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

Inheritance diagram for MzQuantMLHandler:

Public Member Functions
virtual void	endElement (const XMLCh const, const XMLCh const, const XMLCh *const qname)
	Parsing method for closing tags. More...

virtual void	startElement (const XMLCh const, const XMLCh const, const XMLCh *const qname, const xercesc::Attributes &attributes)
	Parsing method for opening tags. More...

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

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

Constructors and destructor
	MzQuantMLHandler (const MSQuantifications &msq, const String &filename, const String &version, const ProgressLogger &logger)
	Constructor for a write-only handler. More...

	MzQuantMLHandler (MSQuantifications &msq, const String &filename, const String &version, const ProgressLogger &logger)
	Constructor for a read-only handler. More...

virtual	~MzQuantMLHandler ()
	Destructor. More...

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

virtual	~XMLHandler ()
	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...

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

void	fatalError (const xercesc::SAXParseException &exception)

void	error (const xercesc::SAXParseException &exception)

void	warning (const xercesc::SAXParseException &exception)

Protected Member Functions
void	handleCVParam_ (const String &parent_parent_tag, const String &parent_tag, const String &accession, const String &name, const String &value, const xercesc::Attributes &attributes, const String &cv_ref, const String &unit_accession="")
	Handles CV terms. More...

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

void	writeCVParams_ (String &s, const Map< String, std::vector< CVTerm > > &, UInt indent)
	Write CV term. More...

void	writeUserParams_ (std::ostream &os, const MetaInfoInterface &meta, UInt indent)
	Writes user terms. More...

void	writeUserParams_ (String &s, const MetaInfoInterface &meta, UInt indent)

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

void	writeFeature_ (String &feature_xml, const std::vector< FeatureMap > &fm, UInt indentation_level)
	Helper method that writes the featuremaps. 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...

char *	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...

char *	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
const ProgressLogger &	logger_
	Progress logger. More...

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

String	tag_

MSQuantifications *	msq_

const MSQuantifications *	cmsq_

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...

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
	MzQuantMLHandler ()
	Helper method that writes a source file. More...

	MzQuantMLHandler (const MzQuantMLHandler &rhs)

MzQuantMLHandler &	operator= (const MzQuantMLHandler &rhs)

Private Attributes
std::map< String, std::vector< ExperimentalSettings > >	current_files_

String	current_id_

String	current_cf_id_

Size	current_count_

std::vector< MetaInfo >	up_stack_

std::vector< CVTerm >	cvp_stack_

MSQuantifications::Assay	current_assay_

std::multimap< String, String >	cm_cf_ids_

std::map< String, String >	f_cf_ids_

std::map< String, ConsensusFeature >	cf_cf_obj_

std::map< String, FeatureHandle >	f_f_obj_

std::map< String, ConsensusFeature::Ratio >	r_rtemp_

std::map< String, String >	numden_r_ids_

std::map< String, ConsensusFeature::Ratio >	r_r_obj_

std::map< String, Software >	current_sws_

std::map< int, DataProcessing >	current_orderedps_

std::pair< int, DataProcessing >	current_dp_

std::set< DataProcessing::ProcessingAction >	current_pas_

std::vector< String >	current_col_types_

std::vector< double >	current_dm_values_

std::vector< double >	current_row_

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

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

XML handler for MzQuantMLFile.

Note: Do not use this class. It is only needed in MzQuantMLFile.

Constructor & Destructor Documentation

◆ MzQuantMLHandler() [1/4]

MzQuantMLHandler	(	const MSQuantifications &	msq,
		const String &	filename,
		const String &	version,
		const ProgressLogger &	logger
	)

Constructor for a write-only handler.

◆ MzQuantMLHandler() [2/4]

MzQuantMLHandler	(	MSQuantifications &	msq,
		const String &	filename,
		const String &	version,
		const ProgressLogger &	logger
	)

Constructor for a read-only handler.

◆ ~MzQuantMLHandler()

virtual ~MzQuantMLHandler ( )

virtual

Destructor.

◆ MzQuantMLHandler() [3/4]

MzQuantMLHandler ( )

private

Helper method that writes a source file.

◆ MzQuantMLHandler() [4/4]

MzQuantMLHandler ( const MzQuantMLHandler & rhs )

private

Member Function Documentation

◆ characters()

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

virtual

Parsing method for character data.

Reimplemented from XMLHandler.

