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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.molbio;
import junit.framework.TestCase;
import org.biojava.bio.BioError;
import org.biojava.bio.BioException;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.symbol.IllegalSymbolException;
import org.biojava.bio.symbol.SymbolList;
/**
* <code>RestrictionEnzymeTest</code> tests enzyme functionality.
*
* @author Keith James
*/
public class RestrictionEnzymeTest extends TestCase
{
public RestrictionEnzymeTest(String name)
{
super(name);
}
public void testGetName() throws BioException
{
RestrictionEnzyme ecoRI = RestrictionEnzymeManager.getEnzyme("EcoRI");
assertEquals("EcoRI", ecoRI.getName());
}
public void testGetRecognitionSite() throws BioException
{
RestrictionEnzyme ecoRI = RestrictionEnzymeManager.getEnzyme("EcoRI");
SymbolList site = ecoRI.getRecognitionSite();
SymbolList test = null;
try
{
test = DNATools.createDNA("GAATTC");
}
catch (IllegalSymbolException ise)
{
throw new BioError(ise, "Internal error in test");
}
for (int i = 1; i <= site.length(); i++)
{
assertEquals(test.symbolAt(i), site.symbolAt(i));
}
}
public void testIsPalindromic()
{
RestrictionEnzyme ecoRI = RestrictionEnzymeManager.getEnzyme("EcoRI");
assertTrue(ecoRI.isPalindromic());
RestrictionEnzyme bsp24I = RestrictionEnzymeManager.getEnzyme("Bsp24I");
assertTrue(! bsp24I.isPalindromic());
}
public void testGetCutType()
{
RestrictionEnzyme ecoRI = RestrictionEnzymeManager.getEnzyme("EcoRI");
assertEquals(RestrictionEnzyme.CUT_SIMPLE, ecoRI.getCutType());
RestrictionEnzyme bsp24I = RestrictionEnzymeManager.getEnzyme("Bsp24I");
assertEquals(RestrictionEnzyme.CUT_COMPOUND, bsp24I.getCutType());
}
public void testGetDownstreamCut() throws BioException
{
RestrictionEnzyme ecoRI = RestrictionEnzymeManager.getEnzyme("EcoRI");
int [] ds = ecoRI.getDownstreamCut();
assertEquals(1, ds[0]);
assertEquals(5, ds[1]);
}
public void testGetUpstreamCut() throws BioException
{
RestrictionEnzyme bsp24I = RestrictionEnzymeManager.getEnzyme("Bsp24I");
int [] us = bsp24I.getUpstreamCut();
assertEquals(8, us[0]);
assertEquals(13, us[1]);
RestrictionEnzyme ecoRI = RestrictionEnzymeManager.getEnzyme("EcoRI");
try
{
us = ecoRI.getUpstreamCut();
}
catch (BioException be)
{
return;
}
fail("Expected BioException");
}
public void testGetDownstreamEndType() throws BioException
{
RestrictionEnzyme ecoRI = RestrictionEnzymeManager.getEnzyme("EcoRI");
assertEquals(RestrictionEnzyme.OVERHANG_3PRIME,
ecoRI.getDownstreamEndType());
RestrictionEnzyme apaI = RestrictionEnzymeManager.getEnzyme("ApaI");
assertEquals(RestrictionEnzyme.OVERHANG_5PRIME,
apaI.getDownstreamEndType());
RestrictionEnzyme smaI = RestrictionEnzymeManager.getEnzyme("SmaI");
assertEquals(RestrictionEnzyme.BLUNT,
smaI.getDownstreamEndType());
}
public void testGetUpstreamEndType() throws BioException
{
RestrictionEnzyme bsp24I = RestrictionEnzymeManager.getEnzyme("Bsp24I");
assertEquals(RestrictionEnzyme.OVERHANG_3PRIME,
bsp24I.getUpstreamEndType());
RestrictionEnzyme ecoRI = RestrictionEnzymeManager.getEnzyme("EcoRI");
try
{
ecoRI.getUpstreamEndType();
}
catch (BioException be)
{
return;
}
fail("Expected BioException");
}
}
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