Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
GenBankFileTest	44	115	2	1.0100%	Show methods

Class GenBankFileTest

Class GenBankFileTest	Line # 44	Total Statements 115	Complexity 2	TOTAL Coverage 1.0100%
setUp() : void   setUp() : void	4646	1.01	1.01	1.0 1.0100%
testParse() : void   testParse() : void	5959	114.0114	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.982906	jalview.io.GenBankFileTest.testParsejalview.io.GenBankFileTest.testParse	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.io;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertTrue;
25		import static org.testng.AssertJUnit.assertNull;
26
27		import java.io.File;
28		import java.io.IOException;
29		import java.net.MalformedURLException;
30		import java.util.List;
31		import java.util.Set;
32
33		import org.testng.annotations.BeforeClass;
34		import org.testng.annotations.Test;
35
36		import jalview.bin.Console;
37		import jalview.datamodel.DBRefEntry;
38		import jalview.datamodel.Mapping;
39		import jalview.datamodel.SequenceFeature;
40		import jalview.datamodel.SequenceI;
41		import jalview.datamodel.features.SequenceFeatures;
42		import jalview.util.MapList;
43
		100% Uncovered Elements: 0 (117) Complexity: 2 Complexity Density: 0.02
44		public class GenBankFileTest
45		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
46	1	@BeforeClass(alwaysRun = true)...
47		public void setUp()
48		{
49	1	Console.initLogger();
50		}
51
52		/**
53		* A fairly tough test, using J03321 (circular DNA), which has 8 CDS features,
54		* one of them reverse strand
55		*
56		* @throws MalformedURLException
57		* @throws IOException
58		*/
		100% Uncovered Elements: 0 (114) Complexity: 1 Complexity Density: 0.01 1PASS
59	1	@Test(groups = "Functional")...
60		public void testParse() throws MalformedURLException, IOException
61		{
62	1	File dataFile = new File("test/jalview/io/J03321.gb");
63	1	FileParse fp = new FileParse(dataFile.getAbsolutePath(),
64		DataSourceType.FILE);
65	1	EMBLLikeFlatFile parser = new GenBankFile(fp, "GenBankTest");
66	1	List<SequenceI> seqs = parser.getSeqs();
67
68	1	assertEquals(seqs.size(), 1);
69	1	SequenceI seq = seqs.get(0);
70	1	assertEquals(seq.getName(), "GenBankTest|J03321");
71	1	assertEquals(seq.getLength(), 7502);
72	1	assertEquals(seq.getDescription(),
73		"Chlamydia trachomatis plasmid pCHL1, complete sequence");
74
75		/*
76		* should be 9 CDS features (one is a 'join' of two exons)
77		*/
78	1	Set<String> featureTypes = seq.getFeatures().getFeatureTypes();
79	1	assertEquals(featureTypes.size(), 1);
80	1	assertTrue(featureTypes.contains("CDS"));
81
82		/*
83		* inspect some features (sorted just for convenience of test assertions)
84		*/
85	1	List<SequenceFeature> features = seq.getFeatures()
86		.getAllFeatures("CDS");
87	1	SequenceFeatures.sortFeatures(features, true);
88	1	assertEquals(features.size(), 9);
89
90	1	SequenceFeature sf = features.get(0);
91	1	assertEquals(sf.getBegin(), 1);
92	1	assertEquals(sf.getEnd(), 437);
93	1	assertEquals(sf.getDescription(),
94		"Exon 2 for protein EMBLCDS:AAA91567.1");
95	1	assertEquals(sf.getFeatureGroup(), "GenBankTest");
96	1	assertEquals(sf.getEnaLocation(), "join(7022..7502,1..437)");
97	1	assertEquals(sf.getPhase(), "0");
98	1	assertEquals(sf.getStrand(), 1);
99	1	assertEquals(sf.getValue("note"), "pGP7-D");
100		// this is the second exon of circular CDS!
101	1	assertEquals(sf.getValue("exon number"), 2);
102	1	assertEquals(sf.getValue("product"), "hypothetical protein");
103	1	assertEquals(sf.getValue("transl_table"), "11");
104
105	1	sf = features.get(1);
106	1	assertEquals(sf.getBegin(), 488);
107	1	assertEquals(sf.getEnd(), 1480);
108	1	assertEquals(sf.getDescription(),
109		"Exon 1 for protein EMBLCDS:AAA91568.1");
110	1	assertEquals(sf.getFeatureGroup(), "GenBankTest");
111	1	assertEquals(sf.getEnaLocation(), "complement(488..1480)");
112	1	assertEquals(sf.getPhase(), "0");
113	1	assertEquals(sf.getStrand(), -1); // reverse strand!
