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 java.awt.BorderLayout;
24 import java.awt.Color;
25 import java.awt.Dimension;
26 import java.awt.Graphics;
27 import java.awt.event.ActionEvent;
28 import java.awt.event.ActionListener;
29 import java.awt.print.PageFormat;
30 import java.awt.print.Printable;
31 import java.awt.print.PrinterException;
32 import java.awt.print.PrinterJob;
34 import javax.swing.ButtonGroup;
35 import javax.swing.JMenuItem;
36 import javax.swing.JRadioButtonMenuItem;
37 import javax.swing.event.InternalFrameAdapter;
38 import javax.swing.event.InternalFrameEvent;
40 import jalview.analysis.scoremodels.ScoreModels;
41 import jalview.api.AlignViewportI;
42 import jalview.api.analysis.ScoreModelI;
43 import jalview.api.analysis.SimilarityParamsI;
44 import jalview.bin.Console;
45 import jalview.datamodel.Alignment;
46 import jalview.datamodel.AlignmentI;
47 import jalview.datamodel.AlignmentView;
48 import jalview.datamodel.HiddenColumns;
49 import jalview.datamodel.SequenceI;
50 import jalview.gui.ImageExporter.ImageWriterI;
51 import jalview.gui.JalviewColourChooser.ColourChooserListener;
52 import jalview.io.exceptions.ImageOutputException;
53 import jalview.jbgui.GPCAPanel;
54 import jalview.math.RotatableMatrix.Axis;
55 import jalview.util.IdUtils;
56 import jalview.util.IdUtils.IdType;
57 import jalview.util.ImageMaker;
58 import jalview.util.MessageManager;
59 import jalview.viewmodel.AlignmentViewport;
60 import jalview.viewmodel.PCAModel;
63 * The panel holding the Principal Component Analysis 3-D visualisation
65 public class PCAPanel extends GPCAPanel
66 implements Runnable, IProgressIndicator
68 private static final int MIN_WIDTH = 470;
70 private static final int MIN_HEIGHT = 250;
72 private RotatableCanvas rc;
78 private PCAModel pcaModel;
82 private IProgressIndicator progressBar;
84 private boolean working;
87 * Constructor given sequence data, a similarity (or distance) score model
88 * name, and score calculation parameters
94 public PCAPanel(AlignmentPanel alignPanel, String modelName,
95 SimilarityParamsI params)
98 this.setFrameIcon(null);
99 this.av = alignPanel.av;
100 this.ap = alignPanel;
101 boolean nucleotide = av.getAlignment().isNucleotide();
103 progressBar = new ProgressBar(statusPanel, statusBar);
105 addInternalFrameListener(new InternalFrameAdapter()
108 public void internalFrameClosed(InternalFrameEvent e)
110 close_actionPerformed();
114 boolean selected = av.getSelectionGroup() != null
115 && av.getSelectionGroup().getSize() > 0;
116 AlignmentView seqstrings = av.getAlignmentView(selected);
120 seqs = av.getAlignment().getSequencesArray();
124 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
127 ScoreModelI scoreModel = ScoreModels.getInstance()
128 .getScoreModel(modelName, ap);
130 new PCAModel(seqstrings, seqs, nucleotide, scoreModel, params));
131 PaintRefresher.Register(this, av.getSequenceSetId());
133 setRotatableCanvas(new RotatableCanvas(alignPanel));
134 this.getContentPane().add(getRotatableCanvas(), BorderLayout.CENTER);
136 addKeyListener(getRotatableCanvas());
141 * Ensure references to potentially very large objects (the PCA matrices) are
142 * nulled when the frame is closed
144 protected void close_actionPerformed()
