public void AddToMap(string protein, string peptide, string precursorCharge, string rt, FDRValue fdrValue)
{
this.FDRValueMap.Add($"{protein}-{peptide}-{rt}-{precursorCharge}", fdrValue);
}
public FDRFile(string filePath, double fdrCutOff)
{
this.FDRCutOff = fdrCutOff;
FDRValueMap = new Dictionary <string, FDRValue>();
TextReader reader = new StreamReader(filePath);
var csvReader = new CsvReader(reader, CultureInfo.CurrentCulture);
csvReader.Read();
csvReader.ReadHeader();
this.Header = csvReader.Context.HeaderRecord;
while (csvReader.Read())
{
var row = new FDRRow();
for (var index = 0; index < 7; index++)
{
switch (this.Header[index])
{
case "Protein":
row.Protein = csvReader.GetField(index);
break;
case "Peptide":
row.Peptide = csvReader.GetField(index);
break;
case "Label":
row.Label = csvReader.GetField(index);
break;
case "Precursor MZ":
row.PrecursorMZ = csvReader.GetField(index);
break;
case "Precursor Charge":
row.PrecursorCharge = csvReader.GetField(index);
break;
case "RT":
row.RT = csvReader.GetField(index);
break;
case "Decoy":
row.Decoy = csvReader.GetField(index) != "FALSE";
break;
default:
Console.WriteLine($"Unexpected column name: {this.Header[index]}");
break;
}
}
var values = new List <double>();
var valuesPass = new List <bool>();
var rowPass = false;
for (var index = 7; index < this.Header.Length; index++)
{
var value = Convert.ToDouble(csvReader.GetField(index));
values.Add(value);
if (value < this.FDRCutOff)
{
valuesPass.Add(true);
rowPass = true;
}
else
{
valuesPass.Add(false);
}
}
var samples = new FDRValue(values, row.Decoy, valuesPass, rowPass);
this.AddToMap(row.Protein, row.Peptide, row.PrecursorCharge, row.RT, samples);
//Console.WriteLine(csvReader.GetField(0));
}
reader.Close();
}
