2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, 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()
54 * Creates a new TreePanel object.
69 public TreePanel(AlignmentPanel ap, String type, String pwtype)
74 this.setMenuBar(jMenuBar1);
75 } catch (Exception ex)
80 initTreePanel(ap, type, pwtype, null);
84 * Creates a new TreePanel object.
97 public TreePanel(AlignmentPanel ap, String type, String pwtype,
103 this.setMenuBar(jMenuBar1);
104 } catch (Exception e)
109 initTreePanel(ap, type, pwtype, newtree);
112 void initTreePanel(AlignmentPanel ap, String type, String pwtype,
119 this.pwtype = pwtype;
121 treeCanvas = new TreeCanvas(ap, scrollPane);
122 TreeLoader tl = new TreeLoader(newTree);
124 embedMenuIfNeeded(treeCanvas);
125 scrollPane.add(treeCanvas, BorderLayout.CENTER);
128 void showOriginalData()
130 // decide if av alignment is sufficiently different to original data to
131 // warrant a new window to be created
132 // create new alignmnt window with hidden regions (unhiding hidden regions
133 // yields unaligned seqs)
134 // or create a selection box around columns in alignment view
135 // test Alignment(SeqCigar[])
136 if (tree.seqData != null)
141 // we try to get the associated view's gap character
142 // but this may fail if the view was closed...
143 gc = av.getGapCharacter();
144 } catch (Exception ex)
148 Object[] alAndColsel = tree.seqData
149 .getAlignmentAndColumnSelection(gc);
151 if (alAndColsel != null && alAndColsel[0] != null)
153 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
154 AlignFrame af = new AlignFrame(al, av.applet,
155 "Original Data for Tree", false);
157 af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
162 System.out.println("Original Tree Data not available");
166 class TreeLoader extends Thread
170 jalview.datamodel.AlignmentView odata = null;
172 public TreeLoader(NewickFile newtree)
174 this.newtree = newtree;
183 tree = new NJTree(av.alignment.getSequencesArray(), newtree);
187 tree = new NJTree(av.alignment.getSequencesArray(), odata,
196 AlignmentView seqStrings = av.getAlignmentView(av
197 .getSelectionGroup() != null);
198 if (av.getSelectionGroup() == null)
201 end = av.alignment.getWidth();
202 seqs = av.alignment.getSequencesArray();
206 start = av.getSelectionGroup().getStartRes();
207 end = av.getSelectionGroup().getEndRes() + 1;
208 seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
211 tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
214 tree.reCount(tree.getTopNode());
215 tree.findHeight(tree.getTopNode());
216 treeCanvas.setTree(tree);
219 // Set default view, paying lip service to any overriding tree view
220 // parameter settings
221 boolean showDist = newtree.HasDistances()
222 && av.applet.getDefaultParameter("showTreeDistances",
223 newtree.HasDistances());
224 boolean showBoots = newtree.HasBootstrap()
225 && av.applet.getDefaultParameter("showTreeBootstraps",
226 newtree.HasBootstrap());
227 distanceMenu.setState(showDist);
228 bootstrapMenu.setState(showBoots);
229 treeCanvas.setShowBootstrap(showBoots);
230 treeCanvas.setShowDistances(showDist);
231 treeCanvas.setMarkPlaceholders(av.applet.getDefaultParameter(
232 "showUnlinkedTreeNodes", false));
235 treeCanvas.repaint();
237 av.setCurrentTree(tree);
242 public void actionPerformed(ActionEvent evt)
244 if (evt.getSource() == newickOutput)
246 newickOutput_actionPerformed();
248 else if (evt.getSource() == fontSize)
250 fontSize_actionPerformed();
252 else if (evt.getSource() == inputData)
258 public void itemStateChanged(ItemEvent evt)
260 if (evt.getSource() == fitToWindow)
262 treeCanvas.fitToWindow = fitToWindow.getState();
265 else if (evt.getSource() == distanceMenu)
267 treeCanvas.setShowDistances(distanceMenu.getState());
270 else if (evt.getSource() == bootstrapMenu)
272 treeCanvas.setShowBootstrap(bootstrapMenu.getState());
275 else if (evt.getSource() == placeholdersMenu)
277 treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
280 treeCanvas.repaint();
283 public void newickOutput_actionPerformed()
285 jalview.io.NewickFile fout = new jalview.io.NewickFile(
287 String output = fout.print(false, true);
288 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
290 java.awt.Frame frame = new java.awt.Frame();
292 jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
295 public java.awt.Font getTreeFont()
297 return treeCanvas.font;
300 public void setTreeFont(java.awt.Font font)
302 treeCanvas.font = font;
303 treeCanvas.repaint();
306 protected void fontSize_actionPerformed()
308 if (treeCanvas == null)
313 new FontChooser(this);
316 BorderLayout borderLayout1 = new BorderLayout();
318 protected ScrollPane scrollPane = new ScrollPane();
320 MenuBar jMenuBar1 = new MenuBar();
322 Menu jMenu2 = new Menu();
324 protected MenuItem fontSize = new MenuItem();
326 protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();
328 protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();
330 protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();
332 protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();
334 Menu fileMenu = new Menu();
336 MenuItem newickOutput = new MenuItem();
338 MenuItem inputData = new MenuItem();
340 private void jbInit() throws Exception
342 setLayout(borderLayout1);
343 this.setBackground(Color.white);
344 this.setFont(new java.awt.Font("Verdana", 0, 12));
345 jMenu2.setLabel("View");
346 fontSize.setLabel("Font...");
347 fontSize.addActionListener(this);
348 bootstrapMenu.setLabel("Show Bootstrap Values");
349 bootstrapMenu.addItemListener(this);
350 distanceMenu.setLabel("Show Distances");
351 distanceMenu.addItemListener(this);
352 placeholdersMenu.setLabel("Mark Unassociated Leaves");
353 placeholdersMenu.addItemListener(this);
354 fitToWindow.setState(true);
355 fitToWindow.setLabel("Fit To Window");
356 fitToWindow.addItemListener(this);
357 fileMenu.setLabel("File");
358 newickOutput.setLabel("Newick Format");
359 newickOutput.addActionListener(this);
360 inputData.setLabel("Input Data...");
362 add(scrollPane, BorderLayout.CENTER);
363 jMenuBar1.add(fileMenu);
364 jMenuBar1.add(jMenu2);
365 jMenu2.add(fitToWindow);
366 jMenu2.add(fontSize);
367 jMenu2.add(distanceMenu);
368 jMenu2.add(bootstrapMenu);
369 jMenu2.add(placeholdersMenu);
370 fileMenu.add(newickOutput);
371 fileMenu.add(inputData);
372 inputData.addActionListener(this);