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.bin.JalviewLite;
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 awt2swing.Button;
34 import awt2swing.CheckboxMenuItem;
35 import awt2swing.Choice;
36 import java.awt.Color;
37 import java.awt.FlowLayout;
38 import awt2swing.Frame;
39 import awt2swing.Label;
40 import awt2swing.Menu;
41 import awt2swing.MenuBar;
42 import awt2swing.MenuItem;
43 import awt2swing.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);
105 rc = new RotatableCanvas(av);
106 embedMenuIfNeeded(rc);
107 add(rc, BorderLayout.CENTER);
109 JalviewLite.addFrame(this,
110 MessageManager.getString("label.principal_component_analysis"),
113 Thread worker = new Thread(this);
122 // TODO progress indicator
123 calcSettings.setEnabled(false);
124 rc.setEnabled(false);
127 nuclSetting.setState(pcaModel.isNucleotide());
128 protSetting.setState(!pcaModel.isNucleotide());
135 pcaModel.updateRc(rc);
137 top = pcaModel.getTop();
138 } catch (OutOfMemoryError x)
140 System.err.println("Out of memory when calculating PCA.");
143 calcSettings.setEnabled(true);
145 // TODO revert progress indicator
151 void doDimensionChange()
158 int dim1 = top - xCombobox.getSelectedIndex();
159 int dim2 = top - yCombobox.getSelectedIndex();
160 int dim3 = top - zCombobox.getSelectedIndex();
161 pcaModel.updateRcView(dim1, dim2, dim3);
163 rc.rotmat.setIdentity();
165 rc.paint(rc.getGraphics());
168 public void actionPerformed(ActionEvent evt)
170 if (evt.getSource() == inputData)
174 if (evt.getSource() == resetButton)
181 if (evt.getSource() == values)
183 values_actionPerformed();
187 public void itemStateChanged(ItemEvent evt)
189 if (evt.getSource() == xCombobox)
191 xCombobox_actionPerformed();
193 else if (evt.getSource() == yCombobox)
195 yCombobox_actionPerformed();
197 else if (evt.getSource() == zCombobox)
199 zCombobox_actionPerformed();
201 else if (evt.getSource() == labels)
203 labels_itemStateChanged(evt);
205 else if (evt.getSource() == nuclSetting)
207 if (!pcaModel.isNucleotide())
209 pcaModel.setNucleotide(true);
210 new Thread(this).start();
213 else if (evt.getSource() == protSetting)
215 if (pcaModel.isNucleotide())
217 pcaModel.setNucleotide(false);
218 new Thread(this).start();
223 protected void xCombobox_actionPerformed()
228 protected void yCombobox_actionPerformed()
233 protected void zCombobox_actionPerformed()
238 public void values_actionPerformed()
241 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
242 Frame frame = new Frame();
244 JalviewLite.addFrame(frame,
245 MessageManager.getString("label.pca_details"), 500, 500);
247 cap.setText(pcaModel.getDetails());
250 void showOriginalData()
252 // decide if av alignment is sufficiently different to original data to
253 // warrant a new window to be created
254 // create new alignmnt window with hidden regions (unhiding hidden regions
255 // yields unaligned seqs)
256 // or create a selection box around columns in alignment view
257 // test Alignment(SeqCigar[])
261 // we try to get the associated view's gap character
262 // but this may fail if the view was closed...
263 gc = av.getGapCharacter();
264 } catch (Exception ex)
268 Object[] alAndColsel = pcaModel.getSeqtrings()
269 .getAlignmentAndColumnSelection(gc);
271 if (alAndColsel != null && alAndColsel[0] != null)
273 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
274 AlignFrame af = new AlignFrame(al, av.applet,
275 "Original Data for PCA", false);
277 af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
281 public void labels_itemStateChanged(ItemEvent itemEvent)
283 rc.showLabels(labels.getState());
286 Panel jPanel2 = new Panel();
288 Label jLabel1 = new Label();
290 Label jLabel2 = new Label();
292 Label jLabel3 = new Label();
294 protected Choice xCombobox = new Choice();
296 protected Choice yCombobox = new Choice();
298 protected Choice zCombobox = new Choice();
300 protected Button resetButton = new Button();
302 FlowLayout flowLayout1 = new FlowLayout();
304 BorderLayout borderLayout1 = new BorderLayout();
306 MenuBar menuBar1 = new MenuBar();
308 Menu menu1 = new Menu();
310 Menu menu2 = new Menu();
312 Menu calcSettings = new Menu();
314 protected CheckboxMenuItem labels = new CheckboxMenuItem();
316 protected CheckboxMenuItem protSetting = new CheckboxMenuItem();
318 protected CheckboxMenuItem nuclSetting = new CheckboxMenuItem();
320 MenuItem values = new MenuItem();
322 MenuItem inputData = new MenuItem();
324 private void jbInit() throws Exception
326 this.setLayout(borderLayout1);
327 jPanel2.setLayout(flowLayout1);
328 jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
329 jLabel1.setText("x=");
330 jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));
331 jLabel2.setText("y=");
332 jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));
333 jLabel3.setText("z=");
334 jPanel2.setBackground(Color.white);
335 zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
336 zCombobox.addItemListener(this);
337 yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
338 yCombobox.addItemListener(this);
339 xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
340 xCombobox.addItemListener(this);
341 resetButton.setFont(new java.awt.Font("Verdana", 0, 12));
342 resetButton.setLabel(MessageManager.getString("action.reset"));
343 resetButton.addActionListener(this);
344 this.setMenuBar(menuBar1);
345 menu1.setLabel(MessageManager.getString("action.file"));
346 menu2.setLabel(MessageManager.getString("action.view"));
347 calcSettings.setLabel(MessageManager.getString("action.change_params"));
348 labels.setLabel(MessageManager.getString("label.labels"));
349 labels.addItemListener(this);
350 values.setLabel(MessageManager.getString("label.output_values"));
351 values.addActionListener(this);
352 inputData.setLabel(MessageManager.getString("label.input_data"));
353 nuclSetting.setLabel(MessageManager
354 .getString("label.nucleotide_matrix"));
355 nuclSetting.addItemListener(this);
356 protSetting.setLabel(MessageManager.getString("label.protein_matrix"));
357 protSetting.addItemListener(this);
358 this.add(jPanel2, BorderLayout.SOUTH);
359 jPanel2.add(jLabel1, null);
360 jPanel2.add(xCombobox, null);
361 jPanel2.add(jLabel2, null);
362 jPanel2.add(yCombobox, null);
363 jPanel2.add(jLabel3, null);
364 jPanel2.add(zCombobox, null);
365 jPanel2.add(resetButton, null);
368 menuBar1.add(calcSettings);
371 menu1.add(inputData);
372 calcSettings.add(nuclSetting);
373 calcSettings.add(protSetting);
374 inputData.addActionListener(this);