Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PCAPanel	67	191	70	0.4176245341.8%	Show methods
PCAPanel.PCAPrinter	386	18	7	0.00%	Show methods

Class PCAPanel

Class PCAPanel	Line # 67	Total Statements 191	Complexity 70	TOTAL Coverage 0.4176245341.8%
internalFrameClosed(InternalFrameEvent) : void   internalFrameClosed(InternalFrameEvent) : void	110110	1.01	1.01	1.0 1.0100%
PCAPanel(AlignmentPanel,String,SimilarityParamsI)   PCAPanel(AlignmentPanel,String,SimilarityParamsI)	9797	24.024	3.03	0.8214286 0.821428682.1%
close_actionPerformed() : void   close_actionPerformed() : void	164164	5.05	2.02	0.85714287 0.8571428785.7%
colourSelected(Color) : void   colourSelected(Color) : void	181181	2.02	1.01	0.0 0.00%
bgcolour_actionPerformed() : void   bgcolour_actionPerformed() : void	175175	3.03	1.01	0.0 0.00%
run() : void   run() : void	195195	24.024	4.04	0.8214286 0.821428682.1%
doDimensionChange() : void   doDimensionChange() : void	243243	7.07	2.02	0.33333334 0.3333333433.3%
setSelectedDimensionIndex(int,Axis) : void   setSelectedDimensionIndex(int,Axis) : void	265265	11.011	4.04	0.90909094 0.9090909490.9%
outputValues_actionPerformed() : void   outputValues_actionPerformed() : void	282282	6.06	2.02	0.0 0.00%
showLabels_actionPerformed() : void   showLabels_actionPerformed() : void	298298	1.01	1.01	0.0 0.00%
print_actionPerformed() : void   print_actionPerformed() : void	304304	2.02	1.01	0.0 0.00%
originalSeqData_actionPerformed() : void   originalSeqData_actionPerformed() : void	315315	15.015	8.08	0.0 0.00%
exportImage(Graphics) : void   exportImage(Graphics) : void	447447	5.05	2.02	0.0 0.00%
makePCAImage(ImageMaker.TYPE) : void   makePCAImage(ImageMaker.TYPE) : void	441441	8.08	2.02	0.0 0.00%
viewMenu_menuSelected() : void   viewMenu_menuSelected() : void	471471	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	513513	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	531531	1.01	1.01	0.0 0.00%
buildAssociatedViewMenu() : void   buildAssociatedViewMenu() : void	481481	22.022	5.05	0.0 0.00%
outputPoints_actionPerformed() : void   outputPoints_actionPerformed() : void	548548	6.06	2.02	0.0 0.00%
outputProjPoints_actionPerformed() : void   outputProjPoints_actionPerformed() : void	574574	6.06	2.02	0.0 0.00%
setProgressBar(String,long) : void   setProgressBar(String,long) : void	598598	1.01	1.01	0.0 0.00%
addProgressBar(long,String) : void   addProgressBar(long,String) : void	647647	1.01	1.01	0.0 0.00%
removeProgressBar(long) : void   removeProgressBar(long) : void	653653	1.01	1.01	0.0 0.00%
registerHandler(long,IProgressIndicatorHandler) : void   registerHandler(long,IProgressIndicatorHandler) : void	659659	1.01	1.01	0.0 0.00%
operationInProgress() : boolean   operationInProgress() : boolean	696696	1.01	1.01	0.0 0.00%
resetButton_actionPerformed() : void   resetButton_actionPerformed() : void	702702	6.06	1.01	0.0 0.00%
isWorking() : boolean   isWorking() : boolean	718718	1.01	1.01	0.0 0.00%
getSelectedDimensionIndex(Axis) : int   getSelectedDimensionIndex(Axis) : int	730730	7.07	3.03	1.0 1.0100%
setShowLabels(boolean) : void   setShowLabels(boolean) : void	743743	1.01	1.01	1.0 1.0100%
setInputData(AlignmentView) : void   setInputData(AlignmentView) : void	755755	2.02	1.01	1.0 1.0100%
getAlignViewport() : AlignViewportI   getAlignViewport() : AlignViewportI	761761	1.01	1.01	1.0 1.0100%
getPcaModel() : PCAModel   getPcaModel() : PCAModel	766766	1.01	1.01	1.0 1.0100%
setPcaModel(PCAModel) : void   setPcaModel(PCAModel) : void	771771	1.01	1.01	1.0 1.0100%
