public TrinucCalculation Calc()
{
TrinucCalculation tri = new TrinucCalculation();
TrinucArray trinucArray = new TrinucArray();
string seqTrinuc = string.Empty;
int trinucIndex = 0;
int firstFrame = 0;
int secondFrame = 0;
int thirdFrame = 0;
string seqCalc = seq + seq.Substring(0, 6);
for (int i = 0; i < seq.Length; i += 3)
{
seqTrinuc = seqCalc.Substring(i, 3);
trinucIndex = Array.FindIndex(trinucArray.trinuc, item => item == seqTrinuc);
tri.trinucleotides[trinucIndex].Trinuc1st += 1;
firstFrame += 1;
}
for (int i = 1; i < seq.Length + 1; i += 3)
{
seqTrinuc = seqCalc.Substring(i, 3);
trinucIndex = Array.FindIndex(trinucArray.trinuc, item => item == seqTrinuc);
tri.trinucleotides[trinucIndex].Trinuc2nd += 1;
secondFrame += 1;
}
for (int i = 2; i < seq.Length + 2; i += 3)
{
seqTrinuc = seqCalc.Substring(i, 3);
trinucIndex = Array.FindIndex(trinucArray.trinuc, item => item == seqTrinuc);
tri.trinucleotides[trinucIndex].Trinuc3rd += 1;
thirdFrame += 1;
}
foreach (var item in tri.trinucleotides)
{
item.TrinucFrq1st = (double)item.Trinuc1st / (double)firstFrame;
item.TrinucFrq2nd = (double)item.Trinuc2nd / (double)secondFrame;
item.TrinucFrq3rd = (double)item.Trinuc3rd / (double)thirdFrame;
}
foreach (var item in tri.trinucleotides)
{
item.TrinucDiff1st2nd = Math.Abs(item.TrinucFrq1st - item.TrinucFrq2nd);
item.TrinucDiff2nd3rd = Math.Abs(item.TrinucFrq2nd - item.TrinucFrq3rd);
item.TrinucDiff1st3rd = Math.Abs(item.TrinucFrq1st - item.TrinucFrq3rd);
}
foreach (var item in tri.trinucleotides)
{
item.TrinucDiffSum = item.TrinucDiff1st2nd + item.TrinucDiff2nd3rd + item.TrinucDiff1st3rd;
}
//TrinucOutput trinucOutput = new TrinucOutput(seq, trinucleotide);
//trinucOutput.TrinucOut();
return(tri);
}
public TrinucCalc()
{
trinucArray = new TrinucArray();
trinucleotideMatch = new List <TrinucleotideMatch>();
}