Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FeatureDistanceModelTest	47	113	14	0.00%	Show methods

Class FeatureDistanceModelTest

Class FeatureDistanceModelTest	Line # 47	Total Statements 113	Complexity 14	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5050	2.02	1.01	0.0 0.00%
getTestAlignmentFrame() : AlignFrame   getTestAlignmentFrame() : AlignFrame	7676	20.020	5.05	0.0 0.00%
testFeatureScoreModel() : void   testFeatureScoreModel() : void	114114	7.07	1.01	0.0 0.00%
testFeatureScoreModel_hiddenFirstColumn() : void   testFeatureScoreModel_hiddenFirstColumn() : void	131131	8.08	1.01	0.0 0.00%
testFeatureScoreModel_HiddenColumns() : void   testFeatureScoreModel_HiddenColumns() : void	149149	11.011	2.02	0.0 0.00%
testFindFeatureAt_PointFeature() : void   testFindFeatureAt_PointFeature() : void	182182	16.016	1.01	0.0 0.00%
testFindDistances() : void   testFindDistances() : void	225225	23.023	1.01	0.0 0.00%
testFindDistances_withParams() : void   testFindDistances_withParams() : void	282282	14.014	1.01	0.0 0.00%
setupAlignmentView() : AlignFrame   setupAlignmentView() : AlignFrame	335335	12.012	1.01	0.0 0.00%

 

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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.AlignViewportI;
27		import jalview.api.analysis.ScoreModelI;
28		import jalview.api.analysis.SimilarityParamsI;
29		import jalview.datamodel.Alignment;
30		import jalview.datamodel.AlignmentI;
31		import jalview.datamodel.AlignmentView;
32		import jalview.datamodel.Sequence;
33		import jalview.datamodel.SequenceFeature;
34		import jalview.datamodel.SequenceI;
35		import jalview.gui.AlignFrame;
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
		0% Uncovered Elements: 132 (132) Complexity: 14 Complexity Density: 0.12
47		public class FeatureDistanceModelTest
48		{
49
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
50	0	@BeforeClass(alwaysRun = true)...
51		public void setUpJvOptionPane()
52		{
53	0	JvOptionPane.setInteractiveMode(false);
54	0	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		*/
		0% Uncovered Elements: 28 (28) Complexity: 5 Complexity Density: 0.25
76	0	public AlignFrame getTestAlignmentFrame()...
77		{
78	0	AlignFrame alf = new FileLoader(false)
79		.LoadFileWaitTillLoaded(alntestFile, DataSourceType.PASTE);
80	0	AlignmentI al = alf.getViewport().getAlignment();
81	0	Assert.assertEquals(al.getHeight(), 4);
82	0	Assert.assertEquals(al.getWidth(), 5);
83	0	for (int i = 0; i < 4; i++)
84		{
85	0	SequenceI ds = al.getSequenceAt(i).getDatasetSequence();
86	0	if (sf1[i * 2] > 0)
87		{
88	0	ds.addSequenceFeature(new SequenceFeature("sf1", "sf1", sf1[i * 2],
89		sf1[i * 2 + 1], "sf1"));
90		}
91	0	if (sf2[i * 2] > 0)
92		{
93	0	ds.addSequenceFeature(new SequenceFeature("sf2", "sf2", sf2[i * 2],
94		sf2[i * 2 + 1], "sf2"));
95		}
96	0	if (sf3[i * 2] > 0)
97		{
98	0	ds.addSequenceFeature(new SequenceFeature("sf3", "sf3", sf3[i * 2],
99		sf3[i * 2 + 1], "sf3"));
100		}
101		}
102	0	alf.setShowSeqFeatures(true);
103	0	alf.getFeatureRenderer().setVisible("sf1");
104	0	alf.getFeatureRenderer().setVisible("sf2");
105	0	alf.getFeatureRenderer().setVisible("sf3");
106	0	alf.getFeatureRenderer().findAllFeatures(true);
107	0	Assert.assertEquals(
108		alf.getFeatureRenderer().getDisplayedFeatureTypes().size(), 3,
109		"Number of feature types");
110	0	assertTrue(alf.getCurrentView().areFeaturesDisplayed());
111	0	return alf;
112		}
113
		0% Uncovered Elements: 7 (7) Complexity: 1 Complexity Density: 0.14 4-
114	0	@Test(groups = { "Functional" })...
