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...
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class | const_iterator |
| provides forward-only, read-only iteration to enumerate peptides More...
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Public Member Functions |
| Digestion (const Peptide &polypeptide, CVID cleavageAgent, const Config &config=Config()) |
| specifies digestion occurs by a commonly used cleavage agent
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| Digestion (const Peptide &polypeptide, const std::vector< CVID > &cleavageAgents, const Config &config=Config()) |
| specifies digestion occurs by a combination of commonly used cleavage agents
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| 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"
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| 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"
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std::vector< DigestedPeptide > | 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!
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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!
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| ~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
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static const std::vector
< std::string > & | getCleavageAgentNames () |
| returns the names of the set of predefined cleavage agents defined in the PSI-MS CV
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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
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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)
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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.
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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.
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Private Attributes |
boost::shared_ptr< Impl > | 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 |
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const Peptide & |
polypeptide, |
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CVID |
cleavageAgent, |
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const Config & |
config = Config() |
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specifies digestion occurs by a commonly used cleavage agent
pwiz::proteome::Digestion::Digestion |
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const Peptide & |
polypeptide, |
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const std::vector< CVID > & |
cleavageAgents, |
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const Config & |
config = Config() |
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specifies digestion occurs by a combination of commonly used cleavage agents
pwiz::proteome::Digestion::Digestion |
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const Peptide & |
polypeptide, |
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const boost::regex & |
cleavageAgentRegex, |
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const Config & |
config = Config() |
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) |
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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 |
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const Peptide & |
polypeptide, |
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const std::vector< boost::regex > & |
cleavageAgentRegexes, |
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const Config & |
config = Config() |
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) |
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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 |
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Member Function Documentation
static const std::set<CVID>& pwiz::proteome::Digestion::getCleavageAgents |
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static |
static const std::vector<std::string>& pwiz::proteome::Digestion::getCleavageAgentNames |
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returns the names of the set of predefined cleavage agents defined in the PSI-MS CV
static CVID pwiz::proteome::Digestion::getCleavageAgentByName |
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const std::string & |
agentName | ) |
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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 |
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const std::string & |
agentRegex | ) |
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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 |
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CVID |
agentCvid | ) |
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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 |
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const std::string & |
cleavageAgentRegex | ) |
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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])
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 |
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const Peptide & |
peptide, |
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size_t |
offsetHint = 0 |
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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().
Friends And Related Function Documentation
friend class const_iterator::Impl |
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friend |
Member Data Documentation
boost::shared_ptr<Impl> pwiz::proteome::Digestion::impl_ |
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private |
The documentation for this class was generated from the following file:
- /Users/parag/_Research/pwiz/svn/trunk/pwiz/pwiz/data/proteome/Digestion.hpp