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.util.Platform;
40 import jalview.viewmodel.AlignmentViewport;
41 import jalview.viewmodel.PCAModel;
43 import java.awt.BorderLayout;
44 import java.awt.Color;
45 import java.awt.Dimension;
46 import java.awt.Graphics;
47 import java.awt.event.ActionEvent;
48 import java.awt.event.ActionListener;
49 import java.awt.print.PageFormat;
50 import java.awt.print.Printable;
51 import java.awt.print.PrinterException;
52 import java.awt.print.PrinterJob;
54 import javax.swing.ButtonGroup;
55 import javax.swing.JMenuItem;
56 import javax.swing.JRadioButtonMenuItem;
57 import javax.swing.event.InternalFrameAdapter;
58 import javax.swing.event.InternalFrameEvent;
61 * The panel holding the Principal Component Analysis 3-D visualisation
63 public class PCAPanel extends GPCAPanel
64 implements Runnable, IProgressIndicator
66 private static final int MIN_WIDTH = 470;
68 private static final int MIN_HEIGHT = 250;
70 private RotatableCanvas rc;
76 private PCAModel pcaModel;
80 private IProgressIndicator progressBar;
82 private boolean working;
85 * Constructor given sequence data, a similarity (or distance) score model
86 * name, and score calculation parameters
92 public PCAPanel(AlignmentPanel alignPanel, String modelName,
93 SimilarityParamsI params)
96 this.av = alignPanel.av;
98 boolean nucleotide = av.getAlignment().isNucleotide();
100 progressBar = new ProgressBar(statusPanel, statusBar);
102 addInternalFrameListener(new InternalFrameAdapter()
105 public void internalFrameClosed(InternalFrameEvent e)
107 close_actionPerformed();
111 boolean selected = av.getSelectionGroup() != null
112 && av.getSelectionGroup().getSize() > 0;
113 AlignmentView seqstrings = av.getAlignmentView(selected);
117 seqs = av.getAlignment().getSequencesArray();
121 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
124 ScoreModelI scoreModel = ScoreModels.getInstance()
125 .getScoreModel(modelName, ap);
126 setPcaModel(new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
128 PaintRefresher.Register(this, av.getSequenceSetId());
130 setRotatableCanvas(new RotatableCanvas(alignPanel));
131 this.getContentPane().add(getRotatableCanvas(), BorderLayout.CENTER);
133 addKeyListener(getRotatableCanvas());
138 * Ensure references to potentially very large objects (the PCA matrices) are
139 * nulled when the frame is closed
141 protected void close_actionPerformed()
147 protected void bgcolour_actionPerformed()
149 String ttl = MessageManager.getString("label.select_background_colour");
150 ColourChooserListener listener = new ColourChooserListener()
153 public void colourSelected(Color c)
159 JalviewColourChooser.showColourChooser(this, ttl, rc.getBgColour(),
164 * Calculates the PCA and displays the results
170 long progId = System.currentTimeMillis();
171 IProgressIndicator progress = this;
172 String message = MessageManager.getString("label.pca_recalculating");
173 if (getParent() == null)
175 progress = ap.alignFrame;
176 message = MessageManager.getString("label.pca_calculating");
178 progress.setProgressBar(message, progId);
181 getPcaModel().calculate();
183 xCombobox.setSelectedIndex(0);
184 yCombobox.setSelectedIndex(1);
185 zCombobox.setSelectedIndex(2);
187 getPcaModel().updateRc(getRotatableCanvas());
189 setTop(getPcaModel().getTop());
191 } catch (OutOfMemoryError er)
193 new OOMWarning("calculating PCA", er);
198 progress.setProgressBar("", progId);
202 if (getParent() == null)
204 addToDesktop(this, getPcaModel().getScoreModelName());
205 this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
211 * Updates the PCA display after a change of component to use for x, y or z
215 protected void doDimensionChange()
222 int dim1 = getTop() - xCombobox.getSelectedIndex();
223 int dim2 = getTop() - yCombobox.getSelectedIndex();
224 int dim3 = getTop() - zCombobox.getSelectedIndex();
225 getPcaModel().updateRcView(dim1, dim2, dim3);
226 getRotatableCanvas().resetView();
230 * Sets the selected checkbox item index for PCA dimension (1, 2, 3...) for
231 * the given axis (X/Y/Z)
236 public void setSelectedDimensionIndex(int index, Axis axis)
241 xCombobox.setSelectedIndex(index);
244 yCombobox.setSelectedIndex(index);
247 zCombobox.setSelectedIndex(index);
254 protected void outputValues_actionPerformed()
256 CutAndPasteTransfer cap = new CutAndPasteTransfer();
259 cap.setText(getPcaModel().getDetails());
260 Desktop.addInternalFrame(cap,
261 MessageManager.getString("label.pca_details"), 500, 500);
262 } catch (OutOfMemoryError oom)
264 new OOMWarning("opening PCA details", oom);
270 protected void showLabels_actionPerformed()
272 getRotatableCanvas().showLabels(showLabels.getState());
276 protected void print_actionPerformed()
278 PCAPrinter printer = new PCAPrinter();
283 * If available, shows the data which formed the inputs for the PCA as a new
287 public void originalSeqData_actionPerformed()
289 // JAL-2647 disabled after load from project (until save to project done)
290 if (getPcaModel().getInputData() == null)
293 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
296 // decide if av alignment is sufficiently different to original data to
297 // warrant a new window to be created
298 // create new alignment window with hidden regions (unhiding hidden regions
299 // yields unaligned seqs)
300 // or create a selection box around columns in alignment view
301 // test Alignment(SeqCigar[])
305 // we try to get the associated view's gap character
306 // but this may fail if the view was closed...
