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.api.analysis.ScoreModelI;
25 import jalview.api.analysis.SimilarityParamsI;
26 import jalview.bin.Cache;
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.math.RotatableMatrix.Axis;
34 import jalview.util.ImageMaker;
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.JColorChooser;
52 import javax.swing.JMenuItem;
53 import javax.swing.JRadioButtonMenuItem;
54 import javax.swing.event.InternalFrameAdapter;
55 import javax.swing.event.InternalFrameEvent;
58 * The panel holding the Principal Component Analysis 3-D visualisation
60 public class PCAPanel extends GPCAPanel
61 implements Runnable, IProgressIndicator
63 private static final int MIN_WIDTH = 470;
65 private static final int MIN_HEIGHT = 250;
77 private IProgressIndicator progressBar;
79 private boolean working;
82 * Constructor given sequence data, a similarity (or distance) score model
83 * name, and score calculation parameters
89 public PCAPanel(AlignmentPanel alignPanel, String modelName,
90 SimilarityParamsI params)
93 this.av = alignPanel.av;
95 boolean nucleotide = av.getAlignment().isNucleotide();
97 progressBar = new ProgressBar(statusPanel, statusBar);
99 addInternalFrameListener(new InternalFrameAdapter()
102 public void internalFrameClosed(InternalFrameEvent e)
104 close_actionPerformed();
108 boolean selected = av.getSelectionGroup() != null
109 && av.getSelectionGroup().getSize() > 0;
110 AlignmentView seqstrings = av.getAlignmentView(selected);
114 seqs = av.getAlignment().getSequencesArray();
118 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
121 ScoreModelI scoreModel = ScoreModels.getInstance()
122 .getScoreModel(modelName, ap);
123 pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
125 PaintRefresher.Register(this, av.getSequenceSetId());
127 rc = new RotatableCanvas(alignPanel);
128 this.getContentPane().add(rc, BorderLayout.CENTER);
133 this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
137 * Ensure references to potentially very large objects (the PCA matrices) are
138 * nulled when the frame is closed
140 protected void close_actionPerformed()
146 protected void bgcolour_actionPerformed()
148 Color col = JColorChooser.showDialog(this,
149 MessageManager.getString("label.select_background_colour"),
160 * Calculates the PCA and displays the results
165 long progId = System.currentTimeMillis();
166 IProgressIndicator progress = this;
167 String message = MessageManager.getString("label.pca_recalculating");
168 if (getParent() == null)
170 progress = ap.alignFrame;
171 message = MessageManager.getString("label.pca_calculating");
173 progress.setProgressBar(message, progId);
177 pcaModel.calculate();
179 xCombobox.setSelectedIndex(0);
180 yCombobox.setSelectedIndex(1);
181 zCombobox.setSelectedIndex(2);
183 pcaModel.updateRc(rc);
185 top = pcaModel.getTop();
187 } catch (OutOfMemoryError er)
189 new OOMWarning("calculating PCA", er);
194 progress.setProgressBar("", progId);
198 if (getParent() == null)
200 Desktop.addInternalFrame(this,
201 MessageManager.formatMessage("label.calc_title", "PCA",
202 pcaModel.getScoreModelName()),
209 * Updates the PCA display after a change of component to use for x, y or z
213 protected void doDimensionChange()
220 int dim1 = top - xCombobox.getSelectedIndex();
221 int dim2 = top - yCombobox.getSelectedIndex();
222 int dim3 = top - zCombobox.getSelectedIndex();
223 pcaModel.updateRcView(dim1, dim2, dim3);
228 * Sets the selected checkbox item index for PCA dimension (1, 2, 3...) for
229 * the given axis (X/Y/Z)
234 public void setSelectedDimensionIndex(int index, Axis axis)
239 xCombobox.setSelectedIndex(index);
242 yCombobox.setSelectedIndex(index);
245 zCombobox.setSelectedIndex(index);
252 protected void outputValues_actionPerformed()
254 CutAndPasteTransfer cap = new CutAndPasteTransfer();
257 cap.setText(pcaModel.getDetails());
258 Desktop.addInternalFrame(cap,
259 MessageManager.getString("label.pca_details"), 500, 500);
260 } catch (OutOfMemoryError oom)
262 new OOMWarning("opening PCA details", oom);
268 protected void showLabels_actionPerformed()
270 rc.showLabels(showLabels.getState());
274 protected void print_actionPerformed()
276 PCAPrinter printer = new PCAPrinter();
281 * If available, shows the data which formed the inputs for the PCA as a new
285 public void originalSeqData_actionPerformed()
287 // JAL-2647 disabled after load from project (until save to project done)
288 if (pcaModel.getInputData() == null)
291 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
294 // decide if av alignment is sufficiently different to original data to
295 // warrant a new window to be created
296 // create new alignment window with hidden regions (unhiding hidden regions
297 // yields unaligned seqs)
298 // or create a selection box around columns in alignment view
299 // test Alignment(SeqCigar[])
303 // we try to get the associated view's gap character
304 // but this may fail if the view was closed...
