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 java.awt.BorderLayout;
24 import java.awt.Color;
25 import java.awt.Dimension;
26 import java.awt.Graphics;
27 import java.awt.event.ActionEvent;
28 import java.awt.event.ActionListener;
29 import java.awt.print.PageFormat;
30 import java.awt.print.Printable;
31 import java.awt.print.PrinterException;
32 import java.awt.print.PrinterJob;
34 import javax.swing.ButtonGroup;
35 import javax.swing.JMenuItem;
36 import javax.swing.JProgressBar;
37 import javax.swing.JRadioButtonMenuItem;
38 import javax.swing.event.InternalFrameAdapter;
39 import javax.swing.event.InternalFrameEvent;
41 import jalview.analysis.scoremodels.ScoreModels;
42 import jalview.api.AlignViewportI;
43 import jalview.api.analysis.ScoreModelI;
44 import jalview.api.analysis.SimilarityParamsI;
45 import jalview.bin.Console;
46 import jalview.datamodel.Alignment;
47 import jalview.datamodel.AlignmentI;
48 import jalview.datamodel.AlignmentView;
49 import jalview.datamodel.HiddenColumns;
50 import jalview.datamodel.SequenceI;
51 import jalview.gui.ImageExporter.ImageWriterI;
52 import jalview.gui.JalviewColourChooser.ColourChooserListener;
53 import jalview.io.exceptions.ImageOutputException;
54 import jalview.jbgui.GPCAPanel;
55 import jalview.math.RotatableMatrix.Axis;
56 import jalview.util.ImageMaker;
57 import jalview.util.MessageManager;
58 import jalview.viewmodel.AlignmentViewport;
59 import jalview.viewmodel.PCAModel;
62 * The panel holding the Principal Component Analysis 3-D visualisation
64 public class PCAPanel extends GPCAPanel
65 implements Runnable, IProgressIndicator
67 private static final int MIN_WIDTH = 470;
69 private static final int MIN_HEIGHT = 250;
71 private RotatableCanvas rc;
77 private PCAModel pcaModel;
81 private IProgressIndicator progressBar;
83 private boolean working;
86 * Constructor given sequence data, a similarity (or distance) score model
87 * name, and score calculation parameters
93 public PCAPanel(AlignmentPanel alignPanel, String modelName,
94 SimilarityParamsI params)
97 this.setFrameIcon(null);
98 this.av = alignPanel.av;
100 boolean nucleotide = av.getAlignment().isNucleotide();
102 progressBar = new ProgressBar(statusPanel, statusBar);
104 addInternalFrameListener(new InternalFrameAdapter()
107 public void internalFrameClosed(InternalFrameEvent e)
109 close_actionPerformed();
113 boolean selected = av.getSelectionGroup() != null
114 && av.getSelectionGroup().getSize() > 0;
115 AlignmentView seqstrings = av.getAlignmentView(selected);
119 seqs = av.getAlignment().getSequencesArray();
123 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
126 ScoreModelI scoreModel = ScoreModels.getInstance()
127 .getScoreModel(modelName, ap);
129 new PCAModel(seqstrings, seqs, nucleotide, scoreModel, params));
130 PaintRefresher.Register(this, av.getSequenceSetId());
132 setRotatableCanvas(new RotatableCanvas(alignPanel));
133 this.getContentPane().add(getRotatableCanvas(), BorderLayout.CENTER);
135 addKeyListener(getRotatableCanvas());
140 * Ensure references to potentially very large objects (the PCA matrices) are
141 * nulled when the frame is closed
143 protected void close_actionPerformed()
148 this.rc.sequencePoints = null;
