test/jalview/io/TCoffeeScoreFileTest.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ 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 jalview.io.TCoffeeScoreFile.Block;
  24 import jalview.io.TCoffeeScoreFile.Header;
  25
  26 import java.io.File;
  27 import java.io.FileNotFoundException;
  28 import java.io.IOException;
  29 import java.util.List;
  30
  31 import org.testng.AssertJUnit;
  32 import org.testng.annotations.Test;
  33
  34 public class TCoffeeScoreFileTest
  35 {
  36
  37   final static File SCORE_FILE = new File(
  38           "test/jalview/io/tcoffee.score_ascii");
  39
  40   final static File ALIGN_FILE = new File(
  41           "test/jalview/io/tcoffee.fasta_aln");
  42
  43   @Test
  44   public void testReadHeader() throws IOException
  45   {
  46
  47     TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),
  48             AppletFormatAdapter.FILE);
  49     AssertJUnit.assertTrue(scoreFile.getWarningMessage(), scoreFile.isValid());
  50
  51     Header header = scoreFile.header;
  52     AssertJUnit.assertNotNull(header);
  53     AssertJUnit.assertEquals(
  54             "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)",
  55             header.head);
  56     AssertJUnit.assertEquals(90, header.score);
  57     AssertJUnit.assertEquals(89, header.getScoreFor("1PHT"));
  58     AssertJUnit.assertEquals(90, header.getScoreFor("1BB9"));
  59     AssertJUnit.assertEquals(94, header.getScoreFor("1UHC"));
  60     AssertJUnit.assertEquals(94, header.getScoreFor("1YCS"));
  61     AssertJUnit.assertEquals(93, header.getScoreFor("1OOT"));
  62     AssertJUnit.assertEquals(94, header.getScoreFor("1ABO"));
  63     AssertJUnit.assertEquals(94, header.getScoreFor("1FYN"));
  64     AssertJUnit.assertEquals(94, header.getScoreFor("1QCF"));
  65     AssertJUnit.assertEquals(90, header.getScoreFor("cons"));
  66   }
  67
  68   @Test
  69   public void testWrongFile()
  70   {
  71     try
  72     {
  73       TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(),
  74               FormatAdapter.FILE);
  75       AssertJUnit.assertFalse(result.isValid());
  76     } catch (IOException x)
  77     {
  78       AssertJUnit.assertTrue("File not found exception thrown",
  79               x instanceof FileNotFoundException);
  80     }
  81   }
  82
  83   @Test
  84   public void testHeightAndWidth() throws IOException
  85   {
  86     TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(),
  87             FormatAdapter.FILE);
  88     AssertJUnit.assertTrue(result.isValid());
  89     AssertJUnit.assertEquals(8, result.getHeight());
  90     AssertJUnit.assertEquals(83, result.getWidth());
  91   }
  92
  93   @Test
  94   public void testReadBlock() throws IOException
  95   {
  96
  97     String BLOCK = "\n" + "\n" + "\n"
  98             + "1PHT   999999999999999999999999998762112222543211112134\n"
  99             + "1BB9   99999999999999999999999999987-------4322----2234  \n"
 100             + "1UHC   99999999999999999999999999987-------5321----2246\n"
 101             + "1YCS   99999999999999999999999999986-------4321----1-35\n"
 102             + "1OOT   999999999999999999999999999861-------3------1135  \n"
 103             + "1ABO   99999999999999999999999999986-------422-------34\n"
 104             + "1FYN   99999999999999999999999999985-------32--------35\n"
 105             + "1QCF   99999999999999999999999999974-------2---------24\n"
 106             + "cons   999999999999999999999999999851000110321100001134\n"
 107             + "\n" + "\n";
 108     FileParse source = new FileParse(BLOCK, FormatAdapter.PASTE);
 109     Block block = TCoffeeScoreFile.readBlock(source, 0);
 110
 111     AssertJUnit.assertNotNull(block);
 112     AssertJUnit.assertEquals("999999999999999999999999998762112222543211112134",
 113             block.getScoresFor("1PHT"));
 114     AssertJUnit.assertEquals("99999999999999999999999999987-------4322----2234",
 115             block.getScoresFor("1BB9"));
 116     AssertJUnit.assertEquals("99999999999999999999999999987-------5321----2246",
 117             block.getScoresFor("1UHC"));
 118     AssertJUnit.assertEquals("99999999999999999999999999986-------4321----1-35",
 119             block.getScoresFor("1YCS"));
 120     AssertJUnit.assertEquals("999999999999999999999999999861-------3------1135",
 121             block.getScoresFor("1OOT"));
 122     AssertJUnit.assertEquals("99999999999999999999999999986-------422-------34",
 123             block.getScoresFor("1ABO"));
 124     AssertJUnit.assertEquals("99999999999999999999999999985-------32--------35",
 125             block.getScoresFor("1FYN"));
 126     AssertJUnit.assertEquals("99999999999999999999999999974-------2---------24",
 127             block.getScoresFor("1QCF"));
 128     AssertJUnit.assertEquals("999999999999999999999999999851000110321100001134",
