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.analysis.scoremodels.SimilarityParams;
25 import jalview.api.analysis.ScoreModelI;
26 import jalview.api.analysis.SimilarityParamsI;
27 import jalview.datamodel.Alignment;
28 import jalview.datamodel.AlignmentI;
29 import jalview.datamodel.AlignmentView;
30 import jalview.datamodel.ColumnSelection;
31 import jalview.datamodel.SequenceI;
32 import jalview.jbgui.GPCAPanel;
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.Graphics;
40 import java.awt.event.ActionEvent;
41 import java.awt.event.ActionListener;
42 import java.awt.print.PageFormat;
43 import java.awt.print.Printable;
44 import java.awt.print.PrinterException;
45 import java.awt.print.PrinterJob;
47 import javax.swing.ButtonGroup;
48 import javax.swing.JCheckBoxMenuItem;
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;
61 public class PCAPanel extends GPCAPanel implements Runnable,
65 private IProgressIndicator progressBar;
78 * Creates a new PCAPanel object using default score model and parameters
82 public PCAPanel(AlignmentPanel alignPanel)
84 this(alignPanel, ScoreModels.getInstance()
85 .getDefaultModel(!alignPanel.av.getAlignment().isNucleotide())
86 .getName(), SimilarityParams.SeqSpace);
90 * Constructor given sequence data, a similarity (or distance) score model
91 * name, and score calculation parameters
97 public PCAPanel(AlignmentPanel alignPanel, String modelName,
98 SimilarityParamsI params)
101 this.av = alignPanel.av;
102 this.ap = alignPanel;
103 boolean nucleotide = av.getAlignment().isNucleotide();
105 progressBar = new ProgressBar(statusPanel, statusBar);
107 addInternalFrameListener(new InternalFrameAdapter()
110 public void internalFrameClosed(InternalFrameEvent e)
112 close_actionPerformed();
116 boolean selected = av.getSelectionGroup() != null
117 && av.getSelectionGroup().getSize() > 0;
118 AlignmentView seqstrings = av.getAlignmentView(selected);
122 seqs = av.getAlignment().getSequencesArray();
126 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
129 ScoreModelI scoreModel = ScoreModels.getInstance().getScoreModel(
131 pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
133 PaintRefresher.Register(this, av.getSequenceSetId());
135 rc = new RotatableCanvas(alignPanel);
136 this.getContentPane().add(rc, BorderLayout.CENTER);
137 Thread worker = new Thread(this);
142 * Ensure references to potentially very large objects (the PCA matrices) are
143 * nulled when the frame is closed
145 protected void close_actionPerformed()
151 * Repopulate the options and actions under the score model menu when it is
152 * selected. Options will depend on whether 'nucleotide' or 'peptide'
153 * modelling is selected (and also possibly on whether any additional score
154 * models have been added).
157 protected void scoreModel_menuSelected()
159 scoreModelMenu.removeAll();
160 for (final ScoreModelI sm : ScoreModels.getInstance().getModels())
162 final String name = sm.getName();
163 JCheckBoxMenuItem jm = new JCheckBoxMenuItem(name);
166 * if the score model doesn't provide a description, try to look one
167 * up in the text bundle, falling back on its name
169 String tooltip = sm.getDescription();
172 tooltip = MessageManager.getStringOrReturn("label.score_model_",
175 jm.setToolTipText(tooltip);
176 jm.setSelected(pcaModel.getScoreModelName().equals(name));
177 if ((pcaModel.isNucleotide() && sm.isDNA())
178 || (!pcaModel.isNucleotide() && sm.isProtein()))
180 jm.addActionListener(new ActionListener()
183 public void actionPerformed(ActionEvent e)
185 if (!pcaModel.getScoreModelName().equals(name))
187 ScoreModelI sm2 = ScoreModels.getInstance().getScoreModel(
189 pcaModel.setScoreModel(sm2);
190 Thread worker = new Thread(PCAPanel.this);
195 scoreModelMenu.add(jm);
201 public void bgcolour_actionPerformed(ActionEvent e)
203 Color col = JColorChooser.showDialog(this,
204 MessageManager.getString("label.select_background_colour"),
220 long progId = System.currentTimeMillis();
221 IProgressIndicator progress = this;
222 String message = MessageManager.getString("label.pca_recalculating");
223 if (getParent() == null)
225 progress = ap.alignFrame;
226 message = MessageManager.getString("label.pca_calculating");
228 progress.setProgressBar(message, progId);
231 calcSettings.setEnabled(false);
234 xCombobox.setSelectedIndex(0);
235 yCombobox.setSelectedIndex(1);
236 zCombobox.setSelectedIndex(2);
238 pcaModel.updateRc(rc);
240 nuclSetting.setSelected(pcaModel.isNucleotide());
241 protSetting.setSelected(!pcaModel.isNucleotide());
242 top = pcaModel.getTop();
244 } catch (OutOfMemoryError er)
246 new OOMWarning("calculating PCA", er);
250 progress.setProgressBar("", progId);
252 calcSettings.setEnabled(true);
254 if (getParent() == null)
257 Desktop.addInternalFrame(this, MessageManager
258 .getString("label.principal_component_analysis"), 475, 450);
263 protected void nuclSetting_actionPerfomed(ActionEvent arg0)
265 if (!pcaModel.isNucleotide())
267 pcaModel.setNucleotide(true);
