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pwiz::proteome::Digestion Class Reference

enumerates the peptides from proteolytic digestion of a polypeptide or protein; More...

#include <Digestion.hpp>

List of all members.

Classes

struct  Config
 sets constraints for valid peptides produced by iterating the digestion More...
class  const_iterator
 provides forward-only, read-only iteration to enumerate peptides More...

Public Member Functions

 Digestion (const Peptide &polypeptide, CVID cleavageAgent, const Config &config=Config())
 specifies digestion occurs by a commonly used cleavage agent
 Digestion (const Peptide &polypeptide, const std::vector< CVID > &cleavageAgents, const Config &config=Config())
 specifies digestion occurs by a combination of commonly used cleavage agents
 Digestion (const Peptide &polypeptide, const boost::regex &cleavageAgentRegex, const Config &config=Config())
 specifies digestion occurs by a user-specified, zero-width Perl regular expression example: "(?<=K)" means "cleaves after K" example: "((?<=D))|((?=D))" means "cleaves before or after D" example: "(?=[DE])" means "cleaves before D or E" example: "(?<=[FYWLKR])(?!P)" means "cleaves after any single residue from FYWLKR except when it is followed by P"
 Digestion (const Peptide &polypeptide, const std::vector< boost::regex > &cleavageAgentRegexes, const Config &config=Config())
 specifies digestion occurs by a combination of user-specified, zero-width Perl regular expressions example: "(?<=K)" means "cleaves after K" example: "((?<=D))|((?=D))" means "cleaves before or after D" example: "(?=[DE])" means "cleaves before D or E" example: "(?<=[FYWLKR])(?!P)" means "cleaves after any single residue from FYWLKR except when it is followed by P"
std::vector< DigestedPeptidefind_all (const Peptide &peptide) const
 returns all instances of the given peptide in the polypeptide under digestion; note: the filters set in Digestion::Config are respected!
DigestedPeptide find_first (const Peptide &peptide, size_t offsetHint=0) const
 returns the first instance of the given peptide in the polypeptide under digestion; if offsetHint is provided, the search will begin at that offset; throws runtime_error if no instance of the peptide is found; note: the filters set in Digestion::Config are respected!
 ~Digestion ()
const_iterator begin () const
const_iterator end () const

Static Public Member Functions

static const std::set< CVID > & getCleavageAgents ()
 returns the set of predefined cleavage agents defined in the PSI-MS CV
static const std::vector
< std::string > & 
getCleavageAgentNames ()
 returns the names of the set of predefined cleavage agents defined in the PSI-MS CV
static CVID getCleavageAgentByName (const std::string &agentName)
 returns the cvid of the specified cleavage agent using a case-insensitive search, or CVID_Unknown if the agent is not found
static CVID getCleavageAgentByRegex (const std::string &agentRegex)
 returns the cvid of the specified cleavage agent looking it up by the Perl regular expression, or CVID_Unknown if the agent is not found (the regex pattern must match exactly)
static const std::string & getCleavageAgentRegex (CVID agentCvid)
 returns the official PSI Perl regular expression defining the places in a polypeptide or protein that the agent will cut.
static std::string disambiguateCleavageAgentRegex (const std::string &cleavageAgentRegex)
 returns a modified version of a cleavage agent regex where any ambiguous AA symbols (BJXZ) are augmented with their unambiguous counterparts (e.g.

Private Attributes

boost::shared_ptr< Impl > impl_

Friends

class const_iterator
class const_iterator::Impl

Detailed Description

enumerates the peptides from proteolytic digestion of a polypeptide or protein;

Definition at line 112 of file Digestion.hpp.


