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Coverage Report

  1. Project Clover database Thu Nov 7 2024 17:01:39 GMT
  2. Package jalview.gui

File PCAPanel.java

 

Coverage histogram

../../img/srcFileCovDistChart0.png
0% of files have more coverage

Code metrics

34
202
41
2
803
517
73
0.36
4.93
20.5
1.78

Classes

Class Line # Actions
PCAPanel 64 184 66
0.00%
PCAPanel.PCAPrinter 373 18 7
0.00%
 

Contributing tests

No tests hitting this source file were found.

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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 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;
33   
34    import javax.swing.ButtonGroup;
35    import javax.swing.JMenuItem;
36    import javax.swing.JProgressBar;
37    import javax.swing.JRadioButtonMenuItem;
38    import javax.swing.event.InternalFrameAdapter;
39    import javax.swing.event.InternalFrameEvent;
40   
41    import jalview.analysis.scoremodels.ScoreModels;
42    import jalview.api.AlignViewportI;
43    import jalview.api.analysis.ScoreModelI;
44    import jalview.api.analysis.SimilarityParamsI;
45    import jalview.bin.Console;
46    import jalview.datamodel.Alignment;
47    import jalview.datamodel.AlignmentI;
48    import jalview.datamodel.AlignmentView;
49    import jalview.datamodel.HiddenColumns;
50    import jalview.datamodel.SequenceI;
51    import jalview.gui.ImageExporter.ImageWriterI;
52    import jalview.gui.JalviewColourChooser.ColourChooserListener;
53    import jalview.io.exceptions.ImageOutputException;
54    import jalview.jbgui.GPCAPanel;
55    import jalview.math.RotatableMatrix.Axis;
56    import jalview.util.ImageMaker;
57    import jalview.util.MessageManager;
58    import jalview.viewmodel.AlignmentViewport;
59    import jalview.viewmodel.PCAModel;
60   
61    /**
62    * The panel holding the Principal Component Analysis 3-D visualisation
63    */
 
64    public class PCAPanel extends SpatialPanel
65    implements Runnable, IProgressIndicator
66    {
67    private static final int MIN_WIDTH = 470;
68   
69    private static final int MIN_HEIGHT = 250;
70   
71    private RotatableCanvas rc;
72   
73    AlignmentPanel ap;
74   
75    AlignmentViewport av;
76   
77    private PCAModel pcaModel;
78   
79    private int top = 0;
80   
81    private IProgressIndicator progressBar;
82   
83    private boolean working;
84   
85    String newPcaTitle = null;
86    /**
87    * Constructor given sequence data, a similarity (or distance) score model
88    * name, and score calculation parameters
89    *
90    * @param alignPanel
91    * @param modelName
92    * @param params
93    */
 
94  0 toggle public PCAPanel(AlignmentPanel alignPanel, String modelName,
95    SimilarityParamsI params)
96    {
97  0 super();
98  0 this.setFrameIcon(null);
99  0 this.av = alignPanel.av;
100  0 this.ap = alignPanel;
101  0 boolean nucleotide = av.getAlignment().isNucleotide();
102   
103  0 progressBar = new ProgressBar(statusPanel, statusBar);
104   
105  0 addInternalFrameListener(new InternalFrameAdapter()
106    {
 
107  0 toggle @Override
108    public void internalFrameClosed(InternalFrameEvent e)
109    {
110  0 close_actionPerformed();
111    }
112    });
113   
114  0 boolean selected = av.getSelectionGroup() != null
115    && av.getSelectionGroup().getSize() > 0;
116  0 AlignmentView seqstrings = av.getAlignmentView(selected);
117  0 SequenceI[] seqs;
118  0 if (!selected)
119    {
120  0 seqs = av.getAlignment().getSequencesArray();
121    }
122    else
123    {
124  0 seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
125    }
126   
127  0 ScoreModelI scoreModel = ScoreModels.getInstance()
128    .getScoreModel(modelName, ap);
129  0 setPcaModel(
130    new PCAModel(seqstrings, seqs, nucleotide, scoreModel, params));
131   
132  0 newPcaTitle = alignPanel.alignFrame.formCalculationTitle(
133    MessageManager.formatMessage("label.calc_title", "PCA",
134    getPcaModel().getScoreModelName()),
135    selected, ap.alignFrame.getTitle());
136   
137  0 PaintRefresher.Register(this, av.getSequenceSetId());
138   
139  0 setRotatableCanvas(new RotatableCanvas(alignPanel));
140  0 this.getContentPane().add(getRotatableCanvas(), BorderLayout.CENTER);
141   
142  0 addKeyListener(getRotatableCanvas());
143  0 validate();
144    }
145   
146    /**
147    * Ensure references to potentially very large objects (the PCA matrices) are
148    * nulled when the frame is closed
149    */
 
