2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
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;
47 public NJTree getTree()
53 * Creates a new TreePanel object.
68 public TreePanel(AlignViewport av, String type, String pwtype)
73 this.setMenuBar(jMenuBar1);
74 } catch (Exception ex)
79 initTreePanel(av, type, pwtype, null);
83 * Creates a new TreePanel object.
96 public TreePanel(AlignViewport av, String type, String pwtype,
102 this.setMenuBar(jMenuBar1);
103 } catch (Exception e)
108 initTreePanel(av, type, pwtype, newtree);
111 void initTreePanel(AlignViewport av, String type, String pwtype,
117 this.pwtype = pwtype;
119 treeCanvas = new TreeCanvas(av, scrollPane);
120 TreeLoader tl = new TreeLoader(newTree);
122 embedMenuIfNeeded(treeCanvas);
123 scrollPane.add(treeCanvas, BorderLayout.CENTER);
126 void showOriginalData()
128 // decide if av alignment is sufficiently different to original data to
129 // warrant a new window to be created
130 // create new alignmnt window with hidden regions (unhiding hidden regions
131 // yields unaligned seqs)
132 // or create a selection box around columns in alignment view
133 // test Alignment(SeqCigar[])
134 if (tree.seqData != null)
139 // we try to get the associated view's gap character
140 // but this may fail if the view was closed...
141 gc = av.getGapCharacter();
142 } catch (Exception ex)
146 Object[] alAndColsel = tree.seqData
147 .getAlignmentAndColumnSelection(gc);
149 if (alAndColsel != null && alAndColsel[0] != null)
151 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
152 AlignFrame af = new AlignFrame(al, av.applet,
153 "Original Data for Tree", false);
155 af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
160 System.out.println("Original Tree Data not available");
164 class TreeLoader extends Thread
168 jalview.datamodel.AlignmentView odata = null;
170 public TreeLoader(NewickFile newtree)
172 this.newtree = newtree;
181 tree = new NJTree(av.alignment.getSequencesArray(), newtree);
185 tree = new NJTree(av.alignment.getSequencesArray(), odata,
194 AlignmentView seqStrings = av.getAlignmentView(av
195 .getSelectionGroup() != null);
196 if (av.getSelectionGroup() == null)
199 end = av.alignment.getWidth();
200 seqs = av.alignment.getSequencesArray();
204 start = av.getSelectionGroup().getStartRes();
205 end = av.getSelectionGroup().getEndRes() + 1;
206 seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
209 tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
212 tree.reCount(tree.getTopNode());
213 tree.findHeight(tree.getTopNode());
214 treeCanvas.setTree(tree);
217 // Set default view, paying lip service to any overriding tree view
218 // parameter settings
219 boolean showDist = newtree.HasDistances()
220 && av.applet.getDefaultParameter("showTreeDistances",
221 newtree.HasDistances());
222 boolean showBoots = newtree.HasBootstrap()
223 && av.applet.getDefaultParameter("showTreeBootstraps",
224 newtree.HasBootstrap());
225 distanceMenu.setState(showDist);
226 bootstrapMenu.setState(showBoots);
227 treeCanvas.setShowBootstrap(showBoots);
228 treeCanvas.setShowDistances(showDist);
229 treeCanvas.setMarkPlaceholders(av.applet.getDefaultParameter(
230 "showUnlinkedTreeNodes", false));
233 treeCanvas.repaint();
235 av.setCurrentTree(tree);
240 public void actionPerformed(ActionEvent evt)
242 if (evt.getSource() == newickOutput)
244 newickOutput_actionPerformed();
246 else if (evt.getSource() == fontSize)
248 fontSize_actionPerformed();
250 else if (evt.getSource() == inputData)
256 public void itemStateChanged(ItemEvent evt)
258 if (evt.getSource() == fitToWindow)
260 treeCanvas.fitToWindow = fitToWindow.getState();
263 else if (evt.getSource() == distanceMenu)
265 treeCanvas.setShowDistances(distanceMenu.getState());
268 else if (evt.getSource() == bootstrapMenu)
270 treeCanvas.setShowBootstrap(bootstrapMenu.getState());
273 else if (evt.getSource() == placeholdersMenu)
275 treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
278 treeCanvas.repaint();
281 public void newickOutput_actionPerformed()
283 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
285 String output = fout.print(false, true);
286 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
288 java.awt.Frame frame = new java.awt.Frame();
290 jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
293 public java.awt.Font getTreeFont()
295 return treeCanvas.font;
298 public void setTreeFont(java.awt.Font font)
300 treeCanvas.font = font;
301 treeCanvas.repaint();
304 protected void fontSize_actionPerformed()
306 if (treeCanvas == null)
311 new FontChooser(this);
314 BorderLayout borderLayout1 = new BorderLayout();
316 protected ScrollPane scrollPane = new ScrollPane();
318 MenuBar jMenuBar1 = new MenuBar();
320 Menu jMenu2 = new Menu();
322 protected MenuItem fontSize = new MenuItem();
324 protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();
326 protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();
328 protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();
330 protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();
332 Menu fileMenu = new Menu();
334 MenuItem newickOutput = new MenuItem();
336 MenuItem inputData = new MenuItem();
338 private void jbInit() throws Exception
340 setLayout(borderLayout1);
341 this.setBackground(Color.white);
342 this.setFont(new java.awt.Font("Verdana", 0, 12));
343 jMenu2.setLabel("View");
344 fontSize.setLabel("Font...");
345 fontSize.addActionListener(this);
346 bootstrapMenu.setLabel("Show Bootstrap Values");
347 bootstrapMenu.addItemListener(this);
348 distanceMenu.setLabel("Show Distances");
349 distanceMenu.addItemListener(this);
350 placeholdersMenu.setLabel("Mark Unassociated Leaves");
351 placeholdersMenu.addItemListener(this);
352 fitToWindow.setState(true);
353 fitToWindow.setLabel("Fit To Window");
354 fitToWindow.addItemListener(this);
355 fileMenu.setLabel("File");
356 newickOutput.setLabel("Newick Format");
357 newickOutput.addActionListener(this);
358 inputData.setLabel("Input Data...");
360 add(scrollPane, BorderLayout.CENTER);
361 jMenuBar1.add(fileMenu);
362 jMenuBar1.add(jMenu2);
363 jMenu2.add(fitToWindow);
364 jMenu2.add(fontSize);
365 jMenu2.add(distanceMenu);
366 jMenu2.add(bootstrapMenu);
367 jMenu2.add(placeholdersMenu);
368 fileMenu.add(newickOutput);
369 fileMenu.add(inputData);
370 inputData.addActionListener(this);