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EnzymaticDigestion Member List

This is the complete list of members for EnzymaticDigestion, including all inherited members.

countInternalCleavageSites(const String &sequence) constEnzymaticDigestion
countMissedCleavages_(const std::vector< int > &cleavage_positions, Size seq_start, Size seq_end) constEnzymaticDigestionprotected
digestAfterTokenize_(const std::vector< int > &fragment_positions, const StringView &sequence, std::vector< StringView > &output, Size min_length=0, Size max_length=-1) constEnzymaticDigestionprotected
digestAfterTokenize_(const std::vector< int > &fragment_positions, const StringView &sequence, std::vector< std::pair< Size, Size >> &output, Size min_length=0, Size max_length=-1) constEnzymaticDigestionprotected
digestUnmodified(const StringView &sequence, std::vector< StringView > &output, Size min_length=1, Size max_length=0) constEnzymaticDigestion
digestUnmodified(const StringView &sequence, std::vector< std::pair< Size, Size >> &output, Size min_length=1, Size max_length=0) constEnzymaticDigestion
EnzymaticDigestion()EnzymaticDigestion
EnzymaticDigestion(const EnzymaticDigestion &rhs)EnzymaticDigestion
enzyme_EnzymaticDigestionprotected
filterByMissedCleavages(const String &sequence, const std::function< bool(const Int)> &filter) constEnzymaticDigestion
getEnzymeName() constEnzymaticDigestion
getMissedCleavages() constEnzymaticDigestion
getSpecificity() constEnzymaticDigestion
getSpecificityByName(const String &name)EnzymaticDigestionstatic
isValidProduct(const String &protein, int pep_pos, int pep_length, bool ignore_missed_cleavages=true) constEnzymaticDigestion
isValidProduct_(const String &sequence, int pos, int length, bool ignore_missed_cleavages, bool allow_nterm_protein_cleavage, bool allow_random_asp_pro_cleavage) constEnzymaticDigestionprotected
missed_cleavages_EnzymaticDigestionprotected
NamesOfSpecificityEnzymaticDigestionstatic
NoCleavageEnzymaticDigestionstatic
operator=(const EnzymaticDigestion &rhs)EnzymaticDigestion
re_EnzymaticDigestionprotected
setEnzyme(const DigestionEnzyme *enzyme)EnzymaticDigestionvirtual
setMissedCleavages(Size missed_cleavages)EnzymaticDigestion
setSpecificity(Specificity spec)EnzymaticDigestion
SIZE_OF_SPECIFICITY enum valueEnzymaticDigestion
SPEC_FULL enum valueEnzymaticDigestion
SPEC_NOCTERM enum valueEnzymaticDigestion
SPEC_NONE enum valueEnzymaticDigestion
SPEC_NONTERM enum valueEnzymaticDigestion
SPEC_SEMI enum valueEnzymaticDigestion
SPEC_UNKNOWN enum valueEnzymaticDigestion
Specificity enum nameEnzymaticDigestion
specificity_EnzymaticDigestionprotected
tokenize_(const String &sequence, int start=0, int end=-1) constEnzymaticDigestionprotected
UnspecificCleavageEnzymaticDigestionstatic
~EnzymaticDigestion()EnzymaticDigestionvirtual