Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
EnsemblSeqProxyTest	47	53	9	15	0.758064575.8%	Show methods

Class EnsemblSeqProxyTest

Class EnsemblSeqProxyTest	Line # 47	Total Statements 53	Complexity 9	Uncovered Elements 15	TOTAL Coverage 0.758064575.8%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5050	2.02	1.01	0.00	1.0 1.0100%
setUp() : void   setUp() : void	136136	1.01	1.01	0.00	1.0 1.0100%
tearDown() : void   tearDown() : void	142142	1.01	1.01	0.00	1.0 1.0100%
createData(Method) : Object[][]   createData(Method) : Object[][]	148148	2.02	1.01	2.02	0.0 0.00%
testGetOneSeqs(EnsemblRestClient,String,String) : void   testGetOneSeqs(EnsemblRestClient,String,String) : void	155155	11.011	1.01	11.011	0.0 0.00%
getGenomicRangesFromFeatures() : void   getGenomicRangesFromFeatures() : void	186186	0.00	1.01	0.00	-1.0 -1.0 -
testReverseComplementAllele() : void   testReverseComplementAllele() : void	196196	12.012	1.01	0.00	1.0 1.0100%
testReverseComplementAlleles() : void   testReverseComplementAlleles() : void	218218	9.09	1.01	0.00	1.0 1.0100%
testSortFeatures() : void   testSortFeatures() : void	237237	15.015	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.2580645	jalview.ext.ensembl.EnsemblSeqProxyTest.testSortFeaturesjalview.ext.ensembl.EnsemblSeqProxyTest.testSortFeatures	1PASS
	0.20967741	jalview.ext.ensembl.EnsemblSeqProxyTest.testReverseComplementAllelejalview.ext.ensembl.EnsemblSeqProxyTest.testReverseComplementAllele	1PASS
	0.16129032	jalview.ext.ensembl.EnsemblSeqProxyTest.testReverseComplementAllelesjalview.ext.ensembl.EnsemblSeqProxyTest.testReverseComplementAlleles	1PASS
	0.016129032	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		import static org.testng.AssertJUnit.assertSame;
25
26		import jalview.datamodel.Alignment;
27		import jalview.datamodel.SequenceFeature;
28		import jalview.datamodel.SequenceI;
29		import jalview.datamodel.features.SequenceFeatures;
30		import jalview.gui.JvOptionPane;
31		import jalview.io.DataSourceType;
32		import jalview.io.FastaFile;
33		import jalview.io.FileParse;
34		import jalview.io.gff.SequenceOntologyFactory;
35		import jalview.io.gff.SequenceOntologyLite;
36
37		import java.lang.reflect.Method;
38		import java.util.Arrays;
39		import java.util.List;
40
41		import org.testng.Assert;
42		import org.testng.annotations.AfterClass;
43		import org.testng.annotations.BeforeClass;
44		import org.testng.annotations.DataProvider;
45		import org.testng.annotations.Test;
46
		75.8% Uncovered Elements: 15 (62) Complexity: 9 Complexity Density: 0.17
47		public class EnsemblSeqProxyTest
48		{
49
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
50	1	@BeforeClass(alwaysRun = true)...
51		public void setUpJvOptionPane()
52		{
53	1	JvOptionPane.setInteractiveMode(false);
54	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
55		}
56
57		private static final Object[][] allSeqs = new Object[][] {
58		{
59		new EnsemblProtein(),
60		"CCDS5863.1",
61		">CCDS5863.1\n"
62		+ "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
63		+ "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
64		+ "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
65		+ "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
66		+ "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
67		+ "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
68		+ "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
69		+ "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
70		+ "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
71		+ "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
72		+ "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
73		+ "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
74		+ "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
75		{
76		new EnsemblCdna(),
77		"CCDS5863.1",
78		">CCDS5863.1\n"
79		+ "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
80		+ "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
81		+ "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
82		+ "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
83		+ "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
84		+ "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
85		+ "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
86		+ "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
87		+ "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
88		+ "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
89		+ "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
90		+ "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
91		+ "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
92		+ "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
93		+ "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
94		+ "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
95		+ "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
96		+ "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
97		+ "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
98		+ "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
99		+ "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
100		+ "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
101		+ "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
102		+ "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
103		+ "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
104		+ "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
105		+ "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
106		+ "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
107		+ "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
108		+ "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
109		+ "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
110		+ "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
111		+ "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
112		+ "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
113		+ "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
114		+ "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
115		+ "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
116		+ "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
117		+ "GGTGCGTTTCCTGTCCACTGA\n" },
118		{
119		new EnsemblProtein(),
120		"ENSP00000288602",
121		">ENSP00000288602\n"
122		+ "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
123		+ "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
124		+ "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
125		+ "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
126		+ "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
127		+ "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
128		+ "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
129		+ "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
130		+ "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
131		+ "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
132		+ "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
133		+ "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
134		+ "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
135
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
136	1	@BeforeClass(alwaysRun = true)...
137		public void setUp()
138		{
139	1	SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
140		}
141
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
142	1	@AfterClass(alwaysRun = true)...
143		public void tearDown()
144		{
145	1	SequenceOntologyFactory.setInstance(null);
146		}
147
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
148	0	@DataProvider(name = "ens_seqs")...
149		public Object[][] createData(Method m)
150		{
151	0	System.out.println(m.getName());
152	0	return allSeqs;
153		}
154
		0% Uncovered Elements: 11 (11) Complexity: 1 Complexity Density: 0.09 4-
155	0	@Test(dataProvider = "ens_seqs", suiteName = "live")...
