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.AlignViewportI;
25 import jalview.api.analysis.ScoreModelI;
26 import jalview.api.analysis.SimilarityParamsI;
27 import jalview.bin.Cache;
28 import jalview.datamodel.Alignment;
29 import jalview.datamodel.AlignmentI;
30 import jalview.datamodel.AlignmentView;
31 import jalview.datamodel.HiddenColumns;
32 import jalview.datamodel.SequenceI;
33 import jalview.gui.ImageExporter.ImageWriterI;
34 import jalview.gui.JalviewColourChooser.ColourChooserListener;
35 import jalview.jbgui.GPCAPanel;
36 import jalview.math.RotatableMatrix.Axis;
37 import jalview.util.ImageMaker;
38 import jalview.util.MessageManager;
39 import jalview.viewmodel.AlignmentViewport;
40 import jalview.viewmodel.PCAModel;
42 import java.awt.BorderLayout;
43 import java.awt.Color;
44 import java.awt.Dimension;
45 import java.awt.Graphics;
46 import java.awt.event.ActionEvent;
47 import java.awt.event.ActionListener;
48 import java.awt.print.PageFormat;
49 import java.awt.print.Printable;
50 import java.awt.print.PrinterException;
51 import java.awt.print.PrinterJob;
53 import javax.swing.ButtonGroup;
54 import javax.swing.JMenuItem;
55 import javax.swing.JRadioButtonMenuItem;
56 import javax.swing.event.InternalFrameAdapter;
57 import javax.swing.event.InternalFrameEvent;
60 * The panel holding the Principal Component Analysis 3-D visualisation
62 public class PCAPanel extends GPCAPanel
63 implements Runnable, IProgressIndicator
65 private static final int MIN_WIDTH = 470;
67 private static final int MIN_HEIGHT = 250;
69 private RotatableCanvas rc;
75 private PCAModel pcaModel;
79 private IProgressIndicator progressBar;
81 private boolean working;
84 * Constructor given sequence data, a similarity (or distance) score model
85 * name, and score calculation parameters
91 public PCAPanel(AlignmentPanel alignPanel, String modelName,
92 SimilarityParamsI params)
95 this.av = alignPanel.av;
97 boolean nucleotide = av.getAlignment().isNucleotide();
99 progressBar = new ProgressBar(statusPanel, statusBar);
101 addInternalFrameListener(new InternalFrameAdapter()
104 public void internalFrameClosed(InternalFrameEvent e)
106 close_actionPerformed();
110 boolean selected = av.getSelectionGroup() != null
111 && av.getSelectionGroup().getSize() > 0;
112 AlignmentView seqstrings = av.getAlignmentView(selected);
116 seqs = av.getAlignment().getSequencesArray();
120 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
123 ScoreModelI scoreModel = ScoreModels.getInstance()
124 .getScoreModel(modelName, ap);
125 setPcaModel(new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
127 PaintRefresher.Register(this, av.getSequenceSetId());
129 setRotatableCanvas(new RotatableCanvas(alignPanel));
130 this.getContentPane().add(getRotatableCanvas(), BorderLayout.CENTER);
132 addKeyListener(getRotatableCanvas());
135 this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
139 * Ensure references to potentially very large objects (the PCA matrices) are
140 * nulled when the frame is closed
142 protected void close_actionPerformed()
148 protected void bgcolour_actionPerformed()
150 String ttl = MessageManager.getString("label.select_background_colour");
151 ColourChooserListener listener = new ColourChooserListener()
154 public void colourSelected(Color c)
160 JalviewColourChooser.showColourChooser(this, ttl, rc.getBgColour(),
165 * Calculates the PCA and displays the results
171 long progId = System.currentTimeMillis();
172 IProgressIndicator progress = this;
173 String message = MessageManager.getString("label.pca_recalculating");
174 if (getParent() == null)
176 progress = ap.alignFrame;
177 message = MessageManager.getString("label.pca_calculating");
179 progress.setProgressBar(message, progId);
182 getPcaModel().calculate();
184 xCombobox.setSelectedIndex(0);
185 yCombobox.setSelectedIndex(1);
186 zCombobox.setSelectedIndex(2);
188 getPcaModel().updateRc(getRotatableCanvas());
190 setTop(getPcaModel().getTop());
192 } catch (OutOfMemoryError er)
194 new OOMWarning("calculating PCA", er);
199 progress.setProgressBar("", progId);
203 if (getParent() == null)
205 Desktop.addInternalFrame(this,
206 MessageManager.formatMessage("label.calc_title", "PCA",
207 getPcaModel().getScoreModelName()),
214 * Updates the PCA display after a change of component to use for x, y or z
218 protected void doDimensionChange()
225 int dim1 = getTop() - xCombobox.getSelectedIndex();
226 int dim2 = getTop() - yCombobox.getSelectedIndex();
227 int dim3 = getTop() - zCombobox.getSelectedIndex();
228 getPcaModel().updateRcView(dim1, dim2, dim3);
229 getRotatableCanvas().resetView();
233 * Sets the selected checkbox item index for PCA dimension (1, 2, 3...) for
234 * the given axis (X/Y/Z)
239 public void setSelectedDimensionIndex(int index, Axis axis)
244 xCombobox.setSelectedIndex(index);
247 yCombobox.setSelectedIndex(index);
250 zCombobox.setSelectedIndex(index);
257 protected void outputValues_actionPerformed()
259 CutAndPasteTransfer cap = new CutAndPasteTransfer();
262 cap.setText(getPcaModel().getDetails());
263 Desktop.addInternalFrame(cap,
264 MessageManager.getString("label.pca_details"), 500, 500);
265 } catch (OutOfMemoryError oom)
267 new OOMWarning("opening PCA details", oom);
273 protected void showLabels_actionPerformed()
275 getRotatableCanvas().showLabels(showLabels.getState());
279 protected void print_actionPerformed()
281 PCAPrinter printer = new PCAPrinter();
286 * If available, shows the data which formed the inputs for the PCA as a new
290 public void originalSeqData_actionPerformed()
292 // JAL-2647 disabled after load from project (until save to project done)
293 if (getPcaModel().getInputData() == null)
296 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
299 // decide if av alignment is sufficiently different to original data to
300 // warrant a new window to be created
301 // create new alignment window with hidden regions (unhiding hidden regions
302 // yields unaligned seqs)
303 // or create a selection box around columns in alignment view
304 // test Alignment(SeqCigar[])
308 // we try to get the associated view's gap character
309 // but this may fail if the view was closed...
