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 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 FDRSearchEThcDEngine(IProteinCreator proteinCreator,
IPeptideCreator peptideCreator,
IGlycanCreator glycanCreator,
ISpectrumFactory spectrumFactory,
ISpectrumProcessing spectrumProcessing,
IMonoMassSpectrumGetter monoMassSpectrumGetter,
IPrecursorMatcher precursorMatcher,
ISpectrumFilter spectrumFilter,
ISearchEThcD searchEThcDRunner,
IResults results,
IReportProducer reportProducer,
double pesudoMass = -526.7728) :
base(proteinCreator, peptideCreator, glycanCreator, spectrumFactory,
spectrumProcessing, monoMassSpectrumGetter, precursorMatcher, spectrumFilter, searchEThcDRunner, results, reportProducer)
{
this.pesudoMass = pesudoMass;
}
public GeneralSearchEThcDEngine(
IProteinCreator proteinCreator,
IPeptideCreator peptideCreator,
IGlycanCreator glycanCreator,
ISpectrumFactory spectrumFactory,
ISpectrumProcessing spectrumProcessing,
IMonoMassSpectrumGetter monoMassSpectrumGetter,
IPrecursorMatcher precursorMatcher,
ISpectrumFilter spectrumFilter,
ISearchEThcD searchEThcDRunner,
IResults results,
IReportProducer reportProducer
)
{
// protein
this.proteinCreator = proteinCreator;
// peptides
this.peptideCreator = peptideCreator;
// glycans
this.glycanCreator = glycanCreator;
// spectrum
this.spectrumFactory = spectrumFactory;
// spectrum processing
this.spectrumProcessing = spectrumProcessing;
this.monoMassSpectrumGetter = monoMassSpectrumGetter;
// glycopeptides
this.precursorMatcher = precursorMatcher;
this.spectrumFilter = spectrumFilter;
// search
this.searchEThcDRunner = searchEThcDRunner;
// result
this.results = results;
this.reportProducer = reportProducer;
}