Representation of 1D spectrum settings. More...

#include <OpenMS/METADATA/SpectrumSettings.h>

Inheritance diagram for SpectrumSettings:

Public Types
enum	SpectrumType { UNKNOWN, PEAKS, RAWDATA, SIZE_OF_SPECTRUMTYPE }
	Spectrum peak type. More...
Public Member Functions
	SpectrumSettings ()
	Constructor.
	SpectrumSettings (const SpectrumSettings &source)
	Copy constructor.
	~SpectrumSettings ()
	Destructor.
SpectrumSettings &	operator= (const SpectrumSettings &source)
bool	operator== (const SpectrumSettings &rhs) const
	Equality operator.
bool	operator!= (const SpectrumSettings &rhs) const
	Equality operator.
void	unify (const SpectrumSettings &rhs)
	merge another spectrum setting into this one (data is usually appended, except for spectrum type which needs to be unambiguous to be kept)
SpectrumType	getType () const
	returns the spectrum type
void	setType (SpectrumType type)
	sets the spectrum type
const String &	getNativeID () const
	returns the native identifier for the spectrum, used by the acquisition software.
void	setNativeID (const String &native_id)
	sets the native identifier for the spectrum, used by the acquisition software.
const String &	getComment () const
	returns the free-text comment
void	setComment (const String &comment)
	sets the free-text comment
const InstrumentSettings &	getInstrumentSettings () const
	returns a const reference to the instrument settings of the current spectrum
InstrumentSettings &	getInstrumentSettings ()
	returns a mutable reference to the instrument settings of the current spectrum
void	setInstrumentSettings (const InstrumentSettings &instrument_settings)
	sets the instrument settings of the current spectrum
const AcquisitionInfo &	getAcquisitionInfo () const
	returns a const reference to the acquisition info
AcquisitionInfo &	getAcquisitionInfo ()
	returns a mutable reference to the acquisition info
void	setAcquisitionInfo (const AcquisitionInfo &acquisition_info)
	sets the acquisition info
const SourceFile &	getSourceFile () const
	returns a const reference to the source file
SourceFile &	getSourceFile ()
	returns a mutable reference to the source file
void	setSourceFile (const SourceFile &source_file)
	sets the source file
const std::vector< Precursor > &	getPrecursors () const
	returns a const reference to the precursors
std::vector< Precursor > &	getPrecursors ()
	returns a mutable reference to the precursors
void	setPrecursors (const std::vector< Precursor > &precursors)
	sets the precursors
const std::vector< Product > &	getProducts () const
	returns a const reference to the products
std::vector< Product > &	getProducts ()
	returns a mutable reference to the products
void	setProducts (const std::vector< Product > &products)
	sets the products
const std::vector < PeptideIdentification > &	getPeptideIdentifications () const
	returns a const reference to the PeptideIdentification vector
std::vector < PeptideIdentification > &	getPeptideIdentifications ()
	returns a mutable reference to the PeptideIdentification vector
void	setPeptideIdentifications (const std::vector< PeptideIdentification > &identifications)
	sets the PeptideIdentification vector
const std::vector < DataProcessing > &	getDataProcessing () const
	returns a const reference to the description of the applied processing
std::vector< DataProcessing > &	getDataProcessing ()
	returns a mutable reference to the description of the applied processing
void	setDataProcessing (const std::vector< DataProcessing > &data_processing)
	sets the description of the applied processing
Static Public Attributes
static const std::string	NamesOfSpectrumType [SIZE_OF_SPECTRUMTYPE]
	Names of spectrum types.
Protected Attributes
SpectrumType	type_
String	native_id_
String	comment_
InstrumentSettings	instrument_settings_
SourceFile	source_file_
AcquisitionInfo	acquisition_info_
std::vector< Precursor >	precursors_
std::vector< Product >	products_
std::vector < PeptideIdentification >	identification_
std::vector< DataProcessing >	data_processing_

Detailed Description

Representation of 1D spectrum settings.

It contains the metadata about spectrum specific instrument settings, acquisition settings, description of the meta values used in the peaks and precursor info.

Precursor info should only be used if this spectrum is a tandem-MS spectrum. The precursor spectrum is the first spectrum before this spectrum, that has a lower MS-level than the current spectrum.

Member Enumeration Documentation

enum SpectrumType

Spectrum peak type.

Enumerator:

UNKNOWN	Unknown spectrum type.
PEAKS	Peak data (also called centroided data or stick data).
RAWDATA	Raw data (also called profile data).
SIZE_OF_SPECTRUMTYPE

Constructor & Destructor Documentation

SpectrumSettings ( )

Constructor.

Referenced by MSSpectrum< RichPeak1D >::clear().

SpectrumSettings ( const SpectrumSettings & source )

Copy constructor.

~SpectrumSettings ( )

Destructor.

Member Function Documentation

const AcquisitionInfo& getAcquisitionInfo ( ) const

returns a const reference to the acquisition info

Referenced by MzMLHandler< MapType >::handleCVParam_(), MzMLHandler< MapType >::handleUserParam_(), MzMLHandler< MapType >::startElement(), MzDataHandler< MapType >::startElement(), MzMLHandler< MapType >::writeTo(), and MzDataHandler< MapType >::writeTo().