310 gc = av.getGapCharacter();
311 } catch (Exception ex)
315 Object[] alAndColsel = getPcaModel().getInputData()
316 .getAlignmentAndHiddenColumns(gc);
318 if (alAndColsel != null && alAndColsel[0] != null)
320 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
322 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
323 AlignmentI dataset = (av != null && av.getAlignment() != null)
324 ? av.getAlignment().getDataset()
328 al.setDataset(dataset);
334 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
335 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
337 // >>>This is a fix for the moment, until a better solution is
339 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
341 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
344 Desktop.addInternalFrame(af, MessageManager.formatMessage(
345 "label.original_data_for_params", new String[]
346 { this.title }), AlignFrame.DEFAULT_WIDTH,
347 AlignFrame.DEFAULT_HEIGHT);
351 * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
352 * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
353 * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
356 * Desktop.addInternalFrame(cap, "Original Data", 400, 400);
360 class PCAPrinter extends Thread implements Printable
365 PrinterJob printJob = PrinterJob.getPrinterJob();
366 PageFormat defaultPage = printJob.defaultPage();
367 PageFormat pf = printJob.pageDialog(defaultPage);
369 if (defaultPage == pf)
377 printJob.setPrintable(this, pf);
379 if (printJob.printDialog())
384 } catch (Exception PrintException)
386 PrintException.printStackTrace();
392 public int print(Graphics pg, PageFormat pf, int pi)
393 throws PrinterException
395 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
397 getRotatableCanvas().drawBackground(pg);
398 getRotatableCanvas().drawScene(pg);
399 if (getRotatableCanvas().drawAxes)
401 getRotatableCanvas().drawAxes(pg);
406 return Printable.PAGE_EXISTS;
410 return Printable.NO_SUCH_PAGE;
415 public void makePCAImage(ImageMaker.TYPE type)
417 int width = getRotatableCanvas().getWidth();
418 int height = getRotatableCanvas().getHeight();
419 ImageWriterI writer = new ImageWriterI()
422 public void exportImage(Graphics g) throws Exception
424 RotatableCanvas canvas = getRotatableCanvas();
425 canvas.drawBackground(g);
433 String pca = MessageManager.getString("label.pca");
434 ImageExporter exporter = new ImageExporter(writer, null, type, pca);
435 exporter.doExport(null, this, width, height, pca);
439 protected void viewMenu_menuSelected()
441 buildAssociatedViewMenu();
445 * Builds the menu showing the choice of possible views (for the associated
446 * sequence data) to which the PCA may be linked
448 void buildAssociatedViewMenu()
450 AlignmentPanel[] aps = PaintRefresher
451 .getAssociatedPanels(av.getSequenceSetId());
452 if (aps.length == 1 && getRotatableCanvas().av == aps[0].av)
454 associateViewsMenu.setVisible(false);
458 associateViewsMenu.setVisible(true);
461 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
463 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
466 associateViewsMenu.removeAll();
468 JRadioButtonMenuItem item;
469 ButtonGroup buttonGroup = new ButtonGroup();
470 int iSize = aps.length;
472 for (int i = 0; i < iSize; i++)
474 final AlignmentPanel panel = aps[i];
475 item = new JRadioButtonMenuItem(panel.av.getViewName(),
476 panel.av == getRotatableCanvas().av);
477 buttonGroup.add(item);
478 item.addActionListener(new ActionListener()
481 public void actionPerformed(ActionEvent evt)
483 selectAssociatedView(panel);
487 associateViewsMenu.add(item);
490 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
493 buttonGroup.add(itemf);
495 itemf.setSelected(getRotatableCanvas().isApplyToAllViews());
496 itemf.addActionListener(new ActionListener()
499 public void actionPerformed(ActionEvent evt)
501 getRotatableCanvas().setApplyToAllViews(itemf.isSelected());
504 associateViewsMenu.add(itemf);
512 * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
516 protected void outputPoints_actionPerformed()
518 CutAndPasteTransfer cap = new CutAndPasteTransfer();
521 cap.setText(getPcaModel().getPointsasCsv(false,
522 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
523 zCombobox.getSelectedIndex()));
524 Desktop.addInternalFrame(cap, MessageManager
525 .formatMessage("label.points_for_params", new String[]
526 { this.getTitle() }), 500, 500);
527 } catch (OutOfMemoryError oom)
529 new OOMWarning("exporting PCA points", oom);