150  0 toggle protected void close_actionPerformed()
151    {
152  0 setPcaModel(null);
153  0 if (this.rc != null)
154    {
155  0 this.rc.sequencePoints = null;
156  0 this.rc.setAxisEndPoints(null);
157  0 this.rc = null;
158    }
159    }
160   
 
161  0 toggle @Override
162    protected void bgcolour_actionPerformed()
163    {
164  0 String ttl = MessageManager.getString("label.select_background_colour");
165  0 ColourChooserListener listener = new ColourChooserListener()
166    {
 
167  0 toggle @Override
168    public void colourSelected(Color c)
169    {
170  0 rc.setBgColour(c);
171  0 rc.repaint();
172    }
173    };
174  0 JalviewColourChooser.showColourChooser(this, ttl, rc.getBgColour(),
175    listener);
176    }
177   
178    /**
179    * Calculates the PCA and displays the results
180    */
 
181  0 toggle @Override
182    public void run()
183    {
184  0 working = true;
185  0 long progId = System.currentTimeMillis();
186  0 IProgressIndicator progress = this;
187  0 String message = MessageManager.getString("label.pca_recalculating");
188  0 if (getParent() == null)
189    {
190  0 progress = ap.alignFrame;
191  0 message = MessageManager.getString("label.pca_calculating");
192    }
193  0 progress.setProgressBar(message, progId);
194  0 try
195    {
196  0 getPcaModel().calculate();
197   
198  0 xCombobox.setSelectedIndex(0);
199  0 yCombobox.setSelectedIndex(1);
200  0 zCombobox.setSelectedIndex(2);
201   
202  0 getPcaModel().updateRc(getRotatableCanvas());
203    // rc.invalidate();
204  0 setTop(getPcaModel().getTop());
205   
206    } catch (OutOfMemoryError er)
207    {
208  0 new OOMWarning("calculating PCA", er);
209  0 working = false;
210  0 return;
211    } finally
212    {
213  0 progress.setProgressBar("", progId);
214    }
215   
216  0 repaint();
217  0 if (getParent() == null)
218    {
219  0 Desktop.addInternalFrame(this, newPcaTitle,
220    475, 450);
221  0 this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
222    }
223  0 working = false;
224    }
225   
226    /**
227    * Updates the PCA display after a change of component to use for x, y or z
228    * axis
229    */
 
230  0 toggle @Override
231    protected void doDimensionChange()
232    {
233  0 if (getTop() == 0)
234    {
235  0 return;
236    }
237   
238  0 int dim1 = getTop() - xCombobox.getSelectedIndex();
239  0 int dim2 = getTop() - yCombobox.getSelectedIndex();
240  0 int dim3 = getTop() - zCombobox.getSelectedIndex();
241  0 getPcaModel().updateRcView(dim1, dim2, dim3);
242  0 getRotatableCanvas().resetView();
243    }
244   
245    /**
246    * Sets the selected checkbox item index for PCA dimension (1, 2, 3...) for
247    * the given axis (X/Y/Z)
248    *
249    * @param index
250    * @param axis
251    */
 
