3 import static org.junit.Assert.*;
4 import jalview.io.TCoffeeScoreFile.Block;
5 import jalview.io.TCoffeeScoreFile.Header;
7 import java.io.BufferedReader;
9 import java.io.FileNotFoundException;
10 import java.io.FileReader;
11 import java.io.IOException;
12 import java.io.StringReader;
13 import java.util.List;
15 import org.junit.Test;
17 public class TCoffeeScoreFileTest {
19 final static File SCORE_FILE = new File("./test/jalview/io/tcoffee.score_ascii");
22 public void testReadHeader() throws FileNotFoundException {
24 Header header = TCoffeeScoreFile.readHeader( new BufferedReader(new FileReader(SCORE_FILE)) );
25 assertNotNull(header);
26 assertEquals( "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)", header.head );
27 assertEquals( 90, header.score );
28 assertEquals( 89, header.getScoreFor("1PHT") );
29 assertEquals( 90, header.getScoreFor("1BB9") );
30 assertEquals( 94, header.getScoreFor("1UHC") );
31 assertEquals( 94, header.getScoreFor("1YCS") );
32 assertEquals( 93, header.getScoreFor("1OOT") );
33 assertEquals( 94, header.getScoreFor("1ABO") );
34 assertEquals( 94, header.getScoreFor("1FYN") );
35 assertEquals( 94, header.getScoreFor("1QCF") );
36 assertEquals( 90, header.getScoreFor("cons") );
41 public void testWrongFile() {
42 TCoffeeScoreFile result = TCoffeeScoreFile.load(new File("./test/jalview/io/tcoffee.fasta_aln"));
47 public void testHeightAndWidth() {
48 TCoffeeScoreFile result = TCoffeeScoreFile.load(new File("./test/jalview/io/tcoffee.score_ascii"));
49 assertNotNull(result);
50 assertEquals( 8, result.getHeight() );
51 assertEquals( 83, result.getWidth() );
55 public void testReadBlock( ) throws IOException {
60 "1PHT 999999999999999999999999998762112222543211112134\n" +
61 "1BB9 99999999999999999999999999987-------4322----2234 \n" +
62 "1UHC 99999999999999999999999999987-------5321----2246\n" +
63 "1YCS 99999999999999999999999999986-------4321----1-35\n" +
64 "1OOT 999999999999999999999999999861-------3------1135 \n" +
65 "1ABO 99999999999999999999999999986-------422-------34\n" +
66 "1FYN 99999999999999999999999999985-------32--------35\n" +
67 "1QCF 99999999999999999999999999974-------2---------24\n" +
68 "cons 999999999999999999999999999851000110321100001134\n" +
72 Block block = TCoffeeScoreFile.readBlock(new BufferedReader(new StringReader(BLOCK)), 0);
74 assertEquals( "999999999999999999999999998762112222543211112134", block.getScoresFor("1PHT") );
75 assertEquals( "99999999999999999999999999987-------4322----2234", block.getScoresFor("1BB9") );
76 assertEquals( "99999999999999999999999999987-------5321----2246", block.getScoresFor("1UHC") );
77 assertEquals( "99999999999999999999999999986-------4321----1-35", block.getScoresFor("1YCS") );
78 assertEquals( "999999999999999999999999999861-------3------1135", block.getScoresFor("1OOT") );
79 assertEquals( "99999999999999999999999999986-------422-------34", block.getScoresFor("1ABO") );
80 assertEquals( "99999999999999999999999999985-------32--------35", block.getScoresFor("1FYN") );
81 assertEquals( "99999999999999999999999999974-------2---------24", block.getScoresFor("1QCF") );
82 assertEquals( "999999999999999999999999999851000110321100001134", block.getConsensus() );
86 public void testParse() throws FileNotFoundException {
88 TCoffeeScoreFile parser = TCoffeeScoreFile.load(new BufferedReader(new FileReader(SCORE_FILE)) );
90 assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", parser.getScoresFor("1PHT") );
91 assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", parser.getScoresFor("1BB9") );
92 assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", parser.getScoresFor("1UHC") );
93 assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", parser.getScoresFor("1YCS") );
94 assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", parser.getScoresFor("1OOT") );
95 assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", parser.getScoresFor("1ABO") );
96 assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", parser.getScoresFor("1FYN") );
97 assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", parser.getScoresFor("1QCF") );
98 assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", parser.getScoresFor("cons") );
103 public void testGetAsList() throws FileNotFoundException {
105 TCoffeeScoreFile parser = TCoffeeScoreFile.load(new BufferedReader(new FileReader(SCORE_FILE)) );
107 List<String> scores = parser.getScoresList();
108 assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", scores.get(0) );
109 assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", scores.get(1) );
110 assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", scores.get(2) );
111 assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", scores.get(3) );
112 assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", scores.get(4) );
113 assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", scores.get(5) );
114 assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", scores.get(6) );
115 assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", scores.get(7) );
116 assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", scores.get(8) );
122 public void testGetAsArray() throws FileNotFoundException {
124 TCoffeeScoreFile parser = TCoffeeScoreFile.load(new BufferedReader(new FileReader(SCORE_FILE)) );
126 byte[][] scores = parser.getScoresArray();
128 assertEquals( 9, scores[0][0] );
129 assertEquals( 9, scores[1][0] );
130 assertEquals( 9, scores[2][0] );
131 assertEquals( 9, scores[3][0] );
132 assertEquals( 9, scores[4][0] );
133 assertEquals( 9, scores[5][0] );
134 assertEquals( 9, scores[6][0] );
135 assertEquals( 9, scores[7][0] );
136 assertEquals( 9, scores[8][0] );
138 assertEquals( 5, scores[0][36] );
139 assertEquals( 4, scores[1][36] );
140 assertEquals( 5, scores[2][36] );
141 assertEquals( 4, scores[3][36] );
142 assertEquals( -1, scores[4][36] );
143 assertEquals( 4, scores[5][36] );
144 assertEquals( 3, scores[6][36] );
145 assertEquals( 2, scores[7][36] );
146 assertEquals( 3, scores[8][36] );