2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ 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;
23 import jalview.analysis.scoremodels.SimilarityParams;
24 import jalview.datamodel.Alignment;
25 import jalview.datamodel.AlignmentView;
26 import jalview.datamodel.ColumnSelection;
27 import jalview.datamodel.SeqCigar;
28 import jalview.datamodel.SequenceI;
29 import jalview.util.MessageManager;
30 import jalview.viewmodel.PCAModel;
32 import java.awt.BorderLayout;
33 import java.awt.Button;
34 import java.awt.CheckboxMenuItem;
35 import java.awt.Choice;
36 import java.awt.Color;
37 import java.awt.FlowLayout;
38 import java.awt.Frame;
39 import java.awt.Label;
41 import java.awt.MenuBar;
42 import java.awt.MenuItem;
43 import java.awt.Panel;
44 import java.awt.event.ActionEvent;
45 import java.awt.event.ActionListener;
46 import java.awt.event.ItemEvent;
47 import java.awt.event.ItemListener;
49 public class PCAPanel extends EmbmenuFrame implements Runnable,
50 ActionListener, ItemListener
60 public PCAPanel(AlignViewport av)
70 for (int i = 1; i < 8; i++)
72 xCombobox.addItem("dim " + i);
73 yCombobox.addItem("dim " + i);
74 zCombobox.addItem("dim " + i);
78 boolean selected = av.getSelectionGroup() != null
79 && av.getSelectionGroup().getSize() > 0;
80 AlignmentView seqstrings = av.getAlignmentView(selected);
81 boolean nucleotide = av.getAlignment().isNucleotide();
85 seqs = av.getAlignment().getSequencesArray();
89 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
91 SeqCigar sq[] = seqstrings.getSequences();
92 int length = sq[0].getWidth();
94 for (int i = 0; i < seqs.length; i++)
96 if (sq[i].getWidth() != length)
99 .println("Sequences must be equal length for PCA analysis");
103 pcaModel = new PCAModel(seqstrings, seqs, nucleotide,
104 SimilarityParams.SeqSpace);
106 rc = new RotatableCanvas(av);
107 embedMenuIfNeeded(rc);
108 add(rc, BorderLayout.CENTER);
110 jalview.bin.JalviewLite.addFrame(this,
111 MessageManager.getString("label.principal_component_analysis"),
114 Thread worker = new Thread(this);
124 // TODO progress indicator
125 calcSettings.setEnabled(false);
126 rc.setEnabled(false);
129 nuclSetting.setState(pcaModel.isNucleotide());
130 protSetting.setState(!pcaModel.isNucleotide());
137 pcaModel.updateRc(rc);
139 top = pcaModel.getTop();
140 } catch (OutOfMemoryError x)
142 System.err.println("Out of memory when calculating PCA.");
145 calcSettings.setEnabled(true);
147 // TODO revert progress indicator
153 void doDimensionChange()
160 int dim1 = top - xCombobox.getSelectedIndex();
161 int dim2 = top - yCombobox.getSelectedIndex();
162 int dim3 = top - zCombobox.getSelectedIndex();
163 pcaModel.updateRcView(dim1, dim2, dim3);
165 rc.rotmat.setIdentity();
167 rc.paint(rc.getGraphics());
171 public void actionPerformed(ActionEvent evt)
173 if (evt.getSource() == inputData)
177 if (evt.getSource() == resetButton)
184 if (evt.getSource() == values)
186 values_actionPerformed();
191 public void itemStateChanged(ItemEvent evt)
193 if (evt.getSource() == xCombobox)
195 xCombobox_actionPerformed();
197 else if (evt.getSource() == yCombobox)
199 yCombobox_actionPerformed();
201 else if (evt.getSource() == zCombobox)
203 zCombobox_actionPerformed();
205 else if (evt.getSource() == labels)
207 labels_itemStateChanged(evt);
209 else if (evt.getSource() == nuclSetting)
211 if (!pcaModel.isNucleotide())
213 pcaModel.setNucleotide(true);
214 new Thread(this).start();
217 else if (evt.getSource() == protSetting)
219 if (pcaModel.isNucleotide())
221 pcaModel.setNucleotide(false);
222 new Thread(this).start();
227 protected void xCombobox_actionPerformed()
232 protected void yCombobox_actionPerformed()
237 protected void zCombobox_actionPerformed()
242 public void values_actionPerformed()
245 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
246 Frame frame = new Frame();
248 jalview.bin.JalviewLite.addFrame(frame,
249 MessageManager.getString("label.pca_details"), 500, 500);
251 cap.setText(pcaModel.getDetails());
254 void showOriginalData()
256 // decide if av alignment is sufficiently different to original data to
257 // warrant a new window to be created
258 // create new alignmnt window with hidden regions (unhiding hidden regions
259 // yields unaligned seqs)
260 // or create a selection box around columns in alignment view
261 // test Alignment(SeqCigar[])
265 // we try to get the associated view's gap character
266 // but this may fail if the view was closed...
