Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
DnaUtilsTest	35	59	5	2	0.967741996.8%	Show methods

Class DnaUtilsTest

Class DnaUtilsTest	Line # 35	Total Statements 59	Complexity 5	Uncovered Elements 2	TOTAL Coverage 0.967741996.8%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	3838	2.02	1.01	0.00	1.0 1.0100%
testParseLocation() : void   testParseLocation() : void	5252	54.054	2.02	1.01	0.9814815 0.981481598.1%
checkForParseException(String) : void   checkForParseException(String) : void	169169	3.03	2.02	1.01	0.6666667 0.666666766.7%

 

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	Test contribution	Test	Result	Actions
	0.91935486	jalview.util.DnaUtilsTest.testParseLocationjalview.util.DnaUtilsTest.testParseLocation	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.util;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertNull;
25		import static org.testng.AssertJUnit.fail;
26
27		import jalview.gui.JvOptionPane;
28
29		import java.text.ParseException;
30		import java.util.List;
31
32		import org.testng.annotations.BeforeClass;
33		import org.testng.annotations.Test;
34
		96.8% Uncovered Elements: 2 (62) Complexity: 5 Complexity Density: 0.08
35		public class DnaUtilsTest
36		{
37
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
38	1	@BeforeClass(alwaysRun = true)...
39		public void setUpJvOptionPane()
40		{
41	1	JvOptionPane.setInteractiveMode(false);
42	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
43		}
44
45		/**
46		* Tests for parsing an ENA/GenBank location specifier
47		*
48		* @throws ParseException
49		*
50		* @see http://www.insdc.org/files/feature_table.html#3.4
51		*/
		98.1% Uncovered Elements: 1 (54) Complexity: 2 Complexity Density: 0.04 1PASS
52	1	@Test(groups = { "Functional" })...
53		public void testParseLocation() throws ParseException
54		{
55		/*
56		* single locus
57		*/
58	1	List<int[]> ranges = DnaUtils.parseLocation("467");
59	1	assertEquals(1, ranges.size());
60	1	assertEquals(467, ranges.get(0)[0]);
61	1	assertEquals(467, ranges.get(0)[1]);
62
63		/*
64		* simple range
65		*/
66	1	ranges = DnaUtils.parseLocation("12..78");
67	1	assertEquals(1, ranges.size());
68	1	assertEquals(12, ranges.get(0)[0]);
69	1	assertEquals(78, ranges.get(0)[1]);
70
71		/*
72		* join of simple ranges
73		*/
74	1	ranges = DnaUtils.parseLocation("join(12..78,134..202,322..345)");
75	1	assertEquals(3, ranges.size());
76	1	assertEquals(12, ranges.get(0)[0]);
77	1	assertEquals(78, ranges.get(0)[1]);
78	1	assertEquals(134, ranges.get(1)[0]);
79	1	assertEquals(202, ranges.get(1)[1]);
80	1	assertEquals(322, ranges.get(2)[0]);
81	1	assertEquals(345, ranges.get(2)[1]);
82
83		/*
84		* complement of a simple range
85		*/
86	1	ranges = DnaUtils.parseLocation("complement(34..126)");
87	1	assertEquals(1, ranges.size());
88	1	assertEquals(126, ranges.get(0)[0]);
89	1	assertEquals(34, ranges.get(0)[1]);
90
91		/*
92		* complement of a join
93		*/
94	1	ranges = DnaUtils
95		.parseLocation("complement(join(2691..4571,4918..5163))");
96	1	assertEquals(2, ranges.size());
97	1	assertEquals(5163, ranges.get(0)[0]);
98	1	assertEquals(4918, ranges.get(0)[1]);
99	1	assertEquals(4571, ranges.get(1)[0]);
100	1	assertEquals(2691, ranges.get(1)[1]);
101
102		/*
103		* join of two complements
104		*/
105	1	ranges = DnaUtils
106		.parseLocation("join(complement(4918..5163),complement(2691..4571))");
107	1	assertEquals(2, ranges.size());
108	1	assertEquals(5163, ranges.get(0)[0]);
109	1	assertEquals(4918, ranges.get(0)[1]);
110	1	assertEquals(4571, ranges.get(1)[0]);
111	1	assertEquals(2691, ranges.get(1)[1]);
112
113		/*
114		* join complement to non-complement
115		* @see http://www.ncbi.nlm.nih.gov/genbank/genomesubmit_annotation/ Transpliced Genes
116		*/
117	1	ranges = DnaUtils
118		.parseLocation("join(complement(36618..36700),86988..87064)");
119	1	assertEquals(2, ranges.size());
120	1	assertEquals(36700, ranges.get(0)[0]);
121	1	assertEquals(36618, ranges.get(0)[1]);
122	1	assertEquals(86988, ranges.get(1)[0]);
123	1	assertEquals(87064, ranges.get(1)[1]);
124
125		/*
126		* valid things we don't yet handle
127		*/
128	1	checkForParseException("<34..126");
129	1	checkForParseException("35..>126");
130	1	checkForParseException("34.126");
131	1	checkForParseException("34^126");
132	1	checkForParseException("order(34..126,130..180)");
133
134		/*
135		* invalid things
136		*/
137	1	checkForParseException("");
138	1	checkForParseException("JOIN(1..2)");
139	1	checkForParseException("join(1..2");
140	1	checkForParseException("join(1..2(");
141	1	checkForParseException("complement(1..2");
142	1	checkForParseException("complement(1..2(");
143	1	try
144		{
145	1	assertNull(DnaUtils.parseLocation(null));
146	0	fail("Expected exception");
147		} catch (NullPointerException e)
148		{
149		// expected
150		}
151
152		/*
153		* nested joins are not allowed; just as well since this fails to parse
154		* (splitting tokens by comma fragments the inner join expression)
155		*/
156	1	checkForParseException("join(1..2,join(4..5,10..12),18..22)");
157		/*
158		* complement may not enclose multiple ranges
159		* parsing fails for the same reason
160		*/
161	1	checkForParseException("join(complement(36618..36700,4000..4200),86988..87064)");
162		}
163
164		/**
165		* Verifies that a ParseException is thrown when the given location is parsed
166		*
167		* @param location
168		*/
		66.7% Uncovered Elements: 1 (3) Complexity: 2 Complexity Density: 0.67
169	13	void checkForParseException(String location)...
170		{
171	13	try
172		{
173	13	DnaUtils.parseLocation(location);
174	0	fail("Expected exception");
175		} catch (ParseException e)
176		{
177		// expected;
178		}
179		}
180
181		}