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.
23 import org.testng.annotations.Test;
24 import org.testng.AssertJUnit;
25 import jalview.io.TCoffeeScoreFile.Block;
26 import jalview.io.TCoffeeScoreFile.Header;
29 import java.io.FileNotFoundException;
30 import java.io.IOException;
31 import java.util.List;
33 import javax.xml.parsers.ParserConfigurationException;
35 import org.xml.sax.SAXException;
37 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
38 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
39 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
40 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
42 public class TCoffeeScoreFileTest
45 final static File SCORE_FILE = new File(
46 "test/jalview/io/tcoffee.score_ascii");
48 final static File ALIGN_FILE = new File(
49 "test/jalview/io/tcoffee.fasta_aln");
52 public void testReadHeader() throws IOException
55 TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),
56 AppletFormatAdapter.FILE);
57 AssertJUnit.assertTrue(scoreFile.getWarningMessage(), scoreFile.isValid());
59 Header header = scoreFile.header;
60 AssertJUnit.assertNotNull(header);
61 AssertJUnit.assertEquals(
62 "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)",
64 AssertJUnit.assertEquals(90, header.score);
65 AssertJUnit.assertEquals(89, header.getScoreFor("1PHT"));
66 AssertJUnit.assertEquals(90, header.getScoreFor("1BB9"));
67 AssertJUnit.assertEquals(94, header.getScoreFor("1UHC"));
68 AssertJUnit.assertEquals(94, header.getScoreFor("1YCS"));
69 AssertJUnit.assertEquals(93, header.getScoreFor("1OOT"));
70 AssertJUnit.assertEquals(94, header.getScoreFor("1ABO"));
71 AssertJUnit.assertEquals(94, header.getScoreFor("1FYN"));
72 AssertJUnit.assertEquals(94, header.getScoreFor("1QCF"));
73 AssertJUnit.assertEquals(90, header.getScoreFor("cons"));
77 public void testWrongFile()
81 TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(),
83 AssertJUnit.assertFalse(result.isValid());
84 } catch (IOException x)
86 AssertJUnit.assertTrue("File not found exception thrown",
87 x instanceof FileNotFoundException);
92 public void testHeightAndWidth() throws IOException
94 TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(),
96 AssertJUnit.assertTrue(result.isValid());
97 AssertJUnit.assertEquals(8, result.getHeight());
98 AssertJUnit.assertEquals(83, result.getWidth());
102 public void testReadBlock() throws IOException
105 String BLOCK = "\n" + "\n" + "\n"
106 + "1PHT 999999999999999999999999998762112222543211112134\n"
107 + "1BB9 99999999999999999999999999987-------4322----2234 \n"
108 + "1UHC 99999999999999999999999999987-------5321----2246\n"
109 + "1YCS 99999999999999999999999999986-------4321----1-35\n"
110 + "1OOT 999999999999999999999999999861-------3------1135 \n"
111 + "1ABO 99999999999999999999999999986-------422-------34\n"
112 + "1FYN 99999999999999999999999999985-------32--------35\n"
113 + "1QCF 99999999999999999999999999974-------2---------24\n"
114 + "cons 999999999999999999999999999851000110321100001134\n"
116 FileParse source = new FileParse(BLOCK, FormatAdapter.PASTE);
117 Block block = TCoffeeScoreFile.readBlock(source, 0);
119 AssertJUnit.assertNotNull(block);
120 AssertJUnit.assertEquals("999999999999999999999999998762112222543211112134",
121 block.getScoresFor("1PHT"));
122 AssertJUnit.assertEquals("99999999999999999999999999987-------4322----2234",
123 block.getScoresFor("1BB9"));
124 AssertJUnit.assertEquals("99999999999999999999999999987-------5321----2246",
125 block.getScoresFor("1UHC"));
126 AssertJUnit.assertEquals("99999999999999999999999999986-------4321----1-35",
127 block.getScoresFor("1YCS"));
128 AssertJUnit.assertEquals("999999999999999999999999999861-------3------1135",
129 block.getScoresFor("1OOT"));
130 AssertJUnit.assertEquals("99999999999999999999999999986-------422-------34",
131 block.getScoresFor("1ABO"));
132 AssertJUnit.assertEquals("99999999999999999999999999985-------32--------35",
