Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
FeatureDistanceModelTest	47	113	14	0	1.0100%	Show methods

Class FeatureDistanceModelTest

Class FeatureDistanceModelTest	Line # 47	Total Statements 113	Complexity 14	Uncovered Elements 0	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5050	2.02	1.01	0.00	1.0 1.0100%
getTestAlignmentFrame() : AlignFrame   getTestAlignmentFrame() : AlignFrame	7676	20.020	5.05	0.00	1.0 1.0100%
testFeatureScoreModel() : void   testFeatureScoreModel() : void	113113	7.07	1.01	0.00	1.0 1.0100%
testFeatureScoreModel_hiddenFirstColumn() : void   testFeatureScoreModel_hiddenFirstColumn() : void	131131	8.08	1.01	0.00	1.0 1.0100%
testFeatureScoreModel_HiddenColumns() : void   testFeatureScoreModel_HiddenColumns() : void	150150	11.011	2.02	0.00	1.0 1.0100%
testFindFeatureAt_PointFeature() : void   testFindFeatureAt_PointFeature() : void	185185	16.016	1.01	0.00	1.0 1.0100%
testFindDistances() : void   testFindDistances() : void	221221	23.023	1.01	0.00	1.0 1.0100%
testFindDistances_withParams() : void   testFindDistances_withParams() : void	279279	14.014	1.01	0.00	1.0 1.0100%
setupAlignmentView() : AlignFrame   setupAlignmentView() : AlignFrame	332332	12.012	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.32575756	jalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModel_HiddenColumnsjalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModel_HiddenColumns	1PASS
	0.28787878	jalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModel_hiddenFirstColumnjalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModel_hiddenFirstColumn	1PASS
	0.28030303	jalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModeljalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModel	1PASS
	0.21212122	jalview.analysis.scoremodels.FeatureDistanceModelTest.testFindDistances_withParamsjalview.analysis.scoremodels.FeatureDistanceModelTest.testFindDistances_withParams	1PASS
	0.18181819	jalview.analysis.scoremodels.FeatureDistanceModelTest.testFindDistancesjalview.analysis.scoremodels.FeatureDistanceModelTest.testFindDistances	1PASS
	0.12878788	jalview.analysis.scoremodels.FeatureDistanceModelTest.testFindFeatureAt_PointFeaturejalview.analysis.scoremodels.FeatureDistanceModelTest.testFindFeatureAt_PointFeature	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.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.AlignmentI;
30		import jalview.datamodel.AlignmentView;
31		import jalview.datamodel.Sequence;
32		import jalview.datamodel.SequenceFeature;
33		import jalview.datamodel.SequenceI;
34		import jalview.gui.AlignFrame;
35		import jalview.gui.AlignViewport;
36		import jalview.gui.JvOptionPane;
37		import jalview.io.DataSourceType;
38		import jalview.io.FileLoader;
39		import jalview.math.MatrixI;
40
41		import java.util.Arrays;
42
43		import org.testng.Assert;
44		import org.testng.annotations.BeforeClass;
45		import org.testng.annotations.Test;
46
		100% Uncovered Elements: 0 (132) Complexity: 14 Complexity Density: 0.12
47		public class FeatureDistanceModelTest
48		{
49
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
50	1	@BeforeClass(alwaysRun = true)...
51		public void setUpJvOptionPane()
52		{
53	1	JvOptionPane.setInteractiveMode(false);
54	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
55		}
56
57		public static String alntestFile = "FER1_MESCR/72-76 DVYIL\nFER1_SPIOL/71-75 DVYIL\nFER3_RAPSA/21-25 DVYVL\nFER1_MAIZE/73-77 DVYIL\n";
58
59		int[] sf1 = new int[] { 74, 74, 73, 73, 23, 23, -1, -1 };
60
61		int[] sf2 = new int[] { -1, -1, 74, 75, -1, -1, 76, 77 };
62
63		int[] sf3 = new int[] { -1, -1, -1, -1, -1, -1, 76, 77 };
64
65		/**
66		* <pre>
67		* Load test alignment and add features to sequences:
68		* FER1_MESCR FER1_SPIOL FER3_RAPSA FER1_MAIZE
69		* sf1 X X X
70		* sf2 X X
71		* sf3 X
72		* </pre>
73		*
74		* @return
75		*/
		100% Uncovered Elements: 0 (28) Complexity: 5 Complexity Density: 0.25
76	3	public AlignFrame getTestAlignmentFrame()...
