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         final static File ALIGN_FILE = new File("test/jalview/io/tcoffee.fasta_aln");
  21
  22         @Test
  23         public void testReadHeader() throws IOException, FileNotFoundException {
  24
  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") );
  40         }
  41
  42
  43         @Test
  44         public void testWrongFile() {
  45             try {
  46                 TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
  47                 assertFalse(result.isValid());
  48             } catch (IOException x)
  49             {
  50               assertTrue("File not found exception thrown",x instanceof FileNotFoundException);
  51             }
  52         }
  53
  54         @Test
  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() );
  60         }
  61
  62         @Test
  63         public void testReadBlock( ) throws IOException {
  64
  65                 String BLOCK = "\n" +
  66                                 "\n" +
  67                                 "\n" +
  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" +
  77                                 "\n" +
  78                                 "\n";
  79                 FileParse source=new FileParse(BLOCK, FormatAdapter.PASTE);
  80                 Block block = TCoffeeScoreFile.readBlock(source, 0);
  81
  82                 assertNotNull(block);
  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() );
  92         }
  93
  94         @Test
  95         public void testParse() throws IOException {
  96
  97                 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
  98
  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") );
 108         }
 109
 110
 111         @Test
 112         public void testGetAsList() throws IOException {
 113
 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) );
 126
 127         }
 128
 129
 130         @Test
 131         public void testGetAsArray() throws IOException {
 132
 133           TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
 134           assertTrue(parser.getWarningMessage(),parser.isValid());
 135                 byte[][] scores = parser.getScoresArray();
 136
 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] );
 146
 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] );
 156
 157         }
 158
 159
 160
 161 }