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.datamodel.Alignment;
24 import jalview.datamodel.AlignmentI;
25 import jalview.datamodel.AlignmentView;
26 import jalview.datamodel.ColumnSelection;
27 import jalview.datamodel.SeqCigar;
28 import jalview.datamodel.SequenceI;
29 import jalview.jbgui.GPCAPanel;
30 import jalview.schemes.ResidueProperties;
31 import jalview.util.MessageManager;
32 import jalview.viewmodel.AlignmentViewport;
33 import jalview.viewmodel.PCAModel;
35 import java.awt.BorderLayout;
36 import java.awt.Color;
37 import java.awt.Dimension;
38 import java.awt.Graphics;
39 import java.awt.event.ActionEvent;
40 import java.awt.event.ActionListener;
41 import java.awt.print.PageFormat;
42 import java.awt.print.Printable;
43 import java.awt.print.PrinterException;
44 import java.awt.print.PrinterJob;
46 import javax.swing.ButtonGroup;
47 import javax.swing.JCheckBoxMenuItem;
48 import javax.swing.JColorChooser;
49 import javax.swing.JMenuItem;
50 import javax.swing.JRadioButtonMenuItem;
51 import javax.swing.event.InternalFrameAdapter;
52 import javax.swing.event.InternalFrameEvent;
60 public class PCAPanel extends GPCAPanel implements Runnable,
64 private IProgressIndicator progressBar;
74 private static final int MIN_WIDTH = 470;
76 private static final int MIN_HEIGHT = 250;
81 * Creates a new PCAPanel object.
88 public PCAPanel(AlignmentPanel ap)
94 progressBar = new ProgressBar(statusPanel, statusBar);
96 boolean sameLength = true;
97 boolean selected = av.getSelectionGroup() != null
98 && av.getSelectionGroup().getSize() > 0;
99 AlignmentView seqstrings = av.getAlignmentView(selected);
100 boolean nucleotide = av.getAlignment().isNucleotide();
104 seqs = av.getAlignment().getSequencesArray();
108 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
110 SeqCigar sq[] = seqstrings.getSequences();
111 int length = sq[0].getWidth();
113 for (int i = 0; i < seqs.length; i++)
115 if (sq[i].getWidth() != length)
124 JvOptionPane.showMessageDialog(Desktop.desktop,
125 MessageManager.getString("label.pca_sequences_not_aligned"),
126 MessageManager.getString("label.sequences_not_aligned"),
127 JvOptionPane.WARNING_MESSAGE);
132 addInternalFrameListener(new InternalFrameAdapter()
135 public void internalFrameClosed(InternalFrameEvent e)
137 close_actionPerformed();
141 pcaModel = new PCAModel(seqstrings, seqs, nucleotide);
142 PaintRefresher.Register(this, av.getSequenceSetId());
144 rc = new RotatableCanvas(ap);
145 this.getContentPane().add(rc, BorderLayout.CENTER);
146 Thread worker = new Thread(this);
151 * Ensure references to potentially very large objects (the PCA matrices) are
152 * nulled when the frame is closed
154 protected void close_actionPerformed()
160 protected void scoreMatrix_menuSelected()
162 scoreMatrixMenu.removeAll();
163 for (final String sm : ResidueProperties.scoreMatrices.keySet())
165 if (ResidueProperties.getScoreMatrix(sm) != null)
167 // create an entry for this score matrix for use in PCA
168 JCheckBoxMenuItem jm = new JCheckBoxMenuItem();
169 jm.setText(MessageManager.getStringOrReturn("label.score_model_",
171 jm.setSelected(pcaModel.getScore_matrix().equals(sm));
172 if ((ResidueProperties.scoreMatrices.get(sm).isDNA() && ResidueProperties.scoreMatrices
173 .get(sm).isProtein())
174 || pcaModel.isNucleotide() == ResidueProperties.scoreMatrices
177 final PCAPanel us = this;
178 jm.addActionListener(new ActionListener()
181 public void actionPerformed(ActionEvent e)
183 if (!pcaModel.getScore_matrix().equals(sm))
185 pcaModel.setScore_matrix(sm);
186 Thread worker = new Thread(us);
