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.jbgui.GPCAPanel;
34 import jalview.math.RotatableMatrix.Axis;
35 import jalview.util.ImageMaker;
36 import jalview.util.MessageManager;
37 import jalview.viewmodel.AlignmentViewport;
38 import jalview.viewmodel.PCAModel;
40 import java.awt.BorderLayout;
41 import java.awt.Color;
42 import java.awt.Dimension;
43 import java.awt.Graphics;
44 import java.awt.event.ActionEvent;
45 import java.awt.event.ActionListener;
46 import java.awt.print.PageFormat;
47 import java.awt.print.Printable;
48 import java.awt.print.PrinterException;
49 import java.awt.print.PrinterJob;
51 import javax.swing.ButtonGroup;
52 import javax.swing.JColorChooser;
53 import javax.swing.JMenuItem;
54 import javax.swing.JRadioButtonMenuItem;
55 import javax.swing.event.InternalFrameAdapter;
56 import javax.swing.event.InternalFrameEvent;
59 * The panel holding the Principal Component Analysis 3-D visualisation
61 public class PCAPanel extends GPCAPanel
62 implements Runnable, IProgressIndicator
64 private static final int MIN_WIDTH = 470;
66 private static final int MIN_HEIGHT = 250;
68 private RotatableCanvas rc;
74 private PCAModel pcaModel;
78 private IProgressIndicator progressBar;
80 private boolean working;
83 * Constructor given sequence data, a similarity (or distance) score model
84 * name, and score calculation parameters
90 public PCAPanel(AlignmentPanel alignPanel, String modelName,
91 SimilarityParamsI params)
94 this.av = alignPanel.av;
96 boolean nucleotide = av.getAlignment().isNucleotide();
98 progressBar = new ProgressBar(statusPanel, statusBar);
100 addInternalFrameListener(new InternalFrameAdapter()
103 public void internalFrameClosed(InternalFrameEvent e)
105 close_actionPerformed();
109 boolean selected = av.getSelectionGroup() != null
110 && av.getSelectionGroup().getSize() > 0;
111 AlignmentView seqstrings = av.getAlignmentView(selected);
115 seqs = av.getAlignment().getSequencesArray();
119 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
122 ScoreModelI scoreModel = ScoreModels.getInstance()
123 .getScoreModel(modelName, ap);
124 setPcaModel(new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
126 PaintRefresher.Register(this, av.getSequenceSetId());
128 setRotatableCanvas(new RotatableCanvas(alignPanel));
129 this.getContentPane().add(getRotatableCanvas(), BorderLayout.CENTER);
131 addKeyListener(getRotatableCanvas());
134 this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
138 * Ensure references to potentially very large objects (the PCA matrices) are
139 * nulled when the frame is closed
141 protected void close_actionPerformed()
146 this.rc.sequencePoints = null;
147 this.rc.setAxisEndPoints(null);
153 protected void bgcolour_actionPerformed()
155 Color col = JColorChooser.showDialog(this,
156 MessageManager.getString("label.select_background_colour"),
157 getRotatableCanvas().getBgColour());
161 getRotatableCanvas().setBgColour(col);
163 getRotatableCanvas().repaint();
167 * Calculates the PCA and displays the results
173 long progId = System.currentTimeMillis();
174 IProgressIndicator progress = this;
175 String message = MessageManager.getString("label.pca_recalculating");
176 if (getParent() == null)
178 progress = ap.alignFrame;
179 message = MessageManager.getString("label.pca_calculating");
181 progress.setProgressBar(message, progId);
184 getPcaModel().calculate();
186 xCombobox.setSelectedIndex(0);
187 yCombobox.setSelectedIndex(1);
188 zCombobox.setSelectedIndex(2);
190 getPcaModel().updateRc(getRotatableCanvas());
192 setTop(getPcaModel().getTop());
194 } catch (OutOfMemoryError er)
196 new OOMWarning("calculating PCA", er);
201 progress.setProgressBar("", progId);
205 if (getParent() == null)
207 Desktop.addInternalFrame(this,
208 MessageManager.formatMessage("label.calc_title", "PCA",
