Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
DbRefFetcherTest	53	51	11	32	0.550%	Show methods

Class DbRefFetcherTest

Class DbRefFetcherTest	Line # 53	Total Statements 51	Complexity 11	Uncovered Elements 32	TOTAL Coverage 0.550%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	5656	2.02	1.01	0.00	1.0 1.0100%
setUpBeforeClass() : void   setUpBeforeClass() : void	6666	1.01	1.01	0.00	1.0 1.0100%
tearDownAfterClass() : void   tearDownAfterClass() : void	7575	0.00	1.01	0.00	-1.0 -1.0 -
testStandardProtDbs() : void   testStandardProtDbs() : void	8585	20.020	5.05	1.01	0.96153843 0.9615384396.2%
testEmblUniprotProductRecovery() : void   testEmblUniprotProductRecovery() : void	134134	4.04	1.01	4.04	0.0 0.00%
testEmblCDSUniprotProductRecovery() : void   testEmblCDSUniprotProductRecovery() : void	150150	4.04	1.01	4.04	0.0 0.00%
verifyProteinNucleotideXref(String,DbSourceProxy) : void   verifyProteinNucleotideXref(String,DbSourceProxy) : void	167167	20.020	1.01	20.020	0.0 0.00%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.40625	jalview.ws.seqfetcher.DbRefFetcherTest.testStandardProtDbsjalview.ws.seqfetcher.DbRefFetcherTest.testStandardProtDbs	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.ws.seqfetcher;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertFalse;
25		import static org.testng.AssertJUnit.assertNotNull;
26		import static org.testng.AssertJUnit.assertTrue;
27
28		import jalview.analysis.CrossRef;
29		import jalview.datamodel.AlignmentI;
30		import jalview.datamodel.DBRefEntry;
31		import jalview.datamodel.DBRefSource;
32		import jalview.datamodel.FeatureProperties;
33		import jalview.datamodel.SequenceFeature;
34		import jalview.datamodel.SequenceI;
35		import jalview.gui.JvOptionPane;
36		import jalview.util.DBRefUtils;
37		import jalview.ws.SequenceFetcher;
38		import jalview.ws.dbsources.Pdb;
39		import jalview.ws.dbsources.Uniprot;
40
41		import java.util.ArrayList;
42		import java.util.Arrays;
43		import java.util.List;
44
45		import org.testng.annotations.AfterClass;
46		import org.testng.annotations.BeforeClass;
47		import org.testng.annotations.Test;
48
49		/**
50		* @author jimp
51		*
52		*/
		50% Uncovered Elements: 32 (64) Complexity: 11 Complexity Density: 0.22
53		public class DbRefFetcherTest
54		{
55
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
56	1	@BeforeClass(alwaysRun = true)...
57		public void setUpJvOptionPane()
58		{
59	1	JvOptionPane.setInteractiveMode(false);
60	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
61		}
62
63		/**
64		* @throws java.lang.Exception
65		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
66	1	@BeforeClass(alwaysRun = true)...
67		public static void setUpBeforeClass() throws Exception
68		{
69	1	jalview.bin.Cache.initLogger();
70		}
71
72		/**
73		* @throws java.lang.Exception
74		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
75	1	@AfterClass(alwaysRun = true)...
76		public static void tearDownAfterClass() throws Exception
77		{
78		}
79
80		/**
81		* Tests that standard protein database sources include Uniprot (as the first)
82		* and also PDB. (Additional sources are dependent on availability of DAS
83		* services.)
84		*/
		96.2% Uncovered Elements: 1 (26) Complexity: 5 Complexity Density: 0.25 1PASS
85	1	@Test(groups = { "Functional" })...