115		public void testFeatureScoreModel() throws Exception
116		{
117	0	AlignFrame alf = getTestAlignmentFrame();
118	0	ScoreModelI sm = new FeatureDistanceModel();
119	0	sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
120		alf.getCurrentView().getAlignPanel());
121	0	alf.selectAllSequenceMenuItem_actionPerformed(null);
122
123	0	MatrixI dm = sm.findDistances(alf.getViewport().getAlignmentView(true),
124		SimilarityParams.Jalview);
125	0	assertEquals(dm.getValue(0, 2), 0d,
126		"FER1_MESCR (0) should be identical with RAPSA (2)");
127	0	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
		0% Uncovered Elements: 8 (8) Complexity: 1 Complexity Density: 0.12 4-
131	0	@Test(groups = { "Functional" })...
132		public void testFeatureScoreModel_hiddenFirstColumn() throws Exception
133		{
134	0	AlignFrame alf = getTestAlignmentFrame();
135		// hiding first two columns shouldn't affect the tree
136	0	alf.getViewport().hideColumns(0, 1);
137	0	ScoreModelI sm = new FeatureDistanceModel();
138	0	sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
139		alf.getCurrentView().getAlignPanel());
140	0	alf.selectAllSequenceMenuItem_actionPerformed(null);
141	0	MatrixI dm = sm.findDistances(alf.getViewport().getAlignmentView(true),
142		SimilarityParams.Jalview);
143	0	assertEquals(dm.getValue(0, 2), 0d,
144		"FER1_MESCR (0) should be identical with RAPSA (2)");
145	0	assertTrue(dm.getValue(0, 1) > dm.getValue(0, 2),
146		"FER1_MESCR (0) should be further from SPIOL (1) than it is from RAPSA (2)");
147		}
148
		0% Uncovered Elements: 13 (13) Complexity: 2 Complexity Density: 0.18 4-
149	0	@Test(groups = { "Functional" })...
150		public void testFeatureScoreModel_HiddenColumns() throws Exception
151		{
152	0	AlignFrame alf = getTestAlignmentFrame();
153		// hide columns and check tree changes
154	0	alf.getViewport().hideColumns(3, 4);
155	0	alf.getViewport().hideColumns(0, 1);
156		// getName() can become static in Java 8
157	0	ScoreModelI sm = new FeatureDistanceModel();
158	0	sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
159		alf.getCurrentView().getAlignPanel());
160	0	alf.selectAllSequenceMenuItem_actionPerformed(null);
161	0	MatrixI dm = sm.findDistances(alf.getViewport().getAlignmentView(true),
162		SimilarityParams.Jalview);
163	0	assertEquals(dm.getValue(0, 2), 0d,
164		"After hiding last two columns FER1_MESCR (0) should still be identical with RAPSA (2)");
165	0	assertEquals(dm.getValue(0, 1), 0d,
166		"After hiding last two columns FER1_MESCR (0) should now also be identical with SPIOL (1)");
167	0	for (int s = 0; s < 3; s++)
168		{
169	0	assertTrue(dm.getValue(s, 3) > 0d,
170		"After hiding last two columns "
171		+ alf.getViewport().getAlignment().getSequenceAt(s)
172		.getName()
173		+ "(" + s
174		+ ") should still be distinct from FER1_MAIZE (3)");
175		}
176		}
177
178		/**
179		* Check findFeatureAt doesn't return contact features except at contact
180		* points TODO:move to under the FeatureRendererModel test suite
181		*/
		0% Uncovered Elements: 16 (16) Complexity: 1 Complexity Density: 0.06 4-
182	0	@Test(groups = { "Functional" })...
