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.Console;
28 import jalview.datamodel.Alignment;
29 import jalview.datamodel.AlignmentI;
30 import jalview.datamodel.AlignmentView;
31 import jalview.datamodel.HiddenColumns;
32 import jalview.datamodel.SequenceGroup;
33 import jalview.datamodel.SequenceI;
34 import jalview.gui.ImageExporter.ImageWriterI;
35 import jalview.gui.JalviewColourChooser.ColourChooserListener;
36 import jalview.jbgui.GPaSiMapPanel;
37 import jalview.math.RotatableMatrix.Axis;
38 import jalview.util.ImageMaker;
39 import jalview.util.MessageManager;
40 import jalview.viewmodel.AlignmentViewport;
41 import jalview.viewmodel.PaSiMapModel;
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;
53 import java.beans.PropertyChangeEvent;
54 import java.beans.PropertyChangeListener;
56 import javax.swing.ButtonGroup;
57 import javax.swing.JMenuItem;
58 import javax.swing.JProgressBar;
59 import javax.swing.JRadioButtonMenuItem;
60 import javax.swing.event.InternalFrameAdapter;
61 import javax.swing.event.InternalFrameEvent;
64 * The panel holding the Pairwise Similarity Map 3-D visualisation
66 public class PaSiMapPanel extends GPaSiMapPanel
67 implements Runnable, IProgressIndicator
69 private static final int MIN_WIDTH = 470;
71 private static final int MIN_HEIGHT = 250;
73 private static final int MAX_PASIMAP_SEQ = 20000;
75 private final int GAP_OPEN_COST = 100;
77 private final int GAP_EXTEND_COST = 5;
79 private RotatableCanvas rc;
85 private PaSiMapModel pasimapModel;
89 private IProgressIndicator progressBar;
93 private boolean working;
96 * Constructor given sequence data, a similarity (or distance) score model
97 * name, and score calculation parameters
103 public PaSiMapPanel(AlignmentPanel alignPanel, String modelName,
104 SimilarityParamsI params)
107 this.av = alignPanel.av;
108 this.ap = alignPanel;
109 boolean nucleotide = av.getAlignment().isNucleotide();
111 //progressBar = new ProgressBar(statusPanel, statusBar);
113 addInternalFrameListener(new InternalFrameAdapter()
116 public void internalFrameClosed(InternalFrameEvent e)
118 close_actionPerformed();
122 boolean selected = av.getSelectionGroup() != null
123 && av.getSelectionGroup().getSize() > 0;
127 seqs = av.getAlignment().getSequencesArray();
131 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
134 ScoreModelI scoreModel = ScoreModels.getInstance()
135 .getScoreModel(modelName, ap);
137 new PaSiMapModel(av, seqs, nucleotide, scoreModel));
138 PaintRefresher.Register(this, av.getSequenceSetId());
140 setRotatableCanvas(new RotatableCanvas(alignPanel));
141 this.getContentPane().add(getRotatableCanvas(), BorderLayout.CENTER);
143 addKeyListener(getRotatableCanvas());
148 * Ensure references to potentially very large objects (the PaSiMap matrices) are
149 * nulled when the frame is closed
151 protected void close_actionPerformed()
153 setPasimapModel(null);
156 this.rc.sequencePoints = null;
157 this.rc.setAxisEndPoints(null);
163 protected void bgcolour_actionPerformed()
165 String ttl = MessageManager.getString("label.select_background_colour");
166 ColourChooserListener listener = new ColourChooserListener()
169 public void colourSelected(Color c)
175 JalviewColourChooser.showColourChooser(this, ttl, rc.getBgColour(),
180 * Calculates the PaSiMap and displays the results
186 progId = System.currentTimeMillis();
188 String message = MessageManager
189 .getString("label.pasimap_recalculating");
190 if (getParent() == null)
192 progressBar = ap.alignFrame;
193 message = MessageManager.getString("label.pasimap_calculating");
195 progressBar.setProgressBar(message, progId);
198 SequenceGroup selGroup=av.getSelectionGroup();
202 selGroup = new SequenceGroup(av.getAlignment().getSequences());
203 selGroup.setStartRes(0);
204 selGroup.setEndRes(av.getAlignment().getWidth()-1);
207 if (selGroup.getSize()>MAX_PASIMAP_SEQ)
209 int start = selGroup.getStartRes(),end=selGroup.getEndRes();
210 selGroup = new SequenceGroup(selGroup.getSequences().subList(0, MAX_PASIMAP_SEQ));
211 selGroup.setStartRes(start);
212 selGroup.setEndRes(end);
213 Console.warn("Truncated input sequences for PASIMAP analysis to "+MAX_PASIMAP_SEQ);
216 PairwiseAlignPanel pap = new PairwiseAlignPanel(av, selGroup, true,
217 GAP_OPEN_COST, GAP_EXTEND_COST, false);
218 System.out.println(pap != null);
219 setPairwiseAlignPanel(pap);
220 getPasimapModel().calculate(pap);
