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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.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import junit.framework.TestCase;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.seq.io.SymbolTokenization;
/**
* Test for tokenization of cross-product symbols.
*
* @author Thomas Down
* @since 1.2
*/
public class CrossProductTokenizationTest extends TestCase {
private FiniteAlphabet simple_alpha;
private FiniteAlphabet cross_alpha;
private SymbolList cross_atomicSymbols;
private SymbolTokenization nameTokenization;
public CrossProductTokenizationTest(String name) {
super(name);
}
protected void setUp() throws Exception {
simple_alpha = DNATools.getDNA();
cross_alpha = (FiniteAlphabet) AlphabetManager.getCrossProductAlphabet(Collections.nCopies(2, simple_alpha));
List atomics = new ArrayList();
for (Iterator i = cross_alpha.iterator(); i.hasNext(); ) {
atomics.add(i.next());
}
cross_atomicSymbols = new SimpleSymbolList(cross_alpha, atomics);
nameTokenization = cross_alpha.getTokenization("name");
}
public void testAtomicNames()
throws Exception
{
String tokenization = nameTokenization.tokenizeSymbolList(cross_atomicSymbols);
SymbolList reconstruction = new SimpleSymbolList(nameTokenization, tokenization);
assertTrue(SymbolUtils.compareSymbolLists(cross_atomicSymbols, reconstruction));
}
// public void testAmbiguousNames()
// throws Exception
// {
// String tokenization = nameTokenization.tokenizeSymbolList(simple_allSymbols);
// System.out.println(tokenization);
// SymbolList reconstruction = AlphabetManager.parse(nameTokenization, tokenization);
// assertTrue(SymbolUtils.compareSymbolLists(simple_allSymbols, reconstruction));
// }
}
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