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.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.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.JCheckBoxMenuItem;
50 import javax.swing.JColorChooser;
51 import javax.swing.JMenuItem;
52 import javax.swing.JRadioButtonMenuItem;
53 import javax.swing.event.InternalFrameAdapter;
54 import javax.swing.event.InternalFrameEvent;
62 public class PCAPanel extends GPCAPanel
63 implements Runnable, IProgressIndicator
66 private IProgressIndicator progressBar;
76 private static final int MIN_WIDTH = 470;
78 private static final int MIN_HEIGHT = 250;
83 * Creates a new PCAPanel object using default score model and parameters
87 public PCAPanel(AlignmentPanel alignPanel)
90 ScoreModels.getInstance()
92 !alignPanel.av.getAlignment().isNucleotide())
94 SimilarityParams.SeqSpace);
98 * Constructor given sequence data, a similarity (or distance) score model
99 * name, and score calculation parameters
105 public PCAPanel(AlignmentPanel alignPanel, String modelName,
106 SimilarityParamsI params)
109 this.av = alignPanel.av;
110 this.ap = alignPanel;
111 boolean nucleotide = av.getAlignment().isNucleotide();
113 progressBar = new ProgressBar(statusPanel, statusBar);
115 addInternalFrameListener(new InternalFrameAdapter()
118 public void internalFrameClosed(InternalFrameEvent e)
120 close_actionPerformed();
124 boolean selected = av.getSelectionGroup() != null
125 && av.getSelectionGroup().getSize() > 0;
126 AlignmentView seqstrings = av.getAlignmentView(selected);
130 seqs = av.getAlignment().getSequencesArray();
134 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
137 ScoreModelI scoreModel = ScoreModels.getInstance()
138 .getScoreModel(modelName, ap);
139 pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
141 PaintRefresher.Register(this, av.getSequenceSetId());
143 rc = new RotatableCanvas(alignPanel);
144 this.getContentPane().add(rc, BorderLayout.CENTER);
145 Thread worker = new Thread(this);
150 * Ensure references to potentially very large objects (the PCA matrices) are
151 * nulled when the frame is closed
153 protected void close_actionPerformed()
159 * Repopulate the options and actions under the score model menu when it is
160 * selected. Options will depend on whether 'nucleotide' or 'peptide'
161 * modelling is selected (and also possibly on whether any additional score
162 * models have been added).
165 protected void scoreModel_menuSelected()
167 scoreModelMenu.removeAll();
168 for (final ScoreModelI sm : ScoreModels.getInstance().getModels())
170 final String name = sm.getName();
171 JCheckBoxMenuItem jm = new JCheckBoxMenuItem(name);
174 * if the score model doesn't provide a description, try to look one
175 * up in the text bundle, falling back on its name
177 String tooltip = sm.getDescription();
180 tooltip = MessageManager.getStringOrReturn("label.score_model_",
183 jm.setToolTipText(tooltip);
184 jm.setSelected(pcaModel.getScoreModelName().equals(name));
185 if ((pcaModel.isNucleotide() && sm.isDNA())
186 || (!pcaModel.isNucleotide() && sm.isProtein()))
188 jm.addActionListener(new ActionListener()
191 public void actionPerformed(ActionEvent e)
193 if (!pcaModel.getScoreModelName().equals(name))
195 ScoreModelI sm2 = ScoreModels.getInstance()
196 .getScoreModel(name, ap);
197 pcaModel.setScoreModel(sm2);
198 Thread worker = new Thread(PCAPanel.this);
203 scoreModelMenu.add(jm);
209 public void bgcolour_actionPerformed(ActionEvent e)
211 Color col = JColorChooser.showDialog(this,
212 MessageManager.getString("label.select_background_colour"),
228 long progId = System.currentTimeMillis();
229 IProgressIndicator progress = this;
230 String message = MessageManager.getString("label.pca_recalculating");
231 if (getParent() == null)
233 progress = ap.alignFrame;
234 message = MessageManager.getString("label.pca_calculating");
236 progress.setProgressBar(message, progId);
239 calcSettings.setEnabled(false);
242 xCombobox.setSelectedIndex(0);
243 yCombobox.setSelectedIndex(1);
244 zCombobox.setSelectedIndex(2);
246 pcaModel.updateRc(rc);
248 nuclSetting.setSelected(pcaModel.isNucleotide());
249 protSetting.setSelected(!pcaModel.isNucleotide());
250 top = pcaModel.getTop();
252 } catch (OutOfMemoryError er)
254 new OOMWarning("calculating PCA", er);
258 progress.setProgressBar("", progId);
260 calcSettings.setEnabled(true);
262 if (getParent() == null)
265 Desktop.addInternalFrame(this, MessageManager
266 .getString("label.principal_component_analysis"), 475, 450);
267 this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
272 protected void nuclSetting_actionPerfomed(ActionEvent arg0)
274 if (!pcaModel.isNucleotide())
276 pcaModel.setNucleotide(true);
277 pcaModel.setScoreModel(
278 ScoreModels.getInstance().getDefaultModel(false));
279 Thread worker = new Thread(this);
286 protected void protSetting_actionPerfomed(ActionEvent arg0)
