Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PCAPanel	64	184	66	0.417670741.8%	Show methods
PCAPanel.PCAPrinter	373	18	7	0.00%	Show methods

Class PCAPanel

Class PCAPanel	Line # 64	Total Statements 184	Complexity 66	TOTAL Coverage 0.417670741.8%
internalFrameClosed(InternalFrameEvent) : void   internalFrameClosed(InternalFrameEvent) : void	107107	1.01	1.01	1.0 1.0100%
PCAPanel(AlignmentPanel,String,SimilarityParamsI)   PCAPanel(AlignmentPanel,String,SimilarityParamsI)	9494	21.021	2.02	0.9130435 0.913043591.3%
close_actionPerformed() : void   close_actionPerformed() : void	150150	5.05	2.02	0.85714287 0.8571428785.7%
colourSelected(Color) : void   colourSelected(Color) : void	167167	2.02	1.01	0.0 0.00%
bgcolour_actionPerformed() : void   bgcolour_actionPerformed() : void	161161	3.03	1.01	0.0 0.00%
run() : void   run() : void	181181	24.024	4.04	0.8214286 0.821428682.1%
doDimensionChange() : void   doDimensionChange() : void	230230	7.07	2.02	0.33333334 0.3333333433.3%
setSelectedDimensionIndex(int,Axis) : void   setSelectedDimensionIndex(int,Axis) : void	252252	11.011	4.04	0.90909094 0.9090909490.9%
outputValues_actionPerformed() : void   outputValues_actionPerformed() : void	269269	6.06	2.02	0.0 0.00%
showLabels_actionPerformed() : void   showLabels_actionPerformed() : void	285285	1.01	1.01	0.0 0.00%
print_actionPerformed() : void   print_actionPerformed() : void	291291	2.02	1.01	0.0 0.00%
originalSeqData_actionPerformed() : void   originalSeqData_actionPerformed() : void	302302	15.015	8.08	0.0 0.00%
exportImage(Graphics) : void   exportImage(Graphics) : void	434434	5.05	2.02	0.0 0.00%
makePCAImage(ImageMaker.TYPE) : void   makePCAImage(ImageMaker.TYPE) : void	428428	8.08	2.02	0.0 0.00%
viewMenu_menuSelected() : void   viewMenu_menuSelected() : void	458458	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	500500	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	518518	1.01	1.01	0.0 0.00%
buildAssociatedViewMenu() : void   buildAssociatedViewMenu() : void	468468	22.022	5.05	0.0 0.00%
outputPoints_actionPerformed() : void   outputPoints_actionPerformed() : void	535535	6.06	2.02	0.0 0.00%
outputProjPoints_actionPerformed() : void   outputProjPoints_actionPerformed() : void	561561	6.06	2.02	0.0 0.00%
setProgressBar(String,long) : void   setProgressBar(String,long) : void	585585	1.01	1.01	0.0 0.00%
registerHandler(long,IProgressIndicatorHandler) : void   registerHandler(long,IProgressIndicatorHandler) : void	634634	1.01	1.01	0.0 0.00%
operationInProgress() : boolean   operationInProgress() : boolean	671671	1.01	1.01	0.0 0.00%
resetButton_actionPerformed() : void   resetButton_actionPerformed() : void	677677	6.06	1.01	0.0 0.00%
isWorking() : boolean   isWorking() : boolean	693693	1.01	1.01	0.0 0.00%
getSelectedDimensionIndex(Axis) : int   getSelectedDimensionIndex(Axis) : int	705705	7.07	3.03	1.0 1.0100%
setShowLabels(boolean) : void   setShowLabels(boolean) : void	718718	1.01	1.01	1.0 1.0100%
setInputData(AlignmentView) : void   setInputData(AlignmentView) : void	730730	2.02	1.01	1.0 1.0100%
getAlignViewport() : AlignViewportI   getAlignViewport() : AlignViewportI	736736	1.01	1.01	1.0 1.0100%
getPcaModel() : PCAModel   getPcaModel() : PCAModel	741741	1.01	1.01	1.0 1.0100%
setPcaModel(PCAModel) : void   setPcaModel(PCAModel) : void	746746	1.01	1.01	1.0 1.0100%
getRotatableCanvas() : RotatableCanvas   getRotatableCanvas() : RotatableCanvas	751751	1.01	1.01	1.0 1.0100%
setRotatableCanvas(RotatableCanvas) : void   setRotatableCanvas(RotatableCanvas) : void	756756	1.01	1.01	1.0 1.0100%
getTop() : int   getTop() : int	761761	1.01	1.01	1.0 1.0100%
setTop(int) : void   setTop(int) : void	766766	1.01	1.01	1.0 1.0100%
selectAssociatedView(AlignmentPanel) : void   selectAssociatedView(AlignmentPanel) : void	776776	6.06	1.01	1.0 1.0100%
getProgressBar(long) : JProgressBar   getProgressBar(long) : JProgressBar	788788	1.01	1.01	0.0 0.00%
getMessage(long) : String   getMessage(long) : String	794794	1.01	1.01	0.0 0.00%
setProgressBarMessage(long,String) : void   setProgressBarMessage(long,String) : void	799799	1.01	1.01	0.0 0.00%

