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

Inheritance diagram for MzXMLHandler:

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

Public Member Functions
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...

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 ()
	Gets the scan count. More...

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

Constructors and destructor
	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...

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 MSSpectrum	SpectrumType
	Spectrum type. More...

Protected Member Functions
std::ostream &	writeAttributeIfExists_ (std::ostream &os, const MetaInfoInterface &meta, const String &metakey, const String &attname)
	write metaInfo to xml (usually in nameValue-tag) More...

void	writeUserParam_ (std::ostream &os, const MetaInfoInterface &meta, int indent=4, 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...

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_
	map pointer for reading More...

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

PeakFileOptions	options_
	Options for loading and storing. 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...

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...

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...

Private Member Functions
	MzXMLHandler ()
	Not implemented. More...

void	init_ ()
	initialize members (call from C'tor) More...

void	initStaticMembers_ ()

Static Private Attributes
static const XMLCh *	s_value_

static const XMLCh *	s_count_

static const XMLCh *	s_type_

static const XMLCh *	s_name_

static const XMLCh *	s_version_

static const XMLCh *	s_filename_

static const XMLCh *	s_filetype_

static const XMLCh *	s_filesha1_

static const XMLCh *	s_completiontime_

static const XMLCh *	s_precision_

static const XMLCh *	s_byteorder_

static const XMLCh *	s_contentType_

static const XMLCh *	s_compressionType_

static const XMLCh *	s_precursorintensity_

static const XMLCh *	s_precursorcharge_

static const XMLCh *	s_windowwideness_

static const XMLCh *	s_mslevel_

static const XMLCh *	s_peakscount_

static const XMLCh *	s_polarity_

static const XMLCh *	s_scantype_

static const XMLCh *	s_filterline_

static const XMLCh *	s_retentiontime_

static const XMLCh *	s_startmz_

static const XMLCh *	s_endmz_

static const XMLCh *	s_first_

static const XMLCh *	s_last_

static const XMLCh *	s_phone_

static const XMLCh *	s_email_

static const XMLCh *	s_uri_

static const XMLCh *	s_num_

static const XMLCh *	s_intensitycutoff_

static const XMLCh *	s_centroided_

static const XMLCh *	s_deisotoped_

static const XMLCh *	s_chargedeconvoluted_

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

◆ 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()

virtual LOADDETAIL getLoadDetail ( ) const

overridevirtual

handler which support partial loading, implement this method

Reimplemented from XMLHandler.

◆ getScanCount()

UInt getScanCount ( )

inline

Gets the scan count.

◆ init_()

void init_ ( )

private

initialize members (call from C'tor)

◆ initStaticMembers_()

void initStaticMembers_ ( )

private

◆ 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()

virtual 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_()

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

inlineprotected

write metaInfo to xml (usually in nameValue-tag)

◆ 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`,
		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.

◆ s_byteorder_

const XMLCh* s_byteorder_

staticprivate

◆ s_centroided_

const XMLCh* s_centroided_

staticprivate

◆ s_chargedeconvoluted_

const XMLCh* s_chargedeconvoluted_

staticprivate

◆ s_completiontime_

const XMLCh* s_completiontime_

staticprivate

◆ s_compressionType_

const XMLCh* s_compressionType_

staticprivate

◆ s_contentType_

const XMLCh* s_contentType_

staticprivate

◆ s_count_

const XMLCh* s_count_

staticprivate

◆ s_deisotoped_

const XMLCh* s_deisotoped_

staticprivate

◆ s_email_

const XMLCh* s_email_

staticprivate

◆ s_endmz_

const XMLCh* s_endmz_

staticprivate

◆ s_filename_

const XMLCh* s_filename_

staticprivate

◆ s_filesha1_

const XMLCh* s_filesha1_

staticprivate

◆ s_filetype_

const XMLCh* s_filetype_

staticprivate

◆ s_filterline_

const XMLCh* s_filterline_

staticprivate

◆ s_first_

const XMLCh* s_first_

staticprivate

◆ s_intensitycutoff_

const XMLCh* s_intensitycutoff_

staticprivate

◆ s_last_

const XMLCh* s_last_

staticprivate

◆ s_mslevel_

const XMLCh* s_mslevel_

staticprivate

◆ s_name_

const XMLCh* s_name_

staticprivate

◆ s_num_

const XMLCh* s_num_

staticprivate

◆ s_peakscount_

const XMLCh* s_peakscount_

staticprivate

◆ s_phone_

const XMLCh* s_phone_

staticprivate

◆ s_polarity_

const XMLCh* s_polarity_

staticprivate

◆ s_precision_

const XMLCh* s_precision_

staticprivate

◆ s_precursorcharge_

const XMLCh* s_precursorcharge_

staticprivate

◆ s_precursorintensity_

const XMLCh* s_precursorintensity_

staticprivate

◆ s_retentiontime_

const XMLCh* s_retentiontime_

staticprivate

◆ s_scantype_

const XMLCh* s_scantype_

staticprivate

◆ s_startmz_

const XMLCh* s_startmz_

staticprivate

◆ s_type_

const XMLCh* s_type_

staticprivate

◆ s_uri_

const XMLCh* s_uri_

staticprivate

◆ s_value_

const XMLCh* s_value_

staticprivate

◆ s_version_

const XMLCh* s_version_

staticprivate

◆ s_windowwideness_

const XMLCh* s_windowwideness_

staticprivate

◆ 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

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Private Member Functions

Static Private Attributes

Additional Inherited Members

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_()

◆ initStaticMembers_()

◆ populateSpectraWithData_()

◆ setLoadDetail()

◆ setMSDataConsumer()

◆ setOptions()

◆ startElement()

◆ writeAttributeIfExists_()

◆ writeTo()

◆ writeUserParam_()

Member Data Documentation

◆ cexp_

◆ consumer_

◆ data_processing_

◆ exp_

◆ logger_

◆ nesting_level_

◆ options_

◆ s_byteorder_

◆ s_centroided_

◆ s_chargedeconvoluted_

◆ s_completiontime_

◆ s_compressionType_

◆ s_contentType_

◆ s_count_

◆ s_deisotoped_

◆ s_email_

◆ s_endmz_

◆ s_filename_

◆ s_filesha1_

◆ s_filetype_

◆ s_filterline_

◆ s_first_

◆ s_intensitycutoff_

◆ s_last_

◆ s_mslevel_

◆ s_name_

◆ s_num_

◆ s_peakscount_

◆ s_phone_

◆ s_polarity_

◆ s_precision_

◆ s_precursorcharge_

◆ s_precursorintensity_

◆ s_retentiontime_

◆ s_scantype_

◆ s_startmz_

◆ s_type_

◆ s_uri_

◆ s_value_

◆ s_version_

◆ s_windowwideness_

◆ scan_count_

◆ skip_spectrum_

◆ spec_write_counter_

◆ spectrum_data_