307 gc = av.getGapCharacter();
308 } catch (Exception ex)
312 Object[] alAndColsel = getPcaModel().getInputData()
313 .getAlignmentAndHiddenColumns(gc);
315 if (alAndColsel != null && alAndColsel[0] != null)
317 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
319 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
320 AlignmentI dataset = (av != null && av.getAlignment() != null)
321 ? av.getAlignment().getDataset()
325 al.setDataset(dataset);
331 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
332 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
334 // >>>This is a fix for the moment, until a better solution is
336 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
338 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
341 Desktop.addInternalFrame(af, MessageManager.formatMessage(
342 "label.original_data_for_params", new String[]
343 { this.title }), AlignFrame.DEFAULT_WIDTH,
344 AlignFrame.DEFAULT_HEIGHT);
348 * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
349 * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
350 * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
353 * Desktop.addInternalFrame(cap, "Original Data", 400, 400);
357 class PCAPrinter extends Thread implements Printable
362 PrinterJob printJob = PrinterJob.getPrinterJob();
363 PageFormat defaultPage = printJob.defaultPage();
364 PageFormat pf = printJob.pageDialog(defaultPage);
366 if (defaultPage == pf)
374 printJob.setPrintable(this, pf);
376 if (printJob.printDialog())
381 } catch (Exception PrintException)
383 PrintException.printStackTrace();
389 public int print(Graphics pg, PageFormat pf, int pi)
390 throws PrinterException
392 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
394 getRotatableCanvas().drawBackground(pg);
395 getRotatableCanvas().drawScene(pg);
396 if (getRotatableCanvas().drawAxes)
398 getRotatableCanvas().drawAxes(pg);
403 return Printable.PAGE_EXISTS;
407 return Printable.NO_SUCH_PAGE;
412 public void makePCAImage(ImageMaker.TYPE type)
414 int width = getRotatableCanvas().getWidth();
415 int height = getRotatableCanvas().getHeight();
416 ImageWriterI writer = new ImageWriterI()
419 public void exportImage(Graphics g) throws Exception
421 RotatableCanvas canvas = getRotatableCanvas();
422 canvas.drawBackground(g);
430 String pca = MessageManager.getString("label.pca");
431 ImageExporter exporter = new ImageExporter(writer, null, type, pca);
432 exporter.doExport(null, this, width, height, pca);
436 protected void viewMenu_menuSelected()
438 buildAssociatedViewMenu();
442 * Builds the menu showing the choice of possible views (for the associated
443 * sequence data) to which the PCA may be linked
445 void buildAssociatedViewMenu()
447 AlignmentPanel[] aps = PaintRefresher
448 .getAssociatedPanels(av.getSequenceSetId());
449 if (aps.length == 1 && getRotatableCanvas().av == aps[0].av)
451 associateViewsMenu.setVisible(false);
455 associateViewsMenu.setVisible(true);
458 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
460 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
463 associateViewsMenu.removeAll();
465 JRadioButtonMenuItem item;
466 ButtonGroup buttonGroup = new ButtonGroup();
467 int iSize = aps.length;
469 for (int i = 0; i < iSize; i++)
471 final AlignmentPanel panel = aps[i];
472 item = new JRadioButtonMenuItem(panel.av.getViewName(),
473 panel.av == getRotatableCanvas().av);
474 buttonGroup.add(item);
475 item.addActionListener(new ActionListener()
478 public void actionPerformed(ActionEvent evt)
480 selectAssociatedView(panel);
484 associateViewsMenu.add(item);
487 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
490 buttonGroup.add(itemf);
492 itemf.setSelected(getRotatableCanvas().isApplyToAllViews());
493 itemf.addActionListener(new ActionListener()
496 public void actionPerformed(ActionEvent evt)
498 getRotatableCanvas().setApplyToAllViews(itemf.isSelected());
501 associateViewsMenu.add(itemf);
509 * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
513 protected void outputPoints_actionPerformed()
515 CutAndPasteTransfer cap = new CutAndPasteTransfer();
518 cap.setText(getPcaModel().getPointsasCsv(false,
519 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
520 zCombobox.getSelectedIndex()));
521 Desktop.addInternalFrame(cap, MessageManager
522 .formatMessage("label.points_for_params", new String[]
523 { this.getTitle() }), 500, 500);
524 } catch (OutOfMemoryError oom)
526 new OOMWarning("exporting PCA points", oom);
535 * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
539 protected void outputProjPoints_actionPerformed()
541 CutAndPasteTransfer cap = new CutAndPasteTransfer();
