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.Annotation;
31 import jalview.datamodel.HiddenColumns;
32 import jalview.datamodel.SequenceI;
33 import jalview.gui.JalviewColourChooser.ColourChooserListener;
34 import jalview.jbgui.GPCAPanel;
35 import jalview.util.MessageManager;
36 import jalview.viewmodel.AlignmentViewport;
37 import jalview.viewmodel.PCAModel;
39 import java.awt.BorderLayout;
40 import java.awt.Color;
41 import java.awt.Dimension;
42 import java.awt.Graphics;
43 import java.awt.event.ActionEvent;
44 import java.awt.event.ActionListener;
45 import java.awt.print.PageFormat;
46 import java.awt.print.Printable;
47 import java.awt.print.PrinterException;
48 import java.awt.print.PrinterJob;
50 import javax.swing.ButtonGroup;
51 import javax.swing.JCheckBoxMenuItem;
52 import javax.swing.JColorChooser;
53 import javax.swing.JDialog;
54 import javax.swing.JMenuItem;
55 import javax.swing.JRadioButtonMenuItem;
56 import javax.swing.event.InternalFrameAdapter;
57 import javax.swing.event.InternalFrameEvent;
65 public class PCAPanel extends GPCAPanel
66 implements Runnable, IProgressIndicator
69 private IProgressIndicator progressBar;
79 private static final int MIN_WIDTH = 470;
81 private static final int MIN_HEIGHT = 250;
85 private boolean working;
88 * Creates a new PCAPanel object using default score model and parameters
92 public PCAPanel(AlignmentPanel alignPanel)
95 ScoreModels.getInstance()
97 !alignPanel.av.getAlignment().isNucleotide())
99 SimilarityParams.SeqSpace);
103 * Constructor given sequence data, a similarity (or distance) score model
104 * name, and score calculation parameters
110 public PCAPanel(AlignmentPanel alignPanel, String modelName,
111 SimilarityParamsI params)
114 this.av = alignPanel.av;
115 this.ap = alignPanel;
116 boolean nucleotide = av.getAlignment().isNucleotide();
118 progressBar = new ProgressBar(statusPanel, statusBar);
120 addInternalFrameListener(new InternalFrameAdapter()
123 public void internalFrameClosed(InternalFrameEvent e)
125 close_actionPerformed();
129 boolean selected = av.getSelectionGroup() != null
130 && av.getSelectionGroup().getSize() > 0;
131 AlignmentView seqstrings = av.getAlignmentView(selected);
135 seqs = av.getAlignment().getSequencesArray();
139 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
142 ScoreModelI scoreModel = ScoreModels.getInstance()
143 .getScoreModel(modelName, ap);
144 pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
146 PaintRefresher.Register(this, av.getSequenceSetId());
148 rc = new RotatableCanvas(alignPanel);
149 this.getContentPane().add(rc, BorderLayout.CENTER);
150 Thread worker = new Thread(this);
155 * Ensure references to potentially very large objects (the PCA matrices) are
156 * nulled when the frame is closed
158 protected void close_actionPerformed()
164 * Repopulate the options and actions under the score model menu when it is
165 * selected. Options will depend on whether 'nucleotide' or 'peptide'
166 * modelling is selected (and also possibly on whether any additional score
167 * models have been added).