 129             block.getConsensus());
 130   }
 131
 132   @Test
 133   public void testParse() throws IOException
 134   {
 135
 136     TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
 137             FormatAdapter.FILE);
 138
 139     AssertJUnit.assertEquals(
 140             "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
 141             parser.getScoresFor("1PHT"));
 142     AssertJUnit.assertEquals(
 143             "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
 144             parser.getScoresFor("1BB9"));
 145     AssertJUnit.assertEquals(
 146             "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
 147             parser.getScoresFor("1UHC"));
 148     AssertJUnit.assertEquals(
 149             "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
 150             parser.getScoresFor("1YCS"));
 151     AssertJUnit.assertEquals(
 152             "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
 153             parser.getScoresFor("1OOT"));
 154     AssertJUnit.assertEquals(
 155             "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
 156             parser.getScoresFor("1ABO"));
 157     AssertJUnit.assertEquals(
 158             "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
 159             parser.getScoresFor("1FYN"));
 160     AssertJUnit.assertEquals(
 161             "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
 162             parser.getScoresFor("1QCF"));
 163     AssertJUnit.assertEquals(
 164             "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
 165             parser.getScoresFor("cons"));
 166   }
 167
 168   @Test
 169   public void testGetAsList() throws IOException
 170   {
 171
 172     TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
 173             FormatAdapter.FILE);
 174     AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
 175     List<String> scores = parser.getScoresList();
 176     AssertJUnit.assertEquals(
 177             "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
 178             scores.get(0));
 179     AssertJUnit.assertEquals(
 180             "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
 181             scores.get(1));
 182     AssertJUnit.assertEquals(
 183             "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
 184             scores.get(2));
 185     AssertJUnit.assertEquals(
 186             "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
 187             scores.get(3));
 188     AssertJUnit.assertEquals(
 189             "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
 190             scores.get(4));
 191     AssertJUnit.assertEquals(
 192             "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
 193             scores.get(5));
 194     AssertJUnit.assertEquals(
 195             "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
 196             scores.get(6));
 197     AssertJUnit.assertEquals(
 198             "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
 199             scores.get(7));
 200     AssertJUnit.assertEquals(
 201             "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
 202             scores.get(8));
 203
 204   }
 205
 206   @Test
 207   public void testGetAsArray() throws IOException
 208   {
 209
 210     TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
 211             FormatAdapter.FILE);
 212     AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
 213     byte[][] scores = parser.getScoresArray();
 214
 215     AssertJUnit.assertEquals(9, scores[0][0]);
 216     AssertJUnit.assertEquals(9, scores[1][0]);
 217     AssertJUnit.assertEquals(9, scores[2][0]);
 218     AssertJUnit.assertEquals(9, scores[3][0]);
 219     AssertJUnit.assertEquals(9, scores[4][0]);
 220     AssertJUnit.assertEquals(9, scores[5][0]);
 221     AssertJUnit.assertEquals(9, scores[6][0]);
 222     AssertJUnit.assertEquals(9, scores[7][0]);
 223     AssertJUnit.assertEquals(9, scores[8][0]);
 224
 225     AssertJUnit.assertEquals(5, scores[0][36]);
 226     AssertJUnit.assertEquals(4, scores[1][36]);
 227     AssertJUnit.assertEquals(5, scores[2][36]);
 228     AssertJUnit.assertEquals(4, scores[3][36]);
 229     AssertJUnit.assertEquals(-1, scores[4][36]);
 230     AssertJUnit.assertEquals(4, scores[5][36]);
 231     AssertJUnit.assertEquals(3, scores[6][36]);
 232     AssertJUnit.assertEquals(2, scores[7][36]);
 233     AssertJUnit.assertEquals(3, scores[8][36]);
 234
 235   }
 236
 237   @Test
 238   public void testHeightAndWidthWithResidueNumbers() throws Exception
 239   {
 240     String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
 241     TCoffeeScoreFile result = new TCoffeeScoreFile(file, FormatAdapter.FILE);
 242     AssertJUnit.assertTrue(result.isValid());
 243     AssertJUnit.assertEquals(5, result.getHeight());
 244     AssertJUnit.assertEquals(84, result.getWidth());
 245   }
 246
 247 }