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 javax.xml.parsers.ParserConfigurationException;
  16
  17 import org.junit.Test;
  18 import org.xml.sax.SAXException;
  19
  20 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
  21 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
  22 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
  23 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
  24
  25 public class TCoffeeScoreFileTest {
  26
  27         final static File SCORE_FILE = new File("test/jalview/io/tcoffee.score_ascii");
  28         final static File ALIGN_FILE = new File("test/jalview/io/tcoffee.fasta_aln");
  29
  30         @Test
  31         public void testReadHeader() throws IOException, FileNotFoundException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
  32
  33                 TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE);
  34                 assertTrue(scoreFile.getWarningMessage(),scoreFile.isValid());
  35                 Header header = scoreFile.header;
  36                 assertNotNull(header);
  37                 assertEquals( "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)", header.head );
  38                 assertEquals( 90, header.score );
  39                 assertEquals( 89, header.getScoreFor("1PHT") );
  40                 assertEquals( 90, header.getScoreFor("1BB9") );
  41                 assertEquals( 94, header.getScoreFor("1UHC") );
  42                 assertEquals( 94, header.getScoreFor("1YCS") );
  43                 assertEquals( 93, header.getScoreFor("1OOT") );
  44                 assertEquals( 94, header.getScoreFor("1ABO") );
  45                 assertEquals( 94, header.getScoreFor("1FYN") );
  46                 assertEquals( 94, header.getScoreFor("1QCF") );
  47                 assertEquals( 90, header.getScoreFor("cons") );
  48         }
  49
  50
  51         @Test
  52         public void testWrongFile() throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
  53             try {
  54                 TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
  55                 assertFalse(result.isValid());
  56             } catch (IOException x)
  57             {
  58               assertTrue("File not found exception thrown",x instanceof FileNotFoundException);
  59             }
  60         }
  61
  62         @Test
  63         public void testHeightAndWidth() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
  64                 TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
  65                 assertTrue(result.isValid());
  66                 assertEquals( 8, result.getHeight() );
  67                 assertEquals( 83, result.getWidth() );
  68         }
  69
  70         @Test
  71         public void testReadBlock( ) throws IOException {
  72
  73                 String BLOCK = "\n" +
  74                                 "\n" +
  75                                 "\n" +
  76                                 "1PHT   999999999999999999999999998762112222543211112134\n" +
  77                                 "1BB9   99999999999999999999999999987-------4322----2234  \n" +
  78                                 "1UHC   99999999999999999999999999987-------5321----2246\n" +
  79                                 "1YCS   99999999999999999999999999986-------4321----1-35\n" +
  80                                 "1OOT   999999999999999999999999999861-------3------1135  \n" +
  81                                 "1ABO   99999999999999999999999999986-------422-------34\n" +
  82                                 "1FYN   99999999999999999999999999985-------32--------35\n" +
  83                                 "1QCF   99999999999999999999999999974-------2---------24\n" +
  84                                 "cons   999999999999999999999999999851000110321100001134\n" +
  85                                 "\n" +
  86                                 "\n";
  87                 FileParse source=new FileParse(BLOCK, FormatAdapter.PASTE);
  88                 Block block = TCoffeeScoreFile.readBlock(source, 0);
  89
  90                 assertNotNull(block);
  91                 assertEquals( "999999999999999999999999998762112222543211112134", block.getScoresFor("1PHT") );
  92                 assertEquals( "99999999999999999999999999987-------4322----2234", block.getScoresFor("1BB9") );
  93                 assertEquals( "99999999999999999999999999987-------5321----2246", block.getScoresFor("1UHC") );
  94                 assertEquals( "99999999999999999999999999986-------4321----1-35", block.getScoresFor("1YCS") );
  95                 assertEquals( "999999999999999999999999999861-------3------1135", block.getScoresFor("1OOT") );
  96                 assertEquals( "99999999999999999999999999986-------422-------34", block.getScoresFor("1ABO") );
  97                 assertEquals( "99999999999999999999999999985-------32--------35", block.getScoresFor("1FYN") );
  98                 assertEquals( "99999999999999999999999999974-------2---------24", block.getScoresFor("1QCF") );
  99                 assertEquals( "999999999999999999999999999851000110321100001134", block.getConsensus() );
 100         }
 101
 102         @Test
 103         public void testParse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
 104
 105                 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
 106
 107                 assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", parser.getScoresFor("1PHT") );
 108                 assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", parser.getScoresFor("1BB9") );
 109                 assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", parser.getScoresFor("1UHC") );
 110                 assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", parser.getScoresFor("1YCS") );
 111                 assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", parser.getScoresFor("1OOT") );
 112                 assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", parser.getScoresFor("1ABO") );
 113                 assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", parser.getScoresFor("1FYN") );
 114                 assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", parser.getScoresFor("1QCF") );
 115                 assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", parser.getScoresFor("cons") );
 116         }
 117
 118
 119         @Test
 120         public void testGetAsList() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
 121
 122           TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
 123           assertTrue(parser.getWarningMessage(),parser.isValid());
 124                 List<String> scores = parser.getScoresList();
 125                 assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", scores.get(0) );
 126                 assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", scores.get(1) );
 127                 assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", scores.get(2) );
 128                 assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", scores.get(3) );
 129                 assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", scores.get(4) );
 130                 assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", scores.get(5) );
 131                 assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", scores.get(6) );
 132                 assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", scores.get(7) );
 133                 assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", scores.get(8) );
 134
 135         }
 136
 137
 138         @Test
 139         public void testGetAsArray() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {
 140
 141           TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
 142           assertTrue(parser.getWarningMessage(),parser.isValid());
 143                 byte[][] scores = parser.getScoresArray();
 144
 145                 assertEquals( 9, scores[0][0] );
 146                 assertEquals( 9, scores[1][0] );
 147                 assertEquals( 9, scores[2][0] );
 148                 assertEquals( 9, scores[3][0] );
 149                 assertEquals( 9, scores[4][0] );
 150                 assertEquals( 9, scores[5][0] );
 151                 assertEquals( 9, scores[6][0] );
 152                 assertEquals( 9, scores[7][0] );
 153                 assertEquals( 9, scores[8][0] );
 154
 155                 assertEquals( 5, scores[0][36] );
 156                 assertEquals( 4, scores[1][36] );
 157                 assertEquals( 5, scores[2][36] );
 158                 assertEquals( 4, scores[3][36] );
 159                 assertEquals( -1, scores[4][36] );
 160                 assertEquals( 4, scores[5][36] );
 161                 assertEquals( 3, scores[6][36] );
 162                 assertEquals( 2, scores[7][36] );
 163                 assertEquals( 3, scores[8][36] );
 164
 165         }
 166
 167
 168
 169 }