Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
GffHelperBaseTest	37	134	5	0.00%	Show methods

Class GffHelperBaseTest

Class GffHelperBaseTest	Line # 37	Total Statements 134	Complexity 5	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4040	2.02	1.01	0.0 0.00%
testParseNameValuePairs() : void   testParseNameValuePairs() : void	5151	22.022	1.01	0.0 0.00%
testTrimMapping() : void   testTrimMapping() : void	9999	75.075	1.01	0.0 0.00%
testParseAttributeMap() : void   testParseAttributeMap() : void	211211	35.035	2.02	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.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
		0% Uncovered Elements: 138 (138) Complexity: 5 Complexity Density: 0.04
37		public class GffHelperBaseTest
38		{
39
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
40	0	@BeforeClass(alwaysRun = true)...
41		public void setUpJvOptionPane()
42		{
43	0	JvOptionPane.setInteractiveMode(false);
44	0	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		*/
		0% Uncovered Elements: 22 (22) Complexity: 1 Complexity Density: 0.05 4-
51	0	@Test(groups = { "Functional" })...
52		public void testParseNameValuePairs()
53		{
54	0	assertTrue(GffHelperBase.parseNameValuePairs(null, ";", ' ', ",")
55		.isEmpty());
56	0	assertTrue(
57		GffHelperBase.parseNameValuePairs("", ";", ' ', ",").isEmpty());
58	0	assertTrue(GffHelperBase
59		.parseNameValuePairs("hello=world", ";", ' ', ",").isEmpty());
60
61	0	Map<String, List<String>> map = GffHelperBase
62		.parseNameValuePairs("hello world", ";", ' ', ", ");
63	0	assertEquals(map.size(), 1);
64	0	assertEquals(map.get("hello").size(), 1);
65	0	assertEquals(map.get("hello").get(0), "world");
66
67	0	map = GffHelperBase.parseNameValuePairs(
68		"Method= manual curation ;nothing; Notes=F2 S ; Notes=Metal,Shiny%2Csmooth; Type=",
69		";", '=', ",");
70
71		// Type is ignored as no value was supplied
72	0	assertEquals(map.size(), 2);
73
74	0	assertEquals(map.get("Method").size(), 1);
75	0	assertEquals(map.get("Method").get(0), "manual curation"); // trimmed
76
77	0	assertEquals(map.get("Notes").size(), 3);
78	0	assertEquals(map.get("Notes").get(0), "F2 S");
79	0	assertEquals(map.get("Notes").get(1), "Metal");
80	0	assertEquals(map.get("Notes").get(2), "Shiny%2Csmooth"); // not decoded here
81
82		/*
83		* gff3 style with nested attribute values
84		*/
85	0	String csqValue = "POLYPHEN=possibly_damaging,probably_damaging,SIFT=tolerated%2Cdeleterious";
86	0	map = GffHelperBase.parseNameValuePairs("hello=world;CSQ=" + csqValue,
87		";", '=', ",");
88	0	assertEquals(map.size(), 2); // keys hello, CSQ
89	0	assertEquals(map.get("hello").size(), 1);
90	0	assertEquals(map.get("hello").get(0), "world");
91		// CSQ values is read 'raw' here, and parsed further elsewhere
92	0	assertEquals(map.get("CSQ").size(), 1);
93	0	assertEquals(map.get("CSQ").get(0), csqValue);
94		}
95
96		/**
97		* Test for the method that tries to trim mappings to equivalent lengths
98		*/
		0% Uncovered Elements: 75 (75) Complexity: 1 Complexity Density: 0.01 4-
99	0	@Test(groups = "Functional")...
