Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
EnsemblGenomeTest	41	73	6	0	1.0100%	Show methods

Class EnsemblGenomeTest

Class EnsemblGenomeTest	Line # 41	Total Statements 73	Complexity 6	Uncovered Elements 0	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4444	2.02	1.01	0.00	1.0 1.0100%
setUp() : void   setUp() : void	5151	1.01	1.01	0.00	1.0 1.0100%
tearDown() : void   tearDown() : void	5757	1.01	1.01	0.00	1.0 1.0100%
testGetGenomicRangesFromFeatures() : void   testGetGenomicRangesFromFeatures() : void	6767	35.035	1.01	0.00	1.0 1.0100%
testRetainFeature() : void   testRetainFeature() : void	129129	14.014	1.01	0.00	1.0 1.0100%
testIdentifiesSequence() : void   testIdentifiesSequence() : void	164164	20.020	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.4556962	jalview.ext.ensembl.EnsemblGenomeTest.testGetGenomicRangesFromFeaturesjalview.ext.ensembl.EnsemblGenomeTest.testGetGenomicRangesFromFeatures	1PASS
	0.2658228	jalview.ext.ensembl.EnsemblGenomeTest.testIdentifiesSequencejalview.ext.ensembl.EnsemblGenomeTest.testIdentifiesSequence	1PASS
	0.18987341	jalview.ext.ensembl.EnsemblGenomeTest.testRetainFeaturejalview.ext.ensembl.EnsemblGenomeTest.testRetainFeature	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.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.SequenceDummy;
28		import jalview.datamodel.SequenceFeature;
29		import jalview.datamodel.SequenceI;
30		import jalview.gui.JvOptionPane;
31		import jalview.io.gff.SequenceOntologyFactory;
32		import jalview.io.gff.SequenceOntologyLite;
33		import jalview.util.MapList;
34
35		import java.util.List;
36
37		import org.testng.annotations.AfterClass;
38		import org.testng.annotations.BeforeClass;
39		import org.testng.annotations.Test;
40
		100% Uncovered Elements: 0 (79) Complexity: 6 Complexity Density: 0.08
41		public class EnsemblGenomeTest
42		{
43
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
44	1	@BeforeClass(alwaysRun = true)...
45		public void setUpJvOptionPane()
46		{
47	1	JvOptionPane.setInteractiveMode(false);
48	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
49		}
50
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
51	1	@BeforeClass(alwaysRun = true)...
52		public void setUp()
53		{
54	1	SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
55		}
56
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
57	1	@AfterClass(alwaysRun = true)...
58		public void tearDown()
59		{
60	1	SequenceOntologyFactory.setInstance(null);
61		}
62
63		/**
64		* Test that the genomic sequence part of genomic sequence is correctly
65		* identified by 'transcript' features (or subtypes) with the correct gene ID
66		*/
		100% Uncovered Elements: 0 (35) Complexity: 1 Complexity Density: 0.03 1PASS
67	1	@Test(groups = "Functional")...
68		public void testGetGenomicRangesFromFeatures()
69		{
70	1	EnsemblGenome testee = new EnsemblGenome();
71	1	SequenceI genomic = new SequenceDummy("chr7");
72	1	genomic.setStart(10000);
73	1	genomic.setEnd(50000);
74	1	String transcriptId = "ABC123";
75
76		// transcript at (start+10000) length 501
77	1	SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
78		20500, 0f, null);
79	1	sf.setValue("ID", "transcript:" + transcriptId);
80	1	sf.setStrand("+");
81	1	genomic.addSequenceFeature(sf);
82
83		// transcript (sub-type) at (start + 10500) length 101
84	1	sf = new SequenceFeature("ncRNA", "", 10500, 10600, 0f, null);
85	1	sf.setValue("ID", "transcript:" + transcriptId);
86	1	sf.setStrand("+");
87	1	genomic.addSequenceFeature(sf);
88
89		// Ensembl treats NMD_transcript_variant as if transcript
90		// although strictly it is a sequence_variant in SO
91	1	sf = new SequenceFeature("NMD_transcript_variant", "", 11000, 12000,
92		0f, null);
93	1	sf.setValue("ID", "transcript:" + transcriptId);
94	1	sf.setStrand("+");
95	1	genomic.addSequenceFeature(sf);
96
97		// transcript with a different ID doesn't count
98	1	sf = new SequenceFeature("transcript", "", 11500, 12600, 0f, null);
99	1	sf.setValue("ID", "transcript:anotherOne");
