public virtual void Read(string peptideFileLocation, string spectrumFileLocation)
{
List <IPeptide> peptides = initializer.GetPeptides(peptideFileLocation);
spectrumRunner = initializer.GetSpectrumReader(spectrumFileLocation);
int lastScan = spectrumRunner.GetLastScan();
resultTable = new IGlycoPeptideScoreResultProduct[lastScan + 1];
glycanGenerator = new BruteForceNGlycanCreator(initializer.GetGlycanCreatorParameter());
glycans = glycanGenerator.Generate();
// data process
specProcessor = initializer.GetSpectrumProcessing();
monoRunner = new BinSearchMonoMassSpectrumRun();
// precursor
double preTol = initializer.GetParameter().GetMS1Tolereance();
precursorMatcher = new Y1PeptidesFilterPrecursorMatcher(
new GlycoPeptidePrecursorMatcher(peptides, glycans, preTol), peptides);
// search spectrum
double tol = initializer.GetParameter().GetMSMSTolereance();
searchWorker = new DPSearchSpectrumCID(tol);
//result
analyzer = new GeneralGlycoPeptideScoreResultAnalyzer();
}
public virtual void Read(string peptideFileLocation, string spectrumFileLocation)
{
List <IPeptide> peptides = initializer.GetPeptides(peptideFileLocation);
spectrumRunner = initializer.GetSpectrumReader(spectrumFileLocation);
int lastScan = spectrumRunner.GetLastScan();
resultTable = new IGlycoPeptideScoreResultProduct[lastScan + 1];
resultFDRTable = new IGlycoPeptideScoreResultProduct[lastScan + 1];
glycanGenerator = new AccumulatedMSBruteForceNGlycanCreator(initializer.GetGlycanCreatorParameter());
glycans = glycanGenerator.Generate();
// data process
specProcessor = initializer.GetSpectrumProcessing();
monoRunner = new BinSearchMonoMassSpectrumRun();
// precursor
double preTol = initializer.GetParameter().GetMS1Tolereance();
precursorMatcher = new Y1PeptidesFilterPrecursorMatcher(
new AccumulatedMSNGlycoPeptidePrecursorMatcher(peptides, glycans, preTol), peptides);
//precursorMatcher = new AccumulatedMSNGlycoPeptidePrecursorMatcher(peptides, glycans, preTol);
// search spectrum
double tol = initializer.GetParameter().GetMSMSTolereance();
searchWorker = new BinSearchSpectrumEThcD(tol);
(searchWorker as BinSearchSpectrumEThcD).SetAlphaValue(initializer.GetParameter().GetAlphaFactor());
(searchWorker as BinSearchSpectrumEThcD).SetBetaValue(initializer.GetParameter().GetBetaFactor());
//result
fdr = initializer.GetParameter().GetFDRlevel();
discover = new GeneralGlycoPeptideScoreResultFDR(fdr);
}
public ISpectrumSearchRun GetSpectrumReader(string file)
{
ISpectrumSearchRun specRunner = null;
string pext = Path.GetExtension(file);
switch (pext)
{
case ".raw":
specRunner = new ThermoRawSearchRunSpectrum();
specRunner.Run(file);
return(specRunner);
}
return(specRunner);
}
