Consumer class that writes MS data to disk using the mzML format. More...

#include <OpenMS/FORMAT/DATAACCESS/MSDataWritingConsumer.h>

Inheritance diagram for PlainMSDataWritingConsumer:

Collaboration diagram for PlainMSDataWritingConsumer:

Public Member Functions
	PlainMSDataWritingConsumer (String filename)

Public Member Functions inherited from MSDataWritingConsumer
	MSDataWritingConsumer (const String &filename)
	Constructor. More...

	~MSDataWritingConsumer () override
	Destructor. More...

void	setExperimentalSettings (const ExperimentalSettings &exp) override
	Set experimental settings for the whole file. More...

void	setExpectedSize (Size expectedSpectra, Size expectedChromatograms) override
	Set expected size of spectra and chromatograms to be written. More...

void	consumeSpectrum (SpectrumType &s) override
	Consume a spectrum. More...

void	consumeChromatogram (ChromatogramType &c) override
	Consume a chromatogram. More...

virtual void	addDataProcessing (DataProcessing d)
	Optionally add a data processing method to each chromatogram and spectrum. More...

virtual Size	getNrSpectraWritten ()
	Return the number of spectra written. More...

virtual Size	getNrChromatogramsWritten ()
	Return the number of chromatograms written. More...

Public Member Functions inherited from MzMLHandler
	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...

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...

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...

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

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

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

DataValue	cvParamToValue (const ControlledVocabulary &cv, const String &parent_tag, const String &accession, const String &name, const String &value, const String &unit_accession) const
	Convert the value of a <cvParam value=.> (as commonly found in PSI schemata) to the DataValue with the correct type (e.g. int) according to the type stored in the CV (usually PSI-MS CV), as well as set its unit. More...

DataValue	cvParamToValue (const ControlledVocabulary &cv, const CVTerm &raw_term) const
	Convert the value of a <cvParam value=.> (as commonly found in PSI schemata) to the DataValue with the correct type (e.g. int) according to the type stored in the CV (usually PSI-MS CV), as well as set its unit. More...

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

Public Member Functions inherited from IMSDataConsumer
virtual	~IMSDataConsumer ()

Private Member Functions
void	processSpectrum_ (MapType::SpectrumType &) override
	Process a spectrum before storing to disk. More...

void	processChromatogram_ (MapType::ChromatogramType &) override
	Process a chromatogram before storing to disk. More...

Additional Inherited Members
Public Types inherited from MSDataWritingConsumer
typedef PeakMap	MapType

typedef MapType::SpectrumType	SpectrumType

typedef MapType::ChromatogramType	ChromatogramType

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 }

Public Types inherited from IMSDataConsumer
typedef MSSpectrum	SpectrumType

typedef MSChromatogram	ChromatogramType

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

static DataValue	fromXSDString (const String &type, const String &value)
	Convert an XSD type (e.g. 'xsd:double') to a DataValue. More...

Protected Types inherited from MzMLHandler
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 inherited from MzMLHandler
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...

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

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 inherited from MSDataWritingConsumer
std::ofstream	ofs_
	File stream (to write mzML) More...

bool	started_writing_
	Stores whether we have already started writing any data. More...

bool	writing_spectra_
	Stores whether we are currently writing spectra. More...

bool	writing_chromatograms_
	Stores whether we are currently writing chromatograms. More...

Size	spectra_written_
	Number of spectra written. More...

Size	chromatograms_written_
	Number of chromatograms written. More...

Size	spectra_expected_
	Number of spectra expected. More...

Size	chromatograms_expected_
	Number of chromatograms expected. More...

bool	add_dataprocessing_
	Whether to add dataprocessing term to the data before writing. More...

Internal::MzMLValidator *	validator_
	Validator that knows about CV terms. More...

ExperimentalSettings	settings_
	Experimental settings to use for the whole file. More...

std::vector< std::vector< ConstDataProcessingPtr > >	dps_
	Vector of data processing objects -> will be filled by writeHeader_. More...

DataProcessingPtr	additional_dataprocessing_
	The dataprocessing to be added to each spectrum/chromatogram. More...

Protected Attributes inherited from MzMLHandler
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...

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

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

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

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

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

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

std::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...

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...

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_

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...

Protected Attributes inherited from XMLHandler
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...

Detailed Description

Consumer class that writes MS data to disk using the mzML format.

A very simple implementation of MSDataWritingConsumer, not offering the ability to modify the spectra before writing. This is probably the class you want if you want to write mzML files to disk by providing spectra and chromatograms sequentially.

Constructor & Destructor Documentation

◆ PlainMSDataWritingConsumer()

PlainMSDataWritingConsumer ( String filename )

inlineexplicit

Member Function Documentation

◆ processChromatogram_()

void processChromatogram_ ( MapType::ChromatogramType & c )

inlineoverrideprivatevirtual

Process a chromatogram before storing to disk.

Redefine this function to determine chromatogram processing before writing to disk.

Implements MSDataWritingConsumer.

◆ processSpectrum_()

void processSpectrum_ ( MapType::SpectrumType & s )

inlineoverrideprivatevirtual

Process a spectrum before storing to disk.

Redefine this function to determine spectra processing before writing to disk.