The structure that captures the generation of a peak list (including the underlying acquisitions) More...

#include <MSData.hpp>

Inheritance diagram for pwiz::msdata::Spectrum:

Public Member Functions
	Spectrum ()
bool	empty () const
	returns true iff the element contains no params and all members are empty or null
bool	hasBinaryData () const
	returns true iff has nonnull and nonempty BinaryDataArrayPtr
void	getMZIntensityPairs (std::vector< MZIntensityPair > &output) const
	copy binary data arrays into m/z-intensity pair array
void	getMZIntensityPairs (MZIntensityPair *output, size_t expectedSize) const
	copy binary data arrays into m/z-intensity pair array note: this overload is to allow client to allocate own buffer; the client must determine the correct size beforehand, or an exception will be thrown
BinaryDataArrayPtr	getMZArray () const
	get m/z array (may be null)
BinaryDataArrayPtr	getIntensityArray () const
	get intensity array (may be null)
void	setMZIntensityPairs (const std::vector< MZIntensityPair > &input, CVID intensityUnits)
	set binary data arrays
void	setMZIntensityPairs (const MZIntensityPair *input, size_t size, CVID intensityUnits)
	set binary data arrays
void	setMZIntensityArrays (const std::vector< double > &mzArray, const std::vector< double > &intensityArray, CVID intensityUnits)
	set m/z and intensity arrays separately (they must be the same size)
Public Member Functions inherited from pwiz::msdata::SpectrumIdentity
	SpectrumIdentity ()
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< CVParam >	cvParamChildren (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
size_t	defaultArrayLength
	default length of binary data arrays contained in this element.
DataProcessingPtr	dataProcessingPtr
	this attribute can optionally reference the 'id' of the appropriate dataProcessing.
SourceFilePtr	sourceFilePtr
	this attribute can optionally reference the 'id' of the appropriate sourceFile.
ScanList	scanList
	list of scans
std::vector< Precursor >	precursors
	list and descriptions of precursors to the spectrum currently being described.
std::vector< Product >	products
	list and descriptions of product ion information
std::vector< BinaryDataArrayPtr >	binaryDataArrayPtrs
	list of binary data arrays.
Public Attributes inherited from pwiz::msdata::SpectrumIdentity
size_t	index
	the zero-based, consecutive index of the spectrum in the SpectrumList.
std::string	id
	a unique identifier for this spectrum. It should be expected that external files may use this identifier together with the mzML filename or accession to reference a particular spectrum.
std::string	spotID
	the identifier for the spot from which this spectrum was derived, if a MALDI or similar run.
boost::iostreams::stream_offset	sourceFilePosition
	for file-based MSData implementations, this attribute may refer to the spectrum's position in the file
Public Attributes inherited from pwiz::data::ParamContainer
std::vector< ParamGroupPtr >	paramGroupPtrs
	a collection of references to ParamGroups
std::vector< CVParam >	cvParams
	a collection of controlled vocabulary terms
std::vector< UserParam >	userParams
	a collection of uncontrolled user terms

Detailed Description

The structure that captures the generation of a peak list (including the underlying acquisitions)

Definition at line 503 of file MSData.hpp.

Constructor & Destructor Documentation

pwiz::msdata::Spectrum::Spectrum ( )

inline

Definition at line 527 of file MSData.hpp.

: defaultArrayLength(0) {}

Member Function Documentation

bool pwiz::msdata::Spectrum::empty ( ) const

returns true iff the element contains no params and all members are empty or null

Reimplemented from pwiz::data::ParamContainer.

bool pwiz::msdata::Spectrum::hasBinaryData ( ) const

inline

returns true iff has nonnull and nonempty BinaryDataArrayPtr

Definition at line 533 of file MSData.hpp.

Referenced by spectrumHasBinaryData().

                               {
        return binaryDataArrayPtrs.size() && 
               binaryDataArrayPtrs[0] &&
              !binaryDataArrayPtrs[0]->data.empty();
    };

void pwiz::msdata::Spectrum::getMZIntensityPairs ( std::vector< MZIntensityPair > & output ) const

copy binary data arrays into m/z-intensity pair array

Referenced by doSomething().

void pwiz::msdata::Spectrum::getMZIntensityPairs	(	MZIntensityPair *	output,
		size_t	expectedSize
	)		const

copy binary data arrays into m/z-intensity pair array note: this overload is to allow client to allocate own buffer; the client must determine the correct size beforehand, or an exception will be thrown

BinaryDataArrayPtr pwiz::msdata::Spectrum::getMZArray ( ) const

get m/z array (may be null)

Referenced by initializeTinyMGF(), initializeTinyMS1(), and initializeTinyMS2().

BinaryDataArrayPtr pwiz::msdata::Spectrum::getIntensityArray ( ) const

get intensity array (may be null)

Referenced by initializeTinyMGF(), initializeTinyMS1(), and initializeTinyMS2().

void pwiz::msdata::Spectrum::setMZIntensityPairs	(	const std::vector< MZIntensityPair > &	input,
		CVID	intensityUnits
	)

set binary data arrays

void pwiz::msdata::Spectrum::setMZIntensityPairs	(	const MZIntensityPair *	input,
		size_t	size,
		CVID	intensityUnits
	)

set binary data arrays

void pwiz::msdata::Spectrum::setMZIntensityArrays	(	const std::vector< double > &	mzArray,
		const std::vector< double > &	intensityArray,
		CVID	intensityUnits
	)