getRotatableCanvas() : RotatableCanvas   getRotatableCanvas() : RotatableCanvas	776776	1.01	1.01	1.0 1.0100%
setRotatableCanvas(RotatableCanvas) : void   setRotatableCanvas(RotatableCanvas) : void	781781	1.01	1.01	1.0 1.0100%
getTop() : int   getTop() : int	786786	1.01	1.01	1.0 1.0100%
setTop(int) : void   setTop(int) : void	791791	1.01	1.01	1.0 1.0100%
selectAssociatedView(AlignmentPanel) : void   selectAssociatedView(AlignmentPanel) : void	801801	6.06	1.01	1.0 1.0100%
getProgressBar(long) : JProgressBar   getProgressBar(long) : JProgressBar	813813	1.01	1.01	0.0 0.00%
getMessage(long) : String   getMessage(long) : String	819819	1.01	1.01	0.0 0.00%
setProgressBarMessage(long,String) : void   setProgressBarMessage(long,String) : void	824824	1.01	1.01	0.0 0.00%
addToDesktop(PCAPanel,String) : void   addToDesktop(PCAPanel,String) : void	829829	2.02	1.01	1.0 1.0100%

 

Class PCAPanel.PCAPrinter

Class PCAPanel.PCAPrinter	Line # 386	Total Statements 18	Complexity 7	TOTAL Coverage 0.00%
run() : void   run() : void	388388	10.010	4.04	0.0 0.00%
print(Graphics,PageFormat,int) : int   print(Graphics,PageFormat,int) : int	417417	8.08	3.03	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.37716264	jalview.project.Jalview2xmlTests.testPcaViewAssociationjalview.project.Jalview2xmlTests.testPcaViewAssociation	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 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.JLabel;
36		import javax.swing.JMenuItem;
37		import javax.swing.JProgressBar;
38		import javax.swing.JRadioButtonMenuItem;
39		import javax.swing.SwingConstants;
40		import javax.swing.event.InternalFrameAdapter;
41		import javax.swing.event.InternalFrameEvent;
42
43		import jalview.analysis.scoremodels.ScoreModels;
44		import jalview.api.AlignViewportI;
45		import jalview.api.analysis.ScoreModelI;
46		import jalview.api.analysis.SimilarityParamsI;
47		import jalview.bin.Console;
48		import jalview.datamodel.Alignment;
49		import jalview.datamodel.AlignmentI;
50		import jalview.datamodel.AlignmentView;
51		import jalview.datamodel.HiddenColumns;
52		import jalview.datamodel.SequenceI;
53		import jalview.gui.ImageExporter.ImageWriterI;
54		import jalview.gui.JalviewColourChooser.ColourChooserListener;
55		import jalview.io.exceptions.ImageOutputException;
56		import jalview.jbgui.GPCAPanel;
57		import jalview.math.RotatableMatrix.Axis;
58		import jalview.util.ImageMaker;
59		import jalview.util.MessageManager;
60		import jalview.util.Platform;
61		import jalview.viewmodel.AlignmentViewport;
62		import jalview.viewmodel.PCAModel;
63
64		/**
65		* The panel holding the Principal Component Analysis 3-D visualisation
66		*/
		41.8% Uncovered Elements: 152 (261) Complexity: 70 Complexity Density: 0.37
67		public class PCAPanel extends GPCAPanel
68		implements Runnable, IProgressIndicator
69		{
70		private static final int MIN_WIDTH = 470;
71
72		private static final int MIN_HEIGHT = 250;
73
74		private RotatableCanvas rc;
75
76		AlignmentPanel ap;
77
78		AlignmentViewport av;
79
80		private PCAModel pcaModel;
81
82		private int top = 0;
83
84		private IProgressIndicator progressBar;
85
86		private boolean working;
87
88		String newPcaTitle = null;
89		/**
90		* Constructor given sequence data, a similarity (or distance) score model
91		* name, and score calculation parameters
92		*
93		* @param alignPanel
94		* @param modelName
95		* @param params
96		*/
		82.1% Uncovered Elements: 5 (28) Complexity: 3 Complexity Density: 0.12
97	2	public PCAPanel(AlignmentPanel alignPanel, String modelName,...
