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

#include <IdentData.hpp>

Inheritance diagram for pwiz::identdata::Modification:

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

Public Attributes
int	location
std::vector< char >	residues
double	avgMassDelta
double	monoisotopicMassDelta
Public Attributes inherited from pwiz::data::ParamContainer
std::vector< ParamGroupPtr >	paramGroupPtrs
	a collection of references to ParamGroups
std::vector< CVParam >	cvParams
	a collection of controlled vocabulary terms
std::vector< UserParam >	userParams
	a collection of uncontrolled user terms

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 â€œunknown modificationâ€ 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.