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.HiddenColumns;
31 import jalview.datamodel.SequenceI;
32 import jalview.gui.ImageExporter.ImageWriterI;
33 import jalview.gui.JalviewColourChooser.ColourChooserListener;
34 import jalview.jbgui.GPCAPanel;
35 import jalview.util.ImageMaker;
36 import jalview.util.MessageManager;
37 import jalview.viewmodel.AlignmentViewport;
38 import jalview.viewmodel.PCAModel;
40 import java.awt.BorderLayout;
41 import java.awt.Color;
42 import java.awt.Dimension;
43 import java.awt.Graphics;
44 import java.awt.event.ActionEvent;
45 import java.awt.event.ActionListener;
46 import java.awt.print.PageFormat;
47 import java.awt.print.Printable;
48 import java.awt.print.PrinterException;
49 import java.awt.print.PrinterJob;
51 import javax.swing.ButtonGroup;
52 import javax.swing.JCheckBoxMenuItem;
53 import javax.swing.JMenuItem;
54 import javax.swing.JRadioButtonMenuItem;
55 import javax.swing.event.InternalFrameAdapter;
56 import javax.swing.event.InternalFrameEvent;
64 public class PCAPanel extends GPCAPanel
65 implements Runnable, IProgressIndicator
68 private IProgressIndicator progressBar;
78 private static final int MIN_WIDTH = 470;
80 private static final int MIN_HEIGHT = 250;
84 private boolean working;
87 * Creates a new PCAPanel object using default score model and parameters
91 public PCAPanel(AlignmentPanel alignPanel)
94 ScoreModels.getInstance()
96 !alignPanel.av.getAlignment().isNucleotide())
98 SimilarityParams.SeqSpace);
102 * Constructor given sequence data, a similarity (or distance) score model
103 * name, and score calculation parameters
109 public PCAPanel(AlignmentPanel alignPanel, String modelName,
110 SimilarityParamsI params)
113 this.av = alignPanel.av;
114 this.ap = alignPanel;
115 boolean nucleotide = av.getAlignment().isNucleotide();
117 progressBar = new ProgressBar(statusPanel, statusBar);
119 addInternalFrameListener(new InternalFrameAdapter()
122 public void internalFrameClosed(InternalFrameEvent e)
124 close_actionPerformed();
128 boolean selected = av.getSelectionGroup() != null
129 && av.getSelectionGroup().getSize() > 0;
130 AlignmentView seqstrings = av.getAlignmentView(selected);
134 seqs = av.getAlignment().getSequencesArray();
138 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
141 ScoreModelI scoreModel = ScoreModels.getInstance()
142 .getScoreModel(modelName, ap);
143 pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
145 PaintRefresher.Register(this, av.getSequenceSetId());
147 rc = new RotatableCanvas(alignPanel);
148 this.getContentPane().add(rc, BorderLayout.CENTER);
149 Thread worker = new Thread(this);
154 * Ensure references to potentially very large objects (the PCA matrices) are
155 * nulled when the frame is closed
157 protected void close_actionPerformed()
163 * Repopulate the options and actions under the score model menu when it is
164 * selected. Options will depend on whether 'nucleotide' or 'peptide'
165 * modelling is selected (and also possibly on whether any additional score
166 * models have been added).