222 xCombobox.setSelectedIndex(0);
223 yCombobox.setSelectedIndex(1);
224 zCombobox.setSelectedIndex(2);
226 getPasimapModel().updateRc(getRotatableCanvas());
228 setTop(getPasimapModel().getTop());
230 } catch (OutOfMemoryError er)
232 new OOMWarning("calculating PaSiMap", er);
237 progressBar.setProgressBar("", progId);
241 if (getParent() == null)
243 Desktop.addInternalFrame(
244 this, MessageManager.formatMessage("label.calc_title",
245 "PaSiMap", ap.alignFrame.getTitle()),
247 this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
253 * Updates the PaSiMap display after a change of component to use for x, y or z
257 protected void doDimensionChange()
264 int dim1 = getTop() - xCombobox.getSelectedIndex();
265 int dim2 = getTop() - yCombobox.getSelectedIndex();
266 int dim3 = getTop() - zCombobox.getSelectedIndex();
267 getPasimapModel().updateRcView(dim1, dim2, dim3);
268 getRotatableCanvas().resetView();
272 * Sets the selected checkbox item index for PaSiMap dimension (1, 2, 3...) for
273 * the given axis (X/Y/Z)
278 public void setSelectedDimensionIndex(int index, Axis axis)
283 xCombobox.setSelectedIndex(index);
286 yCombobox.setSelectedIndex(index);
289 zCombobox.setSelectedIndex(index);
296 protected void outputValues_actionPerformed()
298 CutAndPasteTransfer cap = new CutAndPasteTransfer();
301 cap.setText(getPasimapModel().getDetails());
302 Desktop.addInternalFrame(cap,
303 MessageManager.getString("label.pasimap_details"), 500, 500);
304 } catch (OutOfMemoryError oom)
306 new OOMWarning("opening PaSiMap details", oom);
312 protected void showLabels_actionPerformed()
314 getRotatableCanvas().showLabels(showLabels.getState());
318 protected void print_actionPerformed()
320 PaSiMapPrinter printer = new PaSiMapPrinter();
325 * If available, shows the data which formed the inputs for the PaSiMap as a new
329 public void originalSeqData_actionPerformed()
331 // JAL-2647 disabled after load from project (until save to project done)
332 if (getPasimapModel().getInputData() == null)
335 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
338 // decide if av alignment is sufficiently different to original data to
339 // warrant a new window to be created
340 // create new alignment window with hidden regions (unhiding hidden regions
341 // yields unaligned seqs)
342 // or create a selection box around columns in alignment view
343 // test Alignment(SeqCigar[])
347 // we try to get the associated view's gap character
348 // but this may fail if the view was closed...
349 gc = av.getGapCharacter();
350 } catch (Exception ex)
354 Object[] alAndColsel = getPasimapModel().getInputData()
355 .getAlignmentView(false).getAlignmentAndHiddenColumns(gc);
357 if (alAndColsel != null && alAndColsel[0] != null)
359 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
361 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
362 AlignmentI dataset = (av != null && av.getAlignment() != null)
363 ? av.getAlignment().getDataset()
367 al.setDataset(dataset);
373 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
374 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
376 // >>>This is a fix for the moment, until a better solution is
378 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
380 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
383 Desktop.addInternalFrame(af, MessageManager.formatMessage(
384 "label.original_data_for_params", new String[]
385 { this.title }), AlignFrame.DEFAULT_WIDTH,
386 AlignFrame.DEFAULT_HEIGHT);
390 * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
391 * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
392 * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
395 * Desktop.addInternalFrame(cap, "Original Data", 400, 400);
399 class PaSiMapPrinter extends Thread implements Printable
404 PrinterJob printJob = PrinterJob.getPrinterJob();
405 PageFormat defaultPage = printJob.defaultPage();
406 PageFormat pf = printJob.pageDialog(defaultPage);
408 if (defaultPage == pf)
416 printJob.setPrintable(this, pf);
418 if (printJob.printDialog())
423 } catch (Exception PrintException)
425 PrintException.printStackTrace();
431 public int print(Graphics pg, PageFormat pf, int pi)
432 throws PrinterException
434 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
436 getRotatableCanvas().drawBackground(pg);
437 getRotatableCanvas().drawScene(pg);
438 if (getRotatableCanvas().drawAxes)
