Public Member Functions | Public Attributes
pwiz::identdata::SpectrumIdentificationItem Struct Reference

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

#include <IdentData.hpp>

Inheritance diagram for pwiz::identdata::SpectrumIdentificationItem:
pwiz::identdata::IdentifiableParamContainer pwiz::data::ParamContainer

List of all members.

Public Member Functions

 SpectrumIdentificationItem (const std::string &id="", const std::string &name="")
bool empty () const
 returns true iff the element contains no params or param groups
- Public Member Functions inherited from pwiz::identdata::IdentifiableParamContainer
 IdentifiableParamContainer (const std::string &id_="", const std::string &name_="")
virtual ~IdentifiableParamContainer ()
- 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)
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 chargeState
double experimentalMassToCharge
double calculatedMassToCharge
double calculatedPI
PeptidePtr peptidePtr
int rank
bool passThreshold
MassTablePtr massTablePtr
SamplePtr samplePtr
std::vector< PeptideEvidencePtr > peptideEvidencePtr
std::vector< IonTypePtr > fragmentation
- Public Attributes inherited from pwiz::identdata::IdentifiableParamContainer
std::string id
std::string name
- 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

Implementation of SpectrumIdentificationItemType from the mzIdentML schema.

An identification of a single (poly)peptide, resulting from querying an input spectra, along with the set of confidence values for that identification. PeptideEvidence elements should be given for all mappings of the corresponding Peptide sequence within protein sequences.

Definition at line 669 of file IdentData.hpp.

Constructor & Destructor Documentation

pwiz::identdata::SpectrumIdentificationItem::SpectrumIdentificationItem ( const std::string &  id = "",
const std::string &  name = "" 

Member Function Documentation

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

returns true iff the element contains no params or param groups

Reimplemented from pwiz::identdata::IdentifiableParamContainer.

Referenced by pwiz::identdata::TextWriter::operator()().

Member Data Documentation

int pwiz::identdata::SpectrumIdentificationItem::chargeState
double pwiz::identdata::SpectrumIdentificationItem::experimentalMassToCharge
double pwiz::identdata::SpectrumIdentificationItem::calculatedMassToCharge
double pwiz::identdata::SpectrumIdentificationItem::calculatedPI
PeptidePtr pwiz::identdata::SpectrumIdentificationItem::peptidePtr
int pwiz::identdata::SpectrumIdentificationItem::rank
bool pwiz::identdata::SpectrumIdentificationItem::passThreshold
MassTablePtr pwiz::identdata::SpectrumIdentificationItem::massTablePtr
SamplePtr pwiz::identdata::SpectrumIdentificationItem::samplePtr
std::vector<PeptideEvidencePtr> pwiz::identdata::SpectrumIdentificationItem::peptideEvidencePtr
std::vector<IonTypePtr> pwiz::identdata::SpectrumIdentificationItem::fragmentation

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