AcquisitionInfo& getAcquisitionInfo ( )

returns a mutable reference to the acquisition info

const String& getComment ( ) const

returns the free-text comment

Referenced by MzXMLHandler< MapType >::writeTo().

const std::vector<DataProcessing>& getDataProcessing ( ) const

returns a const reference to the description of the applied processing

Referenced by MzDataHandler< MapType >::startElement(), and MzMLHandler< MapType >::writeTo().

std::vector<DataProcessing>& getDataProcessing ( )

returns a mutable reference to the description of the applied processing

const InstrumentSettings& getInstrumentSettings ( ) const

returns a const reference to the instrument settings of the current spectrum

Referenced by MzDataHandler< MapType >::cvParam_(), MzMLHandler< MapType >::handleCVParam_(), MzMLHandler< MapType >::handleUserParam_(), MzMLHandler< MapType >::startElement(), MzDataHandler< MapType >::startElement(), MzXMLHandler< MapType >::writeTo(), MzMLHandler< MapType >::writeTo(), and MzDataHandler< MapType >::writeTo().

InstrumentSettings& getInstrumentSettings ( )

returns a mutable reference to the instrument settings of the current spectrum

const String& getNativeID ( ) const

returns the native identifier for the spectrum, used by the acquisition software.

Referenced by MzMLHandler< MapType >::fillData_(), FeatureFinderAlgorithmSH< PeakType, FeatureType >::run(), MzXMLHandler< MapType >::writeTo(), MzMLHandler< MapType >::writeTo(), and MzDataHandler< MapType >::writeTo().

const std::vector<PeptideIdentification>& getPeptideIdentifications ( ) const

returns a const reference to the PeptideIdentification vector

std::vector<PeptideIdentification>& getPeptideIdentifications ( )

returns a mutable reference to the PeptideIdentification vector

const std::vector<Precursor>& getPrecursors ( ) const

returns a const reference to the precursors

Referenced by MzDataHandler< MapType >::cvParam_(), MzMLHandler< MapType >::handleCVParam_(), MzMLHandler< MapType >::handleUserParam_(), MzMLHandler< MapType >::startElement(), MzDataHandler< MapType >::startElement(), MzXMLHandler< MapType >::writeTo(), MzMLHandler< MapType >::writeTo(), and MzDataHandler< MapType >::writeTo().

std::vector<Precursor>& getPrecursors ( )

returns a mutable reference to the precursors

std::vector<Product>& getProducts ( )

returns a mutable reference to the products

const std::vector<Product>& getProducts ( ) const

returns a const reference to the products

Referenced by MzMLHandler< MapType >::handleCVParam_(), MzMLHandler< MapType >::handleUserParam_(), MzMLHandler< MapType >::startElement(), and MzMLHandler< MapType >::writeTo().

const SourceFile& getSourceFile ( ) const

returns a const reference to the source file

Referenced by MzMLHandler< MapType >::writeTo().

SourceFile& getSourceFile ( )

returns a mutable reference to the source file

SpectrumType getType ( ) const

returns the spectrum type

Referenced by MzMLHandler< MapType >::writeTo(), and MzDataHandler< MapType >::writeTo().

bool operator!= ( const SpectrumSettings & rhs ) const

Equality operator.

SpectrumSettings& operator= ( const SpectrumSettings & source )

bool operator== ( const SpectrumSettings & rhs ) const

Equality operator.

void setAcquisitionInfo ( const AcquisitionInfo & acquisition_info )

sets the acquisition info

Referenced by XMassFile::load().

void setComment ( const String & comment )

sets the free-text comment

Referenced by MzDataHandler< MapType >::characters(), XMassFile::load(), and TOPPRNPxl::main_().

void setDataProcessing ( const std::vector< DataProcessing > & data_processing )

sets the description of the applied processing

Referenced by XMassFile::load(), and MzMLHandler< MapType >::startElement().

void setInstrumentSettings ( const InstrumentSettings & instrument_settings )

sets the instrument settings of the current spectrum

Referenced by XMassFile::load().

void setNativeID ( const String & native_id )

sets the native identifier for the spectrum, used by the acquisition software.

Referenced by XMassFile::load(), MzMLHandler< MapType >::startElement(), and MzDataHandler< MapType >::startElement().

void setPeptideIdentifications ( const std::vector< PeptideIdentification > & identifications )

sets the PeptideIdentification vector

void setPrecursors ( const std::vector< Precursor > & precursors )

sets the precursors

Referenced by TOPPRNPxl::main_(), OfflinePrecursorIonSelection::makePrecursorSelectionForKnownLCMSMap(), and TOPPViewBase::showSpectrumGenerationDialog().

void setProducts ( const std::vector< Product > & products )

sets the products

void setSourceFile ( const SourceFile & source_file )

sets the source file

Referenced by XMassFile::load(), and MzMLHandler< MapType >::startElement().

void setType ( SpectrumType type )

sets the spectrum type

Referenced by MorphologicalFilter::filter(), GaussFilter::filter(), MzMLHandler< MapType >::handleCVParam_(), XMassFile::load(), PeakPickerHiRes::pick(), and MzDataHandler< MapType >::startElement().

void unify ( const SpectrumSettings & rhs )

merge another spectrum setting into this one (data is usually appended, except for spectrum type which needs to be unambiguous to be kept)

Member Data Documentation

AcquisitionInfo acquisition_info_ [protected]

String comment_ [protected]

std::vector<DataProcessing> data_processing_ [protected]

std::vector<PeptideIdentification> identification_ [protected]

InstrumentSettings instrument_settings_ [protected]

const std::string NamesOfSpectrumType[SIZE_OF_SPECTRUMTYPE] [static]

Names of spectrum types.

String native_id_ [protected]

std::vector<Precursor> precursors_ [protected]

std::vector<Product> products_ [protected]

SourceFile source_file_ [protected]

SpectrumType type_ [protected]

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:56 using doxygen 1.7.1

SpectrumSettings Class Reference [Metadata]

Public Types

Public Member Functions

Static Public Attributes

Protected Attributes

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

SpectrumSettings Class Reference
[Metadata]