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jalviewX

  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.gui

File PCAPanel.java

 

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42
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2
779
504
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0.34
5.88
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Classes

Class Line # Actions
PCAPanel 64 182 60 248
0.00%
PCAPanel.PCAPrinter 466 18 7 28
0.00%
 

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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.
11    *
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.
16    *
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.
20    */
21    package jalview.gui;
22   
23    import jalview.analysis.scoremodels.ScoreModels;
24    import jalview.analysis.scoremodels.SimilarityParams;
25    import jalview.api.analysis.ScoreModelI;
26    import jalview.api.analysis.SimilarityParamsI;
27    import jalview.datamodel.Alignment;
28    import jalview.datamodel.AlignmentI;
29    import jalview.datamodel.AlignmentView;
30    import jalview.datamodel.HiddenColumns;
31    import jalview.datamodel.SequenceI;
32    import jalview.gui.ImageExporter.ImageWriterI;
33    import jalview.gui.JalviewColourChooser.ColourChooserListener;
34    import jalview.jbgui.GPCAPanel;
35    import jalview.util.ImageMaker;
36    import jalview.util.MessageManager;
37    import jalview.viewmodel.AlignmentViewport;
38    import jalview.viewmodel.PCAModel;
39   
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;
50   
51    import javax.swing.ButtonGroup;
52    import javax.swing.JCheckBoxMenuItem;
53    import javax.swing.JMenuItem;
54    import javax.swing.JRadioButtonMenuItem;
55    import javax.swing.event.InternalFrameAdapter;
56    import javax.swing.event.InternalFrameEvent;
57   
58    /**
59    * DOCUMENT ME!
60    *
61    * @author $author$
62    * @version $Revision$
63    */
 
64    public class PCAPanel extends GPCAPanel
65    implements Runnable, IProgressIndicator
66    {
67   
68    private IProgressIndicator progressBar;
69   
70    RotatableCanvas rc;
71   
72    AlignmentPanel ap;
73   
74    AlignmentViewport av;
75   
76    PCAModel pcaModel;
77   
78    private static final int MIN_WIDTH = 470;
79   
80    private static final int MIN_HEIGHT = 250;
81   
82    int top = 0;
83   
84    private boolean working;
85   
86    /**
87    * Creates a new PCAPanel object using default score model and parameters
88    *
89    * @param alignPanel
90    */
 
91  0 toggle public PCAPanel(AlignmentPanel alignPanel)
92    {
93  0 this(alignPanel,
94    ScoreModels.getInstance()
95    .getDefaultModel(
96    !alignPanel.av.getAlignment().isNucleotide())
97    .getName(),
98    SimilarityParams.SeqSpace);
99    }
100   
101    /**
102    * Constructor given sequence data, a similarity (or distance) score model
103    * name, and score calculation parameters
104    *
105    * @param alignPanel
106    * @param modelName
107    * @param params
108    */
 
109  0 toggle public PCAPanel(AlignmentPanel alignPanel, String modelName,
110    SimilarityParamsI params)
111    {
112  0 super();
113  0 this.av = alignPanel.av;
114  0 this.ap = alignPanel;
115  0 boolean nucleotide = av.getAlignment().isNucleotide();
116   
117  0 progressBar = new ProgressBar(statusPanel, statusBar);
118   
119  0 addInternalFrameListener(new InternalFrameAdapter()
120    {
 
