public ProteinHoarder(IEnumerable<CsvFile> csvFiles,
string fastaFile,
string outputDirectory,
int minPeptidesPerGroup = 1,
int maxMissedCleavages = 3,
double maxFDR = 1,
AnnotationType annotationType = AnnotationType.None,
bool useConservativePScore = true,
bool useQuant = false,
bool useMedian = false,
bool duplexQuantitation = false,
bool useNoiseBandCap = false,
HashSet<Modification> modstoignore = null,
bool filterquantInterference = true,
double quantInterferenceCutoff = 0.25,
bool includeUnfilteredResults = false,
bool ignorePeptideWithMissingData = false,
bool semiDigestion = false,
bool proteinPerMinute = false,
bool sequenceCoverageMap = false)
{
CsvFiles = new List<CsvFile>(csvFiles);
FastaFile = fastaFile;
OutputDirectory = outputDirectory;
MaxMissedCleavages = maxMissedCleavages;
MaxFdr = maxFDR;
MinPeptidesPerGroup = minPeptidesPerGroup;
AnnotationType = annotationType;
UseConservativePScore = useConservativePScore;
UseQuant = useQuant;
UseMedianForQuantitation = useMedian;
DuplexQuantitation = duplexQuantitation;
UseOnlyCompleteSets = useNoiseBandCap;
Quantitation.UseMedian = useMedian;
ModificationsToIgnore = modstoignore;
FilterQuantInterference = filterquantInterference;
QuantInterferenceCutoff = quantInterferenceCutoff;
IncludeNonFilteredResults = includeUnfilteredResults;
IgnorePeptideWithMissingData = ignorePeptideWithMissingData;
SemiDigestion = semiDigestion;
ProteinsPerMinute = proteinPerMinute;
SequenceCoverageMap = sequenceCoverageMap;
}