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 org.junit.Test;
32 public class TCoffeeScoreFileTest {
34 final static File SCORE_FILE = new File("test/jalview/io/tcoffee.score_ascii");
35 final static File ALIGN_FILE = new File("test/jalview/io/tcoffee.fasta_aln");
38 public void testReadHeader() throws IOException, FileNotFoundException {
40 TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE);
41 assertTrue(scoreFile.getWarningMessage(),scoreFile.isValid());
43 Header header = scoreFile.header;
44 assertNotNull(header);
45 assertEquals( "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)", header.head );
46 assertEquals( 90, header.score );
47 assertEquals( 89, header.getScoreFor("1PHT") );
48 assertEquals( 90, header.getScoreFor("1BB9") );
49 assertEquals( 94, header.getScoreFor("1UHC") );
50 assertEquals( 94, header.getScoreFor("1YCS") );
51 assertEquals( 93, header.getScoreFor("1OOT") );
52 assertEquals( 94, header.getScoreFor("1ABO") );
53 assertEquals( 94, header.getScoreFor("1FYN") );
54 assertEquals( 94, header.getScoreFor("1QCF") );
55 assertEquals( 90, header.getScoreFor("cons") );
60 public void testWrongFile() {
62 TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
63 assertFalse(result.isValid());
67 assertTrue("File not found exception thrown",x instanceof FileNotFoundException);
72 public void testHeightAndWidth() throws IOException {
73 TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
74 assertTrue(result.isValid());
75 assertEquals( 8, result.getHeight() );
76 assertEquals( 83, result.getWidth() );
80 public void testReadBlock( ) throws IOException {
85 "1PHT 999999999999999999999999998762112222543211112134\n" +
86 "1BB9 99999999999999999999999999987-------4322----2234 \n" +
87 "1UHC 99999999999999999999999999987-------5321----2246\n" +
88 "1YCS 99999999999999999999999999986-------4321----1-35\n" +
89 "1OOT 999999999999999999999999999861-------3------1135 \n" +
90 "1ABO 99999999999999999999999999986-------422-------34\n" +
91 "1FYN 99999999999999999999999999985-------32--------35\n" +
92 "1QCF 99999999999999999999999999974-------2---------24\n" +
93 "cons 999999999999999999999999999851000110321100001134\n" +
96 FileParse source=new FileParse(BLOCK, FormatAdapter.PASTE);
97 Block block = TCoffeeScoreFile.readBlock(source, 0);
100 assertEquals( "999999999999999999999999998762112222543211112134", block.getScoresFor("1PHT") );
101 assertEquals( "99999999999999999999999999987-------4322----2234", block.getScoresFor("1BB9") );
102 assertEquals( "99999999999999999999999999987-------5321----2246", block.getScoresFor("1UHC") );
103 assertEquals( "99999999999999999999999999986-------4321----1-35", block.getScoresFor("1YCS") );
104 assertEquals( "999999999999999999999999999861-------3------1135", block.getScoresFor("1OOT") );
105 assertEquals( "99999999999999999999999999986-------422-------34", block.getScoresFor("1ABO") );
106 assertEquals( "99999999999999999999999999985-------32--------35", block.getScoresFor("1FYN") );
107 assertEquals( "99999999999999999999999999974-------2---------24", block.getScoresFor("1QCF") );
108 assertEquals( "999999999999999999999999999851000110321100001134", block.getConsensus() );
112 public void testParse() throws IOException {
114 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
116 assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", parser.getScoresFor("1PHT") );
117 assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", parser.getScoresFor("1BB9") );
118 assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", parser.getScoresFor("1UHC") );
119 assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", parser.getScoresFor("1YCS") );
120 assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", parser.getScoresFor("1OOT") );
121 assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", parser.getScoresFor("1ABO") );
122 assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", parser.getScoresFor("1FYN") );
123 assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", parser.getScoresFor("1QCF") );
124 assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", parser.getScoresFor("cons") );
129 public void testGetAsList() throws IOException {
131 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
132 assertTrue(parser.getWarningMessage(),parser.isValid());
133 List<String> scores = parser.getScoresList();
134 assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", scores.get(0) );
135 assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", scores.get(1) );
136 assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", scores.get(2) );
137 assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", scores.get(3) );
138 assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", scores.get(4) );
139 assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", scores.get(5) );
140 assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", scores.get(6) );
141 assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", scores.get(7) );
142 assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", scores.get(8) );
148 public void testGetAsArray() throws IOException {
150 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
151 assertTrue(parser.getWarningMessage(),parser.isValid());
152 byte[][] scores = parser.getScoresArray();
154 assertEquals( 9, scores[0][0] );
155 assertEquals( 9, scores[1][0] );
156 assertEquals( 9, scores[2][0] );
157 assertEquals( 9, scores[3][0] );
158 assertEquals( 9, scores[4][0] );
159 assertEquals( 9, scores[5][0] );
160 assertEquals( 9, scores[6][0] );
161 assertEquals( 9, scores[7][0] );
162 assertEquals( 9, scores[8][0] );
164 assertEquals( 5, scores[0][36] );
165 assertEquals( 4, scores[1][36] );
166 assertEquals( 5, scores[2][36] );
167 assertEquals( 4, scores[3][36] );
168 assertEquals( -1, scores[4][36] );
169 assertEquals( 4, scores[5][36] );
170 assertEquals( 3, scores[6][36] );
171 assertEquals( 2, scores[7][36] );
172 assertEquals( 3, scores[8][36] );
177 public void testHeightAndWidthWithResidueNumbers() throws IOException {
178 String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
179 TCoffeeScoreFile result = new TCoffeeScoreFile(file, FormatAdapter.FILE);
180 assertTrue(result.isValid());
181 assertEquals( 5, result.getHeight() );
182 assertEquals( 84, result.getWidth() );