Handler for mzML file format. More...

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

Inheritance diagram for MzMLHandler:

Collaboration 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
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 and data parsing

void	endElement (const XMLCh const, const XMLCh const, const XMLCh *const qname) override
	Docu in base class XMLHandler::endElement. More...

void	startElement (const XMLCh const, const XMLCh const, const XMLCh *const qname, const xercesc::Attributes &attributes) override
	Docu in base class XMLHandler::startElelement. More...

void	characters (const XMLCh *const chars, const XMLSize_t length) override
	Docu in base class XMLHandler::characters. More...

void	writeTo (std::ostream &os) override
	Docu in base class XMLHandler::writeTo. 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...

void	getCounts (Size &spectra_counts, Size &chromatogram_counts)
	Get the spectra and chromatogram counts of a file. 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 (const xercesc::SAXParseException &exception) override

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

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

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	checkUniqueIdentifiers_ (const std::vector< ProteinIdentification > &prot_ids)

Protected Member Functions
Helper functions for storing data in memory

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
	Add extra data arrays to a spectrum. More...

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

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, const String &unit_accession="")
	Handles user terms. More...

Protected Member Functions inherited from XMLHandler
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) const
	Conversion of a String to an integer value. More...

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

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

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

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

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

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

bool	equal_ (const XMLCh a, const XMLCh b) const
	Returns if two Xerces strings are equal. More...

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

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...

Protected Attributes
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< std::pair< String, String >, bool >	cached_terms_
	CV terms-path-combinations that have been checked in validateCV_() 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...

UInt	selected_ion_count_ { 0 }
	Count of selected ions. 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
These data structures are used to store binary offsets required by the indexedMzML format, specifically the start of each <spectrum> and <chromatogram> tag is stored and will then be stored at the end of the file.
std::vector< std::pair< std::string, Int64 > >	spectra_offsets_
	Stores binary offsets for each <spectrum> tag. More...

std::vector< std::pair< std::string, Int64 > >	chromatograms_offsets_
	Stores binary offsets for each <chromatogram> tag. More...

const ProgressLogger &	logger_
	Progress logger. More...

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

temporary data structures for counting spectra and chromatograms
UInt	scan_count_ { 0 }
	number of scans which pass the options-filter More...

UInt	chromatogram_count_ { 0 }
	number of chromatograms which pass the options-filter More...

Int	scan_count_total_ { -1 }
	total number of scans in mzML file (according to 'count' attribute) More...

Int	chrom_count_total_ { -1 }
	total number of chromatograms in mzML file (according to 'count' attribute) More...

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

CVMappings	mapping_

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...

IMSDataConsumer setter
The IMSDataConsumer object allows the user to specify a callback object which can consume spectra and chromatograms on the fly. The consumer does not have to wait until data is read fully into memory, but will start receiving data as soon as it is available (read from disk).
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

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...

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

Helper functions for writing data

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...

void	writeHeader_ (std::ostream &os, const MapType &exp, std::vector< std::vector< ConstDataProcessingPtr > > &dps, const Internal::MzMLValidator &validator)
	Write out XML header including (everything up to spectrumList / chromatogramList. More...

void	writeSpectrum_ (std::ostream &os, const SpectrumType &spec, Size spec_idx, const Internal::MzMLValidator &validator, bool renew_native_ids, std::vector< std::vector< ConstDataProcessingPtr > > &dps)
	Write out a single spectrum. More...

void	writeChromatogram_ (std::ostream &os, const ChromatogramType &chromatogram, Size chrom_idx, const Internal::MzMLValidator &validator)
	Write out a single chromatogram. More...

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

template<typename DataType >
void	writeBinaryDataArray_ (std::ostream &os, const PeakFileOptions &options, std::vector< DataType > &data, bool is32bit, String array_type)
	Write a single <binaryDataArray> element to the output. More...

void	writeBinaryFloatDataArray_ (std::ostream &os, const PeakFileOptions &options, const OpenMS::DataArrays::FloatDataArray &array, const Size spec_chrom_idx, const Size array_idx, bool is_spectrum, const Internal::MzMLValidator &validator)
	Write a single <binaryDataArray> element for a float data array to the output. More...

void	writeUserParam_ (std::ostream &os, const MetaInfoInterface &meta, UInt indent, const String &path, const Internal::MzMLValidator &validator, const std::set< String > &exclude={}) const
	Writes user terms. More...

