// private const string DebugFileName = @"C:\Users\wilk011\Documents\DataFiles\TestFolder\debug_HCD_QCShew_Precursor.txt";
private IEnumerable<SpectrumMatch> InitTest()
{
var ionTypeFactory = new IonTypeFactory(_baseIons, _neutralLosses, MaxCharge);
_ionTypes = ionTypeFactory.GetAllKnownIonTypes().ToList();
var lcms = new LazyLcMsRun(RawFile, NoiseFiltration, NoiseFiltration);
var spectrumMatches = (new SpectrumMatchList(lcms, TsvFile, DataFileFormat.IcBottomUp));
return spectrumMatches;
}
public PrecursorFilter(PrecursorOffsets offsets, Tolerance tolerance)
{
_offsets = offsets;
_tolerance = tolerance;
var maxCharge = offsets.Charge;
BaseIonType[] baseIons = { BaseIonType.Y };
NeutralLoss[] neutralLosses = { NeutralLoss.NoLoss };
var ionTypeFactory = new IonTypeFactory(baseIons, neutralLosses, maxCharge);
_precursorIonTypes = ionTypeFactory.GetAllKnownIonTypes().ToList();
}
public PrecursorOffsetFrequencyTable(double searchWidth, int charge = 1, double binWidth = 1.005)
{
_offsetCounts = new Histogram<double>();
_searchWidth = searchWidth;
_binWidth = binWidth;
Charge = charge;
Total = 0;
GenerateEdges();
BaseIonType[] baseIons = { BaseIonType.Y };
NeutralLoss[] neutralLosses = { NeutralLoss.NoLoss };
var ionTypeFactory = new IonTypeFactory(baseIons, neutralLosses, charge);
_precursorIonTypes = ionTypeFactory.GetAllKnownIonTypes().ToList();
}
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 = _defaultToleranceTh;
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 = _defaultToleranceTh;
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"];
}
public void TestPpmErrorCalculation(string seqText, string rawFilePath, int scanNum)
{
var methodName = MethodBase.GetCurrentMethod().Name;
ShowStarting(methodName, rawFilePath);
var tolerance = new Tolerance(10, ToleranceUnit.Ppm);
const int maxCharge = 15;
const double relIntThres = 0.1;
if (!File.Exists(rawFilePath))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFilePath);
}
// init
var sequence = Sequence.GetSequenceFromMsGfPlusPeptideStr(seqText);
var lcms = PbfLcMsRun.GetLcMsRun(rawFilePath);
var spectrum = lcms.GetSpectrum(scanNum);
var ionTypeFactory = new IonTypeFactory(maxCharge);
var iontypes = ionTypeFactory.GetAllKnownIonTypes();
foreach (var iontype in iontypes)
{
var ion = iontype.GetIon(sequence.Composition);
var obsPeaks = spectrum.GetAllIsotopePeaks(ion, tolerance, relIntThres);
if (obsPeaks == null) continue;
var isotopes = ion.GetIsotopes(relIntThres).ToArray();
for (int i = 0; i < isotopes.Length; i++)
{
if (obsPeaks[i] == null) continue;
var obsMz = obsPeaks[i].Mz;
var theoMz = ion.GetIsotopeMz(isotopes[i].Index);
var ppmError = (obsMz - theoMz)/theoMz*1e6;
Assert.True(ppmError <= tolerance.GetValue());
}
}
}
public void TestIonTypeGeneration()
{
var methodName = MethodBase.GetCurrentMethod().Name;
ShowStarting(methodName);
var ionTypeFactory = new IonTypeFactory();
int index = 0;
foreach (var ionType in ionTypeFactory.GetAllKnownIonTypes())
{
Console.WriteLine(++index + ": " + ionType);
}
var yIon = ionTypeFactory.GetIonType("y2-H2O");
Console.WriteLine(yIon.GetMz(0));
}
public void TestGetProductIons()
{
var methodName = MethodBase.GetCurrentMethod().Name;
ShowStarting(methodName);
var aaSet = new AminoAcidSet(Modification.Carbamidomethylation);
var sequence = new Sequence("CCAADDKEACFAVEGPK", aaSet);
var ionTypeFactory = new IonTypeFactory(
new[] {BaseIonType.B, BaseIonType.Y},
new[] {NeutralLoss.NoLoss, NeutralLoss.H2O},
maxCharge: 2);
Console.WriteLine("Precursor Ion: {0}\t{1}", sequence.GetPrecursorIon(2).Composition, sequence.GetPrecursorIon(2).GetMonoIsotopicMz());
Console.WriteLine("Product ions: ");
var productIons = sequence.GetProductIons(ionTypeFactory.GetAllKnownIonTypes());
foreach (var theoIon in productIons)
{
var ionTypeAndIndex = theoIon.Key;
var ionType = ionTypeAndIndex.Item1;
var index = ionTypeAndIndex.Item2;
var ion = theoIon.Value;
Console.WriteLine("{0}\t{1}\t{2}\t{3}\t{4}", ionType.Name, index, ion.Composition, ion.Charge, ion.GetMonoIsotopicMz());
}
}
// 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;
}
