Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
GffHelperBaseTest	37	134	5	0.992753699.3%	Show methods

Class GffHelperBaseTest

Class GffHelperBaseTest	Line # 37	Total Statements 134	Complexity 5	TOTAL Coverage 0.992753699.3%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4040	2.02	1.01	1.0 1.0100%
testParseNameValuePairs() : void   testParseNameValuePairs() : void	5151	22.022	1.01	1.0 1.0100%
testTrimMapping() : void   testTrimMapping() : void	100100	75.075	1.01	1.0 1.0100%
testParseAttributeMap() : void   testParseAttributeMap() : void	212212	35.035	2.02	0.9714286 0.971428697.1%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.5507246	jalview.io.gff.GffHelperBaseTest.testTrimMappingjalview.io.gff.GffHelperBaseTest.testTrimMapping	1PASS
	0.2536232	jalview.io.gff.GffHelperBaseTest.testParseAttributeMapjalview.io.gff.GffHelperBaseTest.testParseAttributeMap	1PASS
	0.16666667	jalview.io.gff.GffHelperBaseTest.testParseNameValuePairsjalview.io.gff.GffHelperBaseTest.testParseNameValuePairs	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.gff;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertFalse;
25		import static org.testng.Assert.assertTrue;
26		import static org.testng.Assert.fail;
27
28		import jalview.gui.JvOptionPane;
29
30		import java.util.Arrays;
31		import java.util.List;
32		import java.util.Map;
33
34		import org.testng.annotations.BeforeClass;
35		import org.testng.annotations.Test;
36
		99.3% Uncovered Elements: 1 (138) Complexity: 5 Complexity Density: 0.04
37		public class GffHelperBaseTest
38		{
39
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
40	1	@BeforeClass(alwaysRun = true)...
41		public void setUpJvOptionPane()
42		{
43	1	JvOptionPane.setInteractiveMode(false);
44	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
45		}
46
47		/**
48		* Test the method that parses lines like <br>
49		* ID=2345;Name=Something,Another thing;Notes=Hello;Notes=World
50		*/
		100% Uncovered Elements: 0 (22) Complexity: 1 Complexity Density: 0.05 1PASS
51	1	@Test(groups = { "Functional" })...
52		public void testParseNameValuePairs()
53		{
54	1	assertTrue(GffHelperBase.parseNameValuePairs(null, ";", ' ', ",")
55		.isEmpty());
56	1	assertTrue(GffHelperBase.parseNameValuePairs("", ";", ' ', ",")
57		.isEmpty());
58	1	assertTrue(GffHelperBase.parseNameValuePairs("hello=world", ";", ' ',
59		",").isEmpty());
60
61	1	Map<String, List<String>> map = GffHelperBase.parseNameValuePairs(
62		"hello world", ";", ' ', ", ");
63	1	assertEquals(map.size(), 1);
64	1	assertEquals(map.get("hello").size(), 1);
65	1	assertEquals(map.get("hello").get(0), "world");
66
67	1	map = GffHelperBase
68		.parseNameValuePairs(
69		"Method= manual curation ;nothing; Notes=F2 S ; Notes=Metal,Shiny%2Csmooth; Type=",
70		";", '=', ",");
71
72		// Type is ignored as no value was supplied
73	1	assertEquals(map.size(), 2);
74
75	1	assertEquals(map.get("Method").size(), 1);
76	1	assertEquals(map.get("Method").get(0), "manual curation"); // trimmed
77
78	1	assertEquals(map.get("Notes").size(), 3);
79	1	assertEquals(map.get("Notes").get(0), "F2 S");
80	1	assertEquals(map.get("Notes").get(1), "Metal");
81	1	assertEquals(map.get("Notes").get(2), "Shiny%2Csmooth"); // not decoded here
82
83		/*
84		* gff3 style with nested attribute values
85		*/
86	1	String csqValue = "POLYPHEN=possibly_damaging,probably_damaging,SIFT=tolerated%2Cdeleterious";
87	1	map = GffHelperBase.parseNameValuePairs("hello=world;CSQ=" + csqValue,
88		";", '=', ",");
89	1	assertEquals(map.size(), 2); // keys hello, CSQ
90	1	assertEquals(map.get("hello").size(), 1);
91	1	assertEquals(map.get("hello").get(0), "world");
92		// CSQ values is read 'raw' here, and parsed further elsewhere
93	1	assertEquals(map.get("CSQ").size(), 1);
94	1	assertEquals(map.get("CSQ").get(0), csqValue);
95		}
96
97		/**
98		* Test for the method that tries to trim mappings to equivalent lengths
99		*/
		100% Uncovered Elements: 0 (75) Complexity: 1 Complexity Density: 0.01 1PASS
100	1	@Test(groups = "Functional")...
