Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EnsemblGenomeTest	42	83	6	0.00%	Show methods

Class EnsemblGenomeTest

Class EnsemblGenomeTest	Line # 42	Total Statements 83	Complexity 6	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4545	2.02	1.01	0.0 0.00%
setUp() : void   setUp() : void	5252	1.01	1.01	0.0 0.00%
tearDown() : void   tearDown() : void	5858	1.01	1.01	0.0 0.00%
testGetGenomicRangesFromFeatures() : void   testGetGenomicRangesFromFeatures() : void	6868	35.035	1.01	0.0 0.00%
testRetainFeature() : void   testRetainFeature() : void	130130	14.014	1.01	0.0 0.00%
testGetIdentifyingFeatures() : void   testGetIdentifyingFeatures() : void	165165	30.030	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.ext.ensembl;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertFalse;
25		import static org.testng.AssertJUnit.assertTrue;
26
27		import jalview.datamodel.Sequence;
28		import jalview.datamodel.SequenceDummy;
29		import jalview.datamodel.SequenceFeature;
30		import jalview.datamodel.SequenceI;
31		import jalview.gui.JvOptionPane;
32		import jalview.io.gff.SequenceOntologyFactory;
33		import jalview.io.gff.SequenceOntologyLite;
34		import jalview.util.MapList;
35
36		import java.util.List;
37
38		import org.testng.annotations.AfterClass;
39		import org.testng.annotations.BeforeClass;
40		import org.testng.annotations.Test;
41
		0% Uncovered Elements: 89 (89) Complexity: 6 Complexity Density: 0.07
42		public class EnsemblGenomeTest
43		{
44
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
45	0	@BeforeClass(alwaysRun = true)...
46		public void setUpJvOptionPane()
47		{
48	0	JvOptionPane.setInteractiveMode(false);
49	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
50		}
51
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
52	0	@BeforeClass(alwaysRun = true)...
53		public void setUp()
54		{
55	0	SequenceOntologyFactory.setSequenceOntology(new SequenceOntologyLite());
56		}
57
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
58	0	@AfterClass(alwaysRun = true)...
59		public void tearDown()
60		{
61	0	SequenceOntologyFactory.setSequenceOntology(null);
62		}
63
64		/**
65		* Test that the genomic sequence part of genomic sequence is correctly
66		* identified by 'transcript' features (or subtypes) with the correct gene ID
67		*/
		0% Uncovered Elements: 35 (35) Complexity: 1 Complexity Density: 0.03 4-
68	0	@Test(groups = "Functional")...
69		public void testGetGenomicRangesFromFeatures()
70		{
71	0	EnsemblGenome testee = new EnsemblGenome();
72	0	SequenceI genomic = new SequenceDummy("chr7");
73	0	genomic.setStart(10000);
74	0	genomic.setEnd(50000);
75	0	String transcriptId = "ABC123";
76
77		// transcript at (start+10000) length 501
78	0	SequenceFeature sf = new SequenceFeature("transcript", "", 20000, 20500,
79		0f, null);
80	0	sf.setValue("id", transcriptId);
81	0	sf.setStrand("+");
82	0	genomic.addSequenceFeature(sf);
83
84		// transcript (sub-type) at (start + 10500) length 101
85	0	sf = new SequenceFeature("ncRNA", "", 10500, 10600, 0f, null);
86	0	sf.setValue("id", transcriptId);
87	0	sf.setStrand("+");
88	0	genomic.addSequenceFeature(sf);
89
90		// Ensembl treats NMD_transcript_variant as if transcript
91		// although strictly it is a sequence_variant in SO
92	0	sf = new SequenceFeature("NMD_transcript_variant", "", 11000, 12000, 0f,
93		null);
94	0	sf.setValue("id", transcriptId);
95	0	sf.setStrand("+");
96	0	genomic.addSequenceFeature(sf);
97
98		// transcript with a different ID doesn't count
99	0	sf = new SequenceFeature("transcript", "", 11500, 12600, 0f, null);
100	0	sf.setValue("id", "anotherOne");
101	0	genomic.addSequenceFeature(sf);
102
103		// parent of transcript feature doesn't count
104	0	sf = new SequenceFeature("gene_member_region", "", 10000, 50000, 0f,
105		null);
106	0	genomic.addSequenceFeature(sf);
107
108	0	MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
109		transcriptId, 23);
110	0	List<int[]> fromRanges = ranges.getFromRanges();
111	0	assertEquals(3, fromRanges.size());
112		// from ranges should be sorted by start order
113	0	assertEquals(10500, fromRanges.get(0)[0]);
114	0	assertEquals(10600, fromRanges.get(0)[1]);
115	0	assertEquals(11000, fromRanges.get(1)[0]);
116	0	assertEquals(12000, fromRanges.get(1)[1]);
117	0	assertEquals(20000, fromRanges.get(2)[0]);
118	0	assertEquals(20500, fromRanges.get(2)[1]);
119		// to range should start from given start numbering
120	0	List<int[]> toRanges = ranges.getToRanges();
121	0	assertEquals(1, toRanges.size());
122	0	assertEquals(23, toRanges.get(0)[0]);
123	0	assertEquals(1625, toRanges.get(0)[1]);
124		}
125
126		/**
127		* Test the method that retains features except for 'transcript' (or
128		* sub-type), or those with parent other than the given id
129		*/
		0% Uncovered Elements: 14 (14) Complexity: 1 Complexity Density: 0.07 4-
130	0	@Test(groups = "Functional")...
