Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
MappedFeaturesTest	34	45	1	1.0100%	Show methods

Class MappedFeaturesTest

Class MappedFeaturesTest	Line # 34	Total Statements 45	Complexity 1	TOTAL Coverage 1.0100%
testFindProteinVariants() : void   testFindProteinVariants() : void	3636	45.045	1.01	1.0 1.0100%

 

Contributing tests

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	Test contribution	Test	Result	Actions
	1.0	jalview.datamodel.MappedFeaturesTest.testFindProteinVariantsjalview.datamodel.MappedFeaturesTest.testFindProteinVariants	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.datamodel;
22
23		import static org.testng.Assert.assertEquals;
24
25		import jalview.util.MapList;
26
27		import java.util.ArrayList;
28		import java.util.HashMap;
29		import java.util.List;
30		import java.util.Map;
31
32		import org.testng.annotations.Test;
33
		100% Uncovered Elements: 0 (46) Complexity: 1 Complexity Density: 0.02
34		public class MappedFeaturesTest
35		{
		100% Uncovered Elements: 0 (45) Complexity: 1 Complexity Density: 0.02 1PASS
36	1	@Test(groups = "Functional")...
37		public void testFindProteinVariants()
38		{
39		/*
40		* scenario:
41		* dna/10-20 aCGTaGctGAa (codons CGT=R, GGA = G)
42		* mapping: 3:1 from [11-13,15,18-19] to peptide/1-2 RG
43		*/
44	1	SequenceI from = new Sequence("dna/10-20", "acgTAGCTGAA");
45	1	SequenceI to = new Sequence("peptide", "RG");
46	1	MapList map = new MapList(new int[] { 11, 13, 15, 15, 18, 19 },
47		new int[]
48		{ 1, 2 }, 3, 1);
49	1	Mapping mapping = new Mapping(to, map);
50
51		/*
52		* variants
53		* C>T at dna11, consequence CGT>TGT=C
54		* T>C at dna13, consequence CGT>CGC synonymous
55		*/
56	1	List<SequenceFeature> features = new ArrayList<>();
57	1	SequenceFeature sf1 = new SequenceFeature("sequence_variant", "C,T", 11,
58		11, null);
59	1	sf1.setValue("alleles", "C,T");
60	1	features.add(sf1);
61	1	SequenceFeature sf2 = new SequenceFeature("sequence_variant", "T,C", 13,
62		13, null);
63	1	sf2.setValue("alleles", "T,C");
64	1	features.add(sf2);
65
66		/*
67		* missense variant in first codon
68		*/
69	1	MappedFeatures mf = new MappedFeatures(mapping, from, 1, 'R', features);
70	1	String variant = mf.findProteinVariants(sf1);
71	1	assertEquals(variant, "p.Arg1Cys");
72
73		/*
74		* more than one alternative allele
75		* C>G consequence is GGT=G
76		* peptide variants as a comma-separated list
77		*/
78	1	sf1.setValue("alleles", "C,T,G");
79	1	variant = mf.findProteinVariants(sf1);
80	1	assertEquals(variant, "p.Arg1Cys,p.Arg1Gly");
81
82		/*
83		* synonymous variant in first codon
84		* shown in HGVS notation on peptide
85		*/
86	1	variant = mf.findProteinVariants(sf2);
87	1	assertEquals(variant, "c.13T>C(p.=)");
88
89		/*
90		* CSQ:HGVSp value is used if present
91		* _and_ it contains "p." following a colon
92		*/
93	1	Map<String, String> csq = new HashMap<>();
94	1	csq.put("HGVSp", "hello:world");
95	1	sf2.setValue("CSQ", csq);
96	1	variant = mf.findProteinVariants(sf2);
97	1	assertEquals(variant, "c.13T>C(p.=)");
98	1	csq.put("HGVSp", "p.HelloWorld");
99	1	variant = mf.findProteinVariants(sf2);
100	1	assertEquals(variant, "c.13T>C(p.=)");
101	1	csq.put("HGVSp", "try this:hellop.world");
102	1	variant = mf.findProteinVariants(sf2);
103	1	assertEquals(variant, "hellop.world");
104
105		/*
106		* missense and indel variants in second codon
107		* - codon is GGA spliced from dna positions 15,18,19
108		* - SNP G>T in second position mutates GGA>G to GTA>V
109		* - indel variants are not computed or reported
110		*/
111	1	mf = new MappedFeatures(mapping, from, 2, 'G', features);
112	1	features.clear();
113	1	SequenceFeature sf3 = new SequenceFeature("sequence_variant",
114		"G,-,CG,T", 18, 18, null);
115	1	sf3.setValue("alleles", "G,-,CG,T");
116	1	features.add(sf3);
117	1	variant = mf.findProteinVariants(sf3);
118	1	assertEquals(variant, "p.Gly2Val");
119
120		/*
121		* G>T in first position gives TGA Stop
122		* shown with HGVS notation as 'Ter'
123		*/
124	1	SequenceFeature sf4 = new SequenceFeature("sequence_variant", "G,T", 15,
125		15, null);
126	1	sf4.setValue("alleles", "G,-,CG,T");
127	1	features.add(sf4);
128	1	variant = mf.findProteinVariants(sf4);
129	1	assertEquals(variant, "p.Gly2Ter");
130
131		/*
132		* feature must be one of those in MappedFeatures
133		*/
134	1	SequenceFeature sf9 = new SequenceFeature("sequence_variant", "G,C", 15,
135		15, null);
136	1	variant = mf.findProteinVariants(sf9);
137	1	assertEquals(variant, "");
138		}
139		}