156		public void testGetOneSeqs(EnsemblRestClient proxy, String sq,
157		String fastasq) throws Exception
158		{
159	0	FileParse fp = proxy.getSequenceReader(Arrays
160		.asList(new String[] { sq }));
161	0	SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
162	0	FastaFile trueRes = new FastaFile(fastasq, DataSourceType.PASTE);
163	0	SequenceI[] trueSqs = trueRes.getSeqsAsArray();
164	0	Assert.assertEquals(sqs.length, trueSqs.length,
165		"Different number of sequences retrieved for query " + sq);
166	0	Alignment ral = new Alignment(sqs);
167	0	for (SequenceI tr : trueSqs)
168		{
169	0	SequenceI[] rseq;
170	0	Assert.assertNotNull(
171		rseq = ral.findSequenceMatch(tr.getName()),
172		"Couldn't find sequences matching expected sequence "
173		+ tr.getName());
174	0	Assert.assertEquals(rseq.length, 1,
175		"Expected only one sequence for sequence ID " + tr.getName());
176	0	Assert.assertEquals(
177		rseq[0].getSequenceAsString(),
178		tr.getSequenceAsString(),
179		"Sequences differ for " + tr.getName() + "\n" + "Exp:"
180		+ tr.getSequenceAsString() + "\n" + "Got:"
181		+ rseq[0].getSequenceAsString());
182
183		}
184		}
185
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: - 1PASS
186	1	@Test(groups = "Functional")...
187		public void getGenomicRangesFromFeatures()
188		{
189
190		}
191
192		/**
193		* Test the method that appends a single allele's reverse complement to a
194		* string buffer
195		*/
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
196	1	@Test(groups = "Functional")...
197		public void testReverseComplementAllele()
198		{
199	1	StringBuilder sb = new StringBuilder();
200	1	EnsemblSeqProxy.reverseComplementAllele(sb, "G"); // comp=C
201	1	EnsemblSeqProxy.reverseComplementAllele(sb, "g"); // comp=c
202	1	EnsemblSeqProxy.reverseComplementAllele(sb, "C"); // comp=G
203	1	EnsemblSeqProxy.reverseComplementAllele(sb, "T"); // comp=A
204	1	EnsemblSeqProxy.reverseComplementAllele(sb, "A"); // comp=T
205	1	assertEquals("C,c,G,A,T", sb.toString());
206
207	1	sb = new StringBuilder();
208	1	EnsemblSeqProxy.reverseComplementAllele(sb, "-GATt"); // revcomp=aATC-
209	1	EnsemblSeqProxy.reverseComplementAllele(sb, "hgmd_mutation");
210	1	EnsemblSeqProxy.reverseComplementAllele(sb, "PhenCode_variation");
211	1	assertEquals("aATC-,hgmd_mutation,PhenCode_variation", sb.toString());
212		}
213
214		/**
215		* Test the method that computes the reverse complement of the alleles in a
216		* sequence_variant feature
217		*/
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11 1PASS
218	1	@Test(groups = "Functional")...
219		public void testReverseComplementAlleles()
220		{
221	1	String alleles = "C,G,-TAC,HGMD_MUTATION,gac";
222	1	SequenceFeature sf = new SequenceFeature("sequence_variant", alleles,
223		1, 2, 0f, null);
224	1	sf.setValue("alleles", alleles);
225	1	sf.setAttributes("x=y,z;alleles=" + alleles + ";a=b,c");
226
227	1	EnsemblSeqProxy.reverseComplementAlleles(sf);
228	1	String revcomp = "G,C,GTA-,HGMD_MUTATION,gtc";
229		// verify description is updated with reverse complement
230	1	assertEquals(revcomp, sf.getDescription());
231		// verify alleles attribute is updated with reverse complement
232	1	assertEquals(revcomp, sf.getValue("alleles"));
233		// verify attributes string is updated with reverse complement
234	1	assertEquals("x=y,z;alleles=" + revcomp + ";a=b,c", sf.getAttributes());
235		}
236
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
237	1	@Test(groups = "Functional")...
238		public void testSortFeatures()
239		{
240	1	SequenceFeature sf1 = new SequenceFeature("", "", 10, 15, 0f, null);
241	1	SequenceFeature sf2 = new SequenceFeature("", "", 8, 12, 0f, null);
242	1	SequenceFeature sf3 = new SequenceFeature("", "", 8, 13, 0f, null);
243	1	SequenceFeature sf4 = new SequenceFeature("", "", 11, 11, 0f, null);
244	1	List<SequenceFeature> sfs = Arrays.asList(new SequenceFeature[] { sf1,
245		sf2, sf3, sf4 });
246
247		// sort by start position ascending (forward strand)
248		// sf2 and sf3 tie and should not be reordered by sorting
249	1	SequenceFeatures.sortFeatures(sfs, true);
250	1	assertSame(sfs.get(0), sf2);
251	1	assertSame(sfs.get(1), sf3);
252	1	assertSame(sfs.get(2), sf1);
253	1	assertSame(sfs.get(3), sf4);
254
255		// sort by end position descending (reverse strand)
256	1	SequenceFeatures.sortFeatures(sfs, false);
257	1	assertSame(sfs.get(0), sf1);
258	1	assertSame(sfs.get(1), sf3);
259	1	assertSame(sfs.get(2), sf2);
260	1	assertSame(sfs.get(3), sf4);
261		}
262		}