191 scoreMatrixMenu.add(jm);
198 public void bgcolour_actionPerformed(ActionEvent e)
200 Color col = JColorChooser.showDialog(this,
201 MessageManager.getString("label.select_background_colour"),
217 long progId = System.currentTimeMillis();
218 IProgressIndicator progress = this;
219 String message = MessageManager.getString("label.pca_recalculating");
220 if (getParent() == null)
222 progress = ap.alignFrame;
223 message = MessageManager.getString("label.pca_calculating");
225 progress.setProgressBar(message, progId);
228 calcSettings.setEnabled(false);
231 xCombobox.setSelectedIndex(0);
232 yCombobox.setSelectedIndex(1);
233 zCombobox.setSelectedIndex(2);
235 pcaModel.updateRc(rc);
237 nuclSetting.setSelected(pcaModel.isNucleotide());
238 protSetting.setSelected(!pcaModel.isNucleotide());
239 jvVersionSetting.setSelected(pcaModel.isJvCalcMode());
240 top = pcaModel.getTop();
242 } catch (OutOfMemoryError er)
244 new OOMWarning("calculating PCA", er);
248 progress.setProgressBar("", progId);
250 calcSettings.setEnabled(true);
252 if (getParent() == null)
255 Desktop.addInternalFrame(this, MessageManager
256 .getString("label.principal_component_analysis"), 475, 450);
257 this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
262 protected void nuclSetting_actionPerfomed(ActionEvent arg0)
264 if (!pcaModel.isNucleotide())
266 pcaModel.setNucleotide(true);
267 pcaModel.setScore_matrix("DNA");
268 Thread worker = new Thread(this);
275 protected void protSetting_actionPerfomed(ActionEvent arg0)
278 if (pcaModel.isNucleotide())
280 pcaModel.setNucleotide(false);
281 pcaModel.setScore_matrix("BLOSUM62");
282 Thread worker = new Thread(this);
288 protected void jvVersionSetting_actionPerfomed(ActionEvent arg0)
290 pcaModel.setJvCalcMode(jvVersionSetting.isSelected());
291 Thread worker = new Thread(this);
298 void doDimensionChange()
305 int dim1 = top - xCombobox.getSelectedIndex();
306 int dim2 = top - yCombobox.getSelectedIndex();
307 int dim3 = top - zCombobox.getSelectedIndex();
308 pcaModel.updateRcView(dim1, dim2, dim3);
310 rc.rotmat.setIdentity();
312 rc.paint(rc.getGraphics());
322 protected void xCombobox_actionPerformed(ActionEvent e)
334 protected void yCombobox_actionPerformed(ActionEvent e)
346 protected void zCombobox_actionPerformed(ActionEvent e)
352 public void outputValues_actionPerformed(ActionEvent e)
354 CutAndPasteTransfer cap = new CutAndPasteTransfer();
357 cap.setText(pcaModel.getDetails());
358 Desktop.addInternalFrame(cap,
359 MessageManager.getString("label.pca_details"), 500, 500);
360 } catch (OutOfMemoryError oom)
362 new OOMWarning("opening PCA details", oom);
368 public void showLabels_actionPerformed(ActionEvent e)
370 rc.showLabels(showLabels.getState());
374 public void print_actionPerformed(ActionEvent e)
376 PCAPrinter printer = new PCAPrinter();
381 public void originalSeqData_actionPerformed(ActionEvent e)
383 // this was cut'n'pasted from the equivalent TreePanel method - we should
384 // make this an abstract function of all jalview analysis windows
385 if (pcaModel.getSeqtrings() == null)
387 jalview.bin.Cache.log
388 .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
391 // decide if av alignment is sufficiently different to original data to
392 // warrant a new window to be created
393 // create new alignmnt window with hidden regions (unhiding hidden regions
394 // yields unaligned seqs)
395 // or create a selection box around columns in alignment view
396 // test Alignment(SeqCigar[])
400 // we try to get the associated view's gap character
401 // but this may fail if the view was closed...