268 pcaModel.setScoreModel(ScoreModels.getInstance().getDefaultModel(
270 Thread worker = new Thread(this);
277 protected void protSetting_actionPerfomed(ActionEvent arg0)
280 if (pcaModel.isNucleotide())
282 pcaModel.setNucleotide(false);
283 pcaModel.setScoreModel(ScoreModels.getInstance()
284 .getDefaultModel(true));
285 Thread worker = new Thread(this);
293 void doDimensionChange()
300 int dim1 = top - xCombobox.getSelectedIndex();
301 int dim2 = top - yCombobox.getSelectedIndex();
302 int dim3 = top - zCombobox.getSelectedIndex();
303 pcaModel.updateRcView(dim1, dim2, dim3);
305 rc.rotmat.setIdentity();
307 rc.paint(rc.getGraphics());
317 protected void xCombobox_actionPerformed(ActionEvent e)
329 protected void yCombobox_actionPerformed(ActionEvent e)
341 protected void zCombobox_actionPerformed(ActionEvent e)
347 public void outputValues_actionPerformed(ActionEvent e)
349 CutAndPasteTransfer cap = new CutAndPasteTransfer();
352 cap.setText(pcaModel.getDetails());
353 Desktop.addInternalFrame(cap,
354 MessageManager.getString("label.pca_details"), 500, 500);
355 } catch (OutOfMemoryError oom)
357 new OOMWarning("opening PCA details", oom);
363 public void showLabels_actionPerformed(ActionEvent e)
365 rc.showLabels(showLabels.getState());
369 public void print_actionPerformed(ActionEvent e)
371 PCAPrinter printer = new PCAPrinter();
376 public void originalSeqData_actionPerformed(ActionEvent e)
378 // this was cut'n'pasted from the equivalent TreePanel method - we should
379 // make this an abstract function of all jalview analysis windows
380 if (pcaModel.getSeqtrings() == null)
382 jalview.bin.Cache.log
383 .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
386 // decide if av alignment is sufficiently different to original data to
387 // warrant a new window to be created
388 // create new alignmnt window with hidden regions (unhiding hidden regions
389 // yields unaligned seqs)
390 // or create a selection box around columns in alignment view
391 // test Alignment(SeqCigar[])
395 // we try to get the associated view's gap character
396 // but this may fail if the view was closed...
397 gc = av.getGapCharacter();
398 } catch (Exception ex)
402 Object[] alAndColsel = pcaModel.getSeqtrings()
403 .getAlignmentAndColumnSelection(gc);
405 if (alAndColsel != null && alAndColsel[0] != null)
407 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
409 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
410 AlignmentI dataset = (av != null && av.getAlignment() != null) ? av
411 .getAlignment().getDataset() : null;
414 al.setDataset(dataset);
420 AlignFrame af = new AlignFrame(al,
421 (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
422 AlignFrame.DEFAULT_HEIGHT);
424 // >>>This is a fix for the moment, until a better solution is
426 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
428 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
431 Desktop.addInternalFrame(af, MessageManager.formatMessage(
432 "label.original_data_for_params",
433 new String[] { this.title }), AlignFrame.DEFAULT_WIDTH,
434 AlignFrame.DEFAULT_HEIGHT);
438 * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
439 * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
440 * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
443 * Desktop.addInternalFrame(cap, "Original Data", 400, 400);
447 class PCAPrinter extends Thread implements Printable
452 PrinterJob printJob = PrinterJob.getPrinterJob();
453 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
455 printJob.setPrintable(this, pf);
457 if (printJob.printDialog())
462 } catch (Exception PrintException)
464 PrintException.printStackTrace();
470 public int print(Graphics pg, PageFormat pf, int pi)
471 throws PrinterException
473 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
475 rc.drawBackground(pg, rc.bgColour);
477 if (rc.drawAxes == true)
484 return Printable.PAGE_EXISTS;
488 return Printable.NO_SUCH_PAGE;
500 public void eps_actionPerformed(ActionEvent e)
502 makePCAImage(jalview.util.ImageMaker.TYPE.EPS);
512 public void png_actionPerformed(ActionEvent e)
514 makePCAImage(jalview.util.ImageMaker.TYPE.PNG);
517 void makePCAImage(jalview.util.ImageMaker.TYPE type)
519 int width = rc.getWidth();
520 int height = rc.getHeight();
522 jalview.util.ImageMaker im;
524 if (type == jalview.util.ImageMaker.TYPE.PNG)
526 im = new jalview.util.ImageMaker(this,
527 jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from PCA",
528 width, height, null, null, null, 0, false);
530 else if (type == jalview.util.ImageMaker.TYPE.EPS)
532 im = new jalview.util.ImageMaker(this,
533 jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from PCA",
534 width, height, null, this.getTitle(), null, 0, false);
538 im = new jalview.util.ImageMaker(this,
539 jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
540 width, height, null, this.getTitle(), null, 0, false);
544 if (im.getGraphics() != null)
546 rc.drawBackground(im.getGraphics(), Color.black);
547 rc.drawScene(im.getGraphics());