252  0 toggle public void setSelectedDimensionIndex(int index, Axis axis)
253    {
254  0 switch (axis)
255    {
256  0 case X:
257  0 xCombobox.setSelectedIndex(index);
258  0 break;
259  0 case Y:
260  0 yCombobox.setSelectedIndex(index);
261  0 break;
262  0 case Z:
263  0 zCombobox.setSelectedIndex(index);
264  0 break;
265  0 default:
266    }
267    }
268   
 
269  0 toggle @Override
270    protected void outputValues_actionPerformed()
271    {
272  0 CutAndPasteTransfer cap = new CutAndPasteTransfer();
273  0 try
274    {
275  0 cap.setText(getPcaModel().getDetails());
276  0 Desktop.addInternalFrame(cap,
277    MessageManager.getString("label.pca_details"), 500, 500);
278    } catch (OutOfMemoryError oom)
279    {
280  0 new OOMWarning("opening PCA details", oom);
281  0 cap.dispose();
282    }
283    }
284   
 
285  0 toggle @Override
286    protected void showLabels_actionPerformed()
287    {
288  0 getRotatableCanvas().showLabels(showLabels.getState());
289    }
290   
 
291  0 toggle @Override
292    protected void print_actionPerformed()
293    {
294  0 PCAPrinter printer = new PCAPrinter();
295  0 printer.start();
296    }
297   
298    /**
299    * If available, shows the data which formed the inputs for the PCA as a new
300    * alignment
301    */
 
302  0 toggle @Override
303    public void originalSeqData_actionPerformed()
304    {
305    // JAL-2647 disabled after load from project (until save to project done)
306  0 if (getPcaModel().getInputData() == null)
307    {
308  0 Console.info(
309    "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
310  0 return;
311    }
312    // decide if av alignment is sufficiently different to original data to
313    // warrant a new window to be created
314    // create new alignment window with hidden regions (unhiding hidden regions
315    // yields unaligned seqs)
316    // or create a selection box around columns in alignment view
317    // test Alignment(SeqCigar[])
318  0 char gc = '-';
319  0 try
320    {
321    // we try to get the associated view's gap character
322    // but this may fail if the view was closed...
323  0 gc = av.getGapCharacter();
324    } catch (Exception ex)
325    {
326    }
327   
328  0 Object[] alAndColsel = getPcaModel().getInputData()
329    .getAlignmentAndHiddenColumns(gc);
330   
331  0 if (alAndColsel != null && alAndColsel[0] != null)
332    {
333    // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
334   
335  0 AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
336  0 AlignmentI dataset = (av != null && av.getAlignment() != null)
337    ? av.getAlignment().getDataset()
338    : null;
339  0 if (dataset != null)
340    {
341  0 al.setDataset(dataset);
342    }
343   
344  0 if (true)
345    {
346    // make a new frame!
347  0 AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
348    AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
349   
350    // >>>This is a fix for the moment, until a better solution is
351    // found!!<<<
352    // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
353   
354    // af.addSortByOrderMenuItem(ServiceName + " Ordering",
355    // msaorder);
356   
357  0 Desktop.addInternalFrame(af, MessageManager.formatMessage(
358    "label.original_data_for_params", new String[]
359    { this.title }), AlignFrame.DEFAULT_WIDTH,
360    AlignFrame.DEFAULT_HEIGHT);
361    }
362    }
363    /*
364    * CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
365    * seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
366    * "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
367    * "\n"); }
368    *
369    * Desktop.addInternalFrame(cap, "Original Data", 400, 400);
370    */
371    }
372   
 
373    class PCAPrinter extends Thread implements Printable
374    {
 
375  0 toggle @Override
376    public void run()
377    {
378  0 PrinterJob printJob = PrinterJob.getPrinterJob();
379  0 PageFormat defaultPage = printJob.defaultPage();
380  0 PageFormat pf = printJob.pageDialog(defaultPage);
381   
382  0 if (defaultPage == pf)
383    {
384    /*
385    * user cancelled
386    */
387  0 return;
388    }
389   
390  0 printJob.setPrintable(this, pf);
391   
392  0 if (printJob.printDialog())
393    {
394  0 try
395    {
396  0 printJob.print();
397    } catch (Exception PrintException)
398    {
399  0 PrintException.printStackTrace();
400    }
401    }
402    }
403   
 
