/// <summary>
/// Reads information returned from query and stores it as a protein level SNP
/// </summary>
/// <param name="curRow"></param>
/// <param name="function"></param>
/// <param name="snplist"></param>
public void ProcessSequenceChangeResult(DataRow curRow, string function, List <Snp> snplist)
{
Snp result = new Snp();
result.LoadData(curRow);
if (function == "41")
{
result.ModifiedPeptideString = "Stop-Gain";
}
else if (function == "43")
{
result.ModifiedPeptideString = "Stop-Loss";
}
else if (function == "44")
{
result.ModifiedPeptideString = "Frameshift";
}
else if (function == "45")
{
result.ModifiedPeptideString = "CDS-Indel";
}
else
{
result.ModifiedPeptideString = "Unknown";
}
if (result.MinorAlleleFrequency != -1)
{
snplist.Add(result);
}
}
/// <summary>
/// Reads information returned from query and stores it in the peptide it corresponds to
/// </summary>
/// <param name="curRow"></param>
/// <param name="plist"></param>
public void ProcessMissenseResult(DataRow curRow, List <Peptide> plist)
{
//Find the SNP's position...
int pos = DbCInt(curRow["aa_pos"]);
foreach (Peptide pep in plist)
{
//...see if it lies within a peptide in our list...
if (pos > pep.IndexStart && pos < pep.IndexStop)
{
//...then make a Snp object for it...
Snp result = new Snp();
result.LoadData(curRow);
//...and add that object to the Snp List for that peptide
pep.Snps.Add(result);
pep.FoundVariantInQuery = true;
}
}
}