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GffHelperBaseTest | 37 | 134 | 5 |
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 | ||
37 | public class GffHelperBaseTest | |
38 | { | |
39 | ||
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 | */ | |
51 | 1 | @Test(groups = { "Functional" }) |
52 | public void testParseNameValuePairs() | |
53 | { | |
54 | 1 | assertTrue(GffHelperBase.parseNameValuePairs(null, ";", ' ', ",") |
55 | .isEmpty()); | |
56 | 1 | assertTrue( |
57 | GffHelperBase.parseNameValuePairs("", ";", ' ', ",").isEmpty()); | |
58 | 1 | assertTrue(GffHelperBase |
59 | .parseNameValuePairs("hello=world", ";", ' ', ",").isEmpty()); | |
60 | ||
61 | 1 | Map<String, List<String>> map = GffHelperBase |
62 | .parseNameValuePairs("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.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 | 1 | assertEquals(map.size(), 2); |
73 | ||
74 | 1 | assertEquals(map.get("Method").size(), 1); |
75 | 1 | assertEquals(map.get("Method").get(0), "manual curation"); // trimmed |
76 | ||
77 | 1 | assertEquals(map.get("Notes").size(), 3); |
78 | 1 | assertEquals(map.get("Notes").get(0), "F2 S"); |
79 | 1 | assertEquals(map.get("Notes").get(1), "Metal"); |
80 | 1 | assertEquals(map.get("Notes").get(2), "Shiny%2Csmooth"); // not decoded here |
81 | ||
82 | /* | |
83 | * gff3 style with nested attribute values | |
84 | */ | |
85 | 1 | String csqValue = "POLYPHEN=possibly_damaging,probably_damaging,SIFT=tolerated%2Cdeleterious"; |
86 | 1 | map = GffHelperBase.parseNameValuePairs("hello=world;CSQ=" + csqValue, |
87 | ";", '=', ","); | |
88 | 1 | assertEquals(map.size(), 2); // keys hello, CSQ |
89 | 1 | assertEquals(map.get("hello").size(), 1); |
90 | 1 | assertEquals(map.get("hello").get(0), "world"); |
91 | // CSQ values is read 'raw' here, and parsed further elsewhere | |
92 | 1 | assertEquals(map.get("CSQ").size(), 1); |
93 | 1 | assertEquals(map.get("CSQ").get(0), csqValue); |
94 | } | |
95 | ||
96 | /** | |
97 | * Test for the method that tries to trim mappings to equivalent lengths | |
98 | */ | |
99 | 1 | @Test(groups = "Functional") |
100 | public void testTrimMapping() | |
101 | { | |
102 | 1 | int[] from = { 1, 12 }; |
103 | 1 | int[] to = { 20, 31 }; |
104 | 1 | assertTrue(GffHelperBase.trimMapping(from, to, 1, 1)); |
105 | 1 | assertEquals(Arrays.toString(from), "[1, 12]"); // unchanged |
106 | 1 | assertEquals(Arrays.toString(to), "[20, 31]"); // unchanged |
107 | ||
108 | // from too long: | |
109 | 1 | from = new int[] { 1, 13 }; |
110 | 1 | assertTrue(GffHelperBase.trimMapping(from, to, 1, 1)); |
111 | 1 | assertEquals(Arrays.toString(from), "[1, 12]"); // trimmed |
112 | 1 | assertEquals(Arrays.toString(to), "[20, 31]"); // unchanged |
113 | ||
114 | // to too long: | |
115 | 1 | to = new int[] { 20, 33 }; |
116 | 1 | assertTrue(GffHelperBase.trimMapping(from, to, 1, 1)); |
117 | 1 | assertEquals(Arrays.toString(from), "[1, 12]"); // unchanged |
118 | 1 | assertEquals(Arrays.toString(to), "[20, 31]"); // trimmed |
119 | ||
120 | // from reversed: | |
121 | 1 | from = new int[] { 12, 1 }; |
122 | 1 | assertTrue(GffHelperBase.trimMapping(from, to, 1, 1)); |
123 | 1 | assertEquals(Arrays.toString(from), "[12, 1]"); // unchanged |
