test/jalview/io/TCoffeeScoreFileTest.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
   3  * Copyright (C) 2014 The Jalview Authors
   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
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.io;
  22
  23 import static org.junit.Assert.*;
  24 import jalview.io.TCoffeeScoreFile.Block;
  25 import jalview.io.TCoffeeScoreFile.Header;
  26
  27 import java.io.File;
  28 import java.io.FileNotFoundException;
  29 import java.io.IOException;
  30 import java.util.List;
  31
  32 import javax.xml.parsers.ParserConfigurationException;
  33
  34 import org.junit.Test;
  35 import org.xml.sax.SAXException;
  36
  37 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
  38 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
  39 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
  40 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
  41
  42 public class TCoffeeScoreFileTest
  43 {
  44
  45   final static File SCORE_FILE = new File(
  46           "test/jalview/io/tcoffee.score_ascii");
  47
  48   final static File ALIGN_FILE = new File(
  49           "test/jalview/io/tcoffee.fasta_aln");
  50
  51   @Test
  52   public void testReadHeader() throws IOException
  53   {
  54
  55     TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),
  56             AppletFormatAdapter.FILE);
  57     assertTrue(scoreFile.getWarningMessage(), scoreFile.isValid());
  58
  59     Header header = scoreFile.header;
  60     assertNotNull(header);
  61     assertEquals(
  62             "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)",
  63             header.head);
  64     assertEquals(90, header.score);
  65     assertEquals(89, header.getScoreFor("1PHT"));
  66     assertEquals(90, header.getScoreFor("1BB9"));
  67     assertEquals(94, header.getScoreFor("1UHC"));
  68     assertEquals(94, header.getScoreFor("1YCS"));
  69     assertEquals(93, header.getScoreFor("1OOT"));
  70     assertEquals(94, header.getScoreFor("1ABO"));
  71     assertEquals(94, header.getScoreFor("1FYN"));
  72     assertEquals(94, header.getScoreFor("1QCF"));
  73     assertEquals(90, header.getScoreFor("cons"));
  74   }
  75
  76   @Test
  77   public void testWrongFile()
  78   {
  79     try
  80     {
  81       TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(),
  82               FormatAdapter.FILE);
  83       assertFalse(result.isValid());
  84     } catch (IOException x)
  85     {
  86       assertTrue("File not found exception thrown",
  87               x instanceof FileNotFoundException);
  88     }
  89   }
  90
  91   @Test
  92   public void testHeightAndWidth() throws IOException
  93   {
  94     TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(),
  95             FormatAdapter.FILE);
  96     assertTrue(result.isValid());
  97     assertEquals(8, result.getHeight());
  98     assertEquals(83, result.getWidth());
  99   }
 100
 101   @Test
 102   public void testReadBlock() throws IOException
 103   {
 104
 105     String BLOCK = "\n" + "\n" + "\n"
 106             + "1PHT   999999999999999999999999998762112222543211112134\n"
 107             + "1BB9   99999999999999999999999999987-------4322----2234  \n"
 108             + "1UHC   99999999999999999999999999987-------5321----2246\n"
 109             + "1YCS   99999999999999999999999999986-------4321----1-35\n"
 110             + "1OOT   999999999999999999999999999861-------3------1135  \n"
 111             + "1ABO   99999999999999999999999999986-------422-------34\n"
 112             + "1FYN   99999999999999999999999999985-------32--------35\n"
 113             + "1QCF   99999999999999999999999999974-------2---------24\n"
 114             + "cons   999999999999999999999999999851000110321100001134\n"
 115             + "\n" + "\n";
 116     FileParse source = new FileParse(BLOCK, FormatAdapter.PASTE);
 117     Block block = TCoffeeScoreFile.readBlock(source, 0);
 118
 119     assertNotNull(block);
 120     assertEquals("999999999999999999999999998762112222543211112134",
 121             block.getScoresFor("1PHT"));
 122     assertEquals("99999999999999999999999999987-------4322----2234",
 123             block.getScoresFor("1BB9"));
 124     assertEquals("99999999999999999999999999987-------5321----2246",
 125             block.getScoresFor("1UHC"));
 126     assertEquals("99999999999999999999999999986-------4321----1-35",
 127             block.getScoresFor("1YCS"));
 128     assertEquals("999999999999999999999999999861-------3------1135",
 129             block.getScoresFor("1OOT"));
 130     assertEquals("99999999999999999999999999986-------422-------34",
 131             block.getScoresFor("1ABO"));
 132     assertEquals("99999999999999999999999999985-------32--------35",
