25 #ifndef _DIGESTION_HPP_ 26 #define _DIGESTION_HPP_ 33 #include "boost/shared_ptr.hpp" 55 std::string::const_iterator end,
57 size_t missedCleavages,
58 bool NTerminusIsSpecific,
59 bool CTerminusIsSpecific,
60 std::string NTerminusPrefix =
"",
61 std::string CTerminusSuffix =
"");
65 size_t missedCleavages,
66 bool NTerminusIsSpecific,
67 bool CTerminusIsSpecific,
68 std::string NTerminusPrefix =
"",
69 std::string CTerminusSuffix =
"");
77 size_t offset()
const;
80 size_t missedCleavages()
const;
83 size_t specificTermini()
const;
86 bool NTerminusIsSpecific()
const;
89 bool CTerminusIsSpecific()
const;
92 std::string NTerminusPrefix()
const;
95 std::string CTerminusSuffix()
const;
139 Config(
int maximumMissedCleavages = 100000,
142 int minimumLength = 0,
143 int maximumLength = 100000,
144 Specificity minimumSpecificity = FullySpecific,
145 bool clipNTerminalMethionine =
true);
149 static const std::set<CVID>& getCleavageAgents();
152 static const std::vector<std::string>& getCleavageAgentNames();
156 static CVID getCleavageAgentByName(
const std::string& agentName);
160 static CVID getCleavageAgentByRegex(
const std::string& agentRegex);
164 static const std::string& getCleavageAgentRegex(CVID agentCvid);
168 static std::string disambiguateCleavageAgentRegex(
const std::string&
cleavageAgentRegex);
200 std::vector<DigestedPeptide> find_all(
const Peptide&
peptide)
const;
242 friend class Digestion::Impl;
245 boost::shared_ptr<Impl>
impl_;
253 friend class const_iterator::Impl;
262 #endif // _DIGESTION_HPP_
std::forward_iterator_tag iterator_category
bool NTerminusIsSpecific_
provides forward-only, read-only iteration to enumerate peptides
PWIZ_API_DECL proteome::Peptide peptide(const Peptide &peptide)
creates a proteome::Peptide from an identdata::Peptide
boost::shared_ptr< Impl > impl_
DigestedPeptide value_type
sets constraints for valid peptides produced by iterating the digestion
int maximumMissedCleavages
bool clipNTerminalMethionine
Specificity minimumSpecificity
PWIZ_API_DECL std::vector< CVID > cleavageAgents(const Enzymes &enzymes)
returns a list of cleavage agent CVIDs for an identdata::Enzymes instance
represents a peptide or polypeptide (a sequence of amino acids)
SemiSpecific
neither termini must match digestion motif(s)
std::string NTerminusPrefix_
PWIZ_API_DECL std::vector< std::string > cleavageAgentRegexes(const Enzymes &enzymes)
returns a list of regular expressions for an identdata::Enzymes instance
std::string CTerminusSuffix_
PWIZ_API_DECL Formula operator*(const Formula &a, int scalar)
bool CTerminusIsSpecific_
PWIZ_API_DECL bool operator==(const TruncatedLorentzianParameters &t, const TruncatedLorentzianParameters &u)
PWIZ_API_DECL std::string cleavageAgentRegex(const Enzyme &ez)
returns a regular expression for an identdata::Enzyme
PWIZ_API_DECL CVID cleavageAgent(const Enzyme &ez)
returns a cleavage agent CVID for an identdata::Enzyme
enumerates the peptides from proteolytic digestion of a polypeptide or protein;
PWIZ_API_DECL bool operator!=(const TruncatedLorentzianParameters &t, const TruncatedLorentzianParameters &u)
peptide subclass that contains extra metadata provided by digestion
boost::shared_ptr< Impl > impl_