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;
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)
205 Dimension dim = Platform.getDimIfEmbedded(this, 475, 450);
206 Desktop.addInternalFrame(this,
207 MessageManager.formatMessage("label.calc_title", "PCA",
208 getPcaModel().getScoreModelName()),
209 dim.width, dim.height);
210 setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
216 * Updates the PCA display after a change of component to use for x, y or z
220 protected void doDimensionChange()
227 int dim1 = getTop() - xCombobox.getSelectedIndex();
228 int dim2 = getTop() - yCombobox.getSelectedIndex();
229 int dim3 = getTop() - zCombobox.getSelectedIndex();
230 getPcaModel().updateRcView(dim1, dim2, dim3);
231 getRotatableCanvas().resetView();
235 * Sets the selected checkbox item index for PCA dimension (1, 2, 3...) for
236 * the given axis (X/Y/Z)
241 public void setSelectedDimensionIndex(int index, Axis axis)
246 xCombobox.setSelectedIndex(index);
249 yCombobox.setSelectedIndex(index);
252 zCombobox.setSelectedIndex(index);
259 protected void outputValues_actionPerformed()
261 CutAndPasteTransfer cap = new CutAndPasteTransfer();
264 cap.setText(getPcaModel().getDetails());
265 Desktop.addInternalFrame(cap,
266 MessageManager.getString("label.pca_details"), 500, 500);
267 } catch (OutOfMemoryError oom)
269 new OOMWarning("opening PCA details", oom);
275 protected void showLabels_actionPerformed()
277 getRotatableCanvas().showLabels(showLabels.getState());
281 protected void print_actionPerformed()
283 PCAPrinter printer = new PCAPrinter();
288 * If available, shows the data which formed the inputs for the PCA as a new
292 public void originalSeqData_actionPerformed()
294 // JAL-2647 disabled after load from project (until save to project done)
295 if (getPcaModel().getInputData() == null)
298 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
301 // decide if av alignment is sufficiently different to original data to
302 // warrant a new window to be created
303 // create new alignment window with hidden regions (unhiding hidden regions
304 // yields unaligned seqs)
305 // or create a selection box around columns in alignment view
306 // test Alignment(SeqCigar[])
310 // we try to get the associated view's gap character
311 // but this may fail if the view was closed...
312 gc = av.getGapCharacter();
313 } catch (Exception ex)
317 Object[] alAndColsel = getPcaModel().getInputData()
318 .getAlignmentAndHiddenColumns(gc);
320 if (alAndColsel != null && alAndColsel[0] != null)
322 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
324 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
325 AlignmentI dataset = (av != null && av.getAlignment() != null)
326 ? av.getAlignment().getDataset()
330 al.setDataset(dataset);
336 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
337 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
339 // >>>This is a fix for the moment, until a better solution is
341 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
343 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
346 Desktop.addInternalFrame(af, MessageManager.formatMessage(
347 "label.original_data_for_params", new String[]
348 { this.title }), AlignFrame.DEFAULT_WIDTH,
349 AlignFrame.DEFAULT_HEIGHT);
353 * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
354 * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
355 * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
358 * Desktop.addInternalFrame(cap, "Original Data", 400, 400);
362 class PCAPrinter extends Thread implements Printable
367 PrinterJob printJob = PrinterJob.getPrinterJob();
368 PageFormat defaultPage = printJob.defaultPage();
369 PageFormat pf = printJob.pageDialog(defaultPage);
371 if (defaultPage == pf)
379 printJob.setPrintable(this, pf);
381 if (printJob.printDialog())
386 } catch (Exception PrintException)
388 PrintException.printStackTrace();
394 public int print(Graphics pg, PageFormat pf, int pi)
395 throws PrinterException
397 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
399 getRotatableCanvas().drawBackground(pg);
400 getRotatableCanvas().drawScene(pg);
401 if (getRotatableCanvas().drawAxes)
403 getRotatableCanvas().drawAxes(pg);
408 return Printable.PAGE_EXISTS;
412 return Printable.NO_SUCH_PAGE;
418 public void makePCAImage(ImageMaker.TYPE type)
420 int width = getRotatableCanvas().getWidth();
421 int height = getRotatableCanvas().getHeight();
422 ImageWriterI writer = new ImageWriterI()
425 public void exportImage(Graphics g) throws Exception
427 RotatableCanvas canvas = getRotatableCanvas();
428 canvas.drawBackground(g);
