Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PCAPanel	62	173	61	0.41630941.6%	Show methods
PCAPanel.PCAPrinter	359	18	7	0.00%	Show methods

Class PCAPanel

Class PCAPanel	Line # 62	Total Statements 173	Complexity 61	TOTAL Coverage 0.41630941.6%
internalFrameClosed(InternalFrameEvent) : void   internalFrameClosed(InternalFrameEvent) : void	103103	1.01	1.01	1.0 1.0100%
PCAPanel(AlignmentPanel,String,SimilarityParamsI)   PCAPanel(AlignmentPanel,String,SimilarityParamsI)	9191	19.019	2.02	0.9047619 0.904761990.5%
close_actionPerformed() : void   close_actionPerformed() : void	140140	1.01	1.01	1.0 1.0100%
colourSelected(Color) : void   colourSelected(Color) : void	151151	2.02	1.01	0.0 0.00%
bgcolour_actionPerformed() : void   bgcolour_actionPerformed() : void	145145	3.03	1.01	0.0 0.00%
run() : void   run() : void	165165	24.024	4.04	0.8214286 0.821428682.1%
doDimensionChange() : void   doDimensionChange() : void	216216	7.07	2.02	0.33333334 0.3333333433.3%
setSelectedDimensionIndex(int,Axis) : void   setSelectedDimensionIndex(int,Axis) : void	238238	11.011	4.04	0.90909094 0.9090909490.9%
outputValues_actionPerformed() : void   outputValues_actionPerformed() : void	255255	6.06	2.02	0.0 0.00%
showLabels_actionPerformed() : void   showLabels_actionPerformed() : void	271271	1.01	1.01	0.0 0.00%
print_actionPerformed() : void   print_actionPerformed() : void	277277	2.02	1.01	0.0 0.00%
originalSeqData_actionPerformed() : void   originalSeqData_actionPerformed() : void	288288	15.015	8.08	0.0 0.00%
exportImage(Graphics) : void   exportImage(Graphics) : void	420420	5.05	2.02	0.0 0.00%
makePCAImage(ImageMaker.TYPE) : void   makePCAImage(ImageMaker.TYPE) : void	414414	6.06	1.01	0.0 0.00%
viewMenu_menuSelected() : void   viewMenu_menuSelected() : void	437437	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	479479	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	497497	1.01	1.01	0.0 0.00%
buildAssociatedViewMenu() : void   buildAssociatedViewMenu() : void	447447	22.022	5.05	0.0 0.00%
outputPoints_actionPerformed() : void   outputPoints_actionPerformed() : void	514514	6.06	2.02	0.0 0.00%
outputProjPoints_actionPerformed() : void   outputProjPoints_actionPerformed() : void	540540	6.06	2.02	0.0 0.00%
setProgressBar(String,long) : void   setProgressBar(String,long) : void	564564	1.01	1.01	0.0 0.00%
registerHandler(long,IProgressIndicatorHandler) : void   registerHandler(long,IProgressIndicatorHandler) : void	613613	1.01	1.01	0.0 0.00%
operationInProgress() : boolean   operationInProgress() : boolean	649649	1.01	1.01	0.0 0.00%
resetButton_actionPerformed() : void   resetButton_actionPerformed() : void	655655	6.06	1.01	0.0 0.00%
isWorking() : boolean   isWorking() : boolean	671671	1.01	1.01	0.0 0.00%
getSelectedDimensionIndex(Axis) : int   getSelectedDimensionIndex(Axis) : int	683683	7.07	3.03	1.0 1.0100%
setShowLabels(boolean) : void   setShowLabels(boolean) : void	696696	1.01	1.01	1.0 1.0100%
setInputData(AlignmentView) : void   setInputData(AlignmentView) : void	708708	2.02	1.01	1.0 1.0100%
getAlignViewport() : AlignViewportI   getAlignViewport() : AlignViewportI	714714	1.01	1.01	1.0 1.0100%
getPcaModel() : PCAModel   getPcaModel() : PCAModel	719719	1.01	1.01	1.0 1.0100%
