test/jalview/io/TCoffeeScoreFileTest.java

   1 package jalview.io;
   2
   3 import static org.junit.Assert.*;
   4 import jalview.io.TCoffeeScoreFile.Block;
   5 import jalview.io.TCoffeeScoreFile.Header;
   6
   7 import java.io.BufferedReader;
   8 import java.io.File;
   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;
  14
  15 import org.junit.Test;
  16
  17 public class TCoffeeScoreFileTest {
  18
  19         final static File SCORE_FILE = new File("./test/jalview/io/tcoffee.score_ascii");
  20
  21         @Test
  22         public void testReadHeader() throws FileNotFoundException {
  23
  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") );
  37         }
  38
  39
  40         @Test
  41         public void testWrongFile() {
  42                 TCoffeeScoreFile result = TCoffeeScoreFile.load(new File("./test/jalview/io/tcoffee.fasta_aln"));
  43                 assertNull(result);
  44         }
  45
  46         @Test
  47         public void testReadBlock( ) throws IOException {
  48
  49                 String BLOCK = "\n" +
  50                                 "\n" +
  51                                 "\n" +
  52                                 "1PHT   999999999999999999999999998762112222543211112134\n" +
  53                                 "1BB9   99999999999999999999999999987-------4322----2234  \n" +
  54                                 "1UHC   99999999999999999999999999987-------5321----2246\n" +
  55                                 "1YCS   99999999999999999999999999986-------4321----1-35\n" +
  56                                 "1OOT   999999999999999999999999999861-------3------1135  \n" +
  57                                 "1ABO   99999999999999999999999999986-------422-------34\n" +
  58                                 "1FYN   99999999999999999999999999985-------32--------35\n" +
  59                                 "1QCF   99999999999999999999999999974-------2---------24\n" +
  60                                 "cons   999999999999999999999999999851000110321100001134\n" +
  61                                 "\n" +
  62                                 "\n";
  63
  64                 Block block = TCoffeeScoreFile.readBlock(new BufferedReader(new StringReader(BLOCK)), 0);
  65                 assertNotNull(block);
  66                 assertEquals( "999999999999999999999999998762112222543211112134", block.getScoresFor("1PHT") );
  67                 assertEquals( "99999999999999999999999999987-------4322----2234", block.getScoresFor("1BB9") );
  68                 assertEquals( "99999999999999999999999999987-------5321----2246", block.getScoresFor("1UHC") );
  69                 assertEquals( "99999999999999999999999999986-------4321----1-35", block.getScoresFor("1YCS") );
  70                 assertEquals( "999999999999999999999999999861-------3------1135", block.getScoresFor("1OOT") );
  71                 assertEquals( "99999999999999999999999999986-------422-------34", block.getScoresFor("1ABO") );
  72                 assertEquals( "99999999999999999999999999985-------32--------35", block.getScoresFor("1FYN") );
  73                 assertEquals( "99999999999999999999999999974-------2---------24", block.getScoresFor("1QCF") );
  74                 assertEquals( "999999999999999999999999999851000110321100001134", block.getConsensus() );
  75         }
  76
  77         @Test
  78         public void testParse() throws FileNotFoundException {
  79
  80                 TCoffeeScoreFile parser = TCoffeeScoreFile.load(new BufferedReader(new FileReader(SCORE_FILE)) );
  81
  82                 assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", parser.getScoresFor("1PHT") );
  83                 assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", parser.getScoresFor("1BB9") );
  84                 assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", parser.getScoresFor("1UHC") );
  85                 assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", parser.getScoresFor("1YCS") );
  86                 assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", parser.getScoresFor("1OOT") );
  87                 assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", parser.getScoresFor("1ABO") );
  88                 assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", parser.getScoresFor("1FYN") );
  89                 assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", parser.getScoresFor("1QCF") );
  90                 assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", parser.getScoresFor("cons") );
  91         }
  92
  93
  94         @Test
  95         public void testGetAsList() throws FileNotFoundException {
  96
  97                 TCoffeeScoreFile parser = TCoffeeScoreFile.load(new BufferedReader(new FileReader(SCORE_FILE)) );
  98
  99                 List<String> scores = parser.getScoresList();
 100                 assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", scores.get(0) );
 101                 assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", scores.get(1) );
 102                 assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", scores.get(2) );
 103                 assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", scores.get(3) );
 104                 assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", scores.get(4) );
 105                 assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", scores.get(5) );
 106                 assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", scores.get(6) );
 107                 assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", scores.get(7) );
 108                 assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", scores.get(8) );
 109
 110         }
 111
 112
 113         @Test
 114         public void testGetAsArray() throws FileNotFoundException {
 115
 116                 TCoffeeScoreFile parser = TCoffeeScoreFile.load(new BufferedReader(new FileReader(SCORE_FILE)) );
 117
 118                 byte[][] scores = parser.getScoresArray();
 119
 120                 assertEquals( 9, scores[0][0] );
 121                 assertEquals( 9, scores[1][0] );
 122                 assertEquals( 9, scores[2][0] );
 123                 assertEquals( 9, scores[3][0] );
 124                 assertEquals( 9, scores[4][0] );
 125                 assertEquals( 9, scores[5][0] );
 126                 assertEquals( 9, scores[6][0] );
 127                 assertEquals( 9, scores[7][0] );
 128                 assertEquals( 9, scores[8][0] );
 129
 130                 assertEquals( 5, scores[0][36] );
 131                 assertEquals( 4, scores[1][36] );
 132                 assertEquals( 5, scores[2][36] );
 133                 assertEquals( 4, scores[3][36] );
 134                 assertEquals( -1, scores[4][36] );
 135                 assertEquals( 4, scores[5][36] );
 136                 assertEquals( 3, scores[6][36] );
 137                 assertEquals( 2, scores[7][36] );
 138                 assertEquals( 3, scores[8][36] );
 139
 140         }
 141
 142
 143
 144 }