2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ 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.
23 import jalview.analysis.scoremodels.ScoreModels;
24 import jalview.api.analysis.ScoreModelI;
25 import jalview.api.analysis.SimilarityParamsI;
26 import jalview.datamodel.Alignment;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.AlignmentView;
29 import jalview.datamodel.HiddenColumns;
30 import jalview.datamodel.SequenceI;
31 import jalview.jbgui.GPCAPanel;
32 import jalview.util.ImageMaker;
33 import jalview.util.MessageManager;
34 import jalview.viewmodel.AlignmentViewport;
35 import jalview.viewmodel.PCAModel;
37 import java.awt.BorderLayout;
38 import java.awt.Color;
39 import java.awt.Dimension;
40 import java.awt.Graphics;
41 import java.awt.event.ActionEvent;
42 import java.awt.event.ActionListener;
43 import java.awt.print.PageFormat;
44 import java.awt.print.Printable;
45 import java.awt.print.PrinterException;
46 import java.awt.print.PrinterJob;
48 import javax.swing.ButtonGroup;
49 import javax.swing.JColorChooser;
50 import javax.swing.JMenuItem;
51 import javax.swing.JRadioButtonMenuItem;
52 import javax.swing.event.InternalFrameAdapter;
53 import javax.swing.event.InternalFrameEvent;
56 * The panel holding the Principal Component Analysis 3-d visualisation
58 public class PCAPanel extends GPCAPanel
59 implements Runnable, IProgressIndicator
71 private static final int MIN_WIDTH = 470;
73 private static final int MIN_HEIGHT = 250;
75 private IProgressIndicator progressBar;
77 private boolean working;
80 * Constructor given sequence data, a similarity (or distance) score model
81 * name, and score calculation parameters
87 public PCAPanel(AlignmentPanel alignPanel, String modelName,
88 SimilarityParamsI params)
91 this.av = alignPanel.av;
93 boolean nucleotide = av.getAlignment().isNucleotide();
95 progressBar = new ProgressBar(statusPanel, statusBar);
97 addInternalFrameListener(new InternalFrameAdapter()
100 public void internalFrameClosed(InternalFrameEvent e)
102 close_actionPerformed();
106 boolean selected = av.getSelectionGroup() != null
107 && av.getSelectionGroup().getSize() > 0;
108 AlignmentView seqstrings = av.getAlignmentView(selected);
112 seqs = av.getAlignment().getSequencesArray();
116 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
119 ScoreModelI scoreModel = ScoreModels.getInstance()
120 .getScoreModel(modelName, ap);
121 pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
123 PaintRefresher.Register(this, av.getSequenceSetId());
125 rc = new RotatableCanvas(alignPanel);
126 this.getContentPane().add(rc, BorderLayout.CENTER);
129 * perform calculation in a new Thread
131 Thread worker = new Thread(this);
136 * Ensure references to potentially very large objects (the PCA matrices) are
137 * nulled when the frame is closed
139 protected void close_actionPerformed()
145 protected void bgcolour_actionPerformed()
147 Color col = JColorChooser.showDialog(this,
148 MessageManager.getString("label.select_background_colour"),
159 * Calculates the PCA and displays the results
164 long progId = System.currentTimeMillis();
165 IProgressIndicator progress = this;
166 String message = MessageManager.getString("label.pca_recalculating");
167 if (getParent() == null)
169 progress = ap.alignFrame;
170 message = MessageManager.getString("label.pca_calculating");
172 progress.setProgressBar(message, progId);
176 pcaModel.calculate();
178 xCombobox.setSelectedIndex(0);
179 yCombobox.setSelectedIndex(1);
180 zCombobox.setSelectedIndex(2);
182 pcaModel.updateRc(rc);
184 top = pcaModel.getTop();
186 } catch (OutOfMemoryError er)
188 new OOMWarning("calculating PCA", er);
193 progress.setProgressBar("", progId);
197 if (getParent() == null)
200 Desktop.addInternalFrame(this,
201 MessageManager.formatMessage("label.calc_title", "PCA",
202 pcaModel.getScoreModelName()),
204 this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
210 * Updates the PCA display after a change of component to use for x, y or z
214 protected void doDimensionChange()
221 int dim1 = top - xCombobox.getSelectedIndex();
222 int dim2 = top - yCombobox.getSelectedIndex();
223 int dim3 = top - zCombobox.getSelectedIndex();
224 pcaModel.updateRcView(dim1, dim2, dim3);
226 rc.paint(rc.getGraphics());
230 protected void outputValues_actionPerformed()
232 CutAndPasteTransfer cap = new CutAndPasteTransfer();
235 cap.setText(pcaModel.getDetails());
236 Desktop.addInternalFrame(cap,
237 MessageManager.getString("label.pca_details"), 500, 500);
238 } catch (OutOfMemoryError oom)
240 new OOMWarning("opening PCA details", oom);
246 protected void showLabels_actionPerformed()
248 rc.showLabels(showLabels.getState());
252 protected void print_actionPerformed()
254 PCAPrinter printer = new PCAPrinter();
259 public void originalSeqData_actionPerformed()
261 // this was cut'n'pasted from the equivalent TreePanel method - we should
262 // make this an abstract function of all jalview analysis windows
263 if (pcaModel.getSeqtrings() == null)
265 jalview.bin.Cache.log.info(
266 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
269 // decide if av alignment is sufficiently different to original data to
270 // warrant a new window to be created
271 // create new alignmnt window with hidden regions (unhiding hidden regions
272 // yields unaligned seqs)
273 // or create a selection box around columns in alignment view
274 // test Alignment(SeqCigar[])
278 // we try to get the associated view's gap character
279 // but this may fail if the view was closed...
