Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SecondaryStructureDistanceModelTest	49	139	12	0.651612965.2%	Show methods

Class SecondaryStructureDistanceModelTest

Class SecondaryStructureDistanceModelTest	Line # 49	Total Statements 139	Complexity 12	TOTAL Coverage 0.651612965.2%
testFindDistances_withGap() : void   testFindDistances_withGap() : void	5555	17.017	1.01	1.0 1.0100%
testFindDistances_withSSUndefinedInEitherOneSeq() : void   testFindDistances_withSSUndefinedInEitherOneSeq() : void	101101	17.017	1.01	1.0 1.0100%
testFindDistances_withSSUndefinedInBothSeqs() : void   testFindDistances_withSSUndefinedInBothSeqs() : void	147147	17.017	1.01	1.0 1.0100%
setupAlignmentView(String) : AlignFrame   setupAlignmentView(String) : AlignFrame	201201	32.032	4.04	0.0 0.00%
setupAlignmentViewWithGap() : AlignFrame   setupAlignmentViewWithGap() : AlignFrame	324324	23.023	1.01	1.0 1.0100%
setupAlignmentViewWithoutSS(String) : AlignFrame   setupAlignmentViewWithoutSS(String) : AlignFrame	367367	20.020	2.02	1.0 1.0100%
testData() : Object[][]   testData() : Object[][]	407407	1.01	1.01	0.0 0.00%
testFindDistances(String,double,double,double,double) : void   testFindDistances(String,double,double,double,double) : void	416416	12.012	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.27096775	jalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withGapjalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withGap	1PASS
	0.2580645	jalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withSSUndefinedInEitherOneSeqjalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withSSUndefinedInEitherOneSeq	1PASS
	0.21290323	jalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withSSUndefinedInBothSeqsjalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withSSUndefinedInBothSeqs	1PASS

 

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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.analysis.scoremodels;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertTrue;
25
26		import jalview.api.analysis.ScoreModelI;
27		import jalview.api.analysis.SimilarityParamsI;
28		import jalview.datamodel.Alignment;
29		import jalview.datamodel.AlignmentAnnotation;
30		import jalview.datamodel.AlignmentI;
31		import jalview.datamodel.AlignmentView;
32		import jalview.datamodel.Annotation;
33		import jalview.datamodel.Sequence;
34		import jalview.datamodel.SequenceFeature;
35		import jalview.datamodel.SequenceI;
36		import jalview.gui.AlignFrame;
37		import jalview.gui.AlignViewport;
38		import jalview.gui.JvOptionPane;
39		import jalview.io.DataSourceType;
40		import jalview.io.FileLoader;
41		import jalview.math.MatrixI;
42
43		import org.testng.Assert;
44		import org.testng.annotations.BeforeClass;
45		import org.testng.annotations.DataProvider;
46		import org.testng.annotations.Test;
47
48		// This class tests methods in Class SecondaryStructureDistanceModel
		65.2% Uncovered Elements: 54 (155) Complexity: 12 Complexity Density: 0.09
49		public class SecondaryStructureDistanceModelTest
50		{
51
52		/**
53		* Verify computed distances of sequences with gap
54		*/
		100% Uncovered Elements: 0 (17) Complexity: 1 Complexity Density: 0.06 1PASS
55	1	@Test(groups = "Functional")...
56		public void testFindDistances_withGap()
57		{
58	1	AlignFrame af = setupAlignmentViewWithGap();
59	1	AlignViewport viewport = af.getViewport();
60	1	AlignmentView view = viewport.getAlignmentView(false);
61
62	1	ScoreModelI sm = new SecondaryStructureDistanceModel();
63	1	sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
64		af.alignPanel);
65
66		/*
67		* feature distance model always normalises by region width
68		* gap-gap is always included (but scores zero)
69		* the only variable parameter is 'includeGaps'
70		*/
71
72		/*
73		* include gaps
74		* score = 0 + 0 + 1 + 0 = 1/4
75		*/
76	1	SimilarityParamsI params = new SimilarityParams(false, true, true,
77		true);
78	1	params.setSecondaryStructureSource("3D Structures");
79	1	MatrixI distances = sm.findDistances(view, params);
80	1	assertEquals(distances.getValue(0, 0), 1d);
81	1	assertEquals(distances.getValue(1, 1), 1d);
82	1	assertEquals(distances.getValue(0, 1), 0d);
83	1	assertEquals(distances.getValue(1, 0), 0d);
84
85		/*
86		* exclude gaps
87		* score = 0 + 0 + 0 + 0 = 0/4
88		*/
89
90	1	SimilarityParamsI params2 = new SimilarityParams(false, true, false,
91		true);
92	1	params2.setSecondaryStructureSource("3D Structures");
93	1	MatrixI distances2 = sm.findDistances(view, params2);
94	1	assertEquals(distances2.getValue(0, 1), 0d);
95	1	assertEquals(distances2.getValue(1, 0), 0d);
96		}
97
98		/**
99		* Verify computed distances of sequences with gap
100		*/
		100% Uncovered Elements: 0 (17) Complexity: 1 Complexity Density: 0.06 1PASS
101	1	@Test(groups = "Functional")...
