Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
MappedFeaturesTest	14	45	1	1.0100%	Show methods

Class MappedFeaturesTest

Class MappedFeaturesTest	Line # 14	Total Statements 45	Complexity 1	TOTAL Coverage 1.0100%
testFindProteinVariants() : void   testFindProteinVariants() : void	1616	45.045	1.01	1.0 1.0100%

 

Contributing tests

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		package jalview.datamodel;
2
3		import static org.testng.Assert.assertEquals;
4
5		import jalview.util.MapList;
6
7		import java.util.ArrayList;
8		import java.util.HashMap;
9		import java.util.List;
10		import java.util.Map;
11
12		import org.testng.annotations.Test;
13
		100% Uncovered Elements: 0 (46) Complexity: 1 Complexity Density: 0.02
14		public class MappedFeaturesTest
15		{
		100% Uncovered Elements: 0 (45) Complexity: 1 Complexity Density: 0.02 1PASS
16	1	@Test(groups = "Functional")...
17		public void testFindProteinVariants()
18		{
19		/*
20		* scenario:
21		* dna/10-20 aCGTaGctGAa (codons CGT=R, GGA = G)
22		* mapping: 3:1 from [11-13,15,18-19] to peptide/1-2 RG
23		*/
24	1	SequenceI from = new Sequence("dna/10-20", "acgTAGCTGAA");
25	1	SequenceI to = new Sequence("peptide", "RG");
26	1	MapList map = new MapList(new int[] { 11, 13, 15, 15, 18, 19 },
27		new int[]
28		{ 1, 2 }, 3, 1);
29	1	Mapping mapping = new Mapping(to, map);
30
31		/*
32		* variants
33		* C>T at dna11, consequence CGT>TGT=C
34		* T>C at dna13, consequence CGT>CGC synonymous
35		*/
36	1	List<SequenceFeature> features = new ArrayList<>();
37	1	SequenceFeature sf1 = new SequenceFeature("sequence_variant", "C,T",
38		11, 11, null);
39	1	sf1.setValue("alleles", "C,T");
40	1	features.add(sf1);
41	1	SequenceFeature sf2 = new SequenceFeature("sequence_variant", "T,C", 13,
42		13, null);
43	1	sf2.setValue("alleles", "T,C");
44	1	features.add(sf2);
45
46		/*
47		* missense variant in first codon
48		*/
49	1	MappedFeatures mf = new MappedFeatures(mapping, from, 1, 'R',
50		features);
51	1	String variant = mf.findProteinVariants(sf1);
52	1	assertEquals(variant, "p.Arg1Cys");
53
54		/*
55		* more than one alternative allele
56		* C>G consequence is GGT=G
57		* peptide variants as a comma-separated list
58		*/
59	1	sf1.setValue("alleles", "C,T,G");
60	1	variant = mf.findProteinVariants(sf1);
61	1	assertEquals(variant, "p.Arg1Cys,p.Arg1Gly");
62
63		/*
64		* synonymous variant in first codon
65		* shown in HGVS notation on peptide
66		*/
67	1	variant = mf.findProteinVariants(sf2);
68	1	assertEquals(variant, "c.13T>C(p.=)");
69
70		/*
71		* CSQ:HGVSp value is used if present
72		* _and_ it contains "p." following a colon
73		*/
74	1	Map<String, String> csq = new HashMap<>();
75	1	csq.put("HGVSp", "hello:world");
76	1	sf2.setValue("CSQ", csq);
77	1	variant = mf.findProteinVariants(sf2);
78	1	assertEquals(variant, "c.13T>C(p.=)");
79	1	csq.put("HGVSp", "p.HelloWorld");
80	1	variant = mf.findProteinVariants(sf2);
81	1	assertEquals(variant, "c.13T>C(p.=)");
82	1	csq.put("HGVSp", "try this:hellop.world");
83	1	variant = mf.findProteinVariants(sf2);
84	1	assertEquals(variant, "hellop.world");
85
86		/*
87		* missense and indel variants in second codon
88		* - codon is GGA spliced from dna positions 15,18,19
89		* - SNP G>T in second position mutates GGA>G to GTA>V
90		* - indel variants are not computed or reported
91		*/
92	1	mf = new MappedFeatures(mapping, from, 2, 'G', features);
93	1	features.clear();
94	1	SequenceFeature sf3 = new SequenceFeature("sequence_variant",
95		"G,-,CG,T", 18, 18, null);
96	1	sf3.setValue("alleles", "G,-,CG,T");
97	1	features.add(sf3);
98	1	variant = mf.findProteinVariants(sf3);
99	1	assertEquals(variant, "p.Gly2Val");
100
101		/*
102		* G>T in first position gives TGA Stop
103		* shown with HGVS notation as 'Ter'
104		*/
105	1	SequenceFeature sf4 = new SequenceFeature("sequence_variant", "G,T", 15,
106		15, null);
107	1	sf4.setValue("alleles", "G,-,CG,T");
108	1	features.add(sf4);
109	1	variant = mf.findProteinVariants(sf4);
110	1	assertEquals(variant, "p.Gly2Ter");
111
112		/*
113		* feature must be one of those in MappedFeatures
114		*/
115	1	SequenceFeature sf9 = new SequenceFeature("sequence_variant", "G,C", 15,
116		15, null);
117	1	variant = mf.findProteinVariants(sf9);
118	1	assertEquals(variant, "");
119		}
120		}