pwiz::msdata::SpectrumListSimple Struct Reference

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

#include <MSData.hpp>

Inheritance diagram for pwiz::msdata::SpectrumListSimple:

List of all members.

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 SpectrumIdentity &	spectrumIdentity (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 DataProcessing >	dataProcessingPtr () 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 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	~SpectrumList ()

Public Attributes
std::vector< SpectrumPtr >	spectra
DataProcessingPtr	dp

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Detailed Description

Simple writeable in-memory implementation of SpectrumList.

Note: This spectrum() implementation returns internal SpectrumPtrs.

Definition at line 710 of file MSData.hpp.

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Member Function Documentation

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

inlinevirtual

returns the number of spectra

Implements pwiz::msdata::SpectrumList.

Definition at line 717 of file MSData.hpp.

{return spectra.size();}

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 718 of file MSData.hpp.

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

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

virtual

access to a spectrum index

Implements pwiz::msdata::SpectrumList.

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.

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.

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Member Data Documentation

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

Definition at line 712 of file MSData.hpp.

Referenced by initializeSpectrumList(), test(), testDeisotoping(), testIntensityThresholding(), testMS2Denoising(), testPrecursorMassRemoval(), testSpectrumList(), testSpectrumListWithPositions(), testSpectrumListWriteProgress(), and testZeroSamplesFilter().

DataProcessingPtr pwiz::msdata::SpectrumListSimple::dp

Definition at line 713 of file MSData.hpp.

Referenced by testSpectrumList().

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

• /Users/parag/_Research/pwiz/svn/trunk/pwiz/pwiz/data/msdata/MSData.hpp