public void SimpleMatchTestStartLater()
{
var match = ProteinMatcher.Match("XAAAA", 1, "A2A", 1);
Assert.IsTrue(match.HasMatch, "Has Match");
Assert.AreEqual(0, match.Distance, "Distance is 0");
}
public List <ProteinMatch> FindInSequence(ProteinSequenceWithFundaments sequence, int fundamentIndex, string expression, int maximumDistance)
{
var result = new List <ProteinMatch>();
var minimalDistance = maximumDistance;
var startFrom = 0;
//if (fundamentIndex > 1)
//{
// var lastFundament = sequence[fundamentIndex - 1];
// if (lastFundament != null)
// {
// startFrom = lastFundament.Index + lastFundament.Length;
// }
//}
for (var i = startFrom; i < sequence.ProteinSequence.Sequence.Length; i++)
{
var match = ProteinMatcher.Match(sequence.ProteinSequence.Sequence, i, expression, maximumDistance);
if (!match.HasMatch || match.Distance >= minimalDistance)
{
continue;
}
if (match.Distance < minimalDistance)
{
result.Clear();
minimalDistance = match.Distance;
}
if (match.Distance == minimalDistance)
{
sequence[fundamentIndex] = match;
}
}
return(result);
}
public ProteinMatcherTests()
{
_matcher = new ProteinMatcher();
}
