#include <OpenMS/FORMAT/HANDLERS/MzMLHandler.h>

Inheritance diagram for MzMLHandler:

Classes
struct	ChromatogramData
	Data necessary to generate a single chromatogram. More...

struct	SpectrumData
	Data necessary to generate a single spectrum. More...

Public Member Functions
void	getCounts (Size &spectra_counts, Size &chromatogram_counts)
	Get the spectra and chromatogram counts of a file. More...

void	setMSDataConsumer (Interfaces::IMSDataConsumer *consumer)
	Set the IMSDataConsumer consumer which will consume the read data. More...

virtual LOADDETAIL	getLoadDetail () const override
	handler which support partial loading, implement this method More...

virtual void	setLoadDetail (const LOADDETAIL d) override
	handler which support partial loading, implement this method More...

Constructors and destructor
	MzMLHandler (MapType &exp, const String &filename, const String &version, const ProgressLogger &logger)
	Constructor for a read-only handler. More...

	MzMLHandler (const MapType &exp, const String &filename, const String &version, const ProgressLogger &logger)
	Constructor for a write-only handler. More...

	~MzMLHandler () override
	Destructor. More...

XML Handling functions and output writing
void	endElement (const XMLCh const, const XMLCh const, const XMLCh *const qname) override

void	startElement (const XMLCh const, const XMLCh const, const XMLCh *const qname, const xercesc::Attributes &attributes) override

void	characters (const XMLCh *const chars, const XMLSize_t length) override

void	writeTo (std::ostream &os) override
	Writes the contents to a stream. More...

PeakFileOptions setters/getters
The PeakFileOptions object determine the reading and writing of the MzML file. In read-mode the lazy-loading options determine whether meta-data only or the full raw data is read into memory and how this data should be handled. The MS-level, m/z, RT and Intensity range options determine which part of the MzML file is read into memory.
void	setOptions (const PeakFileOptions &opt)
	Set the peak file options. More...

PeakFileOptions &	getOptions ()
	Get the peak file options. More...

Public Member Functions inherited from XMLHandler
	XMLHandler (const String &filename, const String &version)
	Default constructor. More...

	~XMLHandler () override
	Destructor. More...

void	reset ()
	Release internal memory used for parsing (call. More...

void	fatalError (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const
	Fatal error handler. Throws a ParseError exception. More...

void	error (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const
	Error handler for recoverable errors. More...

void	warning (ActionMode mode, const String &msg, UInt line=0, UInt column=0) const
	Warning handler. More...

void	characters (const XMLCh *const chars, const XMLSize_t length) override
	Parsing method for character data. More...

void	startElement (const XMLCh const uri, const XMLCh const localname, const XMLCh *const qname, const xercesc::Attributes &attrs) override
	Parsing method for opening tags. More...

void	endElement (const XMLCh const uri, const XMLCh const localname, const XMLCh *const qname) override
	Parsing method for closing tags. More...

String	errorString ()
	Returns the last error description. More...

void	fatalError (const xercesc::SAXParseException &exception) override

void	error (const xercesc::SAXParseException &exception) override

void	warning (const xercesc::SAXParseException &exception) override

Protected Types
typedef MapType::PeakType	PeakType
	Peak type. More...

typedef MapType::ChromatogramPeakType	ChromatogramPeakType
	Chromatogram peak type. More...

typedef MSSpectrum	SpectrumType
	Spectrum type. More...

typedef MSChromatogram	ChromatogramType
	Spectrum type. More...

typedef MzMLHandlerHelper::BinaryData	BinaryData

Protected Member Functions
	MzMLHandler (const String &filename, const String &version, const ProgressLogger &logger)
	delegated constructor for the two public versions More...

void	writeSpectrum_ (std::ostream &os, const SpectrumType &spec, Size s, Internal::MzMLValidator &validator, bool renew_native_ids, std::vector< std::vector< ConstDataProcessingPtr > > &dps)

void	writeChromatogram_ (std::ostream &os, const ChromatogramType &chromatogram, Size c, Internal::MzMLValidator &validator)

template<typename ContainerT >
void	writeContainerData_ (std::ostream &os, const PeakFileOptions &pf_options_, const ContainerT &container, String array_type)

void	populateSpectraWithData_ ()
	Populate all spectra on the stack with data from input. More...

