2 * Jalview - A Sequence Alignment Editor and Viewer
\r
3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
5 * This program is free software; you can redistribute it and/or
\r
6 * modify it under the terms of the GNU General Public License
\r
7 * as published by the Free Software Foundation; either version 2
\r
8 * of the License, or (at your option) any later version.
\r
10 * This program is distributed in the hope that it will be useful,
\r
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
13 * GNU General Public License for more details.
\r
15 * You should have received a copy of the GNU General Public License
\r
16 * along with this program; if not, write to the Free Software
\r
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
19 package jalview.gui;
\r
21 import jalview.analysis.*;
\r
23 import jalview.datamodel.*;
\r
25 import jalview.jbgui.*;
\r
28 import java.awt.event.*;
\r
31 import javax.swing.*;
\r
32 import java.awt.print.*;
\r
39 * @version $Revision$
\r
41 public class PCAPanel extends GPCAPanel implements Runnable
\r
47 AlignmentView seqstrings;
\r
51 * Creates a new PCAPanel object.
\r
53 * @param av DOCUMENT ME!
\r
54 * @param s DOCUMENT ME!
\r
56 public PCAPanel(AlignViewport av)
\r
60 boolean sameLength = true;
\r
62 seqstrings = av.getAlignmentView(av.getSelectionGroup()!=null);
\r
63 if(av.getSelectionGroup()==null)
\r
65 seqs = av.alignment.getSequencesArray();
\r
69 seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
\r
71 SeqCigar sq[]=seqstrings.getSequences();
\r
72 int length = sq[0].getWidth();
\r
74 for (int i = 0; i < seqs.length; i++)
\r
76 if (sq[i].getWidth() != length)
\r
85 JOptionPane.showMessageDialog(Desktop.desktop,
\r
86 "The sequences must be aligned before calculating PCA.\n" +
\r
87 "Try using the Pad function in the edit menu,\n" +
\r
88 "or one of the multiple sequence alignment web services.",
\r
89 "Sequences not aligned",
\r
90 JOptionPane.WARNING_MESSAGE);
\r
96 Desktop.addInternalFrame(this, "Principal component analysis",
\r
100 rc = new RotatableCanvas(av);
\r
101 this.getContentPane().add(rc, BorderLayout.CENTER);
\r
102 Thread worker = new Thread(this);
\r
106 public void bgcolour_actionPerformed(ActionEvent e)
\r
108 Color col = JColorChooser.showDialog(this, "Select Background Colour",
\r
125 pca = new PCA(seqstrings.getSequenceStrings(' '));
\r
128 // Now find the component coordinates
\r
131 while ( (ii < seqs.length) && (seqs[ii] != null))
\r
136 double[][] comps = new double[ii][ii];
\r
138 for (int i = 0; i < ii; i++)
\r
140 if (pca.getEigenvalue(i) > 1e-4)
\r
142 comps[i] = pca.component(i);
\r
147 xCombobox.setSelectedIndex(0);
\r
148 yCombobox.setSelectedIndex(1);
\r
149 zCombobox.setSelectedIndex(2);
\r
151 top = pca.getM().rows - 1;
\r
153 Vector points = new Vector();
\r
154 float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
\r
156 for (int i = 0; i < pca.getM().rows; i++)
\r
158 SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
\r
159 points.addElement(sp);
\r
162 rc.setPoints(points, pca.getM().rows);
\r
165 addKeyListener(rc);
\r
168 catch(OutOfMemoryError er)
\r
169 { JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
170 "Out of memory calculating PCA!!"
\r
172 "\nSee help files for increasing Java Virtual Machine memory."
\r
174 JOptionPane.WARNING_MESSAGE);
\r
175 System.out.println("PCAPanel: "+er);
\r
185 void doDimensionChange()
\r
192 int dim1 = top - xCombobox.getSelectedIndex();
\r
193 int dim2 = top - yCombobox.getSelectedIndex();
\r
194 int dim3 = top - zCombobox.getSelectedIndex();
\r
196 float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);
\r
198 for (int i = 0; i < pca.getM().rows; i++)
\r
200 ((SequencePoint) rc.points.elementAt(i)).coord = scores[i];
\r
204 rc.rotmat.setIdentity();
\r
206 rc.paint(rc.getGraphics());
\r
212 * @param e DOCUMENT ME!
\r
214 protected void xCombobox_actionPerformed(ActionEvent e)
\r
216 doDimensionChange();
\r
222 * @param e DOCUMENT ME!