 133             block.getScoresFor("1FYN"));
 134     assertEquals("99999999999999999999999999974-------2---------24",
 135             block.getScoresFor("1QCF"));
 136     assertEquals("999999999999999999999999999851000110321100001134",
 137             block.getConsensus());
 138   }
 139
 140   @Test
 141   public void testParse() throws IOException
 142   {
 143
 144     TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
 145             FormatAdapter.FILE);
 146
 147     assertEquals(
 148             "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
 149             parser.getScoresFor("1PHT"));
 150     assertEquals(
 151             "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
 152             parser.getScoresFor("1BB9"));
 153     assertEquals(
 154             "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
 155             parser.getScoresFor("1UHC"));
 156     assertEquals(
 157             "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
 158             parser.getScoresFor("1YCS"));
 159     assertEquals(
 160             "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
 161             parser.getScoresFor("1OOT"));
 162     assertEquals(
 163             "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
 164             parser.getScoresFor("1ABO"));
 165     assertEquals(
 166             "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
 167             parser.getScoresFor("1FYN"));
 168     assertEquals(
 169             "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
 170             parser.getScoresFor("1QCF"));
 171     assertEquals(
 172             "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
 173             parser.getScoresFor("cons"));
 174   }
 175
 176   @Test
 177   public void testGetAsList() throws IOException
 178   {
 179
 180     TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
 181             FormatAdapter.FILE);
 182     assertTrue(parser.getWarningMessage(), parser.isValid());
 183     List<String> scores = parser.getScoresList();
 184     assertEquals(
 185             "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
 186             scores.get(0));
 187     assertEquals(
 188             "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
 189             scores.get(1));
 190     assertEquals(
 191             "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
 192             scores.get(2));
 193     assertEquals(
 194             "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
 195             scores.get(3));
 196     assertEquals(
 197             "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
 198             scores.get(4));
 199     assertEquals(
 200             "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
 201             scores.get(5));
 202     assertEquals(
 203             "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
 204             scores.get(6));
 205     assertEquals(
 206             "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
 207             scores.get(7));
 208     assertEquals(
 209             "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
 210             scores.get(8));
 211
 212   }
 213
 214   @Test
 215   public void testGetAsArray() throws IOException
 216   {
 217
 218     TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
 219             FormatAdapter.FILE);
 220     assertTrue(parser.getWarningMessage(), parser.isValid());
 221     byte[][] scores = parser.getScoresArray();
 222
 223     assertEquals(9, scores[0][0]);
 224     assertEquals(9, scores[1][0]);
 225     assertEquals(9, scores[2][0]);
 226     assertEquals(9, scores[3][0]);
 227     assertEquals(9, scores[4][0]);
 228     assertEquals(9, scores[5][0]);
 229     assertEquals(9, scores[6][0]);
 230     assertEquals(9, scores[7][0]);
 231     assertEquals(9, scores[8][0]);
 232
 233     assertEquals(5, scores[0][36]);
 234     assertEquals(4, scores[1][36]);
 235     assertEquals(5, scores[2][36]);
 236     assertEquals(4, scores[3][36]);
 237     assertEquals(-1, scores[4][36]);
 238     assertEquals(4, scores[5][36]);
 239     assertEquals(3, scores[6][36]);
 240     assertEquals(2, scores[7][36]);
 241     assertEquals(3, scores[8][36]);
 242
 243   }
 244
 245   @Test
 246   public void testHeightAndWidthWithResidueNumbers() throws Exception
 247   {
 248     String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
 249     TCoffeeScoreFile result = new TCoffeeScoreFile(file, FormatAdapter.FILE);
 250     assertTrue(result.isValid());
 251     assertEquals(5, result.getHeight());
 252     assertEquals(84, result.getWidth());
 253   }
 254
 255 }