void	populateChromatogramsWithData_ ()
	Populate all chromatograms on the stack with data from input. More...

void	addSpectrumMetaData_ (const std::vector< MzMLHandlerHelper::BinaryData > &input_data, const Size n, SpectrumType &spectrum) const

void	populateSpectraWithData_ (std::vector< MzMLHandlerHelper::BinaryData > &input_data, Size &default_arr_length, const PeakFileOptions &peak_file_options, SpectrumType &spectrum)
	Fill a single spectrum with data from input. More...

void	populateChromatogramsWithData_ (std::vector< MzMLHandlerHelper::BinaryData > &input_data, Size &default_arr_length, const PeakFileOptions &peak_file_options, ChromatogramType &inp_chromatogram)
	Fill a single chromatogram with data from input. More...

template<typename DataType >
void	writeBinaryDataArray_ (std::ostream &os, const PeakFileOptions &pf_options_, std::vector< DataType > data_to_encode, bool is32bit, String array_type)

void	writeHeader_ (std::ostream &os, const MapType &exp, std::vector< std::vector< ConstDataProcessingPtr > > &dps, Internal::MzMLValidator &validator)

void	fillChromatogramData_ ()
	Fills the current chromatogram with data points and meta data. More...

void	handleCVParam_ (const String &parent_parent_tag, const String &parent_tag, const String &accession, const String &name, const String &value, const String &unit_accession="")
	Handles CV terms. More...

void	handleUserParam_ (const String &parent_parent_tag, const String &parent_tag, const String &name, const String &type, const String &value)
	Handles user terms. More...

void	writeUserParam_ (std::ostream &os, const MetaInfoInterface &meta, UInt indent, String path, Internal::MzMLValidator &validator) const
	Writes user terms. More...

ControlledVocabulary::CVTerm	getChildWithName_ (const String &parent_accession, const String &name) const
	Looks up a child CV term of `parent_accession` with the name `name`. If no such term is found, an empty term is returned. More...

void	writeSoftware_ (std::ostream &os, const String &id, const Software &software, Internal::MzMLValidator &validator)
	Helper method that writes a software. More...

void	writeSourceFile_ (std::ostream &os, const String &id, const SourceFile &software, Internal::MzMLValidator &validator)
	Helper method that writes a source file. More...

void	writeDataProcessing_ (std::ostream &os, const String &id, const std::vector< ConstDataProcessingPtr > &dps, Internal::MzMLValidator &validator)
	Helper method that writes a data processing list. More...

void	writePrecursor_ (std::ostream &os, const Precursor &precursor, Internal::MzMLValidator &validator)
	Helper method that write precursor information from spectra and chromatograms. More...

void	writeProduct_ (std::ostream &os, const Product &product, Internal::MzMLValidator &validator)
	Helper method that write precursor information from spectra and chromatograms. More...

String	writeCV_ (const ControlledVocabulary::CVTerm &c, const DataValue &metaValue) const
	Helper method to write an CV based on a meta value. More...

bool	validateCV_ (const ControlledVocabulary::CVTerm &c, const String &path, const Internal::MzMLValidator &validator) const
	Helper method to validate if the given CV is allowed in the current location (path) More...

Protected Member Functions inherited from XMLHandler
bool	equal_ (const XMLCh a, const XMLCh b) const
	Returns if two Xerces strings are equal. More...

void	writeUserParam_ (const String &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const
	Writes the content of MetaInfoInterface to the file. More...

Int	asInt_ (const String &in)
	Conversion of a String to an integer value. More...

Int	asInt_ (const XMLCh *in)
	Conversion of a Xerces string to an integer value. More...

UInt	asUInt_ (const String &in)
	Conversion of a String to an unsigned integer value. More...

double	asDouble_ (const String &in)
	Conversion of a String to a double value. More...

float	asFloat_ (const String &in)
	Conversion of a String to a float value. More...

bool	asBool_ (const String &in)
	Conversion of a string to a boolean value. More...

DateTime	asDateTime_ (String date_string)
	Conversion of a xs:datetime string to a DateTime value. More...

