/// <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);
species.DeconvolutionFeature = deconFeature;
return(species);
}
private static AnnotatedSpecies GetTdPortalSpecies(string line)
{
string[] items = line.Split(ItemDelimiter);
string baseSequence = items[SpeciesNameColumn];
string modSequence = items[SpeciesNameColumn];
double mass = double.Parse(items[MonoisotopicMassColumn]);
// TD portal does not report precursor charge
var id = new Identification(baseSequence, modSequence, mass, -1);
var species = new AnnotatedSpecies(id);
return(species);
}
private static AnnotatedSpecies GetMetaMorpheusSpecies(string line)
{
string[] items = line.Split(ItemDelimiter);
string baseSequence = items[SpeciesNameColumn];
string modSequence = items[SpeciesNameColumn];
double mass = double.Parse(items[MonoisotopicMassColumn]);
int charge = int.Parse(items[ChargeColumn]);
var id = new Identification(baseSequence, modSequence, mass, charge);
var species = new AnnotatedSpecies(id);
species.Identification = id;
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);
species.DeconvolutionFeature = deconFeature;
return(species);
}
public static List <AnnotatedSpecies> ReadSpeciesFromFile(string filePath, out List <string> errors)
{
var fileType = InputSourceType.Unknown;
errors = new List <string>();
var listOfSpecies = new List <AnnotatedSpecies>();
// open the file to read
StreamReader reader;
try
{
reader = new StreamReader(filePath);
}
catch (Exception e)
{
errors.Add("Error reading file " + filePath + "\n" + e.Message);
return(listOfSpecies);
}
// read the file
int lineNum = 0;
while (reader.Peek() > 0)
{
string line = reader.ReadLine();
lineNum++;
// determine file type from the header
if (lineNum == 1)
{
fileType = GetFileTypeFromHeader(line);
if (fileType == InputSourceType.Unknown)
{
errors.Add("Could not interpret header labels from file: " + filePath);
return(listOfSpecies);
}
continue;
}
// read the line + create the species object
AnnotatedSpecies species = null;
switch (fileType)
{
case InputSourceType.MetaMorpheus:
species = GetMetaMorpheusSpecies(line);
break;
case InputSourceType.FlashDeconv:
species = GetFlashDeconvSpecies(line);
break;
case InputSourceType.TDPortal:
species = GetTdPortalSpecies(line);
break;
case InputSourceType.ThermoDecon:
species = GetThermoDeconSpecies(line, reader, filePath);
break;
}
// add the item to the list
if (species != null)
{
listOfSpecies.Add(species);
}
}
return(listOfSpecies);
}
