2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
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.util.MessageManager;
26 import jalview.viewmodel.PCAModel;
28 public class PCAPanel extends EmbmenuFrame implements Runnable,
29 ActionListener, ItemListener
39 public PCAPanel(AlignViewport av)
49 for (int i = 1; i < 8; i++)
51 xCombobox.addItem("dim " + i);
52 yCombobox.addItem("dim " + i);
53 zCombobox.addItem("dim " + i);
57 boolean selected = av.getSelectionGroup() != null
58 && av.getSelectionGroup().getSize() > 0;
59 AlignmentView seqstrings = av.getAlignmentView(selected);
60 boolean nucleotide = av.getAlignment().isNucleotide();
64 seqs = av.getAlignment().getSequencesArray();
68 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
70 SeqCigar sq[] = seqstrings.getSequences();
71 int length = sq[0].getWidth();
73 for (int i = 0; i < seqs.length; i++)
75 if (sq[i].getWidth() != length)
78 .println("Sequences must be equal length for PCA analysis");
82 pcaModel = new PCAModel(seqstrings, seqs, nucleotide);
84 rc = new RotatableCanvas(av);
85 embedMenuIfNeeded(rc);
86 add(rc, BorderLayout.CENTER);
88 jalview.bin.JalviewLite.addFrame(this, MessageManager.getString("label.principal_component_analysis"),
91 Thread worker = new Thread(this);
100 // TODO progress indicator
101 calcSettings.setEnabled(false);
102 rc.setEnabled(false);
105 nuclSetting.setState(pcaModel.isNucleotide());
106 protSetting.setState(!pcaModel.isNucleotide());
113 pcaModel.updateRc(rc);
115 top = pcaModel.getTop();
116 } catch (OutOfMemoryError x)
118 System.err.println("Out of memory when calculating PCA.");
121 calcSettings.setEnabled(true);
123 // TODO revert progress indicator
129 void doDimensionChange()
136 int dim1 = top - xCombobox.getSelectedIndex();
137 int dim2 = top - yCombobox.getSelectedIndex();
138 int dim3 = top - zCombobox.getSelectedIndex();
139 pcaModel.updateRcView(dim1, dim2, dim3);
141 rc.rotmat.setIdentity();
143 rc.paint(rc.getGraphics());
146 public void actionPerformed(ActionEvent evt)
148 if (evt.getSource() == inputData)
152 if (evt.getSource() == resetButton)
159 if (evt.getSource() == values)
161 values_actionPerformed();
165 public void itemStateChanged(ItemEvent evt)
167 if (evt.getSource() == xCombobox)
169 xCombobox_actionPerformed();
171 else if (evt.getSource() == yCombobox)
173 yCombobox_actionPerformed();
175 else if (evt.getSource() == zCombobox)
177 zCombobox_actionPerformed();
179 else if (evt.getSource() == labels)
181 labels_itemStateChanged(evt);
183 else if (evt.getSource() == nuclSetting)
185 if (!pcaModel.isNucleotide())
187 pcaModel.setNucleotide(true);
188 new Thread(this).start();
191 else if (evt.getSource() == protSetting)
193 if (pcaModel.isNucleotide())
195 pcaModel.setNucleotide(false);
196 new Thread(this).start();
201 protected void xCombobox_actionPerformed()
206 protected void yCombobox_actionPerformed()
211 protected void zCombobox_actionPerformed()
216 public void values_actionPerformed()
219 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
220 Frame frame = new Frame();
222 jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.pca_details"), 500, 500);
224 cap.setText(pcaModel.getDetails());
227 void showOriginalData()
229 // decide if av alignment is sufficiently different to original data to
230 // warrant a new window to be created
231 // create new alignmnt window with hidden regions (unhiding hidden regions
232 // yields unaligned seqs)
233 // or create a selection box around columns in alignment view
234 // test Alignment(SeqCigar[])
238 // we try to get the associated view's gap character
239 // but this may fail if the view was closed...
240 gc = av.getGapCharacter();
241 } catch (Exception ex)
245 Object[] alAndColsel = pcaModel.getSeqtrings()
246 .getAlignmentAndColumnSelection(gc);
248 if (alAndColsel != null && alAndColsel[0] != null)
250 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
251 AlignFrame af = new AlignFrame(al, av.applet,
252 "Original Data for PCA", false);
254 af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
258 public void labels_itemStateChanged(ItemEvent itemEvent)
260 rc.showLabels(labels.getState());
263 Panel jPanel2 = new Panel();
265 Label jLabel1 = new Label();
267 Label jLabel2 = new Label();
269 Label jLabel3 = new Label();
271 protected Choice xCombobox = new Choice();
273 protected Choice yCombobox = new Choice();
275 protected Choice zCombobox = new Choice();
277 protected Button resetButton = new Button();
279 FlowLayout flowLayout1 = new FlowLayout();
281 BorderLayout borderLayout1 = new BorderLayout();
283 MenuBar menuBar1 = new MenuBar();
285 Menu menu1 = new Menu();
287 Menu menu2 = new Menu();
289 Menu calcSettings = new Menu();
291 protected CheckboxMenuItem labels = new CheckboxMenuItem();
293 protected CheckboxMenuItem protSetting = new CheckboxMenuItem();
295 protected CheckboxMenuItem nuclSetting = new CheckboxMenuItem();
297 MenuItem values = new MenuItem();
299 MenuItem inputData = new MenuItem();
301 private void jbInit() throws Exception
303 this.setLayout(borderLayout1);
304 jPanel2.setLayout(flowLayout1);
305 jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
306 jLabel1.setText("x=");
307 jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));
308 jLabel2.setText("y=");
309 jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));
310 jLabel3.setText("z=");
311 jPanel2.setBackground(Color.white);
312 zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
313 zCombobox.addItemListener(this);
314 yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
315 yCombobox.addItemListener(this);
316 xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
317 xCombobox.addItemListener(this);
318 resetButton.setFont(new java.awt.Font("Verdana", 0, 12));
319 resetButton.setLabel(MessageManager.getString("action.reset"));
320 resetButton.addActionListener(this);
321 this.setMenuBar(menuBar1);
322 menu1.setLabel(MessageManager.getString("action.file"));
323 menu2.setLabel(MessageManager.getString("action.view"));
324 calcSettings.setLabel(MessageManager.getString("action.change_params"));
325 labels.setLabel(MessageManager.getString("label.labels"));
326 labels.addItemListener(this);
327 values.setLabel(MessageManager.getString("label.output_values"));
328 values.addActionListener(this);
329 inputData.setLabel(MessageManager.getString("label.input_data"));
330 nuclSetting.setLabel(MessageManager.getString("label.nucleotide_matrix"));
331 nuclSetting.addItemListener(this);
332 protSetting.setLabel(MessageManager.getString("label.protein_matrix"));
333 protSetting.addItemListener(this);
334 this.add(jPanel2, BorderLayout.SOUTH);
335 jPanel2.add(jLabel1, null);
336 jPanel2.add(xCombobox, null);
337 jPanel2.add(jLabel2, null);
338 jPanel2.add(yCombobox, null);
339 jPanel2.add(jLabel3, null);
340 jPanel2.add(zCombobox, null);
341 jPanel2.add(resetButton, null);
344 menuBar1.add(calcSettings);
347 menu1.add(inputData);
348 calcSettings.add(nuclSetting);
349 calcSettings.add(protSetting);
350 inputData.addActionListener(this);