149 this.rc.sequencePoints = null;
150 this.rc.setAxisEndPoints(null);
156 protected void bgcolour_actionPerformed()
158 String ttl = MessageManager.getString("label.select_background_colour");
159 ColourChooserListener listener = new ColourChooserListener()
162 public void colourSelected(Color c)
168 JalviewColourChooser.showColourChooser(this, ttl, rc.getBgColour(),
173 * Calculates the PCA and displays the results
179 long progId = IdUtils.newId(IdType.PROGRESS);
180 IProgressIndicator progress = this;
181 String message = MessageManager.getString("label.pca_recalculating");
182 if (getParent() == null)
184 progress = ap.alignFrame;
185 message = MessageManager.getString("label.pca_calculating");
187 progress.setProgressBar(message, progId);
190 getPcaModel().calculate();
192 xCombobox.setSelectedIndex(0);
193 yCombobox.setSelectedIndex(1);
194 zCombobox.setSelectedIndex(2);
196 getPcaModel().updateRc(getRotatableCanvas());
198 setTop(getPcaModel().getTop());
200 } catch (OutOfMemoryError er)
202 new OOMWarning("calculating PCA", er);
207 progress.setProgressBar("", progId);
211 if (getParent() == null)
213 Desktop.addInternalFrame(this,
214 MessageManager.formatMessage("label.calc_title", "PCA",
215 getPcaModel().getScoreModelName()),
217 this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
223 * Updates the PCA display after a change of component to use for x, y or z
227 protected void doDimensionChange()
234 int dim1 = getTop() - xCombobox.getSelectedIndex();
235 int dim2 = getTop() - yCombobox.getSelectedIndex();
236 int dim3 = getTop() - zCombobox.getSelectedIndex();
237 getPcaModel().updateRcView(dim1, dim2, dim3);
238 getRotatableCanvas().resetView();
242 * Sets the selected checkbox item index for PCA dimension (1, 2, 3...) for
243 * the given axis (X/Y/Z)
248 public void setSelectedDimensionIndex(int index, Axis axis)
253 xCombobox.setSelectedIndex(index);
256 yCombobox.setSelectedIndex(index);
259 zCombobox.setSelectedIndex(index);
266 protected void outputValues_actionPerformed()
268 CutAndPasteTransfer cap = new CutAndPasteTransfer();
271 cap.setText(getPcaModel().getDetails());
272 Desktop.addInternalFrame(cap,
273 MessageManager.getString("label.pca_details"), 500, 500);
274 } catch (OutOfMemoryError oom)
276 new OOMWarning("opening PCA details", oom);
282 protected void showLabels_actionPerformed()
284 getRotatableCanvas().showLabels(showLabels.getState());
288 protected void print_actionPerformed()
290 PCAPrinter printer = new PCAPrinter();
295 * If available, shows the data which formed the inputs for the PCA as a new
299 public void originalSeqData_actionPerformed()
301 // JAL-2647 disabled after load from project (until save to project done)
302 if (getPcaModel().getInputData() == null)
305 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
308 // decide if av alignment is sufficiently different to original data to
309 // warrant a new window to be created
310 // create new alignment window with hidden regions (unhiding hidden regions
311 // yields unaligned seqs)
312 // or create a selection box around columns in alignment view
313 // test Alignment(SeqCigar[])
317 // we try to get the associated view's gap character
318 // but this may fail if the view was closed...