133 block.getScoresFor("1FYN"));
134 AssertJUnit.assertEquals("99999999999999999999999999974-------2---------24",
135 block.getScoresFor("1QCF"));
136 AssertJUnit.assertEquals("999999999999999999999999999851000110321100001134",
137 block.getConsensus());
141 public void testParse() throws IOException
144 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
147 AssertJUnit.assertEquals(
148 "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
149 parser.getScoresFor("1PHT"));
150 AssertJUnit.assertEquals(
151 "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
152 parser.getScoresFor("1BB9"));
153 AssertJUnit.assertEquals(
154 "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
155 parser.getScoresFor("1UHC"));
156 AssertJUnit.assertEquals(
157 "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
158 parser.getScoresFor("1YCS"));
159 AssertJUnit.assertEquals(
160 "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
161 parser.getScoresFor("1OOT"));
162 AssertJUnit.assertEquals(
163 "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
164 parser.getScoresFor("1ABO"));
165 AssertJUnit.assertEquals(
166 "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
167 parser.getScoresFor("1FYN"));
168 AssertJUnit.assertEquals(
169 "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
170 parser.getScoresFor("1QCF"));
171 AssertJUnit.assertEquals(
172 "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
173 parser.getScoresFor("cons"));
177 public void testGetAsList() throws IOException
180 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
182 AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
183 List<String> scores = parser.getScoresList();
184 AssertJUnit.assertEquals(
185 "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
187 AssertJUnit.assertEquals(
188 "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
190 AssertJUnit.assertEquals(
191 "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
193 AssertJUnit.assertEquals(
194 "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
196 AssertJUnit.assertEquals(
197 "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
199 AssertJUnit.assertEquals(
200 "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
202 AssertJUnit.assertEquals(
203 "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
205 AssertJUnit.assertEquals(
206 "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
208 AssertJUnit.assertEquals(
209 "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
215 public void testGetAsArray() throws IOException
218 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
220 AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
221 byte[][] scores = parser.getScoresArray();
223 AssertJUnit.assertEquals(9, scores[0][0]);
224 AssertJUnit.assertEquals(9, scores[1][0]);
225 AssertJUnit.assertEquals(9, scores[2][0]);
226 AssertJUnit.assertEquals(9, scores[3][0]);
227 AssertJUnit.assertEquals(9, scores[4][0]);
228 AssertJUnit.assertEquals(9, scores[5][0]);
229 AssertJUnit.assertEquals(9, scores[6][0]);
230 AssertJUnit.assertEquals(9, scores[7][0]);
231 AssertJUnit.assertEquals(9, scores[8][0]);
233 AssertJUnit.assertEquals(5, scores[0][36]);
234 AssertJUnit.assertEquals(4, scores[1][36]);
235 AssertJUnit.assertEquals(5, scores[2][36]);
236 AssertJUnit.assertEquals(4, scores[3][36]);
237 AssertJUnit.assertEquals(-1, scores[4][36]);
238 AssertJUnit.assertEquals(4, scores[5][36]);
239 AssertJUnit.assertEquals(3, scores[6][36]);
240 AssertJUnit.assertEquals(2, scores[7][36]);
241 AssertJUnit.assertEquals(3, scores[8][36]);
246 public void testHeightAndWidthWithResidueNumbers() throws Exception
248 String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
249 TCoffeeScoreFile result = new TCoffeeScoreFile(file, FormatAdapter.FILE);
250 AssertJUnit.assertTrue(result.isValid());
251 AssertJUnit.assertEquals(5, result.getHeight());
252 AssertJUnit.assertEquals(84, result.getWidth());