77		{
78	3	AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(
79		alntestFile, DataSourceType.PASTE);
80	3	AlignmentI al = alf.getViewport().getAlignment();
81	3	Assert.assertEquals(al.getHeight(), 4);
82	3	Assert.assertEquals(al.getWidth(), 5);
83	15	for (int i = 0; i < 4; i++)
84		{
85	12	SequenceI ds = al.getSequenceAt(i).getDatasetSequence();
86	12	if (sf1[i * 2] > 0)
87		{
88	9	ds.addSequenceFeature(new SequenceFeature("sf1", "sf1", sf1[i * 2],
89		sf1[i * 2 + 1], "sf1"));
90		}
91	12	if (sf2[i * 2] > 0)
92		{
93	6	ds.addSequenceFeature(new SequenceFeature("sf2", "sf2", sf2[i * 2],
94		sf2[i * 2 + 1], "sf2"));
95		}
96	12	if (sf3[i * 2] > 0)
97		{
98	3	ds.addSequenceFeature(new SequenceFeature("sf3", "sf3", sf3[i * 2],
99		sf3[i * 2 + 1], "sf3"));
100		}
101		}
102	3	alf.setShowSeqFeatures(true);
103	3	alf.getFeatureRenderer().setVisible("sf1");
104	3	alf.getFeatureRenderer().setVisible("sf2");
105	3	alf.getFeatureRenderer().setVisible("sf3");
106	3	alf.getFeatureRenderer().findAllFeatures(true);
107	3	Assert.assertEquals(alf.getFeatureRenderer().getDisplayedFeatureTypes()
108		.size(), 3, "Number of feature types");
109	3	assertTrue(alf.getCurrentView().areFeaturesDisplayed());
110	3	return alf;
111		}
112
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14 1PASS
113	1	@Test(groups = { "Functional" })...
114		public void testFeatureScoreModel() throws Exception
115		{
116	1	AlignFrame alf = getTestAlignmentFrame();
117	1	ScoreModelI sm = new FeatureDistanceModel();
118	1	sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
119		alf.getCurrentView().getAlignPanel());
120	1	alf.selectAllSequenceMenuItem_actionPerformed(null);
121
122	1	MatrixI dm = sm.findDistances(
123		alf.getViewport().getAlignmentView(true),
124		SimilarityParams.Jalview);
125	1	assertEquals(dm.getValue(0, 2), 0d,
126		"FER1_MESCR (0) should be identical with RAPSA (2)");
127	1	assertTrue(dm.getValue(0, 1) > dm.getValue(0, 2),
128		"FER1_MESCR (0) should be further from SPIOL (1) than it is from RAPSA (2)");
129		}
130
		100% Uncovered Elements: 0 (8) Complexity: 1 Complexity Density: 0.12 1PASS
131	1	@Test(groups = { "Functional" })...
132		public void testFeatureScoreModel_hiddenFirstColumn() throws Exception
133		{
134	1	AlignFrame alf = getTestAlignmentFrame();
135		// hiding first two columns shouldn't affect the tree
136	1	alf.getViewport().hideColumns(0, 1);
137	1	ScoreModelI sm = new FeatureDistanceModel();
138	1	sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
139		alf.getCurrentView().getAlignPanel());
140	1	alf.selectAllSequenceMenuItem_actionPerformed(null);
141	1	MatrixI dm = sm.findDistances(
142		alf.getViewport().getAlignmentView(true),
143		SimilarityParams.Jalview);
144	1	assertEquals(dm.getValue(0, 2), 0d,
145		"FER1_MESCR (0) should be identical with RAPSA (2)");
146	1	assertTrue(dm.getValue(0, 1) > dm.getValue(0, 2),
147		"FER1_MESCR (0) should be further from SPIOL (1) than it is from RAPSA (2)");
148		}
149
		100% Uncovered Elements: 0 (13) Complexity: 2 Complexity Density: 0.18 1PASS
150	1	@Test(groups = { "Functional" })...
