2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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;
23 import java.awt.event.*;
25 import jalview.analysis.*;
26 import jalview.datamodel.*;
27 import jalview.viewmodel.PCAModel;
29 public class PCAPanel extends EmbmenuFrame implements Runnable,
30 ActionListener, ItemListener
40 public PCAPanel(AlignViewport av)
50 for (int i = 1; i < 8; i++)
52 xCombobox.addItem("dim " + i);
53 yCombobox.addItem("dim " + i);
54 zCombobox.addItem("dim " + i);
58 boolean selected = av.getSelectionGroup() != null
59 && av.getSelectionGroup().getSize() > 0;
60 AlignmentView seqstrings = av.getAlignmentView(selected);
61 boolean nucleotide = av.getAlignment().isNucleotide();
65 seqs = av.getAlignment().getSequencesArray();
69 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
71 SeqCigar sq[] = seqstrings.getSequences();
72 int length = sq[0].getWidth();
74 for (int i = 0; i < seqs.length; i++)
76 if (sq[i].getWidth() != length)
79 .println("Sequences must be equal length for PCA analysis");
83 pcaModel = new PCAModel(seqstrings, seqs, nucleotide);
85 rc = new RotatableCanvas(av);
86 embedMenuIfNeeded(rc);
87 add(rc, BorderLayout.CENTER);
89 jalview.bin.JalviewLite.addFrame(this, "Principal component analysis",
92 Thread worker = new Thread(this);
101 // TODO progress indicator
102 calcSettings.setEnabled(false);
103 rc.setEnabled(false);
106 nuclSetting.setState(pcaModel.isNucleotide());
107 protSetting.setState(!pcaModel.isNucleotide());
114 pcaModel.updateRc(rc);
116 top = pcaModel.getTop();
117 } catch (OutOfMemoryError x)
119 System.err.println("Out of memory when calculating PCA.");
122 calcSettings.setEnabled(true);
124 // TODO revert progress indicator
130 void doDimensionChange()
137 int dim1 = top - xCombobox.getSelectedIndex();
138 int dim2 = top - yCombobox.getSelectedIndex();
139 int dim3 = top - zCombobox.getSelectedIndex();
140 pcaModel.updateRcView(dim1, dim2, dim3);
142 rc.rotmat.setIdentity();
144 rc.paint(rc.getGraphics());
147 public void actionPerformed(ActionEvent evt)
149 if (evt.getSource() == inputData)
153 if (evt.getSource() == resetButton)
160 if (evt.getSource() == values)
162 values_actionPerformed();
166 public void itemStateChanged(ItemEvent evt)
168 if (evt.getSource() == xCombobox)
170 xCombobox_actionPerformed();
172 else if (evt.getSource() == yCombobox)
174 yCombobox_actionPerformed();
176 else if (evt.getSource() == zCombobox)
178 zCombobox_actionPerformed();
180 else if (evt.getSource() == labels)
182 labels_itemStateChanged(evt);
184 else if (evt.getSource() == nuclSetting)
186 if (!pcaModel.isNucleotide())
188 pcaModel.setNucleotide(true);
189 new Thread(this).start();
192 else if (evt.getSource() == protSetting)
194 if (pcaModel.isNucleotide())
196 pcaModel.setNucleotide(false);
197 new Thread(this).start();
202 protected void xCombobox_actionPerformed()
207 protected void yCombobox_actionPerformed()
212 protected void zCombobox_actionPerformed()
217 public void values_actionPerformed()
220 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
221 Frame frame = new Frame();
223 jalview.bin.JalviewLite.addFrame(frame, "PCA details", 500, 500);
225 cap.setText(pcaModel.getDetails());
228 void showOriginalData()
230 // decide if av alignment is sufficiently different to original data to
231 // warrant a new window to be created
232 // create new alignmnt window with hidden regions (unhiding hidden regions
233 // yields unaligned seqs)
234 // or create a selection box around columns in alignment view
235 // test Alignment(SeqCigar[])
239 // we try to get the associated view's gap character
240 // but this may fail if the view was closed...
241 gc = av.getGapCharacter();
242 } catch (Exception ex)
246 Object[] alAndColsel = pcaModel.getSeqtrings()
247 .getAlignmentAndColumnSelection(gc);
249 if (alAndColsel != null && alAndColsel[0] != null)
251 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
252 AlignFrame af = new AlignFrame(al, av.applet,
253 "Original Data for PCA", false);
255 af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
259 public void labels_itemStateChanged(ItemEvent itemEvent)
261 rc.showLabels(labels.getState());
264 Panel jPanel2 = new Panel();
266 Label jLabel1 = new Label();
268 Label jLabel2 = new Label();
270 Label jLabel3 = new Label();
272 protected Choice xCombobox = new Choice();
274 protected Choice yCombobox = new Choice();
276 protected Choice zCombobox = new Choice();
278 protected Button resetButton = new Button();
280 FlowLayout flowLayout1 = new FlowLayout();
282 BorderLayout borderLayout1 = new BorderLayout();
284 MenuBar menuBar1 = new MenuBar();
286 Menu menu1 = new Menu();
288 Menu menu2 = new Menu();
290 Menu calcSettings = new Menu();
292 protected CheckboxMenuItem labels = new CheckboxMenuItem();
294 protected CheckboxMenuItem protSetting = new CheckboxMenuItem();
296 protected CheckboxMenuItem nuclSetting = new CheckboxMenuItem();
298 MenuItem values = new MenuItem();
300 MenuItem inputData = new MenuItem();
302 private void jbInit() throws Exception
304 this.setLayout(borderLayout1);
305 jPanel2.setLayout(flowLayout1);
306 jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
307 jLabel1.setText("x=");
308 jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));
309 jLabel2.setText("y=");
310 jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));
311 jLabel3.setText("z=");
312 jPanel2.setBackground(Color.white);
313 zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
314 zCombobox.addItemListener(this);
315 yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
316 yCombobox.addItemListener(this);
317 xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
318 xCombobox.addItemListener(this);
319 resetButton.setFont(new java.awt.Font("Verdana", 0, 12));
320 resetButton.setLabel("Reset");
321 resetButton.addActionListener(this);
322 this.setMenuBar(menuBar1);
323 menu1.setLabel("File");
324 menu2.setLabel("View");
325 calcSettings.setLabel("Change Parameters");
326 labels.setLabel("Labels");
327 labels.addItemListener(this);
328 values.setLabel("Output Values...");
329 values.addActionListener(this);
330 inputData.setLabel("Input Data...");
331 nuclSetting.setLabel("Nucleotide matrix");
332 nuclSetting.addItemListener(this);
333 protSetting.setLabel("Protein matrix");
334 protSetting.addItemListener(this);
335 this.add(jPanel2, BorderLayout.SOUTH);
336 jPanel2.add(jLabel1, null);
337 jPanel2.add(xCombobox, null);
338 jPanel2.add(jLabel2, null);
339 jPanel2.add(yCombobox, null);
340 jPanel2.add(jLabel3, null);
341 jPanel2.add(zCombobox, null);
342 jPanel2.add(resetButton, null);
345 menuBar1.add(calcSettings);
348 menu1.add(inputData);
349 calcSettings.add(nuclSetting);
350 calcSettings.add(protSetting);
351 inputData.addActionListener(this);