124 | 1 | assertEquals(Arrays.toString(to), "[20, 31]"); // unchanged |
125 | ||
126 | // to reversed: | |
127 | 1 | to = new int[] { 31, 20 }; |
128 | 1 | assertTrue(GffHelperBase.trimMapping(from, to, 1, 1)); |
129 | 1 | assertEquals(Arrays.toString(from), "[12, 1]"); // unchanged |
130 | 1 | assertEquals(Arrays.toString(to), "[31, 20]"); // unchanged |
131 | ||
132 | // from reversed and too long: | |
133 | 1 | from = new int[] { 14, 1 }; |
134 | 1 | assertTrue(GffHelperBase.trimMapping(from, to, 1, 1)); |
135 | 1 | assertEquals(Arrays.toString(from), "[14, 3]"); // end trimmed |
136 | 1 | assertEquals(Arrays.toString(to), "[31, 20]"); // unchanged |
137 | ||
138 | // to reversed and too long: | |
139 | 1 | to = new int[] { 31, 10 }; |
140 | 1 | assertTrue(GffHelperBase.trimMapping(from, to, 1, 1)); |
141 | 1 | assertEquals(Arrays.toString(from), "[14, 3]"); // unchanged |
142 | 1 | assertEquals(Arrays.toString(to), "[31, 20]"); // end trimmed |
143 | ||
144 | // cdna to peptide (matching) | |
145 | 1 | from = new int[] { 1, 18 }; |
146 | 1 | to = new int[] { 4, 9 }; |
147 | 1 | assertTrue(GffHelperBase.trimMapping(from, to, 3, 1)); |
148 | 1 | assertEquals(Arrays.toString(from), "[1, 18]"); // unchanged |
149 | 1 | assertEquals(Arrays.toString(to), "[4, 9]"); // unchanged |
150 | ||
151 | // overlong cdna to peptide | |
152 | 1 | from = new int[] { 1, 20 }; |
153 | 1 | assertTrue(GffHelperBase.trimMapping(from, to, 3, 1)); |
154 | 1 | assertEquals(Arrays.toString(from), "[1, 18]"); // end trimmed |
155 | 1 | assertEquals(Arrays.toString(to), "[4, 9]"); // unchanged |
156 | ||
157 | // overlong cdna (reversed) to peptide | |
158 | 1 | from = new int[] { 20, 1 }; |
159 | 1 | assertTrue(GffHelperBase.trimMapping(from, to, 3, 1)); |
160 | 1 | assertEquals(Arrays.toString(from), "[20, 3]"); // end trimmed |
161 | 1 | assertEquals(Arrays.toString(to), "[4, 9]"); // unchanged |
162 | ||
163 | // overlong cdna (reversed) to peptide (reversed) | |
164 | 1 | from = new int[] { 20, 1 }; |
165 | 1 | to = new int[] { 9, 4 }; |
166 | 1 | assertTrue(GffHelperBase.trimMapping(from, to, 3, 1)); |
167 | 1 | assertEquals(Arrays.toString(from), "[20, 3]"); // end trimmed |
168 | 1 | assertEquals(Arrays.toString(to), "[9, 4]"); // unchanged |
169 | ||
170 | // peptide to cdna (matching) | |
171 | 1 | from = new int[] { 4, 9 }; |
172 | 1 | to = new int[] { 1, 18 }; |
173 | 1 | assertTrue(GffHelperBase.trimMapping(from, to, 1, 3)); |
174 | 1 | assertEquals(Arrays.toString(from), "[4, 9]"); // unchanged |
175 | 1 | assertEquals(Arrays.toString(to), "[1, 18]"); // unchanged |
176 | ||
177 | // peptide to overlong cdna | |
178 | 1 | to = new int[] { 1, 20 }; |
179 | 1 | assertTrue(GffHelperBase.trimMapping(from, to, 1, 3)); |
180 | 1 | assertEquals(Arrays.toString(from), "[4, 9]"); // unchanged |
181 | 1 | assertEquals(Arrays.toString(to), "[1, 18]"); // end trimmed |
182 | ||
183 | // peptide to overlong cdna (reversed) | |
184 | 1 | to = new int[] { 20, 1 }; |
185 | 1 | assertTrue(GffHelperBase.trimMapping(from, to, 1, 3)); |
186 | 1 | assertEquals(Arrays.toString(from), "[4, 9]"); // unchanged |
187 | 1 | assertEquals(Arrays.toString(to), "[20, 3]"); // end trimmed |
188 | ||
189 | // peptide (reversed) to overlong cdna (reversed) | |
190 | 1 | from = new int[] { 9, 4 }; |
191 | 1 | to = new int[] { 20, 1 }; |
192 | 1 | assertTrue(GffHelperBase.trimMapping(from, to, 1, 3)); |
193 | 1 | assertEquals(Arrays.toString(from), "[9, 4]"); // unchanged |
194 | 1 | assertEquals(Arrays.toString(to), "[20, 3]"); // end trimmed |
195 | ||
196 | // overlong peptide to word-length cdna | |
197 | 1 | from = new int[] { 4, 10 }; |
198 | 1 | to = new int[] { 1, 18 }; |
199 | 1 | assertTrue(GffHelperBase.trimMapping(from, to, 1, 3)); |
200 | 1 | assertEquals(Arrays.toString(from), "[4, 9]"); // end trimmed |
201 | 1 | assertEquals(Arrays.toString(to), "[1, 18]"); // unchanged |
202 | ||
203 | // overlong peptide to non-word-length cdna | |
204 | 1 | from = new int[] { 4, 10 }; |
205 | 1 | to = new int[] { 1, 19 }; |
206 | 1 | assertFalse(GffHelperBase.trimMapping(from, to, 1, 3)); |
207 | 1 | assertEquals(Arrays.toString(from), "[4, 10]"); // unchanged |
208 | 1 | assertEquals(Arrays.toString(to), "[1, 19]"); // unchanged |
209 | } | |
210 | ||
211 | 1 | @Test(groups = { "Functional" }) |
212 | public void testParseAttributeMap() | |
213 | { | |
214 | 1 | Map<String, String> map = GffHelperBase |
215 | .parseAttributeMap("A=B,C%2C%3D%3B%09%25D,X=Y"); | |
216 | 1 | assertEquals(map.size(), 2); |
217 | // value of A is everything up to and excluding ,X= | |
218 | 1 | assertEquals(map.get("A"), "B,C,=;\t%D"); |
219 | 1 | assertEquals(map.get("X"), "Y"); |
220 | ||
221 | /* | |
222 | * malformed cases should result in an empty map | |
223 | */ | |
224 | 1 | map = GffHelperBase.parseAttributeMap("=B=Y"); |
225 | 1 | assertTrue(map.isEmpty()); |
226 | // first token should be an attribute name only, no commas | |
227 | 1 | map = GffHelperBase.parseAttributeMap("A,B=C"); |
228 | 1 | assertTrue(map.isEmpty()); |
229 | // intermediate tokens need at least one comma (value,name=) | |
230 | 1 | map = GffHelperBase.parseAttributeMap("A=B=C"); |
231 | 1 | assertTrue(map.isEmpty()); |
232 | // last token may have a comma or not | |
233 | 1 | map = GffHelperBase.parseAttributeMap("A=B"); |
234 | 1 | assertEquals(map.get("A"), "B"); |
235 | 1 | map = GffHelperBase.parseAttributeMap("A=B,C"); |
236 | 1 | assertEquals(map.get("A"), "B,C"); |
237 | 1 | map = GffHelperBase.parseAttributeMap("A"); |
238 | 1 | assertTrue(map.isEmpty()); |
239 | 1 | map = GffHelperBase.parseAttributeMap("A="); |
240 | 1 | assertTrue(map.isEmpty()); |
241 | 1 | map = GffHelperBase.parseAttributeMap("A==C"); |
242 | 1 | assertTrue(map.isEmpty()); |
243 | 1 | map = GffHelperBase.parseAttributeMap("=A"); |
244 | 1 | assertTrue(map.isEmpty()); |
245 | 1 | map = GffHelperBase.parseAttributeMap("="); |
246 | 1 | assertTrue(map.isEmpty()); |
247 | 1 | map = GffHelperBase.parseAttributeMap(","); |
248 | 1 | assertTrue(map.isEmpty()); |
249 | 1 | map = GffHelperBase.parseAttributeMap(" "); |
250 | 1 | assertTrue(map.isEmpty()); |
251 | 1 | map = GffHelperBase.parseAttributeMap(""); |
252 | 1 | assertTrue(map.isEmpty()); |
253 | 1 | map = GffHelperBase.parseAttributeMap("A=B, =C"); |
254 | 1 | assertTrue(map.isEmpty()); |
255 | ||
256 | 1 | try |
257 | { | |
258 | 1 | GffHelperBase.parseAttributeMap(null); |
259 | 0 | fail("expected exception"); |
260 | } catch (NullPointerException e) | |
261 | { | |
262 | // expected | |
263 | } | |
264 | } | |
265 | } |