98		SimilarityParamsI params)
99		{
100	2	super();
101	2	this.setFrameIcon(null);
102	2	this.av = alignPanel.av;
103	2	this.ap = alignPanel;
104	2	boolean nucleotide = av.getAlignment().isNucleotide();
105
106	2	progressBar = new ProgressBar(statusPanel, statusBar);
107
108	2	addInternalFrameListener(new InternalFrameAdapter()
109		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
110	2	@Override...
111		public void internalFrameClosed(InternalFrameEvent e)
112		{
113	2	close_actionPerformed();
114		}
115		});
116
117	2	boolean selected = av.getSelectionGroup() != null
118		&& av.getSelectionGroup().getSize() > 0;
119	2	AlignmentView seqstrings = av.getAlignmentView(selected);
120	2	SequenceI[] seqs;
121	2	if (!selected)
122		{
123	2	seqs = av.getAlignment().getSequencesArray();
124		}
125		else
126		{
127	0	seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
128		}
129
130	2	ScoreModelI scoreModel = ScoreModels.getInstance()
131		.getScoreModel(modelName, ap);
132	2	setPcaModel(
133		new PCAModel(seqstrings, seqs, nucleotide, scoreModel, params));
134
135	2	newPcaTitle = alignPanel.alignFrame.formCalculationTitle(
136		MessageManager.formatMessage("label.calc_title", "PCA",
137		getPcaModel().getScoreModelName()),
138		selected, ap.alignFrame.getTitle());
139
140	2	PaintRefresher.Register(this, av.getSequenceSetId());
141
142	2	setRotatableCanvas(new RotatableCanvas(alignPanel));
143
144	2	if (params.getSecondaryStructureSource() != null)
145		{
146		// Initialize and set subtitle text
147	0	JLabel subtitleLabel = new JLabel(
148		" Secondary Structure Provider : "
149		+ params.getSecondaryStructureSource(),
150		SwingConstants.LEFT);
151	0	this.getContentPane().add(subtitleLabel, BorderLayout.NORTH);
152
153		}
154	2	this.getContentPane().add(getRotatableCanvas(), BorderLayout.CENTER);
155
156	2	addKeyListener(getRotatableCanvas());
157	2	validate();
158		}
159
160		/**
161		* Ensure references to potentially very large objects (the PCA matrices) are
162		* nulled when the frame is closed
163		*/
		85.7% Uncovered Elements: 1 (7) Complexity: 2 Complexity Density: 0.4
164	2	protected void close_actionPerformed()...
165		{
166	2	setPcaModel(null);
167	2	if (this.rc != null)
168		{
169	2	this.rc.sequencePoints = null;
170	2	this.rc.setAxisEndPoints(null);
171	2	this.rc = null;
172		}
173		}
174
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
175	0	@Override...
176		protected void bgcolour_actionPerformed()
177		{
178	0	String ttl = MessageManager.getString("label.select_background_colour");
179	0	ColourChooserListener listener = new ColourChooserListener()
180		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
181	0	@Override...
182		public void colourSelected(Color c)
183		{
184	0	rc.setBgColour(c);
185	0	rc.repaint();
186		}
187		};
188	0	JalviewColourChooser.showColourChooser(this, ttl, rc.getBgColour(),
189		listener);
190		}
191
192		/**
193		* Calculates the PCA and displays the results
194		*/
		82.1% Uncovered Elements: 5 (28) Complexity: 4 Complexity Density: 0.17
195	1	@Override...
