Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
ClustalFileTest	12	18	2	0	1.0100%	Show methods

Class ClustalFileTest

Class ClustalFileTest	Line # 12	Total Statements 18	Complexity 2	Uncovered Elements 0	TOTAL Coverage 1.0100%
testParse_withNumbering() : void   testParse_withNumbering() : void	1414	9.09	1.01	0.00	1.0 1.0100%
testParse_noNumbering() : void   testParse_noNumbering() : void	4242	9.09	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.5	jalview.io.ClustalFileTest.testParse_withNumberingjalview.io.ClustalFileTest.testParse_withNumbering	1PASS
	0.5	jalview.io.ClustalFileTest.testParse_noNumberingjalview.io.ClustalFileTest.testParse_noNumbering	1PASS

 

Source view

1		package jalview.io;
2
3		import static org.testng.Assert.assertEquals;
4		import static org.testng.Assert.assertTrue;
5
6		import jalview.datamodel.SequenceI;
7
8		import java.io.IOException;
9
10		import org.testng.annotations.Test;
11
		100% Uncovered Elements: 0 (20) Complexity: 2 Complexity Density: 0.11
12		public class ClustalFileTest
13		{
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11 1PASS
14	1	@Test(groups="Functional")...
15		public void testParse_withNumbering() throws IOException
16		{
17		//@formatter:off
18	1	String data = "CLUSTAL\n\n"
19		+ "FER_CAPAA/1-8 -----------------------------------------------------------A\t1\n"
20		+ "FER_CAPAN/1-55 MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMA 48\n"
21		+ "FER1_SOLLC/1-55 MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA 48\n"
22		+ "Q93XJ9_SOLTU/1-55 MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA 48\n"
23		+ "FER1_PEA/1-60 MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA 53\n\n"
24		+ "FER_CAPAA/1-8 SYKVKLI 8\n"
25		+ "FER_CAPAN/1-55 SYKVKLI 55\n"
26		+ "FER1_SOLLC/1-55 SYKVKLI 55\n"
27		+ "Q93XJ9_SOLTU/1-55 SYKVKLI 55\n"
28		+ "FER1_PEA/1-60 SYKVKLV 60\n"
29		+ " .* .:....*******..** ..........** ********...*:::* ...\n"
30		+ "\t\t.:.::. *\n";
31		//@formatter:on
32	1	ClustalFile cf = new ClustalFile(data, DataSourceType.PASTE);
33	1	cf.parse();
34	1	SequenceI[] seqs = cf.getSeqsAsArray();
35	1	assertEquals(seqs.length, 5);
36	1	assertEquals(seqs[0].getName(), "FER_CAPAA");
37	1	assertEquals(seqs[0].getStart(), 1);
38	1	assertEquals(seqs[0].getEnd(), 8);
39	1	assertTrue(seqs[0].getSequenceAsString().endsWith("ASYKVKLI"));
40		}
41
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11 1PASS
42	1	@Test(groups="Functional")...
43		public void testParse_noNumbering() throws IOException
44		{
45		//@formatter:off
46	1	String data = "CLUSTAL\n\n"
47		+ "FER_CAPAA/1-8 -----------------------------------------------------------A\n"
48		+ "FER_CAPAN/1-55 MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMA\n"
49		+ "FER1_SOLLC/1-55 MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA\n"
50		+ "Q93XJ9_SOLTU/1-55 MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA\n"
51		+ "FER1_PEA/1-60 MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA\n\n"
52		+ "FER_CAPAA/1-8 SYKVKLI\n"
53		+ "FER_CAPAN/1-55 SYKVKLI\n"
54		+ "FER1_SOLLC/1-55 SYKVKLI\n"
55		+ "Q93XJ9_SOLTU/1-55 SYKVKLI\n"
56		+ "FER1_PEA/1-60 SYKVKLV\n";
57		//@formatter:on
58	1	ClustalFile cf = new ClustalFile(data, DataSourceType.PASTE);
59	1	cf.parse();
60	1	SequenceI[] seqs = cf.getSeqsAsArray();
61	1	assertEquals(seqs.length, 5);
62	1	assertEquals(seqs[0].getName(), "FER_CAPAA");
63	1	assertEquals(seqs[0].getStart(), 1);
64	1	assertEquals(seqs[0].getEnd(), 8);
65	1	assertTrue(seqs[0].getSequenceAsString().endsWith("ASYKVKLI"));
66		}
67		}