149 this.rc.setAxisEndPoints(null);
155 protected void bgcolour_actionPerformed()
157 String ttl = MessageManager.getString("label.select_background_colour");
158 ColourChooserListener listener = new ColourChooserListener()
161 public void colourSelected(Color c)
167 JalviewColourChooser.showColourChooser(this, ttl, rc.getBgColour(),
172 * Calculates the PCA and displays the results
178 long progId = System.currentTimeMillis();
179 IProgressIndicator progress = this;
180 String message = MessageManager.getString("label.pca_recalculating");
181 if (getParent() == null)
183 progress = ap.alignFrame;
184 message = MessageManager.getString("label.pca_calculating");
186 progress.setProgressBar(message, progId);
189 getPcaModel().calculate();
191 xCombobox.setSelectedIndex(0);
192 yCombobox.setSelectedIndex(1);
193 zCombobox.setSelectedIndex(2);
195 getPcaModel().updateRc(getRotatableCanvas());
197 setTop(getPcaModel().getTop());
199 } catch (OutOfMemoryError er)
201 new OOMWarning("calculating PCA", er);
206 progress.setProgressBar("", progId);
210 if (getParent() == null)
212 Desktop.addInternalFrame(this,
213 MessageManager.formatMessage("label.calc_title", "PCA",
214 getPcaModel().getScoreModelName()),
216 this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
222 * Updates the PCA display after a change of component to use for x, y or z
226 protected void doDimensionChange()
233 int dim1 = getTop() - xCombobox.getSelectedIndex();
234 int dim2 = getTop() - yCombobox.getSelectedIndex();
235 int dim3 = getTop() - zCombobox.getSelectedIndex();
236 getPcaModel().updateRcView(dim1, dim2, dim3);
237 getRotatableCanvas().resetView();
241 * Sets the selected checkbox item index for PCA dimension (1, 2, 3...) for
242 * the given axis (X/Y/Z)
247 public void setSelectedDimensionIndex(int index, Axis axis)
252 xCombobox.setSelectedIndex(index);
255 yCombobox.setSelectedIndex(index);
258 zCombobox.setSelectedIndex(index);
265 protected void outputValues_actionPerformed()
267 CutAndPasteTransfer cap = new CutAndPasteTransfer();
270 cap.setText(getPcaModel().getDetails());
271 Desktop.addInternalFrame(cap,
272 MessageManager.getString("label.pca_details"), 500, 500);
273 } catch (OutOfMemoryError oom)
275 new OOMWarning("opening PCA details", oom);
281 protected void showLabels_actionPerformed()
283 getRotatableCanvas().showLabels(showLabels.getState());
287 protected void print_actionPerformed()
289 PCAPrinter printer = new PCAPrinter();
294 * If available, shows the data which formed the inputs for the PCA as a new
298 public void originalSeqData_actionPerformed()
300 // JAL-2647 disabled after load from project (until save to project done)
301 if (getPcaModel().getInputData() == null)
304 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
307 // decide if av alignment is sufficiently different to original data to
308 // warrant a new window to be created
309 // create new alignment window with hidden regions (unhiding hidden regions
310 // yields unaligned seqs)
311 // or create a selection box around columns in alignment view
312 // test Alignment(SeqCigar[])
316 // we try to get the associated view's gap character
317 // but this may fail if the view was closed...
