// Read Configuration file
private void InitTest(ConfigFileReader reader)
{
// Read program variables
var config = reader.GetNodes("vars").First();
var actStr = config.Contents["activationmethod"].ToLower();
_noiseFiltration = Convert.ToDouble(config.Contents["noisefiltration"]);
_precursorCharge = Convert.ToInt32(config.Contents["precursorcharge"]);
_searchWidth = Convert.ToDouble(config.Contents["searchwidth"]);
_binWidth = Convert.ToDouble(config.Contents["binwidth"]);
// Read input and output file names
var fileInfo = reader.GetNodes("fileinfo").First();
_names = fileInfo.Contents["name"].Split(',');
_preTsv = fileInfo.Contents["tsvpath"];
_preRaw = fileInfo.Contents["rawpath"];
var outPathtemp = fileInfo.Contents["outpath"];
_outPre = outPathtemp;
var outFiletemp = fileInfo.Contents["outfile"];
_outFileName = _outPre + outFiletemp;
}
// Read Configuration file
private void InitTest(ConfigFileReader reader)
{
// Read program variables
var config = reader.GetNodes("vars").First();
_precursorCharge = Convert.ToInt32(config.Contents["precursorcharge"]);
var actStr = config.Contents["activationmethod"].ToLower();
_combineCharges = (config.Contents.ContainsKey("combinecharges") &&
config.Contents["combinecharges"].ToLower() == "true");
_useDecoy = (config.Contents.ContainsKey("usedecoy") &&
config.Contents["usedecoy"].ToLower() == "true");
_relativeIntensityThreshold = Convert.ToDouble(config.Contents["relativeintensitythreshold"]);
// Read ion data
var ionInfo = reader.GetNodes("ion").First();
int totalCharges = Convert.ToInt32(ionInfo.Contents["totalcharges"]);
var ionTypeStr = ionInfo.Contents["iontype"].Split(',');
var ions = new BaseIonType[ionTypeStr.Length];
for (int i = 0; i < ionTypeStr.Length; i++)
{
switch (ionTypeStr[i].ToLower())
{
case "a":
ions[i] = BaseIonType.A;
break;
case "b":
ions[i] = BaseIonType.B;
break;
case "c":
ions[i] = BaseIonType.C;
break;
case "x":
ions[i] = BaseIonType.X;
break;
case "y":
ions[i] = BaseIonType.Y;
break;
case "z":
ions[i] = BaseIonType.Z;
break;
}
}
var ionLossStr = ionInfo.Contents["losses"].Split(',');
var ionLosses = new NeutralLoss[ionLossStr.Length];
for (int i = 0; i < ionLossStr.Length; i++)
{
switch (ionLossStr[i].ToLower())
{
case "noloss":
ionLosses[i] = NeutralLoss.NoLoss;
break;
case "nh3":
ionLosses[i] = NeutralLoss.NH3;
break;
case "h2o":
ionLosses[i] = NeutralLoss.H2O;
break;
}
}
_ionTypeFactory = new IonTypeFactory(ions, ionLosses, totalCharges);
_ionTypes = _ionTypeFactory.GetAllKnownIonTypes().ToList();
var tempIonList = new List <IonType>();
if (ionInfo.Contents.ContainsKey("exclusions"))
{
var ionExclusions = ionInfo.Contents["exclusions"].Split(',');
tempIonList.AddRange(_ionTypes.Where(ionType => !ionExclusions.Contains(ionType.Name)));
_ionTypes = tempIonList;
}
// Read input and output file names
var fileInfo = reader.GetNodes("fileinfo").First();
_names = fileInfo.Contents["name"].Split(',');
_preTsv = fileInfo.Contents["tsvpath"];
_preRaw = fileInfo.Contents["rawpath"];
var outPathtemp = fileInfo.Contents["outpath"];
_outPre = outPathtemp;
var outFiletemp = fileInfo.Contents["outfile"];
_outFileName = _outPre + outFiletemp;
}