102		public void testFindDistances_withSSUndefinedInEitherOneSeq()
103		{
104	1	AlignFrame af = setupAlignmentViewWithoutSS("either");
105	1	AlignViewport viewport = af.getViewport();
106	1	AlignmentView view = viewport.getAlignmentView(false);
107
108	1	ScoreModelI sm = new SecondaryStructureDistanceModel();
109	1	sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
110		af.alignPanel);
111
112		/*
113		* feature distance model always normalises by region width
114		* gap-gap is always included (but scores zero)
115		* the only variable parameter is 'includeGaps'
116		*/
117
118		/*
119		* include gaps
120		* score = 0 + 0 + 2 + 2 = 2/4
121		*/
122	1	SimilarityParamsI params = new SimilarityParams(false, true, true,
123		true);
124	1	params.setSecondaryStructureSource("3D Structures");
125	1	MatrixI distances = sm.findDistances(view, params);
126	1	assertEquals(distances.getValue(0, 0), 1d);
127	1	assertEquals(distances.getValue(1, 1), 1d);
128	1	assertEquals(distances.getValue(0, 1), 0d);
129	1	assertEquals(distances.getValue(1, 0), 0d);
130
131		/*
132		* exclude gaps
133		* score = 0 + 0 + 2 + 2 = 2/4
134		*/
135
136	1	SimilarityParamsI params2 = new SimilarityParams(false, true, false,
137		true);
138	1	params2.setSecondaryStructureSource("3D Structures");
139	1	MatrixI distances2 = sm.findDistances(view, params2);
140	1	assertEquals(distances2.getValue(0, 1), 0d);
141	1	assertEquals(distances2.getValue(1, 0), 0d);
142		}
143
144		/**
145		* Verify computed distances of sequences with gap
146		*/
		100% Uncovered Elements: 0 (17) Complexity: 1 Complexity Density: 0.06 1PASS
147	1	@Test(groups = "Functional")...
148		public void testFindDistances_withSSUndefinedInBothSeqs()
149		{
150	1	AlignFrame af = setupAlignmentViewWithoutSS("both");
151	1	AlignViewport viewport = af.getViewport();
152	1	AlignmentView view = viewport.getAlignmentView(false);
153
154	1	ScoreModelI sm = new SecondaryStructureDistanceModel();
155	1	sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
156		af.alignPanel);
157
158		/*
159		* feature distance model always normalises by region width
160		* gap-gap is always included (but scores zero)
161		* the only variable parameter is 'includeGaps'
162		*/
163
164		/*
165		* include gaps
166		* score = 0 + 0 + 2 + 2 = 2/4
167		*/
168	1	SimilarityParamsI params = new SimilarityParams(false, true, true,
169		true);
170	1	params.setSecondaryStructureSource("3D Structures");
171	1	MatrixI distances = sm.findDistances(view, params);
172	1	assertEquals(distances.getValue(0, 0), 1d);
173	1	assertEquals(distances.getValue(1, 1), 1d);
174	1	assertEquals(distances.getValue(0, 1), 0d);
175	1	assertEquals(distances.getValue(1, 0), 0d);
176
177		/*
178		* exclude gaps
179		* score = 0 + 0 + 2 + 2 = 2/4
180		*/
181
182	1	SimilarityParamsI params2 = new SimilarityParams(false, true, false,
183		true);
184	1	params2.setSecondaryStructureSource("3D Structures");
185	1	MatrixI distances2 = sm.findDistances(view, params2);
186	1	assertEquals(distances2.getValue(0, 1), 0d);
187	1	assertEquals(distances2.getValue(1, 0), 0d);
188		}
189
190		/**
191		* <pre>
192		* Set up
193		* column 1 2 3 4
194		* seq s1 F R K S
195		*
196		* seq s2 F S J L
197		* </pre>
198		*
199		* @return
200		*/
		0% Uncovered Elements: 38 (38) Complexity: 4 Complexity Density: 0.12
201	0	protected AlignFrame setupAlignmentView(String similar)...
