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.event.ActionEvent;
38 import java.awt.event.ActionListener;
39 import java.awt.print.PageFormat;
40 import java.awt.print.Printable;
41 import java.awt.print.PrinterException;
42 import java.awt.print.PrinterJob;
44 import javax.swing.ButtonGroup;
45 import javax.swing.JCheckBoxMenuItem;
46 import javax.swing.JColorChooser;
47 import javax.swing.JMenuItem;
48 import javax.swing.JOptionPane;
49 import javax.swing.JRadioButtonMenuItem;
57 public class PCAPanel extends GPCAPanel implements Runnable,
61 private IProgressIndicator progressBar;
74 * Creates a new PCAPanel object.
81 public PCAPanel(AlignmentPanel ap)
86 progressBar = new ProgressBar(statusPanel, statusBar);
88 boolean sameLength = true;
89 boolean selected = av.getSelectionGroup() != null
90 && av.getSelectionGroup().getSize() > 0;
91 AlignmentView seqstrings = av.getAlignmentView(selected);
92 boolean nucleotide = av.getAlignment().isNucleotide();
96 seqs = av.getAlignment().getSequencesArray();
100 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
102 SeqCigar sq[] = seqstrings.getSequences();
103 int length = sq[0].getWidth();
105 for (int i = 0; i < seqs.length; i++)
107 if (sq[i].getWidth() != length)
116 JOptionPane.showMessageDialog(Desktop.desktop,
117 MessageManager.getString("label.pca_sequences_not_aligned"),
118 MessageManager.getString("label.sequences_not_aligned"),
119 JOptionPane.WARNING_MESSAGE);
123 pcaModel = new PCAModel(seqstrings, seqs, nucleotide);
124 PaintRefresher.Register(this, av.getSequenceSetId());
126 rc = new RotatableCanvas(ap);
127 this.getContentPane().add(rc, BorderLayout.CENTER);
128 Thread worker = new Thread(this);
133 protected void scoreMatrix_menuSelected()
135 scoreMatrixMenu.removeAll();
136 for (final String sm : ResidueProperties.scoreMatrices.keySet())
138 if (ResidueProperties.getScoreMatrix(sm) != null)
140 // create an entry for this score matrix for use in PCA
141 JCheckBoxMenuItem jm = new JCheckBoxMenuItem();
142 jm.setText(MessageManager
143 .getStringOrReturn("label.score_model", sm));
144 jm.setSelected(pcaModel.getScore_matrix().equals(sm));
145 if ((ResidueProperties.scoreMatrices.get(sm).isDNA() && ResidueProperties.scoreMatrices
146 .get(sm).isProtein())
147 || pcaModel.isNucleotide() == ResidueProperties.scoreMatrices
150 final PCAPanel us = this;
151 jm.addActionListener(new ActionListener()
154 public void actionPerformed(ActionEvent e)
156 if (!pcaModel.getScore_matrix().equals(sm))
158 pcaModel.setScore_matrix(sm);
159 Thread worker = new Thread(us);
164 scoreMatrixMenu.add(jm);
171 public void bgcolour_actionPerformed(ActionEvent e)
173 Color col = JColorChooser.showDialog(this,
174 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());
294 protected void xCombobox_actionPerformed(ActionEvent e)
306 protected void yCombobox_actionPerformed(ActionEvent e)
318 protected void zCombobox_actionPerformed(ActionEvent e)
324 public void outputValues_actionPerformed(ActionEvent e)
326 CutAndPasteTransfer cap = new CutAndPasteTransfer();
329 cap.setText(pcaModel.getDetails());
330 Desktop.addInternalFrame(cap,
331 MessageManager.getString("label.pca_details"), 500, 500);
332 } catch (OutOfMemoryError oom)
334 new OOMWarning("opening PCA details", oom);
340 public void showLabels_actionPerformed(ActionEvent e)
342 rc.showLabels(showLabels.getState());
346 public void print_actionPerformed(ActionEvent e)
348 PCAPrinter printer = new PCAPrinter();
353 public void originalSeqData_actionPerformed(ActionEvent e)
355 // this was cut'n'pasted from the equivalent TreePanel method - we should
356 // make this an abstract function of all jalview analysis windows
357 if (pcaModel.getSeqtrings() == null)
359 jalview.bin.Cache.log
360 .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
363 // decide if av alignment is sufficiently different to original data to
364 // warrant a new window to be created
365 // create new alignmnt window with hidden regions (unhiding hidden regions
366 // yields unaligned seqs)
367 // or create a selection box around columns in alignment view
368 // test Alignment(SeqCigar[])
372 // we try to get the associated view's gap character
373 // but this may fail if the view was closed...
