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EmbossTableParserTest.java 2.15 KiB
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    /*
     * Copyright (C) 2009  Genome Research Limited
     *
     * This program is free software; you can redistribute it and/or
     * modify it under the terms of the GNU General Public License
     * as published by the Free Software Foundation; either version 2
     * of the License, or (at your option) any later version.
     *
     * This program is distributed in the hope that it will be useful,
     * but WITHOUT ANY WARRANTY; without even the implied warranty of
     * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     * GNU General Public License for more details.
     *
     * You should have received a copy of the GNU General Public License
     * along with this program; if not, write to the Free Software
     * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
     *
     */
    package uk.ac.sanger.artemis.circular.digest;
    
    import static org.junit.Assert.assertEquals;
    import static org.junit.Assert.assertNotNull;
    import static org.junit.Assert.assertTrue;
    
    import java.io.InputStream;
    import java.io.InputStreamReader;
    import java.io.BufferedReader;
    import java.io.IOException;
    import java.util.List;
    
    import org.junit.Test;
    
    import uk.ac.sanger.artemis.circular.digest.CutSite;
    import uk.ac.sanger.artemis.circular.digest.EmbossTableParser;
    
    public class EmbossTableParserTest
    {
    
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      /**
       * Test that restrict output is parsed
       */
      @Test
      public void testParser() throws IOException
      {
        final InputStream inputStream = EmbossTableParserTest.class
            .getResourceAsStream("/data/foo.restrict");
    
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        InputStreamReader reader = new InputStreamReader(inputStream);
        EmbossTableParser etp = new EmbossTableParser();
    
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        List<CutSite> cutSites = etp.parse(new BufferedReader(reader));
        CutSite firstCutSite = cutSites.get(0);
    
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        assertEquals("Number of cut sites", cutSites.size(), 4);
        assertEquals("Enzyme name", firstCutSite.getEnzymeName(), "HindIII");
        assertEquals("3prime", firstCutSite.getThreePrime(), 85);
        assertEquals("5prime", firstCutSite.getFivePrime(), 81);
        assertEquals("3prime-rev", firstCutSite.getThreePrimeRev(), 0);
        assertEquals("5prime-rev", firstCutSite.getFivePrimeRev(), 0);
        assertTrue("Cut site strand", firstCutSite.isForward());
      }
    
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    }