404  0 toggle @Override
405    public int print(Graphics pg, PageFormat pf, int pi)
406    throws PrinterException
407    {
408  0 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
409   
410  0 getRotatableCanvas().drawBackground(pg);
411  0 getRotatableCanvas().drawScene(pg);
412  0 if (getRotatableCanvas().drawAxes)
413    {
414  0 getRotatableCanvas().drawAxes(pg);
415    }
416   
417  0 if (pi == 0)
418    {
419  0 return Printable.PAGE_EXISTS;
420    }
421    else
422    {
423  0 return Printable.NO_SUCH_PAGE;
424    }
425    }
426    }
427   
 
428  0 toggle public void makePCAImage(ImageMaker.TYPE type)
429    {
430  0 int width = getRotatableCanvas().getWidth();
431  0 int height = getRotatableCanvas().getHeight();
432  0 ImageWriterI writer = new ImageWriterI()
433    {
 
434  0 toggle @Override
435    public void exportImage(Graphics g) throws Exception
436    {
437  0 RotatableCanvas canvas = getRotatableCanvas();
438  0 canvas.drawBackground(g);
439  0 canvas.drawScene(g);
440  0 if (canvas.drawAxes)
441    {
442  0 canvas.drawAxes(g);
443    }
444    }
445    };
446  0 String pca = MessageManager.getString("label.pca");
447  0 ImageExporter exporter = new ImageExporter(writer, null, type, pca);
448  0 try
449    {
450  0 exporter.doExport(null, this, width, height, pca);
451    } catch (ImageOutputException ioex)
452    {
453  0 Console.error("Unexpected error whilst writing " + type.toString(),
454    ioex);
455    }
456    }
457   
 
458  0 toggle @Override
459    protected void viewMenu_menuSelected()
460    {
461  0 buildAssociatedViewMenu();
462    }
463   
464    /**
465    * Builds the menu showing the choice of possible views (for the associated
466    * sequence data) to which the PCA may be linked
467    */
 
468  0 toggle void buildAssociatedViewMenu()
469    {
470  0 AlignmentPanel[] aps = PaintRefresher
471    .getAssociatedPanels(av.getSequenceSetId());
472  0 if (aps.length == 1 && getRotatableCanvas().av == aps[0].av)
473    {
474  0 associateViewsMenu.setVisible(false);
475  0 return;
476    }
477   
478  0 associateViewsMenu.setVisible(true);
479   
480  0 if ((viewMenu
481    .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
482    {
483  0 viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
484    }
485   
486  0 associateViewsMenu.removeAll();
487   
488  0 JRadioButtonMenuItem item;
489  0 ButtonGroup buttonGroup = new ButtonGroup();
490  0 int iSize = aps.length;
491   
492  0 for (int i = 0; i < iSize; i++)
493    {
494  0 final AlignmentPanel panel = aps[i];
495  0 item = new JRadioButtonMenuItem(panel.av.getViewName(),
496    panel.av == getRotatableCanvas().av);
497  0 buttonGroup.add(item);
498  0 item.addActionListener(new ActionListener()
499    {
 
500  0 toggle @Override
501    public void actionPerformed(ActionEvent evt)
502    {
503  0 selectAssociatedView(panel);
504    }
505    });
506   
507  0 associateViewsMenu.add(item);
508    }
509   
510  0 final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
511    "All Views");
512   
513  0 buttonGroup.add(itemf);
514   
515  0 itemf.setSelected(getRotatableCanvas().isApplyToAllViews());
516  0 itemf.addActionListener(new ActionListener()
517    {
 
518  0 toggle @Override
519    public void actionPerformed(ActionEvent evt)
520    {
521  0 getRotatableCanvas().setApplyToAllViews(itemf.isSelected());
522    }
523    });
524  0 associateViewsMenu.add(itemf);
525   
526    }
527   
528    /*
529    * (non-Javadoc)
530    *
531    * @see
532    * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
533    * )
534    */
 
