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.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.PaSiMapModel;
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 Pairwise Similarity Map 3-D visualisation
62 public class PaSiMapPanel extends GPCAPanel
63 implements Runnable, IProgressIndicator
65 private static final int MIN_WIDTH = 470;
67 private static final int MIN_HEIGHT = 250;
69 private RotatableCanvas rc;
75 private PaSiMapModel pasimapModel;
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 PaSiMapPanel(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;
115 seqs = av.getAlignment().getSequencesArray();
119 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
122 ScoreModelI scoreModel = ScoreModels.getInstance()
123 .getScoreModel(modelName, ap);
125 new PaSiMapModel(av, seqs, nucleotide, scoreModel, params));
126 PaintRefresher.Register(this, av.getSequenceSetId());
128 setRotatableCanvas(new RotatableCanvas(alignPanel));
129 this.getContentPane().add(getRotatableCanvas(), BorderLayout.CENTER);
131 addKeyListener(getRotatableCanvas());
136 * Ensure references to potentially very large objects (the PaSiMap matrices) are
137 * nulled when the frame is closed
139 protected void close_actionPerformed()
141 setPasimapModel(null);
144 this.rc.sequencePoints = null;
145 this.rc.setAxisEndPoints(null);
151 protected void bgcolour_actionPerformed()
153 String ttl = MessageManager.getString("label.select_background_colour");
154 ColourChooserListener listener = new ColourChooserListener()
157 public void colourSelected(Color c)
163 JalviewColourChooser.showColourChooser(this, ttl, rc.getBgColour(),
168 * Calculates the PaSiMap and displays the results
174 long progId = System.currentTimeMillis();
175 IProgressIndicator progress = this;
176 String message = MessageManager.getString("label.pasimap_recalculating");
177 if (getParent() == null)
179 progress = ap.alignFrame;
180 message = MessageManager.getString("label.pasimap_calculating");
182 progress.setProgressBar(message, progId);
185 getPasimapModel().calculate();
187 xCombobox.setSelectedIndex(0);
188 yCombobox.setSelectedIndex(1);
189 zCombobox.setSelectedIndex(2);
191 getPasimapModel().updateRc(getRotatableCanvas());
193 setTop(getPasimapModel().getTop());
195 } catch (OutOfMemoryError er)
197 new OOMWarning("calculating PaSiMap", er);
202 progress.setProgressBar("", progId);
206 if (getParent() == null)
208 Desktop.addInternalFrame(this,
209 MessageManager.formatMessage("label.calc_title", "PaSiMap",
210 getPasimapModel().getScoreModelName()),
212 this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
218 * Updates the PaSiMap display after a change of component to use for x, y or z
222 protected void doDimensionChange()
229 int dim1 = getTop() - xCombobox.getSelectedIndex();
230 int dim2 = getTop() - yCombobox.getSelectedIndex();
231 int dim3 = getTop() - zCombobox.getSelectedIndex();
232 getPasimapModel().updateRcView(dim1, dim2, dim3);
233 getRotatableCanvas().resetView();
237 * Sets the selected checkbox item index for PaSiMap dimension (1, 2, 3...) for
238 * the given axis (X/Y/Z)
243 public void setSelectedDimensionIndex(int index, Axis axis)
248 xCombobox.setSelectedIndex(index);
251 yCombobox.setSelectedIndex(index);
254 zCombobox.setSelectedIndex(index);
261 protected void outputValues_actionPerformed()
263 CutAndPasteTransfer cap = new CutAndPasteTransfer();
266 cap.setText(getPasimapModel().getDetails());
267 Desktop.addInternalFrame(cap,
268 MessageManager.getString("label.pasimap_details"), 500, 500);
269 } catch (OutOfMemoryError oom)
271 new OOMWarning("opening PaSiMap details", oom);
277 protected void showLabels_actionPerformed()
279 getRotatableCanvas().showLabels(showLabels.getState());
283 protected void print_actionPerformed()
285 PaSiMapPrinter printer = new PaSiMapPrinter();
290 * If available, shows the data which formed the inputs for the PaSiMap as a new
294 public void originalSeqData_actionPerformed()
296 // JAL-2647 disabled after load from project (until save to project done)
297 if (getPasimapModel().getInputData() == null)
300 "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
303 // decide if av alignment is sufficiently different to original data to
304 // warrant a new window to be created
305 // create new alignment window with hidden regions (unhiding hidden regions
306 // yields unaligned seqs)
307 // or create a selection box around columns in alignment view
308 // test Alignment(SeqCigar[])
312 // we try to get the associated view's gap character
313 // but this may fail if the view was closed...