114	1	assertEquals(sf.getValue("note"), "pGP8-D");
115	1	assertEquals(sf.getValue("exon number"), 1);
116	1	assertEquals(sf.getValue("product"), "hypothetical protein");
117
118	1	sf = features.get(7);
119	1	assertEquals(sf.getBegin(), 6045);
120	1	assertEquals(sf.getEnd(), 6788);
121	1	assertEquals(sf.getDescription(),
122		"Exon 1 for protein EMBLCDS:AAA91574.1");
123	1	assertEquals(sf.getFeatureGroup(), "GenBankTest");
124	1	assertEquals(sf.getEnaLocation(), "6045..6788");
125	1	assertEquals(sf.getPhase(), "0");
126	1	assertEquals(sf.getStrand(), 1);
127	1	assertEquals(sf.getValue("note"), "pGP6-D (gtg start codon)");
128	1	assertEquals(sf.getValue("exon number"), 1);
129	1	assertEquals(sf.getValue("product"), "hypothetical protein");
130
131		/*
132		* CDS at 7022-7502 is the first exon of the circular CDS
133		*/
134	1	sf = features.get(8);
135	1	assertEquals(sf.getBegin(), 7022);
136	1	assertEquals(sf.getEnd(), 7502);
137	1	assertEquals(sf.getDescription(),
138		"Exon 1 for protein EMBLCDS:AAA91567.1");
139	1	assertEquals(sf.getFeatureGroup(), "GenBankTest");
140	1	assertEquals(sf.getEnaLocation(), "join(7022..7502,1..437)");
141	1	assertEquals(sf.getPhase(), "0");
142	1	assertEquals(sf.getStrand(), 1);
143	1	assertEquals(sf.getValue("note"), "pGP7-D");
144	1	assertEquals(sf.getValue("exon number"), 1);
145	1	assertEquals(sf.getValue("product"), "hypothetical protein");
146
147		/*
148		* GenBank doesn't declare accession or CDS xrefs;
149		* dbrefs are added by Jalview for
150		* xref to self : 1
151		* protein products: 8
152		*/
153	1	List<DBRefEntry> dbrefs = seq.getDBRefs();
154
155	1	assertEquals(dbrefs.size(), 9);
156		// xref to 'self':
157	1	DBRefEntry selfRef = new DBRefEntry("GENBANKTEST", "1", "J03321");
158	1	int[] range = new int[] { 1, seq.getLength() };
159	1	selfRef.setMap(new Mapping(null, range, range, 1, 1));
160	1	assertTrue(dbrefs.contains(selfRef));
161
162		/*
163		* dna should have dbref to itself, and to EMBLCDSPROTEIN
164		* for each /protein_id (synthesized as no UNIPROT xref)
165		*/
166		// TODO check if we should synthesize EMBLCDSPROTEIN dbrefs
167	1	DBRefEntry dbref = dbrefs.get(0);
168	1	assertEquals(dbref.getSource(), "GENBANKTEST");
169	1	assertEquals(dbref.getAccessionId(), "J03321");
170	1	Mapping mapping = dbref.getMap();
171	1	assertNull(mapping.getTo());
172	1	MapList map = mapping.getMap();
173	1	assertEquals(map.getFromLowest(), 1);
174	1	assertEquals(map.getFromHighest(), 7502);
175	1	assertEquals(map.getToLowest(), 1);
176	1	assertEquals(map.getToHighest(), 7502);
177	1	assertEquals(map.getFromRatio(), 1);
178	1	assertEquals(map.getToRatio(), 1);
179
180		// dbref to inferred EMBLCDSPROTEIN for first CDS
181	1	dbref = dbrefs.get(1);
182	1	assertEquals(dbref.getSource(), "EMBLCDSPROTEIN");
183	1	assertEquals(dbref.getAccessionId(), "AAA91567.1");
184	1	mapping = dbref.getMap();
185	1	SequenceI mapTo = mapping.getTo();
186	1	assertEquals(mapTo.getName(), "AAA91567.1");
187		// the /product qualifier transfers to protein product description
188	1	assertEquals(mapTo.getDescription(), "hypothetical protein");
189	1	String seqString = mapTo.getSequenceAsString();
190	1	assertEquals(seqString.length(), 305);
191	1	assertTrue(seqString.startsWith("MGSMAF"));
192	1	assertTrue(seqString.endsWith("QTPTIL"));
193	1	map = mapping.getMap();
194	1	assertEquals(map.getFromLowest(), 1);
195	1	assertEquals(map.getFromHighest(), 7502);
196	1	assertEquals(map.getToLowest(), 1);
197	1	assertEquals(map.getToHighest(), 305);
198	1	assertEquals(map.getFromRatio(), 3);
199	1	assertEquals(map.getToRatio(), 1);
200
201		// dbref to inferred EMBLCDSPROTEIN for last CDS
202	1	dbref = dbrefs.get(8);
203	1	assertEquals(dbref.getSource(), "EMBLCDSPROTEIN");
204	1	assertEquals(dbref.getAccessionId(), "AAA91574.1");
205	1	mapping = dbref.getMap();
206	1	mapTo = mapping.getTo();
207	1	assertEquals(mapTo.getName(), "AAA91574.1");
208		// the /product qualifier transfers to protein product description
209	1	assertEquals(mapTo.getDescription(), "hypothetical protein");
210	1	seqString = mapTo.getSequenceAsString();
211	1	assertEquals(seqString.length(), 247);
212	1	assertTrue(seqString.startsWith("MNKLK"));
213	1	assertTrue(seqString.endsWith("FKQKS"));
214	1	map = mapping.getMap();
215	1	assertEquals(map.getFromLowest(), 6045);
216	1	assertEquals(map.getFromHighest(), 6785); // excludes stop at 6788
217	1	assertEquals(map.getToLowest(), 1);
218	1	assertEquals(map.getToHighest(), 247);
219	1	assertEquals(map.getFromRatio(), 3);
220	1	assertEquals(map.getToRatio(), 1);
221		}
222		}