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.AlignmentView;
25 import jalview.datamodel.ColumnSelection;
26 import jalview.datamodel.SeqCigar;
27 import jalview.datamodel.SequenceI;
28 import jalview.jbgui.GPCAPanel;
29 import jalview.schemes.ResidueProperties;
30 import jalview.util.MessageManager;
31 import jalview.viewmodel.AlignmentViewport;
32 import jalview.viewmodel.PCAModel;
34 import java.awt.BorderLayout;
35 import java.awt.Color;
36 import java.awt.Graphics;
37 import java.awt.GridLayout;
38 import java.awt.event.ActionEvent;
39 import java.awt.event.ActionListener;
40 import java.awt.print.PageFormat;
41 import java.awt.print.Printable;
42 import java.awt.print.PrinterException;
43 import java.awt.print.PrinterJob;
44 import java.util.Hashtable;
46 import javax.swing.ButtonGroup;
47 import javax.swing.JButton;
48 import javax.swing.JCheckBoxMenuItem;
49 import javax.swing.JColorChooser;
50 import javax.swing.JLabel;
51 import javax.swing.JMenuItem;
52 import javax.swing.JOptionPane;
53 import javax.swing.JPanel;
54 import javax.swing.JProgressBar;
55 import javax.swing.JRadioButtonMenuItem;
63 public class PCAPanel extends GPCAPanel implements Runnable,
78 * Creates a new PCAPanel object.
85 public PCAPanel(AlignmentPanel ap)
90 boolean sameLength = true;
91 boolean selected = av.getSelectionGroup() != null
92 && av.getSelectionGroup().getSize() > 0;
93 AlignmentView seqstrings = av.getAlignmentView(selected);
94 boolean nucleotide = av.getAlignment().isNucleotide();
98 seqs = av.getAlignment().getSequencesArray();
102 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
104 SeqCigar sq[] = seqstrings.getSequences();
105 int length = sq[0].getWidth();
107 for (int i = 0; i < seqs.length; i++)
109 if (sq[i].getWidth() != length)
121 MessageManager.getString("label.pca_sequences_not_aligned"),
122 MessageManager.getString("label.sequences_not_aligned"), JOptionPane.WARNING_MESSAGE);
126 pcaModel = new PCAModel(seqstrings, seqs, nucleotide);
127 PaintRefresher.Register(this, av.getSequenceSetId());
129 rc = new RotatableCanvas(ap);
130 this.getContentPane().add(rc, BorderLayout.CENTER);
131 Thread worker = new Thread(this);
136 protected void scoreMatrix_menuSelected()
138 scoreMatrixMenu.removeAll();
139 for (final String sm : ResidueProperties.scoreMatrices.keySet())
141 if (ResidueProperties.getScoreMatrix(sm) != null)
143 // create an entry for this score matrix for use in PCA
144 JCheckBoxMenuItem jm = new JCheckBoxMenuItem();
145 jm.setText(MessageManager
146 .getStringOrReturn("label.score_model", sm));
147 jm.setSelected(pcaModel.getScore_matrix().equals(sm));
148 if ((ResidueProperties.scoreMatrices.get(sm).isDNA() && ResidueProperties.scoreMatrices
149 .get(sm).isProtein())
150 || pcaModel.isNucleotide() == ResidueProperties.scoreMatrices
153 final PCAPanel us = this;
154 jm.addActionListener(new ActionListener()
157 public void actionPerformed(ActionEvent e)
159 if (!pcaModel.getScore_matrix().equals(sm))
161 pcaModel.setScore_matrix(sm);
162 Thread worker = new Thread(us);
167 scoreMatrixMenu.add(jm);
173 public void bgcolour_actionPerformed(ActionEvent e)
175 Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_backgroud_colour"),
190 long progId = System.currentTimeMillis();
191 IProgressIndicator progress = this;
192 String message = MessageManager.getString("label.pca_recalculating");
193 if (getParent() == null)
195 progress = ap.alignFrame;
196 message = MessageManager.getString("label.pca_calculating");
198 progress.setProgressBar(message, progId);
201 calcSettings.setEnabled(false);
204 xCombobox.setSelectedIndex(0);
205 yCombobox.setSelectedIndex(1);
206 zCombobox.setSelectedIndex(2);
208 pcaModel.updateRc(rc);
210 nuclSetting.setSelected(pcaModel.isNucleotide());
211 protSetting.setSelected(!pcaModel.isNucleotide());
212 jvVersionSetting.setSelected(pcaModel.isJvCalcMode());
213 top = pcaModel.getTop();
215 } catch (OutOfMemoryError er)
217 new OOMWarning("calculating PCA", er);
221 progress.setProgressBar("", progId);
223 calcSettings.setEnabled(true);
225 if (getParent() == null)
228 Desktop.addInternalFrame(this, MessageManager
229 .getString("label.principal_component_analysis"), 475, 450);
234 protected void nuclSetting_actionPerfomed(ActionEvent arg0)
236 if (!pcaModel.isNucleotide())
238 pcaModel.setNucleotide(true);
239 pcaModel.setScore_matrix("DNA");
240 Thread worker = new Thread(this);
247 protected void protSetting_actionPerfomed(ActionEvent arg0)
250 if (pcaModel.isNucleotide())
252 pcaModel.setNucleotide(false);
253 pcaModel.setScore_matrix("BLOSUM62");
254 Thread worker = new Thread(this);
260 protected void jvVersionSetting_actionPerfomed(ActionEvent arg0)
262 pcaModel.setJvCalcMode(jvVersionSetting.isSelected());