169 protected void scoreModel_menuSelected()
171 scoreModelMenu.removeAll();
172 for (final ScoreModelI sm : ScoreModels.getInstance().getModels())
174 final String name = sm.getName();
175 JCheckBoxMenuItem jm = new JCheckBoxMenuItem(name);
178 * if the score model doesn't provide a description, try to look one
179 * up in the text bundle, falling back on its name
181 String tooltip = sm.getDescription();
184 tooltip = MessageManager.getStringOrReturn("label.score_model_",
187 jm.setToolTipText(tooltip);
188 jm.setSelected(pcaModel.getScoreModelName().equals(name));
189 if ((pcaModel.isNucleotide() && sm.isDNA())
190 || (!pcaModel.isNucleotide() && sm.isProtein()))
192 jm.addActionListener(new ActionListener()
195 public void actionPerformed(ActionEvent e)
197 if (!pcaModel.getScoreModelName().equals(name))
199 ScoreModelI sm2 = ScoreModels.getInstance()
200 .getScoreModel(name, ap);
201 pcaModel.setScoreModel(sm2);
202 Thread worker = new Thread(PCAPanel.this);
207 scoreModelMenu.add(jm);
213 public void bgcolour_actionPerformed(ActionEvent e)
215 String ttl = MessageManager.getString("label.select_background_colour");
216 ColourChooserListener listener = new ColourChooserListener()
219 public void colourSelected(Color c)
225 JalviewColourChooser.showColourChooser(this, ttl, rc.bgColour,
235 long progId = System.currentTimeMillis();
236 IProgressIndicator progress = this;
237 String message = MessageManager.getString("label.pca_recalculating");
238 if (getParent() == null)
240 progress = ap.alignFrame;
241 message = MessageManager.getString("label.pca_calculating");
243 progress.setProgressBar(message, progId);
247 calcSettings.setEnabled(false);
250 xCombobox.setSelectedIndex(0);
251 yCombobox.setSelectedIndex(1);
252 zCombobox.setSelectedIndex(2);
254 pcaModel.updateRc(rc);
256 nuclSetting.setSelected(pcaModel.isNucleotide());
257 protSetting.setSelected(!pcaModel.isNucleotide());
258 top = pcaModel.getTop();
260 } catch (OutOfMemoryError er)
262 new OOMWarning("calculating PCA", er);
267 progress.setProgressBar("", progId);
269 calcSettings.setEnabled(true);
271 if (getParent() == null)
274 Desktop.addInternalFrame(this, MessageManager
275 .getString("label.principal_component_analysis"), 475, 450);
276 this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
282 protected void nuclSetting_actionPerfomed(ActionEvent arg0)
284 if (!pcaModel.isNucleotide())
286 pcaModel.setNucleotide(true);
287 pcaModel.setScoreModel(
288 ScoreModels.getInstance().getDefaultModel(false));
289 Thread worker = new Thread(this);
296 protected void protSetting_actionPerfomed(ActionEvent arg0)
299 if (pcaModel.isNucleotide())
301 pcaModel.setNucleotide(false);
302 pcaModel.setScoreModel(
303 ScoreModels.getInstance().getDefaultModel(true));
304 Thread worker = new Thread(this);
312 void doDimensionChange()
319 int dim1 = top - xCombobox.getSelectedIndex();
320 int dim2 = top - yCombobox.getSelectedIndex();
321 int dim3 = top - zCombobox.getSelectedIndex();
322 pcaModel.updateRcView(dim1, dim2, dim3);
324 rc.rotmat.setIdentity();
326 rc.paint(rc.getGraphics());
336 protected void xCombobox_actionPerformed(ActionEvent e)
348 protected void yCombobox_actionPerformed(ActionEvent e)
360 protected void zCombobox_actionPerformed(ActionEvent e)
366 public void outputValues_actionPerformed(ActionEvent e)
368 CutAndPasteTransfer cap = new CutAndPasteTransfer();
371 cap.setText(pcaModel.getDetails());
372 Desktop.addInternalFrame(cap,
373 MessageManager.getString("label.pca_details"), 500, 500);
374 } catch (OutOfMemoryError oom)
376 new OOMWarning("opening PCA details", oom);
382 public void showLabels_actionPerformed(ActionEvent e)
384 rc.showLabels(showLabels.getState());
388 public void print_actionPerformed(ActionEvent e)
390 PCAPrinter printer = new PCAPrinter();
395 public void originalSeqData_actionPerformed(ActionEvent e)
397 // this was cut'n'pasted from the equivalent TreePanel method - we should
398 // make this an abstract function of all jalview analysis windows
399 if (pcaModel.getSeqtrings() == null)
401 jalview.bin.Cache.log.info(
402 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
405 // decide if av alignment is sufficiently different to original data to
406 // warrant a new window to be created
407 // create new alignmnt window with hidden regions (unhiding hidden regions
408 // yields unaligned seqs)
409 // or create a selection box around columns in alignment view
410 // test Alignment(SeqCigar[])
414 // we try to get the associated view's gap character
415 // but this may fail if the view was closed...