267 gc = av.getGapCharacter();
268 } catch (Exception ex)
272 Object[] alAndColsel = pcaModel.getSeqtrings()
273 .getAlignmentAndColumnSelection(gc);
275 if (alAndColsel != null && alAndColsel[0] != null)
277 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
278 AlignFrame af = new AlignFrame(al, av.applet,
279 "Original Data for PCA", false);
281 af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
285 public void labels_itemStateChanged(ItemEvent itemEvent)
287 rc.showLabels(labels.getState());
290 Panel jPanel2 = new Panel();
292 Label jLabel1 = new Label();
294 Label jLabel2 = new Label();
296 Label jLabel3 = new Label();
298 protected Choice xCombobox = new Choice();
300 protected Choice yCombobox = new Choice();
302 protected Choice zCombobox = new Choice();
304 protected Button resetButton = new Button();
306 FlowLayout flowLayout1 = new FlowLayout();
308 BorderLayout borderLayout1 = new BorderLayout();
310 MenuBar menuBar1 = new MenuBar();
312 Menu menu1 = new Menu();
314 Menu menu2 = new Menu();
316 Menu calcSettings = new Menu();
318 protected CheckboxMenuItem labels = new CheckboxMenuItem();
320 protected CheckboxMenuItem protSetting = new CheckboxMenuItem();
322 protected CheckboxMenuItem nuclSetting = new CheckboxMenuItem();
324 MenuItem values = new MenuItem();
326 MenuItem inputData = new MenuItem();
328 private void jbInit() throws Exception
330 this.setLayout(borderLayout1);
331 jPanel2.setLayout(flowLayout1);
332 jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
333 jLabel1.setText("x=");
334 jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));
335 jLabel2.setText("y=");
336 jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));
337 jLabel3.setText("z=");
338 jPanel2.setBackground(Color.white);
339 zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
340 zCombobox.addItemListener(this);
341 yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
342 yCombobox.addItemListener(this);
343 xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
344 xCombobox.addItemListener(this);
345 resetButton.setFont(new java.awt.Font("Verdana", 0, 12));
346 resetButton.setLabel(MessageManager.getString("action.reset"));
347 resetButton.addActionListener(this);
348 this.setMenuBar(menuBar1);
349 menu1.setLabel(MessageManager.getString("action.file"));
350 menu2.setLabel(MessageManager.getString("action.view"));
351 calcSettings.setLabel(MessageManager.getString("action.change_params"));
352 labels.setLabel(MessageManager.getString("label.labels"));
353 labels.addItemListener(this);
354 values.setLabel(MessageManager.getString("label.output_values"));
355 values.addActionListener(this);
356 inputData.setLabel(MessageManager.getString("label.input_data"));
357 nuclSetting.setLabel(MessageManager
358 .getString("label.nucleotide_matrix"));
359 nuclSetting.addItemListener(this);
360 protSetting.setLabel(MessageManager.getString("label.protein_matrix"));
361 protSetting.addItemListener(this);
362 this.add(jPanel2, BorderLayout.SOUTH);
363 jPanel2.add(jLabel1, null);
364 jPanel2.add(xCombobox, null);
365 jPanel2.add(jLabel2, null);
366 jPanel2.add(yCombobox, null);
367 jPanel2.add(jLabel3, null);
368 jPanel2.add(zCombobox, null);
369 jPanel2.add(resetButton, null);
372 menuBar1.add(calcSettings);
375 menu1.add(inputData);
376 calcSettings.add(nuclSetting);
377 calcSettings.add(protSetting);
378 inputData.addActionListener(this);