263 Thread worker = new Thread(this);
270 void doDimensionChange()
277 int dim1 = top - xCombobox.getSelectedIndex();
278 int dim2 = top - yCombobox.getSelectedIndex();
279 int dim3 = top - zCombobox.getSelectedIndex();
280 pcaModel.updateRcView(dim1, dim2, dim3);
282 rc.rotmat.setIdentity();
284 rc.paint(rc.getGraphics());
293 protected void xCombobox_actionPerformed(ActionEvent e)
304 protected void yCombobox_actionPerformed(ActionEvent e)
315 protected void zCombobox_actionPerformed(ActionEvent e)
320 public void outputValues_actionPerformed(ActionEvent e)
322 CutAndPasteTransfer cap = new CutAndPasteTransfer();
325 cap.setText(pcaModel.getDetails());
326 Desktop.addInternalFrame(cap,
327 MessageManager.getString("label.pca_details"), 500, 500);
328 } catch (OutOfMemoryError oom)
330 new OOMWarning("opening PCA details", oom);
335 public void showLabels_actionPerformed(ActionEvent e)
337 rc.showLabels(showLabels.getState());
340 public void print_actionPerformed(ActionEvent e)
342 PCAPrinter printer = new PCAPrinter();
346 public void originalSeqData_actionPerformed(ActionEvent e)
348 // this was cut'n'pasted from the equivalent TreePanel method - we should
349 // make this an abstract function of all jalview analysis windows
350 if (pcaModel.getSeqtrings() == null)
352 jalview.bin.Cache.log
353 .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
356 // decide if av alignment is sufficiently different to original data to
357 // warrant a new window to be created
358 // create new alignmnt window with hidden regions (unhiding hidden regions
359 // yields unaligned seqs)
360 // or create a selection box around columns in alignment view
361 // test Alignment(SeqCigar[])
365 // we try to get the associated view's gap character
366 // but this may fail if the view was closed...
367 gc = av.getGapCharacter();
368 } catch (Exception ex)
372 Object[] alAndColsel = pcaModel.getSeqtrings()
373 .getAlignmentAndColumnSelection(gc);
375 if (alAndColsel != null && alAndColsel[0] != null)
377 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
379 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
380 Alignment dataset = (av != null && av.getAlignment() != null) ? av
381 .getAlignment().getDataset() : null;
384 al.setDataset(dataset);
390 AlignFrame af = new AlignFrame(al,
391 (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
392 AlignFrame.DEFAULT_HEIGHT);
394 // >>>This is a fix for the moment, until a better solution is
396 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
398 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
401 Desktop.addInternalFrame(af, MessageManager.formatMessage(
402 "label.original_data_for_params", new String[]
403 { this.title }), AlignFrame.DEFAULT_WIDTH,
404 AlignFrame.DEFAULT_HEIGHT);
408 * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
409 * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
410 * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
413 * Desktop.addInternalFrame(cap, "Original Data", 400, 400);
417 class PCAPrinter extends Thread implements Printable
421 PrinterJob printJob = PrinterJob.getPrinterJob();
422 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
424 printJob.setPrintable(this, pf);
426 if (printJob.printDialog())
431 } catch (Exception PrintException)
433 PrintException.printStackTrace();
438 public int print(Graphics pg, PageFormat pf, int pi)
439 throws PrinterException
441 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
443 rc.drawBackground(pg, rc.bgColour);
445 if (rc.drawAxes == true)
452 return Printable.PAGE_EXISTS;
456 return Printable.NO_SUCH_PAGE;
467 public void eps_actionPerformed(ActionEvent e)
469 makePCAImage(jalview.util.ImageMaker.TYPE.EPS);
478 public void png_actionPerformed(ActionEvent e)
480 makePCAImage(jalview.util.ImageMaker.TYPE.PNG);
483 void makePCAImage(jalview.util.ImageMaker.TYPE type)
485 int width = rc.getWidth();
486 int height = rc.getHeight();
488 jalview.util.ImageMaker im;
490 if (type == jalview.util.ImageMaker.TYPE.PNG)
492 im = new jalview.util.ImageMaker(this,
493 jalview.util.ImageMaker.TYPE.PNG,
494 "Make PNG image from PCA", width, height, null, null);
496 else if (type == jalview.util.ImageMaker.TYPE.EPS)
498 im = new jalview.util.ImageMaker(this,
499 jalview.util.ImageMaker.TYPE.EPS,
500 "Make EPS file from PCA", width, height, null,
505 im = new jalview.util.ImageMaker(this,
506 jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
507 width, height, null, this.getTitle());
511 if (im.getGraphics() != null)
513 rc.drawBackground(im.getGraphics(), Color.black);
514 rc.drawScene(im.getGraphics());
515 if (rc.drawAxes == true)
517 rc.drawAxes(im.getGraphics());
523 public void viewMenu_menuSelected()
525 buildAssociatedViewMenu();