416 gc = av.getGapCharacter();
417 } catch (Exception ex)
421 Object[] alAndColsel = pcaModel.getSeqtrings()
422 .getAlignmentAndHiddenColumns(gc);
424 if (alAndColsel != null && alAndColsel[0] != null)
426 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
428 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
429 AlignmentI dataset = (av != null && av.getAlignment() != null)
430 ? av.getAlignment().getDataset()
434 al.setDataset(dataset);
440 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
441 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
443 // >>>This is a fix for the moment, until a better solution is
445 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
447 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
450 Desktop.addInternalFrame(af, MessageManager.formatMessage(
451 "label.original_data_for_params", new String[]
452 { this.title }), AlignFrame.DEFAULT_WIDTH,
453 AlignFrame.DEFAULT_HEIGHT);
457 * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
458 * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
459 * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
462 * Desktop.addInternalFrame(cap, "Original Data", 400, 400);
466 class PCAPrinter extends Thread implements Printable
471 PrinterJob printJob = PrinterJob.getPrinterJob();
472 PageFormat defaultPage = printJob.defaultPage();
473 PageFormat pf = printJob.pageDialog(defaultPage);
475 if (defaultPage == pf)
483 printJob.setPrintable(this, pf);
485 if (printJob.printDialog())
490 } catch (Exception PrintException)
492 PrintException.printStackTrace();
498 public int print(Graphics pg, PageFormat pf, int pi)
499 throws PrinterException
501 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
503 rc.drawBackground(pg, rc.bgColour);
505 if (rc.drawAxes == true)
512 return Printable.PAGE_EXISTS;
516 return Printable.NO_SUCH_PAGE;
521 public void makePCAImage(ImageMaker.TYPE type)
523 int width = rc.getWidth();
524 int height = rc.getHeight();
525 ImageWriterI writer = new ImageWriterI()
528 public void exportImage(Graphics g) throws Exception
530 rc.drawBackground(g, Color.black);
538 String pca = MessageManager.getString("label.pca");
539 ImageExporter exporter = new ImageExporter(writer, null, type, pca);
540 exporter.doExport(null, this, width, height, pca);
544 public void viewMenu_menuSelected()
546 buildAssociatedViewMenu();
549 void buildAssociatedViewMenu()
551 AlignmentPanel[] aps = PaintRefresher
552 .getAssociatedPanels(av.getSequenceSetId());
553 if (aps.length == 1 && rc.av == aps[0].av)
555 associateViewsMenu.setVisible(false);
559 associateViewsMenu.setVisible(true);
562 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
564 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
567 associateViewsMenu.removeAll();
569 JRadioButtonMenuItem item;
570 ButtonGroup buttonGroup = new ButtonGroup();
571 int i, iSize = aps.length;
572 final PCAPanel thisPCAPanel = this;
573 for (i = 0; i < iSize; i++)
575 final AlignmentPanel ap = aps[i];
576 item = new JRadioButtonMenuItem(ap.av.getViewName(), ap.av == rc.av);
577 buttonGroup.add(item);
578 item.addActionListener(new ActionListener()
581 public void actionPerformed(ActionEvent evt)
583 rc.applyToAllViews = false;
586 PaintRefresher.Register(thisPCAPanel, ap.av.getSequenceSetId());
590 associateViewsMenu.add(item);
593 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
596 buttonGroup.add(itemf);
598 itemf.setSelected(rc.applyToAllViews);
599 itemf.addActionListener(new ActionListener()
602 public void actionPerformed(ActionEvent evt)
604 rc.applyToAllViews = itemf.isSelected();
607 associateViewsMenu.add(itemf);
615 * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
