Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
EmblFileTest	34	96	2	0	1.0100%	Show methods

Class EmblFileTest

Class EmblFileTest	Line # 34	Total Statements 96	Complexity 2	Uncovered Elements 0	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	3737	2.02	1.01	0.00	1.0 1.0100%
testGetEmblFile() : void   testGetEmblFile() : void	4444	94.094	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.96938777	jalview.datamodel.xdb.embl.EmblFileTest.testGetEmblFilejalview.datamodel.xdb.embl.EmblFileTest.testGetEmblFile	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.datamodel.xdb.embl;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertNull;
25
26		import jalview.datamodel.DBRefEntry;
27		import jalview.gui.JvOptionPane;
28
29		import java.util.Vector;
30
31		import org.testng.annotations.BeforeClass;
32		import org.testng.annotations.Test;
33
		100% Uncovered Elements: 0 (98) Complexity: 2 Complexity Density: 0.02
34		public class EmblFileTest
35		{
36
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
37	1	@BeforeClass(alwaysRun = true)...
38		public void setUpJvOptionPane()
39		{
40	1	JvOptionPane.setInteractiveMode(false);
41	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
42		}
43
		100% Uncovered Elements: 0 (94) Complexity: 1 Complexity Density: 0.01 1PASS
44	1	@Test(groups = { "Functional" })...
45		public void testGetEmblFile()
46		{
47	1	Vector<EmblEntry> entries = EmblTestHelper.getEmblFile().getEntries();
48	1	assertEquals(1, entries.size());
49	1	EmblEntry entry = entries.get(0);
50
51	1	assertEquals("X07547", entry.getAccession());
52	1	assertEquals("C. trachomatis plasmid", entry.getDescription());
53	1	assertEquals("STD", entry.getDataClass());
54	1	assertEquals("PRO", entry.getTaxonomicDivision());
55	1	assertEquals("1999-02-10", entry.getLastUpdatedDate());
56	1	assertEquals("58", entry.getLastUpdatedRelease());
57	1	assertEquals("1988-11-10", entry.getFirstPublicDate());
58	1	assertEquals("18", entry.getFirstPublicRelease());
59	1	assertEquals("genomic DNA", entry.getMoleculeType());
60	1	assertEquals("1", entry.getSequenceVersion());
61	1	assertEquals("8", entry.getEntryVersion());
62	1	assertEquals("linear", entry.getTopology());
63	1	assertEquals("7499", entry.getSequenceLength());
64
65		/*
66		* FIXME these assertions fail - values are null - why?? Adding or removing
67		* attributes in the test XML modifies behaviour. eg. inserting an attribute
68		* _before_ lastUpdated results in a null value in this field.
69		*/
70	1	assertEquals("1988-11-10", entry.getFirstPublicDate());
71	1	assertEquals("18", entry.getFirstPublicRelease());
72
73	1	assertEquals(2, entry.getKeywords().size());
74	1	assertEquals("plasmid", entry.getKeywords().get(0));
75	1	assertEquals("unidentified reading frame", entry.getKeywords().get(1));
76
77		/*
78		* dbrefs
79		*/
80	1	assertEquals(2, entry.getDbRefs().size());
81	1	DBRefEntry dbref = entry.getDbRefs().get(0);
82	1	assertEquals("EuropePMC", dbref.getSource());
83	1	assertEquals("PMC107176", dbref.getAccessionId());
84	1	assertEquals("9573186", dbref.getVersion());
85	1	dbref = entry.getDbRefs().get(1);
86	1	assertEquals("MD5", dbref.getSource());
87	1	assertEquals("ac73317", dbref.getAccessionId());
88		// blank version has been converted to "0"
89	1	assertEquals("0", dbref.getVersion());
90
91		/*
92		* three sequence features for CDS
93		*/
94	1	assertEquals(3, entry.getFeatures().size());