121  0 toggle @Override
122    public void internalFrameClosed(InternalFrameEvent e)
123    {
124  0 close_actionPerformed();
125    }
126    });
127   
128  0 boolean selected = av.getSelectionGroup() != null
129    && av.getSelectionGroup().getSize() > 0;
130  0 AlignmentView seqstrings = av.getAlignmentView(selected);
131  0 SequenceI[] seqs;
132  0 if (!selected)
133    {
134  0 seqs = av.getAlignment().getSequencesArray();
135    }
136    else
137    {
138  0 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
139    }
140   
141  0 ScoreModelI scoreModel = ScoreModels.getInstance()
142    .getScoreModel(modelName, ap);
143  0 pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
144    params);
145  0 PaintRefresher.Register(this, av.getSequenceSetId());
146   
147  0 rc = new RotatableCanvas(alignPanel);
148  0 this.getContentPane().add(rc, BorderLayout.CENTER);
149  0 Thread worker = new Thread(this);
150  0 worker.start();
151    }
152   
153    /**
154    * Ensure references to potentially very large objects (the PCA matrices) are
155    * nulled when the frame is closed
156    */
 
157  0 toggle protected void close_actionPerformed()
158    {
159  0 pcaModel = null;
160    }
161   
162    /**
163    * Repopulate the options and actions under the score model menu when it is
164    * selected. Options will depend on whether 'nucleotide' or 'peptide'
165    * modelling is selected (and also possibly on whether any additional score
166    * models have been added).
167    */
 
168  0 toggle @Override
169    protected void scoreModel_menuSelected()
170    {
171  0 scoreModelMenu.removeAll();
172  0 for (final ScoreModelI sm : ScoreModels.getInstance().getModels())
173    {
174  0 final String name = sm.getName();
175  0 JCheckBoxMenuItem jm = new JCheckBoxMenuItem(name);
176   
177    /*
178    * if the score model doesn't provide a description, try to look one
179    * up in the text bundle, falling back on its name
180    */
181  0 String tooltip = sm.getDescription();
182  0 if (tooltip == null)
183    {
184  0 tooltip = MessageManager.getStringOrReturn("label.score_model_",
185    name);
186    }
187  0 jm.setToolTipText(tooltip);
188  0 jm.setSelected(pcaModel.getScoreModelName().equals(name));
189  0 if ((pcaModel.isNucleotide() && sm.isDNA())
190    || (!pcaModel.isNucleotide() && sm.isProtein()))
191    {
192  0 jm.addActionListener(new ActionListener()
193    {
 
194  0 toggle @Override
195    public void actionPerformed(ActionEvent e)
196    {
197  0 if (!pcaModel.getScoreModelName().equals(name))
198    {
199  0 ScoreModelI sm2 = ScoreModels.getInstance()
200    .getScoreModel(name, ap);
201  0 pcaModel.setScoreModel(sm2);
202  0 Thread worker = new Thread(PCAPanel.this);
203  0 worker.start();
204    }
205    }
206    });
207  0 scoreModelMenu.add(jm);
208    }
209    }
210    }
211   
 
212  0 toggle @Override
213    public void bgcolour_actionPerformed(ActionEvent e)
214    {
215  0 String ttl = MessageManager.getString("label.select_background_colour");
216  0 ColourChooserListener listener = new ColourChooserListener()
217    {
 
218  0 toggle @Override
219    public void colourSelected(Color c)
220    {
221  0 rc.bgColour = c;
222  0 rc.repaint();
223    }
224    };
225  0 JalviewColourChooser.showColourChooser(this, ttl, rc.bgColour,
226    listener);
227    }
228   
229    /**
230    * DOCUMENT ME!
231    */
 