196		public void run()
197		{
198	1	working = true;
199	1	long progId = System.currentTimeMillis();
200	1	IProgressIndicator progress = this;
201	1	String message = MessageManager.getString("label.pca_recalculating");
202	1	if (getParent() == null)
203		{
204	1	progress = ap.alignFrame;
205	1	message = MessageManager.getString("label.pca_calculating");
206		}
207	1	progress.setProgressBar(message, progId);
208	1	try
209		{
210	1	getPcaModel().calculate();
211
212	1	xCombobox.setSelectedIndex(0);
213	1	yCombobox.setSelectedIndex(1);
214	1	zCombobox.setSelectedIndex(2);
215
216	1	getPcaModel().updateRc(getRotatableCanvas());
217		// rc.invalidate();
218	1	setTop(getPcaModel().getTop());
219
220		} catch (OutOfMemoryError er)
221		{
222	0	new OOMWarning("calculating PCA", er);
223	0	working = false;
224	0	return;
225		} finally
226		{
227	1	progress.setProgressBar("", progId);
228		}
229
230	1	repaint();
231	1	if (getParent() == null)
232		{
233	1	addToDesktop(this, newPcaTitle);
234	1	this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
235		}
236	1	working = false;
237		}
238
239		/**
240		* Updates the PCA display after a change of component to use for x, y or z
241		* axis
242		*/
		33.3% Uncovered Elements: 6 (9) Complexity: 2 Complexity Density: 0.29
243	12	@Override...
244		protected void doDimensionChange()
245		{
246	12	if (getTop() == 0)
247		{
248	12	return;
249		}
250
251	0	int dim1 = getTop() - xCombobox.getSelectedIndex();
252	0	int dim2 = getTop() - yCombobox.getSelectedIndex();
253	0	int dim3 = getTop() - zCombobox.getSelectedIndex();
254	0	getPcaModel().updateRcView(dim1, dim2, dim3);
255	0	getRotatableCanvas().resetView();
256		}
257
258		/**
259		* Sets the selected checkbox item index for PCA dimension (1, 2, 3...) for
260		* the given axis (X/Y/Z)
261		*
262		* @param index
263		* @param axis
264		*/
		90.9% Uncovered Elements: 1 (11) Complexity: 4 Complexity Density: 0.36
265	3	public void setSelectedDimensionIndex(int index, Axis axis)...
266		{
267	3	switch (axis)
268		{
269	1	case X:
270	1	xCombobox.setSelectedIndex(index);
271	1	break;
272	1	case Y:
273	1	yCombobox.setSelectedIndex(index);
274	1	break;
275	1	case Z:
276	1	zCombobox.setSelectedIndex(index);
277	1	break;
278	0	default:
279		}
280		}
281
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.33
282	0	@Override...
283		protected void outputValues_actionPerformed()
284		{
285	0	CutAndPasteTransfer cap = new CutAndPasteTransfer();
286	0	try
287		{
288	0	cap.setText(getPcaModel().getDetails());
289	0	Desktop.addInternalFrame(cap,
290		MessageManager.getString("label.pca_details"), 500, 500);
291		} catch (OutOfMemoryError oom)
292		{
293	0	new OOMWarning("opening PCA details", oom);
294	0	cap.dispose();
295		}
296		}
297
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
298	0	@Override...
299		protected void showLabels_actionPerformed()
300		{
301	0	getRotatableCanvas().showLabels(showLabels.getState());
302		}
303
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
304	0	@Override...
305		protected void print_actionPerformed()
306		{
307	0	PCAPrinter printer = new PCAPrinter();
308	0	printer.start();
309		}
310
311		/**
312		* If available, shows the data which formed the inputs for the PCA as a new
313		* alignment
314		*/
		0% Uncovered Elements: 23 (23) Complexity: 8 Complexity Density: 0.53
315	0	@Override...
