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pwiz::msdata::SpectrumList Class Referenceabstract

Interface for accessing spectra, which may be stored in memory or backed by a data file (RAW, mzXML, mzML). More...

#include <MSData.hpp>

Inheritance diagram for pwiz::msdata::SpectrumList:
pwiz::msdata::SpectrumListBase pwiz::msdata::SpectrumListSimple pwiz::msdata::SpectrumListWrapper MyBase pwiz::msdata::detail::SpectrumList_ABI pwiz::msdata::detail::SpectrumList_ABI_T2D pwiz::msdata::detail::SpectrumList_Agilent pwiz::msdata::detail::SpectrumList_Bruker pwiz::msdata::detail::SpectrumList_Thermo pwiz::msdata::detail::SpectrumList_UIMF pwiz::msdata::detail::SpectrumList_Waters pwiz::msdata::SpectrumList_BTDX pwiz::msdata::SpectrumList_MGF pwiz::msdata::SpectrumList_MSn pwiz::msdata::SpectrumList_mzML pwiz::msdata::SpectrumList_mzXML pwiz::analysis::SpectrumList_3D pwiz::analysis::SpectrumList_ChargeFromIsotope pwiz::analysis::SpectrumList_ChargeStateCalculator pwiz::analysis::SpectrumList_Filter pwiz::analysis::SpectrumList_IonMobility pwiz::analysis::SpectrumList_LockmassRefiner pwiz::analysis::SpectrumList_MetadataFixer pwiz::analysis::SpectrumList_MZRefiner pwiz::analysis::SpectrumList_MZWindow pwiz::analysis::SpectrumList_PeakFilter pwiz::analysis::SpectrumList_PeakPicker pwiz::analysis::SpectrumList_PrecursorRecalculator pwiz::analysis::SpectrumList_PrecursorRefine pwiz::analysis::SpectrumList_ScanSummer pwiz::analysis::SpectrumList_Smoother pwiz::analysis::SpectrumList_Sorter pwiz::analysis::SpectrumList_TitleMaker pwiz::analysis::SpectrumList_ZeroSamplesFilter pwiz::msdata::SpectrumListCache

Public Member Functions

virtual size_t size () const =0
 returns the number of spectra More...
 
virtual bool empty () const
 returns true iff (size() == 0) and (dataProcessingPtr.get() == NULL) More...
 
virtual const SpectrumIdentityspectrumIdentity (size_t index) const =0
 access to a spectrum index More...
 
virtual size_t find (const std::string &id) const
 find id in the spectrum index (returns size() on failure) More...
 
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) More...
 
virtual IndexList findNameValue (const std::string &name, const std::string &value) const
 find all spectrum indexes with specified name/value pair More...
 
virtual IndexList findSpotID (const std::string &spotID) const
 find all spectrum indexes with spotID (returns empty vector on failure) More...
 
virtual SpectrumPtr spectrum (size_t index, bool getBinaryData=false) const =0
 retrieve a spectrum by index More...
 
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 More...
 
virtual SpectrumPtr spectrum (size_t index, DetailLevel detailLevel) const
 retrieve a spectrum by index More...
 
virtual const boost::shared_ptr< const DataProcessingdataProcessingPtr () const
 returns the data processing affecting spectra retrieved through this interface More...
 
virtual void warn_once (const char *msg) const
 issues a warning once per SpectrumList instance (based on string hash) More...
 
virtual ~SpectrumList ()
 

Detailed Description

Interface for accessing spectra, which may be stored in memory or backed by a data file (RAW, mzXML, mzML).

Implementation notes:

Definition at line 656 of file MSData.hpp.

Constructor & Destructor Documentation

§ ~SpectrumList()

virtual pwiz::msdata::SpectrumList::~SpectrumList ( )
inlinevirtual

Definition at line 703 of file MSData.hpp.

703 {}

Member Function Documentation

§ size()

virtual size_t pwiz::msdata::SpectrumList::size ( ) const
pure virtual

§ empty()

virtual bool pwiz::msdata::SpectrumList::empty ( ) const
virtual

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

Reimplemented in pwiz::msdata::SpectrumListSimple, and pwiz::msdata::SpectrumListWrapper.