232  0 toggle @Override
233    public void run()
234    {
235  0 long progId = System.currentTimeMillis();
236  0 IProgressIndicator progress = this;
237  0 String message = MessageManager.getString("label.pca_recalculating");
238  0 if (getParent() == null)
239    {
240  0 progress = ap.alignFrame;
241  0 message = MessageManager.getString("label.pca_calculating");
242    }
243  0 progress.setProgressBar(message, progId);
244  0 working = true;
245  0 try
246    {
247  0 calcSettings.setEnabled(false);
248  0 pcaModel.run();
249    // ////////////////
250  0 xCombobox.setSelectedIndex(0);
251  0 yCombobox.setSelectedIndex(1);
252  0 zCombobox.setSelectedIndex(2);
253   
254  0 pcaModel.updateRc(rc);
255    // rc.invalidate();
256  0 nuclSetting.setSelected(pcaModel.isNucleotide());
257  0 protSetting.setSelected(!pcaModel.isNucleotide());
258  0 top = pcaModel.getTop();
259   
260    } catch (OutOfMemoryError er)
261    {
262  0 new OOMWarning("calculating PCA", er);
263  0 working = false;
264  0 return;
265    } finally
266    {
267  0 progress.setProgressBar("", progId);
268    }
269  0 calcSettings.setEnabled(true);
270  0 repaint();
271  0 if (getParent() == null)
272    {
273  0 addKeyListener(rc);
274  0 Desktop.addInternalFrame(this, MessageManager
275    .getString("label.principal_component_analysis"), 475, 450);
276  0 this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
277    }
278  0 working = false;
279    }
280   
 
281  0 toggle @Override
282    protected void nuclSetting_actionPerfomed(ActionEvent arg0)
283    {
284  0 if (!pcaModel.isNucleotide())
285    {
286  0 pcaModel.setNucleotide(true);
287  0 pcaModel.setScoreModel(
288    ScoreModels.getInstance().getDefaultModel(false));
289  0 Thread worker = new Thread(this);
290  0 worker.start();
291    }
292   
293    }
294   
 
295  0 toggle @Override
296    protected void protSetting_actionPerfomed(ActionEvent arg0)
297    {
298   
299  0 if (pcaModel.isNucleotide())
300    {
301  0 pcaModel.setNucleotide(false);
302  0 pcaModel.setScoreModel(
303    ScoreModels.getInstance().getDefaultModel(true));
304  0 Thread worker = new Thread(this);
305  0 worker.start();
306    }
307    }
308   
309    /**
310    * DOCUMENT ME!
311    */
 
312  0 toggle void doDimensionChange()
313    {
314  0 if (top == 0)
315    {
316  0 return;
317    }
318   
319  0 int dim1 = top - xCombobox.getSelectedIndex();
320  0 int dim2 = top - yCombobox.getSelectedIndex();
321  0 int dim3 = top - zCombobox.getSelectedIndex();
322  0 pcaModel.updateRcView(dim1, dim2, dim3);
323  0 rc.img = null;
324  0 rc.rotmat.setIdentity();
325  0 rc.initAxes();
326  0 rc.paint(rc.getGraphics());
327    }
328   
329    /**
330    * DOCUMENT ME!
331    *
332    * @param e
333    * DOCUMENT ME!
334    */
 
335  0 toggle @Override
336    protected void xCombobox_actionPerformed(ActionEvent e)
337    {
338  0 doDimensionChange();
339    }
340   
341    /**
342    * DOCUMENT ME!
343    *
344    * @param e
345    * DOCUMENT ME!
346    */
 
347  0 toggle @Override
348    protected void yCombobox_actionPerformed(ActionEvent e)
349    {
350  0 doDimensionChange();
351    }
352   
353    /**
354    * DOCUMENT ME!
355    *
356    * @param e
357    * DOCUMENT ME!
358    */
 
359  0 toggle @Override
360    protected void zCombobox_actionPerformed(ActionEvent e)
361    {
362  0 doDimensionChange();
363    }
364   
 
365  0 toggle @Override
366    public void outputValues_actionPerformed(ActionEvent e)
367    {
368  0 CutAndPasteTransfer cap = new CutAndPasteTransfer();
369  0 try
370    {
371  0 cap.setText(pcaModel.getDetails());
372  0 Desktop.addInternalFrame(cap,
373    MessageManager.getString("label.pca_details"), 500, 500);
374    } catch (OutOfMemoryError oom)
375    {
376  0 new OOMWarning("opening PCA details", oom);
377  0 cap.dispose();
378    }
379    }
380   
 
381  0 toggle @Override
382    public void showLabels_actionPerformed(ActionEvent e)
383    {
384  0 rc.showLabels(showLabels.getState());
385    }
386   
 