setPcaModel(PCAModel) : void   setPcaModel(PCAModel) : void	724724	1.01	1.01	1.0 1.0100%
getRotatableCanvas() : RotatableCanvas   getRotatableCanvas() : RotatableCanvas	729729	1.01	1.01	1.0 1.0100%
setRotatableCanvas(RotatableCanvas) : void   setRotatableCanvas(RotatableCanvas) : void	734734	1.01	1.01	1.0 1.0100%
getTop() : int   getTop() : int	739739	1.01	1.01	1.0 1.0100%
setTop(int) : void   setTop(int) : void	744744	1.01	1.01	1.0 1.0100%
selectAssociatedView(AlignmentPanel) : void   selectAssociatedView(AlignmentPanel) : void	754754	6.06	1.01	1.0 1.0100%

 

Class PCAPanel.PCAPrinter

Class PCAPanel.PCAPrinter	Line # 359	Total Statements 18	Complexity 7	TOTAL Coverage 0.00%
run() : void   run() : void	361361	10.010	4.04	0.0 0.00%
print(Graphics,PageFormat,int) : int   print(Graphics,PageFormat,int) : int	390390	8.08	3.03	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.3716475	jalview.project.Jalview2xmlTests.testPcaViewAssociationjalview.project.Jalview2xmlTests.testPcaViewAssociation	1PASS
	0.022988506	jalview.project.Jalview2xmlTests.testStoreAndRecoverColourThresholdsjalview.project.Jalview2xmlTests.testStoreAndRecoverColourThresholds	1PASS
	0.007662835	jalview.project.Jalview2xmlTests.testSaveLoadFeatureColoursAndFiltersjalview.project.Jalview2xmlTests.testSaveLoadFeatureColoursAndFilters	1PASS
	0.007662835	jalview.project.Jalview2xmlTests.testRNAStructureRecoveryjalview.project.Jalview2xmlTests.testRNAStructureRecovery	1PASS

 

Source view

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.api.AlignViewportI;
25		import jalview.api.analysis.ScoreModelI;
26		import jalview.api.analysis.SimilarityParamsI;
27		import jalview.bin.Cache;
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.PCAModel;
41
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;
52
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;
58
59		/**
60		* The panel holding the Principal Component Analysis 3-D visualisation
61		*/
		41.6% Uncovered Elements: 136 (233) Complexity: 61 Complexity Density: 0.35
62		public class PCAPanel extends GPCAPanel
63		implements Runnable, IProgressIndicator
64		{
65		private static final int MIN_WIDTH = 470;
66
67		private static final int MIN_HEIGHT = 250;
68
69		private RotatableCanvas rc;
70
71		AlignmentPanel ap;
72
73		AlignmentViewport av;
74
75		private PCAModel pcaModel;
76
77		private int top = 0;
78
79		private IProgressIndicator progressBar;
80
81		private boolean working;
82
83		/**
84		* Constructor given sequence data, a similarity (or distance) score model
85		* name, and score calculation parameters
86		*
87		* @param alignPanel
88		* @param modelName
89		* @param params
90		*/
		90.5% Uncovered Elements: 2 (21) Complexity: 2 Complexity Density: 0.11
91	2	public PCAPanel(AlignmentPanel alignPanel, String modelName,...
92		SimilarityParamsI params)
93		{
94	2	super();
95	2	this.av = alignPanel.av;
96	2	this.ap = alignPanel;
97	2	boolean nucleotide = av.getAlignment().isNucleotide();
98
99	2	progressBar = new ProgressBar(statusPanel, statusBar);
100
101	2	addInternalFrameListener(new InternalFrameAdapter()
102		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
103	2	@Override...
