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pwiz::identdata::Modification Struct Reference

Implementation of ModificationType from the mzIdentML schema. More...

#include <IdentData.hpp>

Inheritance diagram for pwiz::identdata::Modification:
pwiz::data::ParamContainer

Public Member Functions

 Modification ()
 
bool empty () const
 
- Public Member Functions inherited from pwiz::data::ParamContainer
CVParam cvParam (CVID cvid) const
 finds cvid in the container: More...
 
CVParam cvParamChild (CVID cvid) const
 finds child of cvid in the container: More...
 
std::vector< CVParamcvParamChildren (CVID cvid) const
 finds all children of cvid in the container: More...
 
bool hasCVParam (CVID cvid) const
 returns true iff cvParams contains exact cvid (recursive) More...
 
bool hasCVParamChild (CVID cvid) const
 returns true iff cvParams contains a child (is_a) of cvid (recursive) More...
 
UserParam userParam (const std::string &) const
 finds UserParam with specified name More...
 
void set (CVID cvid, const std::string &value="", CVID units=CVID_Unknown)
 set/add a CVParam (not recursive) More...
 
void set (CVID cvid, double value, CVID units=CVID_Unknown)
 set/add a CVParam (not recursive) More...
 
void set (CVID cvid, int value, CVID units=CVID_Unknown)
 set/add a CVParam (not recursive) More...
 
template<typename value_type >
void set (CVID cvid, value_type value, CVID units=CVID_Unknown)
 set/add a CVParam (not recursive) More...
 
bool empty () const
 returns true iff the element contains no params or param groups More...
 
void clear ()
 clears the collections More...
 
bool operator== (const ParamContainer &that) const
 returns true iff this and that have the exact same cvParams and userParams More...
 
bool operator!= (const ParamContainer &that) const
 returns !(this==that) More...
 
template<>
void set (CVID cvid, bool value, CVID units)
 special case for bool (outside the class for gcc 3.4, and inline for msvc) More...
 

Public Attributes

int location
 
std::vector< char > residues
 
double avgMassDelta
 
double monoisotopicMassDelta
 
- Public Attributes inherited from pwiz::data::ParamContainer
std::vector< ParamGroupPtrparamGroupPtrs
 a collection of references to ParamGroups More...
 
std::vector< CVParamcvParams
 a collection of controlled vocabulary terms More...
 
std::vector< UserParamuserParams
 a collection of uncontrolled user terms More...
 

Detailed Description

Implementation of ModificationType from the mzIdentML schema.

A molecule modification specification. If n modifications have been found on a peptide, there should be n instances of Modification. If multiple modifications are provided as cvParams, it is assumed that the modification is ambiguous i.e. one modification or another. A cvParam must be provided with the identification of the modification sourced from a suitable CV e.g. UNIMOD. If the modification is not present in the CV (and this will be checked by the semantic validator within a given tolerance window), there is a “unknown modification” CV term that must be used instead. A neutral loss should be defined as an additional CVParam within Modification. If more complex information should be given about neutral losses (such as presence/absence on particular product ions), this can additionally be encoded within the FragmentationArray.

Definition at line 329 of file IdentData.hpp.

Constructor & Destructor Documentation

§ Modification()

pwiz::identdata::Modification::Modification ( )

Member Function Documentation

§ empty()

bool pwiz::identdata::Modification::empty ( ) const

Member Data Documentation

§ location

int pwiz::identdata::Modification::location

§ residues

std::vector<char> pwiz::identdata::Modification::residues

§ avgMassDelta

double pwiz::identdata::Modification::avgMassDelta

§ monoisotopicMassDelta

double pwiz::identdata::Modification::monoisotopicMassDelta

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