314 gc = av.getGapCharacter();
315 } catch (Exception ex)
319 Object[] alAndColsel = getPasimapModel().getInputData()
320 .getAlignmentView(false).getAlignmentAndHiddenColumns(gc);
322 if (alAndColsel != null && alAndColsel[0] != null)
324 // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
326 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
327 AlignmentI dataset = (av != null && av.getAlignment() != null)
328 ? av.getAlignment().getDataset()
332 al.setDataset(dataset);
338 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
339 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
341 // >>>This is a fix for the moment, until a better solution is
343 // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
345 // af.addSortByOrderMenuItem(ServiceName + " Ordering",
348 Desktop.addInternalFrame(af, MessageManager.formatMessage(
349 "label.original_data_for_params", new String[]
350 { this.title }), AlignFrame.DEFAULT_WIDTH,
351 AlignFrame.DEFAULT_HEIGHT);
355 * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
356 * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
357 * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
360 * Desktop.addInternalFrame(cap, "Original Data", 400, 400);
364 class PaSiMapPrinter extends Thread implements Printable
369 PrinterJob printJob = PrinterJob.getPrinterJob();
370 PageFormat defaultPage = printJob.defaultPage();
371 PageFormat pf = printJob.pageDialog(defaultPage);
373 if (defaultPage == pf)
381 printJob.setPrintable(this, pf);
383 if (printJob.printDialog())
388 } catch (Exception PrintException)
390 PrintException.printStackTrace();
396 public int print(Graphics pg, PageFormat pf, int pi)
397 throws PrinterException
399 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
401 getRotatableCanvas().drawBackground(pg);
402 getRotatableCanvas().drawScene(pg);
403 if (getRotatableCanvas().drawAxes)
405 getRotatableCanvas().drawAxes(pg);
410 return Printable.PAGE_EXISTS;
414 return Printable.NO_SUCH_PAGE;
419 public void makePaSiMapImage(ImageMaker.TYPE type) throws Exception
421 int width = getRotatableCanvas().getWidth();
422 int height = getRotatableCanvas().getHeight();
423 ImageWriterI writer = new ImageWriterI()
426 public void exportImage(Graphics g) throws Exception
428 RotatableCanvas canvas = getRotatableCanvas();
429 canvas.drawBackground(g);
437 String pasimap = MessageManager.getString("label.pasimap");
438 ImageExporter exporter = new ImageExporter(writer, null, type, pasimap);
439 exporter.doExport(null, this, width, height, pasimap);
443 protected void viewMenu_menuSelected()
445 buildAssociatedViewMenu();
449 * Builds the menu showing the choice of possible views (for the associated
450 * sequence data) to which the PaSiMap may be linked
452 void buildAssociatedViewMenu()
454 AlignmentPanel[] aps = PaintRefresher
455 .getAssociatedPanels(av.getSequenceSetId());
456 if (aps.length == 1 && getRotatableCanvas().av == aps[0].av)
458 associateViewsMenu.setVisible(false);
462 associateViewsMenu.setVisible(true);
465 .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
467 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
470 associateViewsMenu.removeAll();
472 JRadioButtonMenuItem item;
473 ButtonGroup buttonGroup = new ButtonGroup();
474 int iSize = aps.length;
476 for (int i = 0; i < iSize; i++)
478 final AlignmentPanel panel = aps[i];
479 item = new JRadioButtonMenuItem(panel.av.getViewName(),
480 panel.av == getRotatableCanvas().av);
481 buttonGroup.add(item);
482 item.addActionListener(new ActionListener()
485 public void actionPerformed(ActionEvent evt)
487 selectAssociatedView(panel);
491 associateViewsMenu.add(item);
494 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
497 buttonGroup.add(itemf);
499 itemf.setSelected(getRotatableCanvas().isApplyToAllViews());
500 itemf.addActionListener(new ActionListener()
503 public void actionPerformed(ActionEvent evt)
505 getRotatableCanvas().setApplyToAllViews(itemf.isSelected());
508 associateViewsMenu.add(itemf);
516 * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
520 protected void outputPoints_actionPerformed()
522 CutAndPasteTransfer cap = new CutAndPasteTransfer();
525 cap.setText(getPasimapModel().getPointsasCsv(false,
526 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
527 zCombobox.getSelectedIndex()));
528 Desktop.addInternalFrame(cap, MessageManager
529 .formatMessage("label.points_for_params", new String[]
530 { this.getTitle() }), 500, 500);
531 } catch (OutOfMemoryError oom)
533 new OOMWarning("exporting PaSiMap points", oom);
542 * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
546 protected void outputProjPoints_actionPerformed()
548 CutAndPasteTransfer cap = new CutAndPasteTransfer();
551 cap.setText(getPasimapModel().getPointsasCsv(true,
