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.gui.JvOptionPane;
  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 org.testng.AssertJUnit;
  33 import org.testng.annotations.BeforeClass;
  34 import org.testng.annotations.Test;
  35
  36 public class TCoffeeScoreFileTest
  37 {
  38
  39   @BeforeClass(alwaysRun = true)
  40   public void setUpJvOptionPane()
  41   {
  42     JvOptionPane.setInteractiveMode(false);
  43     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  44   }
  45
  46   final static File SCORE_FILE = new File(
  47           "test/jalview/io/tcoffee.score_ascii");
  48
  49   final static File ALIGN_FILE = new File(
  50           "test/jalview/io/tcoffee.fasta_aln");
  51
  52   @Test(groups = { "Functional" })
  53   public void testReadHeader() throws IOException
  54   {
  55
  56     TCoffeeScoreFile scoreFile = new TCoffeeScoreFile(SCORE_FILE.getPath(),
  57             DataSourceType.FILE);
  58     AssertJUnit.assertTrue(scoreFile.getWarningMessage(),
  59             scoreFile.isValid());
  60
  61     Header header = scoreFile.header;
  62     AssertJUnit.assertNotNull(header);
  63     AssertJUnit
  64             .assertEquals(
  65                     "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)",
  66                     header.head);
  67     AssertJUnit.assertEquals(90, header.score);
  68     AssertJUnit.assertEquals(89, header.getScoreFor("1PHT"));
  69     AssertJUnit.assertEquals(90, header.getScoreFor("1BB9"));
  70     AssertJUnit.assertEquals(94, header.getScoreFor("1UHC"));
  71     AssertJUnit.assertEquals(94, header.getScoreFor("1YCS"));
  72     AssertJUnit.assertEquals(93, header.getScoreFor("1OOT"));
  73     AssertJUnit.assertEquals(94, header.getScoreFor("1ABO"));
  74     AssertJUnit.assertEquals(94, header.getScoreFor("1FYN"));
  75     AssertJUnit.assertEquals(94, header.getScoreFor("1QCF"));
  76     AssertJUnit.assertEquals(90, header.getScoreFor("cons"));
  77   }
  78
  79   @Test(groups = { "Functional" })
  80   public void testWrongFile()
  81   {
  82     try
  83     {
  84       TCoffeeScoreFile result = new TCoffeeScoreFile(ALIGN_FILE.getPath(),
  85               DataSourceType.FILE);
  86       AssertJUnit.assertFalse(result.isValid());
  87     } catch (IOException x)
  88     {
  89       AssertJUnit.assertTrue("File not found exception thrown",
  90               x instanceof FileNotFoundException);
  91     }
  92   }
  93
  94   @Test(groups = { "Functional" })
  95   public void testHeightAndWidth() throws IOException
  96   {
  97     TCoffeeScoreFile result = new TCoffeeScoreFile(SCORE_FILE.getPath(),
  98             DataSourceType.FILE);
  99     AssertJUnit.assertTrue(result.isValid());
 100     AssertJUnit.assertEquals(8, result.getHeight());
 101     AssertJUnit.assertEquals(83, result.getWidth());
 102   }
 103
 104   @Test(groups = { "Functional" })
 105   public void testReadBlock() throws IOException
 106   {
 107
 108     String BLOCK = "\n" + "\n" + "\n"
 109             + "1PHT   999999999999999999999999998762112222543211112134\n"
 110             + "1BB9   99999999999999999999999999987-------4322----2234  \n"
 111             + "1UHC   99999999999999999999999999987-------5321----2246\n"
 112             + "1YCS   99999999999999999999999999986-------4321----1-35\n"
 113             + "1OOT   999999999999999999999999999861-------3------1135  \n"
 114             + "1ABO   99999999999999999999999999986-------422-------34\n"
 115             + "1FYN   99999999999999999999999999985-------32--------35\n"
 116             + "1QCF   99999999999999999999999999974-------2---------24\n"
 117             + "cons   999999999999999999999999999851000110321100001134\n"
 118             + "\n" + "\n";
 119     FileParse source = new FileParse(BLOCK, DataSourceType.PASTE);
 120     Block block = TCoffeeScoreFile.readBlock(source, 0);
 121
 122     AssertJUnit.assertNotNull(block);
 123     AssertJUnit.assertEquals(
 124             "999999999999999999999999998762112222543211112134",
 125             block.getScoresFor("1PHT"));
 126     AssertJUnit.assertEquals(
 127             "99999999999999999999999999987-------4322----2234",
 128             block.getScoresFor("1BB9"));
 129     AssertJUnit.assertEquals(
 130             "99999999999999999999999999987-------5321----2246",
 131             block.getScoresFor("1UHC"));
 132     AssertJUnit.assertEquals(
 133             "99999999999999999999999999986-------4321----1-35",
 134             block.getScoresFor("1YCS"));
 135     AssertJUnit.assertEquals(
 136             "999999999999999999999999999861-------3------1135",
 137             block.getScoresFor("1OOT"));
 138     AssertJUnit.assertEquals(
 139             "99999999999999999999999999986-------422-------34",
 140             block.getScoresFor("1ABO"));
 141     AssertJUnit.assertEquals(
 142             "99999999999999999999999999985-------32--------35",
 143             block.getScoresFor("1FYN"));
 144     AssertJUnit.assertEquals(
 145             "99999999999999999999999999974-------2---------24",
 146             block.getScoresFor("1QCF"));
 147     AssertJUnit.assertEquals(
 148             "999999999999999999999999999851000110321100001134",
 149             block.getConsensus());
 150   }
 151
 152   @Test(groups = { "Functional" })
 153   public void testParse() throws IOException
 154   {
 155
 156     TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
