Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ClustalFileTest	32	18	2	0.00%	Show methods

Class ClustalFileTest

Class ClustalFileTest	Line # 32	Total Statements 18	Complexity 2	TOTAL Coverage 0.00%
testParse_withNumbering() : void   testParse_withNumbering() : void	3434	9.09	1.01	0.0 0.00%
testParse_noNumbering() : void   testParse_noNumbering() : void	6262	9.09	1.01	0.0 0.00%

 

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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
26		import jalview.datamodel.SequenceI;
27
28		import java.io.IOException;
29
30		import org.testng.annotations.Test;
31
		0% Uncovered Elements: 20 (20) Complexity: 2 Complexity Density: 0.11
32		public class ClustalFileTest
33		{
		0% Uncovered Elements: 9 (9) Complexity: 1 Complexity Density: 0.11 4-
34	0	@Test(groups = "Functional")...
35		public void testParse_withNumbering() throws IOException
36		{
37		//@formatter:off
38	0	String data = "CLUSTAL\n\n"
39		+ "FER_CAPAA/1-8 -----------------------------------------------------------A\t1\n"
40		+ "FER_CAPAN/1-55 MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMA 48\n"
41		+ "FER1_SOLLC/1-55 MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA 48\n"
42		+ "Q93XJ9_SOLTU/1-55 MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA 48\n"
43		+ "FER1_PEA/1-60 MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA 53\n\n"
44		+ "FER_CAPAA/1-8 SYKVKLI 8\n"
45		+ "FER_CAPAN/1-55 SYKVKLI 55\n"
46		+ "FER1_SOLLC/1-55 SYKVKLI 55\n"
47		+ "Q93XJ9_SOLTU/1-55 SYKVKLI 55\n"
48		+ "FER1_PEA/1-60 SYKVKLV 60\n"
49		+ " .* .:....*******..** ..........** ********...*:::* ...\n"
50		+ "\t\t.:.::. *\n";
51		//@formatter:on
52	0	ClustalFile cf = new ClustalFile(data, DataSourceType.PASTE);
53	0	cf.parse();
54	0	SequenceI[] seqs = cf.getSeqsAsArray();
55	0	assertEquals(seqs.length, 5);
56	0	assertEquals(seqs[0].getName(), "FER_CAPAA");
57	0	assertEquals(seqs[0].getStart(), 1);
58	0	assertEquals(seqs[0].getEnd(), 8);
59	0	assertTrue(seqs[0].getSequenceAsString().endsWith("ASYKVKLI"));
60		}
61
		0% Uncovered Elements: 9 (9) Complexity: 1 Complexity Density: 0.11 4-
62	0	@Test(groups = "Functional")...
63		public void testParse_noNumbering() throws IOException
64		{
65		//@formatter:off
66	0	String data = "CLUSTAL\n\n"
67		+ "FER_CAPAA/1-8 -----------------------------------------------------------A\n"
68		+ "FER_CAPAN/1-55 MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMA\n"
69		+ "FER1_SOLLC/1-55 MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA\n"
70		+ "Q93XJ9_SOLTU/1-55 MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA\n"
71		+ "FER1_PEA/1-60 MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA\n\n"
72		+ "FER_CAPAA/1-8 SYKVKLI\n"
73		+ "FER_CAPAN/1-55 SYKVKLI\n"
74		+ "FER1_SOLLC/1-55 SYKVKLI\n"
75		+ "Q93XJ9_SOLTU/1-55 SYKVKLI\n"
76		+ "FER1_PEA/1-60 SYKVKLV\n";
77		//@formatter:on
78	0	ClustalFile cf = new ClustalFile(data, DataSourceType.PASTE);
79	0	cf.parse();
80	0	SequenceI[] seqs = cf.getSeqsAsArray();
81	0	assertEquals(seqs.length, 5);
82	0	assertEquals(seqs[0].getName(), "FER_CAPAA");
83	0	assertEquals(seqs[0].getStart(), 1);
84	0	assertEquals(seqs[0].getEnd(), 8);
85	0	assertTrue(seqs[0].getSequenceAsString().endsWith("ASYKVKLI"));
86		}
87		}