private void Assembly()
{
profile.AddSequence(sequences[0], 0);
var lastSegment = 0;
var firstSegment = 0;
AssemblyInit(sequences[0]);
int change = 0; // 0 - there was align, 1 - there wasn't align on last, 2 - there wasn't align at all
while (true)
{
int seq;
if (change == 0)
{
seq = lastSegment;
}
else if (change == 1)
{
seq = firstSegment;
}
else
{
break;
}
var list = GetProbablyBest(seq);
if (list.Count == 0)
{
if (change == 0)
{
seq = firstSegment;
list = GetProbablyBest(seq);
if (list.Count == 0)
{
break;
}
}
else
{
break;
}
}
var wasAlign = false;
foreach (var probSeq in list)
{
var sm = new SmithWaterman(profile, sequences[probSeq]);
sm.Calculate();
var alignment = sm.GetBest();
AssemblyCandidate(sequences[probSeq], alignment.First.Value.Item1 - alignment.First.Value.Item2);
if (IsGoodAlignment(sequences[probSeq], alignment))
{
var side = AddSequence(sequences[probSeq], alignment);
if ((side & 1) != 0)
{
firstSegment = probSeq;
}
else if ((side & 2) != 0)
{
lastSegment = probSeq;
change = 0;
}
RemoveSeq(probSeq);
//AssemblyGoodAlignmentAdded(profile);
AssemblyGoodAlignment();
wasAlign = true;
break;
}
}
if (!wasAlign)
{
change++;
}
}
AssemblyEnd();
}
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));
}
}