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

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

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

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

void	writeProduct_ (std::ostream &os, const Product &product, const 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...

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

Detailed Description

Handler for mzML file format.

This class handles parsing and writing of the mzML file format. It supports reading data directly into memory or parsing on-the-fly using a consumer (see Setting a consumer). In read-mode, this class will parse an MzML XML file and append the input spectra to the provided MSExperiment object or to the provided Interfaces::IMSDataConsumer (needs to be provided separately through setMSDataConsumer()).

Functions constituting the XML reading/writing interface can be found under XML Handling functions, helper functions specifically used for writing out to XML are organized under Writing functions and helper functions used for reading in XML from disk are organized under Readingfunctions".

See the MzMLHandlerHelper for additional helper functions that are independent of state.

Note: Do not use this class directly. It is only needed in MzMLFile.; Only upon destruction of this class it can be guaranteed that all data has been appended to the appropriate consumer of the data. Do not try to access the data before that.

Todo:: replace hardcoded cv stuff with more flexible handling via obo r/w.

Class Documentation

◆ OpenMS::Internal::MzMLHandler::ChromatogramData

struct OpenMS::Internal::MzMLHandler::ChromatogramData

Data necessary to generate a single chromatogram.

Small struct holds all data necessary to populate a chromatogram at a later timepoint (since reading of the base64 data and generation of chromatogram can be done at distinct timepoints).

Collaboration diagram for MzMLHandler::ChromatogramData:

[legend]

Class Members
ChromatogramType	chromatogram
vector< BinaryData >	data
Size	default_array_length

◆ OpenMS::Internal::MzMLHandler::SpectrumData

struct OpenMS::Internal::MzMLHandler::SpectrumData

Data necessary to generate a single spectrum.

Small struct holds all data necessary to populate a spectrum at a later timepoint (since reading of the base64 data and generation of spectra can be done at distinct timepoints).

Collaboration diagram for MzMLHandler::SpectrumData:

[legend]

Class Members
vector< BinaryData >	data
Size	default_array_length
SpectrumType	spectrum

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

Add extra data arrays to a spectrum.

Add the float, integer and string data arrays to a spectrum.

◆ characters()

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

override

Docu in base class XMLHandler::characters.

◆ endElement()

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

override

Docu in base class XMLHandler::endElement.

◆ 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

Helper method to look 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.

Referenced by MzMLSwathFileConsumer::addNewSwathMap_(), and TOPPOpenSwathBase::prepareChromOutput().

◆ 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,
		const String &	unit_accession = `""`
	)

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 &	length,
		const PeakFileOptions &	peak_file_options,
		ChromatogramType &	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.

Parameters

input_data	The input data with which to fill the spectra
length	The input data length (number of data points)
peak_file_options	Will be used if only part of the data should be copied (RT, mz or intensity range)
chromatogram	The output chromatogram

◆ 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 &	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.; This function takes about 50 % of total load time with a single thread and parallelizes linearly up to at least 10 threads.

Parameters

input_data	The input data with which to fill the spectra
length	The input data length (number of data points)
peak_file_options	Will be used if only part of the data should be copied (RT, mz or intensity range)
spectrum	The output spectrum

◆ 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

Docu in base class XMLHandler::startElelement.

◆ 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 &	options,
		std::vector< DataType > &	data,
		bool	is32bit,
		String	array_type
	)

protected

Write a single <binaryDataArray> element to the output.

