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package org.biojava.bio.dist;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Map;
import junit.framework.TestCase;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.symbol.Alignment;
import org.biojava.bio.symbol.AlphabetManager;
import org.biojava.bio.symbol.SimpleAlignment;
import org.biojava.bio.symbol.Symbol;
/**
* Tests that methods from DistributionTools work as advertised.
*
* @author Mark Schreiber
* @since 1.3
*/
public class DistributionToolsTest extends TestCase {
private Alignment a;
private Distribution random;
private String[] sa;
private Map map;
public DistributionToolsTest(String name) {
super(name);
}
protected void setUp() {
try{
sa = new String[]{"CA-TGGG","AATTGGC","AATTGGG",
"AATTGGC","AA-TGGG","AATTGGC",
"AATTGGG","AATTGGC","AATTGGG",
"AATTGGC"};
map = new HashMap(sa.length);
for (int i = 0; i < sa.length; i++) {
map.put(new Integer(i), DNATools.createDNA(sa[i]));
}
a = new SimpleAlignment(map);
random = new SimpleDistribution(DNATools.getDNA());
DistributionTools.randomizeDistribution(random);
}catch(Exception e){
e.printStackTrace();
}
}
protected void tearDown(){
sa = null;
map = null;
a = null;
random = null;
}
public void testDistOverAlignment() {
try{
Distribution[] d = DistributionTools.distOverAlignment(a,false);
Distribution[] d2 = DistributionTools.distOverAlignment(a,false,10.0);
Distribution[] d3 = DistributionTools.distOverAlignment(a,true);
assertTrue(d[0].getWeight(DNATools.a()) == 0.9);
assertTrue(d[0].getWeight(DNATools.c()) == 0.1);
assertTrue(d[0].getWeight(DNATools.g()) == 0.0);
assertTrue(d[0].getWeight(DNATools.t()) == 0.0);
assertTrue(d[0].getWeight(AlphabetManager.getGapSymbol()) == 0.0);
assertTrue(d2[1].getWeight(DNATools.a()) == 0.625);
assertTrue(d2[1].getWeight(DNATools.c()) == 0.125);
assertTrue(d2[1].getWeight(DNATools.g()) == 0.125);
assertTrue(d2[1].getWeight(DNATools.t()) == 0.125);
assertTrue(d2[1].getWeight(AlphabetManager.getGapSymbol()) == 0.0);
assertEquals( 0.0 , d3[2].getWeight(DNATools.a()) ,0.000001);
assertEquals( 0.0 , d3[2].getWeight(DNATools.c()) ,0.000001);
assertEquals( 0.0 , d3[2].getWeight(DNATools.g()) ,0.000001);
assertEquals( 0.8 , d3[2].getWeight(DNATools.t()), 0.000001);
assertEquals( 0.2 , d3[2].getWeight(AlphabetManager.getGapSymbol()),
0.000001);
}catch(Exception e){
e.printStackTrace();
}
}
/**
* This method tests DistributionTools.shannonEntropy(), DistributionTools.totalEntropy()
* and DistributionTools.bitsOfInformation().
*/
public void testInformationContent(){
Distribution d = new UniformDistribution(DNATools.getDNA());
assertTrue(DistributionTools.bitsOfInformation(d) == 0.0);
assertTrue(DistributionTools.totalEntropy(d) == 2.0);
Map map = DistributionTools.shannonEntropy(d,2.0);
for(Iterator i = DNATools.getDNA().iterator(); i.hasNext();){
Symbol s = (Symbol)i.next();
double ent = ((Double)map.get(s)).doubleValue();
assertTrue(ent == 2.0);
}
}
public void testGenerateSequence(){
Sequence seq = DistributionTools.generateSequence("seq",random,1000);
assertTrue(seq.length() == 1000);
//this will kick in the PackedSymbolListFactory
Sequence seq2 = DistributionTools.generateSequence("seq", random, 30000);
assertTrue(seq2.length() == 30000);
}
}
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