Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
EnsemblSeqProxyTest	42	34	8	0.690476269%	Show methods

Class EnsemblSeqProxyTest

Class EnsemblSeqProxyTest	Line # 42	Total Statements 34	Complexity 8	TOTAL Coverage 0.690476269%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4545	2.02	1.01	1.0 1.0100%
setUp() : void   setUp() : void	127127	1.01	1.01	1.0 1.0100%
tearDown() : void   tearDown() : void	133133	1.01	1.01	1.0 1.0100%
createData(Method) : Object[][]   createData(Method) : Object[][]	139139	2.02	1.01	0.0 0.00%
testGetSequenceRecords(EnsemblSeqProxy,String,String) : void   testGetSequenceRecords(EnsemblSeqProxy,String,String) : void	146146	9.09	1.01	0.0 0.00%
getGenomicRangesFromFeatures() : void   getGenomicRangesFromFeatures() : void	173173	0.00	1.01	-1.0 -1.0 -
testReverseComplementAllele() : void   testReverseComplementAllele() : void	183183	12.012	1.01	1.0 1.0100%
testReverseComplementAlleles() : void   testReverseComplementAlleles() : void	205205	7.07	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.30952382	jalview.ext.ensembl.EnsemblSeqProxyTest.testReverseComplementAllelejalview.ext.ensembl.EnsemblSeqProxyTest.testReverseComplementAllele	1PASS
	0.1904762	jalview.ext.ensembl.EnsemblSeqProxyTest.testReverseComplementAllelesjalview.ext.ensembl.EnsemblSeqProxyTest.testReverseComplementAlleles	1PASS
	0.023809524	jalview.ext.ensembl.EnsemblSeqProxyTest.getGenomicRangesFromFeaturesjalview.ext.ensembl.EnsemblSeqProxyTest.getGenomicRangesFromFeatures	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
25		import jalview.datamodel.AlignmentI;
26		import jalview.datamodel.SequenceFeature;
27		import jalview.datamodel.SequenceI;
28		import jalview.gui.JvOptionPane;
29		import jalview.io.DataSourceType;
30		import jalview.io.FastaFile;
31		import jalview.io.gff.SequenceOntologyFactory;
32		import jalview.io.gff.SequenceOntologyLite;
33
34		import java.lang.reflect.Method;
35
36		import org.testng.Assert;
37		import org.testng.annotations.AfterClass;
38		import org.testng.annotations.BeforeClass;
39		import org.testng.annotations.DataProvider;
40		import org.testng.annotations.Test;
41
		69% Uncovered Elements: 13 (42) Complexity: 8 Complexity Density: 0.24
42		public class EnsemblSeqProxyTest
43		{
44
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
45	1	@BeforeClass(alwaysRun = true)...
46		public void setUpJvOptionPane()
47		{
48	1	JvOptionPane.setInteractiveMode(false);
49	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
50		}
51
52		private static final Object[][] allSeqs = new Object[][] { {
53		new EnsemblProtein(), "CCDS5863.1",
54		">CCDS5863.1\n"
55		+ "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
56		+ "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
57		+ "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
58		+ "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
59		+ "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
60		+ "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
61		+ "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
62		+ "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
63		+ "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
64		+ "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
65		+ "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
66		+ "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
67		+ "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
68		{ new EnsemblCdna(), "CCDS5863.1", ">CCDS5863.1\n"
69		+ "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
70		+ "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
71		+ "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
72		+ "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
73		+ "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
74		+ "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
75		+ "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
76		+ "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
77		+ "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
78		+ "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
79		+ "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
80		+ "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
81		+ "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
82		+ "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
83		+ "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
84		+ "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
85		+ "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
86		+ "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
87		+ "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
88		+ "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
89		+ "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
90		+ "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
91		+ "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
92		+ "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
93		+ "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
94		+ "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
95		+ "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
96		+ "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
97		+ "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
98		+ "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
99		+ "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
100		+ "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
101		+ "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
102		+ "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
103		+ "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
104		+ "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
105		+ "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
106		+ "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
107		+ "GGTGCGTTTCCTGTCCACTGA\n" },
108		{ new EnsemblProtein(), "ENSP00000288602", ">ENSP00000288602\n"
109		+ "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
110		+ "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
111		+ "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
112		+ "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
113		+ "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
114		+ "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
115		+ "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDG\n"
116		// ? insertion added in ENSP00000288602.11, not in P15056
117		+ "APLNQLMRCLRKYQSRTPSPLLHSVPSEIVFDFEPGPVFR\n"
118		// end insertion
119		+ "GSTTGLSATPPASLPGSLTNVKALQKSP\n"
120		+ "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
121		+ "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
122		+ "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
123		+ "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
124		+ "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
125		+ "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
126
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
127	1	@BeforeClass(alwaysRun = true)...
