2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 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 static org.junit.Assert.*;
24 import jalview.io.TCoffeeScoreFile.Block;
25 import jalview.io.TCoffeeScoreFile.Header;
28 import java.io.FileNotFoundException;
29 import java.io.IOException;
30 import java.util.List;
32 import javax.xml.parsers.ParserConfigurationException;
34 import org.junit.Test;
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 {
44 final static File SCORE_FILE = new File("test/jalview/io/tcoffee.score_ascii");
45 final static File ALIGN_FILE = new File("test/jalview/io/tcoffee.fasta_aln");
48 public void testReadHeader() throws IOException {
50 TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE);
51 assertTrue(scoreFile.getWarningMessage(),scoreFile.isValid());
53 Header header = scoreFile.header;
54 assertNotNull(header);
55 assertEquals( "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)", header.head );
56 assertEquals( 90, header.score );
57 assertEquals( 89, header.getScoreFor("1PHT") );
58 assertEquals( 90, header.getScoreFor("1BB9") );
59 assertEquals( 94, header.getScoreFor("1UHC") );
60 assertEquals( 94, header.getScoreFor("1YCS") );
61 assertEquals( 93, header.getScoreFor("1OOT") );
62 assertEquals( 94, header.getScoreFor("1ABO") );
63 assertEquals( 94, header.getScoreFor("1FYN") );
64 assertEquals( 94, header.getScoreFor("1QCF") );
65 assertEquals( 90, header.getScoreFor("cons") );
70 public void testWrongFile() {
72 TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
73 assertFalse(result.isValid());
77 assertTrue("File not found exception thrown",x instanceof FileNotFoundException);
82 public void testHeightAndWidth() throws IOException {
83 TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
84 assertTrue(result.isValid());
85 assertEquals( 8, result.getHeight() );
86 assertEquals( 83, result.getWidth() );
90 public void testReadBlock( ) throws IOException {
95 "1PHT 999999999999999999999999998762112222543211112134\n" +
96 "1BB9 99999999999999999999999999987-------4322----2234 \n" +
97 "1UHC 99999999999999999999999999987-------5321----2246\n" +
98 "1YCS 99999999999999999999999999986-------4321----1-35\n" +
99 "1OOT 999999999999999999999999999861-------3------1135 \n" +
100 "1ABO 99999999999999999999999999986-------422-------34\n" +
101 "1FYN 99999999999999999999999999985-------32--------35\n" +
102 "1QCF 99999999999999999999999999974-------2---------24\n" +
103 "cons 999999999999999999999999999851000110321100001134\n" +
106 FileParse source=new FileParse(BLOCK, FormatAdapter.PASTE);
107 Block block = TCoffeeScoreFile.readBlock(source, 0);
109 assertNotNull(block);
110 assertEquals( "999999999999999999999999998762112222543211112134", block.getScoresFor("1PHT") );
111 assertEquals( "99999999999999999999999999987-------4322----2234", block.getScoresFor("1BB9") );
112 assertEquals( "99999999999999999999999999987-------5321----2246", block.getScoresFor("1UHC") );
113 assertEquals( "99999999999999999999999999986-------4321----1-35", block.getScoresFor("1YCS") );
114 assertEquals( "999999999999999999999999999861-------3------1135", block.getScoresFor("1OOT") );
115 assertEquals( "99999999999999999999999999986-------422-------34", block.getScoresFor("1ABO") );
116 assertEquals( "99999999999999999999999999985-------32--------35", block.getScoresFor("1FYN") );
117 assertEquals( "99999999999999999999999999974-------2---------24", block.getScoresFor("1QCF") );
118 assertEquals( "999999999999999999999999999851000110321100001134", block.getConsensus() );
122 public void testParse() throws IOException {
124 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
126 assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", parser.getScoresFor("1PHT") );
127 assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", parser.getScoresFor("1BB9") );
128 assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", parser.getScoresFor("1UHC") );
129 assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", parser.getScoresFor("1YCS") );
130 assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", parser.getScoresFor("1OOT") );
131 assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", parser.getScoresFor("1ABO") );
132 assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", parser.getScoresFor("1FYN") );
133 assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", parser.getScoresFor("1QCF") );
134 assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", parser.getScoresFor("cons") );
139 public void testGetAsList() throws IOException {
141 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
142 assertTrue(parser.getWarningMessage(),parser.isValid());
143 List<String> scores = parser.getScoresList();
144 assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", scores.get(0) );
145 assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", scores.get(1) );
146 assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", scores.get(2) );
147 assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", scores.get(3) );
148 assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", scores.get(4) );
149 assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", scores.get(5) );
150 assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", scores.get(6) );
151 assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", scores.get(7) );
152 assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", scores.get(8) );
158 public void testGetAsArray() throws IOException {
160 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
161 assertTrue(parser.getWarningMessage(),parser.isValid());
162 byte[][] scores = parser.getScoresArray();
164 assertEquals( 9, scores[0][0] );
165 assertEquals( 9, scores[1][0] );
166 assertEquals( 9, scores[2][0] );
167 assertEquals( 9, scores[3][0] );
168 assertEquals( 9, scores[4][0] );
169 assertEquals( 9, scores[5][0] );
170 assertEquals( 9, scores[6][0] );
171 assertEquals( 9, scores[7][0] );
172 assertEquals( 9, scores[8][0] );
174 assertEquals( 5, scores[0][36] );
175 assertEquals( 4, scores[1][36] );
176 assertEquals( 5, scores[2][36] );
177 assertEquals( 4, scores[3][36] );
178 assertEquals( -1, scores[4][36] );
179 assertEquals( 4, scores[5][36] );
180 assertEquals( 3, scores[6][36] );
181 assertEquals( 2, scores[7][36] );
182 assertEquals( 3, scores[8][36] );
187 public void testHeightAndWidthWithResidueNumbers() throws Exception {
188 String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
189 TCoffeeScoreFile result = new TCoffeeScoreFile(file, FormatAdapter.FILE);
190 assertTrue(result.isValid());
191 assertEquals( 5, result.getHeight() );
192 assertEquals( 84, result.getWidth() );