 157             DataSourceType.FILE);
 158
 159     AssertJUnit
 160             .assertEquals(
 161                     "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
 162                     parser.getScoresFor("1PHT"));
 163     AssertJUnit
 164             .assertEquals(
 165                     "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
 166                     parser.getScoresFor("1BB9"));
 167     AssertJUnit
 168             .assertEquals(
 169                     "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
 170                     parser.getScoresFor("1UHC"));
 171     AssertJUnit
 172             .assertEquals(
 173                     "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
 174                     parser.getScoresFor("1YCS"));
 175     AssertJUnit
 176             .assertEquals(
 177                     "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
 178                     parser.getScoresFor("1OOT"));
 179     AssertJUnit
 180             .assertEquals(
 181                     "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
 182                     parser.getScoresFor("1ABO"));
 183     AssertJUnit
 184             .assertEquals(
 185                     "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
 186                     parser.getScoresFor("1FYN"));
 187     AssertJUnit
 188             .assertEquals(
 189                     "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
 190                     parser.getScoresFor("1QCF"));
 191     AssertJUnit
 192             .assertEquals(
 193                     "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
 194                     parser.getScoresFor("cons"));
 195   }
 196
 197   @Test(groups = { "Functional" })
 198   public void testGetAsList() throws IOException
 199   {
 200
 201     TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
 202             DataSourceType.FILE);
 203     AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
 204     List<String> scores = parser.getScoresList();
 205     AssertJUnit
 206             .assertEquals(
 207                     "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
 208                     scores.get(0));
 209     AssertJUnit
 210             .assertEquals(
 211                     "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
 212                     scores.get(1));
 213     AssertJUnit
 214             .assertEquals(
 215                     "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
 216                     scores.get(2));
 217     AssertJUnit
 218             .assertEquals(
 219                     "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
 220                     scores.get(3));
 221     AssertJUnit
 222             .assertEquals(
 223                     "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
 224                     scores.get(4));
 225     AssertJUnit
 226             .assertEquals(
 227                     "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
 228                     scores.get(5));
 229     AssertJUnit
 230             .assertEquals(
 231                     "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
 232                     scores.get(6));
 233     AssertJUnit
 234             .assertEquals(
 235                     "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
 236                     scores.get(7));
 237     AssertJUnit
 238             .assertEquals(
 239                     "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
 240                     scores.get(8));
 241
 242   }
 243
 244   @Test(groups = { "Functional" })
 245   public void testGetAsArray() throws IOException
 246   {
 247
 248     TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
 249             DataSourceType.FILE);
 250     AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
 251     byte[][] scores = parser.getScoresArray();
 252
 253     AssertJUnit.assertEquals(9, scores[0][0]);
 254     AssertJUnit.assertEquals(9, scores[1][0]);
 255     AssertJUnit.assertEquals(9, scores[2][0]);
 256     AssertJUnit.assertEquals(9, scores[3][0]);
 257     AssertJUnit.assertEquals(9, scores[4][0]);
 258     AssertJUnit.assertEquals(9, scores[5][0]);
 259     AssertJUnit.assertEquals(9, scores[6][0]);
 260     AssertJUnit.assertEquals(9, scores[7][0]);
 261     AssertJUnit.assertEquals(9, scores[8][0]);
 262
 263     AssertJUnit.assertEquals(5, scores[0][36]);
 264     AssertJUnit.assertEquals(4, scores[1][36]);
 265     AssertJUnit.assertEquals(5, scores[2][36]);
 266     AssertJUnit.assertEquals(4, scores[3][36]);
 267     AssertJUnit.assertEquals(-1, scores[4][36]);
 268     AssertJUnit.assertEquals(4, scores[5][36]);
 269     AssertJUnit.assertEquals(3, scores[6][36]);
 270     AssertJUnit.assertEquals(2, scores[7][36]);
 271     AssertJUnit.assertEquals(3, scores[8][36]);
 272
 273   }
 274
 275   @Test(groups = { "Functional" })
 276   public void testHeightAndWidthWithResidueNumbers() throws Exception
 277   {
 278     String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
 279     TCoffeeScoreFile result = new TCoffeeScoreFile(file, DataSourceType.FILE);
 280     AssertJUnit.assertTrue(result.isValid());
 281     AssertJUnit.assertEquals(5, result.getHeight());
 282     AssertJUnit.assertEquals(84, result.getWidth());
 283   }
 284
 285 }