128		public void setUp()
129		{
130	1	SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
131		}
132
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
133	1	@AfterClass(alwaysRun = true)...
134		public void tearDown()
135		{
136	1	SequenceOntologyFactory.setInstance(null);
137		}
138
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
139	0	@DataProvider(name = "ens_seqs")...
140		public Object[][] createData(Method m)
141		{
142	0	System.out.println(m.getName());
143	0	return allSeqs;
144		}
145
		0% Uncovered Elements: 9 (9) Complexity: 1 Complexity Density: 0.11 4-
146	0	@Test(dataProvider = "ens_seqs", suiteName = "live")...
147		public void testGetSequenceRecords(EnsemblSeqProxy proxy, String sq,
148		String fastasq) throws Exception
149		{
150	0	FastaFile trueRes = new FastaFile(fastasq, DataSourceType.PASTE);
151	0	SequenceI[] expected = trueRes.getSeqsAsArray();
152	0	AlignmentI retrieved = proxy.getSequenceRecords(sq);
153
154	0	Assert.assertEquals(retrieved.getHeight(), expected.length,
155		"Different number of sequences retrieved for query " + sq);
156
157	0	for (SequenceI tr : expected)
158		{
159	0	SequenceI[] rseq;
160	0	Assert.assertNotNull(rseq = retrieved.findSequenceMatch(tr.getName()),
161		"Couldn't find sequences matching expected sequence "
162		+ tr.getName());
163	0	Assert.assertEquals(rseq.length, 1,
164		"Expected only one sequence for sequence ID " + tr.getName());
165	0	Assert.assertEquals(rseq[0].getSequenceAsString(),
166		tr.getSequenceAsString(),
167		"Sequences differ for " + tr.getName() + "\n" + "Exp:"
168		+ tr.getSequenceAsString() + "\n" + "Got:"
169		+ rseq[0].getSequenceAsString());
170		}
171		}
172
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: - 1PASS
173	1	@Test(groups = "Functional")...
174		public void getGenomicRangesFromFeatures()
175		{
176
177		}
178
179		/**
180		* Test the method that appends a single allele's reverse complement to a
181		* string buffer
182		*/
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
183	1	@Test(groups = "Functional")...
184		public void testReverseComplementAllele()
185		{
186	1	StringBuilder sb = new StringBuilder();
187	1	EnsemblSeqProxy.reverseComplementAllele(sb, "G"); // comp=C
188	1	EnsemblSeqProxy.reverseComplementAllele(sb, "g"); // comp=c
189	1	EnsemblSeqProxy.reverseComplementAllele(sb, "C"); // comp=G
190	1	EnsemblSeqProxy.reverseComplementAllele(sb, "T"); // comp=A
191	1	EnsemblSeqProxy.reverseComplementAllele(sb, "A"); // comp=T
192	1	assertEquals("C,c,G,A,T", sb.toString());
193
194	1	sb = new StringBuilder();
195	1	EnsemblSeqProxy.reverseComplementAllele(sb, "-GATt"); // revcomp=aATC-
196	1	EnsemblSeqProxy.reverseComplementAllele(sb, "hgmd_mutation");
197	1	EnsemblSeqProxy.reverseComplementAllele(sb, "PhenCode_variation");
198	1	assertEquals("aATC-,hgmd_mutation,PhenCode_variation", sb.toString());
199		}
200
201		/**
202		* Test the method that computes the reverse complement of the alleles in a
203		* sequence_variant feature
204		*/
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14 1PASS
205	1	@Test(groups = "Functional")...
206		public void testReverseComplementAlleles()
207		{
208	1	String alleles = "C,G,-TAC,HGMD_MUTATION,gac";
209	1	SequenceFeature sf = new SequenceFeature("sequence_variant", alleles, 1,
210		2, 0f, null);
211	1	sf.setValue("alleles", alleles);
212
213	1	EnsemblSeqProxy.reverseComplementAlleles(sf);
214	1	String revcomp = "G,C,GTA-,HGMD_MUTATION,gtc";
215		// verify description is updated with reverse complement
216	1	assertEquals(revcomp, sf.getDescription());
217		// verify alleles attribute is updated with reverse complement
218	1	assertEquals(revcomp, sf.getValue("alleles"));
219		}
220		}