316		public void originalSeqData_actionPerformed()
317		{
318		// JAL-2647 disabled after load from project (until save to project done)
319	0	if (getPcaModel().getInputData() == null)
320		{
321	0	Console.info(
322		"Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
323	0	return;
324		}
325		// decide if av alignment is sufficiently different to original data to
326		// warrant a new window to be created
327		// create new alignment window with hidden regions (unhiding hidden regions
328		// yields unaligned seqs)
329		// or create a selection box around columns in alignment view
330		// test Alignment(SeqCigar[])
331	0	char gc = '-';
332	0	try
333		{
334		// we try to get the associated view's gap character
335		// but this may fail if the view was closed...
336	0	gc = av.getGapCharacter();
337		} catch (Exception ex)
338		{
339		}
340
341	0	Object[] alAndColsel = getPcaModel().getInputData()
342		.getAlignmentAndHiddenColumns(gc);
343
344	0	if (alAndColsel != null && alAndColsel[0] != null)
345		{
346		// AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
347
348	0	AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
349	0	AlignmentI dataset = (av != null && av.getAlignment() != null)
350		? av.getAlignment().getDataset()
351		: null;
352	0	if (dataset != null)
353		{
354	0	al.setDataset(dataset);
355		}
356
357	0	if (true)
358		{
359		// make a new frame!
360	0	AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
361		AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
362
363		// >>>This is a fix for the moment, until a better solution is
364		// found!!<<<
365		// af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
366
367		// af.addSortByOrderMenuItem(ServiceName + " Ordering",
368		// msaorder);
369
370	0	Desktop.addInternalFrame(af, MessageManager.formatMessage(
371		"label.original_data_for_params", new String[]
372		{ this.title }), AlignFrame.DEFAULT_WIDTH,
373		AlignFrame.DEFAULT_HEIGHT);
374		}
375		}
376		/*
377		* CutAndPasteTransfer cap = new CutAndPasteTransfer(); for (int i = 0; i <
378		* seqs.length; i++) { cap.appendText(new jalview.util.Format("%-" + 15 +
379		* "s").form( seqs[i].getName())); cap.appendText(" " + seqstrings[i] +
380		* "\n"); }
381		*
382		* Desktop.addInternalFrame(cap, "Original Data", 400, 400);
383		*/
384		}
385
		0% Uncovered Elements: 28 (28) Complexity: 7 Complexity Density: 0.39
386		class PCAPrinter extends Thread implements Printable
387		{
		0% Uncovered Elements: 14 (14) Complexity: 4 Complexity Density: 0.4
388	0	@Override...
389		public void run()
390		{
391	0	PrinterJob printJob = PrinterJob.getPrinterJob();
392	0	PageFormat defaultPage = printJob.defaultPage();
393	0	PageFormat pf = printJob.pageDialog(defaultPage);
394
395	0	if (defaultPage == pf)
396		{
397		/*
398		* user cancelled
399		*/
400	0	return;
401		}
402
403	0	printJob.setPrintable(this, pf);
404
405	0	if (printJob.printDialog())
406		{
407	0	try
408		{
409	0	printJob.print();
410		} catch (Exception PrintException)
411		{
412	0	PrintException.printStackTrace();
413		}
414		}
415		}
416
		0% Uncovered Elements: 12 (12) Complexity: 3 Complexity Density: 0.38
417	0	@Override...
418		public int print(Graphics pg, PageFormat pf, int pi)
419		throws PrinterException
420		{
421	0	pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
422
423	0	getRotatableCanvas().drawBackground(pg);
424	0	getRotatableCanvas().drawScene(pg);
425	0	if (getRotatableCanvas().drawAxes)
426		{
427	0	getRotatableCanvas().drawAxes(pg);
428		}
429
430	0	if (pi == 0)
431		{
432	0	return Printable.PAGE_EXISTS;
433		}
434		else
435		{
436	0	return Printable.NO_SUCH_PAGE;
437		}
438		}
439		}
440
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.25
441	0	public void makePCAImage(ImageMaker.TYPE type)...