95		/*
96		* first CDS
97		*/
98	1	EmblFeature ef = entry.getFeatures().get(0);
99	1	assertEquals("CDS", ef.getName());
100	1	assertEquals("complement(46..57)", ef.getLocation());
101	1	assertEquals(2, ef.getDbRefs().size());
102	1	dbref = ef.getDbRefs().get(0);
103	1	assertEquals("UniProtKB/Swiss-Prot", dbref.getSource());
104	1	assertEquals("B0BCM4", dbref.getAccessionId());
105	1	assertEquals("2.1", dbref.getVersion());
106	1	dbref = ef.getDbRefs().get(1);
107	1	assertEquals("UniProtKB/Swiss-Prot", dbref.getSource());
108	1	assertEquals("P0CE20", dbref.getAccessionId());
109		// blank version gets converted to "0":
110	1	assertEquals("0", dbref.getVersion());
111		// CDS feature qualifiers
112	1	assertEquals(3, ef.getQualifiers().size());
113	1	Qualifier q = ef.getQualifiers().get(0);
114	1	assertEquals("note", q.getName());
115	1	assertEquals(2, q.getValues().length);
116	1	assertEquals("ORF 8 (AA 1-330)", q.getValues()[0]);
117	1	assertEquals("pickle", q.getValues()[1]);
118	1	assertNull(q.getEvidence());
119	1	q = ef.getQualifiers().get(1);
120	1	assertEquals("protein_id", q.getName());
121	1	assertEquals(1, q.getValues().length);
122	1	assertEquals("CAA30420.1", q.getValues()[0]);
123	1	q = ef.getQualifiers().get(2);
124	1	assertEquals("translation", q.getName());
125	1	assertEquals(1, q.getValues().length);
126	1	assertEquals("MLCF", q.getValues()[0]);
127	1	assertEquals(1, q.getEvidence().length);
128	1	assertEquals("Keith", q.getEvidence()[0]);
129
130		/*
131		* second CDS
132		*/
133	1	ef = entry.getFeatures().get(1);
134	1	assertEquals("CDS", ef.getName());
135	1	assertEquals("4..15", ef.getLocation());
136	1	assertEquals(1, ef.getDbRefs().size());
137	1	dbref = ef.getDbRefs().get(0);
138	1	assertEquals("UniProtKB/Swiss-Prot", dbref.getSource());
139	1	assertEquals("B0BCM3", dbref.getAccessionId());
140	1	assertEquals("0", dbref.getVersion());
141	1	assertEquals(2, ef.getQualifiers().size());
142	1	q = ef.getQualifiers().get(0);
143	1	assertEquals("protein_id", q.getName());
144	1	assertEquals(1, q.getValues().length);
145	1	assertEquals("CAA30421.1", q.getValues()[0]);
146	1	q = ef.getQualifiers().get(1);
147	1	assertEquals("translation", q.getName());
148	1	assertEquals(1, q.getValues().length);
149	1	assertEquals("MSSS", q.getValues()[0]);
150
151		/*
152		* third CDS
153		*/
154	1	ef = entry.getFeatures().get(2);
155	1	assertEquals("CDS", ef.getName());
156	1	assertEquals("join(4..6,10..15)", ef.getLocation());
157	1	assertNull(ef.getDbRefs());
158	1	assertEquals(2, ef.getQualifiers().size());
159	1	q = ef.getQualifiers().get(0);
160	1	assertEquals("protein_id", q.getName());
161	1	assertEquals(1, q.getValues().length);
162	1	assertEquals("CAA12345.6", q.getValues()[0]);
163	1	q = ef.getQualifiers().get(1);
164	1	assertEquals("translation", q.getName());
165	1	assertEquals(1, q.getValues().length);
166	1	assertEquals("MSS", q.getValues()[0]);
167
168		/*
169		* Sequence - verify newline not converted to space (JAL-2029)
170		*/
171	1	EmblSequence seq = entry.getSequence();
172	1	assertEquals(
173		"GGTATGTCCTCTAGTACAAACACCCCCAATATTGTGATATAATTAAAAACATAGCAT",
174		seq.getSequence());
175
176		/*
177		* getSequence() converts empty DBRefEntry.version to "0"
178		*/
179	1	assertEquals("0", entry.getDbRefs().get(1).getVersion());
180	1	assertEquals("0", entry.getFeatures().get(0).getDbRefs().get(1)
181		.getVersion());
182		}
183		}