String	attributeAsString_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to a String. More...

Int	attributeAsInt_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to a Int. More...

double	attributeAsDouble_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to a double. More...

DoubleList	attributeAsDoubleList_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to a DoubleList. More...

IntList	attributeAsIntList_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to an IntList. More...

StringList	attributeAsStringList_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to an StringList. More...

bool	optionalAttributeAsString_ (String &value, const xercesc::Attributes &a, const char *name) const
	Assigns the attribute content to the String value if the attribute is present. More...

bool	optionalAttributeAsInt_ (Int &value, const xercesc::Attributes &a, const char *name) const
	Assigns the attribute content to the Int value if the attribute is present. More...

bool	optionalAttributeAsUInt_ (UInt &value, const xercesc::Attributes &a, const char *name) const
	Assigns the attribute content to the UInt value if the attribute is present. More...

bool	optionalAttributeAsDouble_ (double &value, const xercesc::Attributes &a, const char *name) const
	Assigns the attribute content to the double value if the attribute is present. More...

bool	optionalAttributeAsDoubleList_ (DoubleList &value, const xercesc::Attributes &a, const char *name) const
	Assigns the attribute content to the DoubleList value if the attribute is present. More...

bool	optionalAttributeAsStringList_ (StringList &value, const xercesc::Attributes &a, const char *name) const
	Assigns the attribute content to the StringList value if the attribute is present. More...

bool	optionalAttributeAsIntList_ (IntList &value, const xercesc::Attributes &a, const char *name) const
	Assigns the attribute content to the IntList value if the attribute is present. More...

String	attributeAsString_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a String. More...

Int	attributeAsInt_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a Int. More...

double	attributeAsDouble_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a double. More...

DoubleList	attributeAsDoubleList_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a DoubleList. More...

IntList	attributeAsIntList_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a IntList. More...

StringList	attributeAsStringList_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a StringList. More...

bool	optionalAttributeAsString_ (String &value, const xercesc::Attributes &a, const XMLCh *name) const
	Assigns the attribute content to the String value if the attribute is present. More...

bool	optionalAttributeAsInt_ (Int &value, const xercesc::Attributes &a, const XMLCh *name) const
	Assigns the attribute content to the Int value if the attribute is present. More...

bool	optionalAttributeAsUInt_ (UInt &value, const xercesc::Attributes &a, const XMLCh *name) const
	Assigns the attribute content to the UInt value if the attribute is present. More...

bool	optionalAttributeAsDouble_ (double &value, const xercesc::Attributes &a, const XMLCh *name) const
	Assigns the attribute content to the double value if the attribute is present. More...

bool	optionalAttributeAsDoubleList_ (DoubleList &value, const xercesc::Attributes &a, const XMLCh *name) const
	Assigns the attribute content to the DoubleList value if the attribute is present. More...

bool	optionalAttributeAsIntList_ (IntList &value, const xercesc::Attributes &a, const XMLCh *name) const
	Assigns the attribute content to the IntList value if the attribute is present. More...

bool	optionalAttributeAsStringList_ (StringList &value, const xercesc::Attributes &a, const XMLCh *name) const
	Assigns the attribute content to the StringList value if the attribute is present. More...

SignedSize	cvStringToEnum_ (const Size section, const String &term, const char *message, const SignedSize result_on_error=0)

Protected Attributes
MapType *	exp_ { nullptr }
	map pointer for reading More...

const MapType *	cexp_ { nullptr }
	map pointer for writing More...

PeakFileOptions	options_
	Options that can be set for loading/storing. More...

const ProgressLogger &	logger_
	Progress logger. More...

Interfaces::IMSDataConsumer *	consumer_ { nullptr }
	Consumer class to work on spectra. More...

UInt	scan_count_ { 0 }
	Counting spectra and chromatograms. More...

UInt	chromatogram_count_ { 0 }

Int	scan_count_total_ { -1 }

Int	chrom_count_total_ { -1 }

ControlledVocabulary	cv_
	Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo) More...

CVMappings	mapping_

UInt	selected_ion_count_ { 0 }
	Count of selected ions. More...

temporary data structures to hold parsed data
SpectrumType	spec_
	The current spectrum. More...

