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pwiz::msdata::SpectrumListSimple Struct Reference

Simple writeable in-memory implementation of SpectrumList. More...

#include <MSData.hpp>

Inheritance diagram for pwiz::msdata::SpectrumListSimple:
pwiz::msdata::SpectrumList

Public Member Functions

virtual size_t size () const
 returns the number of spectra
 
virtual bool empty () const
 returns true iff (size() == 0) and (dataProcessingPtr.get() == NULL)
 
virtual const SpectrumIdentityspectrumIdentity (size_t index) const
 access to a spectrum index
 
virtual SpectrumPtr spectrum (size_t index, bool getBinaryData) const
 retrieve a spectrum by index
 
virtual const boost::shared_ptr< const DataProcessingdataProcessingPtr () const
 returns the data processing affecting spectra retrieved through this interface
 
- Public Member Functions inherited from pwiz::msdata::SpectrumList
virtual size_t find (const std::string &id) const
 find id in the spectrum index (returns size() on failure)
 
virtual size_t findAbbreviated (const std::string &abbreviatedId, char delimiter='.') const
 find an abbreviated id (e.g. "1.1.123.2" for "sample=1 period=1 cycle=123 experiment=2") in the spectrum index (returns size() on failure)
 
virtual IndexList findNameValue (const std::string &name, const std::string &value) const
 find all spectrum indexes with specified name/value pair
 
virtual IndexList findSpotID (const std::string &spotID) const
 find all spectrum indexes with spotID (returns empty vector on failure)
 
virtual SpectrumPtr spectrum (const SpectrumPtr &seed, bool getBinaryData) const
 get a copy of the seed spectrum, optionally with its binary data populated this is useful for formats like mzML that can delay loading of binary data
 
virtual SpectrumPtr spectrum (size_t index, DetailLevel detailLevel) const
 retrieve a spectrum by index
 
virtual void warn_once (const char *msg) const
 issues a warning once per SpectrumList instance (based on string hash)
 
virtual ~SpectrumList ()
 

Public Attributes

std::vector< SpectrumPtrspectra
 
DataProcessingPtr dp
 

Detailed Description

Simple writeable in-memory implementation of SpectrumList.

Note: This spectrum() implementation returns internal SpectrumPtrs.

Definition at line 716 of file MSData.hpp.

Member Function Documentation

◆ size()

virtual size_t pwiz::msdata::SpectrumListSimple::size ( ) const
inlinevirtual

returns the number of spectra

Implements pwiz::msdata::SpectrumList.

Definition at line 723 of file MSData.hpp.

723{return spectra.size();}
std::vector< SpectrumPtr > spectra
Definition MSData.hpp:718

◆ empty()

virtual bool pwiz::msdata::SpectrumListSimple::empty ( ) const
inlinevirtual

returns true iff (size() == 0) and (dataProcessingPtr.get() == NULL)

Reimplemented from pwiz::msdata::SpectrumList.

Definition at line 724 of file MSData.hpp.

724{return spectra.empty() && !dp.get();}

◆ spectrumIdentity()

virtual const SpectrumIdentity & pwiz::msdata::SpectrumListSimple::spectrumIdentity ( size_t  index) const
virtual

access to a spectrum index

Implements pwiz::msdata::SpectrumList.

◆ spectrum()

virtual SpectrumPtr pwiz::msdata::SpectrumListSimple::spectrum ( size_t  index,
bool  getBinaryData 
) const
virtual

retrieve a spectrum by index

  • binary data arrays will be provided if (getBinaryData == true);
  • client may assume the underlying Spectrum* is valid

Implements pwiz::msdata::SpectrumList.

◆ dataProcessingPtr()

virtual const boost::shared_ptr< const DataProcessing > pwiz::msdata::SpectrumListSimple::dataProcessingPtr ( ) const
virtual

returns the data processing affecting spectra retrieved through this interface

  • may return a null shared pointer

Reimplemented from pwiz::msdata::SpectrumList.

Member Data Documentation

◆ spectra

std::vector<SpectrumPtr> pwiz::msdata::SpectrumListSimple::spectra

◆ dp

DataProcessingPtr pwiz::msdata::SpectrumListSimple::dp

Definition at line 719 of file MSData.hpp.

Referenced by testSpectrumList().


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