Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
BSMLFileTest	15	15	1	1.0100%	Show methods

Class BSMLFileTest

Class BSMLFileTest	Line # 15	Total Statements 15	Complexity 1	TOTAL Coverage 1.0100%
testParse_BSML() : void   testParse_BSML() : void	1717	15.015	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	1.0	jalview.io.BSMLFileTest.testParse_BSMLjalview.io.BSMLFileTest.testParse_BSML	1PASS

 

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1		package jalview.io;
2
3		import static org.testng.Assert.assertEquals;
4		import static org.testng.Assert.assertTrue;
5
6		import jalview.datamodel.SequenceFeature;
7		import jalview.datamodel.SequenceI;
8		import jalview.datamodel.features.SequenceFeaturesI;
9
10		import java.io.IOException;
11		import java.util.List;
12
13		import org.testng.annotations.Test;
14
		100% Uncovered Elements: 0 (16) Complexity: 1 Complexity Density: 0.07
15		public class BSMLFileTest
16		{
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07 1PASS
17	1	@Test(groups="Functional")...
18		public void testParse_BSML() throws IOException
19		{
20		//@formatter:off
21	1	String data = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\r\n" +
22		"<Bsml>\r\n" +
23		" <Definitions>\r\n" +
24		" <Sequences>\r\n" +
25		" <Sequence\r\n" +
26		" comment=\"Sequence Data Contained in 'Multiple-alignment' section\"\r\n" +
27		" id=\"SEQ-ID:181170\" length=\"30\" molecule=\"dna\" title=\"EP1\">\r\n" +
28		" <Feature-tables>\r\n" +
29		" <Feature-table title=\"GENE\">\r\n" +
30		" <Feature class=\"GENE\" title=\"TEST-001\">\r\n" +
31		" <Interval-loc complement=\"0\" endpos=\"20\" startpos=\"10\"/>\r\n" +
32		" <Resource id=\"GENE-ID:181171\"/>\r\n" +
33		" </Feature>\r\n" +
34		" </Feature-table>\r\n" +
35		" </Feature-tables>\r\n" +
36		" </Sequence>\r\n" +
37		" </Sequences>\r\n" +
38		" <Tables>\r\n" +
39		" <Multiple-alignment-table molecule-type=\"nucleotide\">\r\n" +
40		" <Sequence-alignment sequences=\"1\">\r\n" +
41		" <Sequence-data seq-name=\"EP1\">--AATTTT-ATTTAGTGTCT-----------</Sequence-data>\r\n" +
42		" <Alignment-consensus/>\r\n" +
43		" </Sequence-alignment>\r\n" +
44		" </Multiple-alignment-table>\r\n" +
45		" </Tables>\r\n" +
46		" <Notebook notebook=\"\"/>\r\n" +
47		" </Definitions>\r\n" +
48		"</Bsml>\r\n" +
49		"";
50	1	BSMLFile cf = new BSMLFile(data, DataSourceType.PASTE);
51		// why twice? cf.parse();
52	1	SequenceI[] seqs = cf.getSeqsAsArray();
53	1	assertEquals(seqs.length, 1);
54	1	SequenceI seq = seqs[0];
55	1	assertEquals(seq.getName(), "EP1");
56	1	assertEquals(seq.getStart(), 1);
57	1	assertEquals(seq.getEnd(), 31);
58	1	assertTrue(seq.getSequenceAsString().equals("--AATTTT-ATTTAGTGTCT-----------"));
59	1	SequenceFeaturesI features = seq.getFeatures();
60	1	List<SequenceFeature> genes = features.getAllFeatures("GENE");
61	1	assertEquals(genes.size(), 1);
62	1	SequenceFeature sf = genes.get(0);
63	1	assertEquals(sf.getDescription(), "TEST-001");
64	1	assertEquals(sf.begin + "," + sf.end, "10,20");
65
66		}
67
68		}