Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
EmblEntryTest	41	129	5	1	0.992592699.3%	Show methods

Class EmblEntryTest

Class EmblEntryTest	Line # 41	Total Statements 129	Complexity 5	Uncovered Elements 1	TOTAL Coverage 0.992592699.3%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4444	2.02	1.01	0.00	1.0 1.0100%
testGetCdsRanges() : void   testGetCdsRanges() : void	5151	5.05	1.01	0.00	1.0 1.0100%
testParseCodingFeature() : void   testParseCodingFeature() : void	6767	110.0110	2.02	1.01	0.9910714 0.991071499.1%
testAdjustForProteinLength() : void   testAdjustForProteinLength() : void	236236	12.012	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.8296296	jalview.datamodel.xdb.embl.EmblEntryTest.testParseCodingFeaturejalview.datamodel.xdb.embl.EmblEntryTest.testParseCodingFeature	1PASS
	0.096296296	jalview.datamodel.xdb.embl.EmblEntryTest.testAdjustForProteinLengthjalview.datamodel.xdb.embl.EmblEntryTest.testAdjustForProteinLength	1PASS
	0.044444446	jalview.datamodel.xdb.embl.EmblEntryTest.testGetCdsRangesjalview.datamodel.xdb.embl.EmblEntryTest.testGetCdsRanges	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.datamodel.xdb.embl;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertNull;
25		import static org.testng.AssertJUnit.assertSame;
26
27		import jalview.analysis.SequenceIdMatcher;
28		import jalview.datamodel.DBRefEntry;
29		import jalview.datamodel.DBRefSource;
30		import jalview.datamodel.SequenceI;
31		import jalview.gui.JvOptionPane;
32		import jalview.util.MapList;
33
34		import java.util.ArrayList;
35		import java.util.Arrays;
36		import java.util.List;
37
38		import org.testng.annotations.BeforeClass;
39		import org.testng.annotations.Test;
40
		99.3% Uncovered Elements: 1 (135) Complexity: 5 Complexity Density: 0.04
41		public class EmblEntryTest
42		{
43
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
44	1	@BeforeClass(alwaysRun = true)...
45		public void setUpJvOptionPane()
46		{
47	1	JvOptionPane.setInteractiveMode(false);
48	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
49		}
50
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2 1PASS
51	1	@Test(groups = "Functional")...
52		public void testGetCdsRanges()
53		{
54	1	EmblEntry testee = new EmblEntry();
55
56		/*
57		* Make a (CDS) Feature with 5 locations
58		*/
59	1	EmblFeature cds = new EmblFeature();
60	1	cds.setLocation("join(10..20,complement(30..40),50..60,70..80,complement(110..120))");
61
62	1	int[] exons = testee.getCdsRanges(cds);
63	1	assertEquals("[10, 20, 40, 30, 50, 60, 70, 80, 120, 110]",
64		Arrays.toString(exons));
65		}
66
		99.1% Uncovered Elements: 1 (112) Complexity: 2 Complexity Density: 0.02 1PASS
67	1	@Test(groups = "Functional")...
68		public void testParseCodingFeature()
69		{
70		// not the whole sequence but enough for this test...
71	1	List<SequenceI> peptides = new ArrayList<SequenceI>();
72	1	SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
73	1	EmblFile ef = EmblTestHelper.getEmblFile();
74	1	assertEquals(1, ef.getEntries().size());
75	1	EmblEntry testee = ef.getEntries().get(0);
76	1	String sourceDb = "EMBL";
77	1	SequenceI dna = testee.makeSequence(sourceDb);
78
79		/*
80		* parse three CDS features, with two/one/no Uniprot cross-refs
81		*/
82	1	for (EmblFeature feature : ef.getEntries().get(0).getFeatures())
83		{
84	3	if ("CDS".equals(feature.getName()))
85		{
86	3	testee.parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
87		}
88		}
89
90		/*
91		* peptides should now have five entries:
92		* EMBL product and two Uniprot accessions for the first CDS / translation
93		* EMBL product and one Uniprot accession for the second CDS / "
94		* EMBL product only for the third
95		*/
96	1	assertEquals(6, peptides.size());
97	1	assertEquals("CAA30420.1", peptides.get(0).getName());
98	1	assertEquals("MLCF", peptides.get(0).getSequenceAsString());