440 getRotatableCanvas().drawAxes(pg);
445 return Printable.PAGE_EXISTS;
449 return Printable.NO_SUCH_PAGE;
454 public void makePaSiMapImage(ImageMaker.TYPE type) throws Exception
456 int width = getRotatableCanvas().getWidth();
457 int height = getRotatableCanvas().getHeight();
458 ImageWriterI writer = new ImageWriterI()
461 public void exportImage(Graphics g) throws Exception
463 RotatableCanvas canvas = getRotatableCanvas();
464 canvas.drawBackground(g);
472 String pasimap = MessageManager.getString("label.pasimap");
473 ImageExporter exporter = new ImageExporter(writer, null, type, pasimap);
474 exporter.doExport(null, this, width, height, pasimap);
478 protected void viewMenu_menuSelected()
480 buildAssociatedViewMenu();
484 * Builds the menu showing the choice of possible views (for the associated
485 * sequence data) to which the PaSiMap may be linked
487 void buildAssociatedViewMenu()
489 AlignmentPanel[] aps = PaintRefresher
490 .getAssociatedPanels(av.getSequenceSetId());
491 if (aps.length == 1 && getRotatableCanvas().av == aps[0].av)
493 associateViewsMenu.setVisible(false);
497 associateViewsMenu.setVisible(true);
500 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
502 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
505 associateViewsMenu.removeAll();
507 JRadioButtonMenuItem item;
508 ButtonGroup buttonGroup = new ButtonGroup();
509 int iSize = aps.length;
511 for (int i = 0; i < iSize; i++)
513 final AlignmentPanel panel = aps[i];
514 item = new JRadioButtonMenuItem(panel.av.getViewName(),
515 panel.av == getRotatableCanvas().av);
516 buttonGroup.add(item);
517 item.addActionListener(new ActionListener()
520 public void actionPerformed(ActionEvent evt)
522 selectAssociatedView(panel);
526 associateViewsMenu.add(item);
529 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
532 buttonGroup.add(itemf);
534 itemf.setSelected(getRotatableCanvas().isApplyToAllViews());
535 itemf.addActionListener(new ActionListener()
538 public void actionPerformed(ActionEvent evt)
540 getRotatableCanvas().setApplyToAllViews(itemf.isSelected());
543 associateViewsMenu.add(itemf);
551 * jalview.jbgui.GPaSiMapPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
555 protected void outputPoints_actionPerformed()
557 CutAndPasteTransfer cap = new CutAndPasteTransfer();
560 cap.setText(getPasimapModel().getPointsasCsv(false,
561 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
562 zCombobox.getSelectedIndex()));
563 Desktop.addInternalFrame(cap, MessageManager
564 .formatMessage("label.points_for_params", new String[]
565 { this.getTitle() }), 500, 500);
566 } catch (OutOfMemoryError oom)
568 new OOMWarning("exporting PaSiMap points", oom);
577 * jalview.jbgui.GPaSiMapPanel#outputProjPoints_actionPerformed(java.awt.event
581 protected void outputProjPoints_actionPerformed()
583 CutAndPasteTransfer cap = new CutAndPasteTransfer();
586 cap.setText(getPasimapModel().getPointsasCsv(true,
587 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
588 zCombobox.getSelectedIndex()));
589 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
590 "label.transformed_points_for_params", new String[]
591 { this.getTitle() }), 500, 500);
592 } catch (OutOfMemoryError oom)
594 new OOMWarning("exporting transformed PaSiMap points", oom);
603 * jalview.jbgui.GPaSiMapPanel#outputAlignment_actionPerformed(java.awt.event
607 protected void outputAlignment_actionPerformed()
609 CutAndPasteTransfer cap = new CutAndPasteTransfer();
612 cap.setText(getPasimapModel().getAlignmentOutput());
613 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
614 "label.pairwise_alignment_for_params", new String[] { this.getTitle() }), 500, 500);
615 } catch (OutOfMemoryError oom)
617 new OOMWarning("exporting pairwise alignments", oom);
625 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
628 public void setProgressBar(String message, long id)
630 progressBar.setProgressBar(message, id);
631 // if (progressBars == null)
633 // progressBars = new Hashtable();
634 // progressBarHandlers = new Hashtable();
637 // JPanel progressPanel;
638 // Long lId = Long.valueOf(id);
639 // GridLayout layout = (GridLayout) statusPanel.getLayout();
640 // if (progressBars.get(lId) != null)
642 // progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
643 // statusPanel.remove(progressPanel);
644 // progressBars.remove(lId);
645 // progressPanel = null;