436 String pca = MessageManager.getString("label.pca");
437 ImageExporter exporter = new ImageExporter(writer, null, type, pca);
438 exporter.doExport(null, this, width, height, pca);
442 protected void viewMenu_menuSelected()
444 buildAssociatedViewMenu();
448 * Builds the menu showing the choice of possible views (for the associated
449 * sequence data) to which the PCA may be linked
451 void buildAssociatedViewMenu()
453 AlignmentPanel[] aps = PaintRefresher
454 .getAssociatedPanels(av.getSequenceSetId());
455 if (aps.length == 1 && getRotatableCanvas().av == aps[0].av)
457 associateViewsMenu.setVisible(false);
461 associateViewsMenu.setVisible(true);
464 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
466 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
469 associateViewsMenu.removeAll();
471 JRadioButtonMenuItem item;
472 ButtonGroup buttonGroup = new ButtonGroup();
473 int iSize = aps.length;
475 for (int i = 0; i < iSize; i++)
477 final AlignmentPanel panel = aps[i];
478 item = new JRadioButtonMenuItem(panel.av.getViewName(),
479 panel.av == getRotatableCanvas().av);
480 buttonGroup.add(item);
481 item.addActionListener(new ActionListener()
484 public void actionPerformed(ActionEvent evt)
486 selectAssociatedView(panel);
490 associateViewsMenu.add(item);
493 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
496 buttonGroup.add(itemf);
498 itemf.setSelected(getRotatableCanvas().isApplyToAllViews());
499 itemf.addActionListener(new ActionListener()
502 public void actionPerformed(ActionEvent evt)
504 getRotatableCanvas().setApplyToAllViews(itemf.isSelected());
507 associateViewsMenu.add(itemf);
512 protected void outputPoints_actionPerformed()
514 CutAndPasteTransfer cap = new CutAndPasteTransfer();
517 cap.setText(getPcaModel().getPointsasCsv(false,
518 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
519 zCombobox.getSelectedIndex()));
520 Desktop.addInternalFrame(cap, MessageManager
521 .formatMessage("label.points_for_params", new String[]
522 { this.getTitle() }), 500, 500);
523 } catch (OutOfMemoryError oom)
525 new OOMWarning("exporting PCA points", oom);
531 protected void outputProjPoints_actionPerformed()
533 CutAndPasteTransfer cap = new CutAndPasteTransfer();
536 cap.setText(getPcaModel().getPointsasCsv(true,
537 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
538 zCombobox.getSelectedIndex()));
539 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
540 "label.transformed_points_for_params", new String[]
541 { this.getTitle() }), 500, 500);
542 } catch (OutOfMemoryError oom)
544 new OOMWarning("exporting transformed PCA points", oom);
550 public void setProgressBar(String message, long id)
552 progressBar.setProgressBar(message, id);
556 public void registerHandler(final long id,
557 final IProgressIndicatorHandler handler)
559 progressBar.registerHandler(id, handler);
564 * @return true if any progress bars are still active
567 public boolean operationInProgress()
569 return progressBar.operationInProgress();
573 protected void resetButton_actionPerformed()
576 setTop(0); // ugly - prevents dimensionChanged events from being processed
577 xCombobox.setSelectedIndex(0);
578 yCombobox.setSelectedIndex(1);
580 zCombobox.setSelectedIndex(2);
584 * Answers true if PCA calculation is in progress, else false
588 public boolean isWorking()
594 * Answers the selected checkbox item index for PCA dimension for the X, Y or
595 * Z axis of the display
600 public int getSelectedDimensionIndex(Axis axis)
605 return xCombobox.getSelectedIndex();
607 return yCombobox.getSelectedIndex();
609 return zCombobox.getSelectedIndex();
613 public void setShowLabels(boolean show)
615 showLabels.setSelected(show);
619 * Sets the input data used to calculate the PCA. This is provided for
620 * 'restore from project', which does not currently support this (AL-2647), so
621 * sets the value to null, and hides the menu option for "Input Data...". J
625 public void setInputData(AlignmentView data)
627 getPcaModel().setInputData(data);
628 originalSeqData.setVisible(data != null);
631 public AlignViewportI getAlignViewport()
636 public PCAModel getPcaModel()
641 public void setPcaModel(PCAModel pcaModel)
643 this.pcaModel = pcaModel;
646 public RotatableCanvas getRotatableCanvas()
651 public void setRotatableCanvas(RotatableCanvas rc)
661 public void setTop(int top)
667 * set the associated view for this PCA.
671 public void selectAssociatedView(AlignmentPanel panel)
673 getRotatableCanvas().setApplyToAllViews(false);
678 getRotatableCanvas().av = panel.av;
679 getRotatableCanvas().ap = panel;
680 PaintRefresher.Register(PCAPanel.this, panel.av.getSequenceSetId());