UtilsTest.java

/*
 * 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.*;

import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.List;
import org.junit.Ignore;
import org.junit.Test;

import uk.ac.sanger.artemis.circular.digest.CutSite;

public class UtilsTest
{
	/**
	 * Test that restrict output is parsed
	 */
	@Ignore("Use EmbossTableParserTest")
	@Test
	public void testFindCutSitesFromEmbossReport()
	{
    final InputStream inputStream =
      UtilsTest.class.getResourceAsStream("/data/foo.restrict");

    InputStreamReader reader = new InputStreamReader(inputStream);
    ReportDetails report = Utils.findCutSitesFromEmbossReport(reader);
    
		assertNotNull("ReportDetails null",report);
		assertEquals("Sequence length",report.length, 41243);
		
		List<CutSite> cutSites = report.cutSites;
		CutSite firstCutSite = cutSites.get(0);
		
		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());
	}
	
}