202		{
203		/*
204		* sequences without gaps
205		*/
206	0	SequenceI s1 = new Sequence("s1", "FRKS");
207	0	SequenceI s2 = new Sequence("s2", "FSJL");
208
209	0	s1.addSequenceFeature(
210		new SequenceFeature("chain", null, 1, 4, 0f, null));
211	0	s1.addSequenceFeature(
212		new SequenceFeature("domain", null, 1, 4, 0f, null));
213	0	s2.addSequenceFeature(
214		new SequenceFeature("chain", null, 1, 4, 0f, null));
215	0	s2.addSequenceFeature(
216		new SequenceFeature("metal", null, 1, 4, 0f, null));
217	0	s2.addSequenceFeature(
218		new SequenceFeature("Pfam", null, 1, 4, 0f, null));
219
220		/*
221		* Set up secondary structure annotations
222		*/
223	0	Annotation ssE = new Annotation("", "", 'E', 0);
224	0	Annotation ssH = new Annotation("", "", 'H', 0);
225	0	Annotation ssC = new Annotation(".", "", ' ', 0);
226
227	0	Annotation[] anns1;
228	0	Annotation[] anns2;
229
230		/* All secondary structure annotations are similar for each column
231		* Set up
232		* column 1 2 3 4
233		* seq s1 F R K S
234		* ss E H S E
235		*
236		* seq s2 F S J L
237		* ss E H S E
238		*/
239	0	if (similar == "All Similar")
240		{
241
242	0	anns1 = new Annotation[] { ssE, ssH, ssC, ssE };
243	0	anns2 = new Annotation[] { ssE, ssH, ssC, ssE };
244
245		}
246
247		/* All secondary structure annotations are dissimilar for each column
248		* Set up
249		* column 1 2 3 4
250		* seq s1 F R K S
251		* ss E E C E
252		*
253		* seq s2 F S J L
254		* ss H E E C
255		*/
256	0	else if (similar == "Not Similar")
257		{
258
259	0	anns1 = new Annotation[] { ssE, ssE, ssC, ssE };
260	0	anns2 = new Annotation[] { ssH, ssH, ssE, ssC };
261
262		}
263
264		/* All secondary structure annotations are dissimilar for each column
265		* Set up
266		* column 1 2 3 4
267		* seq s1 F R K S
268		* ss E E C E
269		*
270		* seq s2 F S J L
271		* ss H E E C
272		*/
273	0	else if (similar == "With Coil")
274		{
275
276	0	anns1 = new Annotation[] { ssE, ssE, null, ssE };
277	0	anns2 = new Annotation[] { ssH, ssH, ssE, null };
278
279		}
280
281		/* Set up
282		* column 1 2 3 4
283		* seq s1 F R K S
284		* ss H E C E
285		*
286		* seq s2 F S J L
287		* ss H E E C
288		*/
289		else
290		{
291
292	0	anns1 = new Annotation[] { ssH, ssE, ssC, ssE };
293	0	anns2 = new Annotation[] { ssH, ssE, ssE, ssC };
294		}
295
296	0	AlignmentAnnotation ann1 = new AlignmentAnnotation(
297		"Secondary Structure", "Secondary Structure", anns1);
298	0	AlignmentAnnotation ann2 = new AlignmentAnnotation(
299		"Secondary Structure", "Secondary Structure", anns2);
300
301	0	s1.addAlignmentAnnotation(ann1);
302	0	s2.addAlignmentAnnotation(ann2);
303
304	0	AlignmentI al = new Alignment(new SequenceI[] { s1, s2 });
305	0	AlignFrame af = new AlignFrame(al, 300, 300);
306	0	af.setShowSeqFeatures(true);
307	0	af.getFeatureRenderer().findAllFeatures(true);
308	0	return af;
309		}
310
311		/**
312		* <pre>
313		* Set up
314		* column 1 2 3 4
315		* seq s1 F R S
316		* SS H E C
317		*
318		* seq s2 F S J L
319		* ss H E E C
320		* </pre>
321		*
322		* @return
323		*/
		100% Uncovered Elements: 0 (23) Complexity: 1 Complexity Density: 0.04
324	1	protected AlignFrame setupAlignmentViewWithGap()...
