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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 java.util.Set;
import junit.framework.TestCase;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.seq.ProteinTools;
public class AlphabetManagerTest extends TestCase {
// public static void main(String[] args) throws Exception{
// AlphabetManagerTest amt = new AlphabetManagerTest("");
// amt.testGapInCrossProductAlphabet();
//}
public AlphabetManagerTest(String s) {
super(s);
}
protected void setUp() {
}
protected void tearDown() {
}
public void testAlphabetForName() {
String name1= "DNA";
String name2 = "PROTEIN";
String name3 = "(DNA x DNA x DNA)";
String name4 = "((DNA x DNA x DNA) x PROTEIN)";
String name5 = "(PROTEIN x (DNA x DNA x DNA))";
String name6 = "((DNA x DNA x DNA) x DNA x (PROTEIN x DNA))";
try {
Alphabet alphabetRet = AlphabetManager.alphabetForName(name1);
assertEquals(DNATools.getDNA(),alphabetRet);
alphabetRet = AlphabetManager.alphabetForName(name2);
assertEquals(ProteinTools.getAlphabet(),alphabetRet);
alphabetRet = AlphabetManager.alphabetForName(name3);
assertEquals(alphabetRet.getName(), name3);
alphabetRet = AlphabetManager.alphabetForName(name4);
assertEquals(alphabetRet.getName(), name4);
alphabetRet = AlphabetManager.alphabetForName(name5);
assertEquals(alphabetRet.getName(), name5);
alphabetRet = AlphabetManager.alphabetForName(name6);
assertEquals(alphabetRet.getName(), name6);
}
catch(Exception e) {
System.err.println("Exception thrown: "+e);
}
}
public void testGetAllSymbols()
throws Exception
{
FiniteAlphabet dna = DNATools.getDNA();
Set allDna = AlphabetManager.getAllSymbols(dna);
Symbol n = DNATools.n();
Set allN = AlphabetManager.getAllSymbols((FiniteAlphabet) n.getMatches());
assertEquals(allDna.size(), 16);
assertEquals(allN.size(), 16);
for (Iterator i = allN.iterator(); i.hasNext(); ) {
Symbol is = (Symbol) i.next();
boolean found = false;
for (Iterator j = allDna.iterator(); j.hasNext(); ) {
Symbol js = (Symbol) j.next();
if (is == js) {
found = true;
}
}
assertTrue(found);
}
}
public void testSharedSymbols()
throws Exception
{
Alphabet protein = ProteinTools.getAlphabet();
String protString = "RVQZ";
SymbolList sl_protein = new SimpleSymbolList(
protein.getTokenization("token"),
protString
);
SymbolList sl_proteinT = new SimpleSymbolList(
protein.getTokenization("token"),
protString
);
for (int i = 1; i <= sl_protein.length(); ++i) {
assertEquals(sl_protein.symbolAt(i), sl_proteinT.symbolAt(i));
}
}
public void testGapInCrossProductAlphabet()
throws Exception
{
Alphabet protein = ProteinTools.getAlphabet();
Alphabet alph = AlphabetManager.getCrossProductAlphabet(Collections.nCopies(2, protein));
List s = new ArrayList();
s.add(protein.getGapSymbol());
s.add(ProteinTools.createProtein("V").symbolAt(1));
Symbol sym = alph.getSymbol(s);
List l = ((BasisSymbol)sym ).getSymbols();
assertEquals(s.get(0), l.get(0));
assertEquals(s.get(1), l.get(1));
}
}
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