374 gc = av.getGapCharacter();
375 } catch (Exception ex)
379 Object[] alAndColsel = pcaModel.getSeqtrings()
380 .getAlignmentAndColumnSelection(gc);
382 if (alAndColsel != null && alAndColsel[0] != null)
384 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
386 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
387 Alignment dataset = (av != null && av.getAlignment() != null) ? av
388 .getAlignment().getDataset() : null;
391 al.setDataset(dataset);
397 AlignFrame af = new AlignFrame(al,
398 (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
399 AlignFrame.DEFAULT_HEIGHT);
401 // >>>This is a fix for the moment, until a better solution is
403 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
405 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
408 Desktop.addInternalFrame(af, MessageManager.formatMessage(
409 "label.original_data_for_params",
410 new String[] { this.title }), AlignFrame.DEFAULT_WIDTH,
411 AlignFrame.DEFAULT_HEIGHT);
415 * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
416 * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
417 * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
420 * Desktop.addInternalFrame(cap, "Original Data", 400, 400);
424 class PCAPrinter extends Thread implements Printable
429 PrinterJob printJob = PrinterJob.getPrinterJob();
430 PageFormat pf = printJob.pageDialog(printJob.defaultPage());
432 printJob.setPrintable(this, pf);
434 if (printJob.printDialog())
439 } catch (Exception PrintException)
441 PrintException.printStackTrace();
447 public int print(Graphics pg, PageFormat pf, int pi)
448 throws PrinterException
450 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
452 rc.drawBackground(pg, rc.bgColour);
454 if (rc.drawAxes == true)
461 return Printable.PAGE_EXISTS;
465 return Printable.NO_SUCH_PAGE;
477 public void eps_actionPerformed(ActionEvent e)
479 makePCAImage(jalview.util.ImageMaker.TYPE.EPS);
489 public void png_actionPerformed(ActionEvent e)
491 makePCAImage(jalview.util.ImageMaker.TYPE.PNG);
494 void makePCAImage(jalview.util.ImageMaker.TYPE type)
496 int width = rc.getWidth();
497 int height = rc.getHeight();
499 jalview.util.ImageMaker im;
501 if (type == jalview.util.ImageMaker.TYPE.PNG)
503 im = new jalview.util.ImageMaker(this,
504 jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from PCA",
505 width, height, null, null, null, 0, false);
507 else if (type == jalview.util.ImageMaker.TYPE.EPS)
509 im = new jalview.util.ImageMaker(this,
510 jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from PCA",
511 width, height, null, this.getTitle(), null, 0, false);
515 im = new jalview.util.ImageMaker(this,
516 jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
517 width, height, null, this.getTitle(), null, 0, false);
521 if (im.getGraphics() != null)
523 rc.drawBackground(im.getGraphics(), Color.black);
524 rc.drawScene(im.getGraphics());
525 if (rc.drawAxes == true)
527 rc.drawAxes(im.getGraphics());
534 public void viewMenu_menuSelected()
536 buildAssociatedViewMenu();
539 void buildAssociatedViewMenu()
541 AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
542 .getSequenceSetId());
543 if (aps.length == 1 && rc.av == aps[0].av)
545 associateViewsMenu.setVisible(false);
549 associateViewsMenu.setVisible(true);
551 if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
553 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
556 associateViewsMenu.removeAll();
558 JRadioButtonMenuItem item;
559 ButtonGroup buttonGroup = new ButtonGroup();
560 int i, iSize = aps.length;
561 final PCAPanel thisPCAPanel = this;
562 for (i = 0; i < iSize; i++)
564 final AlignmentPanel ap = aps[i];
565 item = new JRadioButtonMenuItem(ap.av.viewName, ap.av == rc.av);
566 buttonGroup.add(item);
567 item.addActionListener(new ActionListener()
570 public void actionPerformed(ActionEvent evt)
572 rc.applyToAllViews = false;
575 PaintRefresher.Register(thisPCAPanel, ap.av.getSequenceSetId());
