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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;
public class SeqContentPatternTest
extends TestCase {
public void testTooShort()
throws IllegalSymbolException, IllegalAlphabetException {
SymbolList zero = DNATools.createDNA("");
SymbolList one = DNATools.createDNA("a");
SymbolList five = DNATools.createDNA("aaaaa");
SymbolList sixMatch = DNATools.createDNA("aaaaaa");
SymbolList sixNoMatch = DNATools.createDNA("tttttt");
SymbolList sevenMatch1 = DNATools.createDNA("aaaaaat");
SymbolList sevenMatch2 = DNATools.createDNA("taaaaaa");
SymbolList sevenMatchAll = DNATools.createDNA("aaaaaaa");
SymbolList sevenNoMatch = DNATools.createDNA("ttttttt");
SeqContentPattern scp = new SeqContentPattern(DNATools.getDNA());
scp.setLength(6);
scp.setMinCounts(DNATools.a(), 6);
BioMatcher scm;
scm = scp.matcher(zero);
assertFalse("No hits of length 6 in seq length 0", scm.find());
scm = scp.matcher(one);
assertFalse("No hits of length 6 in seq length 1", scm.find());
scm = scp.matcher(five);
assertFalse("No hits of length 6 in seq length 5", scm.find());
scm = scp.matcher(sixMatch);
assertTrue("Hit found in matching 6", scm.find());
assertFalse("Just the one hit", scm.find());
scm = scp.matcher(sixNoMatch);
assertFalse("No hit in non-matching 6", scm.find());
scm = scp.matcher(sevenMatch1);
assertTrue("Hit in 7-1", scm.find());
assertEquals("Hit in 7-1 at 1", 1, scm.start());
assertFalse("No more hits in 7-1", scm.find());
scm = scp.matcher(sevenMatch2);
assertTrue("Hit in 7-2", scm.find());
assertEquals("Hit in 7-2 at 2", 2, scm.start());
assertFalse("No more hits in 7-2", scm.find());
scm = scp.matcher(sevenMatchAll);
assertTrue("Hit in 7-all", scm.find());
assertEquals("Hit in 7-all at 1", 1, scm.start());
assertTrue("Hit in 7-all", scm.find());
assertEquals("Hit in 7-all at 2", 2, scm.start());
scm = scp.matcher(sevenNoMatch);
assertFalse("No hit in seven no hits", scm.find());
}
// we should have tests for various boundary conditions
// on the counts
// also - check that obviously impossible count ranges never match
}
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