public IDictionary <string, IList <int> > GetMatches(SequenceModel sequenceData, string[] searches, bool ignoreCase = false, int startIndex = 0)
{
var sequence = _sequenceProvider.Provide(sequenceData?.FileName, sequenceData?.Content)?.First();
_boyerMoore.IgnoreCase = ignoreCase;
_boyerMoore.StartIndex = startIndex;
return(_boyerMoore.FindMatch(sequence, searches));
}
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 MatchWildcardPatternMiddle()
{
ISequence sequence = new Sequence(DnaAlphabet.Instance, "AGCTAGGTAGCTCAAAAAABCD");
IPatternFinder patternFinder = new BoyerMoore();
IList <int> actual = patternFinder.FindMatch(sequence, "AGCTAGGTAGCTCA*BCD");
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));
}
