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/**
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.bio.seq.io;
import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import junit.framework.TestCase;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.symbol.Alignment;
/**
* JUnit test for MSFAlignmentFormat
* @author Thomas Down
* @since 1.4
*/
public class MSFAlignmentFormatTest extends TestCase
{
public MSFAlignmentFormatTest(String name)
{
super(name);
}
public void testReadDNAAlignment()
{
// get access to the test file
InputStream inputS = this.getClass().getResourceAsStream("/files/dna.msf");
assertNotNull(inputS);
Alignment alignment = new MSFAlignmentFormat().read(new BufferedReader(new InputStreamReader(inputS)));
assertNotNull(alignment);
assertEquals(alignment.length(), 120);
assertEquals(alignment.getAlphabet().getAlphabets().get(0), DNATools.getDNA());
}
}
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