535  0 toggle @Override
536    protected void outputPoints_actionPerformed()
537    {
538  0 CutAndPasteTransfer cap = new CutAndPasteTransfer();
539  0 try
540    {
541  0 cap.setText(getPcaModel().getPointsasCsv(false,
542    xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
543    zCombobox.getSelectedIndex()));
544  0 Desktop.addInternalFrame(cap, MessageManager
545    .formatMessage("label.points_for_params", new String[]
546    { this.getTitle() }), 500, 500);
547    } catch (OutOfMemoryError oom)
548    {
549  0 new OOMWarning("exporting PCA points", oom);
550  0 cap.dispose();
551    }
552    }
553   
554    /*
555    * (non-Javadoc)
556    *
557    * @see
558    * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
559    * .ActionEvent)
560    */
 
561  0 toggle @Override
562    protected void outputProjPoints_actionPerformed()
563    {
564  0 CutAndPasteTransfer cap = new CutAndPasteTransfer();
565  0 try
566    {
567  0 cap.setText(getPcaModel().getPointsasCsv(true,
568    xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
569    zCombobox.getSelectedIndex()));
570  0 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
571    "label.transformed_points_for_params", new String[]
572    { this.getTitle() }), 500, 500);
573    } catch (OutOfMemoryError oom)
574    {
575  0 new OOMWarning("exporting transformed PCA points", oom);
576  0 cap.dispose();
577    }
578    }
579   
580    /*
581    * (non-Javadoc)
582    *
583    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
584    */
 
585  0 toggle @Override
586    public void setProgressBar(String message, long id)
587    {
588  0 progressBar.setProgressBar(message, id);
589    // if (progressBars == null)
590    // {
591    // progressBars = new Hashtable();
592    // progressBarHandlers = new Hashtable();
593    // }
594    //
595    // JPanel progressPanel;
596    // Long lId = Long.valueOf(id);
597    // GridLayout layout = (GridLayout) statusPanel.getLayout();
598    // if (progressBars.get(lId) != null)
599    // {
600    // progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
601    // statusPanel.remove(progressPanel);
602    // progressBars.remove(lId);
603    // progressPanel = null;
604    // if (message != null)
605    // {
606    // statusBar.setText(message);
607    // }
608    // if (progressBarHandlers.contains(lId))
609    // {
610    // progressBarHandlers.remove(lId);
611    // }
612    // layout.setRows(layout.getRows() - 1);
613    // }
614    // else
615    // {
616    // progressPanel = new JPanel(new BorderLayout(10, 5));
617    //
618    // JProgressBar progressBar = new JProgressBar();
619    // progressBar.setIndeterminate(true);
620    //
621    // progressPanel.add(new JLabel(message), BorderLayout.WEST);
622    // progressPanel.add(progressBar, BorderLayout.CENTER);
623    //
624    // layout.setRows(layout.getRows() + 1);
625    // statusPanel.add(progressPanel);
626    //
627    // progressBars.put(lId, progressPanel);
628    // }
629    // // update GUI
630    // // setMenusForViewport();
631    // validate();
632    }
633   
 
634  0 toggle @Override
635    public void registerHandler(final long id,
636    final IProgressIndicatorHandler handler)
637    {
638  0 progressBar.registerHandler(id, handler);
639    // if (progressBarHandlers == null ||
640    // !progressBars.contains(Long.valueOf(id)))
641    // {
642    // throw new
643    // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
644    // }
645    // progressBarHandlers.put(Long.valueOf(id), handler);
646    // final JPanel progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
647    // if (handler.canCancel())
648    // {
649    // JButton cancel = new JButton(
650    // MessageManager.getString("action.cancel"));
651    // final IProgressIndicator us = this;
652    // cancel.addActionListener(new ActionListener()
653    // {
654    //
655    // @Override
656    // public void actionPerformed(ActionEvent e)
657    // {
658    // handler.cancelActivity(id);
659    // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
660    // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
661    // }
662    // });
663    // progressPanel.add(cancel, BorderLayout.EAST);
664    // }
665    }
666   
667    /**
668    *
669    * @return true if any progress bars are still active
670    */
 
