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;
}
public void SetPeptideCreator(IPeptideCreator creator)
{
this.pepRunner = creator;
}
public FastaSearchRunPeptides(IPeptideCreatorParameter parameter)
{
fastaReader = new GeneralFastaProteinCreator();
pepRunner = new GeneralPeptideCreator(parameter);
}
public FastaSearchRunPeptides()
{
fastaReader = new GeneralFastaProteinCreator();
pepRunner = new GeneralPeptideCreator();
}
public DoubleDigestionFastaSearchRunPeptides()
{
parameters = new List <IPeptideCreatorParameter>();
fastaReader = new GeneralFastaProteinCreator();
pepRunner = new DoubleDigestionPeptideCreator();
}