2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
20 package jalview.appletgui;
25 import java.awt.event.*;
27 import jalview.analysis.*;
28 import jalview.datamodel.*;
31 extends EmbmenuFrame implements Runnable, ActionListener, ItemListener
38 AlignmentView seqstrings;
40 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 seqstrings = av.getAlignmentView(av.getSelectionGroup() != null);
60 if (av.getSelectionGroup() == null)
62 seqs = av.alignment.getSequencesArray();
66 seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
68 SeqCigar sq[] = seqstrings.getSequences();
69 int length = sq[0].getWidth();
71 for (int i = 0; i < seqs.length; i++)
73 if (sq[i].getWidth() != length)
75 System.out.println("Sequences must be equal length for PCA analysis");
80 rc = new RotatableCanvas(av);
81 embedMenuIfNeeded(rc);
82 add(rc, BorderLayout.CENTER);
84 jalview.bin.JalviewLite.addFrame(this, "Principal component analysis",
87 Thread worker = new Thread(this);
96 pca = new PCA(seqstrings.getSequenceStrings(' '));
99 // Now find the component coordinates
102 while ( (ii < seqs.length) && (seqs[ii] != null))
107 double[][] comps = new double[ii][ii];
109 for (int i = 0; i < ii; i++)
111 if (pca.getEigenvalue(i) > 1e-4)
113 comps[i] = pca.component(i);
122 top = pca.getM().rows - 1;
124 Vector points = new Vector();
125 float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
127 for (int i = 0; i < pca.getM().rows; i++)
129 SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
130 points.addElement(sp);
133 rc.setPoints(points, pca.getM().rows);
139 void doDimensionChange()
146 int dim1 = top - xCombobox.getSelectedIndex();
147 int dim2 = top - yCombobox.getSelectedIndex();
148 int dim3 = top - zCombobox.getSelectedIndex();
150 float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);
151 for (int i = 0; i < pca.getM().rows; i++)
153 ( (SequencePoint) rc.points.elementAt(i)).coord = scores[i];
157 rc.rotmat.setIdentity();
159 rc.paint(rc.getGraphics());
162 public void actionPerformed(ActionEvent evt)
164 if (evt.getSource() == inputData)
170 values_actionPerformed();
174 public void itemStateChanged(ItemEvent evt)
176 if (evt.getSource() == xCombobox)
178 xCombobox_actionPerformed();
180 else if (evt.getSource() == yCombobox)
182 yCombobox_actionPerformed();
184 else if (evt.getSource() == zCombobox)
186 zCombobox_actionPerformed();
190 protected void xCombobox_actionPerformed()
195 protected void yCombobox_actionPerformed()
200 protected void zCombobox_actionPerformed()
205 public void values_actionPerformed()
208 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
209 Frame frame = new Frame();
211 jalview.bin.JalviewLite.addFrame(frame, "PCA details", 500, 500);
213 cap.setText(pca.getDetails());
216 void showOriginalData()
218 // decide if av alignment is sufficiently different to original data to warrant a new window to be created
219 // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
220 // or create a selection box around columns in alignment view
221 // test Alignment(SeqCigar[])
222 Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(av.
225 if (alAndColsel != null && alAndColsel[0] != null)
227 Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);
228 AlignFrame af = new AlignFrame(al,
230 "Original Data for PCA",
233 af.viewport.setHiddenColumns( (ColumnSelection) alAndColsel[1]);
237 public void labels_itemStateChanged(ItemEvent itemEvent)
239 rc.showLabels(labels.getState());
242 Panel jPanel2 = new Panel();
243 Label jLabel1 = new Label();
244 Label jLabel2 = new Label();
245 Label jLabel3 = new Label();
246 protected Choice xCombobox = new Choice();
247 protected Choice yCombobox = new Choice();
248 protected Choice zCombobox = new Choice();
249 FlowLayout flowLayout1 = new FlowLayout();
250 BorderLayout borderLayout1 = new BorderLayout();
251 MenuBar menuBar1 = new MenuBar();
252 Menu menu1 = new Menu();
253 Menu menu2 = new Menu();
254 protected CheckboxMenuItem labels = new CheckboxMenuItem();
255 MenuItem values = new MenuItem();
256 MenuItem inputData = new MenuItem();
258 private void jbInit()
261 this.setLayout(borderLayout1);
262 jPanel2.setLayout(flowLayout1);
263 jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
264 jLabel1.setText("x=");
265 jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));
266 jLabel2.setText("y=");
267 jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));
268 jLabel3.setText("z=");
269 jPanel2.setBackground(Color.white);
270 zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
271 zCombobox.addItemListener(this);
272 yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
273 yCombobox.addItemListener(this);
274 xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
275 xCombobox.addItemListener(this);
276 this.setMenuBar(menuBar1);
277 menu1.setLabel("File");
278 menu2.setLabel("View");
279 labels.setLabel("Labels");
280 labels.addItemListener(this);
281 values.setLabel("Output Values...");
282 values.addActionListener(this);
283 inputData.setLabel("Input Data...");
284 this.add(jPanel2, BorderLayout.SOUTH);
285 jPanel2.add(jLabel1, null);
286 jPanel2.add(xCombobox, null);
287 jPanel2.add(jLabel2, null);
288 jPanel2.add(yCombobox, null);
289 jPanel2.add(jLabel3, null);
290 jPanel2.add(zCombobox, null);
295 menu1.add(inputData);
296 inputData.addActionListener(this);