671  0 toggle @Override
672    public boolean operationInProgress()
673    {
674  0 return progressBar.operationInProgress();
675    }
676   
 
677  0 toggle @Override
678    protected void resetButton_actionPerformed()
679    {
680  0 int t = getTop();
681  0 setTop(0); // ugly - prevents dimensionChanged events from being processed
682  0 xCombobox.setSelectedIndex(0);
683  0 yCombobox.setSelectedIndex(1);
684  0 setTop(t);
685  0 zCombobox.setSelectedIndex(2);
686    }
687   
688    /**
689    * Answers true if PCA calculation is in progress, else false
690    *
691    * @return
692    */
 
693  0 toggle public boolean isWorking()
694    {
695  0 return working;
696    }
697   
698    /**
699    * Answers the selected checkbox item index for PCA dimension for the X, Y or
700    * Z axis of the display
701    *
702    * @param axis
703    * @return
704    */
 
705  0 toggle public int getSelectedDimensionIndex(Axis axis)
706    {
707  0 switch (axis)
708    {
709  0 case X:
710  0 return xCombobox.getSelectedIndex();
711  0 case Y:
712  0 return yCombobox.getSelectedIndex();
713  0 default:
714  0 return zCombobox.getSelectedIndex();
715    }
716    }
717   
 
718  0 toggle public void setShowLabels(boolean show)
719    {
720  0 showLabels.setSelected(show);
721    }
722   
723    /**
724    * Sets the input data used to calculate the PCA. This is provided for
725    * 'restore from project', which does not currently support this (AL-2647), so
726    * sets the value to null, and hides the menu option for "Input Data...". J
727    *
728    * @param data
729    */
 
730  0 toggle public void setInputData(AlignmentView data)
731    {
732  0 getPcaModel().setInputData(data);
733  0 originalSeqData.setVisible(data != null);
734    }
735   
 
736  0 toggle public AlignViewportI getAlignViewport()
737    {
738  0 return av;
739    }
740   
 
741  0 toggle public PCAModel getPcaModel()
742    {
743  0 return pcaModel;
744    }
745   
 
746  0 toggle public void setPcaModel(PCAModel pcaModel)
747    {
748  0 this.pcaModel = pcaModel;
749    }
750   
 
751  0 toggle public RotatableCanvas getRotatableCanvas()
752    {
753  0 return rc;
754    }
755   
 
756  0 toggle public void setRotatableCanvas(RotatableCanvas rc)
757    {
758  0 this.rc = rc;
759    }
760   
 
761  0 toggle public int getTop()
762    {
763  0 return top;
764    }
765   
 
766  0 toggle public void setTop(int top)
767    {
768  0 this.top = top;
769    }
770   
771    /**
772    * set the associated view for this PCA.
773    *
774    * @param panel
775    */
 
776  0 toggle public void selectAssociatedView(AlignmentPanel panel)
777    {
778  0 getRotatableCanvas().setApplyToAllViews(false);
779   
780  0 ap = panel;
781  0 av = panel.av;
782   
783  0 getRotatableCanvas().av = panel.av;
784  0 getRotatableCanvas().ap = panel;
785  0 PaintRefresher.Register(PCAPanel.this, panel.av.getSequenceSetId());
786    }
787   
 
788  0 toggle @Override
789    public JProgressBar getProgressBar(long id)
790    {
791  0 return progressBar.getProgressBar(id);
792    }
793   
 
794  0 toggle public String getMessage(long id)
795    {
796  0 return progressBar.getMessage(id);
797    }
798   
 
799  0 toggle public void setProgressBarMessage(long id, String message)
800    {
801  0 progressBar.setProgressBarMessage(id, message);
802    }
803    }
  • Report generated by OpenClover v 4.4.1 on Thu Nov 7 2024 17:02:19 GMT using coverage data from Thu Jan 1 1970 01:00:00 GMT.
  • OpenClover is free and open-source software.