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