ChromatogramType	chromatogram_
	The current chromatogram. More...

std::vector< BinaryData >	bin_data_
	The spectrum data (or chromatogram data) More...

Size	default_array_length_
	The default number of peaks in the current spectrum. More...

bool	in_spectrum_list_ { false }
	Flag that indicates that we're inside a spectrum (in contrast to a chromatogram) More...

bool	skip_spectrum_ { false }
	Flag that indicates whether this spectrum should be skipped (e.g. due to options) More...

bool	skip_chromatogram_ { false }
	Flag that indicates whether this chromatogram should be skipped (e.g. due to options) More...

bool	rt_set_ { false }
	Remember whether the RT of the spectrum was set or not. More...

String	current_id_
	Id of the current list. Used for referencing param group, source file, sample, software, ... More...

Map< String, std::vector< SemanticValidator::CVTerm > >	ref_param_
	The referencing param groups: id => array (accession, value) More...

Map< String, SourceFile >	source_files_
	The source files: id => SourceFile. More...

Map< String, Sample >	samples_
	The sample list: id => Sample. More...

Map< String, Software >	software_
	The software list: id => Software. More...

Map< String, Instrument >	instruments_
	The data processing list: id => Instrument. More...

Map< String, std::vector< DataProcessingPtr > >	processing_
	The data processing list: id => Instrument. More...

String	default_processing_
	id of the default data processing (used when no processing is defined) More...

std::vector< SpectrumData >	spectrum_data_
	Vector of spectrum data stored for later parallel processing. More...

std::vector< ChromatogramData >	chromatogram_data_
	Vector of chromatogram data stored for later parallel processing. More...

temporary data structures to hold written data
std::vector< std::pair< std::string, long > >	spectra_offsets_

std::vector< std::pair< std::string, long > >	chromatograms_offsets_

Protected Attributes inherited from XMLHandler
String	error_message_
	Error message of the last error. More...

String	file_
	File name. More...

String	version_
	Schema version. More...

StringManager	sm_
	Helper class for string conversion. More...

std::vector< String >	open_tags_
	Stack of open XML tags. More...

LOADDETAIL	load_detail_
	parse only until total number of scans and chroms have been determined from attributes More...

std::vector< std::vector< String > >	cv_terms_
	Array of CV term lists (one sublist denotes one term and it's children) More...

Additional Inherited Members
Public Types inherited from XMLHandler
enum	ActionMode { LOAD, STORE }
	Action to set the current mode (for error messages) More...

enum	LOADDETAIL { LD_ALLDATA, LD_RAWCOUNTS, LD_COUNTS_WITHOPTIONS }

Static Public Member Functions inherited from XMLHandler
static String	writeXMLEscape (const String &to_escape)
	Escapes a string and returns the escaped string. More...

Member Typedef Documentation

◆ BinaryData

typedef MzMLHandlerHelper::BinaryData BinaryData

protected

◆ ChromatogramPeakType

typedef MapType::ChromatogramPeakType ChromatogramPeakType

protected

Chromatogram peak type.

◆ ChromatogramType

typedef MSChromatogram ChromatogramType

protected

Spectrum type.

◆ PeakType

typedef MapType::PeakType PeakType

protected

Peak type.

◆ SpectrumType

typedef MSSpectrum SpectrumType

protected

Spectrum type.

Constructor & Destructor Documentation

◆ MzMLHandler() [1/3]

MzMLHandler	(	MapType &	exp,
		const String &	filename,
		const String &	version,
		const ProgressLogger &	logger
	)

Constructor for a read-only handler.

◆ MzMLHandler() [2/3]

MzMLHandler	(	const MapType &	exp,
		const String &	filename,
		const String &	version,
		const ProgressLogger &	logger
	)

Constructor for a write-only handler.

◆ ~MzMLHandler()

~MzMLHandler ( )

override

Destructor.