538 * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
542 protected void outputProjPoints_actionPerformed()
544 CutAndPasteTransfer cap = new CutAndPasteTransfer();
547 cap.setText(getPcaModel().getPointsasCsv(true,
548 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
549 zCombobox.getSelectedIndex()));
550 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
551 "label.transformed_points_for_params", new String[]
552 { this.getTitle() }), 500, 500);
553 } catch (OutOfMemoryError oom)
555 new OOMWarning("exporting transformed PCA points", oom);
563 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
566 public void setProgressBar(String message, long id)
568 progressBar.setProgressBar(message, id);
569 // if (progressBars == null)
571 // progressBars = new Hashtable();
572 // progressBarHandlers = new Hashtable();
575 // JPanel progressPanel;
576 // Long lId = new Long(id);
577 // GridLayout layout = (GridLayout) statusPanel.getLayout();
578 // if (progressBars.get(lId) != null)
580 // progressPanel = (JPanel) progressBars.get(new Long(id));
581 // statusPanel.remove(progressPanel);
582 // progressBars.remove(lId);
583 // progressPanel = null;
584 // if (message != null)
586 // statusBar.setText(message);
588 // if (progressBarHandlers.contains(lId))
590 // progressBarHandlers.remove(lId);
592 // layout.setRows(layout.getRows() - 1);
596 // progressPanel = new JPanel(new BorderLayout(10, 5));
598 // JProgressBar progressBar = new JProgressBar();
599 // progressBar.setIndeterminate(true);
601 // progressPanel.add(new JLabel(message), BorderLayout.WEST);
602 // progressPanel.add(progressBar, BorderLayout.CENTER);
604 // layout.setRows(layout.getRows() + 1);
605 // statusPanel.add(progressPanel);
607 // progressBars.put(lId, progressPanel);
610 // // setMenusForViewport();
615 public void registerHandler(final long id,
616 final IProgressIndicatorHandler handler)
618 progressBar.registerHandler(id, handler);
619 // if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
622 // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
624 // progressBarHandlers.put(new Long(id), handler);
625 // final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
626 // if (handler.canCancel())
628 // JButton cancel = new JButton(
629 // MessageManager.getString("action.cancel"));
630 // final IProgressIndicator us = this;
631 // cancel.addActionListener(new ActionListener()
635 // public void actionPerformed(ActionEvent e)
637 // handler.cancelActivity(id);
638 // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
639 // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
642 // progressPanel.add(cancel, BorderLayout.EAST);
648 * @return true if any progress bars are still active
651 public boolean operationInProgress()
653 return progressBar.operationInProgress();
657 protected void resetButton_actionPerformed()
660 setTop(0); // ugly - prevents dimensionChanged events from being processed
661 xCombobox.setSelectedIndex(0);
662 yCombobox.setSelectedIndex(1);
664 zCombobox.setSelectedIndex(2);
668 * Answers true if PCA calculation is in progress, else false
672 public boolean isWorking()
678 * Answers the selected checkbox item index for PCA dimension for the X, Y or
679 * Z axis of the display
684 public int getSelectedDimensionIndex(Axis axis)
689 return xCombobox.getSelectedIndex();
691 return yCombobox.getSelectedIndex();
693 return zCombobox.getSelectedIndex();
697 public void setShowLabels(boolean show)
699 showLabels.setSelected(show);
703 * Sets the input data used to calculate the PCA. This is provided for
704 * 'restore from project', which does not currently support this (AL-2647), so
705 * sets the value to null, and hides the menu option for "Input Data...". J
709 public void setInputData(AlignmentView data)
711 getPcaModel().setInputData(data);
712 originalSeqData.setVisible(data != null);
715 public AlignViewportI getAlignViewport()
720 public PCAModel getPcaModel()
725 public void setPcaModel(PCAModel pcaModel)
727 this.pcaModel = pcaModel;
730 public RotatableCanvas getRotatableCanvas()
735 public void setRotatableCanvas(RotatableCanvas rc)
745 public void setTop(int top)
751 * set the associated view for this PCA.
755 public void selectAssociatedView(AlignmentPanel panel)
757 getRotatableCanvas().setApplyToAllViews(false);
762 getRotatableCanvas().av = panel.av;
763 getRotatableCanvas().ap = panel;
764 PaintRefresher.Register(PCAPanel.this, panel.av.getSequenceSetId());