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.AverageDistanceTree;
24 import jalview.analysis.NJTree;
25 import jalview.analysis.TreeBuilder;
26 import jalview.analysis.TreeModel;
27 import jalview.analysis.scoremodels.ScoreModels;
28 import jalview.analysis.scoremodels.SimilarityParams;
29 import jalview.api.analysis.ScoreModelI;
30 import jalview.datamodel.Alignment;
31 import jalview.datamodel.ColumnSelection;
32 import jalview.datamodel.SequenceI;
33 import jalview.io.NewickFile;
34 import jalview.util.MessageManager;
36 import java.awt.BorderLayout;
37 import java.awt.CheckboxMenuItem;
38 import java.awt.Color;
40 import java.awt.MenuBar;
41 import java.awt.MenuItem;
42 import java.awt.ScrollPane;
43 import java.awt.event.ActionEvent;
44 import java.awt.event.ActionListener;
45 import java.awt.event.ItemEvent;
46 import java.awt.event.ItemListener;
48 public class TreePanel extends EmbmenuFrame implements ActionListener,
61 TreeCanvas treeCanvas;
69 public TreeModel getTree()
75 public void finalize() throws Throwable
83 * Creates a new TreePanel object.
85 public TreePanel(AlignmentPanel alignPanel, String type, String pwtype)
90 this.setMenuBar(jMenuBar1);
91 } catch (Exception ex)
96 initTreePanel(alignPanel, type, pwtype, null);
100 * Creates a new TreePanel object.
103 public TreePanel(AlignmentPanel ap, String type, String pwtype,
109 this.setMenuBar(jMenuBar1);
110 } catch (Exception e)
115 initTreePanel(ap, type, pwtype, newtree);
118 void initTreePanel(AlignmentPanel ap, String type, String pwtype,
125 this.pwtype = pwtype;
127 treeCanvas = new TreeCanvas(ap, scrollPane);
128 TreeLoader tl = new TreeLoader(newTree);
130 embedMenuIfNeeded(treeCanvas);
131 scrollPane.add(treeCanvas, BorderLayout.CENTER);
134 void showOriginalData()
136 // decide if av alignment is sufficiently different to original data to
137 // warrant a new window to be created
138 // create new alignmnt window with hidden regions (unhiding hidden regions
139 // yields unaligned seqs)
140 // or create a selection box around columns in alignment view
141 // test Alignment(SeqCigar[])
142 if (tree.getOriginalData() != null)
147 // we try to get the associated view's gap character
148 // but this may fail if the view was closed...
149 gc = av.getGapCharacter();
150 } catch (Exception ex)
154 Object[] alAndColsel = tree.getOriginalData()
155 .getAlignmentAndColumnSelection(gc);
157 if (alAndColsel != null && alAndColsel[0] != null)
159 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
160 AlignFrame af = new AlignFrame(al, av.applet,
161 "Original Data for Tree", false);
163 af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
168 System.out.println("Original Tree Data not available");
172 class TreeLoader extends Thread
176 jalview.datamodel.AlignmentView odata = null;
178 public TreeLoader(NewickFile newtree)
180 this.newtree = newtree;
188 tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
193 ScoreModelI sm1 = ScoreModels.getInstance().getScoreModel(pwtype,
195 ScoreModelI sm = sm1;
196 TreeBuilder njtree = type.equals(TreeBuilder.NEIGHBOUR_JOINING) ? new NJTree(
197 av, sm, SimilarityParams.Jalview)
198 : new AverageDistanceTree(av, sm, SimilarityParams.Jalview);
199 tree = new TreeModel(njtree);
202 tree.reCount(tree.getTopNode());
203 tree.findHeight(tree.getTopNode());
204 treeCanvas.setTree(tree);
207 // Set default view, paying lip service to any overriding tree view
208 // parameter settings
209 boolean showDist = newtree.HasDistances()
210 && av.applet.getDefaultParameter("showTreeDistances",
211 newtree.HasDistances());
212 boolean showBoots = newtree.HasBootstrap()
213 && av.applet.getDefaultParameter("showTreeBootstraps",
214 newtree.HasBootstrap());