402 gc = av.getGapCharacter();
403 } catch (Exception ex)
407 Object[] alAndColsel = pcaModel.getSeqtrings()
408 .getAlignmentAndColumnSelection(gc);
410 if (alAndColsel != null && alAndColsel[0] != null)
412 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
414 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
415 AlignmentI dataset = (av != null && av.getAlignment() != null) ? av
416 .getAlignment().getDataset() : null;
419 al.setDataset(dataset);
425 AlignFrame af = new AlignFrame(al,
426 (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
427 AlignFrame.DEFAULT_HEIGHT);
429 // >>>This is a fix for the moment, until a better solution is
431 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
433 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
436 Desktop.addInternalFrame(af, MessageManager.formatMessage(
437 "label.original_data_for_params",
438 new String[] { this.title }), AlignFrame.DEFAULT_WIDTH,
439 AlignFrame.DEFAULT_HEIGHT);
443 * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
444 * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
445 * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
448 * Desktop.addInternalFrame(cap, "Original Data", 400, 400);
452 class PCAPrinter extends Thread implements Printable
457 PrinterJob printJob = PrinterJob.getPrinterJob();
458 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
460 printJob.setPrintable(this, pf);
462 if (printJob.printDialog())
467 } catch (Exception PrintException)
469 PrintException.printStackTrace();
475 public int print(Graphics pg, PageFormat pf, int pi)
476 throws PrinterException
478 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
480 rc.drawBackground(pg, rc.bgColour);
482 if (rc.drawAxes == true)
489 return Printable.PAGE_EXISTS;
493 return Printable.NO_SUCH_PAGE;
505 public void eps_actionPerformed(ActionEvent e)
507 makePCAImage(jalview.util.ImageMaker.TYPE.EPS);
517 public void png_actionPerformed(ActionEvent e)
519 makePCAImage(jalview.util.ImageMaker.TYPE.PNG);
522 void makePCAImage(jalview.util.ImageMaker.TYPE type)
524 int width = rc.getWidth();
525 int height = rc.getHeight();
527 jalview.util.ImageMaker im;
529 if (type == jalview.util.ImageMaker.TYPE.PNG)
531 im = new jalview.util.ImageMaker(this,
532 jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from PCA",
533 width, height, null, null, null, 0, false);
535 else if (type == jalview.util.ImageMaker.TYPE.EPS)
537 im = new jalview.util.ImageMaker(this,
538 jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from PCA",
539 width, height, null, this.getTitle(), null, 0, false);
543 im = new jalview.util.ImageMaker(this,
544 jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
545 width, height, null, this.getTitle(), null, 0, false);
549 if (im.getGraphics() != null)
551 rc.drawBackground(im.getGraphics(), Color.black);
552 rc.drawScene(im.getGraphics());
553 if (rc.drawAxes == true)
555 rc.drawAxes(im.getGraphics());
562 public void viewMenu_menuSelected()
564 buildAssociatedViewMenu();
567 void buildAssociatedViewMenu()
569 AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
570 .getSequenceSetId());
571 if (aps.length == 1 && rc.av == aps[0].av)
573 associateViewsMenu.setVisible(false);
577 associateViewsMenu.setVisible(true);
579 if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
581 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
584 associateViewsMenu.removeAll();
586 JRadioButtonMenuItem item;
587 ButtonGroup buttonGroup = new ButtonGroup();
588 int i, iSize = aps.length;
589 final PCAPanel thisPCAPanel = this;
590 for (i = 0; i < iSize; i++)
592 final AlignmentPanel ap = aps[i];
593 item = new JRadioButtonMenuItem(ap.av.viewName, ap.av == rc.av);
594 buttonGroup.add(item);
595 item.addActionListener(new ActionListener()
598 public void actionPerformed(ActionEvent evt)
600 rc.applyToAllViews = false;
603 PaintRefresher.Register(thisPCAPanel, ap.av.getSequenceSetId());