104		public void internalFrameClosed(InternalFrameEvent e)
105		{
106	2	close_actionPerformed();
107		}
108		});
109
110	2	boolean selected = av.getSelectionGroup() != null
111		&& av.getSelectionGroup().getSize() > 0;
112	2	AlignmentView seqstrings = av.getAlignmentView(selected);
113	2	SequenceI[] seqs;
114	2	if (!selected)
115		{
116	2	seqs = av.getAlignment().getSequencesArray();
117		}
118		else
119		{
120	0	seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
121		}
122
123	2	ScoreModelI scoreModel = ScoreModels.getInstance()
124		.getScoreModel(modelName, ap);
125	2	setPcaModel(new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
126		params));
127	2	PaintRefresher.Register(this, av.getSequenceSetId());
128
129	2	setRotatableCanvas(new RotatableCanvas(alignPanel));
130	2	this.getContentPane().add(getRotatableCanvas(), BorderLayout.CENTER);
131
132	2	addKeyListener(getRotatableCanvas());
133	2	validate();
134		}
135
136		/**
137		* Ensure references to potentially very large objects (the PCA matrices) are
138		* nulled when the frame is closed
139		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
140	2	protected void close_actionPerformed()...
141		{
142	2	setPcaModel(null);
143		}
144
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
145	0	@Override...
146		protected void bgcolour_actionPerformed()
147		{
148	0	String ttl = MessageManager.getString("label.select_background_colour");
149	0	ColourChooserListener listener = new ColourChooserListener()
150		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
151	0	@Override...
152		public void colourSelected(Color c)
153		{
154	0	rc.setBgColour(c);
155	0	rc.repaint();
156		}
157		};
158	0	JalviewColourChooser.showColourChooser(this, ttl, rc.getBgColour(),
159		listener);
160		}
161
162		/**
163		* Calculates the PCA and displays the results
164		*/
		82.1% Uncovered Elements: 5 (28) Complexity: 4 Complexity Density: 0.17
165	1	@Override...
166		public void run()
167		{
168	1	working = true;
169	1	long progId = System.currentTimeMillis();
170	1	IProgressIndicator progress = this;
171	1	String message = MessageManager.getString("label.pca_recalculating");
172	1	if (getParent() == null)
173		{
174	1	progress = ap.alignFrame;
175	1	message = MessageManager.getString("label.pca_calculating");
176		}
177	1	progress.setProgressBar(message, progId);
178	1	try
179		{
180	1	getPcaModel().calculate();
181
182	1	xCombobox.setSelectedIndex(0);
183	1	yCombobox.setSelectedIndex(1);
184	1	zCombobox.setSelectedIndex(2);
185
186	1	getPcaModel().updateRc(getRotatableCanvas());
187		// rc.invalidate();
188	1	setTop(getPcaModel().getTop());
189
190		} catch (OutOfMemoryError er)
191		{
192	0	new OOMWarning("calculating PCA", er);
193	0	working = false;
194	0	return;
195		} finally
196		{
197	1	progress.setProgressBar("", progId);
198		}
199
200	1	repaint();
201	1	if (getParent() == null)
202		{
203	1	Desktop.addInternalFrame(this,
204		MessageManager.formatMessage("label.calc_title", "PCA",
205		getPcaModel().getScoreModelName()),
206		475, 450);
207	1	this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
208		}
209	1	working = false;
210		}
211
212		/**
213		* Updates the PCA display after a change of component to use for x, y or z
214		* axis
215		*/
		33.3% Uncovered Elements: 6 (9) Complexity: 2 Complexity Density: 0.29
216	12	@Override...
217		protected void doDimensionChange()
218		{
219	12	if (getTop() == 0)
220		{
221	12	return;
222		}
223
224	0	int dim1 = getTop() - xCombobox.getSelectedIndex();
225	0	int dim2 = getTop() - yCombobox.getSelectedIndex();
226	0	int dim3 = getTop() - zCombobox.getSelectedIndex();
227	0	getPcaModel().updateRcView(dim1, dim2, dim3);
228	0	getRotatableCanvas().resetView();
229		}
230
231		/**
232		* Sets the selected checkbox item index for PCA dimension (1, 2, 3...) for
233		* the given axis (X/Y/Z)
234		*
235		* @param index
236		* @param axis
237		*/
		90.9% Uncovered Elements: 1 (11) Complexity: 4 Complexity Density: 0.36
238	3	public void setSelectedDimensionIndex(int index, Axis axis)...