131		public void testRetainFeature()
132		{
133	0	String accId = "ABC123";
134	0	EnsemblGenome testee = new EnsemblGenome();
135
136	0	SequenceFeature sf = new SequenceFeature("transcript", "", 20000, 20500,
137		0f, null);
138	0	assertFalse(testee.retainFeature(sf, accId));
139
140	0	sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f,
141		null);
142	0	assertFalse(testee.retainFeature(sf, accId));
143
144	0	sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500, 0f,
145		null);
146	0	assertFalse(testee.retainFeature(sf, accId));
147
148		// other feature with no parent is kept
149	0	sf = new SequenceFeature("anything", "", 20000, 20500, 0f, null);
150	0	assertTrue(testee.retainFeature(sf, accId));
151
152		// other feature with correct parent is kept
153	0	sf.setValue("Parent", accId);
154	0	assertTrue(testee.retainFeature(sf, accId));
155
156		// other feature with wrong parent is not kept
157	0	sf.setValue("Parent", "XYZ");
158	0	assertFalse(testee.retainFeature(sf, accId));
159		}
160
161		/**
162		* Test the method that picks out 'transcript' (or subtype) features with the
163		* accession id as ID
164		*/
		0% Uncovered Elements: 30 (30) Complexity: 1 Complexity Density: 0.03 4-
165	0	@Test(groups = "Functional")...
166		public void testGetIdentifyingFeatures()
167		{
168	0	String accId = "ABC123";
169	0	SequenceI seq = new Sequence(accId, "HEARTS");
170
171		// transcript with no ID not valid
172	0	SequenceFeature sf1 = new SequenceFeature("transcript", "", 1, 2, 0f,
173		null);
174	0	seq.addSequenceFeature(sf1);
175
176		// transcript with wrong ID not valid
177		// NB change desc to avoid rejection of duplicate feature!
178	0	SequenceFeature sf2 = new SequenceFeature("transcript", "a", 1, 2, 0f,
179		null);
180	0	sf2.setValue("id", "transcript");
181	0	seq.addSequenceFeature(sf2);
182
183		// transcript with right ID is valid
184	0	SequenceFeature sf3 = new SequenceFeature("transcript", "b", 1, 2, 0f,
185		null);
186	0	sf3.setValue("id", accId);
187	0	seq.addSequenceFeature(sf3);
188
189		// transcript sub-type with right ID is valid
190	0	SequenceFeature sf4 = new SequenceFeature("ncRNA", "", 1, 2, 0f, null);
191	0	sf4.setValue("id", accId);
192	0	seq.addSequenceFeature(sf4);
193
194		// Ensembl treats NMD_transcript_variant as if a transcript
195	0	SequenceFeature sf5 = new SequenceFeature("NMD_transcript_variant", "",
196		1, 2, 0f, null);
197	0	sf5.setValue("id", accId);
198	0	seq.addSequenceFeature(sf5);
199
200		// gene not valid:
201	0	SequenceFeature sf6 = new SequenceFeature("gene", "", 1, 2, 0f, null);
202	0	sf6.setValue("id", accId);
203	0	seq.addSequenceFeature(sf6);
204
205		// exon not valid:
206	0	SequenceFeature sf7 = new SequenceFeature("exon", "", 1, 2, 0f, null);
207	0	sf7.setValue("id", accId);
208	0	seq.addSequenceFeature(sf7);
209
210	0	List<SequenceFeature> sfs = new EnsemblGenome()
211		.getIdentifyingFeatures(seq, accId);
212	0	assertFalse(sfs.contains(sf1));
213	0	assertFalse(sfs.contains(sf2));
214	0	assertTrue(sfs.contains(sf3));
215	0	assertTrue(sfs.contains(sf4));
216	0	assertTrue(sfs.contains(sf5));
217	0	assertFalse(sfs.contains(sf6));
218	0	assertFalse(sfs.contains(sf7));
219		}
220
221		}