/// <summary>
/// Get IonType from IonTypeFactory.
/// </summary>
/// <param name="baseIonType">Base ion type of ion type to get.</param>
/// <param name="neutralLoss">Neutral loss of ion type to get.</param>
/// <param name="charge">Charge of ion type to get</param>
/// <returns>IonType with the given base ion type, neutral loss, and charge.</returns>
public IonType GetIonType(BaseIonType baseIonType, NeutralLoss neutralLoss, int charge)
{
var chargeStr = charge.ToString(CultureInfo.InvariantCulture);
if (charge == 1)
{
chargeStr = string.Empty;
}
var name = baseIonType.Symbol + chargeStr + neutralLoss.Name;
return(IonTypeFactory.GetIonType(name));
}
/// <summary>
/// Get an product ion type from an ion type factory.
/// </summary>
/// <param name="ionTypeFactory">IonTypeFactory for obtaining ion information (mass, charge, etc.)</param>
/// <param name="baseIonType">The base ion type.</param>
/// <param name="neutralLoss">The neutral loss of ion type.</param>
/// <param name="charge">The charge of product ion type.</param>
/// <returns>Ion type with given base ion type, neutral loss, and charge.</returns>
public static IonType GetIonType(
IonTypeFactory ionTypeFactory,
BaseIonType baseIonType,
NeutralLoss neutralLoss,
int charge)
{
var chargeStr = string.Empty;
if (charge > 1)
{
chargeStr = charge.ToString(CultureInfo.InvariantCulture);
}
var name = string.Format("{0}{1}{2}", baseIonType.Symbol, chargeStr, neutralLoss.Name);
return(ionTypeFactory.GetIonType(name));
}
public void ReadConfigurationFile(string configurationFile)
{
var reader = new ConfigFileReader(configurationFile);
// Read program variables
var config = reader.GetNodes("vars").First();
PrecursorCharge = Convert.ToInt32(config.Contents["precursorcharge"]);
PrecursorOffsetThreshold = Convert.ToDouble(config.Contents["precursoroffsetthreshold"]);
WindowWidth = Convert.ToInt32(config.Contents["searchwidth"]);
PrecursorOffsetWidth = Convert.ToInt32(config.Contents["precursoroffsetwidth"]);
RetentionCount = Convert.ToInt32(config.Contents["retentioncount"]);
RelativeIntensityThreshold = Convert.ToDouble(config.Contents["relativeintensitythreshold"]);
SelectedIonThreshold = Convert.ToDouble(config.Contents["selectedionthreshold"]);
MassBinSize = Convert.ToInt32(config.Contents["massbinsize"]);
var actStr = config.Contents["activationmethod"].ToLower();
switch (actStr)
{
case "hcd":
ActivationMethod = ActivationMethod.HCD;
Tolerance = _defaultTolerancePpm;
break;
case "cid":
ActivationMethod = ActivationMethod.CID;
Tolerance = _defaultToleranceMz;
break;
case "etd":
ActivationMethod = ActivationMethod.ETD;
Tolerance = _defaultTolerancePpm;
break;
default:
throw new FormatException("Invalid Activation Method.");
}
var acqStr = config.Contents["acquisitionmethod"].ToLower();
switch (acqStr)
{
case "dia":
AcquisitionMethod = AcquisitionMethod.Dia;
break;
case "dda":
AcquisitionMethod = AcquisitionMethod.Dda;
break;
default:
throw new FormatException("Invalid Acquisition Method.");
}
MassErrorTolerance = _defaultToleranceMz;
MaxRanks = Convert.ToInt32(config.Contents["maxranks"]);
var smoothingRanksStr = config.Contents["smoothingranks"].Split(',');
SmoothingRanks = new int[smoothingRanksStr.Length];
var smoothingWindowSizeStr = config.Contents["smoothingwindowsize"].Split(',');
SmoothingWindowSize = new int[smoothingWindowSizeStr.Length];
if (SmoothingRanks.Length != SmoothingWindowSize.Length)
{
throw new ArgumentException("SmoothingRanks and SmoothingWindowSize unequal lengths.");
}
for (int i = 0; i < SmoothingRanks.Length; i++)
{
if (smoothingRanksStr[i] == "Max")
{
SmoothingRanks[i] = Int32.MaxValue;
}
else
{
SmoothingRanks[i] = Convert.ToInt32(smoothingRanksStr[i]);
}
SmoothingWindowSize[i] = Convert.ToInt32(smoothingWindowSizeStr[i]);
}
// 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().ToArray();
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.ToArray();
}
// Read input and output file names
var fileInfo = reader.GetNodes("fileinfo").First();
DataSets = fileInfo.Contents["name"].Split(',');
var dataFormat = fileInfo.Contents["format"];
switch (dataFormat)
{
case "mgf":
DataFormat = DataFileFormat.Mgf;
break;
case "icbottomup":
DataFormat = DataFileFormat.IcBottomUp;
break;
case "dia":
DataFormat = DataFileFormat.Dia;
break;
default:
throw new FormatException("Invalid Acquisition Method.");
}
TsvPath = fileInfo.Contents["tsvpath"];
DataPath = fileInfo.Contents["datapath"];
var outPathtemp = fileInfo.Contents["outpath"];
OutputPath = outPathtemp;
OutputFileName = OutputPath + fileInfo.Contents["outputfile"];
}
// 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;
}