215 distanceMenu.setState(showDist);
216 bootstrapMenu.setState(showBoots);
217 treeCanvas.setShowBootstrap(showBoots);
218 treeCanvas.setShowDistances(showDist);
219 treeCanvas.setMarkPlaceholders(av.applet.getDefaultParameter(
220 "showUnlinkedTreeNodes", false));
223 treeCanvas.repaint();
225 av.setCurrentTree(tree);
231 public void actionPerformed(ActionEvent evt)
233 if (evt.getSource() == newickOutput)
235 newickOutput_actionPerformed();
237 else if (evt.getSource() == fontSize)
239 fontSize_actionPerformed();
241 else if (evt.getSource() == inputData)
248 public void itemStateChanged(ItemEvent evt)
250 if (evt.getSource() == fitToWindow)
252 treeCanvas.fitToWindow = fitToWindow.getState();
255 else if (evt.getSource() == distanceMenu)
257 treeCanvas.setShowDistances(distanceMenu.getState());
260 else if (evt.getSource() == bootstrapMenu)
262 treeCanvas.setShowBootstrap(bootstrapMenu.getState());
265 else if (evt.getSource() == placeholdersMenu)
267 treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
270 treeCanvas.repaint();
273 public void newickOutput_actionPerformed()
275 jalview.io.NewickFile fout = new jalview.io.NewickFile(
277 String output = fout.print(false, true);
278 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
280 java.awt.Frame frame = new java.awt.Frame();
282 jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
285 public java.awt.Font getTreeFont()
287 return treeCanvas.font;
290 public void setTreeFont(java.awt.Font font)
292 treeCanvas.font = font;
293 treeCanvas.repaint();
296 protected void fontSize_actionPerformed()
298 if (treeCanvas == null)
303 new FontChooser(this);
306 BorderLayout borderLayout1 = new BorderLayout();
308 protected ScrollPane scrollPane = new ScrollPane();
310 MenuBar jMenuBar1 = new MenuBar();
312 Menu jMenu2 = new Menu();
314 protected MenuItem fontSize = new MenuItem();
316 protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();
318 protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();
320 protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();
322 protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();
324 Menu fileMenu = new Menu();
326 MenuItem newickOutput = new MenuItem();
328 MenuItem inputData = new MenuItem();
330 private void jbInit() throws Exception
332 setLayout(borderLayout1);
333 this.setBackground(Color.white);
334 this.setFont(new java.awt.Font("Verdana", 0, 12));
335 jMenu2.setLabel(MessageManager.getString("action.view"));
336 fontSize.setLabel(MessageManager.getString("action.font"));
337 fontSize.addActionListener(this);
338 bootstrapMenu.setLabel(MessageManager
339 .getString("label.show_bootstrap_values"));
340 bootstrapMenu.addItemListener(this);
341 distanceMenu.setLabel(MessageManager.getString("label.show_distances"));
342 distanceMenu.addItemListener(this);
343 placeholdersMenu.setLabel(MessageManager
344 .getString("label.mark_unassociated_leaves"));
345 placeholdersMenu.addItemListener(this);
346 fitToWindow.setState(true);
347 fitToWindow.setLabel(MessageManager.getString("label.fit_to_window"));
348 fitToWindow.addItemListener(this);
349 fileMenu.setLabel(MessageManager.getString("action.file"));
350 newickOutput.setLabel(MessageManager.getString("label.newick_format"));
351 newickOutput.addActionListener(this);
352 inputData.setLabel(MessageManager.getString("label.input_data"));
354 add(scrollPane, BorderLayout.CENTER);
355 jMenuBar1.add(fileMenu);
356 jMenuBar1.add(jMenu2);
357 jMenu2.add(fitToWindow);
358 jMenu2.add(fontSize);
359 jMenu2.add(distanceMenu);
360 jMenu2.add(bootstrapMenu);
361 jMenu2.add(placeholdersMenu);
362 fileMenu.add(newickOutput);
363 fileMenu.add(inputData);
364 inputData.addActionListener(this);