test/jalview/io/TCoffeeScoreFileTest.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
   3  * Copyright (C) 2015 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(groups = { "Functional" })
  44   public void testReadHeader() throws IOException
  45   {
  46
  47     TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),
  48             AppletFormatAdapter.FILE);
  49     AssertJUnit.assertTrue(scoreFile.getWarningMessage(),
  50             scoreFile.isValid());
  51
  52     Header header = scoreFile.header;
  53     AssertJUnit.assertNotNull(header);
  54     AssertJUnit
  55             .assertEquals(
  56                     "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)",
  57                     header.head);
  58     AssertJUnit.assertEquals(90, header.score);
  59     AssertJUnit.assertEquals(89, header.getScoreFor("1PHT"));
  60     AssertJUnit.assertEquals(90, header.getScoreFor("1BB9"));
  61     AssertJUnit.assertEquals(94, header.getScoreFor("1UHC"));
  62     AssertJUnit.assertEquals(94, header.getScoreFor("1YCS"));
  63     AssertJUnit.assertEquals(93, header.getScoreFor("1OOT"));
  64     AssertJUnit.assertEquals(94, header.getScoreFor("1ABO"));
  65     AssertJUnit.assertEquals(94, header.getScoreFor("1FYN"));
  66     AssertJUnit.assertEquals(94, header.getScoreFor("1QCF"));
  67     AssertJUnit.assertEquals(90, header.getScoreFor("cons"));
  68   }
  69
  70   @Test(groups = { "Functional" })
  71   public void testWrongFile()
  72   {
  73     try
  74     {
  75       TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(),
  76               FormatAdapter.FILE);
  77       AssertJUnit.assertFalse(result.isValid());
  78     } catch (IOException x)
  79     {
  80       AssertJUnit.assertTrue("File not found exception thrown",
  81               x instanceof FileNotFoundException);
  82     }
  83   }
  84
  85   @Test(groups = { "Functional" })
  86   public void testHeightAndWidth() throws IOException
  87   {
  88     TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(),
  89             FormatAdapter.FILE);
  90     AssertJUnit.assertTrue(result.isValid());
  91     AssertJUnit.assertEquals(8, result.getHeight());
  92     AssertJUnit.assertEquals(83, result.getWidth());
  93   }
  94
  95   @Test(groups = { "Functional" })
  96   public void testReadBlock() throws IOException
  97   {
  98
  99     String BLOCK = "\n" + "\n" + "\n"
 100             + "1PHT   999999999999999999999999998762112222543211112134\n"
 101             + "1BB9   99999999999999999999999999987-------4322----2234  \n"
 102             + "1UHC   99999999999999999999999999987-------5321----2246\n"
 103             + "1YCS   99999999999999999999999999986-------4321----1-35\n"
 104             + "1OOT   999999999999999999999999999861-------3------1135  \n"
 105             + "1ABO   99999999999999999999999999986-------422-------34\n"
 106             + "1FYN   99999999999999999999999999985-------32--------35\n"
 107             + "1QCF   99999999999999999999999999974-------2---------24\n"
 108             + "cons   999999999999999999999999999851000110321100001134\n"
 109             + "\n" + "\n";
 110     FileParse source = new FileParse(BLOCK, FormatAdapter.PASTE);
 111     Block block = TCoffeeScoreFile.readBlock(source, 0);
 112
 113     AssertJUnit.assertNotNull(block);
 114     AssertJUnit.assertEquals(
 115             "999999999999999999999999998762112222543211112134",
 116             block.getScoresFor("1PHT"));
 117     AssertJUnit.assertEquals(
 118             "99999999999999999999999999987-------4322----2234",
 119             block.getScoresFor("1BB9"));
 120     AssertJUnit.assertEquals(
 121             "99999999999999999999999999987-------5321----2246",
 122             block.getScoresFor("1UHC"));
 123     AssertJUnit.assertEquals(
 124             "99999999999999999999999999986-------4321----1-35",
 125             block.getScoresFor("1YCS"));
 126     AssertJUnit.assertEquals(
 127             "999999999999999999999999999861-------3------1135",
 128             block.getScoresFor("1OOT"));
 129     AssertJUnit.assertEquals(
 130             "99999999999999999999999999986-------422-------34",
 131             block.getScoresFor("1ABO"));
 132     AssertJUnit.assertEquals(
 133             "99999999999999999999999999985-------32--------35",
 134             block.getScoresFor("1FYN"));
 135     AssertJUnit.assertEquals(
 136             "99999999999999999999999999974-------2---------24",
 137             block.getScoresFor("1QCF"));
 138     AssertJUnit.assertEquals(
 139             "999999999999999999999999999851000110321100001134",
 140             block.getConsensus());
 141   }
 142
 143   @Test(groups = { "Functional" })
 144   public void testParse() throws IOException
 145   {
 146
 147     TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
 148             FormatAdapter.FILE);
 149
 150     AssertJUnit
 151             .assertEquals(
 152                     "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
 153                     parser.getScoresFor("1PHT"));
 154     AssertJUnit
 155             .assertEquals(