100	1	genomic.addSequenceFeature(sf);
101
102		// parent of transcript feature doesn't count
103	1	sf = new SequenceFeature("gene_member_region", "", 10000, 50000, 0f,
104		null);
105	1	genomic.addSequenceFeature(sf);
106
107	1	MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
108		transcriptId, 23);
109	1	List<int[]> fromRanges = ranges.getFromRanges();
110	1	assertEquals(3, fromRanges.size());
111		// from ranges should be sorted by start order
112	1	assertEquals(10500, fromRanges.get(0)[0]);
113	1	assertEquals(10600, fromRanges.get(0)[1]);
114	1	assertEquals(11000, fromRanges.get(1)[0]);
115	1	assertEquals(12000, fromRanges.get(1)[1]);
116	1	assertEquals(20000, fromRanges.get(2)[0]);
117	1	assertEquals(20500, fromRanges.get(2)[1]);
118		// to range should start from given start numbering
119	1	List<int[]> toRanges = ranges.getToRanges();
120	1	assertEquals(1, toRanges.size());
121	1	assertEquals(23, toRanges.get(0)[0]);
122	1	assertEquals(1625, toRanges.get(0)[1]);
123		}
124
125		/**
126		* Test the method that retains features except for 'transcript' (or
127		* sub-type), or those with parent other than the given id
128		*/
		100% Uncovered Elements: 0 (14) Complexity: 1 Complexity Density: 0.07 1PASS
129	1	@Test(groups = "Functional")...
130		public void testRetainFeature()
131		{
132	1	String accId = "ABC123";
133	1	EnsemblGenome testee = new EnsemblGenome();
134
135	1	SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
136		20500, 0f, null);
137	1	assertFalse(testee.retainFeature(sf, accId));
138
139	1	sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f,
140		null);
141	1	assertFalse(testee.retainFeature(sf, accId));
142
143	1	sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
144		0f, null);
145	1	assertFalse(testee.retainFeature(sf, accId));
146
147		// other feature with no parent is kept
148	1	sf = new SequenceFeature("anything", "", 20000, 20500, 0f, null);
149	1	assertTrue(testee.retainFeature(sf, accId));
150
151		// other feature with correct parent is kept
152	1	sf.setValue("Parent", "transcript:" + accId);
153	1	assertTrue(testee.retainFeature(sf, accId));
154
155		// other feature with wrong parent is not kept
156	1	sf.setValue("Parent", "transcript:XYZ");
157	1	assertFalse(testee.retainFeature(sf, accId));
158		}
159
160		/**
161		* Test the method that picks out 'transcript' (or subtype) features with the
162		* accession id as ID
163		*/
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
164	1	@Test(groups = "Functional")...
165		public void testIdentifiesSequence()
166		{
167	1	String accId = "ABC123";
168	1	EnsemblGenome testee = new EnsemblGenome();
169
170		// transcript with no ID not valid
171	1	SequenceFeature sf = new SequenceFeature("transcript", "", 1, 2, 0f,
172		null);
173	1	assertFalse(testee.identifiesSequence(sf, accId));
174
175		// transcript with wrong ID not valid
176	1	sf.setValue("ID", "transcript");
177	1	assertFalse(testee.identifiesSequence(sf, accId));
178
179		// transcript with right ID is valid
180	1	sf.setValue("ID", "transcript:" + accId);
181	1	assertTrue(testee.identifiesSequence(sf, accId));
182
183		// transcript sub-type with right ID is valid
184	1	sf = new SequenceFeature("ncRNA", "", 1, 2, 0f, null);
185	1	sf.setValue("ID", "transcript:" + accId);
186	1	assertTrue(testee.identifiesSequence(sf, accId));
187
188		// Ensembl treats NMD_transcript_variant as if a transcript
189	1	sf = new SequenceFeature("NMD_transcript_variant", "", 1, 2, 0f, null);
190	1	sf.setValue("ID", "transcript:" + accId);
191	1	assertTrue(testee.identifiesSequence(sf, accId));
192
193		// gene not valid:
194	1	sf = new SequenceFeature("gene", "", 1, 2, 0f, null);
195	1	sf.setValue("ID", "transcript:" + accId);
196	1	assertFalse(testee.identifiesSequence(sf, accId));
197
198		// exon not valid:
199	1	sf = new SequenceFeature("exon", "", 1, 2, 0f, null);
200	1	sf.setValue("ID", "transcript:" + accId);
201	1	assertFalse(testee.identifiesSequence(sf, accId));
202		}
203
204		}