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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.Arrays;
import java.util.Iterator;
import junit.framework.TestCase;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.seq.ProteinTools;
/**
* <p>Title: CrossProductSybmolIndexTest</p>
* <p>Description: Tests indexing of cross product alphabets</p>
* @author Matthew Pocock
*/
public class CrossProductAlphabetIndexTest extends TestCase {
IntegerAlphabet.SubIntegerAlphabet subint;
FiniteAlphabet dna;
FiniteAlphabet prot;
FiniteAlphabet product;
AlphabetIndex index;
public CrossProductAlphabetIndexTest(String name){
super(name);
}
protected void setUp() throws java.lang.Exception {
super.setUp();
subint = IntegerAlphabet.getSubAlphabet(20,99);
dna = DNATools.getDNA();
prot = ProteinTools.getAlphabet();
product = (FiniteAlphabet) AlphabetManager.getCrossProductAlphabet(
Arrays.asList(new FiniteAlphabet[]
{ subint, dna, prot }
)
);
index = new CrossProductAlphabetIndex(product);
}
protected void tearDown() throws java.lang.Exception {
super.tearDown();
}
public void testIndex2Symbol() throws Exception {
for(int i = 0; i < product.size(); i++) {
product.validate(index.symbolForIndex(i));
}
}
public void testSymbol2Index() throws Exception {
for(Iterator i = product.iterator(); i.hasNext(); ) {
Symbol s = (Symbol) i.next();
int j = index.indexForSymbol(s);
assertTrue(j >= 0 && j < product.size());
}
}
public void testISI() throws Exception {
for(int i = 0; i < product.size(); i++) {
assertTrue(
"index = index->symbol->index\t" +
i + " -> " + index.symbolForIndex(i) + " -> " +
index.indexForSymbol(index.symbolForIndex(i)),
i == index.indexForSymbol(index.symbolForIndex(i))
);
}
}
public void testSIS() throws Exception {
for(Iterator i = product.iterator(); i.hasNext(); ) {
Symbol s = (Symbol) i.next();
assertTrue(
"symbol = symbol -> index -> symbol\t" +
s + " -> " +
index.indexForSymbol(s) + " -> " +
index.symbolForIndex(index.indexForSymbol(s)),
s == index.symbolForIndex(index.indexForSymbol(s))
);
}
}
public static void main(String[] args)
throws Throwable {
CrossProductAlphabetIndexTest test = new CrossProductAlphabetIndexTest("test");
test.setUp();
test.testIndex2Symbol();
test.testSymbol2Index();
test.testISI();
test.testSIS();
test.tearDown();
}
}
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