public gooneJensType getGooneType(ISequence seq1, ISequence seq2)
{
try
{
gooneJensType gt = gooneJensType.unKnown;
dnaSequenceUtil dsc = new dnaSequenceUtil();
string[] seq1ID = dsc.getAbbrID(seq1).Split('_');
string[] seq2ID = dsc.getAbbrID(seq2).Split('_');
if (seq1ID.Count() == 3 && seq2ID.Count() == 3)
{
if (seq1ID[1] == seq2ID[1])
{
if (seq1ID[2] == seq2ID[2])
{
gt = gooneJensType.daroon_goone;
}
else
{
gt = gooneJensType.bein_goone;
}
}
else
{
gt = gooneJensType.bein_jens;
}
}
return(gt);
}
catch (Exception ex)
{
throw ex;
}
}
public double calcK2PDistance(ISequence seq1, ISequence seq2)
{
try
{
double dist = 0;
dnaSequenceUtil dsuc = new dnaSequenceUtil();
double min = dsuc.findMinSequenceLength(new List <ISequence>()
{
seq1, seq2
});
double transitionCount = 0, transversionCount = 0;
for (int i = 0; i < min; i++)
{
if (((char)seq1[i] == 'A' && (char)seq2[i] == 'G') || ((char)seq1[i] == 'C' && (char)seq2[i] == 'T') || ((char)seq1[i] == 'G' && (char)seq2[i] == 'A') || ((char)seq1[i] == 'T' && (char)seq2[i] == 'C'))
{
transitionCount++;
}
if (((char)seq1[i] == 'A' && (char)seq2[i] == 'C') || ((char)seq1[i] == 'G' && (char)seq2[i] == 'T') || ((char)seq1[i] == 'A' && (char)seq2[i] == 'T') || ((char)seq1[i] == 'G' && (char)seq2[i] == 'C') ||
((char)seq1[i] == 'C' && (char)seq2[i] == 'A') || ((char)seq1[i] == 'T' && (char)seq2[i] == 'G') || ((char)seq1[i] == 'T' && (char)seq2[i] == 'A') || ((char)seq1[i] == 'C' && (char)seq2[i] == 'G'))
{
transversionCount++;
}
}
double P = (transitionCount / min);
double Q = (transversionCount / min);
dist = Convert.ToDouble((1F / 2F) * (Math.Log(Convert.ToDouble(1 / (1 - 2 * P - Q)))) + (1F / 4F) * (Math.Log(Convert.ToDouble(1 / (1 - 2 * Q)))));
return(dist);
}
catch (Exception ex)
{
throw ex;
}
}