289 if (pcaModel.isNucleotide())
291 pcaModel.setNucleotide(false);
292 pcaModel.setScoreModel(
293 ScoreModels.getInstance().getDefaultModel(true));
294 Thread worker = new Thread(this);
302 void doDimensionChange()
309 int dim1 = top - xCombobox.getSelectedIndex();
310 int dim2 = top - yCombobox.getSelectedIndex();
311 int dim3 = top - zCombobox.getSelectedIndex();
312 pcaModel.updateRcView(dim1, dim2, dim3);
314 rc.rotmat.setIdentity();
316 rc.paint(rc.getGraphics());
326 protected void xCombobox_actionPerformed(ActionEvent e)
338 protected void yCombobox_actionPerformed(ActionEvent e)
350 protected void zCombobox_actionPerformed(ActionEvent e)
356 public void outputValues_actionPerformed(ActionEvent e)
358 CutAndPasteTransfer cap = new CutAndPasteTransfer();
361 cap.setText(pcaModel.getDetails());
362 Desktop.addInternalFrame(cap,
363 MessageManager.getString("label.pca_details"), 500, 500);
364 } catch (OutOfMemoryError oom)
366 new OOMWarning("opening PCA details", oom);
372 public void showLabels_actionPerformed(ActionEvent e)
374 rc.showLabels(showLabels.getState());
378 public void print_actionPerformed(ActionEvent e)
380 PCAPrinter printer = new PCAPrinter();
385 public void originalSeqData_actionPerformed(ActionEvent e)
387 // this was cut'n'pasted from the equivalent TreePanel method - we should
388 // make this an abstract function of all jalview analysis windows
389 if (pcaModel.getSeqtrings() == null)
391 jalview.bin.Cache.log.info(
392 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
395 // decide if av alignment is sufficiently different to original data to
396 // warrant a new window to be created
397 // create new alignmnt window with hidden regions (unhiding hidden regions
398 // yields unaligned seqs)
399 // or create a selection box around columns in alignment view
400 // test Alignment(SeqCigar[])
404 // we try to get the associated view's gap character
405 // but this may fail if the view was closed...
406 gc = av.getGapCharacter();
407 } catch (Exception ex)
411 Object[] alAndColsel = pcaModel.getSeqtrings()
412 .getAlignmentAndHiddenColumns(gc);
414 if (alAndColsel != null && alAndColsel[0] != null)
416 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
418 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
419 AlignmentI dataset = (av != null && av.getAlignment() != null)
420 ? av.getAlignment().getDataset()
424 al.setDataset(dataset);
430 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
431 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
433 // >>>This is a fix for the moment, until a better solution is
435 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
437 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
440 Desktop.addInternalFrame(af, MessageManager.formatMessage(
441 "label.original_data_for_params", new String[]
442 { this.title }), AlignFrame.DEFAULT_WIDTH,
443 AlignFrame.DEFAULT_HEIGHT);
447 * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
448 * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
449 * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
452 * Desktop.addInternalFrame(cap, "Original Data", 400, 400);
456 class PCAPrinter extends Thread implements Printable
461 PrinterJob printJob = PrinterJob.getPrinterJob();
462 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
464 printJob.setPrintable(this, pf);
466 if (printJob.printDialog())
471 } catch (Exception PrintException)
473 PrintException.printStackTrace();
479 public int print(Graphics pg, PageFormat pf, int pi)
480 throws PrinterException
482 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
484 rc.drawBackground(pg, rc.bgColour);
486 if (rc.drawAxes == true)
493 return Printable.PAGE_EXISTS;
497 return Printable.NO_SUCH_PAGE;
509 public void eps_actionPerformed(ActionEvent e)
511 makePCAImage(jalview.util.ImageMaker.TYPE.EPS);
521 public void png_actionPerformed(ActionEvent e)
523 makePCAImage(jalview.util.ImageMaker.TYPE.PNG);
526 void makePCAImage(jalview.util.ImageMaker.TYPE type)
528 int width = rc.getWidth();
529 int height = rc.getHeight();
531 jalview.util.ImageMaker im;
533 if (type == jalview.util.ImageMaker.TYPE.PNG)
535 im = new jalview.util.ImageMaker(this,
536 jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from PCA",
537 width, height, null, null, null, 0, false);
539 else if (type == jalview.util.ImageMaker.TYPE.EPS)
541 im = new jalview.util.ImageMaker(this,
542 jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from PCA",
543 width, height, null, this.getTitle(), null, 0, false);
547 im = new jalview.util.ImageMaker(this,
548 jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
549 width, height, null, this.getTitle(), null, 0, false);
553 if (im.getGraphics() != null)
555 rc.drawBackground(im.getGraphics(), Color.black);
556 rc.drawScene(im.getGraphics());
557 if (rc.drawAxes == true)
559 rc.drawAxes(im.getGraphics());
566 public void viewMenu_menuSelected()
