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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 java.io.InputStream;
import java.util.Iterator;
import java.util.Set;
import java.util.regex.Pattern;
import junit.framework.TestCase;
import org.biojava.bio.BioError;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.symbol.IllegalAlphabetException;
import org.biojava.bio.symbol.IllegalSymbolException;
import org.biojava.bio.symbol.SymbolList;
/**
* <code>RestrictionEnzymeManagerTest</code> tests manager
* functionality.
*
* @author Keith James
* @author G. Waldon
*/
public class RestrictionEnzymeManagerTest extends TestCase
{
public RestrictionEnzymeManagerTest(String name)
{
super(name);
}
public void testGetAllEnzymes()
{
Set allEnz = RestrictionEnzymeManager.getAllEnzymes();
assertEquals(40, allEnz.size());
}
public void testGetEnzyme()
{
RestrictionEnzyme ecoRI = RestrictionEnzymeManager.getEnzyme("EcoRI");
assertEquals("EcoRI", ecoRI.getName());
try
{
RestrictionEnzyme invalid = RestrictionEnzymeManager.getEnzyme("xxxx");
invalid=invalid==null?null:invalid;//trick
}
catch (IllegalArgumentException iae)
{
return;
}
fail("Expected IllegalArgumentException");
}
public void testGetIsoschizomers()
{
Set isoAvaI = RestrictionEnzymeManager.getIsoschizomers("AvaI");
assertEquals(1, isoAvaI.size());
Set isoAvrI = RestrictionEnzymeManager.getIsoschizomers("AvrI");
assertEquals(1, isoAvrI.size());
RestrictionEnzyme avaI = RestrictionEnzymeManager.getEnzyme("AvaI");
RestrictionEnzyme avrI = RestrictionEnzymeManager.getEnzyme("AvrI");
assertTrue(isoAvaI.contains(avrI));
assertTrue(isoAvrI.contains(avaI));
try
{
Set invalid = RestrictionEnzymeManager.getIsoschizomers("xxxx");
invalid=invalid==null?null:invalid;//trick
}
catch (IllegalArgumentException iae)
{
return;
}
fail("Expected IllegalArgumentException");
}
public void testGetNCutters()
{
Set all6Cutters = RestrictionEnzymeManager.getNCutters(6);
assertEquals(29, all6Cutters.size());
for (Iterator ei = all6Cutters.iterator(); ei.hasNext();)
{
RestrictionEnzyme e = (RestrictionEnzyme) ei.next();
assertEquals(6, e.getRecognitionSite().length());
}
}
public void testGetPatterns()
{
RestrictionEnzyme ecoRI = RestrictionEnzymeManager.getEnzyme("EcoRI");
Pattern [] pat = RestrictionEnzymeManager.getPatterns(ecoRI);
assertEquals("ga{2}t{2}c", pat[0].pattern());
assertEquals("ga{2}t{2}c", pat[1].pattern());
SymbolList site = null;
try
{
site = DNATools.createDNA("a");
}
catch (IllegalSymbolException ise)
{
throw new BioError(ise, "Internal error in test");
}
RestrictionEnzyme custom = null;
try
{
custom = new RestrictionEnzyme("custom", site, 1, 1);
}
catch (IllegalAlphabetException iae)
{
throw new BioError(iae, "Internal error in test");
}
try
{
pat = RestrictionEnzymeManager.getPatterns(custom);
}
catch (IllegalArgumentException iae)
{
return;
}
fail("Expected IllegalArgumentException");
}
/**
* @author G. Waldon
* @since 1.5
*/
public void testGetRecognitionSequence() {
String recognition = RestrictionEnzymeManager.getRecognitionSequence("EcoRI");
assertEquals("G^AATTC",recognition);
}
/** Note: suppliers vary between REBASE releases.
*
* @author G. Waldon
* @since 1.5
*/
public void testgetSuppliers() {
RestrictionEnzyme ecoRI = RestrictionEnzymeManager.getEnzyme("EcoRI");
String suppliers = RestrictionEnzymeManager.getSuppliers(ecoRI);
assertEquals("ABCEFGHIJKLMNOQRSTUVX",suppliers);
}
/**
* @author G. Waldon
* @since 1.5
*/
public void testloadEnzymeFile() {
String rebaseDataFileName = "org/biojava/bio/molbio/rebase.dat";
InputStream is = getClass().getClassLoader().getResourceAsStream(rebaseDataFileName);
RestrictionEnzymeManager.loadEnzymeFile(is,true);
Set re = RestrictionEnzymeManager.getAllEnzymes();
assertEquals(re.size(),1);
try
{
RestrictionEnzyme hind3 = RestrictionEnzymeManager.getEnzyme("HindIII");
assertEquals("HindIII", hind3.getName());
}
catch (IllegalArgumentException iae)
{
fail("IllegalArgumentException not expected");
}
is = getClass().getClassLoader().getResourceAsStream(rebaseDataFileName);
RestrictionEnzymeManager.loadEnzymeFile(is,false);
re = RestrictionEnzymeManager.getAllEnzymes();
assertEquals(re.size(),2);
try
{
RestrictionEnzyme hind3 = RestrictionEnzymeManager.getEnzyme("HindIII");
assertEquals("HindIII", hind3.getName());
RestrictionEnzyme ecor1 = RestrictionEnzymeManager.getEnzyme("EcoRI");
assertEquals("EcoRI", ecor1.getName());
}
catch (IllegalArgumentException iae)
{
fail("IllegalArgumentException not expected");
}
rebaseDataFileName = "/org/biojava/bio/molbio/rebase_common.dat";
is = RestrictionEnzymeManager.class.getResourceAsStream(rebaseDataFileName);
RestrictionEnzymeManager.loadEnzymeFile(is,false);
}
}
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