2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
3 * Copyright (C) 2014 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 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/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.appletgui;
22 import java.awt.event.*;
24 import jalview.datamodel.*;
25 import jalview.viewmodel.PCAModel;
27 public class PCAPanel extends EmbmenuFrame implements Runnable,
28 ActionListener, ItemListener
38 public PCAPanel(AlignViewport av)
48 for (int i = 1; i < 8; i++)
50 xCombobox.addItem("dim " + i);
51 yCombobox.addItem("dim " + i);
52 zCombobox.addItem("dim " + i);
56 boolean selected = av.getSelectionGroup() != null
57 && av.getSelectionGroup().getSize() > 0;
58 AlignmentView seqstrings = av.getAlignmentView(selected);
59 boolean nucleotide = av.getAlignment().isNucleotide();
63 seqs = av.getAlignment().getSequencesArray();
67 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
69 SeqCigar sq[] = seqstrings.getSequences();
70 int length = sq[0].getWidth();
72 for (int i = 0; i < seqs.length; i++)
74 if (sq[i].getWidth() != length)
77 .println("Sequences must be equal length for PCA analysis");
81 pcaModel = new PCAModel(seqstrings, seqs, nucleotide);
83 rc = new RotatableCanvas(av);
84 embedMenuIfNeeded(rc);
85 add(rc, BorderLayout.CENTER);
87 jalview.bin.JalviewLite.addFrame(this, "Principal component analysis",
90 Thread worker = new Thread(this);
99 // TODO progress indicator
100 calcSettings.setEnabled(false);
101 rc.setEnabled(false);
104 nuclSetting.setState(pcaModel.isNucleotide());
105 protSetting.setState(!pcaModel.isNucleotide());
112 pcaModel.updateRc(rc);
114 top = pcaModel.getTop();
115 } catch (OutOfMemoryError x)
117 System.err.println("Out of memory when calculating PCA.");
120 calcSettings.setEnabled(true);
122 // TODO revert progress indicator
128 void doDimensionChange()
135 int dim1 = top - xCombobox.getSelectedIndex();
136 int dim2 = top - yCombobox.getSelectedIndex();
137 int dim3 = top - zCombobox.getSelectedIndex();
138 pcaModel.updateRcView(dim1, dim2, dim3);
140 rc.rotmat.setIdentity();
142 rc.paint(rc.getGraphics());
145 public void actionPerformed(ActionEvent evt)
147 if (evt.getSource() == inputData)
151 if (evt.getSource() == resetButton)
158 if (evt.getSource() == values)
160 values_actionPerformed();
164 public void itemStateChanged(ItemEvent evt)
166 if (evt.getSource() == xCombobox)
168 xCombobox_actionPerformed();
170 else if (evt.getSource() == yCombobox)
172 yCombobox_actionPerformed();
174 else if (evt.getSource() == zCombobox)
176 zCombobox_actionPerformed();
178 else if (evt.getSource() == labels)
180 labels_itemStateChanged(evt);
182 else if (evt.getSource() == nuclSetting)
184 if (!pcaModel.isNucleotide())
186 pcaModel.setNucleotide(true);
187 new Thread(this).start();
190 else if (evt.getSource() == protSetting)
192 if (pcaModel.isNucleotide())
194 pcaModel.setNucleotide(false);
195 new Thread(this).start();
200 protected void xCombobox_actionPerformed()
205 protected void yCombobox_actionPerformed()
210 protected void zCombobox_actionPerformed()
215 public void values_actionPerformed()
218 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
219 Frame frame = new Frame();
221 jalview.bin.JalviewLite.addFrame(frame, "PCA details", 500, 500);
223 cap.setText(pcaModel.getDetails());
226 void showOriginalData()
228 // decide if av alignment is sufficiently different to original data to
229 // warrant a new window to be created
230 // create new alignmnt window with hidden regions (unhiding hidden regions
231 // yields unaligned seqs)
232 // or create a selection box around columns in alignment view
233 // test Alignment(SeqCigar[])
237 // we try to get the associated view's gap character
238 // but this may fail if the view was closed...
239 gc = av.getGapCharacter();
240 } catch (Exception ex)
244 Object[] alAndColsel = pcaModel.getSeqtrings()
245 .getAlignmentAndColumnSelection(gc);
247 if (alAndColsel != null && alAndColsel[0] != null)
249 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
250 AlignFrame af = new AlignFrame(al, av.applet,
251 "Original Data for PCA", false);
253 af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
257 public void labels_itemStateChanged(ItemEvent itemEvent)
259 rc.showLabels(labels.getState());
262 Panel jPanel2 = new Panel();
264 Label jLabel1 = new Label();
266 Label jLabel2 = new Label();
268 Label jLabel3 = new Label();
270 protected Choice xCombobox = new Choice();
272 protected Choice yCombobox = new Choice();
274 protected Choice zCombobox = new Choice();
276 protected Button resetButton = new Button();
278 FlowLayout flowLayout1 = new FlowLayout();
280 BorderLayout borderLayout1 = new BorderLayout();
282 MenuBar menuBar1 = new MenuBar();
284 Menu menu1 = new Menu();
286 Menu menu2 = new Menu();
288 Menu calcSettings = new Menu();
290 protected CheckboxMenuItem labels = new CheckboxMenuItem();
292 protected CheckboxMenuItem protSetting = new CheckboxMenuItem();
294 protected CheckboxMenuItem nuclSetting = new CheckboxMenuItem();
296 MenuItem values = new MenuItem();
298 MenuItem inputData = new MenuItem();
300 private void jbInit() throws Exception
302 this.setLayout(borderLayout1);
303 jPanel2.setLayout(flowLayout1);
304 jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
305 jLabel1.setText("x=");
306 jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));
307 jLabel2.setText("y=");
308 jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));
309 jLabel3.setText("z=");
310 jPanel2.setBackground(Color.white);
311 zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
312 zCombobox.addItemListener(this);
313 yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
314 yCombobox.addItemListener(this);
315 xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
316 xCombobox.addItemListener(this);
317 resetButton.setFont(new java.awt.Font("Verdana", 0, 12));
318 resetButton.setLabel("Reset");
319 resetButton.addActionListener(this);
320 this.setMenuBar(menuBar1);
321 menu1.setLabel("File");
322 menu2.setLabel("View");
323 calcSettings.setLabel("Change Parameters");
324 labels.setLabel("Labels");
325 labels.addItemListener(this);
326 values.setLabel("Output Values...");
327 values.addActionListener(this);
328 inputData.setLabel("Input Data...");
329 nuclSetting.setLabel("Nucleotide matrix");
330 nuclSetting.addItemListener(this);
331 protSetting.setLabel("Protein matrix");
332 protSetting.addItemListener(this);
333 this.add(jPanel2, BorderLayout.SOUTH);
334 jPanel2.add(jLabel1, null);
335 jPanel2.add(xCombobox, null);
336 jPanel2.add(jLabel2, null);
337 jPanel2.add(yCombobox, null);
338 jPanel2.add(jLabel3, null);
339 jPanel2.add(zCombobox, null);
340 jPanel2.add(resetButton, null);
343 menuBar1.add(calcSettings);
346 menu1.add(inputData);
347 calcSettings.add(nuclSetting);
348 calcSettings.add(protSetting);
349 inputData.addActionListener(this);