2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 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;
24 import java.awt.event.*;
26 import jalview.analysis.*;
27 import jalview.datamodel.*;
29 import jalview.util.MessageManager;
31 public class TreePanel extends EmbmenuFrame implements ActionListener,
44 TreeCanvas treeCanvas;
52 public NJTree getTree()
57 public void finalize() throws Throwable
65 * Creates a new TreePanel object.
80 public TreePanel(AlignmentPanel ap, String type, String pwtype)
85 this.setMenuBar(jMenuBar1);
86 } catch (Exception ex)
91 initTreePanel(ap, type, pwtype, null);
95 * Creates a new TreePanel object.
108 public TreePanel(AlignmentPanel ap, String type, String pwtype,
114 this.setMenuBar(jMenuBar1);
115 } catch (Exception e)
120 initTreePanel(ap, type, pwtype, newtree);
123 void initTreePanel(AlignmentPanel ap, String type, String pwtype,
130 this.pwtype = pwtype;
132 treeCanvas = new TreeCanvas(ap, scrollPane);
133 TreeLoader tl = new TreeLoader(newTree);
135 embedMenuIfNeeded(treeCanvas);
136 scrollPane.add(treeCanvas, BorderLayout.CENTER);
139 void showOriginalData()
141 // decide if av alignment is sufficiently different to original data to
142 // warrant a new window to be created
143 // create new alignmnt window with hidden regions (unhiding hidden regions
144 // yields unaligned seqs)
145 // or create a selection box around columns in alignment view
146 // test Alignment(SeqCigar[])
147 if (tree.seqData != null)
152 // we try to get the associated view's gap character
153 // but this may fail if the view was closed...
154 gc = av.getGapCharacter();
155 } catch (Exception ex)
159 Object[] alAndColsel = tree.seqData
160 .getAlignmentAndColumnSelection(gc);
162 if (alAndColsel != null && alAndColsel[0] != null)
164 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
165 AlignFrame af = new AlignFrame(al, av.applet,
166 "Original Data for Tree", false);
168 af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
173 System.out.println("Original Tree Data not available");
177 class TreeLoader extends Thread
181 jalview.datamodel.AlignmentView odata = null;
183 public TreeLoader(NewickFile newtree)
185 this.newtree = newtree;
194 tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
198 tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
207 boolean selview = (av.getSelectionGroup() != null)
208 && (av.getSelectionGroup().getSize() > 1);
209 AlignmentView seqStrings = av.getAlignmentView(selview);
213 end = av.getAlignment().getWidth();
214 seqs = av.getAlignment().getSequencesArray();
218 start = av.getSelectionGroup().getStartRes();
219 end = av.getSelectionGroup().getEndRes() + 1;
220 seqs = av.getSelectionGroup().getSequencesInOrder(
224 tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
227 tree.reCount(tree.getTopNode());
228 tree.findHeight(tree.getTopNode());
229 treeCanvas.setTree(tree);
232 // Set default view, paying lip service to any overriding tree view
233 // parameter settings
234 boolean showDist = newtree.HasDistances()
235 && av.applet.getDefaultParameter("showTreeDistances",
236 newtree.HasDistances());
237 boolean showBoots = newtree.HasBootstrap()
238 && av.applet.getDefaultParameter("showTreeBootstraps",
239 newtree.HasBootstrap());
240 distanceMenu.setState(showDist);
241 bootstrapMenu.setState(showBoots);
242 treeCanvas.setShowBootstrap(showBoots);
243 treeCanvas.setShowDistances(showDist);
244 treeCanvas.setMarkPlaceholders(av.applet.getDefaultParameter(
245 "showUnlinkedTreeNodes", false));
248 treeCanvas.repaint();
250 av.setCurrentTree(tree);
255 public void actionPerformed(ActionEvent evt)
257 if (evt.getSource() == newickOutput)
259 newickOutput_actionPerformed();
261 else if (evt.getSource() == fontSize)
263 fontSize_actionPerformed();
265 else if (evt.getSource() == inputData)
271 public void itemStateChanged(ItemEvent evt)
273 if (evt.getSource() == fitToWindow)
275 treeCanvas.fitToWindow = fitToWindow.getState();
278 else if (evt.getSource() == distanceMenu)
280 treeCanvas.setShowDistances(distanceMenu.getState());
283 else if (evt.getSource() == bootstrapMenu)
285 treeCanvas.setShowBootstrap(bootstrapMenu.getState());
288 else if (evt.getSource() == placeholdersMenu)
290 treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
293 treeCanvas.repaint();
296 public void newickOutput_actionPerformed()
298 jalview.io.NewickFile fout = new jalview.io.NewickFile(
300 String output = fout.print(false, true);
301 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
303 java.awt.Frame frame = new java.awt.Frame();
305 jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
308 public java.awt.Font getTreeFont()
310 return treeCanvas.font;
313 public void setTreeFont(java.awt.Font font)
315 treeCanvas.font = font;
316 treeCanvas.repaint();
319 protected void fontSize_actionPerformed()
321 if (treeCanvas == null)
326 new FontChooser(this);
329 BorderLayout borderLayout1 = new BorderLayout();
331 protected ScrollPane scrollPane = new ScrollPane();
333 MenuBar jMenuBar1 = new MenuBar();
335 Menu jMenu2 = new Menu();
337 protected MenuItem fontSize = new MenuItem();
339 protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();
341 protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();
343 protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();
345 protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();
347 Menu fileMenu = new Menu();
349 MenuItem newickOutput = new MenuItem();
351 MenuItem inputData = new MenuItem();
353 private void jbInit() throws Exception
355 setLayout(borderLayout1);
356 this.setBackground(Color.white);
357 this.setFont(new java.awt.Font("Verdana", 0, 12));
358 jMenu2.setLabel(MessageManager.getString("action.view"));
359 fontSize.setLabel(MessageManager.getString("action.font"));
360 fontSize.addActionListener(this);
361 bootstrapMenu.setLabel(MessageManager
362 .getString("label.show_bootstrap_values"));
363 bootstrapMenu.addItemListener(this);
364 distanceMenu.setLabel(MessageManager.getString("label.show_distances"));
365 distanceMenu.addItemListener(this);
366 placeholdersMenu.setLabel(MessageManager
367 .getString("label.mark_unassociated_leaves"));
368 placeholdersMenu.addItemListener(this);
369 fitToWindow.setState(true);
370 fitToWindow.setLabel(MessageManager.getString("label.fit_to_window"));
371 fitToWindow.addItemListener(this);
372 fileMenu.setLabel(MessageManager.getString("action.file"));
373 newickOutput.setLabel(MessageManager.getString("label.newick_format"));
374 newickOutput.addActionListener(this);
375 inputData.setLabel(MessageManager.getString("label.input_data"));
377 add(scrollPane, BorderLayout.CENTER);
378 jMenuBar1.add(fileMenu);
379 jMenuBar1.add(jMenu2);
380 jMenu2.add(fitToWindow);
381 jMenu2.add(fontSize);
382 jMenu2.add(distanceMenu);
383 jMenu2.add(bootstrapMenu);
384 jMenu2.add(placeholdersMenu);
385 fileMenu.add(newickOutput);
386 fileMenu.add(inputData);
387 inputData.addActionListener(this);