170 protected void scoreModel_menuSelected()
172 scoreModelMenu.removeAll();
173 for (final ScoreModelI sm : ScoreModels.getInstance().getModels())
175 final String name = sm.getName();
176 JCheckBoxMenuItem jm = new JCheckBoxMenuItem(name);
179 * if the score model doesn't provide a description, try to look one
180 * up in the text bundle, falling back on its name
182 String tooltip = sm.getDescription();
185 tooltip = MessageManager.getStringOrReturn("label.score_model_",
188 jm.setToolTipText(tooltip);
189 jm.setSelected(pcaModel.getScoreModelName().equals(name));
190 if ((pcaModel.isNucleotide() && sm.isDNA())
191 || (!pcaModel.isNucleotide() && sm.isProtein()))
193 jm.addActionListener(new ActionListener()
196 public void actionPerformed(ActionEvent e)
198 if (!pcaModel.getScoreModelName().equals(name))
200 ScoreModelI sm2 = ScoreModels.getInstance()
201 .getScoreModel(name, ap);
202 pcaModel.setScoreModel(sm2);
203 Thread worker = new Thread(PCAPanel.this);
208 scoreModelMenu.add(jm);
214 public void bgcolour_actionPerformed(ActionEvent e)
216 String ttl = MessageManager.getString("label.select_background_colour");
217 ColourChooserListener listener = new ColourChooserListener()
220 public void colourSelected(Color c)
226 JalviewColourChooser.showColourChooser(this, ttl, rc.bgColour,
236 long progId = System.currentTimeMillis();
237 IProgressIndicator progress = this;
238 String message = MessageManager.getString("label.pca_recalculating");
239 if (getParent() == null)
241 progress = ap.alignFrame;
242 message = MessageManager.getString("label.pca_calculating");
244 progress.setProgressBar(message, progId);
248 calcSettings.setEnabled(false);
251 xCombobox.setSelectedIndex(0);
252 yCombobox.setSelectedIndex(1);
253 zCombobox.setSelectedIndex(2);
255 pcaModel.updateRc(rc);
257 nuclSetting.setSelected(pcaModel.isNucleotide());
258 protSetting.setSelected(!pcaModel.isNucleotide());
259 top = pcaModel.getTop();
261 } catch (OutOfMemoryError er)
263 new OOMWarning("calculating PCA", er);
268 progress.setProgressBar("", progId);
270 calcSettings.setEnabled(true);
272 if (getParent() == null)
275 Desktop.addInternalFrame(this, MessageManager
276 .getString("label.principal_component_analysis"), 475, 450);
277 this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
283 protected void nuclSetting_actionPerfomed(ActionEvent arg0)
285 if (!pcaModel.isNucleotide())
287 pcaModel.setNucleotide(true);
288 pcaModel.setScoreModel(
289 ScoreModels.getInstance().getDefaultModel(false));
290 Thread worker = new Thread(this);
297 protected void protSetting_actionPerfomed(ActionEvent arg0)
300 if (pcaModel.isNucleotide())
302 pcaModel.setNucleotide(false);
303 pcaModel.setScoreModel(
304 ScoreModels.getInstance().getDefaultModel(true));
305 Thread worker = new Thread(this);
313 void doDimensionChange()
320 int dim1 = top - xCombobox.getSelectedIndex();
321 int dim2 = top - yCombobox.getSelectedIndex();
322 int dim3 = top - zCombobox.getSelectedIndex();
323 pcaModel.updateRcView(dim1, dim2, dim3);
325 rc.rotmat.setIdentity();
327 rc.paint(rc.getGraphics());
337 protected void xCombobox_actionPerformed(ActionEvent e)
349 protected void yCombobox_actionPerformed(ActionEvent e)
361 protected void zCombobox_actionPerformed(ActionEvent e)
367 public void outputValues_actionPerformed(ActionEvent e)
369 CutAndPasteTransfer cap = new CutAndPasteTransfer();
372 cap.setText(pcaModel.getDetails());
373 Desktop.addInternalFrame(cap,
374 MessageManager.getString("label.pca_details"), 500, 500);
375 } catch (OutOfMemoryError oom)
377 new OOMWarning("opening PCA details", oom);
383 public void showLabels_actionPerformed(ActionEvent e)
385 rc.showLabels(showLabels.getState());
389 public void print_actionPerformed(ActionEvent e)
391 PCAPrinter printer = new PCAPrinter();
396 public void originalSeqData_actionPerformed(ActionEvent e)
398 // this was cut'n'pasted from the equivalent TreePanel method - we should
399 // make this an abstract function of all jalview analysis windows
400 if (pcaModel.getSeqtrings() == null)
402 jalview.bin.Cache.log.info(
403 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
406 // decide if av alignment is sufficiently different to original data to
407 // warrant a new window to be created
408 // create new alignmnt window with hidden regions (unhiding hidden regions
409 // yields unaligned seqs)
410 // or create a selection box around columns in alignment view
411 // test Alignment(SeqCigar[])
415 // we try to get the associated view's gap character
416 // but this may fail if the view was closed...
