2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 import static org.junit.Assert.*;
22 import jalview.io.TCoffeeScoreFile.Block;
23 import jalview.io.TCoffeeScoreFile.Header;
26 import java.io.FileNotFoundException;
27 import java.io.IOException;
28 import java.util.List;
30 import javax.xml.parsers.ParserConfigurationException;
32 import org.junit.Test;
33 import org.xml.sax.SAXException;
35 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
36 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
37 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
38 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
40 public class TCoffeeScoreFileTest {
42 final static File SCORE_FILE = new File("test/jalview/io/tcoffee.score_ascii");
43 final static File ALIGN_FILE = new File("test/jalview/io/tcoffee.fasta_aln");
46 public void testReadHeader() throws IOException {
48 TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE);
49 assertTrue(scoreFile.getWarningMessage(),scoreFile.isValid());
51 Header header = scoreFile.header;
52 assertNotNull(header);
53 assertEquals( "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)", header.head );
54 assertEquals( 90, header.score );
55 assertEquals( 89, header.getScoreFor("1PHT") );
56 assertEquals( 90, header.getScoreFor("1BB9") );
57 assertEquals( 94, header.getScoreFor("1UHC") );
58 assertEquals( 94, header.getScoreFor("1YCS") );
59 assertEquals( 93, header.getScoreFor("1OOT") );
60 assertEquals( 94, header.getScoreFor("1ABO") );
61 assertEquals( 94, header.getScoreFor("1FYN") );
62 assertEquals( 94, header.getScoreFor("1QCF") );
63 assertEquals( 90, header.getScoreFor("cons") );
68 public void testWrongFile() {
70 TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
71 assertFalse(result.isValid());
75 assertTrue("File not found exception thrown",x instanceof FileNotFoundException);
80 public void testHeightAndWidth() throws IOException {
81 TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
82 assertTrue(result.isValid());
83 assertEquals( 8, result.getHeight() );
84 assertEquals( 83, result.getWidth() );
88 public void testReadBlock( ) throws IOException {
93 "1PHT 999999999999999999999999998762112222543211112134\n" +
94 "1BB9 99999999999999999999999999987-------4322----2234 \n" +
95 "1UHC 99999999999999999999999999987-------5321----2246\n" +
96 "1YCS 99999999999999999999999999986-------4321----1-35\n" +
97 "1OOT 999999999999999999999999999861-------3------1135 \n" +
98 "1ABO 99999999999999999999999999986-------422-------34\n" +
99 "1FYN 99999999999999999999999999985-------32--------35\n" +
100 "1QCF 99999999999999999999999999974-------2---------24\n" +
101 "cons 999999999999999999999999999851000110321100001134\n" +
104 FileParse source=new FileParse(BLOCK, FormatAdapter.PASTE);
105 Block block = TCoffeeScoreFile.readBlock(source, 0);
107 assertNotNull(block);
108 assertEquals( "999999999999999999999999998762112222543211112134", block.getScoresFor("1PHT") );
109 assertEquals( "99999999999999999999999999987-------4322----2234", block.getScoresFor("1BB9") );
110 assertEquals( "99999999999999999999999999987-------5321----2246", block.getScoresFor("1UHC") );
111 assertEquals( "99999999999999999999999999986-------4321----1-35", block.getScoresFor("1YCS") );
112 assertEquals( "999999999999999999999999999861-------3------1135", block.getScoresFor("1OOT") );
113 assertEquals( "99999999999999999999999999986-------422-------34", block.getScoresFor("1ABO") );
114 assertEquals( "99999999999999999999999999985-------32--------35", block.getScoresFor("1FYN") );
115 assertEquals( "99999999999999999999999999974-------2---------24", block.getScoresFor("1QCF") );
116 assertEquals( "999999999999999999999999999851000110321100001134", block.getConsensus() );
120 public void testParse() throws IOException {
122 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
124 assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", parser.getScoresFor("1PHT") );
125 assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", parser.getScoresFor("1BB9") );
126 assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", parser.getScoresFor("1UHC") );
127 assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", parser.getScoresFor("1YCS") );
128 assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", parser.getScoresFor("1OOT") );
129 assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", parser.getScoresFor("1ABO") );
130 assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", parser.getScoresFor("1FYN") );
131 assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", parser.getScoresFor("1QCF") );
132 assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", parser.getScoresFor("cons") );
137 public void testGetAsList() throws IOException {
139 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
140 assertTrue(parser.getWarningMessage(),parser.isValid());
141 List<String> scores = parser.getScoresList();
142 assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", scores.get(0) );
143 assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", scores.get(1) );
144 assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", scores.get(2) );
145 assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", scores.get(3) );
146 assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", scores.get(4) );
147 assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", scores.get(5) );
148 assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", scores.get(6) );
149 assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", scores.get(7) );
150 assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", scores.get(8) );
156 public void testGetAsArray() throws IOException {
158 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
159 assertTrue(parser.getWarningMessage(),parser.isValid());
160 byte[][] scores = parser.getScoresArray();
162 assertEquals( 9, scores[0][0] );
163 assertEquals( 9, scores[1][0] );
164 assertEquals( 9, scores[2][0] );
165 assertEquals( 9, scores[3][0] );
166 assertEquals( 9, scores[4][0] );
167 assertEquals( 9, scores[5][0] );
168 assertEquals( 9, scores[6][0] );
169 assertEquals( 9, scores[7][0] );
170 assertEquals( 9, scores[8][0] );
172 assertEquals( 5, scores[0][36] );
173 assertEquals( 4, scores[1][36] );
174 assertEquals( 5, scores[2][36] );
175 assertEquals( 4, scores[3][36] );
176 assertEquals( -1, scores[4][36] );
177 assertEquals( 4, scores[5][36] );
178 assertEquals( 3, scores[6][36] );
179 assertEquals( 2, scores[7][36] );
180 assertEquals( 3, scores[8][36] );
185 public void testHeightAndWidthWithResidueNumbers() throws Exception {
186 String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
187 TCoffeeScoreFile result = new TCoffeeScoreFile(file, FormatAdapter.FILE);
188 assertTrue(result.isValid());
189 assertEquals( 5, result.getHeight() );
190 assertEquals( 84, result.getWidth() );