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");
20 final static File ALIGN_FILE = new File("test/jalview/io/tcoffee.fasta_aln");
23 public void testReadHeader() throws IOException, FileNotFoundException {
25 TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE);
26 assertTrue(scoreFile.getWarningMessage(),scoreFile.isValid());
27 Header header = scoreFile.header;
28 assertNotNull(header);
29 assertEquals( "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)", header.head );
30 assertEquals( 90, header.score );
31 assertEquals( 89, header.getScoreFor("1PHT") );
32 assertEquals( 90, header.getScoreFor("1BB9") );
33 assertEquals( 94, header.getScoreFor("1UHC") );
34 assertEquals( 94, header.getScoreFor("1YCS") );
35 assertEquals( 93, header.getScoreFor("1OOT") );
36 assertEquals( 94, header.getScoreFor("1ABO") );
37 assertEquals( 94, header.getScoreFor("1FYN") );
38 assertEquals( 94, header.getScoreFor("1QCF") );
39 assertEquals( 90, header.getScoreFor("cons") );
44 public void testWrongFile() {
46 TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
47 assertFalse(result.isValid());
48 } catch (IOException x)
50 assertTrue("File not found exception thrown",x instanceof FileNotFoundException);
55 public void testHeightAndWidth() throws IOException {
56 TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
57 assertTrue(result.isValid());
58 assertEquals( 8, result.getHeight() );
59 assertEquals( 83, result.getWidth() );
63 public void testReadBlock( ) throws IOException {
68 "1PHT 999999999999999999999999998762112222543211112134\n" +
69 "1BB9 99999999999999999999999999987-------4322----2234 \n" +
70 "1UHC 99999999999999999999999999987-------5321----2246\n" +
71 "1YCS 99999999999999999999999999986-------4321----1-35\n" +
72 "1OOT 999999999999999999999999999861-------3------1135 \n" +
73 "1ABO 99999999999999999999999999986-------422-------34\n" +
74 "1FYN 99999999999999999999999999985-------32--------35\n" +
75 "1QCF 99999999999999999999999999974-------2---------24\n" +
76 "cons 999999999999999999999999999851000110321100001134\n" +
79 FileParse source=new FileParse(BLOCK, FormatAdapter.PASTE);
80 Block block = TCoffeeScoreFile.readBlock(source, 0);
83 assertEquals( "999999999999999999999999998762112222543211112134", block.getScoresFor("1PHT") );
84 assertEquals( "99999999999999999999999999987-------4322----2234", block.getScoresFor("1BB9") );
85 assertEquals( "99999999999999999999999999987-------5321----2246", block.getScoresFor("1UHC") );
86 assertEquals( "99999999999999999999999999986-------4321----1-35", block.getScoresFor("1YCS") );
87 assertEquals( "999999999999999999999999999861-------3------1135", block.getScoresFor("1OOT") );
88 assertEquals( "99999999999999999999999999986-------422-------34", block.getScoresFor("1ABO") );
89 assertEquals( "99999999999999999999999999985-------32--------35", block.getScoresFor("1FYN") );
90 assertEquals( "99999999999999999999999999974-------2---------24", block.getScoresFor("1QCF") );
91 assertEquals( "999999999999999999999999999851000110321100001134", block.getConsensus() );
95 public void testParse() throws IOException {
97 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
99 assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", parser.getScoresFor("1PHT") );
100 assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", parser.getScoresFor("1BB9") );
101 assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", parser.getScoresFor("1UHC") );
102 assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", parser.getScoresFor("1YCS") );
103 assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", parser.getScoresFor("1OOT") );
104 assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", parser.getScoresFor("1ABO") );
105 assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", parser.getScoresFor("1FYN") );
106 assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", parser.getScoresFor("1QCF") );
107 assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", parser.getScoresFor("cons") );
112 public void testGetAsList() throws IOException {
114 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
115 assertTrue(parser.getWarningMessage(),parser.isValid());
116 List<String> scores = parser.getScoresList();
117 assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", scores.get(0) );
118 assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", scores.get(1) );
119 assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", scores.get(2) );
120 assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", scores.get(3) );
121 assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", scores.get(4) );
122 assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", scores.get(5) );
123 assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", scores.get(6) );
124 assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", scores.get(7) );
125 assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", scores.get(8) );
131 public void testGetAsArray() throws IOException {
133 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
134 assertTrue(parser.getWarningMessage(),parser.isValid());
135 byte[][] scores = parser.getScoresArray();
137 assertEquals( 9, scores[0][0] );
138 assertEquals( 9, scores[1][0] );
139 assertEquals( 9, scores[2][0] );
140 assertEquals( 9, scores[3][0] );
141 assertEquals( 9, scores[4][0] );
142 assertEquals( 9, scores[5][0] );
143 assertEquals( 9, scores[6][0] );
144 assertEquals( 9, scores[7][0] );
145 assertEquals( 9, scores[8][0] );
147 assertEquals( 5, scores[0][36] );
148 assertEquals( 4, scores[1][36] );
149 assertEquals( 5, scores[2][36] );
150 assertEquals( 4, scores[3][36] );
151 assertEquals( -1, scores[4][36] );
152 assertEquals( 4, scores[5][36] );
153 assertEquals( 3, scores[6][36] );
154 assertEquals( 2, scores[7][36] );
155 assertEquals( 3, scores[8][36] );