646 // if (message != null)
648 // statusBar.setText(message);
650 // if (progressBarHandlers.contains(lId))
652 // progressBarHandlers.remove(lId);
654 // layout.setRows(layout.getRows() - 1);
658 // progressPanel = new JPanel(new BorderLayout(10, 5));
660 // JProgressBar progressBar = new JProgressBar();
661 // progressBar.setIndeterminate(true);
663 // progressPanel.add(new JLabel(message), BorderLayout.WEST);
664 // progressPanel.add(progressBar, BorderLayout.CENTER);
666 // layout.setRows(layout.getRows() + 1);
667 // statusPanel.add(progressPanel);
669 // progressBars.put(lId, progressPanel);
672 // // setMenusForViewport();
677 * make the progressBar determinate and update its progress
679 public void updateProgressBar(int lengthOfTask, int progress)
681 JProgressBar pBar = progressBar.getProgressBar(progId);
686 if (pBar.isIndeterminate())
688 pBar.setMaximum(lengthOfTask);
690 pBar.setIndeterminate(false);
692 updateProgressBar(progress);
694 public void updateProgressBar(int progress)
696 JProgressBar pBar = progressBar.getProgressBar(progId);
703 pBar.setValue(progress);
708 public void setPairwiseAlignPanel(PairwiseAlignPanel pap)
710 pap.addPropertyChangeListener(new PropertyChangeListener()
713 public void propertyChange(PropertyChangeEvent pcEvent)
715 if (PairwiseAlignPanel.PROGRESS.equals(pcEvent.getPropertyName()))
717 updateProgressBar((int) pcEvent.getNewValue());
718 } else if (PairwiseAlignPanel.TOTAL.equals(pcEvent.getPropertyName())) {
719 updateProgressBar((int) pcEvent.getNewValue(), 0);
726 public void registerHandler(final long id,
727 final IProgressIndicatorHandler handler)
729 progressBar.registerHandler(id, handler);
730 // if (progressBarHandlers == null ||
731 // !progressBars.contains(Long.valueOf(id)))
734 // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
736 // progressBarHandlers.put(Long.valueOf(id), handler);
737 // final JPanel progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
738 // if (handler.canCancel())
740 // JButton cancel = new JButton(
741 // MessageManager.getString("action.cancel"));
742 // final IProgressIndicator us = this;
743 // cancel.addActionListener(new ActionListener()
747 // public void actionPerformed(ActionEvent e)
749 // handler.cancelActivity(id);
750 // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
751 // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
754 // progressPanel.add(cancel, BorderLayout.EAST);
760 * @return true if any progress bars are still active
763 public boolean operationInProgress()
765 return progressBar.operationInProgress();
769 protected void resetButton_actionPerformed()
772 setTop(0); // ugly - prevents dimensionChanged events from being processed
773 xCombobox.setSelectedIndex(0);
774 yCombobox.setSelectedIndex(1);
776 zCombobox.setSelectedIndex(2);
780 * Answers true if PaSiMap calculation is in progress, else false
784 public boolean isWorking()
790 * Answers the selected checkbox item index for PaSiMap dimension for the X, Y or
791 * Z axis of the display
796 public int getSelectedDimensionIndex(Axis axis)
801 return xCombobox.getSelectedIndex();
803 return yCombobox.getSelectedIndex();
805 return zCombobox.getSelectedIndex();
809 public void setShowLabels(boolean show)
811 showLabels.setSelected(show);
815 * Sets the input data used to calculate the PaSiMap. This is provided for
816 * 'restore from project', which does not currently support this (AL-2647), so
817 * sets the value to null, and hides the menu option for "Input Data...". J
821 public void setInputData(AlignmentViewport data)
823 getPasimapModel().setInputData(data);
824 originalSeqData.setVisible(data != null);
827 public AlignViewportI getAlignViewport()
832 public PaSiMapModel getPasimapModel()
837 public void setPasimapModel(PaSiMapModel pasimapModel)
839 this.pasimapModel = pasimapModel;
842 public RotatableCanvas getRotatableCanvas()
847 public void setRotatableCanvas(RotatableCanvas rc)
857 public void setTop(int top)
863 * set the associated view for this PaSiMap.
867 public void selectAssociatedView(AlignmentPanel panel)
869 getRotatableCanvas().setApplyToAllViews(false);
874 getRotatableCanvas().av = panel.av;
875 getRotatableCanvas().ap = panel;
876 PaintRefresher.Register(PaSiMapPanel.this, panel.av.getSequenceSetId());
880 public JProgressBar getProgressBar(long id)
882 return progressBar.getProgressBar(id);