607 associateViewsMenu.add(item);
610 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
612 buttonGroup.add(itemf);
614 itemf.setSelected(rc.applyToAllViews);
615 itemf.addActionListener(new ActionListener()
618 public void actionPerformed(ActionEvent evt)
620 rc.applyToAllViews = itemf.isSelected();
623 associateViewsMenu.add(itemf);
631 * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
635 protected void outputPoints_actionPerformed(ActionEvent e)
637 CutAndPasteTransfer cap = new CutAndPasteTransfer();
640 cap.setText(pcaModel.getPointsasCsv(false,
641 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
642 zCombobox.getSelectedIndex()));
643 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
644 "label.points_for_params", new String[] { this.getTitle() }),
646 } catch (OutOfMemoryError oom)
648 new OOMWarning("exporting PCA points", oom);
657 * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
661 protected void outputProjPoints_actionPerformed(ActionEvent e)
663 CutAndPasteTransfer cap = new CutAndPasteTransfer();
666 cap.setText(pcaModel.getPointsasCsv(true,
667 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
668 zCombobox.getSelectedIndex()));
669 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
670 "label.transformed_points_for_params",
671 new String[] { this.getTitle() }), 500, 500);
672 } catch (OutOfMemoryError oom)
674 new OOMWarning("exporting transformed PCA points", oom);
682 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
685 public void setProgressBar(String message, long id)
687 progressBar.setProgressBar(message, id);
688 // if (progressBars == null)
690 // progressBars = new Hashtable();
691 // progressBarHandlers = new Hashtable();
694 // JPanel progressPanel;
695 // Long lId = new Long(id);
696 // GridLayout layout = (GridLayout) statusPanel.getLayout();
697 // if (progressBars.get(lId) != null)
699 // progressPanel = (JPanel) progressBars.get(new Long(id));
700 // statusPanel.remove(progressPanel);
701 // progressBars.remove(lId);
702 // progressPanel = null;
703 // if (message != null)
705 // statusBar.setText(message);
707 // if (progressBarHandlers.contains(lId))
709 // progressBarHandlers.remove(lId);
711 // layout.setRows(layout.getRows() - 1);
715 // progressPanel = new JPanel(new BorderLayout(10, 5));
717 // JProgressBar progressBar = new JProgressBar();
718 // progressBar.setIndeterminate(true);
720 // progressPanel.add(new JLabel(message), BorderLayout.WEST);
721 // progressPanel.add(progressBar, BorderLayout.CENTER);
723 // layout.setRows(layout.getRows() + 1);
724 // statusPanel.add(progressPanel);
726 // progressBars.put(lId, progressPanel);
729 // // setMenusForViewport();
734 public void registerHandler(final long id,
735 final IProgressIndicatorHandler handler)
737 progressBar.registerHandler(id, handler);
738 // if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
741 // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
743 // progressBarHandlers.put(new Long(id), handler);
744 // final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
745 // if (handler.canCancel())
747 // JButton cancel = new JButton(
748 // MessageManager.getString("action.cancel"));
749 // final IProgressIndicator us = this;
750 // cancel.addActionListener(new ActionListener()
754 // public void actionPerformed(ActionEvent e)
756 // handler.cancelActivity(id);
757 // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
758 // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
761 // progressPanel.add(cancel, BorderLayout.EAST);
767 * @return true if any progress bars are still active
770 public boolean operationInProgress()
772 return progressBar.operationInProgress();
776 protected void resetButton_actionPerformed(ActionEvent e)
779 top = 0; // ugly - prevents dimensionChanged events from being processed
780 xCombobox.setSelectedIndex(0);
781 yCombobox.setSelectedIndex(1);
783 zCombobox.setSelectedIndex(2);