318 gc = av.getGapCharacter();
319 } catch (Exception ex)
323 Object[] alAndColsel = getPcaModel().getInputData()
324 .getAlignmentAndHiddenColumns(gc);
326 if (alAndColsel != null && alAndColsel[0] != null)
328 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
330 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
331 AlignmentI dataset = (av != null && av.getAlignment() != null)
332 ? av.getAlignment().getDataset()
336 al.setDataset(dataset);
342 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
343 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
345 // >>>This is a fix for the moment, until a better solution is
347 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
349 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
352 Desktop.addInternalFrame(af, MessageManager.formatMessage(
353 "label.original_data_for_params", new String[]
354 { this.title }), AlignFrame.DEFAULT_WIDTH,
355 AlignFrame.DEFAULT_HEIGHT);
359 * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
360 * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
361 * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
364 * Desktop.addInternalFrame(cap, "Original Data", 400, 400);
368 class PCAPrinter extends Thread implements Printable
373 PrinterJob printJob = PrinterJob.getPrinterJob();
374 PageFormat defaultPage = printJob.defaultPage();
375 PageFormat pf = printJob.pageDialog(defaultPage);
377 if (defaultPage == pf)
385 printJob.setPrintable(this, pf);
387 if (printJob.printDialog())
392 } catch (Exception PrintException)
394 PrintException.printStackTrace();
400 public int print(Graphics pg, PageFormat pf, int pi)
401 throws PrinterException
403 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
405 getRotatableCanvas().drawBackground(pg);
406 getRotatableCanvas().drawScene(pg);
407 if (getRotatableCanvas().drawAxes)
409 getRotatableCanvas().drawAxes(pg);
414 return Printable.PAGE_EXISTS;
418 return Printable.NO_SUCH_PAGE;
423 public void makePCAImage(ImageMaker.TYPE type)
425 int width = getRotatableCanvas().getWidth();
426 int height = getRotatableCanvas().getHeight();
427 ImageWriterI writer = new ImageWriterI()
430 public void exportImage(Graphics g) throws Exception
432 RotatableCanvas canvas = getRotatableCanvas();
433 canvas.drawBackground(g);
441 String pca = MessageManager.getString("label.pca");
442 ImageExporter exporter = new ImageExporter(writer, null, type, pca);
445 exporter.doExport(null, this, width, height, pca);
446 } catch (ImageOutputException ioex)
448 Console.error("Unexpected error whilst writing " + type.toString(),
454 protected void viewMenu_menuSelected()
456 buildAssociatedViewMenu();
460 * Builds the menu showing the choice of possible views (for the associated
461 * sequence data) to which the PCA may be linked
463 void buildAssociatedViewMenu()
465 AlignmentPanel[] aps = PaintRefresher
466 .getAssociatedPanels(av.getSequenceSetId());
467 if (aps.length == 1 && getRotatableCanvas().av == aps[0].av)
469 associateViewsMenu.setVisible(false);
473 associateViewsMenu.setVisible(true);
476 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
478 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
481 associateViewsMenu.removeAll();
483 JRadioButtonMenuItem item;
484 ButtonGroup buttonGroup = new ButtonGroup();
485 int iSize = aps.length;
487 for (int i = 0; i < iSize; i++)
489 final AlignmentPanel panel = aps[i];
490 item = new JRadioButtonMenuItem(panel.av.getViewName(),
491 panel.av == getRotatableCanvas().av);
492 buttonGroup.add(item);
493 item.addActionListener(new ActionListener()
496 public void actionPerformed(ActionEvent evt)
498 selectAssociatedView(panel);
502 associateViewsMenu.add(item);
505 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
508 buttonGroup.add(itemf);
510 itemf.setSelected(getRotatableCanvas().isApplyToAllViews());
511 itemf.addActionListener(new ActionListener()
514 public void actionPerformed(ActionEvent evt)
516 getRotatableCanvas().setApplyToAllViews(itemf.isSelected());
519 associateViewsMenu.add(itemf);
527 * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
531 protected void outputPoints_actionPerformed()
533 CutAndPasteTransfer cap = new CutAndPasteTransfer();
536 cap.setText(getPcaModel().getPointsasCsv(false,
537 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
538 zCombobox.getSelectedIndex()));
539 Desktop.addInternalFrame(cap, MessageManager
540 .formatMessage("label.points_for_params", new String[]
541 { this.getTitle() }), 500, 500);
542 } catch (OutOfMemoryError oom)
544 new OOMWarning("exporting PCA points", oom);