442		{
443	0	int width = getRotatableCanvas().getWidth();
444	0	int height = getRotatableCanvas().getHeight();
445	0	ImageWriterI writer = new ImageWriterI()
446		{
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
447	0	@Override...
448		public void exportImage(Graphics g) throws Exception
449		{
450	0	RotatableCanvas canvas = getRotatableCanvas();
451	0	canvas.drawBackground(g);
452	0	canvas.drawScene(g);
453	0	if (canvas.drawAxes)
454		{
455	0	canvas.drawAxes(g);
456		}
457		}
458		};
459	0	String pca = MessageManager.getString("label.pca");
460	0	ImageExporter exporter = new ImageExporter(writer, null, type, pca);
461	0	try
462		{
463	0	exporter.doExport(null, this, width, height, pca);
464		} catch (ImageOutputException ioex)
465		{
466	0	Console.error("Unexpected error whilst writing " + type.toString(),
467		ioex);
468		}
469		}
470
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
471	0	@Override...
472		protected void viewMenu_menuSelected()
473		{
474	0	buildAssociatedViewMenu();
475		}
476
477		/**
478		* Builds the menu showing the choice of possible views (for the associated
479		* sequence data) to which the PCA may be linked
480		*/
		0% Uncovered Elements: 28 (28) Complexity: 5 Complexity Density: 0.23
481	0	void buildAssociatedViewMenu()...
482		{
483	0	AlignmentPanel[] aps = PaintRefresher
484		.getAssociatedPanels(av.getSequenceSetId());
485	0	if (aps.length == 1 && getRotatableCanvas().av == aps[0].av)
486		{
487	0	associateViewsMenu.setVisible(false);
488	0	return;
489		}
490
491	0	associateViewsMenu.setVisible(true);
492
493	0	if ((viewMenu
494		.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
495		{
496	0	viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
497		}
498
499	0	associateViewsMenu.removeAll();
500
501	0	JRadioButtonMenuItem item;
502	0	ButtonGroup buttonGroup = new ButtonGroup();
503	0	int iSize = aps.length;
504
505	0	for (int i = 0; i < iSize; i++)
506		{
507	0	final AlignmentPanel panel = aps[i];
508	0	item = new JRadioButtonMenuItem(panel.av.getViewName(),
509		panel.av == getRotatableCanvas().av);
510	0	buttonGroup.add(item);
511	0	item.addActionListener(new ActionListener()
512		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
513	0	@Override...
514		public void actionPerformed(ActionEvent evt)
515		{
516	0	selectAssociatedView(panel);
517		}
518		});
519
520	0	associateViewsMenu.add(item);
521		}
522
523	0	final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
524		"All Views");
525
526	0	buttonGroup.add(itemf);
527
528	0	itemf.setSelected(getRotatableCanvas().isApplyToAllViews());
529	0	itemf.addActionListener(new ActionListener()
530		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
531	0	@Override...
532		public void actionPerformed(ActionEvent evt)
533		{
534	0	getRotatableCanvas().setApplyToAllViews(itemf.isSelected());
535		}
536		});
537	0	associateViewsMenu.add(itemf);
538
539		}
540
541		/*
542		* (non-Javadoc)
543		*
544		* @see
545		* jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
546		* )
547		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.33
548	0	@Override...
549		protected void outputPoints_actionPerformed()
550		{
551	0	CutAndPasteTransfer cap = new CutAndPasteTransfer();
552	0	try
553		{
554	0	cap.setText(getPcaModel().getPointsasCsv(false,
555		xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
556		zCombobox.getSelectedIndex()));
557	0	Desktop.addInternalFrame(cap, MessageManager
558		.formatMessage("label.points_for_params", new String[]
559		{ this.getTitle() }), 500, 500);
560		} catch (OutOfMemoryError oom)
561		{
562	0	new OOMWarning("exporting PCA points", oom);
563	0	cap.dispose();
564		}
565		}
566
567		/*
568		* (non-Javadoc)
569		*
570		* @see
571		* jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
572		* .ActionEvent)
573		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.33
574	0	@Override...