 

Class PCAPanel.PCAPrinter

Class PCAPanel.PCAPrinter	Line # 373	Total Statements 18	Complexity 7	TOTAL Coverage 0.00%
run() : void   run() : void	375375	10.010	4.04	0.0 0.00%
print(Graphics,PageFormat,int) : int   print(Graphics,PageFormat,int) : int	404404	8.08	3.03	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.37545127	jalview.project.Jalview2xmlTests.testPcaViewAssociationjalview.project.Jalview2xmlTests.testPcaViewAssociation	1PASS
	0.039711192	jalview.project.Jalview2xmlTests.testStoreAndRecoverAnnotationRowElementColoursjalview.project.Jalview2xmlTests.testStoreAndRecoverAnnotationRowElementColours	1PASS
	0.0072202166	jalview.project.Jalview2xmlTests.testRNAStructureRecoveryjalview.project.Jalview2xmlTests.testRNAStructureRecovery	1PASS
	0.0072202166	jalview.project.Jalview2xmlTests.testSaveLoadFeatureColoursAndFiltersjalview.project.Jalview2xmlTests.testSaveLoadFeatureColoursAndFilters	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.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		*/
		41.8% Uncovered Elements: 145 (249) Complexity: 66 Complexity Density: 0.36
64		public class PCAPanel extends GPCAPanel
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		*/
		91.3% Uncovered Elements: 2 (23) Complexity: 2 Complexity Density: 0.1
94	2	public PCAPanel(AlignmentPanel alignPanel, String modelName,...
95		SimilarityParamsI params)
96		{
97	2	super();
98	2	this.setFrameIcon(null);
99	2	this.av = alignPanel.av;
100	2	this.ap = alignPanel;
101	2	boolean nucleotide = av.getAlignment().isNucleotide();
102
103	2	progressBar = new ProgressBar(statusPanel, statusBar);
104
105	2	addInternalFrameListener(new InternalFrameAdapter()
106		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
107	2	@Override...
108		public void internalFrameClosed(InternalFrameEvent e)
109		{
110	2	close_actionPerformed();
111		}
112		});
113
114	2	boolean selected = av.getSelectionGroup() != null
115		&& av.getSelectionGroup().getSize() > 0;
116	2	AlignmentView seqstrings = av.getAlignmentView(selected);
117	2	SequenceI[] seqs;
118	2	if (!selected)
119		{
120	2	seqs = av.getAlignment().getSequencesArray();
121		}
122		else
123		{
124	0	seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
125		}
126
127	2	ScoreModelI scoreModel = ScoreModels.getInstance()
128		.getScoreModel(modelName, ap);
129	2	setPcaModel(
130		new PCAModel(seqstrings, seqs, nucleotide, scoreModel, params));
131
132	2	newPcaTitle = alignPanel.alignFrame.formCalculationTitle(
133		MessageManager.formatMessage("label.calc_title", "PCA",
134		getPcaModel().getScoreModelName()),
135		selected, ap.alignFrame.getTitle());
136
137	2	PaintRefresher.Register(this, av.getSequenceSetId());
138
139	2	setRotatableCanvas(new RotatableCanvas(alignPanel));
140	2	this.getContentPane().add(getRotatableCanvas(), BorderLayout.CENTER);
141
142	2	addKeyListener(getRotatableCanvas());
143	2	validate();
144		}
145
146		/**
147		* Ensure references to potentially very large objects (the PCA matrices) are
148		* nulled when the frame is closed
149		*/
		85.7% Uncovered Elements: 1 (7) Complexity: 2 Complexity Density: 0.4
150	2	protected void close_actionPerformed()...
151		{
152	2	setPcaModel(null);
153	2	if (this.rc != null)
154		{
155	2	this.rc.sequencePoints = null;
156	2	this.rc.setAxisEndPoints(null);
157	2	this.rc = null;
158		}
159		}
160
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
161	0	@Override...
162		protected void bgcolour_actionPerformed()
163		{
164	0	String ttl = MessageManager.getString("label.select_background_colour");
165	0	ColourChooserListener listener = new ColourChooserListener()
166		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
167	0	@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		*/
		82.1% Uncovered Elements: 5 (28) Complexity: 4 Complexity Density: 0.17
181	1	@Override...
182		public void run()
183		{
184	1	working = true;
185	1	long progId = System.currentTimeMillis();
186	1	IProgressIndicator progress = this;
187	1	String message = MessageManager.getString("label.pca_recalculating");
188	1	if (getParent() == null)
189		{
190	1	progress = ap.alignFrame;
191	1	message = MessageManager.getString("label.pca_calculating");
192		}
193	1	progress.setProgressBar(message, progId);
194	1	try
195		{
196	1	getPcaModel().calculate();
197
198	1	xCombobox.setSelectedIndex(0);
199	1	yCombobox.setSelectedIndex(1);
200	1	zCombobox.setSelectedIndex(2);
201
202	1	getPcaModel().updateRc(getRotatableCanvas());
203		// rc.invalidate();
204	1	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	1	progress.setProgressBar("", progId);
214		}
215
216	1	repaint();
217	1	if (getParent() == null)
218		{
219	1	Desktop.addInternalFrame(this, newPcaTitle,
220		475, 450);
221	1	this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
222		}
223	1	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		*/
		33.3% Uncovered Elements: 6 (9) Complexity: 2 Complexity Density: 0.29
230	12	@Override...
231		protected void doDimensionChange()
232		{
233	12	if (getTop() == 0)
234		{
235	12	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		*/
		90.9% Uncovered Elements: 1 (11) Complexity: 4 Complexity Density: 0.36
252	3	public void setSelectedDimensionIndex(int index, Axis axis)...
253		{
254	3	switch (axis)
255		{
256	1	case X:
257	1	xCombobox.setSelectedIndex(index);
258	1	break;
259	1	case Y:
260	1	yCombobox.setSelectedIndex(index);
261	1	break;