209 getPcaModel().getScoreModelName()),
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 * Handler for 'Save as EPS' option
421 protected void eps_actionPerformed()
423 makePCAImage(ImageMaker.TYPE.EPS);
427 * Handler for 'Save as PNG' option
430 protected void png_actionPerformed()
432 makePCAImage(ImageMaker.TYPE.PNG);
435 void makePCAImage(ImageMaker.TYPE type)
437 int width = getRotatableCanvas().getWidth();
438 int height = getRotatableCanvas().getHeight();
445 im = new ImageMaker(this, ImageMaker.TYPE.PNG,
446 "Make PNG image from PCA", width, height, null, null, null, 0,
450 im = new ImageMaker(this, ImageMaker.TYPE.EPS,
451 "Make EPS file from PCA", width, height, null,
452 this.getTitle(), null, 0, false);
455 im = new ImageMaker(this, ImageMaker.TYPE.SVG,
456 "Make SVG file from PCA", width, height, null,
457 this.getTitle(), null, 0, false);
460 if (im.getGraphics() != null)
462 getRotatableCanvas().drawBackground(im.getGraphics());
463 getRotatableCanvas().drawScene(im.getGraphics());
464 if (getRotatableCanvas().drawAxes)
466 getRotatableCanvas().drawAxes(im.getGraphics());
473 protected void viewMenu_menuSelected()
475 buildAssociatedViewMenu();
479 * Builds the menu showing the choice of possible views (for the associated
480 * sequence data) to which the PCA may be linked
482 void buildAssociatedViewMenu()
484 AlignmentPanel[] aps = PaintRefresher
485 .getAssociatedPanels(av.getSequenceSetId());
486 if (aps.length == 1 && getRotatableCanvas().av == aps[0].av)
488 associateViewsMenu.setVisible(false);
492 associateViewsMenu.setVisible(true);
495 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
497 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
500 associateViewsMenu.removeAll();
502 JRadioButtonMenuItem item;
503 ButtonGroup buttonGroup = new ButtonGroup();
504 int iSize = aps.length;
506 for (int i = 0; i < iSize; i++)
508 final AlignmentPanel panel = aps[i];
509 item = new JRadioButtonMenuItem(panel.av.getViewName(),
510 panel.av == getRotatableCanvas().av);
511 buttonGroup.add(item);
512 item.addActionListener(new ActionListener()
515 public void actionPerformed(ActionEvent evt)
517 selectAssociatedView(panel);
521 associateViewsMenu.add(item);
524 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
527 buttonGroup.add(itemf);
529 itemf.setSelected(getRotatableCanvas().isApplyToAllViews());
530 itemf.addActionListener(new ActionListener()
533 public void actionPerformed(ActionEvent evt)
535 getRotatableCanvas().setApplyToAllViews(itemf.isSelected());
538 associateViewsMenu.add(itemf);
546 * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
550 protected void outputPoints_actionPerformed()
552 CutAndPasteTransfer cap = new CutAndPasteTransfer();
555 cap.setText(getPcaModel().getPointsasCsv(false,
556 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
557 zCombobox.getSelectedIndex()));
558 Desktop.addInternalFrame(cap, MessageManager
559 .formatMessage("label.points_for_params", new String[]
560 { this.getTitle() }), 500, 500);
561 } catch (OutOfMemoryError oom)
563 new OOMWarning("exporting PCA points", oom);
572 * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
576 protected void outputProjPoints_actionPerformed()
578 CutAndPasteTransfer cap = new CutAndPasteTransfer();
581 cap.setText(getPcaModel().getPointsasCsv(true,
582 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
583 zCombobox.getSelectedIndex()));
584 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
585 "label.transformed_points_for_params", new String[]
586 { this.getTitle() }), 500, 500);
587 } catch (OutOfMemoryError oom)
589 new OOMWarning("exporting transformed PCA points", oom);
597 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
600 public void setProgressBar(String message, long id)