575		protected void outputProjPoints_actionPerformed()
576		{
577	0	CutAndPasteTransfer cap = new CutAndPasteTransfer();
578	0	try
579		{
580	0	cap.setText(getPcaModel().getPointsasCsv(true,
581		xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
582		zCombobox.getSelectedIndex()));
583	0	Desktop.addInternalFrame(cap, MessageManager.formatMessage(
584		"label.transformed_points_for_params", new String[]
585		{ this.getTitle() }), 500, 500);
586		} catch (OutOfMemoryError oom)
587		{
588	0	new OOMWarning("exporting transformed PCA points", oom);
589	0	cap.dispose();
590		}
591		}
592
593		/*
594		* (non-Javadoc)
595		*
596		* @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
597		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
598	0	@Override...
599		public void setProgressBar(String message, long id)
600		{
601	0	progressBar.setProgressBar(message, id);
602		// if (progressBars == null)
603		// {
604		// progressBars = new Hashtable();
605		// progressBarHandlers = new Hashtable();
606		// }
607		//
608		// JPanel progressPanel;
609		// Long lId = Long.valueOf(id);
610		// GridLayout layout = (GridLayout) statusPanel.getLayout();
611		// if (progressBars.get(lId) != null)
612		// {
613		// progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
614		// statusPanel.remove(progressPanel);
615		// progressBars.remove(lId);
616		// progressPanel = null;
617		// if (message != null)
618		// {
619		// statusBar.setText(message);
620		// }
621		// if (progressBarHandlers.contains(lId))
622		// {
623		// progressBarHandlers.remove(lId);
624		// }
625		// layout.setRows(layout.getRows() - 1);
626		// }
627		// else
628		// {
629		// progressPanel = new JPanel(new BorderLayout(10, 5));
630		//
631		// JProgressBar progressBar = new JProgressBar();
632		// progressBar.setIndeterminate(true);
633		//
634		// progressPanel.add(new JLabel(message), BorderLayout.WEST);
635		// progressPanel.add(progressBar, BorderLayout.CENTER);
636		//
637		// layout.setRows(layout.getRows() + 1);
638		// statusPanel.add(progressPanel);
639		//
640		// progressBars.put(lId, progressPanel);
641		// }
642		// // update GUI
643		// // setMenusForViewport();
644		// validate();
645		}
646
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
647	0	@Override...
648		public void addProgressBar(long id, String message)
649		{
650	0	progressBar.addProgressBar(id, message);
651		}
652
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
653	0	@Override...
654		public void removeProgressBar(long id)
655		{
656	0	progressBar.removeProgressBar(id);
657		}
658
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
659	0	@Override...
660		public void registerHandler(final long id,
661		final IProgressIndicatorHandler handler)
662		{
663	0	progressBar.registerHandler(id, handler);
664		// if (progressBarHandlers == null ||
665		// !progressBars.contains(Long.valueOf(id)))
666		// {
667		// throw new
668		// Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
669		// }
670		// progressBarHandlers.put(Long.valueOf(id), handler);
671		// final JPanel progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
672		// if (handler.canCancel())
673		// {
674		// JButton cancel = new JButton(
675		// MessageManager.getString("action.cancel"));
676		// final IProgressIndicator us = this;
677		// cancel.addActionListener(new ActionListener()
678		// {
679		//
680		// @Override
681		// public void actionPerformed(ActionEvent e)
682		// {
683		// handler.cancelActivity(id);
684		// us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
685		// new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
686		// }
687		// });
688		// progressPanel.add(cancel, BorderLayout.EAST);
689		// }
690		}
691
692		/**
693		*
694		* @return true if any progress bars are still active
695		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
696	0	@Override...
