2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.io.gff;
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;
28 import jalview.gui.JvOptionPane;
30 import java.util.Arrays;
31 import java.util.List;
34 import org.testng.annotations.BeforeClass;
35 import org.testng.annotations.Test;
37 public class GffHelperBaseTest
40 @BeforeClass(alwaysRun = true)
41 public void setUpJvOptionPane()
43 JvOptionPane.setInteractiveMode(false);
44 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
48 * Test the method that parses lines like <br>
49 * ID=2345;Name=Something,Another thing;Notes=Hello;Notes=World
51 @Test(groups = { "Functional" })
52 public void testParseNameValuePairs()
54 assertTrue(GffHelperBase.parseNameValuePairs(null, ";", ' ', ",")
56 assertTrue(GffHelperBase.parseNameValuePairs("", ";", ' ', ",")
58 assertTrue(GffHelperBase.parseNameValuePairs("hello=world", ";", ' ',
61 Map<String, List<String>> map = GffHelperBase.parseNameValuePairs(
62 "hello world", ";", ' ', ", ");
63 assertEquals(map.size(), 1);
64 assertEquals(map.get("hello").size(), 1);
65 assertEquals(map.get("hello").get(0), "world");
69 "Method= manual curation ;nothing; Notes=F2 S ; Notes=Metal,Shiny%2Csmooth; Type=",
72 // Type is ignored as no value was supplied
73 assertEquals(map.size(), 2);
75 assertEquals(map.get("Method").size(), 1);
76 assertEquals(map.get("Method").get(0), "manual curation"); // trimmed
78 assertEquals(map.get("Notes").size(), 3);
79 assertEquals(map.get("Notes").get(0), "F2 S");
80 assertEquals(map.get("Notes").get(1), "Metal");
81 assertEquals(map.get("Notes").get(2), "Shiny%2Csmooth"); // not decoded here
84 * gff3 style with nested attribute values
86 String csqValue = "POLYPHEN=possibly_damaging,probably_damaging,SIFT=tolerated%2Cdeleterious";
87 map = GffHelperBase.parseNameValuePairs("hello=world;CSQ=" + csqValue,
89 assertEquals(map.size(), 2); // keys hello, CSQ
90 assertEquals(map.get("hello").size(), 1);
91 assertEquals(map.get("hello").get(0), "world");
92 // CSQ values is read 'raw' here, and parsed further elsewhere
93 assertEquals(map.get("CSQ").size(), 1);
94 assertEquals(map.get("CSQ").get(0), csqValue);
98 * Test for the method that tries to trim mappings to equivalent lengths
100 @Test(groups = "Functional")
101 public void testTrimMapping()
103 int[] from = { 1, 12 };
104 int[] to = { 20, 31 };
105 assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
106 assertEquals(Arrays.toString(from), "[1, 12]"); // unchanged
107 assertEquals(Arrays.toString(to), "[20, 31]"); // unchanged
110 from = new int[] { 1, 13 };
111 assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
112 assertEquals(Arrays.toString(from), "[1, 12]"); // trimmed
113 assertEquals(Arrays.toString(to), "[20, 31]"); // unchanged
116 to = new int[] { 20, 33 };
117 assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
118 assertEquals(Arrays.toString(from), "[1, 12]"); // unchanged
119 assertEquals(Arrays.toString(to), "[20, 31]"); // trimmed
122 from = new int[] { 12, 1 };
123 assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
124 assertEquals(Arrays.toString(from), "[12, 1]"); // unchanged
125 assertEquals(Arrays.toString(to), "[20, 31]"); // unchanged
128 to = new int[] { 31, 20 };
129 assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
130 assertEquals(Arrays.toString(from), "[12, 1]"); // unchanged
131 assertEquals(Arrays.toString(to), "[31, 20]"); // unchanged
133 // from reversed and too long:
134 from = new int[] { 14, 1 };
135 assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
136 assertEquals(Arrays.toString(from), "[14, 3]"); // end trimmed
137 assertEquals(Arrays.toString(to), "[31, 20]"); // unchanged
139 // to reversed and too long:
140 to = new int[] { 31, 10 };
141 assertTrue(GffHelperBase.trimMapping(from, to, 1, 1));
142 assertEquals(Arrays.toString(from), "[14, 3]"); // unchanged
143 assertEquals(Arrays.toString(to), "[31, 20]"); // end trimmed
145 // cdna to peptide (matching)
146 from = new int[] { 1, 18 };
147 to = new int[] { 4, 9 };
148 assertTrue(GffHelperBase.trimMapping(from, to, 3, 1));
149 assertEquals(Arrays.toString(from), "[1, 18]"); // unchanged
150 assertEquals(Arrays.toString(to), "[4, 9]"); // unchanged
152 // overlong cdna to peptide
153 from = new int[] { 1, 20 };
154 assertTrue(GffHelperBase.trimMapping(from, to, 3, 1));
155 assertEquals(Arrays.toString(from), "[1, 18]"); // end trimmed
156 assertEquals(Arrays.toString(to), "[4, 9]"); // unchanged
158 // overlong cdna (reversed) to peptide
159 from = new int[] { 20, 1 };
160 assertTrue(GffHelperBase.trimMapping(from, to, 3, 1));
161 assertEquals(Arrays.toString(from), "[20, 3]"); // end trimmed
162 assertEquals(Arrays.toString(to), "[4, 9]"); // unchanged
164 // overlong cdna (reversed) to peptide (reversed)
165 from = new int[] { 20, 1 };
166 to = new int[] { 9, 4 };
167 assertTrue(GffHelperBase.trimMapping(from, to, 3, 1));
168 assertEquals(Arrays.toString(from), "[20, 3]"); // end trimmed
169 assertEquals(Arrays.toString(to), "[9, 4]"); // unchanged
171 // peptide to cdna (matching)
172 from = new int[] { 4, 9 };
173 to = new int[] { 1, 18 };
174 assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
175 assertEquals(Arrays.toString(from), "[4, 9]"); // unchanged
176 assertEquals(Arrays.toString(to), "[1, 18]"); // unchanged
178 // peptide to overlong cdna
179 to = new int[] { 1, 20 };
180 assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
181 assertEquals(Arrays.toString(from), "[4, 9]"); // unchanged
182 assertEquals(Arrays.toString(to), "[1, 18]"); // end trimmed
184 // peptide to overlong cdna (reversed)
185 to = new int[] { 20, 1 };
186 assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
187 assertEquals(Arrays.toString(from), "[4, 9]"); // unchanged
188 assertEquals(Arrays.toString(to), "[20, 3]"); // end trimmed
190 // peptide (reversed) to overlong cdna (reversed)
191 from = new int[] { 9, 4 };
192 to = new int[] { 20, 1 };
193 assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
194 assertEquals(Arrays.toString(from), "[9, 4]"); // unchanged
195 assertEquals(Arrays.toString(to), "[20, 3]"); // end trimmed
197 // overlong peptide to word-length cdna
198 from = new int[] { 4, 10 };
199 to = new int[] { 1, 18 };
200 assertTrue(GffHelperBase.trimMapping(from, to, 1, 3));
201 assertEquals(Arrays.toString(from), "[4, 9]"); // end trimmed
202 assertEquals(Arrays.toString(to), "[1, 18]"); // unchanged
204 // overlong peptide to non-word-length cdna
205 from = new int[] { 4, 10 };
206 to = new int[] { 1, 19 };
207 assertFalse(GffHelperBase.trimMapping(from, to, 1, 3));
208 assertEquals(Arrays.toString(from), "[4, 10]"); // unchanged
209 assertEquals(Arrays.toString(to), "[1, 19]"); // unchanged
212 @Test(groups = { "Functional" })
213 public void testParseAttributeMap()
215 Map<String, String> map = GffHelperBase
216 .parseAttributeMap("A=B,C%2C%3D%3B%09%25D,X=Y");
217 assertEquals(map.size(), 2);
218 // value of A is everything up to and excluding ,X=
219 assertEquals(map.get("A"), "B,C,=;\t%D");
220 assertEquals(map.get("X"), "Y");
223 * malformed cases should result in an empty map
225 map = GffHelperBase.parseAttributeMap("=B=Y");
226 assertTrue(map.isEmpty());
227 // first token should be an attribute name only, no commas
228 map = GffHelperBase.parseAttributeMap("A,B=C");
229 assertTrue(map.isEmpty());
230 // intermediate tokens need at least one comma (value,name=)
231 map = GffHelperBase.parseAttributeMap("A=B=C");
232 assertTrue(map.isEmpty());
233 // last token may have a comma or not
234 map = GffHelperBase.parseAttributeMap("A=B");
235 assertEquals(map.get("A"), "B");
236 map = GffHelperBase.parseAttributeMap("A=B,C");
237 assertEquals(map.get("A"), "B,C");
238 map = GffHelperBase.parseAttributeMap("A");
239 assertTrue(map.isEmpty());
240 map = GffHelperBase.parseAttributeMap("A=");
241 assertTrue(map.isEmpty());
242 map = GffHelperBase.parseAttributeMap("A==C");
243 assertTrue(map.isEmpty());
244 map = GffHelperBase.parseAttributeMap("=A");
245 assertTrue(map.isEmpty());
246 map = GffHelperBase.parseAttributeMap("=");
247 assertTrue(map.isEmpty());
248 map = GffHelperBase.parseAttributeMap(",");
249 assertTrue(map.isEmpty());
250 map = GffHelperBase.parseAttributeMap(" ");
251 assertTrue(map.isEmpty());
252 map = GffHelperBase.parseAttributeMap("");
253 assertTrue(map.isEmpty());
254 map = GffHelperBase.parseAttributeMap("A=B, =C");
255 assertTrue(map.isEmpty());
259 GffHelperBase.parseAttributeMap(null);
260 fail("expected exception");
261 } catch (NullPointerException e)