183		public void testFindFeatureAt_PointFeature() throws Exception
184		{
185	0	String alignment = "a CCCCCCGGGGGGCCCCCC\n" + "b CCCCCCGGGGGGCCCCCC\n"
186		+ "c CCCCCCGGGGGGCCCCCC\n";
187	0	AlignFrame af = new jalview.io.FileLoader(false)
188		.LoadFileWaitTillLoaded(alignment, DataSourceType.PASTE);
189	0	SequenceI aseq = af.getViewport().getAlignment().getSequenceAt(0);
190	0	SequenceFeature sf = null;
191	0	sf = new SequenceFeature("disulphide bond", "", 2, 5, Float.NaN, "");
192	0	aseq.addSequenceFeature(sf);
193	0	assertTrue(sf.isContactFeature());
194	0	af.refreshFeatureUI(true);
195	0	af.getFeatureRenderer().setAllVisible(Arrays.asList("disulphide bond"));
196	0	Assert.assertEquals(
197		af.getFeatureRenderer().getDisplayedFeatureTypes().size(), 1,
198		"Should be just one feature type displayed");
199		// step through and check for pointwise feature presence/absence
200	0	Assert.assertEquals(
201		af.getFeatureRenderer().findFeaturesAtColumn(aseq, 1).size(),
202		0);
203		// step through and check for pointwise feature presence/absence
204	0	Assert.assertEquals(
205		af.getFeatureRenderer().findFeaturesAtColumn(aseq, 2).size(),
206		1);
207		// step through and check for pointwise feature presence/absence
208	0	Assert.assertEquals(
209		af.getFeatureRenderer().findFeaturesAtColumn(aseq, 3).size(),
210		0);
211		// step through and check for pointwise feature presence/absence
212	0	Assert.assertEquals(
213		af.getFeatureRenderer().findFeaturesAtColumn(aseq, 4).size(),
214		0);
215		// step through and check for pointwise feature presence/absence
216	0	Assert.assertEquals(
217		af.getFeatureRenderer().findFeaturesAtColumn(aseq, 5).size(),
218		1);
219		// step through and check for pointwise feature presence/absence
220	0	Assert.assertEquals(
221		af.getFeatureRenderer().findFeaturesAtColumn(aseq, 6).size(),
222		0);
223		}
224
		0% Uncovered Elements: 23 (23) Complexity: 1 Complexity Density: 0.04 4-
225	0	@Test(groups = { "Functional" })...
226		public void testFindDistances() throws Exception
227		{
228	0	String seqs = ">s1\nABCDE\n>seq2\nABCDE\n";
229	0	AlignFrame alf = new FileLoader().LoadFileWaitTillLoaded(seqs,
230		DataSourceType.PASTE);
231	0	SequenceI s1 = alf.getViewport().getAlignment().getSequenceAt(0);
232	0	SequenceI s2 = alf.getViewport().getAlignment().getSequenceAt(1);
233
234		/*
235		* set domain and variant features thus:
236		* ----5
237		* s1 ddd..
238		* s1 .vvv.
239		* s1 ..vvv
240		* s2 .ddd.
241		* s2 vv..v
242		* The number of unshared feature types per column is
243		* 20120 (two features of the same type doesn't affect score)
244		* giving an average (pairwise distance) of 5/5 or 1.0
245		*/
246	0	s1.addSequenceFeature(
247		new SequenceFeature("domain", null, 1, 3, 0f, null));
248	0	s1.addSequenceFeature(
249		new SequenceFeature("variant", null, 2, 4, 0f, null));
250	0	s1.addSequenceFeature(
251		new SequenceFeature("variant", null, 3, 5, 0f, null));
252	0	s2.addSequenceFeature(
253		new SequenceFeature("domain", null, 2, 4, 0f, null));
254	0	s2.addSequenceFeature(
255		new SequenceFeature("variant", null, 1, 2, 0f, null));
256	0	s2.addSequenceFeature(
257		new SequenceFeature("variant", null, 5, 5, 0f, null));
258	0	alf.setShowSeqFeatures(true);
259	0	alf.getFeatureRenderer().findAllFeatures(true);
260
261	0	ScoreModelI sm = new FeatureDistanceModel();
262	0	sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
263		alf.getCurrentView().getAlignPanel());
264	0	alf.selectAllSequenceMenuItem_actionPerformed(null);
265
266	0	AlignmentView alignmentView = alf.getViewport().getAlignmentView(true);
267	0	MatrixI distances = sm.findDistances(alignmentView,
268		SimilarityParams.Jalview);
269	0	assertEquals(distances.width(), 2);
270	0	assertEquals(distances.height(), 2);
271	0	assertEquals(distances.getValue(0, 0), 0d);
272	0	assertEquals(distances.getValue(1, 1), 0d);
273
274	0	assertEquals(distances.getValue(0, 1), 1d,
275		"expected identical pairs. (check normalisation for similarity score)");
276	0	assertEquals(distances.getValue(1, 0), 1d);
277		}
278
279		/**
280		* Verify computed distances with varying parameter options
281		*/
		0% Uncovered Elements: 14 (14) Complexity: 1 Complexity Density: 0.07 4-
282	0	@Test(groups = "Functional")...