99	1	assertEquals("UNIPROT|B0BCM4", peptides.get(1).getName());
100	1	assertEquals("MLCF", peptides.get(1).getSequenceAsString());
101	1	assertEquals("UNIPROT|P0CE20", peptides.get(2).getName());
102	1	assertEquals("MLCF", peptides.get(2).getSequenceAsString());
103	1	assertEquals("CAA30421.1", peptides.get(3).getName());
104	1	assertEquals("MSSS", peptides.get(3).getSequenceAsString());
105	1	assertEquals("UNIPROT|B0BCM3", peptides.get(4).getName());
106	1	assertEquals("MSSS", peptides.get(4).getSequenceAsString());
107	1	assertEquals("CAA12345.6", peptides.get(5).getName());
108	1	assertEquals("MSS", peptides.get(5).getSequenceAsString());
109
110		/*
111		* verify dna sequence has dbrefs with CDS mappings to the peptide 'products'
112		*/
113	1	MapList cds1Map = new MapList(new int[] { 57, 46 }, new int[] { 1, 4 },
114		3, 1);
115	1	MapList cds2Map = new MapList(new int[] { 4, 15 }, new int[] { 1, 4 },
116		3, 1);
117	1	MapList cds3Map = new MapList(new int[] { 4, 6, 10, 15 }, new int[] {
118		1, 3 }, 3, 1);
119	1	DBRefEntry[] dbrefs = dna.getDBRefs();
120	1	assertEquals(4, dbrefs.length);
121	1	DBRefEntry dbRefEntry = dbrefs[0];
122	1	assertEquals("UNIPROT", dbRefEntry.getSource());
123	1	assertEquals("B0BCM4", dbRefEntry.getAccessionId());
124	1	assertSame(peptides.get(1), dbRefEntry.getMap().getTo());
125	1	assertEquals(cds1Map, dbRefEntry.getMap().getMap());
126
127	1	dbRefEntry = dbrefs[1];
128	1	assertEquals("UNIPROT", dbRefEntry.getSource());
129	1	assertEquals("P0CE20", dbRefEntry.getAccessionId());
130	1	assertSame(peptides.get(2), dbRefEntry.getMap().getTo());
131	1	assertEquals(cds1Map, dbRefEntry.getMap().getMap());
132
133	1	dbRefEntry = dbrefs[2];
134	1	assertEquals("UNIPROT", dbRefEntry.getSource());
135	1	assertEquals("B0BCM3", dbRefEntry.getAccessionId());
136	1	assertSame(peptides.get(4), dbRefEntry.getMap().getTo());
137	1	assertEquals(cds2Map, dbRefEntry.getMap().getMap());
138
139	1	dbRefEntry = dbrefs[3];
140	1	assertEquals("EMBLCDSPROTEIN", dbRefEntry.getSource());
141	1	assertEquals("CAA12345.6", dbRefEntry.getAccessionId());
142	1	assertSame(peptides.get(5), dbRefEntry.getMap().getTo());
143	1	assertEquals(cds3Map, dbRefEntry.getMap().getMap());
144
145		/*
146		* verify peptides have dbrefs
147		* - to EMBL sequence (with inverse 1:3 cds mapping)
148		* - to EMBLCDS (with 1:3 mapping)
149		* - direct (no mapping) to other protein accessions
150		*/
151	1	MapList proteinToCdsMap1 = new MapList(new int[] { 1, 4 }, new int[] {
152		1, 12 }, 1, 3);
153	1	MapList proteinToCdsMap2 = new MapList(new int[] { 1, 3 }, new int[] {
154		1, 9 }, 1, 3);
155
156		// dbrefs for first CDS EMBL product CAA30420.1
157	1	dbrefs = peptides.get(0).getDBRefs();
158	1	assertEquals(5, dbrefs.length);
159	1	assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
160	1	assertEquals("CAA30420.1", dbrefs[0].getAccessionId());
161		// TODO: verify getPrimaryDBRefs() for peptide products
162	1	assertEquals(cds1Map.getInverse(), dbrefs[0].getMap().getMap());
163	1	assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
164	1	assertEquals("CAA30420.1", dbrefs[1].getAccessionId());
165	1	assertEquals(proteinToCdsMap1, dbrefs[1].getMap().getMap());
166	1	assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
167	1	assertEquals("CAA30420.1", dbrefs[2].getAccessionId());
168	1	assertNull(dbrefs[2].getMap());
169	1	assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
170		dbrefs[3]);
171	1	assertNull(dbrefs[3].getMap());
172	1	assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
173		dbrefs[4]);
174	1	assertNull(dbrefs[4].getMap());
175
176		// dbrefs for first CDS first Uniprot xref
177	1	dbrefs = peptides.get(1).getDBRefs();
178	1	assertEquals(2, dbrefs.length);
179	1	assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "2.1", "B0BCM4"),
180		dbrefs[0]);
181	1	assertNull(dbrefs[0].getMap());