417 gc = av.getGapCharacter();
418 } catch (Exception ex)
422 Object[] alAndColsel = pcaModel.getSeqtrings()
423 .getAlignmentAndHiddenColumns(gc);
425 if (alAndColsel != null && alAndColsel[0] != null)
427 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
429 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
430 AlignmentI dataset = (av != null && av.getAlignment() != null)
431 ? av.getAlignment().getDataset()
435 al.setDataset(dataset);
441 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
442 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
444 // >>>This is a fix for the moment, until a better solution is
446 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
448 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
451 Desktop.addInternalFrame(af, MessageManager.formatMessage(
452 "label.original_data_for_params", new String[]
453 { this.title }), AlignFrame.DEFAULT_WIDTH,
454 AlignFrame.DEFAULT_HEIGHT);
458 * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
459 * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
460 * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
463 * Desktop.addInternalFrame(cap, "Original Data", 400, 400);
467 class PCAPrinter extends Thread implements Printable
472 PrinterJob printJob = PrinterJob.getPrinterJob();
473 PageFormat defaultPage = printJob.defaultPage();
474 PageFormat pf = printJob.pageDialog(defaultPage);
476 if (defaultPage == pf)
484 printJob.setPrintable(this, pf);
486 if (printJob.printDialog())
491 } catch (Exception PrintException)
493 PrintException.printStackTrace();
499 public int print(Graphics pg, PageFormat pf, int pi)
500 throws PrinterException
502 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
504 rc.drawBackground(pg, rc.bgColour);
506 if (rc.drawAxes == true)
513 return Printable.PAGE_EXISTS;
517 return Printable.NO_SUCH_PAGE;
529 public void eps_actionPerformed(ActionEvent e)
531 makePCAImage(jalview.util.ImageMaker.TYPE.EPS);
541 public void png_actionPerformed(ActionEvent e)
543 makePCAImage(jalview.util.ImageMaker.TYPE.PNG);
546 void makePCAImage(jalview.util.ImageMaker.TYPE type)
548 int width = rc.getWidth();
549 int height = rc.getHeight();
551 jalview.util.ImageMaker im;
553 if (type == jalview.util.ImageMaker.TYPE.PNG)
555 im = new jalview.util.ImageMaker(this,
556 jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from PCA",
557 width, height, null, null, null, 0, false);
559 else if (type == jalview.util.ImageMaker.TYPE.EPS)
561 im = new jalview.util.ImageMaker(this,
562 jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from PCA",
563 width, height, null, this.getTitle(), null, 0, false);
567 im = new jalview.util.ImageMaker(this,
568 jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
569 width, height, null, this.getTitle(), null, 0, false);
573 if (im.getGraphics() != null)
575 rc.drawBackground(im.getGraphics(), Color.black);
576 rc.drawScene(im.getGraphics());
577 if (rc.drawAxes == true)
579 rc.drawAxes(im.getGraphics());
586 public void viewMenu_menuSelected()
588 buildAssociatedViewMenu();
591 void buildAssociatedViewMenu()
593 AlignmentPanel[] aps = PaintRefresher
594 .getAssociatedPanels(av.getSequenceSetId());
595 if (aps.length == 1 && rc.av == aps[0].av)
597 associateViewsMenu.setVisible(false);
601 associateViewsMenu.setVisible(true);
604 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
606 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
609 associateViewsMenu.removeAll();
611 JRadioButtonMenuItem item;
612 ButtonGroup buttonGroup = new ButtonGroup();
613 int i, iSize = aps.length;
614 final PCAPanel thisPCAPanel = this;
615 for (i = 0; i < iSize; i++)
617 final AlignmentPanel ap = aps[i];
618 item = new JRadioButtonMenuItem(ap.av.viewName, ap.av == rc.av);
619 buttonGroup.add(item);
620 item.addActionListener(new ActionListener()
623 public void actionPerformed(ActionEvent evt)
625 rc.applyToAllViews = false;
628 PaintRefresher.Register(thisPCAPanel, ap.av.getSequenceSetId());
632 associateViewsMenu.add(item);
