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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.Arrays;
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.io.SymbolTokenization;
import org.biojava.utils.AssertionFailure;
public class MotifToolsTest
extends TestCase {
protected String n;
protected void setUp() {
try {
StringBuffer sb = new StringBuffer();
sb.append("[");
SymbolTokenization sTok = DNATools.getDNA().getTokenization("token");
FiniteAlphabet na = (FiniteAlphabet) DNATools.n().getMatches();
Set rawSyms = AlphabetManager.getAllSymbols(na);
List gapSyms = new ArrayList();
for (Iterator si = rawSyms.iterator(); si.hasNext();) {
Symbol rawSym = (Symbol) si.next();
// Crude check for gap symbol
if (((FiniteAlphabet) rawSym.getMatches()).size() == 0) {
gapSyms.add(rawSym);
}
}
rawSyms.removeAll(gapSyms);
// getAllSymbols returns a Set (i.e. unordered) so
// we convert to char array so we can sort tokens
Symbol [] nSyms = (Symbol []) rawSyms.toArray(new Symbol [0]);
char [] nChars = new char [nSyms.length];
for (int i = 0; i < nSyms.length; i++) {
nChars[i] = sTok.tokenizeSymbol(nSyms[i]).charAt(0);
}
Arrays.sort(nChars);
sb.append(nChars);
sb.append("]");
n = sb.toString();
} catch (Exception e) {
throw new AssertionFailure("Couldn't initialize motif tools test", e);
}
}
public MotifToolsTest(String name) {
super(name);
}
public void testPlain() {
doTest("atcg", "atcg");
}
public void testTwoStart() {
doTest("aatcg", "a{2}tcg");
}
public void testThreeStart() {
doTest("aaatcg", "a{3}tcg");
}
public void testTwoInternal() {
doTest("attcg", "at{2}cg");
}
public void testThreeInternal() {
doTest("atttcg", "at{3}cg");
}
public void testTwoEnd() {
doTest("atcgg", "atcg{2}");
}
public void testThreeEnd() {
doTest("atcggg", "atcg{3}");
}
public void testTwoOnly() {
doTest("aa", "a{2}");
}
public void testThreeOnly() {
doTest("aaa", "a{3}");
}
public void testAmbStart() {
doTest("ngct", n + "gct");
}
public void testAmbMiddle() {
doTest("anct", "a" + n + "ct");
}
public void testAmbEnd() {
doTest("agcn", "agc" + n);
}
public void testTwoAmbOnly() {
doTest("nn", n + "{2}");
}
void doTest(String pattern, String target) {
try {
assertEquals(target, MotifTools.createRegex(DNATools.createDNA(pattern)));
} catch (IllegalSymbolException ise) {
throw new AssertionFailure(ise);
}
}
}
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