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;
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());
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 String ttl = MessageManager.getString("label.select_background_colour");
149 ColourChooserListener listener = new ColourChooserListener()
152 public void colourSelected(Color c)
158 JalviewColourChooser.showColourChooser(this, ttl, rc.getBgColour(),
163 * Calculates the PCA and displays the results
169 long progId = System.currentTimeMillis();
170 IProgressIndicator progress = this;
171 String message = MessageManager.getString("label.pca_recalculating");
172 if (getParent() == null)
174 progress = ap.alignFrame;
175 message = MessageManager.getString("label.pca_calculating");
177 progress.setProgressBar(message, progId);
180 getPcaModel().calculate();
182 xCombobox.setSelectedIndex(0);
183 yCombobox.setSelectedIndex(1);
184 zCombobox.setSelectedIndex(2);
186 getPcaModel().updateRc(getRotatableCanvas());
188 setTop(getPcaModel().getTop());
190 } catch (OutOfMemoryError er)
192 new OOMWarning("calculating PCA", er);
197 progress.setProgressBar("", progId);
201 if (getParent() == null)
203 Desktop.addInternalFrame(this,
204 MessageManager.formatMessage("label.calc_title", "PCA",
205 getPcaModel().getScoreModelName()),
207 this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
213 * Updates the PCA display after a change of component to use for x, y or z
217 protected void doDimensionChange()
224 int dim1 = getTop() - xCombobox.getSelectedIndex();
225 int dim2 = getTop() - yCombobox.getSelectedIndex();
226 int dim3 = getTop() - zCombobox.getSelectedIndex();
227 getPcaModel().updateRcView(dim1, dim2, dim3);
228 getRotatableCanvas().resetView();
232 * Sets the selected checkbox item index for PCA dimension (1, 2, 3...) for
233 * the given axis (X/Y/Z)
238 public void setSelectedDimensionIndex(int index, Axis axis)
243 xCombobox.setSelectedIndex(index);
246 yCombobox.setSelectedIndex(index);
249 zCombobox.setSelectedIndex(index);
256 protected void outputValues_actionPerformed()
258 CutAndPasteTransfer cap = new CutAndPasteTransfer();
261 cap.setText(getPcaModel().getDetails());
262 Desktop.addInternalFrame(cap,
263 MessageManager.getString("label.pca_details"), 500, 500);
264 } catch (OutOfMemoryError oom)
266 new OOMWarning("opening PCA details", oom);
272 protected void showLabels_actionPerformed()
274 getRotatableCanvas().showLabels(showLabels.getState());
278 protected void print_actionPerformed()
280 PCAPrinter printer = new PCAPrinter();
285 * If available, shows the data which formed the inputs for the PCA as a new
289 public void originalSeqData_actionPerformed()
291 // JAL-2647 disabled after load from project (until save to project done)
292 if (getPcaModel().getInputData() == null)
295 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
298 // decide if av alignment is sufficiently different to original data to
299 // warrant a new window to be created
300 // create new alignment window with hidden regions (unhiding hidden regions
301 // yields unaligned seqs)
302 // or create a selection box around columns in alignment view
303 // test Alignment(SeqCigar[])
307 // we try to get the associated view's gap character
308 // but this may fail if the view was closed...