387  0 toggle @Override
388    public void print_actionPerformed(ActionEvent e)
389    {
390  0 PCAPrinter printer = new PCAPrinter();
391  0 printer.start();
392    }
393   
 
394  0 toggle @Override
395    public void originalSeqData_actionPerformed(ActionEvent e)
396    {
397    // this was cut'n'pasted from the equivalent TreePanel method - we should
398    // make this an abstract function of all jalview analysis windows
399  0 if (pcaModel.getSeqtrings() == null)
400    {
401  0 jalview.bin.Cache.log.info(
402    "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
403  0 return;
404    }
405    // decide if av alignment is sufficiently different to original data to
406    // warrant a new window to be created
407    // create new alignmnt window with hidden regions (unhiding hidden regions
408    // yields unaligned seqs)
409    // or create a selection box around columns in alignment view
410    // test Alignment(SeqCigar[])
411  0 char gc = '-';
412  0 try
413    {
414    // we try to get the associated view's gap character
415    // but this may fail if the view was closed...
416  0 gc = av.getGapCharacter();
417    } catch (Exception ex)
418    {
419    }
420  0 ;
421  0 Object[] alAndColsel = pcaModel.getSeqtrings()
422    .getAlignmentAndHiddenColumns(gc);
423   
424  0 if (alAndColsel != null && alAndColsel[0] != null)
425    {
426    // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
427   
428  0 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
429  0 AlignmentI dataset = (av != null && av.getAlignment() != null)
430    ? av.getAlignment().getDataset()
431    : null;
432  0 if (dataset != null)
433    {
434  0 al.setDataset(dataset);
435    }
436   
437  0 if (true)
438    {
439    // make a new frame!
440  0 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
441    AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
442   
443    // >>>This is a fix for the moment, until a better solution is
444    // found!!<<<
445    // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
446   
447    // af.addSortByOrderMenuItem(ServiceName + " Ordering",
448    // msaorder);
449   
450  0 Desktop.addInternalFrame(af, MessageManager.formatMessage(
451    "label.original_data_for_params", new String[]
452    { this.title }), AlignFrame.DEFAULT_WIDTH,
453    AlignFrame.DEFAULT_HEIGHT);
454    }
455    }
456    /*
457    * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
458    * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
459    * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
460    * "\n"); }
461    *
462    * Desktop.addInternalFrame(cap, "Original Data", 400, 400);
463    */
464    }
465   
 
466    class PCAPrinter extends Thread implements Printable
467    {
 
468  0 toggle @Override
469    public void run()
470    {
471  0 PrinterJob printJob = PrinterJob.getPrinterJob();
472  0 PageFormat defaultPage = printJob.defaultPage();
473  0 PageFormat pf = printJob.pageDialog(defaultPage);
474   
475  0 if (defaultPage == pf)
476    {
477    /*
478    * user cancelled
479    */
480  0 return;
481    }
482   
483  0 printJob.setPrintable(this, pf);
484   
485  0 if (printJob.printDialog())
486    {
487  0 try
488    {
489  0 printJob.print();
490    } catch (Exception PrintException)
491    {
492  0 PrintException.printStackTrace();
493    }
494    }
495    }
496   
 
497  0 toggle @Override
498    public int print(Graphics pg, PageFormat pf, int pi)
499    throws PrinterException
500    {
501  0 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
502   
503  0 rc.drawBackground(pg, rc.bgColour);
504  0 rc.drawScene(pg);
505  0 if (rc.drawAxes == true)
506    {
507  0 rc.drawAxes(pg);
508    }
509   
510  0 if (pi == 0)
511    {
512  0 return Printable.PAGE_EXISTS;
513    }
514    else
515    {
516  0 return Printable.NO_SUCH_PAGE;
517    }
518    }
519    }
520   
 