239		{
240	3	switch (axis)
241		{
242	1	case X:
243	1	xCombobox.setSelectedIndex(index);
244	1	break;
245	1	case Y:
246	1	yCombobox.setSelectedIndex(index);
247	1	break;
248	1	case Z:
249	1	zCombobox.setSelectedIndex(index);
250	1	break;
251	0	default:
252		}
253		}
254
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.33
255	0	@Override...
256		protected void outputValues_actionPerformed()
257		{
258	0	CutAndPasteTransfer cap = new CutAndPasteTransfer();
259	0	try
260		{
261	0	cap.setText(getPcaModel().getDetails());
262	0	Desktop.addInternalFrame(cap,
263		MessageManager.getString("label.pca_details"), 500, 500);
264		} catch (OutOfMemoryError oom)
265		{
266	0	new OOMWarning("opening PCA details", oom);
267	0	cap.dispose();
268		}
269		}
270
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
271	0	@Override...
272		protected void showLabels_actionPerformed()
273		{
274	0	getRotatableCanvas().showLabels(showLabels.getState());
275		}
276
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
277	0	@Override...
278		protected void print_actionPerformed()
279		{
280	0	PCAPrinter printer = new PCAPrinter();
281	0	printer.start();
282		}
283
284		/**
285		* If available, shows the data which formed the inputs for the PCA as a new
286		* alignment
287		*/
		0% Uncovered Elements: 23 (23) Complexity: 8 Complexity Density: 0.53
288	0	@Override...
289		public void originalSeqData_actionPerformed()
290		{
291		// JAL-2647 disabled after load from project (until save to project done)
292	0	if (getPcaModel().getInputData() == null)
293		{
294	0	Cache.log.info(
295		"Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
296	0	return;
297		}
298		// decide if av alignment is sufficiently different to original data to
299		// warrant a new window to be created
300		// create new alignment window with hidden regions (unhiding hidden regions
301		// yields unaligned seqs)
302		// or create a selection box around columns in alignment view
303		// test Alignment(SeqCigar[])
304	0	char gc = '-';
305	0	try
306		{
307		// we try to get the associated view's gap character
308		// but this may fail if the view was closed...
309	0	gc = av.getGapCharacter();
310		} catch (Exception ex)
311		{
312		}
313
314	0	Object[] alAndColsel = getPcaModel().getInputData()
315		.getAlignmentAndHiddenColumns(gc);
316
317	0	if (alAndColsel != null && alAndColsel[0] != null)
318		{
319		// AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
320
321	0	AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
322	0	AlignmentI dataset = (av != null && av.getAlignment() != null)
323		? av.getAlignment().getDataset()
324		: null;
325	0	if (dataset != null)
326		{
327	0	al.setDataset(dataset);
328		}
329
330	0	if (true)
331		{
332		// make a new frame!
333	0	AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
334		AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
335
336		// >>>This is a fix for the moment, until a better solution is
337		// found!!<<<
338		// af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
339
340		// af.addSortByOrderMenuItem(ServiceName + " Ordering",
341		// msaorder);
342
343	0	Desktop.addInternalFrame(af, MessageManager.formatMessage(
344		"label.original_data_for_params", new String[]
345		{ this.title }), AlignFrame.DEFAULT_WIDTH,
346		AlignFrame.DEFAULT_HEIGHT);
347		}
348		}
349		/*
350		* CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
351		* seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
352		* "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
353		* "\n"); }
354		*
355		* Desktop.addInternalFrame(cap, "Original Data", 400, 400);
356		*/
357		}
358
		0% Uncovered Elements: 28 (28) Complexity: 7 Complexity Density: 0.39
359		class PCAPrinter extends Thread implements Printable
360		{
		0% Uncovered Elements: 14 (14) Complexity: 4 Complexity Density: 0.4
361	0	@Override...