101		public void testTrimMapping()
102		{
103	1	int[] from = { 1, 12 };
104	1	int[] to = { 20, 31 };
105	1	assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
106	1	assertEquals(Arrays.toString(from), "[1, 12]"); // unchanged
107	1	assertEquals(Arrays.toString(to), "[20, 31]"); // unchanged
108
109		// from too long:
110	1	from = new int[] { 1, 13 };
111	1	assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
112	1	assertEquals(Arrays.toString(from), "[1, 12]"); // trimmed
113	1	assertEquals(Arrays.toString(to), "[20, 31]"); // unchanged
114
115		// to too long:
116	1	to = new int[] { 20, 33 };
117	1	assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
118	1	assertEquals(Arrays.toString(from), "[1, 12]"); // unchanged
119	1	assertEquals(Arrays.toString(to), "[20, 31]"); // trimmed
120
121		// from reversed:
122	1	from = new int[] { 12, 1 };
123	1	assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
124	1	assertEquals(Arrays.toString(from), "[12, 1]"); // unchanged
125	1	assertEquals(Arrays.toString(to), "[20, 31]"); // unchanged
126
127		// to reversed:
128	1	to = new int[] { 31, 20 };
129	1	assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
130	1	assertEquals(Arrays.toString(from), "[12, 1]"); // unchanged
131	1	assertEquals(Arrays.toString(to), "[31, 20]"); // unchanged
132
133		// from reversed and too long:
134	1	from = new int[] { 14, 1 };
135	1	assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
136	1	assertEquals(Arrays.toString(from), "[14, 3]"); // end trimmed
137	1	assertEquals(Arrays.toString(to), "[31, 20]"); // unchanged
138
139		// to reversed and too long:
140	1	to = new int[] { 31, 10 };
141	1	assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
142	1	assertEquals(Arrays.toString(from), "[14, 3]"); // unchanged
143	1	assertEquals(Arrays.toString(to), "[31, 20]"); // end trimmed
144
145		// cdna to peptide (matching)
146	1	from = new int[] { 1, 18 };
147	1	to = new int[] { 4, 9 };
148	1	assertTrue(GffHelperBase.trimMapping(from, to, 3, 1));
149	1	assertEquals(Arrays.toString(from), "[1, 18]"); // unchanged
150	1	assertEquals(Arrays.toString(to), "[4, 9]"); // unchanged
151
152		// overlong cdna to peptide
153	1	from = new int[] { 1, 20 };
154	1	assertTrue(GffHelperBase.trimMapping(from, to, 3, 1));
155	1	assertEquals(Arrays.toString(from), "[1, 18]"); // end trimmed
156	1	assertEquals(Arrays.toString(to), "[4, 9]"); // unchanged
157
158		// overlong cdna (reversed) to peptide
159	1	from = new int[] { 20, 1 };
160	1	assertTrue(GffHelperBase.trimMapping(from, to, 3, 1));
161	1	assertEquals(Arrays.toString(from), "[20, 3]"); // end trimmed
162	1	assertEquals(Arrays.toString(to), "[4, 9]"); // unchanged
163
164		// overlong cdna (reversed) to peptide (reversed)
165	1	from = new int[] { 20, 1 };
166	1	to = new int[] { 9, 4 };
167	1	assertTrue(GffHelperBase.trimMapping(from, to, 3, 1));
168	1	assertEquals(Arrays.toString(from), "[20, 3]"); // end trimmed
169	1	assertEquals(Arrays.toString(to), "[9, 4]"); // unchanged
170
171		// peptide to cdna (matching)
172	1	from = new int[] { 4, 9 };
173	1	to = new int[] { 1, 18 };
174	1	assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
175	1	assertEquals(Arrays.toString(from), "[4, 9]"); // unchanged
176	1	assertEquals(Arrays.toString(to), "[1, 18]"); // unchanged
177
178		// peptide to overlong cdna
179	1	to = new int[] { 1, 20 };
180	1	assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
