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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;
import java.util.Collections;
import java.util.List;
import junit.framework.TestCase;
import org.biojava.bio.seq.io.SymbolTokenization;
import org.biojava.bio.symbol.AlphabetManager;
import org.biojava.bio.symbol.SymbolList;
/**
* <code>DNAToolsTest</code> tests are to ensure that the class can be
* instantiated and that the results are internally consistent. The
* functionality of the classes to which <code>DNATools</code>
* delegates e.g. <code>AlphabetManager</code> and
* <code>SymbolTokenization</code> should be tested in their own unit
* tests.
*
* @author Keith James
*/
public class DNAToolsTest extends TestCase
{
protected SymbolTokenization dnaTokens;
public DNAToolsTest(String name)
{
super(name);
}
protected void setUp() throws Exception
{
dnaTokens =
AlphabetManager.alphabetForName("DNA").getTokenization("token");
}
public void testSymbols() throws Exception
{
assertEquals("a", dnaTokens.tokenizeSymbol(DNATools.a()));
assertEquals("g", dnaTokens.tokenizeSymbol(DNATools.g()));
assertEquals("c", dnaTokens.tokenizeSymbol(DNATools.c()));
assertEquals("t", dnaTokens.tokenizeSymbol(DNATools.t()));
assertEquals("n", dnaTokens.tokenizeSymbol(DNATools.n()));
}
public void testGetDNA()
{
assertEquals(AlphabetManager.alphabetForName("DNA"),
DNATools.getDNA());
}
public void testGetCodon(){
List l = Collections.nCopies(3, DNATools.getDNA());
assertEquals(DNATools.getCodonAlphabet(), AlphabetManager.getCrossProductAlphabet(l));
}
public void testCreateDNA() throws Exception
{
SymbolList dnaSyms = DNATools.createDNA("agctn");
assertEquals(5, dnaSyms.length());
assertEquals("a", dnaTokens.tokenizeSymbol(dnaSyms.symbolAt(1)));
assertEquals("g", dnaTokens.tokenizeSymbol(dnaSyms.symbolAt(2)));
assertEquals("c", dnaTokens.tokenizeSymbol(dnaSyms.symbolAt(3)));
assertEquals("t", dnaTokens.tokenizeSymbol(dnaSyms.symbolAt(4)));
assertEquals("n", dnaTokens.tokenizeSymbol(dnaSyms.symbolAt(5)));
}
public void testIndex() throws Exception
{
assertEquals(0, DNATools.index(DNATools.a()));
assertEquals(1, DNATools.index(DNATools.g()));
assertEquals(2, DNATools.index(DNATools.c()));
assertEquals(3, DNATools.index(DNATools.t()));
}
public void testForIndex()
{
assertEquals(DNATools.a(), DNATools.forIndex(0));
assertEquals(DNATools.g(), DNATools.forIndex(1));
assertEquals(DNATools.c(), DNATools.forIndex(2));
assertEquals(DNATools.t(), DNATools.forIndex(3));
}
public void testComplement() throws Exception
{
assertEquals(DNATools.a(), DNATools.complement(DNATools.t()));
assertEquals(DNATools.g(), DNATools.complement(DNATools.c()));
assertEquals(DNATools.c(), DNATools.complement(DNATools.g()));
assertEquals(DNATools.t(), DNATools.complement(DNATools.a()));
assertEquals(DNATools.n(), DNATools.complement(DNATools.n()));
SymbolList dnaSyms =
DNATools.complement(DNATools.createDNA("agctn"));
assertEquals(5, dnaSyms.length());
assertEquals("t", dnaTokens.tokenizeSymbol(dnaSyms.symbolAt(1)));
assertEquals("c", dnaTokens.tokenizeSymbol(dnaSyms.symbolAt(2)));
assertEquals("g", dnaTokens.tokenizeSymbol(dnaSyms.symbolAt(3)));
assertEquals("a", dnaTokens.tokenizeSymbol(dnaSyms.symbolAt(4)));
assertEquals("n", dnaTokens.tokenizeSymbol(dnaSyms.symbolAt(5)));
}
public void testForSymbol() throws Exception
{
assertEquals("a", dnaTokens.tokenizeSymbol(DNATools.forSymbol('a')));
assertEquals("g", dnaTokens.tokenizeSymbol(DNATools.forSymbol('g')));
assertEquals("c", dnaTokens.tokenizeSymbol(DNATools.forSymbol('c')));
assertEquals("t", dnaTokens.tokenizeSymbol(DNATools.forSymbol('t')));
}
public void testReverseComplement() throws Exception
{
SymbolList dnaSyms =
DNATools.reverseComplement(DNATools.createDNA("agctn"));
assertEquals(5, dnaSyms.length());
assertEquals("n", dnaTokens.tokenizeSymbol(dnaSyms.symbolAt(1)));
assertEquals("a", dnaTokens.tokenizeSymbol(dnaSyms.symbolAt(2)));
assertEquals("g", dnaTokens.tokenizeSymbol(dnaSyms.symbolAt(3)));
assertEquals("c", dnaTokens.tokenizeSymbol(dnaSyms.symbolAt(4)));
assertEquals("t", dnaTokens.tokenizeSymbol(dnaSyms.symbolAt(5)));
}
public void testDNAToken() throws Exception
{
assertEquals('a', DNATools.dnaToken(DNATools.a()));
assertEquals('g', DNATools.dnaToken(DNATools.g()));
assertEquals('c', DNATools.dnaToken(DNATools.c()));
assertEquals('t', DNATools.dnaToken(DNATools.t()));
assertEquals('n', DNATools.dnaToken(DNATools.n()));
}
}
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