305 gc = av.getGapCharacter();
306 } catch (Exception ex)
310 Object[] alAndColsel = pcaModel.getInputData()
311 .getAlignmentAndHiddenColumns(gc);
313 if (alAndColsel != null && alAndColsel[0] != null)
315 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
317 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
318 AlignmentI dataset = (av != null && av.getAlignment() != null)
319 ? av.getAlignment().getDataset()
323 al.setDataset(dataset);
329 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
330 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
332 // >>>This is a fix for the moment, until a better solution is
334 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
336 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
339 Desktop.addInternalFrame(af, MessageManager.formatMessage(
340 "label.original_data_for_params", new String[]
341 { this.title }), AlignFrame.DEFAULT_WIDTH,
342 AlignFrame.DEFAULT_HEIGHT);
346 * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
347 * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
348 * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
351 * Desktop.addInternalFrame(cap, "Original Data", 400, 400);
355 class PCAPrinter extends Thread implements Printable
360 PrinterJob printJob = PrinterJob.getPrinterJob();
361 PageFormat defaultPage = printJob.defaultPage();
362 PageFormat pf = printJob.pageDialog(defaultPage);
364 if (defaultPage == pf)
372 printJob.setPrintable(this, pf);
374 if (printJob.printDialog())
379 } catch (Exception PrintException)
381 PrintException.printStackTrace();
387 public int print(Graphics pg, PageFormat pf, int pi)
388 throws PrinterException
390 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
392 rc.drawBackground(pg, rc.bgColour);
401 return Printable.PAGE_EXISTS;
405 return Printable.NO_SUCH_PAGE;
411 * Handler for 'Save as EPS' option
414 protected void eps_actionPerformed()
416 makePCAImage(ImageMaker.TYPE.EPS);
420 * Handler for 'Save as PNG' option
423 protected void png_actionPerformed()
425 makePCAImage(ImageMaker.TYPE.PNG);
428 void makePCAImage(ImageMaker.TYPE type)
430 int width = rc.getWidth();
431 int height = rc.getHeight();
435 if (type == ImageMaker.TYPE.PNG)
437 im = new ImageMaker(this, ImageMaker.TYPE.PNG,
438 "Make PNG image from PCA", width, height, null, null, null, 0,
441 else if (type == jalview.util.ImageMaker.TYPE.EPS)
443 im = new ImageMaker(this, ImageMaker.TYPE.EPS,
444 "Make EPS file from PCA", width, height, null,
445 this.getTitle(), null, 0, false);
449 im = new ImageMaker(this, ImageMaker.TYPE.SVG,
450 "Make SVG file from PCA", width, height, null,
451 this.getTitle(), null, 0, false);
454 if (im.getGraphics() != null)
456 rc.drawBackground(im.getGraphics(), Color.black);
457 rc.drawScene(im.getGraphics());
460 rc.drawAxes(im.getGraphics());
467 protected void viewMenu_menuSelected()
469 buildAssociatedViewMenu();
473 * Builds the menu showing the choice of possible views (for the associated
474 * sequence data) to which the PCA may be linked
476 void buildAssociatedViewMenu()
478 AlignmentPanel[] aps = PaintRefresher
479 .getAssociatedPanels(av.getSequenceSetId());
480 if (aps.length == 1 && rc.av == aps[0].av)
482 associateViewsMenu.setVisible(false);
486 associateViewsMenu.setVisible(true);
489 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
491 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
494 associateViewsMenu.removeAll();
496 JRadioButtonMenuItem item;
497 ButtonGroup buttonGroup = new ButtonGroup();
498 int iSize = aps.length;
500 for (int i = 0; i < iSize; i++)
502 final AlignmentPanel panel = aps[i];
503 item = new JRadioButtonMenuItem(panel.av.viewName, panel.av == rc.av);
504 buttonGroup.add(item);
505 item.addActionListener(new ActionListener()
508 public void actionPerformed(ActionEvent evt)
510 rc.applyToAllViews = false;
513 PaintRefresher.Register(PCAPanel.this,
514 panel.av.getSequenceSetId());
518 associateViewsMenu.add(item);
521 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
524 buttonGroup.add(itemf);
526 itemf.setSelected(rc.applyToAllViews);
527 itemf.addActionListener(new ActionListener()
530 public void actionPerformed(ActionEvent evt)
532 rc.applyToAllViews = itemf.isSelected();
535 associateViewsMenu.add(itemf);
543 * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
