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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.symbol;
import java.util.Iterator;
import java.util.Set;
import junit.framework.TestCase;
import org.biojava.bio.dist.Distribution;
import org.biojava.bio.seq.ProteinTools;
import org.biojava.bio.seq.RNATools;
/**
* Tests the CodonPrefTools class and
* the CodonPref functionality.
* @author David Huen
* @since 1.3
*/
public class SimpleCodonPrefTest extends TestCase
{
CodonPref testPref;
FiniteAlphabet aaAlfa = ProteinTools.getTAlphabet();
public SimpleCodonPrefTest(String name)
{
super(name);
}
protected void setUp() throws Exception
{
testPref = CodonPrefTools.getCodonPreference(CodonPrefTools.JUNIT);
assertNotNull(testPref);
}
public void testGetGeneticCode()
{
// get a copy of the genetic code and confirm
// correct one retrieved
ManyToOneTranslationTable prefGCode = testPref.getGeneticCode();
// retrieve the UNIVERSAL code and check
// that we have the same object
ManyToOneTranslationTable correctGCode = RNATools.getGeneticCode(TranslationTable.UNIVERSAL);
assertSame(prefGCode, correctGCode);
}
public void testGetFrequency()
{
// check that the sum is correct
try {
Distribution codonUse = testPref.getFrequency();
assertNotNull(codonUse);
// sum frequencies over all codons and check that it comes to one
FiniteAlphabet codons = RNATools.getCodonAlphabet();
double sum = 0.0;
for (Iterator codonI = codons.iterator(); codonI.hasNext(); ) {
sum += codonUse.getWeight((Symbol) codonI.next());
}
assertTrue( Math.abs(sum - 1.0) < 0.00001 );
// pick up a specific known frequency and check
SymbolList agc = RNATools.createRNA("agc");
Symbol testCodon = codons.getSymbol(agc.toList());
assertTrue(Math.abs(codonUse.getWeight(testCodon) - 0.0234375) < 0.0001);
}
catch (IllegalSymbolException ise) {
fail("IllegalSymbolException occurred on codon frequency lookup");
}
}
public void testGetFrequencyForSynonyms()
{
try {
// get synonyms for this residue
ManyToOneTranslationTable gCode = testPref.getGeneticCode();
for (Iterator residueI = ProteinTools.getTAlphabet().iterator(); residueI.hasNext(); ) {
Symbol residue = (Symbol) residueI.next();
// filter out selenocysteine!
if (residue.getName().equals("SEC")) continue;
// filter out pyrrolysine!
if (residue.getName().equals("PYL")) continue;
Distribution synonymUse = testPref.getFrequencyForSynonyms(residue);
assertNotNull(synonymUse);
// get set of synonyms
Set synonyms = gCode.untranslate(residue);
double sum = 0.0;
for (Iterator synonymsI = synonyms.iterator(); synonymsI.hasNext(); ) {
Symbol synonym = (Symbol) synonymsI.next();
sum += synonymUse.getWeight(synonym);
}
assertTrue(Math.abs(sum - 1.0) < 0.0001);
}
// check specific value: serine and agc
SymbolList serine = ProteinTools.createProtein("S");
assertNotNull(serine);
Distribution serineDist = testPref.getFrequencyForSynonyms(serine.symbolAt(1));
SymbolList agc = RNATools.createRNA("agc");
Symbol testCodon = RNATools.getCodonAlphabet().getSymbol(agc.toList());
assertTrue(Math.abs(serineDist.getWeight(testCodon) - 0.25) < 0.0001);
}
catch (IllegalSymbolException ise) {
fail("IllegalSymbolException occurred on codon frequency lookup");
}
}
public void testGetWobbleDistributionForSynonyms()
{
try {
// check that I can get back a WobbleDistribution
SymbolList serine = ProteinTools.createProtein("S");
assertNotNull(serine);
WobbleDistribution wobbleDist = testPref.getWobbleDistributionForSynonyms(serine.symbolAt(1));
assertNotNull(wobbleDist);
}
catch (IllegalSymbolException ise) {
fail("IllegalSymbolException occurred on wobble frequency lookup");
}
}
}
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