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
102 public PaSiMapPanel(AlignmentPanel alignPanel, String modelName)
105 this.av = alignPanel.av;
106 this.ap = alignPanel;
107 boolean nucleotide = av.getAlignment().isNucleotide();
109 //progressBar = new ProgressBar(statusPanel, statusBar);
111 addInternalFrameListener(new InternalFrameAdapter()
114 public void internalFrameClosed(InternalFrameEvent e)
116 close_actionPerformed();
120 boolean selected = av.getSelectionGroup() != null
121 && av.getSelectionGroup().getSize() > 0;
125 seqs = av.getAlignment().getSequencesArray();
129 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
132 ScoreModelI scoreModel = ScoreModels.getInstance()
133 .getScoreModel(modelName, ap);
135 new PaSiMapModel(av, seqs, nucleotide, scoreModel));
136 PaintRefresher.Register(this, av.getSequenceSetId());
138 setRotatableCanvas(new RotatableCanvas(alignPanel));
139 this.getContentPane().add(getRotatableCanvas(), BorderLayout.CENTER);
141 addKeyListener(getRotatableCanvas());
146 * Ensure references to potentially very large objects (the PaSiMap matrices) are
147 * nulled when the frame is closed
149 protected void close_actionPerformed()
151 setPasimapModel(null);
154 this.rc.sequencePoints = null;
155 this.rc.setAxisEndPoints(null);
161 protected void bgcolour_actionPerformed()
163 String ttl = MessageManager.getString("label.select_background_colour");
164 ColourChooserListener listener = new ColourChooserListener()
167 public void colourSelected(Color c)
173 JalviewColourChooser.showColourChooser(this, ttl, rc.getBgColour(),
178 * Calculates the PaSiMap and displays the results
184 progId = System.currentTimeMillis();
186 String message = MessageManager
187 .getString("label.pasimap_recalculating");
188 if (getParent() == null)
190 progressBar = ap.alignFrame;
191 message = MessageManager.getString("label.pasimap_calculating");
193 progressBar.setProgressBar(message, progId);
196 SequenceGroup selGroup=av.getSelectionGroup();
200 selGroup = new SequenceGroup(av.getAlignment().getSequences());
201 selGroup.setStartRes(0);
202 selGroup.setEndRes(av.getAlignment().getWidth()-1);
205 if (selGroup.getSize()>MAX_PASIMAP_SEQ)
207 int start = selGroup.getStartRes(),end=selGroup.getEndRes();
208 selGroup = new SequenceGroup(selGroup.getSequences().subList(0, MAX_PASIMAP_SEQ));
209 selGroup.setStartRes(start);
210 selGroup.setEndRes(end);
211 Console.warn("Truncated input sequences for PASIMAP analysis to "+MAX_PASIMAP_SEQ);
214 PairwiseAlignPanel pap = new PairwiseAlignPanel(av, selGroup, true,
215 GAP_OPEN_COST, GAP_EXTEND_COST, false, null);
216 pap.setDiscardAlignments(true);
219 System.out.println(pap != null);
220 setPairwiseAlignPanel(pap);
221 getPasimapModel().calculate(pap);
223 xCombobox.setSelectedIndex(0);
224 yCombobox.setSelectedIndex(1);
225 zCombobox.setSelectedIndex(2);
227 getPasimapModel().updateRc(getRotatableCanvas());
229 setTop(getPasimapModel().getTop());
231 } catch (OutOfMemoryError er)
233 new OOMWarning("calculating PaSiMap", er);
238 progressBar.setProgressBar("", progId);
242 if (getParent() == null)
244 Desktop.addInternalFrame(
245 this, MessageManager.formatMessage("label.calc_title",
246 "PaSiMap", ap.alignFrame.getTitle()),
248 this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
254 * Updates the PaSiMap display after a change of component to use for x, y or z
258 protected void doDimensionChange()
265 int dim1 = getTop() - xCombobox.getSelectedIndex();
266 int dim2 = getTop() - yCombobox.getSelectedIndex();
267 int dim3 = getTop() - zCombobox.getSelectedIndex();
268 getPasimapModel().updateRcView(dim1, dim2, dim3);
269 getRotatableCanvas().resetView();
273 * Sets the selected checkbox item index for PaSiMap dimension (1, 2, 3...) for
274 * the given axis (X/Y/Z)
279 public void setSelectedDimensionIndex(int index, Axis axis)
284 xCombobox.setSelectedIndex(index);
287 yCombobox.setSelectedIndex(index);
290 zCombobox.setSelectedIndex(index);
297 protected void outputValues_actionPerformed()
299 CutAndPasteTransfer cap = new CutAndPasteTransfer();
302 cap.setText(getPasimapModel().getDetails());
303 Desktop.addInternalFrame(cap,
304 MessageManager.getString("label.pasimap_details"), 500, 500);
305 } catch (OutOfMemoryError oom)
