RNaseDigestion Member List

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

countInternalCleavageSites(const String &sequence) const	EnzymaticDigestion
countMissedCleavages_(const std::vector< int > &cleavage_positions, Size seq_start, Size seq_end) const	EnzymaticDigestion	protected
cuts_after_regexes_	RNaseDigestion	protected
cuts_before_regexes_	RNaseDigestion	protected
digest(const NASequence &rna, std::vector< NASequence > &output, Size min_length=0, Size max_length=0) const	RNaseDigestion
digest(IdentificationData &id_data, Size min_length=0, Size max_length=0) const	RNaseDigestion
digestAfterTokenize_(const std::vector< int > &fragment_positions, const StringView &sequence, std::vector< StringView > &output, Size min_length=0, Size max_length=-1) const	EnzymaticDigestion	protected
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) const	EnzymaticDigestion	protected
digestUnmodified(const StringView &sequence, std::vector< StringView > &output, Size min_length=1, Size max_length=0) const	EnzymaticDigestion
digestUnmodified(const StringView &sequence, std::vector< std::pair< Size, Size >> &output, Size min_length=1, Size max_length=0) const	EnzymaticDigestion
EnzymaticDigestion()	EnzymaticDigestion
EnzymaticDigestion(const EnzymaticDigestion &rhs)	EnzymaticDigestion
enzyme_	EnzymaticDigestion	protected
filterByMissedCleavages(const String &sequence, const std::function< bool(const Int)> &filter) const	EnzymaticDigestion
five_prime_gain_	RNaseDigestion	protected
getEnzymeName() const	EnzymaticDigestion
getFragmentPositions_(const NASequence &rna, Size min_length, Size max_length) const	RNaseDigestion	protected
getMissedCleavages() const	EnzymaticDigestion
getSpecificity() const	EnzymaticDigestion
getSpecificityByName(const String &name)	EnzymaticDigestion	static
isValidProduct(const String &protein, int pep_pos, int pep_length, bool ignore_missed_cleavages=true) const	EnzymaticDigestion
isValidProduct_(const String &sequence, int pos, int length, bool ignore_missed_cleavages, bool allow_nterm_protein_cleavage, bool allow_random_asp_pro_cleavage) const	EnzymaticDigestion	protected
missed_cleavages_	EnzymaticDigestion	protected
NamesOfSpecificity	EnzymaticDigestion	static
NoCleavage	EnzymaticDigestion	static
operator=(const EnzymaticDigestion &rhs)	EnzymaticDigestion
re_	EnzymaticDigestion	protected
setEnzyme(const DigestionEnzyme *enzyme) override	RNaseDigestion	virtual
setEnzyme(const String &name)	RNaseDigestion
setMissedCleavages(Size missed_cleavages)	EnzymaticDigestion
setSpecificity(Specificity spec)	EnzymaticDigestion
SIZE_OF_SPECIFICITY enum value	EnzymaticDigestion
SPEC_FULL enum value	EnzymaticDigestion
SPEC_NOCTERM enum value	EnzymaticDigestion
SPEC_NONE enum value	EnzymaticDigestion
SPEC_NONTERM enum value	EnzymaticDigestion
SPEC_SEMI enum value	EnzymaticDigestion
SPEC_UNKNOWN enum value	EnzymaticDigestion
Specificity enum name	EnzymaticDigestion
specificity_	EnzymaticDigestion	protected
three_prime_gain_	RNaseDigestion	protected
tokenize_(const String &sequence, int start=0, int end=-1) const	EnzymaticDigestion	protected
UnspecificCleavage	EnzymaticDigestion	static
~EnzymaticDigestion()	EnzymaticDigestion	virtual