test/jalview/io/TCoffeeScoreFileTest.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   3  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.io;
  19
  20 import static org.junit.Assert.*;
  21 import jalview.io.TCoffeeScoreFile.Block;
  22 import jalview.io.TCoffeeScoreFile.Header;
  23
  24 import java.io.File;
  25 import java.io.FileNotFoundException;
  26 import java.io.IOException;
  27 import java.util.List;
  28
  29 import org.junit.Test;
  30
  31 public class TCoffeeScoreFileTest {
  32
  33         final static File SCORE_FILE = new File("test/jalview/io/tcoffee.score_ascii");
  34     final static File ALIGN_FILE = new File("test/jalview/io/tcoffee.fasta_aln");
  35
  36         @Test
  37         public void testReadHeader() throws IOException, FileNotFoundException {
  38
  39             TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE);
  40             assertTrue(scoreFile.getWarningMessage(),scoreFile.isValid());
  41
  42             Header header = scoreFile.header;
  43                 assertNotNull(header);
  44                 assertEquals( "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)", header.head );
  45                 assertEquals( 90, header.score );
  46                 assertEquals( 89, header.getScoreFor("1PHT") );
  47                 assertEquals( 90, header.getScoreFor("1BB9") );
  48                 assertEquals( 94, header.getScoreFor("1UHC") );
  49                 assertEquals( 94, header.getScoreFor("1YCS") );
  50                 assertEquals( 93, header.getScoreFor("1OOT") );
  51                 assertEquals( 94, header.getScoreFor("1ABO") );
  52                 assertEquals( 94, header.getScoreFor("1FYN") );
  53                 assertEquals( 94, header.getScoreFor("1QCF") );
  54                 assertEquals( 90, header.getScoreFor("cons") );
  55         }
  56
  57
  58         @Test
  59         public void testWrongFile() {
  60             try {
  61                         TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
  62                         assertFalse(result.isValid());
  63             }
  64             catch (IOException x)
  65             {
  66               assertTrue("File not found exception thrown",x instanceof FileNotFoundException);
  67             }
  68         }
  69
  70         @Test
  71         public void testHeightAndWidth() throws IOException {
  72                 TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
  73                 assertTrue(result.isValid());
  74                 assertEquals( 8, result.getHeight() );
  75                 assertEquals( 83, result.getWidth() );
  76         }
  77
  78         @Test
  79         public void testReadBlock( ) throws IOException {
  80
  81                 String BLOCK = "\n" +
  82                                 "\n" +
  83                                 "\n" +
  84                                 "1PHT   999999999999999999999999998762112222543211112134\n" +
  85                                 "1BB9   99999999999999999999999999987-------4322----2234  \n" +
  86                                 "1UHC   99999999999999999999999999987-------5321----2246\n" +
  87                                 "1YCS   99999999999999999999999999986-------4321----1-35\n" +
  88                                 "1OOT   999999999999999999999999999861-------3------1135  \n" +
  89                                 "1ABO   99999999999999999999999999986-------422-------34\n" +
  90                                 "1FYN   99999999999999999999999999985-------32--------35\n" +
  91                                 "1QCF   99999999999999999999999999974-------2---------24\n" +
  92                                 "cons   999999999999999999999999999851000110321100001134\n" +
  93                                 "\n" +
  94                                 "\n";
  95                 FileParse source=new FileParse(BLOCK, FormatAdapter.PASTE);
  96                 Block block = TCoffeeScoreFile.readBlock(source, 0);
  97
  98                 assertNotNull(block);
  99                 assertEquals( "999999999999999999999999998762112222543211112134", block.getScoresFor("1PHT") );
 100                 assertEquals( "99999999999999999999999999987-------4322----2234", block.getScoresFor("1BB9") );
 101                 assertEquals( "99999999999999999999999999987-------5321----2246", block.getScoresFor("1UHC") );
 102                 assertEquals( "99999999999999999999999999986-------4321----1-35", block.getScoresFor("1YCS") );
 103                 assertEquals( "999999999999999999999999999861-------3------1135", block.getScoresFor("1OOT") );
 104                 assertEquals( "99999999999999999999999999986-------422-------34", block.getScoresFor("1ABO") );
 105                 assertEquals( "99999999999999999999999999985-------32--------35", block.getScoresFor("1FYN") );
 106                 assertEquals( "99999999999999999999999999974-------2---------24", block.getScoresFor("1QCF") );
 107                 assertEquals( "999999999999999999999999999851000110321100001134", block.getConsensus() );
 108         }
 109
 110         @Test
 111         public void testParse() throws IOException {
 112
 113                 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
 114
 115                 assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", parser.getScoresFor("1PHT") );
 116                 assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", parser.getScoresFor("1BB9") );
 117                 assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", parser.getScoresFor("1UHC") );
 118                 assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", parser.getScoresFor("1YCS") );
 119                 assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", parser.getScoresFor("1OOT") );
 120                 assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", parser.getScoresFor("1ABO") );
 121                 assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", parser.getScoresFor("1FYN") );
 122                 assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", parser.getScoresFor("1QCF") );
 123                 assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", parser.getScoresFor("cons") );
 124         }
 125
 126
 127         @Test
 128         public void testGetAsList() throws IOException {
 129
 130           TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
 131           assertTrue(parser.getWarningMessage(),parser.isValid());
 132                 List<String> scores = parser.getScoresList();
 133                 assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", scores.get(0) );
 134                 assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", scores.get(1) );
 135                 assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", scores.get(2) );
 136                 assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", scores.get(3) );
 137                 assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", scores.get(4) );
 138                 assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", scores.get(5) );
 139                 assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", scores.get(6) );
 140                 assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", scores.get(7) );
 141                 assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", scores.get(8) );
 142
 143         }
 144
 145
 146         @Test
 147         public void testGetAsArray() throws IOException {
 148
 149           TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
 150           assertTrue(parser.getWarningMessage(),parser.isValid());
 151                 byte[][] scores = parser.getScoresArray();
 152
 153                 assertEquals( 9, scores[0][0] );
 154                 assertEquals( 9, scores[1][0] );
 155                 assertEquals( 9, scores[2][0] );
 156                 assertEquals( 9, scores[3][0] );
 157                 assertEquals( 9, scores[4][0] );
 158                 assertEquals( 9, scores[5][0] );
 159                 assertEquals( 9, scores[6][0] );
 160                 assertEquals( 9, scores[7][0] );
 161                 assertEquals( 9, scores[8][0] );
 162
 163                 assertEquals( 5, scores[0][36] );
 164                 assertEquals( 4, scores[1][36] );
 165                 assertEquals( 5, scores[2][36] );
 166                 assertEquals( 4, scores[3][36] );
 167                 assertEquals( -1, scores[4][36] );
 168                 assertEquals( 4, scores[5][36] );
 169                 assertEquals( 3, scores[6][36] );
 170                 assertEquals( 2, scores[7][36] );
 171                 assertEquals( 3, scores[8][36] );
 172
 173         }
 174
 175         @Test
 176         public void testHeightAndWidthWithResidueNumbers() throws IOException {
 177                 String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
 178                 TCoffeeScoreFile result = new TCoffeeScoreFile(file, FormatAdapter.FILE);
 179                 assertTrue(result.isValid());
 180                 assertEquals( 5, result.getHeight() );
 181                 assertEquals( 84, result.getWidth() );
 182         }
 183
 184
 185
 186 }