262	1	case Z:
263	1	zCombobox.setSelectedIndex(index);
264	1	break;
265	0	default:
266		}
267		}
268
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.33
269	0	@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
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
285	0	@Override...
286		protected void showLabels_actionPerformed()
287		{
288	0	getRotatableCanvas().showLabels(showLabels.getState());
289		}
290
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
291	0	@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		*/
		0% Uncovered Elements: 23 (23) Complexity: 8 Complexity Density: 0.53
302	0	@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
		0% Uncovered Elements: 28 (28) Complexity: 7 Complexity Density: 0.39
373		class PCAPrinter extends Thread implements Printable
374		{
		0% Uncovered Elements: 14 (14) Complexity: 4 Complexity Density: 0.4
375	0	@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
		0% Uncovered Elements: 12 (12) Complexity: 3 Complexity Density: 0.38
404	0	@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
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.25
428	0	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		{
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
434	0	@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
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
458	0	@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		*/
		0% Uncovered Elements: 28 (28) Complexity: 5 Complexity Density: 0.23
468	0	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		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
500	0	@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		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
518	0	@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		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.33
535	0	@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		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.33
561	0	@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		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
585	0	@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
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
634	0	@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		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
671	0	@Override...
672		public boolean operationInProgress()
673		{
674	0	return progressBar.operationInProgress();
675		}
676
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17
677	0	@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		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
693	0	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		*/
		100% Uncovered Elements: 0 (7) Complexity: 3 Complexity Density: 0.43
705	3	public int getSelectedDimensionIndex(Axis axis)...
706		{
707	3	switch (axis)
708		{
709	1	case X:
710	1	return xCombobox.getSelectedIndex();
711	1	case Y:
712	1	return yCombobox.getSelectedIndex();
713	1	default:
714	1	return zCombobox.getSelectedIndex();
715		}
716		}
717
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
718	1	public void setShowLabels(boolean show)...
719		{
720	1	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		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
730	1	public void setInputData(AlignmentView data)...
731		{
732	1	getPcaModel().setInputData(data);
733	1	originalSeqData.setVisible(data != null);
734		}
735
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
736	10	public AlignViewportI getAlignViewport()...
737		{
738	10	return av;
739		}
740
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
741	10	public PCAModel getPcaModel()...
742		{
743	10	return pcaModel;
744		}
745
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
746	4	public void setPcaModel(PCAModel pcaModel)...
747		{
748	4	this.pcaModel = pcaModel;
749		}
750
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
751	24	public RotatableCanvas getRotatableCanvas()...
752		{
753	24	return rc;
754		}
755
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
756	2	public void setRotatableCanvas(RotatableCanvas rc)...
757		{
758	2	this.rc = rc;
759		}
760
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
761	12	public int getTop()...
762		{
763	12	return top;
764		}
765
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
766	2	public void setTop(int top)...
767		{
768	2	this.top = top;
769		}
770
771		/**
772		* set the associated view for this PCA.
773		*
774		* @param panel
775		*/
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17
776	1	public void selectAssociatedView(AlignmentPanel panel)...
777		{
778	1	getRotatableCanvas().setApplyToAllViews(false);
779
780	1	ap = panel;
781	1	av = panel.av;
782
783	1	getRotatableCanvas().av = panel.av;
784	1	getRotatableCanvas().ap = panel;
785	1	PaintRefresher.Register(PCAPanel.this, panel.av.getSequenceSetId());
786		}
787
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
788	0	@Override...
789		public JProgressBar getProgressBar(long id)
790		{
791	0	return progressBar.getProgressBar(id);
792		}
793
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
794	0	public String getMessage(long id)...
795		{
796	0	return progressBar.getMessage(id);
797		}
798
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
799	0	public void setProgressBarMessage(long id, String message)...
800		{
801	0	progressBar.setProgressBarMessage(id, message);
802		}
803		}