◆ MzMLHandler() [3/3]

MzMLHandler	(	const String &	filename,
		const String &	version,
		const ProgressLogger &	logger
	)

protected

delegated constructor for the two public versions

Member Function Documentation

◆ addSpectrumMetaData_()

void addSpectrumMetaData_	(	const std::vector< MzMLHandlerHelper::BinaryData > &	input_data,
		const Size	n,
		SpectrumType &	spectrum
	)		const

protected

◆ characters()

void characters	(	const XMLCh *const	chars,
		const XMLSize_t	length
	)

override

◆ endElement()

void endElement	(	const XMLCh *	const,
		const XMLCh *	const,
		const XMLCh *const	qname
	)

override

◆ fillChromatogramData_()

void fillChromatogramData_ ( )

protected

Fills the current chromatogram with data points and meta data.

◆ getChildWithName_()

ControlledVocabulary::CVTerm getChildWithName_	(	const String &	parent_accession,
		const String &	name
	)		const

protected

Looks up a child CV term of parent_accession with the name name. If no such term is found, an empty term is returned.

◆ getCounts()

void getCounts	(	Size &	spectra_counts,
		Size &	chromatogram_counts
	)

Get the spectra and chromatogram counts of a file.

◆ getLoadDetail()

virtual LOADDETAIL getLoadDetail ( ) const

overridevirtual

handler which support partial loading, implement this method

Reimplemented from XMLHandler.

◆ getOptions()

PeakFileOptions& getOptions ( )

Get the peak file options.

◆ handleCVParam_()

void handleCVParam_	(	const String &	parent_parent_tag,
		const String &	parent_tag,
		const String &	accession,
		const String &	name,
		const String &	value,
		const String &	unit_accession = `""`
	)

protected

Handles CV terms.

◆ handleUserParam_()

void handleUserParam_	(	const String &	parent_parent_tag,
		const String &	parent_tag,
		const String &	name,
		const String &	type,
		const String &	value
	)

protected

Handles user terms.

◆ populateChromatogramsWithData_() [1/2]

void populateChromatogramsWithData_ ( )

protected

Populate all chromatograms on the stack with data from input.

Will populate all chromatograms on the current work stack with data (using multiple threads if available) and append them to the result.

◆ populateChromatogramsWithData_() [2/2]

void populateChromatogramsWithData_	(	std::vector< MzMLHandlerHelper::BinaryData > &	input_data,
		Size &	default_arr_length,
		const PeakFileOptions &	peak_file_options,
		ChromatogramType &	inp_chromatogram
	)

protected

Fill a single chromatogram with data from input.

Note: Do not modify any internal state variables of the class since this function will be executed in parallel.

◆ populateSpectraWithData_() [1/2]

void populateSpectraWithData_ ( )

protected

Populate all spectra on the stack with data from input.

Will populate all spectra on the current work stack with data (using multiple threads if available) and append them to the result.

◆ populateSpectraWithData_() [2/2]

void populateSpectraWithData_	(	std::vector< MzMLHandlerHelper::BinaryData > &	input_data,
		Size &	default_arr_length,
		const PeakFileOptions &	peak_file_options,
		SpectrumType &	spectrum
	)

protected

Fill a single spectrum with data from input.

Note: Do not modify any internal state variables of the class since this function will be executed in parallel.

Speed: this function takes about 50 % of total load time with a single thread and parallelizes linearly up to at least 10 threads.

◆ setLoadDetail()

virtual void setLoadDetail ( const LOADDETAIL d )

overridevirtual

handler which support partial loading, implement this method

Reimplemented from XMLHandler.

◆ setMSDataConsumer()

void setMSDataConsumer ( Interfaces::IMSDataConsumer * consumer )

Set the IMSDataConsumer consumer which will consume the read data.

◆ setOptions()

void setOptions ( const PeakFileOptions & opt )

Set the peak file options.

Referenced by IndexedMzMLFileLoader::store().

