Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
LayeredDBNParserTest	33	25	1	1.0100%	Show methods

Class LayeredDBNParserTest

Class LayeredDBNParserTest	Line # 33	Total Statements 25	Complexity 1	TOTAL Coverage 1.0100%
testParse() : void   testParse() : void	3535	25.025	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	1.0	jalview.io.LayeredDBNParserTest.testParsejalview.io.LayeredDBNParserTest.testParse	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.io;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertTrue;
25
26		import java.io.IOException;
27
28		import org.testng.annotations.Test;
29
30		import jalview.datamodel.AlignmentI;
31		import jalview.io.LayeredDBNParser.Record;
32
		100% Uncovered Elements: 0 (26) Complexity: 1 Complexity Density: 0.04
33		public class LayeredDBNParserTest
34		{
		100% Uncovered Elements: 0 (25) Complexity: 1 Complexity Density: 0.04 1PASS
35	1	@Test(groups = "Functional")...
36		public void testParse() throws IOException
37		{
38
39		// Example text fitting the specification
40	1	String sampleText = ">RNA complex: chains A[1_555](1-59), B[1_555](1-59) ('&' separates chains)\n"
41
42		+ "seq : AAGUACCCUCCAAGCCCUACAGGUUGGAAGAGGGGGCUAUCAGUCCUGUAGGCAGACUC&AAGUACCCUCCAAGCCCUACAGGUUGGAAGAGGGGGCUAUCAGUCCUGUAGGCAGACUC\n"
43
44		+ "L1 cWW : .(((.([[[[[..{.{{{{.{{{...)..].]]]])))......}}}.}}}}}......&.(((.([[[[[..{.{{{{{{{{...)..].]]]])))......}}}}}}}}}......\n"
45
46		+ "L10 tWW : .......................(......)............................&...........................................................\n"
47
48		+ "L11 tWH : ........................(...)..............................&........................(...)..............................\n"
49
50		+ "L12 tWS : ....(....................)..(.............)................&....(....................)..(.............)................\n"
51
52		+ "L13 tHW : ....(....................................).................&....(....................................).................\n"
53
54		+ "L18 tSS : ...........................................................&............(......................................)....... \n"
55		;
56
57		// Init Jalview FileParse in PASTE mode, which means reading directly from a
58		// String block in memory
59
60	1	LayeredDBNParser parser = new LayeredDBNParser(sampleText,
61		DataSourceType.PASTE);
62	1	Record parsedRecord = parser.getRecord();
63	1	String seq1 = "AAGUACCCUCCAAGCCCUACAGGUUGGAAGAGGGGGCUAUCAGUCCUGUAGGCAGACUC", seq2="AAGUACCCUCCAAGCCCUACAGGUUGGAAGAGGGGGCUAUCAGUCCUGUAGGCAGACUC";
64
65	1	assertEquals(parsedRecord.sequences.get(0), seq1);
66	1	assertEquals(parsedRecord.sequences.get(1), seq2);
67	1	assertEquals(parsedRecord.basePairs.get("L1 cWW").get(0).getWuss(),
68		".(((.([[[[[..{.{{{{.{{{...)..].]]]])))......}}}.}}}}}......");
69	1	assertEquals(parsedRecord.basePairs.get("L1 cWW").get(1).getWuss(),
70		".(((.([[[[[..{.{{{{{{{{...)..].]]]])))......}}}}}}}}}......");
71	1	assertEquals(parsedRecord.basePairs.get("L10 tWW").get(0).getWuss(),
72		".......................(......)............................");
73	1	assertEquals(parsedRecord.basePairs.get("L10 tWW").get(1).getWuss(),
74		"...........................................................");
75	1	assertEquals(parsedRecord.basePairs.get("L11 tWH").get(0).getWuss(),
76		"........................(...)..............................");
77	1	assertEquals(parsedRecord.basePairs.get("L11 tWH").get(1).getWuss(),
78		"........................(...)..............................");
79	1	assertEquals(parsedRecord.basePairs.get("L12 tWS").get(0).getWuss(),
80		"....(....................)..(.............)................");
81	1	assertEquals(parsedRecord.basePairs.get("L12 tWS").get(1).getWuss(),
82		"....(....................)..(.............)................");
83	1	assertEquals(parsedRecord.basePairs.get("L13 tHW").get(0).getWuss(),
84		"....(....................................).................");
85	1	assertEquals(parsedRecord.basePairs.get("L13 tHW").get(1).getWuss(),
86		"....(....................................).................");
87	1	assertEquals(parsedRecord.basePairs.get("L18 tSS").get(0).getWuss(),
88		"...........................................................");
89	1	assertEquals(parsedRecord.basePairs.get("L18 tSS").get(1).getWuss(),
90		"............(......................................).......");
91
92		// identifyfile
93
94	1	FileFormatI afr = new IdentifyFile().identify(sampleText, DataSourceType.PASTE);
95	1	assertEquals(afr, FileFormat.LayeredBN);
96		// now check sequence
97	1	AlignmentI al = new AppletFormatAdapter().readFile(sampleText,
98		DataSourceType.PASTE, FileFormat.LayeredBN);
99
100	1	assertEquals(al.getHeight(), 2);
101	1	assertEquals(al.getSequenceAt(0).getAnnotation()[0].isRNA(), true);
102	1	assertTrue(al.getSequenceAt(0).getSequenceAsString().equals(seq1));
103	1	assertTrue(al.getSequenceAt(1).getSequenceAsString().equals(seq2));
104		}
105		}