public void SimpleFindOneOutputPatternTest()
{
ISequence sequence = new Sequence(DnaAlphabet.Instance, "AGCT");
IPatternFinder patternFinder = new BoyerMoore();
IList<int> actual = patternFinder.FindMatch(sequence, "AGCT");
HashSet<int> expected = new HashSet<int>();
expected.Add(0);
Assert.IsTrue(Compare(expected, actual));
}
public void BoyerMooreAlignDnaSequenceWith1000BP()
{
var boyerMoore = new BoyerMoore();
string boyerMooreSequence =
utilityObj.xmlUtil.GetTextValue(Constants.BoyerMooreSequence, Constants.SequenceNode);
string referenceSequence =
utilityObj.xmlUtil.GetTextValue(Constants.BoyerMooreSequence, Constants.SearchSequenceNode);
string expectedMatch =
utilityObj.xmlUtil.GetTextValue(Constants.BoyerMooreSequence, Constants.ExpectedMatch);
ISequence boyerMooreSeq = new Sequence(Alphabets.DNA, boyerMooreSequence);
IList<int> indexList = boyerMoore.FindMatch(boyerMooreSeq,
referenceSequence);
Assert.AreEqual(expectedMatch, indexList[0].ToString((IFormatProvider) null));
}
public void MultipleFindOneOutputPatternTest()
{
ISequence sequence = new Sequence(DnaAlphabet.Instance, "AGCTAGGTTGGCC");
IList<string> patterns = new List<string>();
patterns.Add("AGCT");
patterns.Add("AAAAA");
IPatternFinder patternFinder = new BoyerMoore();
IDictionary<string, IList<int>> actual = patternFinder.FindMatch(sequence, patterns);
IDictionary<string, HashSet<int>> expected = new Dictionary<string, HashSet<int>>();
HashSet<int> indices = new HashSet<int>();
indices.Add(0);
expected.Add("AGCT", indices);
indices = new HashSet<int>();
expected.Add("AAAAA", indices);
Assert.IsTrue(Compare(expected, actual));
}
public void MatchWildcardPatternMiddle()
{
ISequence sequence = new Sequence(DnaAlphabet.Instance, "AGCTAGGTAGCTCAAAAAAGGG");
IPatternFinder patternFinder = new BoyerMoore();
IList<int> actual = patternFinder.FindMatch(sequence, "AGCTAGGTAGCTCA*GGG");
HashSet<int> expected = new HashSet<int>();
expected.Add(0);
Assert.IsTrue(Compare(expected, actual));
}
