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 javax.xml.parsers.ParserConfigurationException;
  30
  31 import org.junit.Test;
  32 import org.xml.sax.SAXException;
  33
  34 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
  35 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
  36 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
  37 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
  38
  39 public class TCoffeeScoreFileTest {
  40
  41         final static File SCORE_FILE = new File("test/jalview/io/tcoffee.score_ascii");
  42     final static File ALIGN_FILE = new File("test/jalview/io/tcoffee.fasta_aln");
  43
  44         @Test
  45         public void testReadHeader() throws IOException {
  46
  47             TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),AppletFormatAdapter.FILE);
  48             assertTrue(scoreFile.getWarningMessage(),scoreFile.isValid());
  49
  50             Header header = scoreFile.header;
  51                 assertNotNull(header);
  52                 assertEquals( "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)", header.head );
  53                 assertEquals( 90, header.score );
  54                 assertEquals( 89, header.getScoreFor("1PHT") );
  55                 assertEquals( 90, header.getScoreFor("1BB9") );
  56                 assertEquals( 94, header.getScoreFor("1UHC") );
  57                 assertEquals( 94, header.getScoreFor("1YCS") );
  58                 assertEquals( 93, header.getScoreFor("1OOT") );
  59                 assertEquals( 94, header.getScoreFor("1ABO") );
  60                 assertEquals( 94, header.getScoreFor("1FYN") );
  61                 assertEquals( 94, header.getScoreFor("1QCF") );
  62                 assertEquals( 90, header.getScoreFor("cons") );
  63         }
  64
  65
  66         @Test
  67         public void testWrongFile()  {
  68             try {
  69                         TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(), FormatAdapter.FILE);
  70                         assertFalse(result.isValid());
  71             }
  72             catch (IOException x)
  73             {
  74               assertTrue("File not found exception thrown",x instanceof FileNotFoundException);
  75             }
  76         }
  77
  78         @Test
  79         public void testHeightAndWidth() throws IOException {
  80                 TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
  81                 assertTrue(result.isValid());
  82                 assertEquals( 8, result.getHeight() );
  83                 assertEquals( 83, result.getWidth() );
  84         }
  85
  86         @Test
  87         public void testReadBlock( ) throws IOException {
  88
  89                 String BLOCK = "\n" +
  90                                 "\n" +
  91                                 "\n" +
  92                                 "1PHT   999999999999999999999999998762112222543211112134\n" +
  93                                 "1BB9   99999999999999999999999999987-------4322----2234  \n" +
  94                                 "1UHC   99999999999999999999999999987-------5321----2246\n" +
  95                                 "1YCS   99999999999999999999999999986-------4321----1-35\n" +
  96                                 "1OOT   999999999999999999999999999861-------3------1135  \n" +
  97                                 "1ABO   99999999999999999999999999986-------422-------34\n" +
  98                                 "1FYN   99999999999999999999999999985-------32--------35\n" +
  99                                 "1QCF   99999999999999999999999999974-------2---------24\n" +
 100                                 "cons   999999999999999999999999999851000110321100001134\n" +
 101                                 "\n" +
 102                                 "\n";
 103                 FileParse source=new FileParse(BLOCK, FormatAdapter.PASTE);
 104                 Block block = TCoffeeScoreFile.readBlock(source, 0);
 105
 106                 assertNotNull(block);
 107                 assertEquals( "999999999999999999999999998762112222543211112134", block.getScoresFor("1PHT") );
 108                 assertEquals( "99999999999999999999999999987-------4322----2234", block.getScoresFor("1BB9") );
 109                 assertEquals( "99999999999999999999999999987-------5321----2246", block.getScoresFor("1UHC") );
 110                 assertEquals( "99999999999999999999999999986-------4321----1-35", block.getScoresFor("1YCS") );
 111                 assertEquals( "999999999999999999999999999861-------3------1135", block.getScoresFor("1OOT") );
 112                 assertEquals( "99999999999999999999999999986-------422-------34", block.getScoresFor("1ABO") );
 113                 assertEquals( "99999999999999999999999999985-------32--------35", block.getScoresFor("1FYN") );
 114                 assertEquals( "99999999999999999999999999974-------2---------24", block.getScoresFor("1QCF") );
 115                 assertEquals( "999999999999999999999999999851000110321100001134", block.getConsensus() );
 116         }
 117
 118         @Test
 119         public void testParse() throws IOException {
 120
 121                 TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(), FormatAdapter.FILE);
 122
 123                 assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", parser.getScoresFor("1PHT") );
 124                 assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", parser.getScoresFor("1BB9") );
 125                 assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", parser.getScoresFor("1UHC") );
 126                 assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", parser.getScoresFor("1YCS") );
 127                 assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", parser.getScoresFor("1OOT") );
 128                 assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", parser.getScoresFor("1ABO") );
 129                 assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", parser.getScoresFor("1FYN") );
 130                 assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", parser.getScoresFor("1QCF") );
 131                 assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", parser.getScoresFor("cons") );
 132         }
 133
 134
 135         @Test
 136         public void testGetAsList() throws IOException {
 137
 138           TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
 139           assertTrue(parser.getWarningMessage(),parser.isValid());
 140                 List<String> scores = parser.getScoresList();
 141                 assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", scores.get(0) );
 142                 assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", scores.get(1) );
 143                 assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", scores.get(2) );
 144                 assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", scores.get(3) );
 145                 assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", scores.get(4) );
 146                 assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", scores.get(5) );
 147                 assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", scores.get(6) );
 148                 assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", scores.get(7) );
 149                 assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", scores.get(8) );
 150
 151         }
 152
 153
 154         @Test
 155         public void testGetAsArray() throws IOException {
 156
 157           TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),FormatAdapter.FILE);
 158           assertTrue(parser.getWarningMessage(),parser.isValid());
 159                 byte[][] scores = parser.getScoresArray();
 160
 161                 assertEquals( 9, scores[0][0] );
 162                 assertEquals( 9, scores[1][0] );
 163                 assertEquals( 9, scores[2][0] );
 164                 assertEquals( 9, scores[3][0] );
 165                 assertEquals( 9, scores[4][0] );
 166                 assertEquals( 9, scores[5][0] );
 167                 assertEquals( 9, scores[6][0] );
 168                 assertEquals( 9, scores[7][0] );
 169                 assertEquals( 9, scores[8][0] );
 170
 171                 assertEquals( 5, scores[0][36] );
 172                 assertEquals( 4, scores[1][36] );
 173                 assertEquals( 5, scores[2][36] );
 174                 assertEquals( 4, scores[3][36] );
 175                 assertEquals( -1, scores[4][36] );
 176                 assertEquals( 4, scores[5][36] );
 177                 assertEquals( 3, scores[6][36] );
 178                 assertEquals( 2, scores[7][36] );
 179                 assertEquals( 3, scores[8][36] );
 180
 181         }
 182
 183         @Test
 184         public void testHeightAndWidthWithResidueNumbers() throws Exception {
 185                 String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
 186                 TCoffeeScoreFile result = new TCoffeeScoreFile(file, FormatAdapter.FILE);
 187                 assertTrue(result.isValid());
 188                 assertEquals( 5, result.getHeight() );
 189                 assertEquals( 84, result.getWidth() );
 190         }
 191
 192
 193
 194 }