100		public void testTrimMapping()
101		{
102	0	int[] from = { 1, 12 };
103	0	int[] to = { 20, 31 };
104	0	assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
105	0	assertEquals(Arrays.toString(from), "[1, 12]"); // unchanged
106	0	assertEquals(Arrays.toString(to), "[20, 31]"); // unchanged
107
108		// from too long:
109	0	from = new int[] { 1, 13 };
110	0	assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
111	0	assertEquals(Arrays.toString(from), "[1, 12]"); // trimmed
112	0	assertEquals(Arrays.toString(to), "[20, 31]"); // unchanged
113
114		// to too long:
115	0	to = new int[] { 20, 33 };
116	0	assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
117	0	assertEquals(Arrays.toString(from), "[1, 12]"); // unchanged
118	0	assertEquals(Arrays.toString(to), "[20, 31]"); // trimmed
119
120		// from reversed:
121	0	from = new int[] { 12, 1 };
122	0	assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
123	0	assertEquals(Arrays.toString(from), "[12, 1]"); // unchanged
124	0	assertEquals(Arrays.toString(to), "[20, 31]"); // unchanged
125
126		// to reversed:
127	0	to = new int[] { 31, 20 };
128	0	assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
129	0	assertEquals(Arrays.toString(from), "[12, 1]"); // unchanged
130	0	assertEquals(Arrays.toString(to), "[31, 20]"); // unchanged
131
132		// from reversed and too long:
133	0	from = new int[] { 14, 1 };
134	0	assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
135	0	assertEquals(Arrays.toString(from), "[14, 3]"); // end trimmed
136	0	assertEquals(Arrays.toString(to), "[31, 20]"); // unchanged
137
138		// to reversed and too long:
139	0	to = new int[] { 31, 10 };
140	0	assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
141	0	assertEquals(Arrays.toString(from), "[14, 3]"); // unchanged
142	0	assertEquals(Arrays.toString(to), "[31, 20]"); // end trimmed
143
144		// cdna to peptide (matching)
145	0	from = new int[] { 1, 18 };
146	0	to = new int[] { 4, 9 };
147	0	assertTrue(GffHelperBase.trimMapping(from, to, 3, 1));
148	0	assertEquals(Arrays.toString(from), "[1, 18]"); // unchanged
149	0	assertEquals(Arrays.toString(to), "[4, 9]"); // unchanged
150
151		// overlong cdna to peptide
152	0	from = new int[] { 1, 20 };
153	0	assertTrue(GffHelperBase.trimMapping(from, to, 3, 1));
154	0	assertEquals(Arrays.toString(from), "[1, 18]"); // end trimmed
155	0	assertEquals(Arrays.toString(to), "[4, 9]"); // unchanged
156
157		// overlong cdna (reversed) to peptide
158	0	from = new int[] { 20, 1 };
159	0	assertTrue(GffHelperBase.trimMapping(from, to, 3, 1));
160	0	assertEquals(Arrays.toString(from), "[20, 3]"); // end trimmed
161	0	assertEquals(Arrays.toString(to), "[4, 9]"); // unchanged
162
163		// overlong cdna (reversed) to peptide (reversed)
164	0	from = new int[] { 20, 1 };
165	0	to = new int[] { 9, 4 };
166	0	assertTrue(GffHelperBase.trimMapping(from, to, 3, 1));
167	0	assertEquals(Arrays.toString(from), "[20, 3]"); // end trimmed
168	0	assertEquals(Arrays.toString(to), "[9, 4]"); // unchanged
169
170		// peptide to cdna (matching)
171	0	from = new int[] { 4, 9 };
172	0	to = new int[] { 1, 18 };
173	0	assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
174	0	assertEquals(Arrays.toString(from), "[4, 9]"); // unchanged
175	0	assertEquals(Arrays.toString(to), "[1, 18]"); // unchanged
176
177		// peptide to overlong cdna
178	0	to = new int[] { 1, 20 };
179	0	assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