151		public void testFeatureScoreModel_HiddenColumns() throws Exception
152		{
153	1	AlignFrame alf = getTestAlignmentFrame();
154		// hide columns and check tree changes
155	1	alf.getViewport().hideColumns(3, 4);
156	1	alf.getViewport().hideColumns(0, 1);
157		// getName() can become static in Java 8
158	1	ScoreModelI sm = new FeatureDistanceModel();
159	1	sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
160		alf.getCurrentView().getAlignPanel());
161	1	alf.selectAllSequenceMenuItem_actionPerformed(null);
162	1	MatrixI dm = sm.findDistances(
163		alf.getViewport().getAlignmentView(true),
164		SimilarityParams.Jalview);
165	1	assertEquals(
166		dm.getValue(0, 2),
167		0d,
168		"After hiding last two columns FER1_MESCR (0) should still be identical with RAPSA (2)");
169	1	assertEquals(
170		dm.getValue(0, 1),
171		0d,
172		"After hiding last two columns FER1_MESCR (0) should now also be identical with SPIOL (1)");
173	4	for (int s = 0; s < 3; s++)
174		{
175	3	assertTrue(dm.getValue(s, 3) > 0d, "After hiding last two columns "
176		+ alf.getViewport().getAlignment().getSequenceAt(s).getName()
177		+ "(" + s + ") should still be distinct from FER1_MAIZE (3)");
178		}
179		}
180
181		/**
182		* Check findFeatureAt doesn't return contact features except at contact
183		* points TODO:move to under the FeatureRendererModel test suite
184		*/
		100% Uncovered Elements: 0 (16) Complexity: 1 Complexity Density: 0.06 1PASS
185	1	@Test(groups = { "Functional" })...
186		public void testFindFeatureAt_PointFeature() throws Exception
187		{
188	1	String alignment = "a CCCCCCGGGGGGCCCCCC\n" + "b CCCCCCGGGGGGCCCCCC\n"
189		+ "c CCCCCCGGGGGGCCCCCC\n";
190	1	AlignFrame af = new jalview.io.FileLoader(false)
191		.LoadFileWaitTillLoaded(alignment, DataSourceType.PASTE);
192	1	SequenceI aseq = af.getViewport().getAlignment().getSequenceAt(0);
193	1	SequenceFeature sf = null;
194	1	sf = new SequenceFeature("disulphide bond", "", 2, 5, Float.NaN, "");
195	1	aseq.addSequenceFeature(sf);
196	1	assertTrue(sf.isContactFeature());
197	1	af.refreshFeatureUI(true);
198	1	af.getFeatureRenderer().setAllVisible(Arrays.asList("disulphide bond"));
199	1	Assert.assertEquals(af.getFeatureRenderer().getDisplayedFeatureTypes()
200		.size(), 1, "Should be just one feature type displayed");
201		// step through and check for pointwise feature presence/absence
202	1	Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 1)
203		.size(), 0);
204		// step through and check for pointwise feature presence/absence
205	1	Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 2)
206		.size(), 1);
207		// step through and check for pointwise feature presence/absence
208	1	Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 3)
209		.size(), 0);
210		// step through and check for pointwise feature presence/absence
211	1	Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 4)
212		.size(), 0);
213		// step through and check for pointwise feature presence/absence
214	1	Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 5)
215		.size(), 1);
216		// step through and check for pointwise feature presence/absence
217	1	Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 6)
218		.size(), 0);
219		}
220
		100% Uncovered Elements: 0 (23) Complexity: 1 Complexity Density: 0.04 1PASS
221	1	@Test(groups = { "Functional" })...
222		public void testFindDistances() throws Exception
223		{
224	1	String seqs = ">s1\nABCDE\n>seq2\nABCDE\n";
225	1	AlignFrame alf = new FileLoader().LoadFileWaitTillLoaded(seqs,
226		DataSourceType.PASTE);
227	1	SequenceI s1 = alf.getViewport().getAlignment().getSequenceAt(0);
228	1	SequenceI s2 = alf.getViewport().getAlignment().getSequenceAt(1);
229
230		/*
231		* set domain and variant features thus:
232		* ----5
233		* s1 ddd..
234		* s1 .vvv.
235		* s1 ..vvv
236		* s2 .ddd.
