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 pairwisedDNA(ISequence _seq1, ISequence _seq2)
{
seq1 = _seq1;
seq2 = _seq2;
k2pDistance = calcK2PDistance(seq1, seq2);
gType = getGooneType(seq1, seq2);
}
public int getFrequency(List <List <pairwisedDNA> > pairwisedDnaMatrix, gooneJensType gt, double min = -1, double max = -1)
{
try
{
int freq = 0;
for (int i = 0; i < pairwisedDnaMatrix.Count; i++)
{
for (int j = 0; j < pairwisedDnaMatrix.Count; j++)
{
if (min != -1 && max != -1)
{
if ((pairwisedDnaMatrix[i][j].k2pDistance > min) && (pairwisedDnaMatrix[i][j].k2pDistance <= max) && pairwisedDnaMatrix[i][j].gType == gt)
{
freq++;
}
}
else if (min != -1 && max == -1)
{
if ((pairwisedDnaMatrix[i][j].k2pDistance <= min) && pairwisedDnaMatrix[i][j].gType == gt)
{
freq++;
}
}
else if (min == -1 && max != -1)
{
if ((pairwisedDnaMatrix[i][j].k2pDistance > max) && pairwisedDnaMatrix[i][j].gType == gt)
{
freq++;
}
}
}
}
return(freq);
}
catch (Exception ex)
{
throw ex;
}
}
public List <pairwisedDNAGraph> createDNAGraph(List <List <pairwisedDNA> > pairwisedDnaMatrix, gooneJensType gt, double intervals = 10)
{
try
{
List <pairwisedDNAGraph> graphValues = new List <pairwisedDNAGraph>();
double maxXValue = getMaxValueInMatrix(pairwisedDnaMatrix);
double minValue = getMinValueInMatrix(pairwisedDnaMatrix);
double difference = maxXValue - minValue;
string xLabel = "";
double yValue = 0;
double xValue = 0, xValue_left = 0, xValue_right = 0;
graphValues.Add(new pairwisedDNAGraph(0, "0", 0, 0, 0));
if (intervals != -1)
{
for (double i = minValue; i < intervals; i++)
{
if (i == 0)
{
xLabel = " <= " + Math.Round(minValue + (difference / intervals), 6);
xValue = Math.Round(minValue + (difference / intervals), 6);
xValue_right = Math.Round(minValue + (difference / intervals), 6);
yValue = getFrequency(pairwisedDnaMatrix, gt, (maxXValue / intervals), -1);
}
else if (i == intervals - 1)
{
xLabel = " > " + Math.Round(minValue + i * (difference / intervals), 6);
xValue = Math.Round(minValue + i * (difference / intervals), 6);
xValue_left = Math.Round(minValue + i * (difference / intervals), 6);
yValue = getFrequency(pairwisedDnaMatrix, gt, -1, i * (maxXValue / intervals));
}
else
{
xLabel = " ( " + Math.Round(minValue + i * (difference / intervals), 6) + " - " + Math.Round(minValue + (i + 1) * (difference / intervals), 6) + " ] ";
xValue = Math.Round((minValue + i * (difference / intervals) + minValue + (i + 1) * (difference / intervals)) / 2, 6);
xValue_left = Math.Round(minValue + i * (difference / intervals), 6);
xValue_right = Math.Round(minValue + (i + 1) * (difference / intervals), 6);
yValue = getFrequency(pairwisedDnaMatrix, gt, (minValue + i * (difference / intervals)), minValue + (i + 1) * (difference / intervals));
}
graphValues.Add(new pairwisedDNAGraph(xValue, xLabel, yValue, xValue_left, xValue_right));
}
}
else
{
}
return(graphValues);
}
catch (Exception ex)
{
throw ex;
}
}