544 cap.setText(getPcaModel().getPointsasCsv(true,
545 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
546 zCombobox.getSelectedIndex()));
547 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
548 "label.transformed_points_for_params", new String[]
549 { this.getTitle() }), 500, 500);
550 } catch (OutOfMemoryError oom)
552 new OOMWarning("exporting transformed PCA points", oom);
560 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
563 public void setProgressBar(String message, long id)
565 progressBar.setProgressBar(message, id);
566 // if (progressBars == null)
568 // progressBars = new Hashtable();
569 // progressBarHandlers = new Hashtable();
572 // JPanel progressPanel;
573 // Long lId = Long.valueOf(id);
574 // GridLayout layout = (GridLayout) statusPanel.getLayout();
575 // if (progressBars.get(lId) != null)
577 // progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
578 // statusPanel.remove(progressPanel);
579 // progressBars.remove(lId);
580 // progressPanel = null;
581 // if (message != null)
583 // statusBar.setText(message);
585 // if (progressBarHandlers.contains(lId))
587 // progressBarHandlers.remove(lId);
589 // layout.setRows(layout.getRows() - 1);
593 // progressPanel = new JPanel(new BorderLayout(10, 5));
595 // JProgressBar progressBar = new JProgressBar();
596 // progressBar.setIndeterminate(true);
598 // progressPanel.add(new JLabel(message), BorderLayout.WEST);
599 // progressPanel.add(progressBar, BorderLayout.CENTER);
601 // layout.setRows(layout.getRows() + 1);
602 // statusPanel.add(progressPanel);
604 // progressBars.put(lId, progressPanel);
607 // // setMenusForViewport();
612 public void removeProgressBar(long id)
614 progressBar.removeProgressBar(id);
618 public void registerHandler(final long id,
619 final IProgressIndicatorHandler handler)
621 progressBar.registerHandler(id, handler);
622 // if (progressBarHandlers == null || !progressBars.contains(Long.valueOf(id)))
625 // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
627 // progressBarHandlers.put(Long.valueOf(id), handler);
628 // final JPanel progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
629 // if (handler.canCancel())
631 // JButton cancel = new JButton(
632 // MessageManager.getString("action.cancel"));
633 // final IProgressIndicator us = this;
634 // cancel.addActionListener(new ActionListener()
638 // public void actionPerformed(ActionEvent e)
640 // handler.cancelActivity(id);
641 // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
642 // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
645 // progressPanel.add(cancel, BorderLayout.EAST);
651 * @return true if any progress bars are still active
654 public boolean operationInProgress()
656 return progressBar.operationInProgress();
660 protected void resetButton_actionPerformed()
663 setTop(0); // ugly - prevents dimensionChanged events from being processed
664 xCombobox.setSelectedIndex(0);
665 yCombobox.setSelectedIndex(1);
667 zCombobox.setSelectedIndex(2);
671 * Answers true if PCA calculation is in progress, else false
675 public boolean isWorking()
681 * Answers the selected checkbox item index for PCA dimension for the X, Y or
682 * Z axis of the display
687 public int getSelectedDimensionIndex(Axis axis)
692 return xCombobox.getSelectedIndex();
694 return yCombobox.getSelectedIndex();
696 return zCombobox.getSelectedIndex();
700 public void setShowLabels(boolean show)
702 showLabels.setSelected(show);
706 * Sets the input data used to calculate the PCA. This is provided for
707 * 'restore from project', which does not currently support this (AL-2647), so
708 * sets the value to null, and hides the menu option for "Input Data...". J
712 public void setInputData(AlignmentView data)
714 getPcaModel().setInputData(data);
715 originalSeqData.setVisible(data != null);
718 public AlignViewportI getAlignViewport()
723 public PCAModel getPcaModel()
728 public void setPcaModel(PCAModel pcaModel)
730 this.pcaModel = pcaModel;
733 public RotatableCanvas getRotatableCanvas()
738 public void setRotatableCanvas(RotatableCanvas rc)
748 public void setTop(int top)
754 * set the associated view for this PCA.
758 public void selectAssociatedView(AlignmentPanel panel)
760 getRotatableCanvas().setApplyToAllViews(false);
765 getRotatableCanvas().av = panel.av;
766 getRotatableCanvas().ap = panel;
767 PaintRefresher.Register(PCAPanel.this, panel.av.getSequenceSetId());
770 public static void addToDesktop(PCAPanel panel, String modelName)
772 Dimension dim = Platform.getDimIfEmbedded(panel, 475, 450);
773 Desktop.addInternalFrame(panel, MessageManager.formatMessage(
774 "label.calc_title", "PCA", modelName), dim.width,