§ spectrumIdentity()

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

§ find()

virtual size_t pwiz::msdata::SpectrumList::find ( const std::string &  id) const
virtual

§ findAbbreviated()

virtual size_t pwiz::msdata::SpectrumList::findAbbreviated ( const std::string &  abbreviatedId,
char  delimiter = '.' 
) const
virtual

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)

Referenced by testSpectrumListSimple().

§ findNameValue()

virtual IndexList pwiz::msdata::SpectrumList::findNameValue ( const std::string &  name,
const std::string &  value 
) const
virtual

find all spectrum indexes with specified name/value pair

Referenced by testSpectrumListSimple().

§ findSpotID()

virtual IndexList pwiz::msdata::SpectrumList::findSpotID ( const std::string &  spotID) const
virtual

find all spectrum indexes with spotID (returns empty vector on failure)

§ spectrum() [1/3]

virtual SpectrumPtr pwiz::msdata::SpectrumList::spectrum ( size_t  index,
bool  getBinaryData = false 
) const
pure virtual

retrieve a spectrum by index

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

Implemented in pwiz::msdata::SpectrumListSimple, pwiz::analysis::SpectrumList_ChargeFromIsotope, pwiz::analysis::SpectrumList_Filter, pwiz::analysis::SpectrumList_Sorter, pwiz::analysis::SpectrumList_MZRefiner, pwiz::analysis::SpectrumList_ScanSummer, pwiz::analysis::SpectrumList_TitleMaker, pwiz::msdata::detail::SpectrumList_UIMF, pwiz::analysis::SpectrumList_PrecursorRefine, pwiz::msdata::detail::SpectrumList_Agilent, pwiz::msdata::detail::SpectrumList_Thermo, pwiz::msdata::SpectrumListWrapper, pwiz::msdata::detail::SpectrumList_Bruker, pwiz::analysis::SpectrumList_ChargeStateCalculator, pwiz::analysis::SpectrumList_PeakPicker, pwiz::analysis::SpectrumList_ZeroSamplesFilter, pwiz::msdata::detail::SpectrumList_Waters, pwiz::msdata::SpectrumListCache, pwiz::analysis::SpectrumList_Smoother, pwiz::msdata::detail::SpectrumList_ABI, pwiz::analysis::SpectrumList_PrecursorRecalculator, pwiz::analysis::SpectrumList_3D, pwiz::analysis::SpectrumList_LockmassRefiner, pwiz::analysis::SpectrumList_PeakFilter, pwiz::analysis::SpectrumList_MetadataFixer, pwiz::analysis::SpectrumList_MZWindow, pwiz::msdata::detail::SpectrumList_ABI_T2D, pwiz::analysis::SpectrumList_IonMobility, and MyBase.

Referenced by pwiz::msdata::TextWriter::operator()(), printSpectrumList(), test(), testSpectrumListSimple(), validateMmgfMzxmlRoundTrip(), and verifySpectrumSize().

§ spectrum() [2/3]

virtual SpectrumPtr pwiz::msdata::SpectrumList::spectrum ( const SpectrumPtr seed,
bool  getBinaryData 
) const
virtual

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

  • client may assume the underlying Spectrum* is valid

§ spectrum() [3/3]

virtual SpectrumPtr pwiz::msdata::SpectrumList::spectrum ( size_t  index,
DetailLevel  detailLevel 
) const
virtual

§ dataProcessingPtr()

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

returns the data processing affecting spectra retrieved through this interface

  • may return a null shared pointer

Reimplemented in pwiz::msdata::SpectrumListSimple, pwiz::msdata::SpectrumListWrapper, pwiz::msdata::SpectrumListBase, and MyBase.

Referenced by pwiz::msdata::TextWriter::operator()(), and testSpectrumListSimple().

§ warn_once()

virtual void pwiz::msdata::SpectrumList::warn_once ( const char *  msg) const
virtual

issues a warning once per SpectrumList instance (based on string hash)

Reimplemented in pwiz::msdata::SpectrumListBase.


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