552 xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
553 zCombobox.getSelectedIndex()));
554 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
555 "label.transformed_points_for_params", new String[]
556 { this.getTitle() }), 500, 500);
557 } catch (OutOfMemoryError oom)
559 new OOMWarning("exporting transformed PaSiMap points", oom);
568 * jalview.jbgui.GPCAPanel#outputAlignment_actionPerformed(java.awt.event
572 protected void outputAlignment_actionPerformed()
574 CutAndPasteTransfer cap = new CutAndPasteTransfer();
577 cap.setText(getPasimapModel().getAlignmentOutput());
578 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
579 "label.pairwise_alignment_for_params", new String[] { this.getTitle() }), 500, 500);
580 } catch (OutOfMemoryError oom)
582 new OOMWarning("exporting pairwise alignments", oom);
590 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
593 public void setProgressBar(String message, long id)
595 progressBar.setProgressBar(message, id);
596 // if (progressBars == null)
598 // progressBars = new Hashtable();
599 // progressBarHandlers = new Hashtable();
602 // JPanel progressPanel;
603 // Long lId = Long.valueOf(id);
604 // GridLayout layout = (GridLayout) statusPanel.getLayout();
605 // if (progressBars.get(lId) != null)
607 // progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
608 // statusPanel.remove(progressPanel);
609 // progressBars.remove(lId);
610 // progressPanel = null;
611 // if (message != null)
613 // statusBar.setText(message);
615 // if (progressBarHandlers.contains(lId))
617 // progressBarHandlers.remove(lId);
619 // layout.setRows(layout.getRows() - 1);
623 // progressPanel = new JPanel(new BorderLayout(10, 5));
625 // JProgressBar progressBar = new JProgressBar();
626 // progressBar.setIndeterminate(true);
628 // progressPanel.add(new JLabel(message), BorderLayout.WEST);
629 // progressPanel.add(progressBar, BorderLayout.CENTER);
631 // layout.setRows(layout.getRows() + 1);
632 // statusPanel.add(progressPanel);
634 // progressBars.put(lId, progressPanel);
637 // // setMenusForViewport();
642 public void registerHandler(final long id,
643 final IProgressIndicatorHandler handler)
645 progressBar.registerHandler(id, handler);
646 // if (progressBarHandlers == null ||
647 // !progressBars.contains(Long.valueOf(id)))
650 // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
652 // progressBarHandlers.put(Long.valueOf(id), handler);
653 // final JPanel progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
654 // if (handler.canCancel())
656 // JButton cancel = new JButton(
657 // MessageManager.getString("action.cancel"));
658 // final IProgressIndicator us = this;
659 // cancel.addActionListener(new ActionListener()
663 // public void actionPerformed(ActionEvent e)
665 // handler.cancelActivity(id);
666 // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
667 // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
670 // progressPanel.add(cancel, BorderLayout.EAST);
676 * @return true if any progress bars are still active
679 public boolean operationInProgress()
681 return progressBar.operationInProgress();
685 protected void resetButton_actionPerformed()
688 setTop(0); // ugly - prevents dimensionChanged events from being processed
689 xCombobox.setSelectedIndex(0);
690 yCombobox.setSelectedIndex(1);
692 zCombobox.setSelectedIndex(2);
696 * Answers true if PaSiMap calculation is in progress, else false
700 public boolean isWorking()
706 * Answers the selected checkbox item index for PaSiMap dimension for the X, Y or
707 * Z axis of the display
712 public int getSelectedDimensionIndex(Axis axis)
717 return xCombobox.getSelectedIndex();
719 return yCombobox.getSelectedIndex();
721 return zCombobox.getSelectedIndex();
725 public void setShowLabels(boolean show)
727 showLabels.setSelected(show);
731 * Sets the input data used to calculate the PaSiMap. This is provided for
732 * 'restore from project', which does not currently support this (AL-2647), so
733 * sets the value to null, and hides the menu option for "Input Data...". J
737 public void setInputData(AlignmentViewport data)
739 getPasimapModel().setInputData(data);
740 originalSeqData.setVisible(data != null);
743 public AlignViewportI getAlignViewport()
748 public PaSiMapModel getPasimapModel()
753 public void setPasimapModel(PaSiMapModel pasimapModel)
755 this.pasimapModel = pasimapModel;
758 public RotatableCanvas getRotatableCanvas()
763 public void setRotatableCanvas(RotatableCanvas rc)
773 public void setTop(int top)
779 * set the associated view for this PaSiMap.
783 public void selectAssociatedView(AlignmentPanel panel)
785 getRotatableCanvas().setApplyToAllViews(false);
790 getRotatableCanvas().av = panel.av;
791 getRotatableCanvas().ap = panel;
792 PaintRefresher.Register(PaSiMapPanel.this, panel.av.getSequenceSetId());