307 new OOMWarning("opening PaSiMap details", oom);
313 protected void showLabels_actionPerformed()
315 getRotatableCanvas().showLabels(showLabels.getState());
319 protected void print_actionPerformed()
321 PaSiMapPrinter printer = new PaSiMapPrinter();
326 * If available, shows the data which formed the inputs for the PaSiMap as a new
330 public void originalSeqData_actionPerformed()
332 // JAL-2647 disabled after load from project (until save to project done)
333 if (getPasimapModel().getInputData() == null)
336 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
339 // decide if av alignment is sufficiently different to original data to
340 // warrant a new window to be created
341 // create new alignment window with hidden regions (unhiding hidden regions
342 // yields unaligned seqs)
343 // or create a selection box around columns in alignment view
344 // test Alignment(SeqCigar[])
348 // we try to get the associated view's gap character
349 // but this may fail if the view was closed...
350 gc = av.getGapCharacter();
351 } catch (Exception ex)
355 Object[] alAndColsel = getPasimapModel().getInputData()
356 .getAlignmentView(false).getAlignmentAndHiddenColumns(gc);
358 if (alAndColsel != null && alAndColsel[0] != null)
360 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
362 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
363 AlignmentI dataset = (av != null && av.getAlignment() != null)
364 ? av.getAlignment().getDataset()
368 al.setDataset(dataset);
374 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
375 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
377 // >>>This is a fix for the moment, until a better solution is
379 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
381 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
384 Desktop.addInternalFrame(af, MessageManager.formatMessage(
385 "label.original_data_for_params", new String[]
386 { this.title }), AlignFrame.DEFAULT_WIDTH,
387 AlignFrame.DEFAULT_HEIGHT);
391 * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
392 * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
393 * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
396 * Desktop.addInternalFrame(cap, "Original Data", 400, 400);
400 class PaSiMapPrinter extends Thread implements Printable
405 PrinterJob printJob = PrinterJob.getPrinterJob();
406 PageFormat defaultPage = printJob.defaultPage();
407 PageFormat pf = printJob.pageDialog(defaultPage);
409 if (defaultPage == pf)
417 printJob.setPrintable(this, pf);
419 if (printJob.printDialog())
424 } catch (Exception PrintException)
426 PrintException.printStackTrace();
432 public int print(Graphics pg, PageFormat pf, int pi)
433 throws PrinterException
435 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
437 getRotatableCanvas().drawBackground(pg);
438 getRotatableCanvas().drawScene(pg);
439 if (getRotatableCanvas().drawAxes)
441 getRotatableCanvas().drawAxes(pg);
446 return Printable.PAGE_EXISTS;
450 return Printable.NO_SUCH_PAGE;
455 public void makePaSiMapImage(ImageMaker.TYPE type) throws Exception
457 int width = getRotatableCanvas().getWidth();
458 int height = getRotatableCanvas().getHeight();
459 ImageWriterI writer = new ImageWriterI()
462 public void exportImage(Graphics g) throws Exception
464 RotatableCanvas canvas = getRotatableCanvas();
465 canvas.drawBackground(g);
473 String pasimap = MessageManager.getString("label.pasimap");
474 ImageExporter exporter = new ImageExporter(writer, null, type, pasimap);
475 exporter.doExport(null, this, width, height, pasimap);
479 protected void viewMenu_menuSelected()
481 buildAssociatedViewMenu();
485 * Builds the menu showing the choice of possible views (for the associated
486 * sequence data) to which the PaSiMap may be linked
488 void buildAssociatedViewMenu()
490 AlignmentPanel[] aps = PaintRefresher
491 .getAssociatedPanels(av.getSequenceSetId());
492 if (aps.length == 1 && getRotatableCanvas().av == aps[0].av)
494 associateViewsMenu.setVisible(false);
498 associateViewsMenu.setVisible(true);
501 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
503 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
506 associateViewsMenu.removeAll();
508 JRadioButtonMenuItem item;
509 ButtonGroup buttonGroup = new ButtonGroup();