579 associateViewsMenu.add(item);
582 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
584 buttonGroup.add(itemf);
586 itemf.setSelected(rc.applyToAllViews);
587 itemf.addActionListener(new ActionListener()
590 public void actionPerformed(ActionEvent evt)
592 rc.applyToAllViews = itemf.isSelected();
595 associateViewsMenu.add(itemf);
603 * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
607 protected void outputPoints_actionPerformed(ActionEvent e)
609 CutAndPasteTransfer cap = new CutAndPasteTransfer();
612 cap.setText(pcaModel.getPointsasCsv(false,
613 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
614 zCombobox.getSelectedIndex()));
615 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
616 "label.points_for_params", new String[] { this.getTitle() }),
618 } catch (OutOfMemoryError oom)
620 new OOMWarning("exporting PCA points", oom);
629 * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
633 protected void outputProjPoints_actionPerformed(ActionEvent e)
635 CutAndPasteTransfer cap = new CutAndPasteTransfer();
638 cap.setText(pcaModel.getPointsasCsv(true,
639 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
640 zCombobox.getSelectedIndex()));
641 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
642 "label.transformed_points_for_params",
643 new String[] { this.getTitle() }), 500, 500);
644 } catch (OutOfMemoryError oom)
646 new OOMWarning("exporting transformed PCA points", oom);
654 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
657 public void setProgressBar(String message, long id)
659 progressBar.setProgressBar(message, id);
660 // if (progressBars == null)
662 // progressBars = new Hashtable();
663 // progressBarHandlers = new Hashtable();
666 // JPanel progressPanel;
667 // Long lId = new Long(id);
668 // GridLayout layout = (GridLayout) statusPanel.getLayout();
669 // if (progressBars.get(lId) != null)
671 // progressPanel = (JPanel) progressBars.get(new Long(id));
672 // statusPanel.remove(progressPanel);
673 // progressBars.remove(lId);
674 // progressPanel = null;
675 // if (message != null)
677 // statusBar.setText(message);
679 // if (progressBarHandlers.contains(lId))
681 // progressBarHandlers.remove(lId);
683 // layout.setRows(layout.getRows() - 1);
687 // progressPanel = new JPanel(new BorderLayout(10, 5));
689 // JProgressBar progressBar = new JProgressBar();
690 // progressBar.setIndeterminate(true);
692 // progressPanel.add(new JLabel(message), BorderLayout.WEST);
693 // progressPanel.add(progressBar, BorderLayout.CENTER);
695 // layout.setRows(layout.getRows() + 1);
696 // statusPanel.add(progressPanel);
698 // progressBars.put(lId, progressPanel);
701 // // setMenusForViewport();
706 public void registerHandler(final long id,
707 final IProgressIndicatorHandler handler)
709 progressBar.registerHandler(id, handler);
710 // if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
713 // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
715 // progressBarHandlers.put(new Long(id), handler);
716 // final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
717 // if (handler.canCancel())
719 // JButton cancel = new JButton(
720 // MessageManager.getString("action.cancel"));
721 // final IProgressIndicator us = this;
722 // cancel.addActionListener(new ActionListener()
726 // public void actionPerformed(ActionEvent e)
728 // handler.cancelActivity(id);
729 // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
730 // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
733 // progressPanel.add(cancel, BorderLayout.EAST);
739 * @return true if any progress bars are still active
742 public boolean operationInProgress()
744 return progressBar.operationInProgress();
748 protected void resetButton_actionPerformed(ActionEvent e)
751 top = 0; // ugly - prevents dimensionChanged events from being processed
752 xCombobox.setSelectedIndex(0);
753 yCombobox.setSelectedIndex(1);
755 zCombobox.setSelectedIndex(2);