521  0 toggle public void makePCAImage(ImageMaker.TYPE type)
522    {
523  0 int width = rc.getWidth();
524  0 int height = rc.getHeight();
525  0 ImageWriterI writer = new ImageWriterI()
526    {
 
527  0 toggle @Override
528    public void exportImage(Graphics g) throws Exception
529    {
530  0 rc.drawBackground(g, Color.black);
531  0 rc.drawScene(g);
532  0 if (rc.drawAxes)
533    {
534  0 rc.drawAxes(g);
535    }
536    }
537    };
538  0 String pca = MessageManager.getString("label.pca");
539  0 ImageExporter exporter = new ImageExporter(writer, null, type, pca);
540  0 exporter.doExport(null, this, width, height, pca);
541    }
542   
 
543  0 toggle @Override
544    public void viewMenu_menuSelected()
545    {
546  0 buildAssociatedViewMenu();
547    }
548   
 
549  0 toggle void buildAssociatedViewMenu()
550    {
551  0 AlignmentPanel[] aps = PaintRefresher
552    .getAssociatedPanels(av.getSequenceSetId());
553  0 if (aps.length == 1 && rc.av == aps[0].av)
554    {
555  0 associateViewsMenu.setVisible(false);
556  0 return;
557    }
558   
559  0 associateViewsMenu.setVisible(true);
560   
561  0 if ((viewMenu
562    .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
563    {
564  0 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
565    }
566   
567  0 associateViewsMenu.removeAll();
568   
569  0 JRadioButtonMenuItem item;
570  0 ButtonGroup buttonGroup = new ButtonGroup();
571  0 int i, iSize = aps.length;
572  0 final PCAPanel thisPCAPanel = this;
573  0 for (i = 0; i < iSize; i++)
574    {
575  0 final AlignmentPanel ap = aps[i];
576  0 item = new JRadioButtonMenuItem(ap.av.viewName, ap.av == rc.av);
577  0 buttonGroup.add(item);
578  0 item.addActionListener(new ActionListener()
579    {
 
580  0 toggle @Override
581    public void actionPerformed(ActionEvent evt)
582    {
583  0 rc.applyToAllViews = false;
584  0 rc.av = ap.av;
585  0 rc.ap = ap;
586  0 PaintRefresher.Register(thisPCAPanel, ap.av.getSequenceSetId());
587    }
588    });
589   
590  0 associateViewsMenu.add(item);
591    }
592   
593  0 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
594    "All Views");
595   
596  0 buttonGroup.add(itemf);
597   
598  0 itemf.setSelected(rc.applyToAllViews);
599  0 itemf.addActionListener(new ActionListener()
600    {
 
601  0 toggle @Override
602    public void actionPerformed(ActionEvent evt)
603    {
604  0 rc.applyToAllViews = itemf.isSelected();
605    }
606    });
607  0 associateViewsMenu.add(itemf);
608   
609    }
610   
611    /*
612    * (non-Javadoc)
613    *
614    * @see
615    * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
616    * )
617    */
 
618  0 toggle @Override
619    protected void outputPoints_actionPerformed(ActionEvent e)
620    {
621  0 CutAndPasteTransfer cap = new CutAndPasteTransfer();
622  0 try
623    {
624  0 cap.setText(pcaModel.getPointsasCsv(false,
625    xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
626    zCombobox.getSelectedIndex()));
627  0 Desktop.addInternalFrame(cap, MessageManager
628    .formatMessage("label.points_for_params", new String[]
629    { this.getTitle() }), 500, 500);
630    } catch (OutOfMemoryError oom)
631    {
632  0 new OOMWarning("exporting PCA points", oom);
633  0 cap.dispose();
634    }
635    }
636   
637    /*
638    * (non-Javadoc)
639    *
640    * @see
641    * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
642    * .ActionEvent)
643    */
 