 156                     "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
 157                     parser.getScoresFor("1BB9"));
 158     AssertJUnit
 159             .assertEquals(
 160                     "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
 161                     parser.getScoresFor("1UHC"));
 162     AssertJUnit
 163             .assertEquals(
 164                     "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
 165                     parser.getScoresFor("1YCS"));
 166     AssertJUnit
 167             .assertEquals(
 168                     "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
 169                     parser.getScoresFor("1OOT"));
 170     AssertJUnit
 171             .assertEquals(
 172                     "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
 173                     parser.getScoresFor("1ABO"));
 174     AssertJUnit
 175             .assertEquals(
 176                     "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
 177                     parser.getScoresFor("1FYN"));
 178     AssertJUnit
 179             .assertEquals(
 180                     "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
 181                     parser.getScoresFor("1QCF"));
 182     AssertJUnit
 183             .assertEquals(
 184                     "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
 185                     parser.getScoresFor("cons"));
 186   }
 187
 188   @Test(groups = { "Functional" })
 189   public void testGetAsList() throws IOException
 190   {
 191
 192     TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
 193             FormatAdapter.FILE);
 194     AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
 195     List<String> scores = parser.getScoresList();
 196     AssertJUnit
 197             .assertEquals(
 198                     "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
 199                     scores.get(0));
 200     AssertJUnit
 201             .assertEquals(
 202                     "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
 203                     scores.get(1));
 204     AssertJUnit
 205             .assertEquals(
 206                     "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
 207                     scores.get(2));
 208     AssertJUnit
 209             .assertEquals(
 210                     "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
 211                     scores.get(3));
 212     AssertJUnit
 213             .assertEquals(
 214                     "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
 215                     scores.get(4));
 216     AssertJUnit
 217             .assertEquals(
 218                     "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
 219                     scores.get(5));
 220     AssertJUnit
 221             .assertEquals(
 222                     "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
 223                     scores.get(6));
 224     AssertJUnit
 225             .assertEquals(
 226                     "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
 227                     scores.get(7));
 228     AssertJUnit
 229             .assertEquals(
 230                     "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
 231                     scores.get(8));
 232
 233   }
 234
 235   @Test(groups = { "Functional" })
 236   public void testGetAsArray() throws IOException
 237   {
 238
 239     TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
 240             FormatAdapter.FILE);
 241     AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
 242     byte[][] scores = parser.getScoresArray();
 243
 244     AssertJUnit.assertEquals(9, scores[0][0]);
 245     AssertJUnit.assertEquals(9, scores[1][0]);
 246     AssertJUnit.assertEquals(9, scores[2][0]);
 247     AssertJUnit.assertEquals(9, scores[3][0]);
 248     AssertJUnit.assertEquals(9, scores[4][0]);
 249     AssertJUnit.assertEquals(9, scores[5][0]);
 250     AssertJUnit.assertEquals(9, scores[6][0]);
 251     AssertJUnit.assertEquals(9, scores[7][0]);
 252     AssertJUnit.assertEquals(9, scores[8][0]);
 253
 254     AssertJUnit.assertEquals(5, scores[0][36]);
 255     AssertJUnit.assertEquals(4, scores[1][36]);
 256     AssertJUnit.assertEquals(5, scores[2][36]);
 257     AssertJUnit.assertEquals(4, scores[3][36]);
 258     AssertJUnit.assertEquals(-1, scores[4][36]);
 259     AssertJUnit.assertEquals(4, scores[5][36]);
 260     AssertJUnit.assertEquals(3, scores[6][36]);
 261     AssertJUnit.assertEquals(2, scores[7][36]);
 262     AssertJUnit.assertEquals(3, scores[8][36]);
 263
 264   }
 265
 266   @Test(groups = { "Functional" })
 267   public void testHeightAndWidthWithResidueNumbers() throws Exception
 268   {
 269     String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
 270     TCoffeeScoreFile result = new TCoffeeScoreFile(file, FormatAdapter.FILE);
 271     AssertJUnit.assertTrue(result.isValid());
 272     AssertJUnit.assertEquals(5, result.getHeight());
 273     AssertJUnit.assertEquals(84, result.getWidth());
 274   }
 275
 276 }