309 gc = av.getGapCharacter();
310 } catch (Exception ex)
314 Object[] alAndColsel = getPcaModel().getInputData()
315 .getAlignmentAndHiddenColumns(gc);
317 if (alAndColsel != null && alAndColsel[0] != null)
319 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
321 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
322 AlignmentI dataset = (av != null && av.getAlignment() != null)
323 ? av.getAlignment().getDataset()
327 al.setDataset(dataset);
333 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
334 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
336 // >>>This is a fix for the moment, until a better solution is
338 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
340 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
343 Desktop.addInternalFrame(af, MessageManager.formatMessage(
344 "label.original_data_for_params", new String[]
345 { this.title }), AlignFrame.DEFAULT_WIDTH,
346 AlignFrame.DEFAULT_HEIGHT);
350 * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
351 * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
352 * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
355 * Desktop.addInternalFrame(cap, "Original Data", 400, 400);
359 class PCAPrinter extends Thread implements Printable
364 PrinterJob printJob = PrinterJob.getPrinterJob();
365 PageFormat defaultPage = printJob.defaultPage();
366 PageFormat pf = printJob.pageDialog(defaultPage);
368 if (defaultPage == pf)
376 printJob.setPrintable(this, pf);
378 if (printJob.printDialog())
383 } catch (Exception PrintException)
385 PrintException.printStackTrace();
391 public int print(Graphics pg, PageFormat pf, int pi)
392 throws PrinterException
394 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
396 getRotatableCanvas().drawBackground(pg);
397 getRotatableCanvas().drawScene(pg);
398 if (getRotatableCanvas().drawAxes)
400 getRotatableCanvas().drawAxes(pg);
405 return Printable.PAGE_EXISTS;
409 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);
509 protected void outputPoints_actionPerformed()
511 CutAndPasteTransfer cap = new CutAndPasteTransfer();
514 cap.setText(getPcaModel().getPointsasCsv(false,
515 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
516 zCombobox.getSelectedIndex()));
517 Desktop.addInternalFrame(cap, MessageManager
518 .formatMessage("label.points_for_params", new String[]
519 { this.getTitle() }), 500, 500);
520 } catch (OutOfMemoryError oom)
522 new OOMWarning("exporting PCA points", oom);
528 protected void outputProjPoints_actionPerformed()
530 CutAndPasteTransfer cap = new CutAndPasteTransfer();
533 cap.setText(getPcaModel().getPointsasCsv(true,
534 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
535 zCombobox.getSelectedIndex()));
536 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
537 "label.transformed_points_for_params", new String[]
538 { this.getTitle() }), 500, 500);
539 } catch (OutOfMemoryError oom)
541 new OOMWarning("exporting transformed PCA points", oom);
547 public void setProgressBar(String message, long id)
549 progressBar.setProgressBar(message, id);
553 public void registerHandler(final long id,
554 final IProgressIndicatorHandler handler)
556 progressBar.registerHandler(id, handler);
561 * @return true if any progress bars are still active
564 public boolean operationInProgress()
566 return progressBar.operationInProgress();
570 protected void resetButton_actionPerformed()
573 setTop(0); // ugly - prevents dimensionChanged events from being processed
574 xCombobox.setSelectedIndex(0);
575 yCombobox.setSelectedIndex(1);
577 zCombobox.setSelectedIndex(2);
581 * Answers true if PCA calculation is in progress, else false
585 public boolean isWorking()
591 * Answers the selected checkbox item index for PCA dimension for the X, Y or
592 * Z axis of the display
597 public int getSelectedDimensionIndex(Axis axis)
602 return xCombobox.getSelectedIndex();
604 return yCombobox.getSelectedIndex();
606 return zCombobox.getSelectedIndex();
610 public void setShowLabels(boolean show)
612 showLabels.setSelected(show);
616 * Sets the input data used to calculate the PCA. This is provided for
617 * 'restore from project', which does not currently support this (AL-2647), so
618 * sets the value to null, and hides the menu option for "Input Data...". J
622 public void setInputData(AlignmentView data)
624 getPcaModel().setInputData(data);
625 originalSeqData.setVisible(data != null);
628 public AlignViewportI getAlignViewport()
633 public PCAModel getPcaModel()
638 public void setPcaModel(PCAModel pcaModel)
640 this.pcaModel = pcaModel;
643 public RotatableCanvas getRotatableCanvas()
648 public void setRotatableCanvas(RotatableCanvas rc)
658 public void setTop(int top)
664 * set the associated view for this PCA.
668 public void selectAssociatedView(AlignmentPanel panel)
670 getRotatableCanvas().setApplyToAllViews(false);
675 getRotatableCanvas().av = panel.av;
676 getRotatableCanvas().ap = panel;
677 PaintRefresher.Register(PCAPanel.this, panel.av.getSequenceSetId());