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package org.biojava.bio.search;
import junit.framework.TestCase;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.symbol.IllegalAlphabetException;
import org.biojava.bio.symbol.IllegalSymbolException;
import org.biojava.bio.symbol.SymbolList;
/**
* Test the MaxMismatchPattern and MaxMismatchMatcher classes.
*
* @author Matthew Pocock
* @since 1.4
*/
public class MaxMismatchPatternTest
extends TestCase {
public void testTooShort()
throws IllegalSymbolException, IllegalAlphabetException{
SymbolList zero = DNATools.createDNA("");
SymbolList one = DNATools.createDNA("a");
SymbolList agct = DNATools.createDNA("agct");
SymbolList aggt = DNATools.createDNA("aggt");
MaxMismatchPattern mmp = new MaxMismatchPattern(agct, 0);
assertFalse("Zero length string has no matches", mmp.matcher(zero).find());
assertFalse("One length string has no matches", mmp.matcher(one).find());
assertTrue("Four length identical string has a match", mmp.matcher(agct).find());
assertFalse("Four length non-identical string has no match", mmp.matcher(aggt).find());
}
}
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