528 void buildAssociatedViewMenu()
530 AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
531 .getSequenceSetId());
532 if (aps.length == 1 && rc.av == aps[0].av)
534 associateViewsMenu.setVisible(false);
538 associateViewsMenu.setVisible(true);
540 if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
542 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
545 associateViewsMenu.removeAll();
547 JRadioButtonMenuItem item;
548 ButtonGroup buttonGroup = new ButtonGroup();
549 int i, iSize = aps.length;
550 final PCAPanel thisPCAPanel = this;
551 for (i = 0; i < iSize; i++)
553 final AlignmentPanel ap = aps[i];
554 item = new JRadioButtonMenuItem(ap.av.viewName, ap.av == rc.av);
555 buttonGroup.add(item);
556 item.addActionListener(new ActionListener()
558 public void actionPerformed(ActionEvent evt)
560 rc.applyToAllViews = false;
563 PaintRefresher.Register(thisPCAPanel, ap.av.getSequenceSetId());
567 associateViewsMenu.add(item);
570 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
572 buttonGroup.add(itemf);
574 itemf.setSelected(rc.applyToAllViews);
575 itemf.addActionListener(new ActionListener()
577 public void actionPerformed(ActionEvent evt)
579 rc.applyToAllViews = itemf.isSelected();
582 associateViewsMenu.add(itemf);
590 * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
593 protected void outputPoints_actionPerformed(ActionEvent e)
595 CutAndPasteTransfer cap = new CutAndPasteTransfer();
598 cap.setText(pcaModel.getPointsasCsv(false,
599 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
600 zCombobox.getSelectedIndex()));
601 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
602 "label.points_for_params", new String[]
603 { this.getTitle() }), 500, 500);
604 } catch (OutOfMemoryError oom)
606 new OOMWarning("exporting PCA points", oom);
615 * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
618 protected void outputProjPoints_actionPerformed(ActionEvent e)
620 CutAndPasteTransfer cap = new CutAndPasteTransfer();
623 cap.setText(pcaModel.getPointsasCsv(true,
624 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
625 zCombobox.getSelectedIndex()));
626 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
627 "label.transformed_points_for_params", new String[]
628 { this.getTitle() }), 500, 500);
629 } catch (OutOfMemoryError oom)
631 new OOMWarning("exporting transformed PCA points", oom);
636 // methods for implementing IProgressIndicator
637 // need to refactor to a reusable stub class
638 Hashtable progressBars, progressBarHandlers;
643 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
646 public void setProgressBar(String message, long id)
648 if (progressBars == null)
650 progressBars = new Hashtable();
651 progressBarHandlers = new Hashtable();
654 JPanel progressPanel;
655 Long lId = new Long(id);
656 GridLayout layout = (GridLayout) statusPanel.getLayout();
657 if (progressBars.get(lId) != null)
659 progressPanel = (JPanel) progressBars.get(new Long(id));
660 statusPanel.remove(progressPanel);
661 progressBars.remove(lId);
662 progressPanel = null;
665 statusBar.setText(message);
667 if (progressBarHandlers.contains(lId))
669 progressBarHandlers.remove(lId);
671 layout.setRows(layout.getRows() - 1);
675 progressPanel = new JPanel(new BorderLayout(10, 5));
677 JProgressBar progressBar = new JProgressBar();
678 progressBar.setIndeterminate(true);
680 progressPanel.add(new JLabel(message), BorderLayout.WEST);
681 progressPanel.add(progressBar, BorderLayout.CENTER);
683 layout.setRows(layout.getRows() + 1);
684 statusPanel.add(progressPanel);
686 progressBars.put(lId, progressPanel);
689 // setMenusForViewport();
694 public void registerHandler(final long id,
695 final IProgressIndicatorHandler handler)
697 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
699 throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
701 progressBarHandlers.put(new Long(id), handler);
702 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
703 if (handler.canCancel())
705 JButton cancel = new JButton(
706 MessageManager.getString("action.cancel"));
707 final IProgressIndicator us = this;
708 cancel.addActionListener(new ActionListener()
712 public void actionPerformed(ActionEvent e)
714 handler.cancelActivity(id);
715 us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
718 progressPanel.add(cancel, BorderLayout.EAST);
724 * @return true if any progress bars are still active
727 public boolean operationInProgress()
729 if (progressBars != null && progressBars.size() > 0)
737 protected void resetButton_actionPerformed(ActionEvent e)
740 top = 0; // ugly - prevents dimensionChanged events from being processed
741 xCombobox.setSelectedIndex(0);
742 yCombobox.setSelectedIndex(1);
744 zCombobox.setSelectedIndex(2);