182	1	assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
183	1	assertEquals("X07547", dbrefs[1].getAccessionId());
184	1	assertEquals(cds1Map.getInverse(), dbrefs[1].getMap().getMap());
185
186		// dbrefs for first CDS second Uniprot xref
187	1	dbrefs = peptides.get(2).getDBRefs();
188	1	assertEquals(2, dbrefs.length);
189	1	assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "P0CE20"),
190		dbrefs[0]);
191	1	assertNull(dbrefs[0].getMap());
192	1	assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
193	1	assertEquals("X07547", dbrefs[1].getAccessionId());
194	1	assertEquals(cds1Map.getInverse(), dbrefs[1].getMap().getMap());
195
196		// dbrefs for second CDS EMBL product CAA30421.1
197	1	dbrefs = peptides.get(3).getDBRefs();
198	1	assertEquals(4, dbrefs.length);
199	1	assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
200	1	assertEquals("CAA30421.1", dbrefs[0].getAccessionId());
201	1	assertEquals(cds2Map.getInverse(), dbrefs[0].getMap().getMap());
202	1	assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
203	1	assertEquals("CAA30421.1", dbrefs[1].getAccessionId());
204	1	assertEquals(proteinToCdsMap1, dbrefs[1].getMap().getMap());
205	1	assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
206	1	assertEquals("CAA30421.1", dbrefs[2].getAccessionId());
207	1	assertNull(dbrefs[2].getMap());
208	1	assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
209		dbrefs[3]);
210	1	assertNull(dbrefs[3].getMap());
211
212		// dbrefs for second CDS second Uniprot xref
213	1	dbrefs = peptides.get(4).getDBRefs();
214	1	assertEquals(2, dbrefs.length);
215	1	assertEquals(new DBRefEntry(DBRefSource.UNIPROT, "0", "B0BCM3"),
216		dbrefs[0]);
217	1	assertNull(dbrefs[0].getMap());
218	1	assertEquals(DBRefSource.EMBL, dbrefs[1].getSource());
219	1	assertEquals("X07547", dbrefs[1].getAccessionId());
220	1	assertEquals(cds2Map.getInverse(), dbrefs[1].getMap().getMap());
221
222		// dbrefs for third CDS inferred EMBL product CAA12345.6
223	1	dbrefs = peptides.get(5).getDBRefs();
224	1	assertEquals(3, dbrefs.length);
225	1	assertEquals(DBRefSource.EMBL, dbrefs[0].getSource());
226	1	assertEquals("CAA12345.6", dbrefs[0].getAccessionId());
227	1	assertEquals(cds3Map.getInverse(), dbrefs[0].getMap().getMap());
228	1	assertEquals(DBRefSource.EMBLCDS, dbrefs[1].getSource());
229	1	assertEquals("CAA12345.6", dbrefs[1].getAccessionId());
230	1	assertEquals(proteinToCdsMap2, dbrefs[1].getMap().getMap());
231	1	assertEquals(DBRefSource.EMBLCDSProduct, dbrefs[2].getSource());
232	1	assertEquals("CAA12345.6", dbrefs[2].getAccessionId());
233	1	assertNull(dbrefs[2].getMap());
234		}
235
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
236	1	@Test(groups = "Functional")...
237		public void testAdjustForProteinLength()
238		{
239	1	int[] exons = new int[] { 11, 15, 21, 25, 31, 38 }; // 18 bp
240
241		// exact length match:
242	1	assertSame(exons, EmblEntry.adjustForProteinLength(6, exons));
243
244		// match if we assume exons include stop codon not in protein:
245	1	assertSame(exons, EmblEntry.adjustForProteinLength(5, exons));
246
247		// truncate last exon by 6bp
248	1	int[] truncated = EmblEntry.adjustForProteinLength(4, exons);
249	1	assertEquals("[11, 15, 21, 25, 31, 32]", Arrays.toString(truncated));
250
251		// remove last exon and truncate preceding by 1bp
252	1	truncated = EmblEntry.adjustForProteinLength(3, exons);
253	1	assertEquals("[11, 15, 21, 24]", Arrays.toString(truncated));
254
255		// exact removal of exon case:
256	1	exons = new int[] { 11, 15, 21, 27, 33, 38 }; // 18 bp
257	1	truncated = EmblEntry.adjustForProteinLength(4, exons);
258	1	assertEquals("[11, 15, 21, 27]", Arrays.toString(truncated));
259
260		// what if exons are too short for protein?
261	1	truncated = EmblEntry.adjustForProteinLength(7, exons);
262	1	assertSame(exons, truncated);
263		}
264		}