181	1	assertEquals(Arrays.toString(from), "[4, 9]"); // unchanged
182	1	assertEquals(Arrays.toString(to), "[1, 18]"); // end trimmed
183
184		// peptide to overlong cdna (reversed)
185	1	to = new int[] { 20, 1 };
186	1	assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
187	1	assertEquals(Arrays.toString(from), "[4, 9]"); // unchanged
188	1	assertEquals(Arrays.toString(to), "[20, 3]"); // end trimmed
189
190		// peptide (reversed) to overlong cdna (reversed)
191	1	from = new int[] { 9, 4 };
192	1	to = new int[] { 20, 1 };
193	1	assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
194	1	assertEquals(Arrays.toString(from), "[9, 4]"); // unchanged
195	1	assertEquals(Arrays.toString(to), "[20, 3]"); // end trimmed
196
197		// overlong peptide to word-length cdna
198	1	from = new int[] { 4, 10 };
199	1	to = new int[] { 1, 18 };
200	1	assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
201	1	assertEquals(Arrays.toString(from), "[4, 9]"); // end trimmed
202	1	assertEquals(Arrays.toString(to), "[1, 18]"); // unchanged
203
204		// overlong peptide to non-word-length cdna
205	1	from = new int[] { 4, 10 };
206	1	to = new int[] { 1, 19 };
207	1	assertFalse(GffHelperBase.trimMapping(from, to, 1, 3));
208	1	assertEquals(Arrays.toString(from), "[4, 10]"); // unchanged
209	1	assertEquals(Arrays.toString(to), "[1, 19]"); // unchanged
210		}
211
		97.1% Uncovered Elements: 1 (35) Complexity: 2 Complexity Density: 0.06 1PASS
212	1	@Test(groups = { "Functional" })...
213		public void testParseAttributeMap()
214		{
215	1	Map<String, String> map = GffHelperBase
216		.parseAttributeMap("A=B,C%2C%3D%3B%09%25D,X=Y");
217	1	assertEquals(map.size(), 2);
218		// value of A is everything up to and excluding ,X=
219	1	assertEquals(map.get("A"), "B,C,=;\t%D");
220	1	assertEquals(map.get("X"), "Y");
221
222		/*
223		* malformed cases should result in an empty map
224		*/
225	1	map = GffHelperBase.parseAttributeMap("=B=Y");
226	1	assertTrue(map.isEmpty());
227		// first token should be an attribute name only, no commas
228	1	map = GffHelperBase.parseAttributeMap("A,B=C");
229	1	assertTrue(map.isEmpty());
230		// intermediate tokens need at least one comma (value,name=)
231	1	map = GffHelperBase.parseAttributeMap("A=B=C");
232	1	assertTrue(map.isEmpty());
233		// last token may have a comma or not
234	1	map = GffHelperBase.parseAttributeMap("A=B");
235	1	assertEquals(map.get("A"), "B");
236	1	map = GffHelperBase.parseAttributeMap("A=B,C");
237	1	assertEquals(map.get("A"), "B,C");
238	1	map = GffHelperBase.parseAttributeMap("A");
239	1	assertTrue(map.isEmpty());
240	1	map = GffHelperBase.parseAttributeMap("A=");
241	1	assertTrue(map.isEmpty());
242	1	map = GffHelperBase.parseAttributeMap("A==C");
243	1	assertTrue(map.isEmpty());
244	1	map = GffHelperBase.parseAttributeMap("=A");
245	1	assertTrue(map.isEmpty());
246	1	map = GffHelperBase.parseAttributeMap("=");
247	1	assertTrue(map.isEmpty());
248	1	map = GffHelperBase.parseAttributeMap(",");
249	1	assertTrue(map.isEmpty());
250	1	map = GffHelperBase.parseAttributeMap(" ");
251	1	assertTrue(map.isEmpty());
252	1	map = GffHelperBase.parseAttributeMap("");
253	1	assertTrue(map.isEmpty());
254	1	map = GffHelperBase.parseAttributeMap("A=B, =C");
255	1	assertTrue(map.isEmpty());
256
257	1	try
258		{
259	1	GffHelperBase.parseAttributeMap(null);
260	0	fail("expected exception");
261		} catch (NullPointerException e)
262		{
263		// expected
264		}
265		}
266		}