2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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/>.
20 import static org.junit.Assert.*;
21 import jalview.io.TCoffeeScoreFile.Block;
22 import jalview.io.TCoffeeScoreFile.Header;
25 import java.io.FileNotFoundException;
26 import java.io.IOException;
27 import java.util.List;
29 import org.junit.Test;
31 public class TCoffeeScoreFileTest {
33 final static File SCORE_FILE = new File("test/jalview/io/tcoffee.score_ascii");
34 final static File ALIGN_FILE = new File("test/jalview/io/tcoffee.fasta_aln");
37 public void testReadHeader() throws IOException, FileNotFoundException {
39 TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE);
40 assertTrue(scoreFile.getWarningMessage(),scoreFile.isValid());
42 Header header = scoreFile.header;
43 assertNotNull(header);
44 assertEquals( "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)", header.head );
45 assertEquals( 90, header.score );
46 assertEquals( 89, header.getScoreFor("1PHT") );
47 assertEquals( 90, header.getScoreFor("1BB9") );
48 assertEquals( 94, header.getScoreFor("1UHC") );
49 assertEquals( 94, header.getScoreFor("1YCS") );
50 assertEquals( 93, header.getScoreFor("1OOT") );
51 assertEquals( 94, header.getScoreFor("1ABO") );
52 assertEquals( 94, header.getScoreFor("1FYN") );
53 assertEquals( 94, header.getScoreFor("1QCF") );
54 assertEquals( 90, header.getScoreFor("cons") );
59 public void testWrongFile() {
61 TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
62 assertFalse(result.isValid());
66 assertTrue("File not found exception thrown",x instanceof FileNotFoundException);
71 public void testHeightAndWidth() throws IOException {
72 TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
73 assertTrue(result.isValid());
74 assertEquals( 8, result.getHeight() );
75 assertEquals( 83, result.getWidth() );
79 public void testReadBlock( ) throws IOException {
84 "1PHT 999999999999999999999999998762112222543211112134\n" +
85 "1BB9 99999999999999999999999999987-------4322----2234 \n" +
86 "1UHC 99999999999999999999999999987-------5321----2246\n" +
87 "1YCS 99999999999999999999999999986-------4321----1-35\n" +
88 "1OOT 999999999999999999999999999861-------3------1135 \n" +
89 "1ABO 99999999999999999999999999986-------422-------34\n" +
90 "1FYN 99999999999999999999999999985-------32--------35\n" +
91 "1QCF 99999999999999999999999999974-------2---------24\n" +
92 "cons 999999999999999999999999999851000110321100001134\n" +
95 FileParse source=new FileParse(BLOCK, FormatAdapter.PASTE);
96 Block block = TCoffeeScoreFile.readBlock(source, 0);
99 assertEquals( "999999999999999999999999998762112222543211112134", block.getScoresFor("1PHT") );
100 assertEquals( "99999999999999999999999999987-------4322----2234", block.getScoresFor("1BB9") );
101 assertEquals( "99999999999999999999999999987-------5321----2246", block.getScoresFor("1UHC") );
102 assertEquals( "99999999999999999999999999986-------4321----1-35", block.getScoresFor("1YCS") );
103 assertEquals( "999999999999999999999999999861-------3------1135", block.getScoresFor("1OOT") );
104 assertEquals( "99999999999999999999999999986-------422-------34", block.getScoresFor("1ABO") );
105 assertEquals( "99999999999999999999999999985-------32--------35", block.getScoresFor("1FYN") );
106 assertEquals( "99999999999999999999999999974-------2---------24", block.getScoresFor("1QCF") );
107 assertEquals( "999999999999999999999999999851000110321100001134", block.getConsensus() );
111 public void testParse() throws IOException {
113 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
115 assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", parser.getScoresFor("1PHT") );
116 assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", parser.getScoresFor("1BB9") );
117 assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", parser.getScoresFor("1UHC") );
118 assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", parser.getScoresFor("1YCS") );
119 assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", parser.getScoresFor("1OOT") );
120 assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", parser.getScoresFor("1ABO") );
121 assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", parser.getScoresFor("1FYN") );
122 assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", parser.getScoresFor("1QCF") );
123 assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", parser.getScoresFor("cons") );
128 public void testGetAsList() throws IOException {
130 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
131 assertTrue(parser.getWarningMessage(),parser.isValid());
132 List<String> scores = parser.getScoresList();
133 assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", scores.get(0) );
134 assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", scores.get(1) );
135 assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", scores.get(2) );
136 assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", scores.get(3) );
137 assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", scores.get(4) );
138 assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", scores.get(5) );
139 assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", scores.get(6) );
140 assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", scores.get(7) );
141 assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", scores.get(8) );
147 public void testGetAsArray() throws IOException {
149 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
150 assertTrue(parser.getWarningMessage(),parser.isValid());
151 byte[][] scores = parser.getScoresArray();
153 assertEquals( 9, scores[0][0] );
154 assertEquals( 9, scores[1][0] );
155 assertEquals( 9, scores[2][0] );
156 assertEquals( 9, scores[3][0] );
157 assertEquals( 9, scores[4][0] );
158 assertEquals( 9, scores[5][0] );
159 assertEquals( 9, scores[6][0] );
160 assertEquals( 9, scores[7][0] );
161 assertEquals( 9, scores[8][0] );
163 assertEquals( 5, scores[0][36] );
164 assertEquals( 4, scores[1][36] );
165 assertEquals( 5, scores[2][36] );
166 assertEquals( 4, scores[3][36] );
167 assertEquals( -1, scores[4][36] );
168 assertEquals( 4, scores[5][36] );
169 assertEquals( 3, scores[6][36] );
170 assertEquals( 2, scores[7][36] );
171 assertEquals( 3, scores[8][36] );
176 public void testHeightAndWidthWithResidueNumbers() throws IOException {
177 String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
178 TCoffeeScoreFile result = new TCoffeeScoreFile(file, FormatAdapter.FILE);
179 assertTrue(result.isValid());
180 assertEquals( 5, result.getHeight() );
181 assertEquals( 84, result.getWidth() );