Constructor & Destructor Documentation

pwiz::proteome::Digestion::Digestion ( const Peptide polypeptide,
CVID  cleavageAgent,
const Config config = Config() 
)

specifies digestion occurs by a commonly used cleavage agent

pwiz::proteome::Digestion::Digestion ( const Peptide polypeptide,
const std::vector< CVID > &  cleavageAgents,
const Config config = Config() 
)

specifies digestion occurs by a combination of commonly used cleavage agents

pwiz::proteome::Digestion::Digestion ( const Peptide polypeptide,
const boost::regex &  cleavageAgentRegex,
const Config config = Config() 
)

specifies digestion occurs by a user-specified, zero-width Perl regular expression example: "(?<=K)" means "cleaves after K" example: "((?<=D))|((?=D))" means "cleaves before or after D" example: "(?=[DE])" means "cleaves before D or E" example: "(?<=[FYWLKR])(?!P)" means "cleaves after any single residue from FYWLKR except when it is followed by P"

pwiz::proteome::Digestion::Digestion ( const Peptide polypeptide,
const std::vector< boost::regex > &  cleavageAgentRegexes,
const Config config = Config() 
)

specifies digestion occurs by a combination of user-specified, zero-width Perl regular expressions example: "(?<=K)" means "cleaves after K" example: "((?<=D))|((?=D))" means "cleaves before or after D" example: "(?=[DE])" means "cleaves before D or E" example: "(?<=[FYWLKR])(?!P)" means "cleaves after any single residue from FYWLKR except when it is followed by P"

pwiz::proteome::Digestion::~Digestion ( )

Member Function Documentation

static const std::set<CVID>& pwiz::proteome::Digestion::getCleavageAgents ( )
static

returns the set of predefined cleavage agents defined in the PSI-MS CV

Referenced by testPepXMLSpecificity().

static const std::vector<std::string>& pwiz::proteome::Digestion::getCleavageAgentNames ( )
static

returns the names of the set of predefined cleavage agents defined in the PSI-MS CV

static CVID pwiz::proteome::Digestion::getCleavageAgentByName ( const std::string &  agentName)
static

returns the cvid of the specified cleavage agent using a case-insensitive search, or CVID_Unknown if the agent is not found

static CVID pwiz::proteome::Digestion::getCleavageAgentByRegex ( const std::string &  agentRegex)
static

returns the cvid of the specified cleavage agent looking it up by the Perl regular expression, or CVID_Unknown if the agent is not found (the regex pattern must match exactly)

static const std::string& pwiz::proteome::Digestion::getCleavageAgentRegex ( CVID  agentCvid)
static

returns the official PSI Perl regular expression defining the places in a polypeptide or protein that the agent will cut.

Referenced by testPepXMLSpecificity().

static std::string pwiz::proteome::Digestion::disambiguateCleavageAgentRegex ( const std::string &  cleavageAgentRegex)
static

returns a modified version of a cleavage agent regex where any ambiguous AA symbols (BJXZ) are augmented with their unambiguous counterparts (e.g.

B -> [BND])

std::vector<DigestedPeptide> pwiz::proteome::Digestion::find_all ( const Peptide peptide) const

returns all instances of the given peptide in the polypeptide under digestion; note: the filters set in Digestion::Config are respected!

Referenced by testFind().

DigestedPeptide pwiz::proteome::Digestion::find_first ( const Peptide peptide,
size_t  offsetHint = 0 
) const

returns the first instance of the given peptide in the polypeptide under digestion; if offsetHint is provided, the search will begin at that offset; throws runtime_error if no instance of the peptide is found; note: the filters set in Digestion::Config are respected!

Referenced by testFind().

const_iterator pwiz::proteome::Digestion::begin ( ) const
const_iterator pwiz::proteome::Digestion::end ( ) const

Friends And Related Function Documentation

friend class const_iterator
friend

Definition at line 253 of file Digestion.hpp.

friend class const_iterator::Impl
friend

Definition at line 254 of file Digestion.hpp.


Member Data Documentation

boost::shared_ptr<Impl> pwiz::proteome::Digestion::impl_
private

Definition at line 255 of file Digestion.hpp.


The documentation for this class was generated from the following file: