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TCoffeeScoreFileTest | 36 | 86 | 10 |
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; | |
22 | ||
23 | import jalview.gui.JvOptionPane; | |
24 | import jalview.io.TCoffeeScoreFile.Block; | |
25 | import jalview.io.TCoffeeScoreFile.Header; | |
26 | ||
27 | import java.io.File; | |
28 | import java.io.FileNotFoundException; | |
29 | import java.io.IOException; | |
30 | import java.util.List; | |
31 | ||
32 | import org.testng.AssertJUnit; | |
33 | import org.testng.annotations.BeforeClass; | |
34 | import org.testng.annotations.Test; | |
35 | ||
36 | public class TCoffeeScoreFileTest | |
37 | { | |
38 | ||
39 | 1 | @BeforeClass(alwaysRun = true) |
40 | public void setUpJvOptionPane() | |
41 | { | |
42 | 1 | JvOptionPane.setInteractiveMode(false); |
43 | 1 | JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
44 | } | |
45 | ||
46 | final static File SCORE_FILE = new File( | |
47 | "test/jalview/io/tcoffee.score_ascii"); | |
48 | ||
49 | final static File ALIGN_FILE = new File( | |
50 | "test/jalview/io/tcoffee.fasta_aln"); | |
51 | ||
52 | 1 | @Test(groups = { "Functional" }) |
53 | public void testReadHeader() throws IOException | |
54 | { | |
55 | ||
56 | 1 | TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(), |
57 | DataSourceType.FILE); | |
58 | 1 | AssertJUnit.assertTrue(scoreFile.getWarningMessage(), |
59 | scoreFile.isValid()); | |
60 | ||
61 | 1 | Header header = scoreFile.header; |
62 | 1 | AssertJUnit.assertNotNull(header); |
63 | 1 | AssertJUnit.assertEquals( |
64 | "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)", | |
65 | header.head); | |
66 | 1 | AssertJUnit.assertEquals(90, header.score); |
67 | 1 | AssertJUnit.assertEquals(89, header.getScoreFor("1PHT")); |
68 | 1 | AssertJUnit.assertEquals(90, header.getScoreFor("1BB9")); |
69 | 1 | AssertJUnit.assertEquals(94, header.getScoreFor("1UHC")); |
70 | 1 | AssertJUnit.assertEquals(94, header.getScoreFor("1YCS")); |
71 | 1 | AssertJUnit.assertEquals(93, header.getScoreFor("1OOT")); |
72 | 1 | AssertJUnit.assertEquals(94, header.getScoreFor("1ABO")); |
73 | 1 | AssertJUnit.assertEquals(94, header.getScoreFor("1FYN")); |
74 | 1 | AssertJUnit.assertEquals(94, header.getScoreFor("1QCF")); |
75 | 1 | AssertJUnit.assertEquals(90, header.getScoreFor("cons")); |
76 | } | |
77 | ||
78 | 1 | @Test(groups = { "Functional" }) |
79 | public void testWrongFile() | |
80 | { | |
81 | 1 | try |
82 | { | |
83 | 1 | TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), |
84 | DataSourceType.FILE); | |
85 | 1 | AssertJUnit.assertFalse(result.isValid()); |
86 | } catch (IOException x) | |
87 | { | |
88 | 0 | AssertJUnit.assertTrue("File not found exception thrown", |
89 | x instanceof FileNotFoundException); | |
90 | } | |
91 | } | |
92 | ||
93 | 1 | @Test(groups = { "Functional" }) |
94 | public void testHeightAndWidth() throws IOException | |
95 | { | |
96 | 1 | TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(), |
97 | DataSourceType.FILE); | |
98 | 1 | AssertJUnit.assertTrue(result.isValid()); |
99 | 1 | AssertJUnit.assertEquals(8, result.getHeight()); |
100 | 1 | AssertJUnit.assertEquals(83, result.getWidth()); |
101 | } | |
102 | ||
103 | 1 | @Test(groups = { "Functional" }) |
104 | public void testReadBlock() throws IOException | |
105 | { | |
106 | ||
107 | 1 | String BLOCK = "\n" + "\n" + "\n" |
108 | + "1PHT 999999999999999999999999998762112222543211112134\n" | |
109 | + "1BB9 99999999999999999999999999987-------4322----2234 \n" | |
110 | + "1UHC 99999999999999999999999999987-------5321----2246\n" | |
111 | + "1YCS 99999999999999999999999999986-------4321----1-35\n" | |
112 | + "1OOT 999999999999999999999999999861-------3------1135 \n" | |
113 | + "1ABO 99999999999999999999999999986-------422-------34\n" | |
114 | + "1FYN 99999999999999999999999999985-------32--------35\n" | |
115 | + "1QCF 99999999999999999999999999974-------2---------24\n" | |
116 | + "cons 999999999999999999999999999851000110321100001134\n" | |
117 | + "\n" + "\n"; | |
118 | 1 | FileParse source = new FileParse(BLOCK, DataSourceType.PASTE); |
119 | 1 | Block block = TCoffeeScoreFile.readBlock(source, 0); |
120 | ||
121 | 1 | AssertJUnit.assertNotNull(block); |
122 | 1 | AssertJUnit.assertEquals( |
123 | "999999999999999999999999998762112222543211112134", | |
124 | block.getScoresFor("1PHT")); | |
125 | 1 | AssertJUnit.assertEquals( |
126 | "99999999999999999999999999987-------4322----2234", | |
127 | block.getScoresFor("1BB9")); | |
128 | 1 | AssertJUnit.assertEquals( |
129 | "99999999999999999999999999987-------5321----2246", | |
130 | block.getScoresFor("1UHC")); | |
131 | 1 | AssertJUnit.assertEquals( |
132 | "99999999999999999999999999986-------4321----1-35", | |
133 | block.getScoresFor("1YCS")); | |
134 | 1 | AssertJUnit.assertEquals( |
135 | "999999999999999999999999999861-------3------1135", | |
136 | block.getScoresFor("1OOT")); | |
137 | 1 | AssertJUnit.assertEquals( |
138 | "99999999999999999999999999986-------422-------34", | |
139 | block.getScoresFor("1ABO")); | |
140 | 1 | AssertJUnit.assertEquals( |
141 | "99999999999999999999999999985-------32--------35", | |
142 | block.getScoresFor("1FYN")); | |
143 | 1 | AssertJUnit.assertEquals( |
144 | "99999999999999999999999999974-------2---------24", | |
145 | block.getScoresFor("1QCF")); | |
146 | 1 | AssertJUnit.assertEquals( |
147 | "999999999999999999999999999851000110321100001134", | |
148 | block.getConsensus()); | |
149 | } | |
150 | ||
151 | 1 | @Test(groups = { "Functional" }) |
152 | public void testParse() throws IOException | |
153 | { | |
154 | ||
155 | 1 | TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(), |
156 | DataSourceType.FILE); | |
157 | ||
158 | 1 | AssertJUnit.assertEquals( |
159 | "999999999999999999999999998762112222543211112134----------5666642367889999999999889", | |
160 | parser.getScoresFor("1PHT")); | |
161 | 1 | AssertJUnit.assertEquals( |
162 | "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", | |
163 | parser.getScoresFor("1BB9")); | |
164 | 1 | AssertJUnit.assertEquals( |
165 | "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", | |
166 | parser.getScoresFor("1UHC")); | |
167 | 1 | AssertJUnit.assertEquals( |
168 | "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", | |
169 | parser.getScoresFor("1YCS")); | |
170 | 1 | AssertJUnit.assertEquals( |
171 | "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", | |
172 | parser.getScoresFor("1OOT")); | |
173 | 1 | AssertJUnit.assertEquals( |
174 | "99999999999999999999999999986-------422-------34----------687774--56779999999999889", | |
175 | parser.getScoresFor("1ABO")); | |
176 | 1 | AssertJUnit.assertEquals( |
177 | "99999999999999999999999999985-------32--------35----------6888842356789999999999889", | |
178 | parser.getScoresFor("1FYN")); | |
179 | 1 | AssertJUnit.assertEquals( |
180 | "99999999999999999999999999974-------2---------24----------6878742356789999999999889", | |
181 | parser.getScoresFor("1QCF")); | |
182 | 1 | AssertJUnit.assertEquals( |
183 | "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", | |
184 | parser.getScoresFor("cons")); | |
185 | } | |
186 | ||
187 | 1 | @Test(groups = { "Functional" }) |
188 | public void testGetAsList() throws IOException | |
189 | { | |
190 | ||
191 | 1 | TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(), |
192 | DataSourceType.FILE); | |
193 | 1 | AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid()); |
194 | 1 | List<String> scores = parser.getScoresList(); |
195 | 1 | AssertJUnit.assertEquals( |
196 | "999999999999999999999999998762112222543211112134----------5666642367889999999999889", | |
197 | scores.get(0)); | |
198 | 1 | AssertJUnit.assertEquals( |
199 | "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", | |
200 | scores.get(1)); | |
201 | 1 | AssertJUnit.assertEquals( |
202 | "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", | |
203 | scores.get(2)); | |
204 | 1 | AssertJUnit.assertEquals( |
205 | "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", | |
206 | scores.get(3)); | |
207 | 1 | AssertJUnit.assertEquals( |
208 | "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", | |
209 | scores.get(4)); | |
210 | 1 | AssertJUnit.assertEquals( |
211 | "99999999999999999999999999986-------422-------34----------687774--56779999999999889", | |
212 | scores.get(5)); | |
213 | 1 | AssertJUnit.assertEquals( |
214 | "99999999999999999999999999985-------32--------35----------6888842356789999999999889", | |
215 | scores.get(6)); | |
216 | 1 | AssertJUnit.assertEquals( |
217 | "99999999999999999999999999974-------2---------24----------6878742356789999999999889", | |
218 | scores.get(7)); | |
219 | 1 | AssertJUnit.assertEquals( |
220 | "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", | |
221 | scores.get(8)); | |
222 | ||
223 | } | |
224 | ||
225 | 1 | @Test(groups = { "Functional" }) |
226 | public void testGetAsArray() throws IOException | |
227 | { | |
228 | ||
229 | 1 | TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(), |
230 | DataSourceType.FILE); | |
231 | 1 | AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid()); |
232 | 1 | byte[][] scores = parser.getScoresArray(); |
233 | ||
234 | 1 | AssertJUnit.assertEquals(9, scores[0][0]); |
235 | 1 | AssertJUnit.assertEquals(9, scores[1][0]); |
236 | 1 | AssertJUnit.assertEquals(9, scores[2][0]); |
237 | 1 | AssertJUnit.assertEquals(9, scores[3][0]); |
238 | 1 | AssertJUnit.assertEquals(9, scores[4][0]); |
239 | 1 | AssertJUnit.assertEquals(9, scores[5][0]); |
240 | 1 | AssertJUnit.assertEquals(9, scores[6][0]); |
241 | 1 | AssertJUnit.assertEquals(9, scores[7][0]); |
242 | 1 | AssertJUnit.assertEquals(9, scores[8][0]); |
243 | ||
244 | 1 | AssertJUnit.assertEquals(5, scores[0][36]); |
245 | 1 | AssertJUnit.assertEquals(4, scores[1][36]); |
246 | 1 | AssertJUnit.assertEquals(5, scores[2][36]); |
247 | 1 | AssertJUnit.assertEquals(4, scores[3][36]); |
248 | 1 | AssertJUnit.assertEquals(-1, scores[4][36]); |
249 | 1 | AssertJUnit.assertEquals(4, scores[5][36]); |
250 | 1 | AssertJUnit.assertEquals(3, scores[6][36]); |
251 | 1 | AssertJUnit.assertEquals(2, scores[7][36]); |
252 | 1 | AssertJUnit.assertEquals(3, scores[8][36]); |
253 | ||
254 | } | |
255 | ||
256 | 1 | @Test(groups = { "Functional" }) |
257 | public void testHeightAndWidthWithResidueNumbers() throws Exception | |
258 | { | |
259 | 1 | String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers"; |
260 | 1 | TCoffeeScoreFile result = new TCoffeeScoreFile(file, |
261 | DataSourceType.FILE); | |
262 | 1 | AssertJUnit.assertTrue(result.isValid()); |
263 | 1 | AssertJUnit.assertEquals(5, result.getHeight()); |
264 | 1 | AssertJUnit.assertEquals(84, result.getWidth()); |
265 | } | |
266 | ||
267 | } |