319 gc = av.getGapCharacter();
320 } catch (Exception ex)
324 Object[] alAndColsel = getPcaModel().getInputData()
325 .getAlignmentAndHiddenColumns(gc);
327 if (alAndColsel != null && alAndColsel[0] != null)
329 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
331 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
332 AlignmentI dataset = (av != null && av.getAlignment() != null)
333 ? av.getAlignment().getDataset()
337 al.setDataset(dataset);
343 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
344 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
346 // >>>This is a fix for the moment, until a better solution is
348 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
350 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
353 Desktop.addInternalFrame(af, MessageManager.formatMessage(
354 "label.original_data_for_params", new String[]
355 { this.title }), AlignFrame.DEFAULT_WIDTH,
356 AlignFrame.DEFAULT_HEIGHT);
360 * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
361 * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
362 * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
365 * Desktop.addInternalFrame(cap, "Original Data", 400, 400);
369 class PCAPrinter extends Thread implements Printable
374 PrinterJob printJob = PrinterJob.getPrinterJob();
375 PageFormat defaultPage = printJob.defaultPage();
376 PageFormat pf = printJob.pageDialog(defaultPage);
378 if (defaultPage == pf)
386 printJob.setPrintable(this, pf);
388 if (printJob.printDialog())
393 } catch (Exception PrintException)
395 PrintException.printStackTrace();
401 public int print(Graphics pg, PageFormat pf, int pi)
402 throws PrinterException
404 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
406 getRotatableCanvas().drawBackground(pg);
407 getRotatableCanvas().drawScene(pg);
408 if (getRotatableCanvas().drawAxes)
410 getRotatableCanvas().drawAxes(pg);
415 return Printable.PAGE_EXISTS;
419 return Printable.NO_SUCH_PAGE;
425 public void makePCAImage(ImageMaker.TYPE type)
427 int width = getRotatableCanvas().getWidth();
428 int height = getRotatableCanvas().getHeight();
429 ImageWriterI writer = new ImageWriterI()
432 public void exportImage(Graphics g) throws Exception
434 RotatableCanvas canvas = getRotatableCanvas();
435 canvas.drawBackground(g);
443 String pca = MessageManager.getString("label.pca");
444 ImageExporter exporter = new ImageExporter(writer, null, type, pca);
447 exporter.doExport(null, this, width, height, pca);
448 } catch (ImageOutputException ioex)
450 Console.error("Unexpected error whilst writing " + type.toString(),
456 protected void viewMenu_menuSelected()
458 buildAssociatedViewMenu();
462 * Builds the menu showing the choice of possible views (for the associated
463 * sequence data) to which the PCA may be linked
465 void buildAssociatedViewMenu()
467 AlignmentPanel[] aps = PaintRefresher
468 .getAssociatedPanels(av.getSequenceSetId());
469 if (aps.length == 1 && getRotatableCanvas().av == aps[0].av)
471 associateViewsMenu.setVisible(false);
475 associateViewsMenu.setVisible(true);
478 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
480 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
483 associateViewsMenu.removeAll();
485 JRadioButtonMenuItem item;
486 ButtonGroup buttonGroup = new ButtonGroup();
487 int iSize = aps.length;
489 for (int i = 0; i < iSize; i++)
491 final AlignmentPanel panel = aps[i];
492 item = new JRadioButtonMenuItem(panel.av.getViewName(),
493 panel.av == getRotatableCanvas().av);
494 buttonGroup.add(item);
495 item.addActionListener(new ActionListener()
498 public void actionPerformed(ActionEvent evt)
500 selectAssociatedView(panel);
504 associateViewsMenu.add(item);
507 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
510 buttonGroup.add(itemf);
512 itemf.setSelected(getRotatableCanvas().isApplyToAllViews());
513 itemf.addActionListener(new ActionListener()
516 public void actionPerformed(ActionEvent evt)
518 getRotatableCanvas().setApplyToAllViews(itemf.isSelected());
521 associateViewsMenu.add(itemf);
529 * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
533 protected void outputPoints_actionPerformed()
535 CutAndPasteTransfer cap = new CutAndPasteTransfer();
538 cap.setText(getPcaModel().getPointsasCsv(false,
539 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
540 zCombobox.getSelectedIndex()));
541 Desktop.addInternalFrame(cap, MessageManager
542 .formatMessage("label.points_for_params", new String[]
543 { this.getTitle() }), 500, 500);
544 } catch (OutOfMemoryError oom)