\r
224 protected void yCombobox_actionPerformed(ActionEvent e)
\r
226 doDimensionChange();
\r
232 * @param e DOCUMENT ME!
\r
234 protected void zCombobox_actionPerformed(ActionEvent e)
\r
236 doDimensionChange();
\r
240 public void outputValues_actionPerformed(ActionEvent e)
\r
242 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
243 Desktop.addInternalFrame(cap, "PCA details", 500,
\r
246 cap.setText(pca.getDetails());
\r
249 public void showLabels_actionPerformed(ActionEvent e)
\r
251 rc.showLabels(showLabels.getState());
\r
254 public void print_actionPerformed(ActionEvent e)
\r
256 PCAPrinter printer = new PCAPrinter();
\r
260 public void originalSeqData_actionPerformed(ActionEvent e)
\r
262 // this was cut'n'pasted from the equivalent TreePanel method - we should make this an abstract function of all jalview analysis windows
\r
263 if (seqstrings==null)
\r
265 jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
\r
268 // decide if av alignment is sufficiently different to original data to warrant a new window to be created
\r
269 // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
\r
270 // or create a selection box around columns in alignment view
\r
271 // test Alignment(SeqCigar[])
\r
272 Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(av.
\r
273 getGapCharacter());
\r
276 if (alAndColsel != null && alAndColsel[0]!=null)
\r
278 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
\r
280 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
\r
281 Alignment dataset = av.getAlignment().getDataset();
\r
282 if (dataset != null)
\r
284 al.setDataset(dataset);
\r
289 // make a new frame!
\r
290 AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],
\r
291 AlignFrame.DEFAULT_WIDTH,
\r
292 AlignFrame.DEFAULT_HEIGHT
\r
295 //>>>This is a fix for the moment, until a better solution is found!!<<<
\r
296 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
\r
298 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
\r
301 Desktop.addInternalFrame(af, "Original Data for " + this.title,
\r
302 AlignFrame.DEFAULT_WIDTH,
\r
303 AlignFrame.DEFAULT_HEIGHT);
\r
306 /* CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
307 for (int i = 0; i < seqs.length; i++)
\r
309 cap.appendText(new jalview.util.Format("%-" + 15 + "s").form(
\r
310 seqs[i].getName()));
\r
311 cap.appendText(" " + seqstrings[i] + "\n");
\r
315 Desktop.addInternalFrame(cap, "Original Data",
\r
322 class PCAPrinter extends Thread implements Printable
\r
326 PrinterJob printJob = PrinterJob.getPrinterJob();
\r
327 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
\r
329 printJob.setPrintable(this, pf);
\r
331 if (printJob.printDialog())
\r
337 catch (Exception PrintException)
\r
339 PrintException.printStackTrace();
\r
344 public int print(Graphics pg, PageFormat pf, int pi)
\r
345 throws PrinterException
\r
347 pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
\r
349 rc.drawBackground(pg, rc.bgColour);
\r
351 if (rc.drawAxes == true)
\r
357 return Printable.PAGE_EXISTS;
\r
359 return Printable.NO_SUCH_PAGE;
\r
368 * @param e DOCUMENT ME!
\r
370 public void eps_actionPerformed(ActionEvent e)
\r
372 makePCAImage(jalview.util.ImageMaker.EPS);
\r
378 * @param e DOCUMENT ME!
\r
380 public void png_actionPerformed(ActionEvent e)
\r
382 makePCAImage(jalview.util.ImageMaker.PNG);
\r
385 void makePCAImage(int type)
\r
387 int width = rc.getWidth();
\r
388 int height = rc.getHeight();
\r
390 jalview.util.ImageMaker im;
\r
392 if(type == jalview.util.ImageMaker.PNG)
\r
393 im = new jalview.util.ImageMaker(this,
\r
394 jalview.util.ImageMaker.PNG,
\r
395 "Make PNG image from PCA",
\r
399 im = new jalview.util.ImageMaker(this,
\r
400 jalview.util.ImageMaker.EPS,
\r
401 "Make EPS file from PCA",
\r
403 null, this.getTitle());
\r
405 if(im.getGraphics()!=null)
\r
407 rc.drawBackground(im.getGraphics(), Color.black);
\r
408 rc.drawScene(im.getGraphics());
\r
409 if (rc.drawAxes == true)
\r
411 rc.drawAxes(im.getGraphics());
\r