547 protected void outputPoints_actionPerformed()
549 CutAndPasteTransfer cap = new CutAndPasteTransfer();
552 cap.setText(pcaModel.getPointsasCsv(false,
553 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
554 zCombobox.getSelectedIndex()));
555 Desktop.addInternalFrame(cap, MessageManager
556 .formatMessage("label.points_for_params", new String[]
557 { this.getTitle() }), 500, 500);
558 } catch (OutOfMemoryError oom)
560 new OOMWarning("exporting PCA points", oom);
569 * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
573 protected void outputProjPoints_actionPerformed()
575 CutAndPasteTransfer cap = new CutAndPasteTransfer();
578 cap.setText(pcaModel.getPointsasCsv(true,
579 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
580 zCombobox.getSelectedIndex()));
581 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
582 "label.transformed_points_for_params", new String[]
583 { this.getTitle() }), 500, 500);
584 } catch (OutOfMemoryError oom)
586 new OOMWarning("exporting transformed PCA points", oom);
594 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
597 public void setProgressBar(String message, long id)
599 progressBar.setProgressBar(message, id);
600 // if (progressBars == null)
602 // progressBars = new Hashtable();
603 // progressBarHandlers = new Hashtable();
606 // JPanel progressPanel;
607 // Long lId = new Long(id);
608 // GridLayout layout = (GridLayout) statusPanel.getLayout();
609 // if (progressBars.get(lId) != null)
611 // progressPanel = (JPanel) progressBars.get(new Long(id));
612 // statusPanel.remove(progressPanel);
613 // progressBars.remove(lId);
614 // progressPanel = null;
615 // if (message != null)
617 // statusBar.setText(message);
619 // if (progressBarHandlers.contains(lId))
621 // progressBarHandlers.remove(lId);
623 // layout.setRows(layout.getRows() - 1);
627 // progressPanel = new JPanel(new BorderLayout(10, 5));
629 // JProgressBar progressBar = new JProgressBar();
630 // progressBar.setIndeterminate(true);
632 // progressPanel.add(new JLabel(message), BorderLayout.WEST);
633 // progressPanel.add(progressBar, BorderLayout.CENTER);
635 // layout.setRows(layout.getRows() + 1);
636 // statusPanel.add(progressPanel);
638 // progressBars.put(lId, progressPanel);
641 // // setMenusForViewport();
646 public void registerHandler(final long id,
647 final IProgressIndicatorHandler handler)
649 progressBar.registerHandler(id, handler);
650 // if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
653 // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
655 // progressBarHandlers.put(new Long(id), handler);
656 // final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
657 // if (handler.canCancel())
659 // JButton cancel = new JButton(
660 // MessageManager.getString("action.cancel"));
661 // final IProgressIndicator us = this;
662 // cancel.addActionListener(new ActionListener()
666 // public void actionPerformed(ActionEvent e)
668 // handler.cancelActivity(id);
669 // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
670 // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
673 // progressPanel.add(cancel, BorderLayout.EAST);
679 * @return true if any progress bars are still active
682 public boolean operationInProgress()
684 return progressBar.operationInProgress();
688 protected void resetButton_actionPerformed()
691 top = 0; // ugly - prevents dimensionChanged events from being processed
692 xCombobox.setSelectedIndex(0);
693 yCombobox.setSelectedIndex(1);
695 zCombobox.setSelectedIndex(2);
699 * Answers true if PCA calculation is in progress, else false
703 public boolean isWorking()
709 * Answers the selected checkbox item index for PCA dimension for the X, Y or
710 * Z axis of the display
715 public int getSelectedDimensionIndex(Axis axis)
720 return xCombobox.getSelectedIndex();
722 return yCombobox.getSelectedIndex();
724 return zCombobox.getSelectedIndex();
728 public void setShowLabels(boolean show)
730 showLabels.setSelected(show);
734 * Sets the input data used to calculate the PCA. This is provided for
735 * 'restore from project', which does not currently support this (AL-2647), so
736 * sets the value to null, and hides the menu option for "Input Data...". J
740 public void setInputData(AlignmentView data)
742 pcaModel.setInputData(data);
743 originalSeqData.setVisible(data != null);