180	0	assertEquals(Arrays.toString(from), "[4, 9]"); // unchanged
181	0	assertEquals(Arrays.toString(to), "[1, 18]"); // end trimmed
182
183		// peptide to overlong cdna (reversed)
184	0	to = new int[] { 20, 1 };
185	0	assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
186	0	assertEquals(Arrays.toString(from), "[4, 9]"); // unchanged
187	0	assertEquals(Arrays.toString(to), "[20, 3]"); // end trimmed
188
189		// peptide (reversed) to overlong cdna (reversed)
190	0	from = new int[] { 9, 4 };
191	0	to = new int[] { 20, 1 };
192	0	assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
193	0	assertEquals(Arrays.toString(from), "[9, 4]"); // unchanged
194	0	assertEquals(Arrays.toString(to), "[20, 3]"); // end trimmed
195
196		// overlong peptide to word-length cdna
197	0	from = new int[] { 4, 10 };
198	0	to = new int[] { 1, 18 };
199	0	assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
200	0	assertEquals(Arrays.toString(from), "[4, 9]"); // end trimmed
201	0	assertEquals(Arrays.toString(to), "[1, 18]"); // unchanged
202
203		// overlong peptide to non-word-length cdna
204	0	from = new int[] { 4, 10 };
205	0	to = new int[] { 1, 19 };
206	0	assertFalse(GffHelperBase.trimMapping(from, to, 1, 3));
207	0	assertEquals(Arrays.toString(from), "[4, 10]"); // unchanged
208	0	assertEquals(Arrays.toString(to), "[1, 19]"); // unchanged
209		}
210
		0% Uncovered Elements: 35 (35) Complexity: 2 Complexity Density: 0.06 4-
211	0	@Test(groups = { "Functional" })...
212		public void testParseAttributeMap()
213		{
214	0	Map<String, String> map = GffHelperBase
215		.parseAttributeMap("A=B,C%2C%3D%3B%09%25D,X=Y");
216	0	assertEquals(map.size(), 2);
217		// value of A is everything up to and excluding ,X=
218	0	assertEquals(map.get("A"), "B,C,=;\t%D");
219	0	assertEquals(map.get("X"), "Y");
220
221		/*
222		* malformed cases should result in an empty map
223		*/
224	0	map = GffHelperBase.parseAttributeMap("=B=Y");
225	0	assertTrue(map.isEmpty());
226		// first token should be an attribute name only, no commas
227	0	map = GffHelperBase.parseAttributeMap("A,B=C");
228	0	assertTrue(map.isEmpty());
229		// intermediate tokens need at least one comma (value,name=)
230	0	map = GffHelperBase.parseAttributeMap("A=B=C");
231	0	assertTrue(map.isEmpty());
232		// last token may have a comma or not
233	0	map = GffHelperBase.parseAttributeMap("A=B");
234	0	assertEquals(map.get("A"), "B");
235	0	map = GffHelperBase.parseAttributeMap("A=B,C");
236	0	assertEquals(map.get("A"), "B,C");
237	0	map = GffHelperBase.parseAttributeMap("A");
238	0	assertTrue(map.isEmpty());
239	0	map = GffHelperBase.parseAttributeMap("A=");
240	0	assertTrue(map.isEmpty());
241	0	map = GffHelperBase.parseAttributeMap("A==C");
242	0	assertTrue(map.isEmpty());
243	0	map = GffHelperBase.parseAttributeMap("=A");
244	0	assertTrue(map.isEmpty());
245	0	map = GffHelperBase.parseAttributeMap("=");
246	0	assertTrue(map.isEmpty());
247	0	map = GffHelperBase.parseAttributeMap(",");
248	0	assertTrue(map.isEmpty());
249	0	map = GffHelperBase.parseAttributeMap(" ");
250	0	assertTrue(map.isEmpty());
251	0	map = GffHelperBase.parseAttributeMap("");
252	0	assertTrue(map.isEmpty());
253	0	map = GffHelperBase.parseAttributeMap("A=B, =C");
254	0	assertTrue(map.isEmpty());
255
256	0	try
257		{
258	0	GffHelperBase.parseAttributeMap(null);
259	0	fail("expected exception");
260		} catch (NullPointerException e)
261		{
262		// expected
263		}
264		}
265		}