280 gc = av.getGapCharacter();
281 } catch (Exception ex)
285 Object[] alAndColsel = pcaModel.getSeqtrings()
286 .getAlignmentAndHiddenColumns(gc);
288 if (alAndColsel != null && alAndColsel[0] != null)
290 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
292 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
293 AlignmentI dataset = (av != null && av.getAlignment() != null)
294 ? av.getAlignment().getDataset()
298 al.setDataset(dataset);
304 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
305 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
307 // >>>This is a fix for the moment, until a better solution is
309 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
311 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
314 Desktop.addInternalFrame(af, MessageManager.formatMessage(
315 "label.original_data_for_params", new String[]
316 { this.title }), AlignFrame.DEFAULT_WIDTH,
317 AlignFrame.DEFAULT_HEIGHT);
321 * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
322 * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
323 * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
326 * Desktop.addInternalFrame(cap, "Original Data", 400, 400);
330 class PCAPrinter extends Thread implements Printable
335 PrinterJob printJob = PrinterJob.getPrinterJob();
336 PageFormat defaultPage = printJob.defaultPage();
337 PageFormat pf = printJob.pageDialog(defaultPage);
339 if (defaultPage == pf)
347 printJob.setPrintable(this, pf);
349 if (printJob.printDialog())
354 } catch (Exception PrintException)
356 PrintException.printStackTrace();
362 public int print(Graphics pg, PageFormat pf, int pi)
363 throws PrinterException
365 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
367 rc.drawBackground(pg, rc.bgColour);
376 return Printable.PAGE_EXISTS;
380 return Printable.NO_SUCH_PAGE;
386 * Handler for 'Save as EPS' option
389 protected void eps_actionPerformed()
391 makePCAImage(ImageMaker.TYPE.EPS);
395 * Handler for 'Save as PNG' option
398 protected void png_actionPerformed()
400 makePCAImage(ImageMaker.TYPE.PNG);
403 void makePCAImage(ImageMaker.TYPE type)
405 int width = rc.getWidth();
406 int height = rc.getHeight();
410 if (type == ImageMaker.TYPE.PNG)
412 im = new ImageMaker(this, ImageMaker.TYPE.PNG,
413 "Make PNG image from PCA", width, height, null, null, null, 0,
416 else if (type == jalview.util.ImageMaker.TYPE.EPS)
418 im = new ImageMaker(this, ImageMaker.TYPE.EPS,
419 "Make EPS file from PCA", width, height, null,
420 this.getTitle(), null, 0, false);
424 im = new ImageMaker(this, ImageMaker.TYPE.SVG,
425 "Make SVG file from PCA", width, height, null,
426 this.getTitle(), null, 0, false);
429 if (im.getGraphics() != null)
431 rc.drawBackground(im.getGraphics(), Color.black);
432 rc.drawScene(im.getGraphics());
435 rc.drawAxes(im.getGraphics());
442 protected void viewMenu_menuSelected()
444 buildAssociatedViewMenu();
448 * Builds the menu showing the choice of possible views (for the associated
449 * sequence data) to which the PCA may be linked
451 void buildAssociatedViewMenu()
453 AlignmentPanel[] aps = PaintRefresher
454 .getAssociatedPanels(av.getSequenceSetId());
455 if (aps.length == 1 && rc.av == aps[0].av)
457 associateViewsMenu.setVisible(false);
461 associateViewsMenu.setVisible(true);
464 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
466 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
469 associateViewsMenu.removeAll();
471 JRadioButtonMenuItem item;
472 ButtonGroup buttonGroup = new ButtonGroup();
473 int iSize = aps.length;
475 for (int i = 0; i < iSize; i++)
477 final AlignmentPanel panel = aps[i];
478 item = new JRadioButtonMenuItem(panel.av.viewName, panel.av == rc.av);
479 buttonGroup.add(item);
480 item.addActionListener(new ActionListener()
483 public void actionPerformed(ActionEvent evt)
485 rc.applyToAllViews = false;
488 PaintRefresher.Register(PCAPanel.this,
489 panel.av.getSequenceSetId());
493 associateViewsMenu.add(item);