325		{
326
327	1	SequenceI s1 = new Sequence("s1", "FR S");
328	1	SequenceI s2 = new Sequence("s2", "FSJL");
329
330	1	s1.addSequenceFeature(
331		new SequenceFeature("chain", null, 1, 3, 0f, null));
332	1	s1.addSequenceFeature(
333		new SequenceFeature("domain", null, 1, 3, 0f, null));
334	1	s2.addSequenceFeature(
335		new SequenceFeature("chain", null, 1, 4, 0f, null));
336	1	s2.addSequenceFeature(
337		new SequenceFeature("metal", null, 1, 4, 0f, null));
338	1	s2.addSequenceFeature(
339		new SequenceFeature("Pfam", null, 1, 4, 0f, null));
340
341	1	Annotation ssE = new Annotation("", "", 'E', 0);
342	1	Annotation ssH = new Annotation("", "", 'H', 0);
343	1	Annotation ssC = new Annotation(".", "", ' ', 0);
344
345	1	Annotation[] anns1;
346	1	Annotation[] anns2;
347
348	1	anns1 = new Annotation[] { ssH, ssE, ssC };
349	1	anns2 = new Annotation[] { ssH, ssE, ssE, ssC };
350
351	1	AlignmentAnnotation ann1 = new AlignmentAnnotation(
352		"Secondary Structure", "Secondary Structure", anns1);
353	1	AlignmentAnnotation ann2 = new AlignmentAnnotation(
354		"Secondary Structure", "Secondary Structure", anns2);
355
356	1	s1.addAlignmentAnnotation(ann1);
357	1	s2.addAlignmentAnnotation(ann2);
358
359	1	AlignmentI al = new Alignment(new SequenceI[] { s1, s2 });
360	1	AlignFrame af = new AlignFrame(al, 300, 300);
361	1	af.setShowSeqFeatures(true);
362	1	af.getFeatureRenderer().findAllFeatures(true);
363
364	1	return af;
365		}
366
		100% Uncovered Elements: 0 (22) Complexity: 2 Complexity Density: 0.1
367	2	protected AlignFrame setupAlignmentViewWithoutSS(String type)...
368		{
369
370	2	SequenceI s1 = new Sequence("s1", "FR S");
371	2	SequenceI s2 = new Sequence("s2", "FSJL");
372
373	2	s1.addSequenceFeature(
374		new SequenceFeature("chain", null, 1, 3, 0f, null));
375	2	s1.addSequenceFeature(
376		new SequenceFeature("domain", null, 1, 3, 0f, null));
377	2	s2.addSequenceFeature(
378		new SequenceFeature("chain", null, 1, 4, 0f, null));
379	2	s2.addSequenceFeature(
380		new SequenceFeature("metal", null, 1, 4, 0f, null));
381	2	s2.addSequenceFeature(
382		new SequenceFeature("Pfam", null, 1, 4, 0f, null));
383
384	2	if (!type.equals("both"))
385		{
386	1	Annotation ssE = new Annotation("", "", 'E', 0);
387	1	Annotation ssH = new Annotation("", "", 'H', 0);
388	1	Annotation ssC = new Annotation(".", "", ' ', 0);
389
390	1	Annotation[] anns1;
391
392	1	anns1 = new Annotation[] { ssH, ssE, ssC };
393
394	1	AlignmentAnnotation ann1 = new AlignmentAnnotation(
395		"Secondary Structure", "Secondary Structure", anns1);
396
397	1	s1.addAlignmentAnnotation(ann1);
398		}
399
400	2	AlignmentI al = new Alignment(new SequenceI[] { s1, s2 });
401	2	AlignFrame af = new AlignFrame(al, 300, 300);
402	2	af.setShowSeqFeatures(true);
403	2	af.getFeatureRenderer().findAllFeatures(true);
404	2	return af;
405		}
406
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1 1PASS
407	0	@DataProvider(name = "testData")...
408		public Object[][] testData()
409		{
410	0	return new Object[][] { { "All Similar", 1d, 1d, 0d, 0d / 4 },
411		{ "Partially Similar", 1d, 1d, 0d, 0d },
412		{ "Not Similar", 1d, 1d, 0d, 0d },
413		{ "With Coil", 1d, 1d, 0d, 0d }, };
414		}
415
		0% Uncovered Elements: 12 (12) Complexity: 1 Complexity Density: 0.08 1PASS
416	0	@Test(dataProvider = "testData")...
417		public void testFindDistances(String scenario, double expectedValue00,
418		double expectedValue11, double expectedValue01,
419		double expectedValue10)
420		{
421	0	AlignFrame af = setupAlignmentView(scenario);
422	0	AlignViewport viewport = af.getViewport();
423	0	AlignmentView view = viewport.getAlignmentView(false);
424
425	0	ScoreModelI sm = new SecondaryStructureDistanceModel();
426	0	sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
427		af.alignPanel);
428
429	0	SimilarityParamsI params = new SimilarityParams(false, true, true,
430		true);
431	0	params.setSecondaryStructureSource("3D Structures");
432	0	MatrixI distances = sm.findDistances(view, params);
433
434	0	assertEquals(distances.getValue(0, 0), expectedValue00);
435	0	assertEquals(distances.getValue(1, 1), expectedValue11);
436	0	assertEquals(distances.getValue(0, 1), expectedValue01);
437	0	assertEquals(distances.getValue(1, 0), expectedValue10);
438		}
439
440		}