public Tigr(int merLength, int maxOverhang, int minOverlap, float minSimilarity, string[] sequences)
{
this.sequences = sequences;
this.merLength = merLength;
this.maxOverhang = maxOverhang;
this.minOverlap = minOverlap;
this.minSimilarity = minSimilarity;
profile = new Profile();
}
public SmithWaterman(Profile profile, string sequence)
{
MatchScore = 2;
MismatchScore = -1;
InsertionScore = -2;
DeletionScore = -2;
this.profile = profile;
this.sequence = sequence;
}
public static void AssemblyGoodAlignmentAdded(Profile profile)
{
Console.WriteLine(string.Format("AssemblyGoodAlignmentAdded: \n{0}", profile));
for (var c = 0; c < profile.Length; ++c)
{
Console.Write(profile[c]);
}
Console.WriteLine();
//Console.ReadKey();
}
public static void SM()
{
var sequence = "AC TGTTTT";
var profile = new Profile();
profile.AddSequence("GGGGACTG", 0);
var sm = new SmithWaterman(profile, sequence);
sm.InsertionScore = -2;
sm.DeletionScore = -2;
sm.MismatchScore = -1;
sm.MatchScore = 2;
sm.Calculate();
sm.PrintResult();
var seq = sm.GetBest();
foreach (var i in seq)
{
Console.Write(string.Format("({0},{1}) ", i.Item1, i.Item2));
}
}
public static void ProfileTest()
{
var profile = new Profile();
while (true)
{
var sequence = Console.ReadLine();
var begin = int.Parse(Console.ReadLine());
profile.AddSequence(sequence, begin);
Console.WriteLine(profile);
}
}