2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
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
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;
24 import java.awt.event.*;
26 import jalview.datamodel.*;
27 import jalview.util.MessageManager;
28 import jalview.viewmodel.PCAModel;
30 public class PCAPanel extends EmbmenuFrame implements Runnable,
31 ActionListener, ItemListener
41 public PCAPanel(AlignViewport av)
51 for (int i = 1; i < 8; i++)
53 xCombobox.addItem("dim " + i);
54 yCombobox.addItem("dim " + i);
55 zCombobox.addItem("dim " + i);
59 boolean selected = av.getSelectionGroup() != null
60 && av.getSelectionGroup().getSize() > 0;
61 AlignmentView seqstrings = av.getAlignmentView(selected);
62 boolean nucleotide = av.getAlignment().isNucleotide();
66 seqs = av.getAlignment().getSequencesArray();
70 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
72 SeqCigar sq[] = seqstrings.getSequences();
73 int length = sq[0].getWidth();
75 for (int i = 0; i < seqs.length; i++)
77 if (sq[i].getWidth() != length)
80 .println("Sequences must be equal length for PCA analysis");
84 pcaModel = new PCAModel(seqstrings, seqs, nucleotide);
86 rc = new RotatableCanvas(av);
87 embedMenuIfNeeded(rc);
88 add(rc, BorderLayout.CENTER);
90 jalview.bin.JalviewLite.addFrame(this, MessageManager.getString("label.principal_component_analysis"),
93 Thread worker = new Thread(this);
102 // TODO progress indicator
103 calcSettings.setEnabled(false);
104 rc.setEnabled(false);
107 nuclSetting.setState(pcaModel.isNucleotide());
108 protSetting.setState(!pcaModel.isNucleotide());
115 pcaModel.updateRc(rc);
117 top = pcaModel.getTop();
118 } catch (OutOfMemoryError x)
120 System.err.println("Out of memory when calculating PCA.");
123 calcSettings.setEnabled(true);
125 // TODO revert progress indicator
131 void doDimensionChange()
138 int dim1 = top - xCombobox.getSelectedIndex();
139 int dim2 = top - yCombobox.getSelectedIndex();
140 int dim3 = top - zCombobox.getSelectedIndex();
141 pcaModel.updateRcView(dim1, dim2, dim3);
143 rc.rotmat.setIdentity();
145 rc.paint(rc.getGraphics());
148 public void actionPerformed(ActionEvent evt)
150 if (evt.getSource() == inputData)
154 if (evt.getSource() == resetButton)
161 if (evt.getSource() == values)
163 values_actionPerformed();
167 public void itemStateChanged(ItemEvent evt)
169 if (evt.getSource() == xCombobox)
171 xCombobox_actionPerformed();
173 else if (evt.getSource() == yCombobox)
175 yCombobox_actionPerformed();
177 else if (evt.getSource() == zCombobox)
179 zCombobox_actionPerformed();
181 else if (evt.getSource() == labels)
183 labels_itemStateChanged(evt);
185 else if (evt.getSource() == nuclSetting)
187 if (!pcaModel.isNucleotide())
189 pcaModel.setNucleotide(true);
190 new Thread(this).start();
193 else if (evt.getSource() == protSetting)
195 if (pcaModel.isNucleotide())
197 pcaModel.setNucleotide(false);
198 new Thread(this).start();
203 protected void xCombobox_actionPerformed()
208 protected void yCombobox_actionPerformed()
213 protected void zCombobox_actionPerformed()
218 public void values_actionPerformed()
221 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
222 Frame frame = new Frame();
224 jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.pca_details"), 500, 500);
226 cap.setText(pcaModel.getDetails());
229 void showOriginalData()
231 // decide if av alignment is sufficiently different to original data to
232 // warrant a new window to be created
233 // create new alignmnt window with hidden regions (unhiding hidden regions
234 // yields unaligned seqs)
235 // or create a selection box around columns in alignment view
236 // test Alignment(SeqCigar[])
240 // we try to get the associated view's gap character
241 // but this may fail if the view was closed...
242 gc = av.getGapCharacter();
243 } catch (Exception ex)
247 Object[] alAndColsel = pcaModel.getSeqtrings()
248 .getAlignmentAndColumnSelection(gc);
250 if (alAndColsel != null && alAndColsel[0] != null)
252 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
253 AlignFrame af = new AlignFrame(al, av.applet,
254 "Original Data for PCA", false);
256 af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
260 public void labels_itemStateChanged(ItemEvent itemEvent)
262 rc.showLabels(labels.getState());
265 Panel jPanel2 = new Panel();
267 Label jLabel1 = new Label();
269 Label jLabel2 = new Label();
271 Label jLabel3 = new Label();
273 protected Choice xCombobox = new Choice();
275 protected Choice yCombobox = new Choice();
277 protected Choice zCombobox = new Choice();
279 protected Button resetButton = new Button();
281 FlowLayout flowLayout1 = new FlowLayout();
283 BorderLayout borderLayout1 = new BorderLayout();
285 MenuBar menuBar1 = new MenuBar();
287 Menu menu1 = new Menu();
289 Menu menu2 = new Menu();
291 Menu calcSettings = new Menu();
293 protected CheckboxMenuItem labels = new CheckboxMenuItem();
295 protected CheckboxMenuItem protSetting = new CheckboxMenuItem();
297 protected CheckboxMenuItem nuclSetting = new CheckboxMenuItem();
299 MenuItem values = new MenuItem();
301 MenuItem inputData = new MenuItem();
303 private void jbInit() throws Exception
305 this.setLayout(borderLayout1);
306 jPanel2.setLayout(flowLayout1);
307 jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
308 jLabel1.setText("x=");
309 jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));
310 jLabel2.setText("y=");
311 jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));
312 jLabel3.setText("z=");
313 jPanel2.setBackground(Color.white);
314 zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
315 zCombobox.addItemListener(this);
316 yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
317 yCombobox.addItemListener(this);
318 xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
319 xCombobox.addItemListener(this);
320 resetButton.setFont(new java.awt.Font("Verdana", 0, 12));
321 resetButton.setLabel(MessageManager.getString("action.reset"));
322 resetButton.addActionListener(this);
323 this.setMenuBar(menuBar1);
324 menu1.setLabel(MessageManager.getString("action.file"));
325 menu2.setLabel(MessageManager.getString("action.view"));
326 calcSettings.setLabel(MessageManager.getString("action.change_params"));
327 labels.setLabel(MessageManager.getString("label.labels"));
328 labels.addItemListener(this);
329 values.setLabel(MessageManager.getString("label.output_values"));
330 values.addActionListener(this);
331 inputData.setLabel(MessageManager.getString("label.input_data"));
332 nuclSetting.setLabel(MessageManager.getString("label.nucleotide_matrix"));
333 nuclSetting.addItemListener(this);
334 protSetting.setLabel(MessageManager.getString("label.protein_matrix"));
335 protSetting.addItemListener(this);
336 this.add(jPanel2, BorderLayout.SOUTH);
337 jPanel2.add(jLabel1, null);
338 jPanel2.add(xCombobox, null);
339 jPanel2.add(jLabel2, null);
340 jPanel2.add(yCombobox, null);
341 jPanel2.add(jLabel3, null);
342 jPanel2.add(zCombobox, null);
343 jPanel2.add(resetButton, null);
346 menuBar1.add(calcSettings);
349 menu1.add(inputData);
350 calcSettings.add(nuclSetting);
351 calcSettings.add(protSetting);
352 inputData.addActionListener(this);