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.datamodel.Alignment;
24 import jalview.datamodel.AlignmentView;
25 import jalview.datamodel.HiddenColumns;
26 import jalview.datamodel.SeqCigar;
27 import jalview.datamodel.SequenceI;
28 import jalview.util.MessageManager;
29 import jalview.viewmodel.PCAModel;
31 import java.awt.BorderLayout;
32 import java.awt.Button;
33 import java.awt.CheckboxMenuItem;
34 import java.awt.Choice;
35 import java.awt.Color;
36 import java.awt.FlowLayout;
37 import java.awt.Frame;
38 import java.awt.Label;
40 import java.awt.MenuBar;
41 import java.awt.MenuItem;
42 import java.awt.Panel;
43 import java.awt.event.ActionEvent;
44 import java.awt.event.ActionListener;
45 import java.awt.event.ItemEvent;
46 import java.awt.event.ItemListener;
48 public class PCAPanel extends EmbmenuFrame implements Runnable,
49 ActionListener, ItemListener
59 public PCAPanel(AlignViewport av)
69 for (int i = 1; i < 8; i++)
71 xCombobox.addItem("dim " + i);
72 yCombobox.addItem("dim " + i);
73 zCombobox.addItem("dim " + i);
77 boolean selected = av.getSelectionGroup() != null
78 && av.getSelectionGroup().getSize() > 0;
79 AlignmentView seqstrings = av.getAlignmentView(selected);
80 boolean nucleotide = av.getAlignment().isNucleotide();
84 seqs = av.getAlignment().getSequencesArray();
88 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
90 SeqCigar sq[] = seqstrings.getSequences();
91 int length = sq[0].getWidth();
93 for (int i = 0; i < seqs.length; i++)
95 if (sq[i].getWidth() != length)
98 .println("Sequences must be equal length for PCA analysis");
102 pcaModel = new PCAModel(seqstrings, seqs, nucleotide);
104 rc = new RotatableCanvas(av);
105 embedMenuIfNeeded(rc);
106 add(rc, BorderLayout.CENTER);
108 jalview.bin.JalviewLite.addFrame(this,
109 MessageManager.getString("label.principal_component_analysis"),
112 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());
169 public void actionPerformed(ActionEvent evt)
171 if (evt.getSource() == inputData)
175 if (evt.getSource() == resetButton)
182 if (evt.getSource() == values)
184 values_actionPerformed();
189 public void itemStateChanged(ItemEvent evt)
191 if (evt.getSource() == xCombobox)
193 xCombobox_actionPerformed();
195 else if (evt.getSource() == yCombobox)
197 yCombobox_actionPerformed();
199 else if (evt.getSource() == zCombobox)
201 zCombobox_actionPerformed();
203 else if (evt.getSource() == labels)
205 labels_itemStateChanged(evt);
207 else if (evt.getSource() == nuclSetting)
209 if (!pcaModel.isNucleotide())
211 pcaModel.setNucleotide(true);
212 new Thread(this).start();
215 else if (evt.getSource() == protSetting)
217 if (pcaModel.isNucleotide())
219 pcaModel.setNucleotide(false);
220 new Thread(this).start();
225 protected void xCombobox_actionPerformed()
230 protected void yCombobox_actionPerformed()
235 protected void zCombobox_actionPerformed()
240 public void values_actionPerformed()
243 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
244 Frame frame = new Frame();
246 jalview.bin.JalviewLite.addFrame(frame,
247 MessageManager.getString("label.pca_details"), 500, 500);
249 cap.setText(pcaModel.getDetails());
252 void showOriginalData()
254 // decide if av alignment is sufficiently different to original data to
255 // warrant a new window to be created
256 // create new alignmnt window with hidden regions (unhiding hidden regions
257 // yields unaligned seqs)
258 // or create a selection box around columns in alignment view
259 // test Alignment(SeqCigar[])
263 // we try to get the associated view's gap character
264 // but this may fail if the view was closed...
265 gc = av.getGapCharacter();
266 } catch (Exception ex)
270 Object[] alAndColsel = pcaModel.getSeqtrings()
271 .getAlignmentAndHiddenColumns(gc);
273 if (alAndColsel != null && alAndColsel[0] != null)
275 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
276 AlignFrame af = new AlignFrame(al, av.applet,
277 "Original Data for PCA", false);
279 af.viewport.getAlignment().setHiddenColumns(
280 (HiddenColumns) alAndColsel[1]);
284 public void labels_itemStateChanged(ItemEvent itemEvent)
286 rc.showLabels(labels.getState());
289 Panel jPanel2 = new Panel();
291 Label jLabel1 = new Label();
293 Label jLabel2 = new Label();
295 Label jLabel3 = new Label();
297 protected Choice xCombobox = new Choice();
299 protected Choice yCombobox = new Choice();
301 protected Choice zCombobox = new Choice();
303 protected Button resetButton = new Button();
305 FlowLayout flowLayout1 = new FlowLayout();
307 BorderLayout borderLayout1 = new BorderLayout();
309 MenuBar menuBar1 = new MenuBar();
311 Menu menu1 = new Menu();
313 Menu menu2 = new Menu();
315 Menu calcSettings = new Menu();
317 protected CheckboxMenuItem labels = new CheckboxMenuItem();
319 protected CheckboxMenuItem protSetting = new CheckboxMenuItem();
321 protected CheckboxMenuItem nuclSetting = new CheckboxMenuItem();
323 MenuItem values = new MenuItem();
325 MenuItem inputData = new MenuItem();
327 private void jbInit() throws Exception
329 this.setLayout(borderLayout1);
330 jPanel2.setLayout(flowLayout1);
331 jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
332 jLabel1.setText("x=");
333 jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));
334 jLabel2.setText("y=");
335 jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));
336 jLabel3.setText("z=");
337 jPanel2.setBackground(Color.white);
338 zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
339 zCombobox.addItemListener(this);
340 yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
341 yCombobox.addItemListener(this);
342 xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
343 xCombobox.addItemListener(this);
344 resetButton.setFont(new java.awt.Font("Verdana", 0, 12));
345 resetButton.setLabel(MessageManager.getString("action.reset"));
346 resetButton.addActionListener(this);
347 this.setMenuBar(menuBar1);
348 menu1.setLabel(MessageManager.getString("action.file"));
349 menu2.setLabel(MessageManager.getString("action.view"));
350 calcSettings.setLabel(MessageManager.getString("action.change_params"));
351 labels.setLabel(MessageManager.getString("label.labels"));
352 labels.addItemListener(this);
353 values.setLabel(MessageManager.getString("label.output_values"));
354 values.addActionListener(this);
355 inputData.setLabel(MessageManager.getString("label.input_data"));
356 nuclSetting.setLabel(MessageManager
357 .getString("label.nucleotide_matrix"));
358 nuclSetting.addItemListener(this);
359 protSetting.setLabel(MessageManager.getString("label.protein_matrix"));
360 protSetting.addItemListener(this);
361 this.add(jPanel2, BorderLayout.SOUTH);
362 jPanel2.add(jLabel1, null);
363 jPanel2.add(xCombobox, null);
364 jPanel2.add(jLabel2, null);
365 jPanel2.add(yCombobox, null);
366 jPanel2.add(jLabel3, null);
367 jPanel2.add(zCombobox, null);
368 jPanel2.add(resetButton, null);
371 menuBar1.add(calcSettings);
374 menu1.add(inputData);
375 calcSettings.add(nuclSetting);
376 calcSettings.add(protSetting);
377 inputData.addActionListener(this);