2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
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 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/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.appletgui;
22 import java.awt.event.*;
24 import jalview.analysis.*;
25 import jalview.datamodel.*;
27 import jalview.util.MessageManager;
29 public class TreePanel extends EmbmenuFrame implements ActionListener,
42 TreeCanvas treeCanvas;
50 public NJTree getTree()
55 public void finalize() throws Throwable
63 * Creates a new TreePanel object.
78 public TreePanel(AlignmentPanel ap, String type, String pwtype)
83 this.setMenuBar(jMenuBar1);
84 } catch (Exception ex)
89 initTreePanel(ap, type, pwtype, null);
93 * Creates a new TreePanel object.
106 public TreePanel(AlignmentPanel ap, String type, String pwtype,
112 this.setMenuBar(jMenuBar1);
113 } catch (Exception e)
118 initTreePanel(ap, type, pwtype, newtree);
121 void initTreePanel(AlignmentPanel ap, String type, String pwtype,
128 this.pwtype = pwtype;
130 treeCanvas = new TreeCanvas(ap, scrollPane);
131 TreeLoader tl = new TreeLoader(newTree);
133 embedMenuIfNeeded(treeCanvas);
134 scrollPane.add(treeCanvas, BorderLayout.CENTER);
137 void showOriginalData()
139 // decide if av alignment is sufficiently different to original data to
140 // warrant a new window to be created
141 // create new alignmnt window with hidden regions (unhiding hidden regions
142 // yields unaligned seqs)
143 // or create a selection box around columns in alignment view
144 // test Alignment(SeqCigar[])
145 if (tree.seqData != null)
150 // we try to get the associated view's gap character
151 // but this may fail if the view was closed...
152 gc = av.getGapCharacter();
153 } catch (Exception ex)
157 Object[] alAndColsel = tree.seqData
158 .getAlignmentAndColumnSelection(gc);
160 if (alAndColsel != null && alAndColsel[0] != null)
162 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
163 AlignFrame af = new AlignFrame(al, av.applet,
164 "Original Data for Tree", false);
166 af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
171 System.out.println("Original Tree Data not available");
175 class TreeLoader extends Thread
179 jalview.datamodel.AlignmentView odata = null;
181 public TreeLoader(NewickFile newtree)
183 this.newtree = newtree;
192 tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
196 tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
205 boolean selview = (av.getSelectionGroup() != null)
206 && (av.getSelectionGroup().getSize() > 1);
207 AlignmentView seqStrings = av.getAlignmentView(selview);
211 end = av.getAlignment().getWidth();
212 seqs = av.getAlignment().getSequencesArray();
216 start = av.getSelectionGroup().getStartRes();
217 end = av.getSelectionGroup().getEndRes() + 1;
218 seqs = av.getSelectionGroup().getSequencesInOrder(
222 tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
225 tree.reCount(tree.getTopNode());
226 tree.findHeight(tree.getTopNode());
227 treeCanvas.setTree(tree);
230 // Set default view, paying lip service to any overriding tree view
231 // parameter settings
232 boolean showDist = newtree.HasDistances()
233 && av.applet.getDefaultParameter("showTreeDistances",
234 newtree.HasDistances());
235 boolean showBoots = newtree.HasBootstrap()
236 && av.applet.getDefaultParameter("showTreeBootstraps",
237 newtree.HasBootstrap());
238 distanceMenu.setState(showDist);
239 bootstrapMenu.setState(showBoots);
240 treeCanvas.setShowBootstrap(showBoots);
241 treeCanvas.setShowDistances(showDist);
242 treeCanvas.setMarkPlaceholders(av.applet.getDefaultParameter(
243 "showUnlinkedTreeNodes", false));
246 treeCanvas.repaint();
248 av.setCurrentTree(tree);
253 public void actionPerformed(ActionEvent evt)
255 if (evt.getSource() == newickOutput)
257 newickOutput_actionPerformed();
259 else if (evt.getSource() == fontSize)
261 fontSize_actionPerformed();
263 else if (evt.getSource() == inputData)
269 public void itemStateChanged(ItemEvent evt)
271 if (evt.getSource() == fitToWindow)
273 treeCanvas.fitToWindow = fitToWindow.getState();
276 else if (evt.getSource() == distanceMenu)
278 treeCanvas.setShowDistances(distanceMenu.getState());
281 else if (evt.getSource() == bootstrapMenu)
283 treeCanvas.setShowBootstrap(bootstrapMenu.getState());
286 else if (evt.getSource() == placeholdersMenu)
288 treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
291 treeCanvas.repaint();
294 public void newickOutput_actionPerformed()
296 jalview.io.NewickFile fout = new jalview.io.NewickFile(
298 String output = fout.print(false, true);
299 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
301 java.awt.Frame frame = new java.awt.Frame();
303 jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
306 public java.awt.Font getTreeFont()
308 return treeCanvas.font;
311 public void setTreeFont(java.awt.Font font)
313 treeCanvas.font = font;
314 treeCanvas.repaint();
317 protected void fontSize_actionPerformed()
319 if (treeCanvas == null)
324 new FontChooser(this);
327 BorderLayout borderLayout1 = new BorderLayout();
329 protected ScrollPane scrollPane = new ScrollPane();
331 MenuBar jMenuBar1 = new MenuBar();
333 Menu jMenu2 = new Menu();
335 protected MenuItem fontSize = new MenuItem();
337 protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();
339 protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();
341 protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();
343 protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();
345 Menu fileMenu = new Menu();
347 MenuItem newickOutput = new MenuItem();
349 MenuItem inputData = new MenuItem();
351 private void jbInit() throws Exception
353 setLayout(borderLayout1);
354 this.setBackground(Color.white);
355 this.setFont(new java.awt.Font("Verdana", 0, 12));
356 jMenu2.setLabel(MessageManager.getString("action.view"));
357 fontSize.setLabel(MessageManager.getString("action.font"));
358 fontSize.addActionListener(this);
359 bootstrapMenu.setLabel(MessageManager.getString("label.show_bootstrap_values"));
360 bootstrapMenu.addItemListener(this);
361 distanceMenu.setLabel(MessageManager.getString("label.show_distances"));
362 distanceMenu.addItemListener(this);
363 placeholdersMenu.setLabel(MessageManager.getString("label.mark_unassociated_leaves"));
364 placeholdersMenu.addItemListener(this);
365 fitToWindow.setState(true);
366 fitToWindow.setLabel(MessageManager.getString("label.fit_to_window"));
367 fitToWindow.addItemListener(this);
368 fileMenu.setLabel(MessageManager.getString("action.file"));
369 newickOutput.setLabel(MessageManager.getString("label.newick_format"));
370 newickOutput.addActionListener(this);
371 inputData.setLabel(MessageManager.getString("label.input_data"));
373 add(scrollPane, BorderLayout.CENTER);
374 jMenuBar1.add(fileMenu);
375 jMenuBar1.add(jMenu2);
376 jMenu2.add(fitToWindow);
377 jMenu2.add(fontSize);
378 jMenu2.add(distanceMenu);
379 jMenu2.add(bootstrapMenu);
380 jMenu2.add(placeholdersMenu);
381 fileMenu.add(newickOutput);
382 fileMenu.add(inputData);
383 inputData.addActionListener(this);