if (evt.getSource() == inputData)
310 public void itemStateChanged(ItemEvent evt)
312 if (evt.getSource() == fitToWindow)
314 treeCanvas.fitToWindow = fitToWindow.getState();
317 else if (evt.getSource() == distanceMenu)
319 treeCanvas.setShowDistances(distanceMenu.getState());
322 else if (evt.getSource() == bootstrapMenu)
324 treeCanvas.setShowBootstrap(bootstrapMenu.getState());
327 else if (evt.getSource() == placeholdersMenu)
329 treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
332 treeCanvas.repaint();
335 public void newickOutput_actionPerformed()
337 jalview.io.NewickFile fout = new jalview.io.NewickFile(
339 String output = fout.print(false, true);
340 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
342 java.awt.Frame frame = new java.awt.Frame();
344 jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
347 public java.awt.Font getTreeFont()
349 return treeCanvas.font;
352 public void setTreeFont(java.awt.Font font)
354 treeCanvas.font = font;
355 treeCanvas.repaint();
358 protected void fontSize_actionPerformed()
360 if (treeCanvas == null)
365 new FontChooser(this);
368 BorderLayout borderLayout1 = new BorderLayout();
370 protected ScrollPane scrollPane = new ScrollPane();
372 MenuBar jMenuBar1 = new MenuBar();
374 Menu jMenu2 = new Menu();
376 protected MenuItem fontSize = new MenuItem();
378 protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();
380 protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();
382 protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();
384 protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();
386 Menu fileMenu = new Menu();
388 MenuItem newickOutput = new MenuItem();
390 MenuItem inputData = new MenuItem();
392 private void jbInit() throws Exception
394 setLayout(borderLayout1);
395 this.setBackground(Color.white);
396 this.setFont(new java.awt.Font("Verdana", 0, 12));
397 jMenu2.setLabel(MessageManager.getString("action.view"));
398 fontSize.setLabel(MessageManager.getString("action.font"));
399 fontSize.addActionListener(this);
400 bootstrapMenu.setLabel(MessageManager
401 .getString("label.show_bootstrap_values"));
402 bootstrapMenu.addItemListener(this);
403 distanceMenu.setLabel(MessageManager.getString("label.show_distances"));
404 distanceMenu.addItemListener(this);
405 placeholdersMenu.setLabel(MessageManager
406 .getString("label.mark_unassociated_leaves"));
407 placeholdersMenu.addItemListener(this);
408 fitToWindow.setState(true);
409 fitToWindow.setLabel(MessageManager.getString("label.fit_to_window"));
410 fitToWindow.addItemListener(this);
411 fileMenu.setLabel(MessageManager.getString("action.file"));
412 newickOutput.setLabel(MessageManager.getString("label.newick_format"));
413 newickOutput.addActionListener(this);
414 inputData.setLabel(MessageManager.getString("label.input_data"));
416 add(scrollPane, BorderLayout.CENTER);
417 jMenuBar1.add(fileMenu);
418 jMenuBar1.add(jMenu2);
419 jMenu2.add(fitToWindow);
420 jMenu2.add(fontSize);
421 jMenu2.add(distanceMenu);
422 jMenu2.add(bootstrapMenu);
423 jMenu2.add(placeholdersMenu);
424 fileMenu.add(newickOutput);
425 fileMenu.add(inputData);
426 inputData.addActionListener(this);