602 progressBar.setProgressBar(message, id);
603 // if (progressBars == null)
605 // progressBars = new Hashtable();
606 // progressBarHandlers = new Hashtable();
609 // JPanel progressPanel;
610 // Long lId = Long.valueOf(id);
611 // GridLayout layout = (GridLayout) statusPanel.getLayout();
612 // if (progressBars.get(lId) != null)
614 // progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
615 // statusPanel.remove(progressPanel);
616 // progressBars.remove(lId);
617 // progressPanel = null;
618 // if (message != null)
620 // statusBar.setText(message);
622 // if (progressBarHandlers.contains(lId))
624 // progressBarHandlers.remove(lId);
626 // layout.setRows(layout.getRows() - 1);
630 // progressPanel = new JPanel(new BorderLayout(10, 5));
632 // JProgressBar progressBar = new JProgressBar();
633 // progressBar.setIndeterminate(true);
635 // progressPanel.add(new JLabel(message), BorderLayout.WEST);
636 // progressPanel.add(progressBar, BorderLayout.CENTER);
638 // layout.setRows(layout.getRows() + 1);
639 // statusPanel.add(progressPanel);
641 // progressBars.put(lId, progressPanel);
644 // // setMenusForViewport();
649 public void registerHandler(final long id,
650 final IProgressIndicatorHandler handler)
652 progressBar.registerHandler(id, handler);
653 // if (progressBarHandlers == null || !progressBars.contains(Long.valueOf(id)))
656 // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
658 // progressBarHandlers.put(Long.valueOf(id), handler);
659 // final JPanel progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
660 // if (handler.canCancel())
662 // JButton cancel = new JButton(
663 // MessageManager.getString("action.cancel"));
664 // final IProgressIndicator us = this;
665 // cancel.addActionListener(new ActionListener()
669 // public void actionPerformed(ActionEvent e)
671 // handler.cancelActivity(id);
672 // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
673 // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
676 // progressPanel.add(cancel, BorderLayout.EAST);
682 * @return true if any progress bars are still active
685 public boolean operationInProgress()
687 return progressBar.operationInProgress();
691 protected void resetButton_actionPerformed()
694 setTop(0); // ugly - prevents dimensionChanged events from being processed
695 xCombobox.setSelectedIndex(0);
696 yCombobox.setSelectedIndex(1);
698 zCombobox.setSelectedIndex(2);
702 * Answers true if PCA calculation is in progress, else false
706 public boolean isWorking()
712 * Answers the selected checkbox item index for PCA dimension for the X, Y or
713 * Z axis of the display
718 public int getSelectedDimensionIndex(Axis axis)
723 return xCombobox.getSelectedIndex();
725 return yCombobox.getSelectedIndex();
727 return zCombobox.getSelectedIndex();
731 public void setShowLabels(boolean show)
733 showLabels.setSelected(show);
737 * Sets the input data used to calculate the PCA. This is provided for
738 * 'restore from project', which does not currently support this (AL-2647), so
739 * sets the value to null, and hides the menu option for "Input Data...". J
743 public void setInputData(AlignmentView data)
745 getPcaModel().setInputData(data);
746 originalSeqData.setVisible(data != null);
749 public AlignViewportI getAlignViewport()
754 public PCAModel getPcaModel()
759 public void setPcaModel(PCAModel pcaModel)
761 this.pcaModel = pcaModel;
764 public RotatableCanvas getRotatableCanvas()
769 public void setRotatableCanvas(RotatableCanvas rc)
779 public void setTop(int top)
785 * set the associated view for this PCA.
789 public void selectAssociatedView(AlignmentPanel panel)
791 getRotatableCanvas().setApplyToAllViews(false);
796 getRotatableCanvas().av = panel.av;
797 getRotatableCanvas().ap = panel;
798 PaintRefresher.Register(PCAPanel.this, panel.av.getSequenceSetId());