237		* s2 vv..v
238		* The number of unshared feature types per column is
239		* 20120 (two features of the same type doesn't affect score)
240		* giving an average (pairwise distance) of 5/5 or 1.0
241		*/
242	1	s1.addSequenceFeature(new SequenceFeature("domain", null, 1, 3, 0f,
243		null));
244	1	s1.addSequenceFeature(new SequenceFeature("variant", null, 2, 4, 0f,
245		null));
246	1	s1.addSequenceFeature(new SequenceFeature("variant", null, 3, 5, 0f,
247		null));
248	1	s2.addSequenceFeature(new SequenceFeature("domain", null, 2, 4, 0f,
249		null));
250	1	s2.addSequenceFeature(new SequenceFeature("variant", null, 1, 2, 0f,
251		null));
252	1	s2.addSequenceFeature(new SequenceFeature("variant", null, 5, 5, 0f,
253		null));
254	1	alf.setShowSeqFeatures(true);
255	1	alf.getFeatureRenderer().findAllFeatures(true);
256
257	1	ScoreModelI sm = new FeatureDistanceModel();
258	1	sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
259		alf.getCurrentView().getAlignPanel());
260	1	alf.selectAllSequenceMenuItem_actionPerformed(null);
261
262	1	AlignmentView alignmentView = alf.getViewport()
263		.getAlignmentView(true);
264	1	MatrixI distances = sm.findDistances(alignmentView,
265		SimilarityParams.Jalview);
266	1	assertEquals(distances.width(), 2);
267	1	assertEquals(distances.height(), 2);
268	1	assertEquals(distances.getValue(0, 0), 0d);
269	1	assertEquals(distances.getValue(1, 1), 0d);
270
271	1	assertEquals(distances.getValue(0, 1), 1d,
272		"expected identical pairs. (check normalisation for similarity score)");
273	1	assertEquals(distances.getValue(1, 0), 1d);
274		}
275
276		/**
277		* Verify computed distances with varying parameter options
278		*/
		100% Uncovered Elements: 0 (14) Complexity: 1 Complexity Density: 0.07 1PASS
279	1	@Test(groups = "Functional")...
280		public void testFindDistances_withParams()
281		{
282	1	AlignFrame af = setupAlignmentView();
283	1	AlignViewport viewport = af.getViewport();
284	1	AlignmentView view = viewport.getAlignmentView(false);
285
286	1	ScoreModelI sm = new FeatureDistanceModel();
287	1	sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
288		af.alignPanel);
289
290		/*
291		* feature distance model always normalises by region width
292		* gap-gap is always included (but scores zero)
293		* the only variable parameter is 'includeGaps'
294		*/
295
296		/*
297		* include gaps
298		* score = 3 + 3 + 0 + 2 + 3 + 2 = 13/6
299		*/
300	1	SimilarityParamsI params = new SimilarityParams(true, true, true, true);
301	1	MatrixI distances = sm.findDistances(view, params);
302	1	assertEquals(distances.getValue(0, 0), 0d);
303	1	assertEquals(distances.getValue(1, 1), 0d);
304	1	assertEquals(distances.getValue(0, 1), 13d / 6); // should be 13d/6
305	1	assertEquals(distances.getValue(1, 0), 13d / 6);
306
307		/*
308		* exclude gaps
309		* score = 3 + 3 + 0 + 0 + 0 + 0 = 6/6
310		*/
311	1	params = new SimilarityParams(true, true, false, true);
312	1	distances = sm.findDistances(view, params);
313	1	assertEquals(distances.getValue(0, 1), 6d / 6);// should be 6d/6
314		}
315
316		/**
317		* <pre>
318		* Set up
319		* column 1 2 3 4 5 6
320		* seq s1 F R - K - S
321		* seq s2 F S - - L
322		* s1 chain c c c c
323		* s1 domain d d d d
324		* s2 chain c c c
325		* s2 metal m m m
326		* s2 Pfam P P P
327		* scores: 3 3 0 2 3 2
328		* </pre>
329		*
330		* @return
331		*/
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08
332	1	protected AlignFrame setupAlignmentView()...
333		{
334		/*
335		* for now, using space for gap to match callers of
336		* AlignmentView.getSequenceStrings()
337		* may change this to '-' (with corresponding change to matrices)
338		*/
339	1	SequenceI s1 = new Sequence("s1", "FR K S");
340	1	SequenceI s2 = new Sequence("s2", "FS L");
341
342	1	s1.addSequenceFeature(new SequenceFeature("chain", null, 1, 4, 0f, null));
343	1	s1.addSequenceFeature(new SequenceFeature("domain", null, 1, 4, 0f,
344		null));
345	1	s2.addSequenceFeature(new SequenceFeature("chain", null, 1, 3, 0f, null));
346	1	s2.addSequenceFeature(new SequenceFeature("metal", null, 1, 3, 0f, null));
347	1	s2.addSequenceFeature(new SequenceFeature("Pfam", null, 1, 3, 0f, null));
348	1	AlignmentI al = new Alignment(new SequenceI[] { s1, s2 });
349	1	AlignFrame af = new AlignFrame(al, 300, 300);
350	1	af.setShowSeqFeatures(true);
351	1	af.getFeatureRenderer().findAllFeatures(true);
352	1	return af;
353		}
354
355		}