635 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
638 buttonGroup.add(itemf);
640 itemf.setSelected(rc.applyToAllViews);
641 itemf.addActionListener(new ActionListener()
644 public void actionPerformed(ActionEvent evt)
646 rc.applyToAllViews = itemf.isSelected();
649 associateViewsMenu.add(itemf);
657 * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
661 protected void outputPoints_actionPerformed(ActionEvent e)
663 CutAndPasteTransfer cap = new CutAndPasteTransfer();
666 cap.setText(pcaModel.getPointsasCsv(false,
667 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
668 zCombobox.getSelectedIndex()));
669 Desktop.addInternalFrame(cap, MessageManager
670 .formatMessage("label.points_for_params", new String[]
671 { this.getTitle() }), 500, 500);
672 } catch (OutOfMemoryError oom)
674 new OOMWarning("exporting PCA points", oom);
683 * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
687 protected void outputProjPoints_actionPerformed(ActionEvent e)
689 CutAndPasteTransfer cap = new CutAndPasteTransfer();
692 cap.setText(pcaModel.getPointsasCsv(true,
693 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
694 zCombobox.getSelectedIndex()));
695 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
696 "label.transformed_points_for_params", new String[]
697 { this.getTitle() }), 500, 500);
698 } catch (OutOfMemoryError oom)
700 new OOMWarning("exporting transformed PCA points", oom);
708 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
711 public void setProgressBar(String message, long id)
713 progressBar.setProgressBar(message, id);
714 // if (progressBars == null)
716 // progressBars = new Hashtable();
717 // progressBarHandlers = new Hashtable();
720 // JPanel progressPanel;
721 // Long lId = new Long(id);
722 // GridLayout layout = (GridLayout) statusPanel.getLayout();
723 // if (progressBars.get(lId) != null)
725 // progressPanel = (JPanel) progressBars.get(new Long(id));
726 // statusPanel.remove(progressPanel);
727 // progressBars.remove(lId);
728 // progressPanel = null;
729 // if (message != null)
731 // statusBar.setText(message);
733 // if (progressBarHandlers.contains(lId))
735 // progressBarHandlers.remove(lId);
737 // layout.setRows(layout.getRows() - 1);
741 // progressPanel = new JPanel(new BorderLayout(10, 5));
743 // JProgressBar progressBar = new JProgressBar();
744 // progressBar.setIndeterminate(true);
746 // progressPanel.add(new JLabel(message), BorderLayout.WEST);
747 // progressPanel.add(progressBar, BorderLayout.CENTER);
749 // layout.setRows(layout.getRows() + 1);
750 // statusPanel.add(progressPanel);
752 // progressBars.put(lId, progressPanel);
755 // // setMenusForViewport();
760 public void registerHandler(final long id,
761 final IProgressIndicatorHandler handler)
763 progressBar.registerHandler(id, handler);
764 // if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
767 // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
769 // progressBarHandlers.put(new Long(id), handler);
770 // final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
771 // if (handler.canCancel())
773 // JButton cancel = new JButton(
774 // MessageManager.getString("action.cancel"));
775 // final IProgressIndicator us = this;
776 // cancel.addActionListener(new ActionListener()
780 // public void actionPerformed(ActionEvent e)
782 // handler.cancelActivity(id);
783 // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
784 // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
787 // progressPanel.add(cancel, BorderLayout.EAST);
793 * @return true if any progress bars are still active
796 public boolean operationInProgress()
798 return progressBar.operationInProgress();
802 protected void resetButton_actionPerformed(ActionEvent e)
805 top = 0; // ugly - prevents dimensionChanged events from being processed
806 xCombobox.setSelectedIndex(0);
807 yCombobox.setSelectedIndex(1);
809 zCombobox.setSelectedIndex(2);
813 * Answers true if PCA calculation is in progress, else false
817 public boolean isWorking()