553 * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
557 protected void outputProjPoints_actionPerformed()
559 CutAndPasteTransfer cap = new CutAndPasteTransfer();
562 cap.setText(getPcaModel().getPointsasCsv(true,
563 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
564 zCombobox.getSelectedIndex()));
565 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
566 "label.transformed_points_for_params", new String[]
567 { this.getTitle() }), 500, 500);
568 } catch (OutOfMemoryError oom)
570 new OOMWarning("exporting transformed PCA points", oom);
578 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
581 public void setProgressBar(String message, long id)
583 progressBar.setProgressBar(message, id);
584 // if (progressBars == null)
586 // progressBars = new Hashtable();
587 // progressBarHandlers = new Hashtable();
590 // JPanel progressPanel;
591 // Long lId = Long.valueOf(id);
592 // GridLayout layout = (GridLayout) statusPanel.getLayout();
593 // if (progressBars.get(lId) != null)
595 // progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
596 // statusPanel.remove(progressPanel);
597 // progressBars.remove(lId);
598 // progressPanel = null;
599 // if (message != null)
601 // statusBar.setText(message);
603 // if (progressBarHandlers.contains(lId))
605 // progressBarHandlers.remove(lId);
607 // layout.setRows(layout.getRows() - 1);
611 // progressPanel = new JPanel(new BorderLayout(10, 5));
613 // JProgressBar progressBar = new JProgressBar();
614 // progressBar.setIndeterminate(true);
616 // progressPanel.add(new JLabel(message), BorderLayout.WEST);
617 // progressPanel.add(progressBar, BorderLayout.CENTER);
619 // layout.setRows(layout.getRows() + 1);
620 // statusPanel.add(progressPanel);
622 // progressBars.put(lId, progressPanel);
625 // // setMenusForViewport();
630 public void registerHandler(final long id,
631 final IProgressIndicatorHandler handler)
633 progressBar.registerHandler(id, handler);
634 // if (progressBarHandlers == null ||
635 // !progressBars.contains(Long.valueOf(id)))
638 // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
640 // progressBarHandlers.put(Long.valueOf(id), handler);
641 // final JPanel progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
642 // if (handler.canCancel())
644 // JButton cancel = new JButton(
645 // MessageManager.getString("action.cancel"));
646 // final IProgressIndicator us = this;
647 // cancel.addActionListener(new ActionListener()
651 // public void actionPerformed(ActionEvent e)
653 // handler.cancelActivity(id);
654 // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
655 // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
658 // progressPanel.add(cancel, BorderLayout.EAST);
664 * @return true if any progress bars are still active
667 public boolean operationInProgress()
669 return progressBar.operationInProgress();
673 protected void resetButton_actionPerformed()
676 setTop(0); // ugly - prevents dimensionChanged events from being processed
677 xCombobox.setSelectedIndex(0);
678 yCombobox.setSelectedIndex(1);
680 zCombobox.setSelectedIndex(2);
684 * Answers true if PCA calculation is in progress, else false
688 public boolean isWorking()
694 * Answers the selected checkbox item index for PCA dimension for the X, Y or
695 * Z axis of the display
700 public int getSelectedDimensionIndex(Axis axis)
705 return xCombobox.getSelectedIndex();
707 return yCombobox.getSelectedIndex();
709 return zCombobox.getSelectedIndex();
713 public void setShowLabels(boolean show)
715 showLabels.setSelected(show);
719 * Sets the input data used to calculate the PCA. This is provided for
720 * 'restore from project', which does not currently support this (AL-2647), so
721 * sets the value to null, and hides the menu option for "Input Data...". J
725 public void setInputData(AlignmentView data)
727 getPcaModel().setInputData(data);
728 originalSeqData.setVisible(data != null);
731 public AlignViewportI getAlignViewport()
736 public PCAModel getPcaModel()
741 public void setPcaModel(PCAModel pcaModel)
743 this.pcaModel = pcaModel;
746 public RotatableCanvas getRotatableCanvas()
751 public void setRotatableCanvas(RotatableCanvas rc)
761 public void setTop(int top)
767 * set the associated view for this PCA.
771 public void selectAssociatedView(AlignmentPanel panel)
773 getRotatableCanvas().setApplyToAllViews(false);
778 getRotatableCanvas().av = panel.av;
779 getRotatableCanvas().ap = panel;
780 PaintRefresher.Register(PCAPanel.this, panel.av.getSequenceSetId());
784 public JProgressBar getProgressBar(long id)
786 return progressBar.getProgressBar(id);