2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, 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.*;
28 public class PCAPanel extends EmbmenuFrame implements Runnable,
29 ActionListener, ItemListener
39 AlignmentView seqstrings;
45 * use the identity matrix for calculating similarity between sequences.
47 private boolean useidentity=false;
50 public PCAPanel(AlignViewport av)
60 for (int i = 1; i < 8; i++)
62 xCombobox.addItem("dim " + i);
63 yCombobox.addItem("dim " + i);
64 zCombobox.addItem("dim " + i);
68 seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
69 useidentity=av.getAlignment().isNucleotide();
70 if (av.getSelectionGroup() == null)
72 seqs = av.alignment.getSequencesArray();
76 seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
78 SeqCigar sq[] = seqstrings.getSequences();
79 int length = sq[0].getWidth();
81 for (int i = 0; i < seqs.length; i++)
83 if (sq[i].getWidth() != length)
86 .println("Sequences must be equal length for PCA analysis");
91 rc = new RotatableCanvas(av);
92 embedMenuIfNeeded(rc);
93 add(rc, BorderLayout.CENTER);
95 jalview.bin.JalviewLite.addFrame(this, "Principal component analysis",
98 Thread worker = new Thread(this);
107 pca = new PCA(seqstrings.getSequenceStrings(' '), useidentity);
110 // Now find the component coordinates
113 while ((ii < seqs.length) && (seqs[ii] != null))
118 double[][] comps = new double[ii][ii];
120 for (int i = 0; i < ii; i++)
122 if (pca.getEigenvalue(i) > 1e-4)
124 comps[i] = pca.component(i);
133 top = pca.getM().rows - 1;
135 Vector points = new Vector();
136 float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
138 for (int i = 0; i < pca.getM().rows; i++)
140 SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
141 points.addElement(sp);
144 rc.setPoints(points, pca.getM().rows);
150 void doDimensionChange()
157 int dim1 = top - xCombobox.getSelectedIndex();
158 int dim2 = top - yCombobox.getSelectedIndex();
159 int dim3 = top - zCombobox.getSelectedIndex();
161 float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);
162 for (int i = 0; i < pca.getM().rows; i++)
164 ((SequencePoint) rc.points.elementAt(i)).coord = scores[i];
168 rc.rotmat.setIdentity();
170 rc.paint(rc.getGraphics());
173 public void actionPerformed(ActionEvent evt)
175 if (evt.getSource() == inputData)
181 values_actionPerformed();
185 public void itemStateChanged(ItemEvent evt)
187 if (evt.getSource() == xCombobox)
189 xCombobox_actionPerformed();
191 else if (evt.getSource() == yCombobox)
193 yCombobox_actionPerformed();
195 else if (evt.getSource() == zCombobox)
197 zCombobox_actionPerformed();
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, "PCA details", 500, 500);
224 cap.setText(pca.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 = seqstrings.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 FlowLayout flowLayout1 = new FlowLayout();
278 BorderLayout borderLayout1 = new BorderLayout();
280 MenuBar menuBar1 = new MenuBar();
282 Menu menu1 = new Menu();
284 Menu menu2 = new Menu();
286 protected CheckboxMenuItem labels = new CheckboxMenuItem();
288 MenuItem values = new MenuItem();
290 MenuItem inputData = new MenuItem();
292 private void jbInit() throws Exception
294 this.setLayout(borderLayout1);
295 jPanel2.setLayout(flowLayout1);
296 jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
297 jLabel1.setText("x=");
298 jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));
299 jLabel2.setText("y=");
300 jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));
301 jLabel3.setText("z=");
302 jPanel2.setBackground(Color.white);
303 zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
304 zCombobox.addItemListener(this);
305 yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
306 yCombobox.addItemListener(this);
307 xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
308 xCombobox.addItemListener(this);
309 this.setMenuBar(menuBar1);
310 menu1.setLabel("File");
311 menu2.setLabel("View");
312 labels.setLabel("Labels");
313 labels.addItemListener(this);
314 values.setLabel("Output Values...");
315 values.addActionListener(this);
316 inputData.setLabel("Input Data...");
317 this.add(jPanel2, BorderLayout.SOUTH);
318 jPanel2.add(jLabel1, null);
319 jPanel2.add(xCombobox, null);
320 jPanel2.add(jLabel2, null);
321 jPanel2.add(yCombobox, null);
322 jPanel2.add(jLabel3, null);
323 jPanel2.add(zCombobox, null);
328 menu1.add(inputData);
329 inputData.addActionListener(this);