568 buildAssociatedViewMenu();
571 void buildAssociatedViewMenu()
573 AlignmentPanel[] aps = PaintRefresher
574 .getAssociatedPanels(av.getSequenceSetId());
575 if (aps.length == 1 && rc.av == aps[0].av)
577 associateViewsMenu.setVisible(false);
581 associateViewsMenu.setVisible(true);
584 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
586 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
589 associateViewsMenu.removeAll();
591 JRadioButtonMenuItem item;
592 ButtonGroup buttonGroup = new ButtonGroup();
593 int i, iSize = aps.length;
594 final PCAPanel thisPCAPanel = this;
595 for (i = 0; i < iSize; i++)
597 final AlignmentPanel ap = aps[i];
598 item = new JRadioButtonMenuItem(ap.av.viewName, ap.av == rc.av);
599 buttonGroup.add(item);
600 item.addActionListener(new ActionListener()
603 public void actionPerformed(ActionEvent evt)
605 rc.applyToAllViews = false;
608 PaintRefresher.Register(thisPCAPanel, ap.av.getSequenceSetId());
612 associateViewsMenu.add(item);
615 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
618 buttonGroup.add(itemf);
620 itemf.setSelected(rc.applyToAllViews);
621 itemf.addActionListener(new ActionListener()
624 public void actionPerformed(ActionEvent evt)
626 rc.applyToAllViews = itemf.isSelected();
629 associateViewsMenu.add(itemf);
637 * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
641 protected void outputPoints_actionPerformed(ActionEvent e)
643 CutAndPasteTransfer cap = new CutAndPasteTransfer();
646 cap.setText(pcaModel.getPointsasCsv(false,
647 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
648 zCombobox.getSelectedIndex()));
649 Desktop.addInternalFrame(cap, MessageManager
650 .formatMessage("label.points_for_params", new String[]
651 { this.getTitle() }), 500, 500);
652 } catch (OutOfMemoryError oom)
654 new OOMWarning("exporting PCA points", oom);
663 * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
667 protected void outputProjPoints_actionPerformed(ActionEvent e)
669 CutAndPasteTransfer cap = new CutAndPasteTransfer();
672 cap.setText(pcaModel.getPointsasCsv(true,
673 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
674 zCombobox.getSelectedIndex()));
675 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
676 "label.transformed_points_for_params", new String[]
677 { this.getTitle() }), 500, 500);
678 } catch (OutOfMemoryError oom)
680 new OOMWarning("exporting transformed PCA points", oom);
688 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
691 public void setProgressBar(String message, long id)
693 progressBar.setProgressBar(message, id);
694 // if (progressBars == null)
696 // progressBars = new Hashtable();
697 // progressBarHandlers = new Hashtable();
700 // JPanel progressPanel;
701 // Long lId = new Long(id);
702 // GridLayout layout = (GridLayout) statusPanel.getLayout();
703 // if (progressBars.get(lId) != null)
705 // progressPanel = (JPanel) progressBars.get(new Long(id));
706 // statusPanel.remove(progressPanel);
707 // progressBars.remove(lId);
708 // progressPanel = null;
709 // if (message != null)
711 // statusBar.setText(message);
713 // if (progressBarHandlers.contains(lId))
715 // progressBarHandlers.remove(lId);
717 // layout.setRows(layout.getRows() - 1);
721 // progressPanel = new JPanel(new BorderLayout(10, 5));
723 // JProgressBar progressBar = new JProgressBar();
724 // progressBar.setIndeterminate(true);
726 // progressPanel.add(new JLabel(message), BorderLayout.WEST);
727 // progressPanel.add(progressBar, BorderLayout.CENTER);
729 // layout.setRows(layout.getRows() + 1);
730 // statusPanel.add(progressPanel);
732 // progressBars.put(lId, progressPanel);
735 // // setMenusForViewport();
740 public void registerHandler(final long id,
741 final IProgressIndicatorHandler handler)
743 progressBar.registerHandler(id, handler);
744 // if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
747 // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
749 // progressBarHandlers.put(new Long(id), handler);
750 // final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
751 // if (handler.canCancel())
753 // JButton cancel = new JButton(
754 // MessageManager.getString("action.cancel"));
755 // final IProgressIndicator us = this;
756 // cancel.addActionListener(new ActionListener()
760 // public void actionPerformed(ActionEvent e)
762 // handler.cancelActivity(id);
763 // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
764 // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
767 // progressPanel.add(cancel, BorderLayout.EAST);
773 * @return true if any progress bars are still active
776 public boolean operationInProgress()
778 return progressBar.operationInProgress();
782 protected void resetButton_actionPerformed(ActionEvent e)
785 top = 0; // ugly - prevents dimensionChanged events from being processed
786 xCombobox.setSelectedIndex(0);
787 yCombobox.setSelectedIndex(1);
789 zCombobox.setSelectedIndex(2);