496 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
499 buttonGroup.add(itemf);
501 itemf.setSelected(rc.applyToAllViews);
502 itemf.addActionListener(new ActionListener()
505 public void actionPerformed(ActionEvent evt)
507 rc.applyToAllViews = itemf.isSelected();
510 associateViewsMenu.add(itemf);
518 * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
522 protected void outputPoints_actionPerformed()
524 CutAndPasteTransfer cap = new CutAndPasteTransfer();
527 cap.setText(pcaModel.getPointsasCsv(false,
528 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
529 zCombobox.getSelectedIndex()));
530 Desktop.addInternalFrame(cap, MessageManager
531 .formatMessage("label.points_for_params", new String[]
532 { this.getTitle() }), 500, 500);
533 } catch (OutOfMemoryError oom)
535 new OOMWarning("exporting PCA points", oom);
544 * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
548 protected void outputProjPoints_actionPerformed()
550 CutAndPasteTransfer cap = new CutAndPasteTransfer();
553 cap.setText(pcaModel.getPointsasCsv(true,
554 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
555 zCombobox.getSelectedIndex()));
556 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
557 "label.transformed_points_for_params", new String[]
558 { this.getTitle() }), 500, 500);
559 } catch (OutOfMemoryError oom)
561 new OOMWarning("exporting transformed PCA points", oom);
569 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
572 public void setProgressBar(String message, long id)
574 progressBar.setProgressBar(message, id);
575 // if (progressBars == null)
577 // progressBars = new Hashtable();
578 // progressBarHandlers = new Hashtable();
581 // JPanel progressPanel;
582 // Long lId = new Long(id);
583 // GridLayout layout = (GridLayout) statusPanel.getLayout();
584 // if (progressBars.get(lId) != null)
586 // progressPanel = (JPanel) progressBars.get(new Long(id));
587 // statusPanel.remove(progressPanel);
588 // progressBars.remove(lId);
589 // progressPanel = null;
590 // if (message != null)
592 // statusBar.setText(message);
594 // if (progressBarHandlers.contains(lId))
596 // progressBarHandlers.remove(lId);
598 // layout.setRows(layout.getRows() - 1);
602 // progressPanel = new JPanel(new BorderLayout(10, 5));
604 // JProgressBar progressBar = new JProgressBar();
605 // progressBar.setIndeterminate(true);
607 // progressPanel.add(new JLabel(message), BorderLayout.WEST);
608 // progressPanel.add(progressBar, BorderLayout.CENTER);
610 // layout.setRows(layout.getRows() + 1);
611 // statusPanel.add(progressPanel);
613 // progressBars.put(lId, progressPanel);
616 // // setMenusForViewport();
621 public void registerHandler(final long id,
622 final IProgressIndicatorHandler handler)
624 progressBar.registerHandler(id, handler);
625 // if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
628 // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
630 // progressBarHandlers.put(new Long(id), handler);
631 // final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
632 // if (handler.canCancel())
634 // JButton cancel = new JButton(
635 // MessageManager.getString("action.cancel"));
636 // final IProgressIndicator us = this;
637 // cancel.addActionListener(new ActionListener()
641 // public void actionPerformed(ActionEvent e)
643 // handler.cancelActivity(id);
644 // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
645 // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
648 // progressPanel.add(cancel, BorderLayout.EAST);
654 * @return true if any progress bars are still active
657 public boolean operationInProgress()
659 return progressBar.operationInProgress();
663 protected void resetButton_actionPerformed()
666 top = 0; // ugly - prevents dimensionChanged events from being processed
667 xCombobox.setSelectedIndex(0);
668 yCombobox.setSelectedIndex(1);
670 zCombobox.setSelectedIndex(2);
674 * Answers true if PCA calculation is in progress, else false
678 public boolean isWorking()