548 if (rc.drawAxes == true)
550 rc.drawAxes(im.getGraphics());
557 public void viewMenu_menuSelected()
559 buildAssociatedViewMenu();
562 void buildAssociatedViewMenu()
564 AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
565 .getSequenceSetId());
566 if (aps.length == 1 && rc.av == aps[0].av)
568 associateViewsMenu.setVisible(false);
572 associateViewsMenu.setVisible(true);
574 if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
576 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
579 associateViewsMenu.removeAll();
581 JRadioButtonMenuItem item;
582 ButtonGroup buttonGroup = new ButtonGroup();
583 int i, iSize = aps.length;
584 final PCAPanel thisPCAPanel = this;
585 for (i = 0; i < iSize; i++)
587 final AlignmentPanel ap = aps[i];
588 item = new JRadioButtonMenuItem(ap.av.viewName, ap.av == rc.av);
589 buttonGroup.add(item);
590 item.addActionListener(new ActionListener()
593 public void actionPerformed(ActionEvent evt)
595 rc.applyToAllViews = false;
598 PaintRefresher.Register(thisPCAPanel, ap.av.getSequenceSetId());
602 associateViewsMenu.add(item);
605 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
607 buttonGroup.add(itemf);
609 itemf.setSelected(rc.applyToAllViews);
610 itemf.addActionListener(new ActionListener()
613 public void actionPerformed(ActionEvent evt)
615 rc.applyToAllViews = itemf.isSelected();
618 associateViewsMenu.add(itemf);
626 * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
630 protected void outputPoints_actionPerformed(ActionEvent e)
632 CutAndPasteTransfer cap = new CutAndPasteTransfer();
635 cap.setText(pcaModel.getPointsasCsv(false,
636 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
637 zCombobox.getSelectedIndex()));
638 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
639 "label.points_for_params", new String[] { this.getTitle() }),
641 } catch (OutOfMemoryError oom)
643 new OOMWarning("exporting PCA points", oom);
652 * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
656 protected void outputProjPoints_actionPerformed(ActionEvent e)
658 CutAndPasteTransfer cap = new CutAndPasteTransfer();
661 cap.setText(pcaModel.getPointsasCsv(true,
662 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
663 zCombobox.getSelectedIndex()));
664 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
665 "label.transformed_points_for_params",
666 new String[] { this.getTitle() }), 500, 500);
667 } catch (OutOfMemoryError oom)
669 new OOMWarning("exporting transformed PCA points", oom);
677 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
680 public void setProgressBar(String message, long id)
682 progressBar.setProgressBar(message, id);
683 // if (progressBars == null)
685 // progressBars = new Hashtable();
686 // progressBarHandlers = new Hashtable();
689 // JPanel progressPanel;
690 // Long lId = new Long(id);
691 // GridLayout layout = (GridLayout) statusPanel.getLayout();
692 // if (progressBars.get(lId) != null)
694 // progressPanel = (JPanel) progressBars.get(new Long(id));
695 // statusPanel.remove(progressPanel);
696 // progressBars.remove(lId);
697 // progressPanel = null;
698 // if (message != null)
700 // statusBar.setText(message);
702 // if (progressBarHandlers.contains(lId))
704 // progressBarHandlers.remove(lId);
706 // layout.setRows(layout.getRows() - 1);
710 // progressPanel = new JPanel(new BorderLayout(10, 5));
712 // JProgressBar progressBar = new JProgressBar();
713 // progressBar.setIndeterminate(true);
715 // progressPanel.add(new JLabel(message), BorderLayout.WEST);
716 // progressPanel.add(progressBar, BorderLayout.CENTER);
718 // layout.setRows(layout.getRows() + 1);
719 // statusPanel.add(progressPanel);
721 // progressBars.put(lId, progressPanel);
724 // // setMenusForViewport();
729 public void registerHandler(final long id,
730 final IProgressIndicatorHandler handler)
732 progressBar.registerHandler(id, handler);
733 // if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
736 // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
738 // progressBarHandlers.put(new Long(id), handler);
739 // final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
740 // if (handler.canCancel())
742 // JButton cancel = new JButton(
743 // MessageManager.getString("action.cancel"));
744 // final IProgressIndicator us = this;
745 // cancel.addActionListener(new ActionListener()
749 // public void actionPerformed(ActionEvent e)
751 // handler.cancelActivity(id);
752 // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
753 // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
756 // progressPanel.add(cancel, BorderLayout.EAST);
762 * @return true if any progress bars are still active
765 public boolean operationInProgress()
767 return progressBar.operationInProgress();
771 protected void resetButton_actionPerformed(ActionEvent e)
774 top = 0; // ugly - prevents dimensionChanged events from being processed
775 xCombobox.setSelectedIndex(0);
776 yCombobox.setSelectedIndex(1);
778 zCombobox.setSelectedIndex(2);