546 new OOMWarning("exporting PCA points", oom);
555 * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
559 protected void outputProjPoints_actionPerformed()
561 CutAndPasteTransfer cap = new CutAndPasteTransfer();
564 cap.setText(getPcaModel().getPointsasCsv(true,
565 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
566 zCombobox.getSelectedIndex()));
567 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
568 "label.transformed_points_for_params", new String[]
569 { this.getTitle() }), 500, 500);
570 } catch (OutOfMemoryError oom)
572 new OOMWarning("exporting transformed PCA points", oom);
580 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
583 public void setProgressBar(String message, long id)
585 progressBar.setProgressBar(message, id);
586 // if (progressBars == null)
588 // progressBars = new Hashtable();
589 // progressBarHandlers = new Hashtable();
592 // JPanel progressPanel;
593 // Long lId = Long.valueOf(id);
594 // GridLayout layout = (GridLayout) statusPanel.getLayout();
595 // if (progressBars.get(lId) != null)
597 // progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
598 // statusPanel.remove(progressPanel);
599 // progressBars.remove(lId);
600 // progressPanel = null;
601 // if (message != null)
603 // statusBar.setText(message);
605 // if (progressBarHandlers.contains(lId))
607 // progressBarHandlers.remove(lId);
609 // layout.setRows(layout.getRows() - 1);
613 // progressPanel = new JPanel(new BorderLayout(10, 5));
615 // JProgressBar progressBar = new JProgressBar();
616 // progressBar.setIndeterminate(true);
618 // progressPanel.add(new JLabel(message), BorderLayout.WEST);
619 // progressPanel.add(progressBar, BorderLayout.CENTER);
621 // layout.setRows(layout.getRows() + 1);
622 // statusPanel.add(progressPanel);
624 // progressBars.put(lId, progressPanel);
627 // // setMenusForViewport();
632 public void registerHandler(final long id,
633 final IProgressIndicatorHandler handler)
635 progressBar.registerHandler(id, handler);
636 // if (progressBarHandlers == null ||
637 // !progressBars.contains(Long.valueOf(id)))
640 // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
642 // progressBarHandlers.put(Long.valueOf(id), handler);
643 // final JPanel progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
644 // if (handler.canCancel())
646 // JButton cancel = new JButton(
647 // MessageManager.getString("action.cancel"));
648 // final IProgressIndicator us = this;
649 // cancel.addActionListener(new ActionListener()
653 // public void actionPerformed(ActionEvent e)
655 // handler.cancelActivity(id);
656 // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
657 // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
660 // progressPanel.add(cancel, BorderLayout.EAST);
666 * @return true if any progress bars are still active
669 public boolean operationInProgress()
671 return progressBar.operationInProgress();
675 protected void resetButton_actionPerformed()
678 setTop(0); // ugly - prevents dimensionChanged events from being processed
679 xCombobox.setSelectedIndex(0);
680 yCombobox.setSelectedIndex(1);
682 zCombobox.setSelectedIndex(2);
686 * Answers true if PCA calculation is in progress, else false
690 public boolean isWorking()
696 * Answers the selected checkbox item index for PCA dimension for the X, Y or
697 * Z axis of the display
702 public int getSelectedDimensionIndex(Axis axis)
707 return xCombobox.getSelectedIndex();
709 return yCombobox.getSelectedIndex();
711 return zCombobox.getSelectedIndex();
715 public void setShowLabels(boolean show)
717 showLabels.setSelected(show);
721 * Sets the input data used to calculate the PCA. This is provided for
722 * 'restore from project', which does not currently support this (AL-2647), so
723 * sets the value to null, and hides the menu option for "Input Data...". J
727 public void setInputData(AlignmentView data)
729 getPcaModel().setInputData(data);
730 originalSeqData.setVisible(data != null);
733 public AlignViewportI getAlignViewport()
738 public PCAModel getPcaModel()
743 public void setPcaModel(PCAModel pcaModel)
745 this.pcaModel = pcaModel;
748 public RotatableCanvas getRotatableCanvas()
753 public void setRotatableCanvas(RotatableCanvas rc)
763 public void setTop(int top)
769 * set the associated view for this PCA.
773 public void selectAssociatedView(AlignmentPanel panel)
775 getRotatableCanvas().setApplyToAllViews(false);
780 getRotatableCanvas().av = panel.av;
781 getRotatableCanvas().ap = panel;
782 PaintRefresher.Register(PCAPanel.this, panel.av.getSequenceSetId());