510 int iSize = aps.length;
512 for (int i = 0; i < iSize; i++)
514 final AlignmentPanel panel = aps[i];
515 item = new JRadioButtonMenuItem(panel.av.getViewName(),
516 panel.av == getRotatableCanvas().av);
517 buttonGroup.add(item);
518 item.addActionListener(new ActionListener()
521 public void actionPerformed(ActionEvent evt)
523 selectAssociatedView(panel);
527 associateViewsMenu.add(item);
530 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
533 buttonGroup.add(itemf);
535 itemf.setSelected(getRotatableCanvas().isApplyToAllViews());
536 itemf.addActionListener(new ActionListener()
539 public void actionPerformed(ActionEvent evt)
541 getRotatableCanvas().setApplyToAllViews(itemf.isSelected());
544 associateViewsMenu.add(itemf);
552 * jalview.jbgui.GPaSiMapPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
556 protected void outputPoints_actionPerformed()
558 CutAndPasteTransfer cap = new CutAndPasteTransfer();
561 cap.setText(getPasimapModel().getPointsasCsv(false,
562 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
563 zCombobox.getSelectedIndex()));
564 Desktop.addInternalFrame(cap, MessageManager
565 .formatMessage("label.points_for_params", new String[]
566 { this.getTitle() }), 500, 500);
567 } catch (OutOfMemoryError oom)
569 new OOMWarning("exporting PaSiMap points", oom);
578 * jalview.jbgui.GPaSiMapPanel#outputProjPoints_actionPerformed(java.awt.event
582 protected void outputProjPoints_actionPerformed()
584 CutAndPasteTransfer cap = new CutAndPasteTransfer();
587 cap.setText(getPasimapModel().getPointsasCsv(true,
588 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
589 zCombobox.getSelectedIndex()));
590 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
591 "label.transformed_points_for_params", new String[]
592 { this.getTitle() }), 500, 500);
593 } catch (OutOfMemoryError oom)
595 new OOMWarning("exporting transformed PaSiMap points", oom);
604 * jalview.jbgui.GPaSiMapPanel#outputAlignment_actionPerformed(java.awt.event
608 protected void outputAlignment_actionPerformed()
610 CutAndPasteTransfer cap = new CutAndPasteTransfer();
613 cap.setText(getPasimapModel().getAlignmentOutput());
614 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
615 "label.pairwise_alignment_for_params", new String[] { this.getTitle() }), 500, 500);
616 } catch (OutOfMemoryError oom)
618 new OOMWarning("exporting pairwise alignments", oom);
626 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
629 public void setProgressBar(String message, long id)
631 progressBar.setProgressBar(message, id);
632 // if (progressBars == null)
634 // progressBars = new Hashtable();
635 // progressBarHandlers = new Hashtable();
638 // JPanel progressPanel;
639 // Long lId = Long.valueOf(id);
640 // GridLayout layout = (GridLayout) statusPanel.getLayout();
641 // if (progressBars.get(lId) != null)
643 // progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
644 // statusPanel.remove(progressPanel);
645 // progressBars.remove(lId);
646 // progressPanel = null;
647 // if (message != null)
649 // statusBar.setText(message);
651 // if (progressBarHandlers.contains(lId))
653 // progressBarHandlers.remove(lId);
655 // layout.setRows(layout.getRows() - 1);
659 // progressPanel = new JPanel(new BorderLayout(10, 5));
661 // JProgressBar progressBar = new JProgressBar();
662 // progressBar.setIndeterminate(true);
664 // progressPanel.add(new JLabel(message), BorderLayout.WEST);
665 // progressPanel.add(progressBar, BorderLayout.CENTER);
667 // layout.setRows(layout.getRows() + 1);
668 // statusPanel.add(progressPanel);
670 // progressBars.put(lId, progressPanel);
673 // // setMenusForViewport();
678 * make the progressBar determinate and update its progress
680 public void updateProgressBar(int lengthOfTask, int progress)
682 JProgressBar pBar = progressBar.getProgressBar(progId);
687 if (pBar.isIndeterminate())
689 pBar.setMaximum(lengthOfTask);
691 pBar.setIndeterminate(false);
693 updateProgressBar(progress);
695 public void updateProgressBar(int progress)
697 JProgressBar pBar = progressBar.getProgressBar(progId);
704 pBar.setValue(progress);
709 * adds a listener for a pairwise alignment panel's progress
710 * TODO: generalise for anything that can report progress ?