86		public void testStandardProtDbs()
87		{
88	1	List<String> defdb = new ArrayList<String>();
89	1	defdb.addAll(Arrays.asList(DBRefSource.PROTEINDBS));
90	1	defdb.add(DBRefSource.PDB);
91	1	List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
92	1	SequenceFetcher sfetcher = new SequenceFetcher();
93	1	boolean pdbFound = false;
94
95	1	for (String ddb : defdb)
96		{
97	5	List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
98
99	5	if (srcesfordb != null)
100		{
101		// TODO is this right? get duplicate entries
102	5	srces.addAll(srcesfordb);
103		}
104		}
105
106	1	int i = 0;
107	1	int uniprotPos = -1;
108	1	for (DbSourceProxy s : srces)
109		{
110	4	if (s instanceof Uniprot && uniprotPos == -1)
111		{
112	1	uniprotPos = i;
113		}
114	4	if (s instanceof Pdb)
115		{
116	1	pdbFound = true;
117		}
118	4	i++;
119		}
120
121	1	assertTrue("Failed to find Uniprot source as first source amongst "
122		+ srces.size() + " sources (source was at position "
123		+ uniprotPos + ")", uniprotPos == 0);
124	1	assertTrue("Failed to find PDB source amongst " + srces.size()
125		+ " sources", pdbFound);
126		}
127
128		/**
129		* Tests retrieval of one entry from EMBL. Test is dependent on availability
130		* of network and the EMBL service.
131		*
132		* @throws Exception
133		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25 1PASS
134	0	@Test(groups = { "External" })...
135		public void testEmblUniprotProductRecovery() throws Exception
136		{
137	0	String retrievalId = "V00488";
138	0	DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
139		DBRefSource.EMBL).get(0);
140	0	assertNotNull("Couldn't find the EMBL retrieval client", embl);
141	0	verifyProteinNucleotideXref(retrievalId, embl);
142		}
143
144		/**
145		* Tests retrieval of one entry from EMBLCDS. Test is dependent on
146		* availability of network and the EMBLCDS service.
147		*
148		* @throws Exception
149		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25 1PASS
150	0	@Test(groups = { "External" })...
151		public void testEmblCDSUniprotProductRecovery() throws Exception
152		{
153	0	String retrievalId = "AAH29712";
154	0	DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
155		DBRefSource.EMBLCDS).get(0);
156	0	assertNotNull("Couldn't find the EMBL retrieval client", embl);
157	0	verifyProteinNucleotideXref(retrievalId, embl);
158		}
159
160		/**
161		* Helper method to perform database retrieval and verification of results.
162		*
163		* @param retrievalId
164		* @param embl
165		* @throws Exception
166		*/
		0% Uncovered Elements: 20 (20) Complexity: 1 Complexity Density: 0.05
167	0	private void verifyProteinNucleotideXref(String retrievalId,...
168		DbSourceProxy embl) throws Exception
169		{
170	0	AlignmentI alsq = embl.getSequenceRecords(retrievalId);
171	0	assertNotNull("Couldn't find the EMBL record " + retrievalId, alsq);
172	0	assertEquals("Didn't retrieve right number of records", 1,
173		alsq.getHeight());
174	0	SequenceI seq = alsq.getSequenceAt(0);
175	0	assertEquals("Wrong sequence name", embl.getDbSource() + "|"
176		+ retrievalId, seq.getName());
177	0	List<SequenceFeature> sfs = seq.getSequenceFeatures();
178	0	assertFalse("Sequence features missing", sfs.isEmpty());
179	0	assertTrue(
180		"Feature not CDS",
181		FeatureProperties.isCodingFeature(embl.getDbSource(),
182		sfs.get(0).getType()));
183	0	assertEquals(embl.getDbSource(), sfs.get(0).getFeatureGroup());
184	0	DBRefEntry[] dr = DBRefUtils.selectRefs(seq.getDBRefs(),
185		new String[] { DBRefSource.UNIPROT });
186	0	assertNotNull(dr);
187	0	assertEquals("Expected a single Uniprot cross reference", 1, dr.length);
188	0	assertEquals("Expected cross reference map to be one amino acid", dr[0]
189		.getMap().getMappedWidth(), 1);
190	0	assertEquals("Expected local reference map to be 3 nucleotides", dr[0]
191		.getMap().getWidth(), 3);
192	0	AlignmentI sprods = new CrossRef(alsq.getSequencesArray(), alsq)
193		.findXrefSequences(dr[0].getSource(), true);
194	0	assertNotNull(
195		"Couldn't recover cross reference sequence from dataset. Was it ever added ?",
196		sprods);
197	0	assertEquals("Didn't xref right number of records", 1,
198		sprods.getHeight());
199	0	SequenceI proteinSeq = sprods.getSequenceAt(0);
200	0	assertEquals(proteinSeq.getSequenceAsString(), dr[0].getMap().getTo()
201		.getSequenceAsString());
202	0	assertEquals(dr[0].getSource() + "|" + dr[0].getAccessionId(),
203		proteinSeq.getName());
204		}
205		}