◆ startElement()

void startElement	(	const XMLCh *	const,
		const XMLCh *	const,
		const XMLCh *const	qname,
		const xercesc::Attributes &	attributes
	)

override

◆ validateCV_()

bool validateCV_	(	const ControlledVocabulary::CVTerm &	c,
		const String &	path,
		const Internal::MzMLValidator &	validator
	)		const

protected

Helper method to validate if the given CV is allowed in the current location (path)

◆ writeBinaryDataArray_()

void writeBinaryDataArray_	(	std::ostream &	os,
		const PeakFileOptions &	pf_options_,
		std::vector< DataType >	data_to_encode,
		bool	is32bit,
		String	array_type
	)

protected

◆ writeChromatogram_()

void writeChromatogram_	(	std::ostream &	os,
		const ChromatogramType &	chromatogram,
		Size	c,
		Internal::MzMLValidator &	validator
	)

protected

◆ writeContainerData_()

void writeContainerData_	(	std::ostream &	os,
		const PeakFileOptions &	pf_options_,
		const ContainerT &	container,
		String	array_type
	)

protected

◆ writeCV_()

String writeCV_	(	const ControlledVocabulary::CVTerm &	c,
		const DataValue &	metaValue
	)		const

protected

Helper method to write an CV based on a meta value.

◆ writeDataProcessing_()

void writeDataProcessing_	(	std::ostream &	os,
		const String &	id,
		const std::vector< ConstDataProcessingPtr > &	dps,
		Internal::MzMLValidator &	validator
	)

protected

Helper method that writes a data processing list.

◆ writeHeader_()

void writeHeader_	(	std::ostream &	os,
		const MapType &	exp,
		std::vector< std::vector< ConstDataProcessingPtr > > &	dps,
		Internal::MzMLValidator &	validator
	)

protected

◆ writePrecursor_()

void writePrecursor_	(	std::ostream &	os,
		const Precursor &	precursor,
		Internal::MzMLValidator &	validator
	)

protected

Helper method that write precursor information from spectra and chromatograms.

◆ writeProduct_()

void writeProduct_	(	std::ostream &	os,
		const Product &	product,
		Internal::MzMLValidator &	validator
	)

protected

Helper method that write precursor information from spectra and chromatograms.

◆ writeSoftware_()

void writeSoftware_	(	std::ostream &	os,
		const String &	id,
		const Software &	software,
		Internal::MzMLValidator &	validator
	)

protected

Helper method that writes a software.

◆ writeSourceFile_()

void writeSourceFile_	(	std::ostream &	os,
		const String &	id,
		const SourceFile &	software,
		Internal::MzMLValidator &	validator
	)

protected

Helper method that writes a source file.

◆ writeSpectrum_()

void writeSpectrum_	(	std::ostream &	os,
		const SpectrumType &	spec,
		Size	s,
		Internal::MzMLValidator &	validator,
		bool	renew_native_ids,
		std::vector< std::vector< ConstDataProcessingPtr > > &	dps
	)

protected

◆ writeTo()

void writeTo ( std::ostream & )

overridevirtual

Writes the contents to a stream.

Reimplemented from XMLHandler.

◆ writeUserParam_()

void writeUserParam_	(	std::ostream &	os,
		const MetaInfoInterface &	meta,
		UInt	indent,
		String	path,
		Internal::MzMLValidator &	validator
	)		const

protected

Writes user terms.

Member Data Documentation

◆ bin_data_

std::vector<BinaryData> bin_data_

protected

The spectrum data (or chromatogram data)

◆ cexp_

const MapType* cexp_ { nullptr }

protected

map pointer for writing

◆ chrom_count_total_

Int chrom_count_total_ { -1 }

protected

◆ chromatogram_

ChromatogramType chromatogram_

protected

The current chromatogram.

◆ chromatogram_count_

UInt chromatogram_count_ { 0 }

protected

◆ chromatogram_data_

std::vector<ChromatogramData> chromatogram_data_

protected

Vector of chromatogram data stored for later parallel processing.

◆ chromatograms_offsets_

std::vector<std::pair<std::string, long> > chromatograms_offsets_

protected

◆ consumer_

Interfaces::IMSDataConsumer* consumer_ { nullptr }

protected

Consumer class to work on spectra.

◆ current_id_

String current_id_

protected

Id of the current list. Used for referencing param group, source file, sample, software, ...

◆ cv_

ControlledVocabulary cv_

protected

Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo)

◆ default_array_length_

Size default_array_length_

protected

The default number of peaks in the current spectrum.