697		public boolean operationInProgress()
698		{
699	0	return progressBar.operationInProgress();
700		}
701
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17
702	0	@Override...
703		protected void resetButton_actionPerformed()
704		{
705	0	int t = getTop();
706	0	setTop(0); // ugly - prevents dimensionChanged events from being processed
707	0	xCombobox.setSelectedIndex(0);
708	0	yCombobox.setSelectedIndex(1);
709	0	setTop(t);
710	0	zCombobox.setSelectedIndex(2);
711		}
712
713		/**
714		* Answers true if PCA calculation is in progress, else false
715		*
716		* @return
717		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
718	0	public boolean isWorking()...
719		{
720	0	return working;
721		}
722
723		/**
724		* Answers the selected checkbox item index for PCA dimension for the X, Y or
725		* Z axis of the display
726		*
727		* @param axis
728		* @return
729		*/
		100% Uncovered Elements: 0 (7) Complexity: 3 Complexity Density: 0.43
730	3	public int getSelectedDimensionIndex(Axis axis)...
731		{
732	3	switch (axis)
733		{
734	1	case X:
735	1	return xCombobox.getSelectedIndex();
736	1	case Y:
737	1	return yCombobox.getSelectedIndex();
738	1	default:
739	1	return zCombobox.getSelectedIndex();
740		}
741		}
742
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
743	1	public void setShowLabels(boolean show)...
744		{
745	1	showLabels.setSelected(show);
746		}
747
748		/**
749		* Sets the input data used to calculate the PCA. This is provided for
750		* 'restore from project', which does not currently support this (AL-2647), so
751		* sets the value to null, and hides the menu option for "Input Data...". J
752		*
753		* @param data
754		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
755	1	public void setInputData(AlignmentView data)...
756		{
757	1	getPcaModel().setInputData(data);
758	1	originalSeqData.setVisible(data != null);
759		}
760
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
761	8	public AlignViewportI getAlignViewport()...
762		{
763	8	return av;
764		}
765
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
766	10	public PCAModel getPcaModel()...
767		{
768	10	return pcaModel;
769		}
770
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
771	4	public void setPcaModel(PCAModel pcaModel)...
772		{
773	4	this.pcaModel = pcaModel;
774		}
775
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
776	24	public RotatableCanvas getRotatableCanvas()...
777		{
778	24	return rc;
779		}
780
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
781	2	public void setRotatableCanvas(RotatableCanvas rc)...
782		{
783	2	this.rc = rc;
784		}
785
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
786	12	public int getTop()...
787		{
788	12	return top;
789		}
790
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
791	2	public void setTop(int top)...
792		{
793	2	this.top = top;
794		}
795
796		/**
797		* set the associated view for this PCA.
798		*
799		* @param panel
800		*/
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17
801	1	public void selectAssociatedView(AlignmentPanel panel)...
802		{
803	1	getRotatableCanvas().setApplyToAllViews(false);
804
805	1	ap = panel;
806	1	av = panel.av;
807
808	1	getRotatableCanvas().av = panel.av;
809	1	getRotatableCanvas().ap = panel;
810	1	PaintRefresher.Register(PCAPanel.this, panel.av.getSequenceSetId());
811		}
812
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
813	0	@Override...
814		public JProgressBar getProgressBar(long id)
815		{
816	0	return progressBar.getProgressBar(id);
817		}
818
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
819	0	public String getMessage(long id)...
820		{
821	0	return progressBar.getMessage(id);
822		}
823
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
824	0	public void setProgressBarMessage(long id, String message)...
825		{
826	0	progressBar.setProgressBarMessage(id, message);
827		}
828
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
829	1	public static void addToDesktop(PCAPanel panel, String modelName)...
830		{
831	1	Dimension dim = Platform.getDimIfEmbedded(panel, 475, 450);
832	1	Desktop.addInternalFrame(panel, MessageManager.formatMessage(
833		"label.calc_title", "PCA", modelName), dim.width,
834		dim.height);
835		}
836		}