619 protected void outputPoints_actionPerformed(ActionEvent e)
621 CutAndPasteTransfer cap = new CutAndPasteTransfer();
624 cap.setText(pcaModel.getPointsasCsv(false,
625 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
626 zCombobox.getSelectedIndex()));
627 Desktop.addInternalFrame(cap, MessageManager
628 .formatMessage("label.points_for_params", new String[]
629 { this.getTitle() }), 500, 500);
630 } catch (OutOfMemoryError oom)
632 new OOMWarning("exporting PCA points", oom);
641 * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
645 protected void outputProjPoints_actionPerformed(ActionEvent e)
647 CutAndPasteTransfer cap = new CutAndPasteTransfer();
650 cap.setText(pcaModel.getPointsasCsv(true,
651 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
652 zCombobox.getSelectedIndex()));
653 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
654 "label.transformed_points_for_params", new String[]
655 { this.getTitle() }), 500, 500);
656 } catch (OutOfMemoryError oom)
658 new OOMWarning("exporting transformed PCA points", oom);
666 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
669 public void setProgressBar(String message, long id)
671 progressBar.setProgressBar(message, id);
672 // if (progressBars == null)
674 // progressBars = new Hashtable();
675 // progressBarHandlers = new Hashtable();
678 // JPanel progressPanel;
679 // Long lId = new Long(id);
680 // GridLayout layout = (GridLayout) statusPanel.getLayout();
681 // if (progressBars.get(lId) != null)
683 // progressPanel = (JPanel) progressBars.get(new Long(id));
684 // statusPanel.remove(progressPanel);
685 // progressBars.remove(lId);
686 // progressPanel = null;
687 // if (message != null)
689 // statusBar.setText(message);
691 // if (progressBarHandlers.contains(lId))
693 // progressBarHandlers.remove(lId);
695 // layout.setRows(layout.getRows() - 1);
699 // progressPanel = new JPanel(new BorderLayout(10, 5));
701 // JProgressBar progressBar = new JProgressBar();
702 // progressBar.setIndeterminate(true);
704 // progressPanel.add(new JLabel(message), BorderLayout.WEST);
705 // progressPanel.add(progressBar, BorderLayout.CENTER);
707 // layout.setRows(layout.getRows() + 1);
708 // statusPanel.add(progressPanel);
710 // progressBars.put(lId, progressPanel);
713 // // setMenusForViewport();
718 public void registerHandler(final long id,
719 final IProgressIndicatorHandler handler)
721 progressBar.registerHandler(id, handler);
722 // if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
725 // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
727 // progressBarHandlers.put(new Long(id), handler);
728 // final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
729 // if (handler.canCancel())
731 // JButton cancel = new JButton(
732 // MessageManager.getString("action.cancel"));
733 // final IProgressIndicator us = this;
734 // cancel.addActionListener(new ActionListener()
738 // public void actionPerformed(ActionEvent e)
740 // handler.cancelActivity(id);
741 // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
742 // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
745 // progressPanel.add(cancel, BorderLayout.EAST);
751 * @return true if any progress bars are still active
754 public boolean operationInProgress()
756 return progressBar.operationInProgress();
760 protected void resetButton_actionPerformed(ActionEvent e)
763 top = 0; // ugly - prevents dimensionChanged events from being processed
764 xCombobox.setSelectedIndex(0);
765 yCombobox.setSelectedIndex(1);
767 zCombobox.setSelectedIndex(2);
771 * Answers true if PCA calculation is in progress, else false
775 public boolean isWorking()