Parameters

os	The stream into which to write
options	The PeakFileOptions which determines the compression type to use
data	The data to write (32bit float or 64 bit double)
is32bit	Whether data is 32bit
array_type	Which type of data array is written (mz, time, intensity or float_data)

Note: The data argument may be modified by the function (see Base64 for reasons why)

◆ writeBinaryFloatDataArray_()

void writeBinaryFloatDataArray_	(	std::ostream &	os,
		const PeakFileOptions &	options,
		const OpenMS::DataArrays::FloatDataArray &	array,
		const Size	spec_chrom_idx,
		const Size	array_idx,
		bool	is_spectrum,
		const Internal::MzMLValidator &	validator
	)

protected

Write a single <binaryDataArray> element for a float data array to the output.

This is only for non-standard data arrays which are treated slightly differently by the standard.

Parameters

os	The stream into which to write
options	The PeakFileOptions which determines the compression type to use
array	The data to write
spec_chrom_idx	The index of the current spectrum or chromatogram
array_idx	The index of the current float data array
is_spectrum	Whether data is associated with a spectrum (if false, a chromatogram is assumed)
validator	Validator object

◆ writeChromatogram_()

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

protected

Write out a single chromatogram.

◆ 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,
		const 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,
		const Internal::MzMLValidator &	validator
	)

protected

Write out XML header including (everything up to spectrumList / chromatogramList.

◆ writePrecursor_()

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

protected

Helper method that write precursor information from spectra and chromatograms.

◆ writeProduct_()

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

protected

Helper method that writes a software.

◆ writeSourceFile_()

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

protected

Helper method that writes a source file.

◆ writeSpectrum_()

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

protected

Write out a single spectrum.

◆ writeTo()

void writeTo ( std::ostream & os )

overridevirtual

Docu in base class XMLHandler::writeTo.

Reimplemented from XMLHandler.

◆ writeUserParam_()

void writeUserParam_	(	std::ostream &	os,
		const MetaInfoInterface &	meta,
		UInt	indent,
		const String &	path,
		const Internal::MzMLValidator &	validator,
		const std::set< String > &	exclude = `{}`
	)		const

protected

Writes user terms.

Member Data Documentation

◆ bin_data_

std::vector<BinaryData> bin_data_

protected

The spectrum data (or chromatogram data)

◆ cached_terms_

Map<std::pair<String, String>, bool> cached_terms_

mutableprotected

CV terms-path-combinations that have been checked in validateCV_()

◆ cexp_

const MapType* cexp_ { nullptr }

protected

map pointer for writing

◆ chrom_count_total_

Int chrom_count_total_ { -1 }

protected

total number of chromatograms in mzML file (according to 'count' attribute)

◆ chromatogram_

ChromatogramType chromatogram_

protected

The current chromatogram.

◆ chromatogram_count_

UInt chromatogram_count_ { 0 }

protected

number of chromatograms which pass the options-filter

◆ 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, Int64> > chromatograms_offsets_

protected

Stores binary offsets for each <chromatogram> tag.

◆ 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_

const 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

number of scans which pass the options-filter

◆ scan_count_total_

Int scan_count_total_ { -1 }

protected

total number of scans in mzML file (according to 'count' attribute)

◆ 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, Int64> > spectra_offsets_

protected

Stores binary offsets for each <spectrum> tag.

◆ spectrum_data_

std::vector<SpectrumData> spectrum_data_

protected

Vector of spectrum data stored for later parallel processing.

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

IMSDataConsumer setter

Helper functions for writing data

Additional Inherited Members

Detailed Description

Class Documentation

◆ OpenMS::Internal::MzMLHandler::ChromatogramData

◆ OpenMS::Internal::MzMLHandler::SpectrumData

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_()

◆ writeBinaryFloatDataArray_()

◆ writeChromatogram_()

◆ writeContainerData_()

◆ writeCV_()

◆ writeDataProcessing_()

◆ writeHeader_()

◆ writePrecursor_()

◆ writeProduct_()

◆ writeSoftware_()

◆ writeSourceFile_()

◆ writeSpectrum_()

◆ writeTo()

◆ writeUserParam_()

Member Data Documentation

◆ bin_data_

◆ cached_terms_

◆ 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_