713 public void setPairwiseAlignPanel(PairwiseAlignPanel pap)
715 pap.addPropertyChangeListener(new PropertyChangeListener()
718 public void propertyChange(PropertyChangeEvent pcEvent)
720 if (PairwiseAlignPanel.PROGRESS.equals(pcEvent.getPropertyName()))
722 updateProgressBar((int) pcEvent.getNewValue());
724 else if (PairwiseAlignPanel.TOTAL.equals(pcEvent.getPropertyName()))
726 updateProgressBar((int) pcEvent.getNewValue(), 0);
733 public void registerHandler(final long id,
734 final IProgressIndicatorHandler handler)
736 progressBar.registerHandler(id, handler);
737 // if (progressBarHandlers == null ||
738 // !progressBars.contains(Long.valueOf(id)))
741 // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
743 // progressBarHandlers.put(Long.valueOf(id), handler);
744 // final JPanel progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
745 // if (handler.canCancel())
747 // JButton cancel = new JButton(
748 // MessageManager.getString("action.cancel"));
749 // final IProgressIndicator us = this;
750 // cancel.addActionListener(new ActionListener()
754 // public void actionPerformed(ActionEvent e)
756 // handler.cancelActivity(id);
757 // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
758 // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
761 // progressPanel.add(cancel, BorderLayout.EAST);
767 * @return true if any progress bars are still active
770 public boolean operationInProgress()
772 return progressBar.operationInProgress();
776 protected void resetButton_actionPerformed()
779 setTop(0); // ugly - prevents dimensionChanged events from being processed
780 xCombobox.setSelectedIndex(0);
781 yCombobox.setSelectedIndex(1);
783 zCombobox.setSelectedIndex(2);
787 * Answers true if PaSiMap calculation is in progress, else false
791 public boolean isWorking()
797 * Answers the selected checkbox item index for PaSiMap dimension for the X, Y or
798 * Z axis of the display
803 public int getSelectedDimensionIndex(Axis axis)
808 return xCombobox.getSelectedIndex();
810 return yCombobox.getSelectedIndex();
812 return zCombobox.getSelectedIndex();
816 public void setShowLabels(boolean show)
818 showLabels.setSelected(show);
822 * Sets the input data used to calculate the PaSiMap. This is provided for
823 * 'restore from project', which does not currently support this (AL-2647), so
824 * sets the value to null, and hides the menu option for "Input Data...". J
828 public void setInputData(AlignmentViewport data)
830 getPasimapModel().setInputData(data);
831 originalSeqData.setVisible(data != null);
834 public AlignViewportI getAlignViewport()
839 public PaSiMapModel getPasimapModel()
844 public void setPasimapModel(PaSiMapModel pasimapModel)
846 this.pasimapModel = pasimapModel;
849 public RotatableCanvas getRotatableCanvas()
854 public void setRotatableCanvas(RotatableCanvas rc)
864 public void setTop(int top)
870 * set the associated view for this PaSiMap.
874 public void selectAssociatedView(AlignmentPanel panel)
876 getRotatableCanvas().setApplyToAllViews(false);
881 getRotatableCanvas().av = panel.av;
882 getRotatableCanvas().ap = panel;
883 PaintRefresher.Register(PaSiMapPanel.this, panel.av.getSequenceSetId());
887 public JProgressBar getProgressBar(long id)
889 return progressBar.getProgressBar(id);