◆ default_processing_

String default_processing_

protected

id of the default data processing (used when no processing is defined)

◆ exp_

MapType* exp_ { nullptr }

protected

map pointer for reading

◆ in_spectrum_list_

bool in_spectrum_list_ { false }

protected

Flag that indicates that we're inside a spectrum (in contrast to a chromatogram)

◆ instruments_

Map<String, Instrument> instruments_

protected

The data processing list: id => Instrument.

◆ logger_

const ProgressLogger& logger_

protected

Progress logger.

◆ mapping_

CVMappings mapping_

protected

◆ options_

PeakFileOptions options_

protected

Options that can be set for loading/storing.

◆ processing_

Map<String, std::vector< DataProcessingPtr > > processing_

protected

The data processing list: id => Instrument.

◆ ref_param_

Map<String, std::vector<SemanticValidator::CVTerm> > ref_param_

protected

The referencing param groups: id => array (accession, value)

◆ rt_set_

bool rt_set_ { false }

protected

Remember whether the RT of the spectrum was set or not.

◆ samples_

Map<String, Sample> samples_

protected

The sample list: id => Sample.

◆ scan_count_

UInt scan_count_ { 0 }

protected

Counting spectra and chromatograms.

◆ scan_count_total_

Int scan_count_total_ { -1 }

protected

◆ selected_ion_count_

UInt selected_ion_count_ { 0 }

protected

Count of selected ions.

◆ skip_chromatogram_

bool skip_chromatogram_ { false }

protected

Flag that indicates whether this chromatogram should be skipped (e.g. due to options)

◆ skip_spectrum_

bool skip_spectrum_ { false }

protected

Flag that indicates whether this spectrum should be skipped (e.g. due to options)

◆ software_

Map<String, Software> software_

protected

The software list: id => Software.

◆ source_files_

Map<String, SourceFile> source_files_

protected

The source files: id => SourceFile.

◆ spec_

SpectrumType spec_

protected

The current spectrum.

◆ spectra_offsets_

std::vector<std::pair<std::string, long> > spectra_offsets_

protected

◆ spectrum_data_

std::vector<SpectrumData> spectrum_data_

protected

Vector of spectrum data stored for later parallel processing.

Classes

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Member Typedef Documentation

◆ BinaryData

◆ ChromatogramPeakType

◆ ChromatogramType

◆ PeakType

◆ SpectrumType

Constructor & Destructor Documentation

◆ MzMLHandler() [1/3]

◆ MzMLHandler() [2/3]

◆ ~MzMLHandler()

◆ MzMLHandler() [3/3]

Member Function Documentation

◆ addSpectrumMetaData_()

◆ characters()

◆ endElement()

◆ fillChromatogramData_()

◆ getChildWithName_()

◆ getCounts()

◆ getLoadDetail()

◆ getOptions()

◆ handleCVParam_()

◆ handleUserParam_()

◆ populateChromatogramsWithData_() [1/2]

◆ populateChromatogramsWithData_() [2/2]

◆ populateSpectraWithData_() [1/2]

◆ populateSpectraWithData_() [2/2]

◆ setLoadDetail()

◆ setMSDataConsumer()

◆ setOptions()

◆ startElement()

◆ validateCV_()

◆ writeBinaryDataArray_()

◆ writeChromatogram_()

◆ writeContainerData_()

◆ writeCV_()

◆ writeDataProcessing_()

◆ writeHeader_()

◆ writePrecursor_()

◆ writeProduct_()

◆ writeSoftware_()

◆ writeSourceFile_()

◆ writeSpectrum_()

◆ writeTo()

◆ writeUserParam_()

Member Data Documentation

◆ bin_data_

◆ cexp_

◆ chrom_count_total_

◆ chromatogram_

◆ chromatogram_count_

◆ chromatogram_data_

◆ chromatograms_offsets_

◆ consumer_

◆ current_id_

◆ cv_

◆ default_array_length_

◆ default_processing_

◆ exp_

◆ in_spectrum_list_

◆ instruments_

◆ logger_

◆ mapping_

◆ options_

◆ processing_

◆ ref_param_

◆ rt_set_

◆ samples_

◆ scan_count_

◆ scan_count_total_

◆ selected_ion_count_

◆ skip_chromatogram_

◆ skip_spectrum_

◆ software_

◆ source_files_