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Public Member Functions | Public Attributes
pwiz::tradata::Modification Struct Reference

A molecule modification specification. More...

#include <TraData.hpp>

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

List of all members.

Public Member Functions

 Modification ()
bool empty () const
 returns true iff all members are zero and contain no params
- 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< CVParamcvParamChildren (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
 Location of the modification within the peptide sequence, counted from the N-terminus, starting at position 1. Specific modifications to the N-terminus should be given the location 0. Modification to the C-terminus should be given as peptide length + 1.
double monoisotopicMassDelta
 Atomic mass delta when assuming only the most common isotope of elements in Daltons.
double averageMassDelta
 Atomic mass delta when considering the natural distribution of isotopes in Daltons.
- Public Attributes inherited from pwiz::data::ParamContainer
std::vector< ParamGroupPtrparamGroupPtrs
 a collection of references to ParamGroups
std::vector< CVParamcvParams
 a collection of controlled vocabulary terms
std::vector< UserParamuserParams
 a collection of uncontrolled user terms

Detailed Description

A molecule modification specification.

If n modifications are present on the peptide, there should be n instances of the modification element. If multiple modifications are provided as cvParams, it is assumed the modification is ambiguous, i.e. one modification or the other. If no cvParams are provided it is assumed that the delta has not been matched to a known modification.

Definition at line 192 of file TraData.hpp.


Constructor & Destructor Documentation

pwiz::tradata::Modification::Modification ( )

Member Function Documentation

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

returns true iff all members are zero and contain no params

Reimplemented from pwiz::data::ParamContainer.


Member Data Documentation

int pwiz::tradata::Modification::location

Location of the modification within the peptide sequence, counted from the N-terminus, starting at position 1. Specific modifications to the N-terminus should be given the location 0. Modification to the C-terminus should be given as peptide length + 1.

Definition at line 197 of file TraData.hpp.

double pwiz::tradata::Modification::monoisotopicMassDelta

Atomic mass delta when assuming only the most common isotope of elements in Daltons.

Definition at line 200 of file TraData.hpp.

double pwiz::tradata::Modification::averageMassDelta

Atomic mass delta when considering the natural distribution of isotopes in Daltons.

Definition at line 203 of file TraData.hpp.


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