362		public void run()
363		{
364	0	PrinterJob printJob = PrinterJob.getPrinterJob();
365	0	PageFormat defaultPage = printJob.defaultPage();
366	0	PageFormat pf = printJob.pageDialog(defaultPage);
367
368	0	if (defaultPage == pf)
369		{
370		/*
371		* user cancelled
372		*/
373	0	return;
374		}
375
376	0	printJob.setPrintable(this, pf);
377
378	0	if (printJob.printDialog())
379		{
380	0	try
381		{
382	0	printJob.print();
383		} catch (Exception PrintException)
384		{
385	0	PrintException.printStackTrace();
386		}
387		}
388		}
389
		0% Uncovered Elements: 12 (12) Complexity: 3 Complexity Density: 0.38
390	0	@Override...
391		public int print(Graphics pg, PageFormat pf, int pi)
392		throws PrinterException
393		{
394	0	pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
395
396	0	getRotatableCanvas().drawBackground(pg);
397	0	getRotatableCanvas().drawScene(pg);
398	0	if (getRotatableCanvas().drawAxes)
399		{
400	0	getRotatableCanvas().drawAxes(pg);
401		}
402
403	0	if (pi == 0)
404		{
405	0	return Printable.PAGE_EXISTS;
406		}
407		else
408		{
409	0	return Printable.NO_SUCH_PAGE;
410		}
411		}
412		}
413
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17
414	0	public void makePCAImage(ImageMaker.TYPE type)...
415		{
416	0	int width = getRotatableCanvas().getWidth();
417	0	int height = getRotatableCanvas().getHeight();
418	0	ImageWriterI writer = new ImageWriterI()
419		{
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
420	0	@Override...
421		public void exportImage(Graphics g) throws Exception
422		{
423	0	RotatableCanvas canvas = getRotatableCanvas();
424	0	canvas.drawBackground(g);
425	0	canvas.drawScene(g);
426	0	if (canvas.drawAxes)
427		{
428	0	canvas.drawAxes(g);
429		}
430		}
431		};
432	0	String pca = MessageManager.getString("label.pca");
433	0	ImageExporter exporter = new ImageExporter(writer, null, type, pca);
434	0	exporter.doExport(null, this, width, height, pca);
435		}
436
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
437	0	@Override...
438		protected void viewMenu_menuSelected()
439		{
440	0	buildAssociatedViewMenu();
441		}
442
443		/**
444		* Builds the menu showing the choice of possible views (for the associated
445		* sequence data) to which the PCA may be linked
446		*/
		0% Uncovered Elements: 28 (28) Complexity: 5 Complexity Density: 0.23
447	0	void buildAssociatedViewMenu()...
448		{
449	0	AlignmentPanel[] aps = PaintRefresher
450		.getAssociatedPanels(av.getSequenceSetId());
451	0	if (aps.length == 1 && getRotatableCanvas().av == aps[0].av)
452		{
453	0	associateViewsMenu.setVisible(false);
454	0	return;
455		}
456
457	0	associateViewsMenu.setVisible(true);
458
459	0	if ((viewMenu
460		.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
461		{
462	0	viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
463		}
464
465	0	associateViewsMenu.removeAll();
466
467	0	JRadioButtonMenuItem item;
468	0	ButtonGroup buttonGroup = new ButtonGroup();
469	0	int iSize = aps.length;
470
471	0	for (int i = 0; i < iSize; i++)
472		{
473	0	final AlignmentPanel panel = aps[i];
474	0	item = new JRadioButtonMenuItem(panel.av.getViewName(),
475		panel.av == getRotatableCanvas().av);
476	0	buttonGroup.add(item);
477	0	item.addActionListener(new ActionListener()
478		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
479	0	@Override...
480		public void actionPerformed(ActionEvent evt)
481		{
482	0	selectAssociatedView(panel);
483		}
484		});
485
486	0	associateViewsMenu.add(item);
487		}
488
489	0	final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
490		"All Views");
491
492	0	buttonGroup.add(itemf);
493
494	0	itemf.setSelected(getRotatableCanvas().isApplyToAllViews());
495	0	itemf.addActionListener(new ActionListener()
496		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
497	0	@Override...
498		public void actionPerformed(ActionEvent evt)
499		{
500	0	getRotatableCanvas().setApplyToAllViews(itemf.isSelected());
501		}
502		});
503	0	associateViewsMenu.add(itemf);
504
505		}
506
507		/*
508		* (non-Javadoc)
509		*
510		* @see
511		* jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
512		* )
513		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.33
514	0	@Override...
515		protected void outputPoints_actionPerformed()
516		{
517	0	CutAndPasteTransfer cap = new CutAndPasteTransfer();
518	0	try
519		{
520	0	cap.setText(getPcaModel().getPointsasCsv(false,
521		xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
522		zCombobox.getSelectedIndex()));
523	0	Desktop.addInternalFrame(cap, MessageManager
524		.formatMessage("label.points_for_params", new String[]
525		{ this.getTitle() }), 500, 500);
526		} catch (OutOfMemoryError oom)
527		{
528	0	new OOMWarning("exporting PCA points", oom);
529	0	cap.dispose();
530		}
531		}
532
533		/*
534		* (non-Javadoc)
535		*
536		* @see
537		* jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
538		* .ActionEvent)
539		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.33
540	0	@Override...
541		protected void outputProjPoints_actionPerformed()
542		{
543	0	CutAndPasteTransfer cap = new CutAndPasteTransfer();
544	0	try
545		{
546	0	cap.setText(getPcaModel().getPointsasCsv(true,
547		xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
548		zCombobox.getSelectedIndex()));
549	0	Desktop.addInternalFrame(cap, MessageManager.formatMessage(
550		"label.transformed_points_for_params", new String[]
551		{ this.getTitle() }), 500, 500);
552		} catch (OutOfMemoryError oom)
553		{
554	0	new OOMWarning("exporting transformed PCA points", oom);
555	0	cap.dispose();
556		}
557		}
558
559		/*
560		* (non-Javadoc)
561		*
562		* @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
563		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
564	0	@Override...
565		public void setProgressBar(String message, long id)
566		{
567	0	progressBar.setProgressBar(message, id);
568		// if (progressBars == null)
569		// {
570		// progressBars = new Hashtable();
571		// progressBarHandlers = new Hashtable();
572		// }
573		//
574		// JPanel progressPanel;
575		// Long lId = Long.valueOf(id);
576		// GridLayout layout = (GridLayout) statusPanel.getLayout();
577		// if (progressBars.get(lId) != null)
578		// {
579		// progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
580		// statusPanel.remove(progressPanel);
581		// progressBars.remove(lId);
582		// progressPanel = null;
583		// if (message != null)
584		// {
585		// statusBar.setText(message);
586		// }
587		// if (progressBarHandlers.contains(lId))
588		// {
589		// progressBarHandlers.remove(lId);
590		// }
591		// layout.setRows(layout.getRows() - 1);
592		// }
593		// else
594		// {
595		// progressPanel = new JPanel(new BorderLayout(10, 5));
596		//
597		// JProgressBar progressBar = new JProgressBar();
598		// progressBar.setIndeterminate(true);
599		//
600		// progressPanel.add(new JLabel(message), BorderLayout.WEST);
601		// progressPanel.add(progressBar, BorderLayout.CENTER);
602		//
603		// layout.setRows(layout.getRows() + 1);
604		// statusPanel.add(progressPanel);
605		//
606		// progressBars.put(lId, progressPanel);
607		// }
608		// // update GUI
609		// // setMenusForViewport();
610		// validate();
611		}
612
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
613	0	@Override...
614		public void registerHandler(final long id,
615		final IProgressIndicatorHandler handler)
616		{
617	0	progressBar.registerHandler(id, handler);
618		// if (progressBarHandlers == null || !progressBars.contains(Long.valueOf(id)))
619		// {
620		// throw new
621		// Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
622		// }
623		// progressBarHandlers.put(Long.valueOf(id), handler);
624		// final JPanel progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
625		// if (handler.canCancel())
626		// {
627		// JButton cancel = new JButton(
628		// MessageManager.getString("action.cancel"));
629		// final IProgressIndicator us = this;
630		// cancel.addActionListener(new ActionListener()
631		// {
632		//
633		// @Override
634		// public void actionPerformed(ActionEvent e)
635		// {
636		// handler.cancelActivity(id);
637		// us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
638		// new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
639		// }
640		// });
641		// progressPanel.add(cancel, BorderLayout.EAST);
642		// }
643		}
644
645		/**
646		*
647		* @return true if any progress bars are still active
648		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
649	0	@Override...
650		public boolean operationInProgress()
651		{
652	0	return progressBar.operationInProgress();
653		}
654
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17
655	0	@Override...
656		protected void resetButton_actionPerformed()
657		{
658	0	int t = getTop();
659	0	setTop(0); // ugly - prevents dimensionChanged events from being processed
660	0	xCombobox.setSelectedIndex(0);
661	0	yCombobox.setSelectedIndex(1);
662	0	setTop(t);
663	0	zCombobox.setSelectedIndex(2);
664		}
665
666		/**
667		* Answers true if PCA calculation is in progress, else false
668		*
669		* @return
670		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
671	0	public boolean isWorking()...
672		{
673	0	return working;
674		}
675
676		/**
677		* Answers the selected checkbox item index for PCA dimension for the X, Y or
678		* Z axis of the display
679		*
680		* @param axis
681		* @return
682		*/
		100% Uncovered Elements: 0 (7) Complexity: 3 Complexity Density: 0.43
683	3	public int getSelectedDimensionIndex(Axis axis)...
684		{
685	3	switch (axis)
686		{
687	1	case X:
688	1	return xCombobox.getSelectedIndex();
689	1	case Y:
690	1	return yCombobox.getSelectedIndex();
691	1	default:
692	1	return zCombobox.getSelectedIndex();
693		}
694		}
695
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
696	1	public void setShowLabels(boolean show)...
697		{
698	1	showLabels.setSelected(show);
699		}
700
701		/**
702		* Sets the input data used to calculate the PCA. This is provided for
703		* 'restore from project', which does not currently support this (AL-2647), so
704		* sets the value to null, and hides the menu option for "Input Data...". J
705		*
706		* @param data
707		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
708	1	public void setInputData(AlignmentView data)...
709		{
710	1	getPcaModel().setInputData(data);
711	1	originalSeqData.setVisible(data != null);
712		}
713
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
714	10	public AlignViewportI getAlignViewport()...
715		{
716	10	return av;
717		}
718
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
719	9	public PCAModel getPcaModel()...
720		{
721	9	return pcaModel;
722		}
723
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
724	4	public void setPcaModel(PCAModel pcaModel)...
725		{
726	4	this.pcaModel = pcaModel;
727		}
728
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
729	24	public RotatableCanvas getRotatableCanvas()...
730		{
731	24	return rc;
732		}
733
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
734	2	public void setRotatableCanvas(RotatableCanvas rc)...
735		{
736	2	this.rc = rc;
737		}
738
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
739	12	public int getTop()...
740		{
741	12	return top;
742		}
743
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
744	2	public void setTop(int top)...
745		{
746	2	this.top = top;
747		}
748
749		/**
750		* set the associated view for this PCA.
751		*
752		* @param panel
753		*/
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17
754	1	public void selectAssociatedView(AlignmentPanel panel)...
755		{
756	1	getRotatableCanvas().setApplyToAllViews(false);
757
758	1	ap = panel;
759	1	av = panel.av;
760
761	1	getRotatableCanvas().av = panel.av;
762	1	getRotatableCanvas().ap = panel;
763	1	PaintRefresher.Register(PCAPanel.this, panel.av.getSequenceSetId());
764		}
765		}