/// <summary>
/// The Thermo decon result filename is assumed to be the same as the spectra file name
/// </summary>
private static AnnotatedSpecies GetThermoDeconSpecies(string line, StreamReader reader, string fileName)
{
string[] items = line.Split(ItemDelimiter);
int numCharges = int.Parse(items[3]); // TODO: get this from header, not hardcoded
List <int> chargeList = new List <int>();
double mass = double.Parse(items[MonoisotopicMassColumn]);
string speciesName = items[SpeciesNameColumn] + " (" + mass.ToString("F1") + ")";
double apexRt = double.Parse(items[RetentionTimeColumn]);
string rtRange = items[FeatureRtStartColumn];
double rtStart = double.Parse(rtRange.Split('-')[0].Trim());
double rtEnd = double.Parse(rtRange.Split('-')[1].Trim());
for (int i = 0; i < numCharges + 1; i++)
{
var nextLine = reader.ReadLine();
var chargeLineSplit = nextLine.Split(ItemDelimiter);
if (chargeLineSplit[1].Trim().Equals("Charge State", StringComparison.OrdinalIgnoreCase))
{
continue;
}
chargeList.Add(int.Parse(chargeLineSplit[1]));
}
var deconFeature = new DeconvolutionFeature(mass, apexRt, rtStart, rtEnd, chargeList, fileName);
var species = new AnnotatedSpecies(deconFeature);
return(species);
}
private static AnnotatedSpecies GetFlashDeconvSpecies(string line)
{
string[] items = line.Split(ItemDelimiter);
string identifier = items[SpeciesNameColumn];
double mass = double.Parse(items[MonoisotopicMassColumn]);
int minChargeState = int.Parse(items[MinChargeColumn]);
int maxChargeState = int.Parse(items[MaxChargeColumn]);
var chargeList = Enumerable.Range(minChargeState, maxChargeState - minChargeState + 1).ToList();
double apexRt = double.Parse(items[RetentionTimeColumn]) / 60;
double rtStart = double.Parse(items[FeatureRtStartColumn]) / 60;
double rtEnd = double.Parse(items[FeatureRtEndColumn]) / 60;
string fileName = items[SpectraFileNameColumn];
var deconFeature = new DeconvolutionFeature(mass, apexRt, rtStart, rtEnd, chargeList, fileName);
var species = new AnnotatedSpecies(deconFeature);
return(species);
}
private static AnnotatedSpecies GetProteoformExplorerSpecies(string line, StreamReader reader)
{
line = line.Replace("\"", string.Empty);
string[] items = line.Split(ItemDelimiter);
string identifier = items[SpeciesNameColumn];
double mass = double.Parse(items[MonoisotopicMassColumn]);
int charge = int.Parse(items[ChargeColumn]);
double apexRt = double.Parse(items[RetentionTimeColumn]);
string fileName = items[SpectraFileNameColumn];
int scan = int.Parse(items[ScanNumberColumn]);
var peaks = items[PeaksListColumn].Split(',').Select(p => double.Parse(p)).ToList();
var annotEnvelope = new AnnotatedEnvelope(scan, apexRt, charge, peaks);
var deconFeature = new DeconvolutionFeature(mass, apexRt, apexRt, apexRt, new List <int> {
charge
}, fileName, new List <AnnotatedEnvelope> {
annotEnvelope
});
var species = new AnnotatedSpecies(deconFeature);
return(species);
}
public AnnotatedSpecies(DeconvolutionFeature deconvolutionFeature, Identification identification)
{
SpeciesLabel = identification.FullSequence;
Identification = identification;
DeconvolutionFeature = deconvolutionFeature;
}
public AnnotatedSpecies(DeconvolutionFeature deconvolutionFeature)
{
SpeciesLabel = deconvolutionFeature.MonoisotopicMass.ToString("F2");
DeconvolutionFeature = deconvolutionFeature;
}