283		public void testFindDistances_withParams()
284		{
285	0	AlignFrame af = setupAlignmentView();
286	0	AlignViewportI viewport = af.getViewport();
287	0	AlignmentView view = viewport.getAlignmentView(false);
288
289	0	ScoreModelI sm = new FeatureDistanceModel();
290	0	sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
291		af.alignPanel);
292
293		/*
294		* feature distance model always normalises by region width
295		* gap-gap is always included (but scores zero)
296		* the only variable parameter is 'includeGaps'
297		*/
298
299		/*
300		* include gaps
301		* score = 3 + 3 + 0 + 2 + 3 + 2 = 13/6
302		*/
303	0	SimilarityParamsI params = new SimilarityParams(true, true, true, true);
304	0	MatrixI distances = sm.findDistances(view, params);
305	0	assertEquals(distances.getValue(0, 0), 0d);
306	0	assertEquals(distances.getValue(1, 1), 0d);
307	0	assertEquals(distances.getValue(0, 1), 13d / 6); // should be 13d/6
308	0	assertEquals(distances.getValue(1, 0), 13d / 6);
309
310		/*
311		* exclude gaps
312		* score = 3 + 3 + 0 + 0 + 0 + 0 = 6/6
313		*/
314	0	params = new SimilarityParams(true, true, false, true);
315	0	distances = sm.findDistances(view, params);
316	0	assertEquals(distances.getValue(0, 1), 6d / 6);// should be 6d/6
317		}
318
319		/**
320		* <pre>
321		* Set up
322		* column 1 2 3 4 5 6
323		* seq s1 F R - K - S
324		* seq s2 F S - - L
325		* s1 chain c c c c
326		* s1 domain d d d d
327		* s2 chain c c c
328		* s2 metal m m m
329		* s2 Pfam P P P
330		* scores: 3 3 0 2 3 2
331		* </pre>
332		*
333		* @return
334		*/
		0% Uncovered Elements: 12 (12) Complexity: 1 Complexity Density: 0.08
335	0	protected AlignFrame setupAlignmentView()...
336		{
337		/*
338		* for now, using space for gap to match callers of
339		* AlignmentView.getSequenceStrings()
340		* may change this to '-' (with corresponding change to matrices)
341		*/
342	0	SequenceI s1 = new Sequence("s1", "FR K S");
343	0	SequenceI s2 = new Sequence("s2", "FS L");
344
345	0	s1.addSequenceFeature(
346		new SequenceFeature("chain", null, 1, 4, 0f, null));
347	0	s1.addSequenceFeature(
348		new SequenceFeature("domain", null, 1, 4, 0f, null));
349	0	s2.addSequenceFeature(
350		new SequenceFeature("chain", null, 1, 3, 0f, null));
351	0	s2.addSequenceFeature(
352		new SequenceFeature("metal", null, 1, 3, 0f, null));
353	0	s2.addSequenceFeature(
354		new SequenceFeature("Pfam", null, 1, 3, 0f, null));
355	0	AlignmentI al = new Alignment(new SequenceI[] { s1, s2 });
356	0	AlignFrame af = new AlignFrame(al, 300, 300);
357	0	af.setShowSeqFeatures(true);
358	0	af.getFeatureRenderer().findAllFeatures(true);
359	0	return af;
360		}
361
362		}