644  0 toggle @Override
645    protected void outputProjPoints_actionPerformed(ActionEvent e)
646    {
647  0 CutAndPasteTransfer cap = new CutAndPasteTransfer();
648  0 try
649    {
650  0 cap.setText(pcaModel.getPointsasCsv(true,
651    xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
652    zCombobox.getSelectedIndex()));
653  0 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
654    "label.transformed_points_for_params", new String[]
655    { this.getTitle() }), 500, 500);
656    } catch (OutOfMemoryError oom)
657    {
658  0 new OOMWarning("exporting transformed PCA points", oom);
659  0 cap.dispose();
660    }
661    }
662   
663    /*
664    * (non-Javadoc)
665    *
666    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
667    */
 
668  0 toggle @Override
669    public void setProgressBar(String message, long id)
670    {
671  0 progressBar.setProgressBar(message, id);
672    // if (progressBars == null)
673    // {
674    // progressBars = new Hashtable();
675    // progressBarHandlers = new Hashtable();
676    // }
677    //
678    // JPanel progressPanel;
679    // Long lId = new Long(id);
680    // GridLayout layout = (GridLayout) statusPanel.getLayout();
681    // if (progressBars.get(lId) != null)
682    // {
683    // progressPanel = (JPanel) progressBars.get(new Long(id));
684    // statusPanel.remove(progressPanel);
685    // progressBars.remove(lId);
686    // progressPanel = null;
687    // if (message != null)
688    // {
689    // statusBar.setText(message);
690    // }
691    // if (progressBarHandlers.contains(lId))
692    // {
693    // progressBarHandlers.remove(lId);
694    // }
695    // layout.setRows(layout.getRows() - 1);
696    // }
697    // else
698    // {
699    // progressPanel = new JPanel(new BorderLayout(10, 5));
700    //
701    // JProgressBar progressBar = new JProgressBar();
702    // progressBar.setIndeterminate(true);
703    //
704    // progressPanel.add(new JLabel(message), BorderLayout.WEST);
705    // progressPanel.add(progressBar, BorderLayout.CENTER);
706    //
707    // layout.setRows(layout.getRows() + 1);
708    // statusPanel.add(progressPanel);
709    //
710    // progressBars.put(lId, progressPanel);
711    // }
712    // // update GUI
713    // // setMenusForViewport();
714    // validate();
715    }
716   
 
717  0 toggle @Override
718    public void registerHandler(final long id,
719    final IProgressIndicatorHandler handler)
720    {
721  0 progressBar.registerHandler(id, handler);
722    // if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
723    // {
724    // throw new
725    // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
726    // }
727    // progressBarHandlers.put(new Long(id), handler);
728    // final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
729    // if (handler.canCancel())
730    // {
731    // JButton cancel = new JButton(
732    // MessageManager.getString("action.cancel"));
733    // final IProgressIndicator us = this;
734    // cancel.addActionListener(new ActionListener()
735    // {
736    //
737    // @Override
738    // public void actionPerformed(ActionEvent e)
739    // {
740    // handler.cancelActivity(id);
741    // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
742    // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
743    // }
744    // });
745    // progressPanel.add(cancel, BorderLayout.EAST);
746    // }
747    }
748   
749    /**
750    *
751    * @return true if any progress bars are still active
752    */
 
753  0 toggle @Override
754    public boolean operationInProgress()
755    {
756  0 return progressBar.operationInProgress();
757    }
758   
 
759  0 toggle @Override
760    protected void resetButton_actionPerformed(ActionEvent e)
761    {
762  0 int t = top;
763  0 top = 0; // ugly - prevents dimensionChanged events from being processed
764  0 xCombobox.setSelectedIndex(0);
765  0 yCombobox.setSelectedIndex(1);
766  0 top = t;
767  0 zCombobox.setSelectedIndex(2);
768    }
769   
770    /**
771    * Answers true if PCA calculation is in progress, else false
772    *
773    * @return
774    */
 
775  0 toggle public boolean isWorking()
776    {
777  0 return working;
778    }
779    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.