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

Inheritance diagram for MzXMLHandler:

Collaboration diagram for MzXMLHandler:

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

Constructors and destructor
typedef MapType::PeakType	PeakType
	Peak type. More...

typedef MSSpectrum	SpectrumType
	Spectrum type. More...

MapType *	exp_
	map pointer for reading More...

const MapType *	cexp_
	map pointer for writing More...

PeakFileOptions	options_
	Options for loading and storing. More...

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

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

	~MzXMLHandler () override
	Destructor. 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...

void	endElement (const XMLCh const uri, const XMLCh const local_name, const XMLCh *const qname) override

void	startElement (const XMLCh const uri, const XMLCh const local_name, 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
	Write the contents to a stream. More...

void	setOptions (const PeakFileOptions &options)
	Sets the options. More...

UInt	getScanCount () const
	Gets the scan count. More...

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

temporary data structures to hold parsed data
Int	nesting_level_

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

bool	skip_spectrum_
	Flag that indicates whether this spectrum should be skipped (due to options) More...

UInt	spec_write_counter_
	spectrum counter (spectra without peaks are not written) More...

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

UInt	scan_count_
	Consumer class to work on spectra. More...

const ProgressLogger &	logger_
	Progress logging class. More...

std::vector< boost::shared_ptr< DataProcessing > >	data_processing_
	data processing auxiliary variable More...

bool	writeAttributeIfExists_ (std::ostream &os, const MetaInfoInterface &meta, const String &metakey, const String &attname)

void	writeUserParam_ (std::ostream &os, const MetaInfoInterface &meta, int indent=4, const String &tag="nameValue")
	write metaInfo to xml (usually in nameValue-tag) More...

void	doPopulateSpectraWithData_ (SpectrumData &spectrum_data)
	Fill a single spectrum with data from input. More...

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

	MzXMLHandler ()
	Not implemented. More...

void	init_ ()
	initialize members (call from C'tor) 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 }

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

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 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 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...

Class Documentation

◆ OpenMS::Internal::MzXMLHandler::SpectrumData

struct OpenMS::Internal::MzXMLHandler::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 MzXMLHandler::SpectrumData:

[legend]

Class Members
String	char_rest_
String	compressionType_
UInt	peak_count_
String	precision_
bool	skip_data
SpectrumType	spectrum

Member Typedef Documentation

◆ PeakType

typedef MapType::PeakType PeakType

protected

Peak type.

◆ SpectrumType

typedef MSSpectrum SpectrumType

protected

Spectrum type.

Constructor & Destructor Documentation

◆ MzXMLHandler() [1/3]

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

Constructor for a read-only handler.

◆ MzXMLHandler() [2/3]

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

Constructor for a write-only handler.

◆ ~MzXMLHandler()

~MzXMLHandler ( )

inlineoverride

Destructor.

◆ MzXMLHandler() [3/3]

MzXMLHandler ( )

private

Not implemented.

Member Function Documentation

◆ characters()

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

override

◆ doPopulateSpectraWithData_()

void doPopulateSpectraWithData_ ( SpectrumData & spectrum_data )

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.

◆ endElement()

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

override

◆ getLoadDetail()

LOADDETAIL getLoadDetail ( ) const

overridevirtual

handler which support partial loading, implement this method

Reimplemented from XMLHandler.

◆ getScanCount()

UInt getScanCount ( ) const

inline

Gets the scan count.

◆ init_()

void init_ ( )

private

initialize members (call from C'tor)

◆ populateSpectraWithData_()

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.

◆ setLoadDetail()

void setLoadDetail ( const LOADDETAIL d )

overridevirtual

handler which support partial loading, implement this method

Reimplemented from XMLHandler.

◆ setMSDataConsumer()

void setMSDataConsumer ( Interfaces::IMSDataConsumer * consumer )

inline

Set the IMSDataConsumer consumer which will consume the read data.

◆ setOptions()

void setOptions ( const PeakFileOptions & options )

inline

Sets the options.

◆ startElement()

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

override

◆ writeAttributeIfExists_()

bool writeAttributeIfExists_	(	std::ostream &	os,
		const MetaInfoInterface &	meta,
		const String &	metakey,
		const String &	attname
	)

inlineprotected

write metaInfo to xml (usually in nameValue-tag) returns true if metavalue existed and data was written to the stream

◆ writeTo()

void writeTo ( std::ostream & os )

overridevirtual

Write the contents to a stream.

Reimplemented from XMLHandler.

◆ writeUserParam_()

void writeUserParam_	(	std::ostream &	os,
		const MetaInfoInterface &	meta,
		int	indent = `4`,
		const String &	tag = `"nameValue"`
	)

inlineprotected

write metaInfo to xml (usually in nameValue-tag)

Member Data Documentation

◆ cexp_

const MapType* cexp_

protected

map pointer for writing

◆ consumer_

Interfaces::IMSDataConsumer* consumer_

protected

Consumer class to work on spectra.

◆ data_processing_

std::vector< boost::shared_ptr< DataProcessing> > data_processing_

protected

data processing auxiliary variable

◆ exp_

MapType* exp_

protected

map pointer for reading

◆ logger_

const ProgressLogger& logger_

protected

Progress logging class.

◆ nesting_level_

Int nesting_level_

protected

◆ options_

PeakFileOptions options_

protected

Options for loading and storing.

◆ scan_count_

UInt scan_count_

protected

Consumer class to work on spectra.

◆ skip_spectrum_

bool skip_spectrum_

protected

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

◆ spec_write_counter_

UInt spec_write_counter_

protected

spectrum counter (spectra without peaks are not written)

◆ spectrum_data_

std::vector< SpectrumData > spectrum_data_

protected

Vector of spectrum data stored for later parallel processing.

Classes

Constructors and destructor

temporary data structures to hold parsed data

Additional Inherited Members

Class Documentation

◆ OpenMS::Internal::MzXMLHandler::SpectrumData

Member Typedef Documentation

◆ PeakType

◆ SpectrumType

Constructor & Destructor Documentation

◆ MzXMLHandler() [1/3]

◆ MzXMLHandler() [2/3]

◆ ~MzXMLHandler()

◆ MzXMLHandler() [3/3]

Member Function Documentation

◆ characters()

◆ doPopulateSpectraWithData_()

◆ endElement()

◆ getLoadDetail()

◆ getScanCount()

◆ init_()

◆ populateSpectraWithData_()

◆ setLoadDetail()

◆ setMSDataConsumer()

◆ setOptions()

◆ startElement()

◆ writeAttributeIfExists_()

◆ writeTo()

◆ writeUserParam_()

Member Data Documentation

◆ cexp_

◆ consumer_

◆ data_processing_

◆ exp_

◆ logger_

◆ nesting_level_

◆ options_

◆ scan_count_

◆ skip_spectrum_

◆ spec_write_counter_

◆ spectrum_data_