2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.*;
22 import java.util.Hashtable;
24 import jalview.analysis.*;
25 import jalview.datamodel.*;
28 public class TreePanel extends EmbmenuFrame implements ActionListener,
41 TreeCanvas treeCanvas;
48 public NJTree getTree()
53 public void finalize() throws Throwable {
60 * Creates a new TreePanel object.
75 public TreePanel(AlignmentPanel ap, String type, String pwtype)
80 this.setMenuBar(jMenuBar1);
81 } catch (Exception ex)
86 initTreePanel(ap, type, pwtype, null);
90 * 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.seqData != 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.seqData
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;
189 tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
193 tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
203 .getSelectionGroup() != null) && (av
204 .getSelectionGroup().getSize()>1);
205 AlignmentView seqStrings = av.getAlignmentView(selview);
209 end = av.getAlignment().getWidth();
210 seqs = av.getAlignment().getSequencesArray();
214 start = av.getSelectionGroup().getStartRes();
215 end = av.getSelectionGroup().getEndRes() + 1;
216 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
219 tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
222 tree.reCount(tree.getTopNode());
223 tree.findHeight(tree.getTopNode());
224 treeCanvas.setTree(tree);
227 // Set default view, paying lip service to any overriding tree view
228 // parameter settings
229 boolean showDist = newtree.HasDistances()
230 && av.applet.getDefaultParameter("showTreeDistances",
231 newtree.HasDistances());
232 boolean showBoots = newtree.HasBootstrap()
233 && av.applet.getDefaultParameter("showTreeBootstraps",
234 newtree.HasBootstrap());
235 distanceMenu.setState(showDist);
236 bootstrapMenu.setState(showBoots);
237 treeCanvas.setShowBootstrap(showBoots);
238 treeCanvas.setShowDistances(showDist);
239 treeCanvas.setMarkPlaceholders(av.applet.getDefaultParameter(
240 "showUnlinkedTreeNodes", false));
243 treeCanvas.repaint();
245 av.setCurrentTree(tree);
250 public void actionPerformed(ActionEvent evt)
252 if (evt.getSource() == newickOutput)
254 newickOutput_actionPerformed();
256 else if (evt.getSource() == fontSize)
258 fontSize_actionPerformed();
260 else if (evt.getSource() == inputData)
266 public void itemStateChanged(ItemEvent evt)
268 if (evt.getSource() == fitToWindow)
270 treeCanvas.fitToWindow = fitToWindow.getState();
273 else if (evt.getSource() == distanceMenu)
275 treeCanvas.setShowDistances(distanceMenu.getState());
278 else if (evt.getSource() == bootstrapMenu)
280 treeCanvas.setShowBootstrap(bootstrapMenu.getState());
283 else if (evt.getSource() == placeholdersMenu)
285 treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
288 treeCanvas.repaint();
291 public void newickOutput_actionPerformed()
293 jalview.io.NewickFile fout = new jalview.io.NewickFile(
295 String output = fout.print(false, true);
296 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
298 java.awt.Frame frame = new java.awt.Frame();
300 jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
303 public java.awt.Font getTreeFont()
305 return treeCanvas.font;
308 public void setTreeFont(java.awt.Font font)
310 treeCanvas.font = font;
311 treeCanvas.repaint();
314 protected void fontSize_actionPerformed()
316 if (treeCanvas == null)
321 new FontChooser(this);
324 BorderLayout borderLayout1 = new BorderLayout();
326 protected ScrollPane scrollPane = new ScrollPane();
328 MenuBar jMenuBar1 = new MenuBar();
330 Menu jMenu2 = new Menu();
332 protected MenuItem fontSize = new MenuItem();
334 protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();
336 protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();
338 protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();
340 protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();
342 Menu fileMenu = new Menu();
344 MenuItem newickOutput = new MenuItem();
346 MenuItem inputData = new MenuItem();
348 private void jbInit() throws Exception
350 setLayout(borderLayout1);
351 this.setBackground(Color.white);
352 this.setFont(new java.awt.Font("Verdana", 0, 12));
353 jMenu2.setLabel("View");
354 fontSize.setLabel("Font...");
355 fontSize.addActionListener(this);
356 bootstrapMenu.setLabel("Show Bootstrap Values");
357 bootstrapMenu.addItemListener(this);
358 distanceMenu.setLabel("Show Distances");
359 distanceMenu.addItemListener(this);
360 placeholdersMenu.setLabel("Mark Unassociated Leaves");
361 placeholdersMenu.addItemListener(this);
362 fitToWindow.setState(true);
363 fitToWindow.setLabel("Fit To Window");
364 fitToWindow.addItemListener(this);
365 fileMenu.setLabel("File");
366 newickOutput.setLabel("Newick Format");
367 newickOutput.addActionListener(this);
368 inputData.setLabel("Input Data...");
370 add(scrollPane, BorderLayout.CENTER);
371 jMenuBar1.add(fileMenu);
372 jMenuBar1.add(jMenu2);
373 jMenu2.add(fitToWindow);
374 jMenu2.add(fontSize);
375 jMenu2.add(distanceMenu);
376 jMenu2.add(bootstrapMenu);
377 jMenu2.add(placeholdersMenu);
378 fileMenu.add(newickOutput);
379 fileMenu.add(inputData);
380 inputData.addActionListener(this);