◆ endElement()

virtual void endElement	(	const XMLCh *	uri,
		const XMLCh *	localname,
		const XMLCh *const	qname
	)

virtual

Parsing method for closing tags.

Reimplemented from XMLHandler.

◆ getChildWithName_()

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

protected

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

◆ handleCVParam_()

void handleCVParam_	(	const String &	parent_parent_tag,
		const String &	parent_tag,
		const String &	accession,
		const String &	name,
		const String &	value,
		const xercesc::Attributes &	attributes,
		const String &	cv_ref,
		const String &	unit_accession = `""`
	)

protected

Handles CV terms.

◆ handleUserParam_()

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

protected

Handles user terms.

◆ operator=()

MzQuantMLHandler& operator= ( const MzQuantMLHandler & rhs )

private

◆ startElement()

virtual void startElement	(	const XMLCh *	uri,
		const XMLCh *	localname,
		const XMLCh *const	qname,
		const xercesc::Attributes &	attrs
	)

virtual

Parsing method for opening tags.

Reimplemented from XMLHandler.

◆ writeCVParams_()

void writeCVParams_	(	String &	s,
		const Map< String, std::vector< CVTerm > > &	,
		UInt	indent
	)

protected

Write CV term.

◆ writeFeature_()

void writeFeature_	(	String &	feature_xml,
		const std::vector< FeatureMap > &	fm,
		UInt	indentation_level
	)

protected

Helper method that writes the featuremaps.

◆ writeTo()

virtual void writeTo ( std::ostream & )

virtual

Writes the contents to a stream.

Reimplemented from XMLHandler.

◆ writeUserParams_() [1/2]

void writeUserParams_	(	std::ostream &	os,
		const MetaInfoInterface &	meta,
		UInt	indent
	)

protected

Writes user terms.

◆ writeUserParams_() [2/2]

void writeUserParams_	(	String &	s,
		const MetaInfoInterface &	meta,
		UInt	indent
	)

protected

Member Data Documentation

◆ cf_cf_obj_

std::map<String, ConsensusFeature> cf_cf_obj_

private

◆ cm_cf_ids_

std::multimap<String, String> cm_cf_ids_

private

◆ cmsq_

const MSQuantifications* cmsq_

protected

◆ current_assay_

MSQuantifications::Assay current_assay_

private

◆ current_cf_id_

String current_cf_id_

private

◆ current_col_types_

std::vector<String> current_col_types_

private

◆ current_count_

Size current_count_

private

◆ current_dm_values_

std::vector<double> current_dm_values_

private

◆ current_dp_

std::pair<int, DataProcessing> current_dp_

private

◆ current_files_

std::map<String, std::vector<ExperimentalSettings> > current_files_

private

◆ current_id_

String current_id_

private

◆ current_orderedps_

std::map<int, DataProcessing> current_orderedps_

private

◆ current_pas_

std::set<DataProcessing::ProcessingAction> current_pas_

private

◆ current_row_

std::vector<double> current_row_

private

◆ current_sws_

std::map<String, Software> current_sws_

private

◆ cv_

ControlledVocabulary cv_

protected

Controlled vocabulary (hopefully the psi-pi from OpenMS/share/OpenMS/CV/psi-pi.obo)

◆ cvp_stack_

std::vector<CVTerm> cvp_stack_

private

◆ f_cf_ids_

std::map<String, String> f_cf_ids_

private

◆ f_f_obj_

std::map<String, FeatureHandle> f_f_obj_

private

◆ logger_

const ProgressLogger& logger_

protected

Progress logger.

◆ msq_

MSQuantifications* msq_

protected

◆ numden_r_ids_

std::map<String, String> numden_r_ids_

private

◆ r_r_obj_

std::map<String, ConsensusFeature::Ratio> r_r_obj_

private

◆ r_rtemp_

std::map<String, ConsensusFeature::Ratio> r_rtemp_

private

◆ tag_

String tag_

protected

◆ up_stack_

std::vector<MetaInfo> up_stack_

private

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MzQuantMLHandler() [1/4]

◆ MzQuantMLHandler() [2/4]

◆ ~MzQuantMLHandler()

◆ MzQuantMLHandler() [3/4]

◆ MzQuantMLHandler() [4/4]

Member Function Documentation

◆ characters()

◆ endElement()

◆ getChildWithName_()

◆ handleCVParam_()

◆ handleUserParam_()

◆ operator=()

◆ startElement()

◆ writeCVParams_()

◆ writeFeature_()

◆ writeTo()

◆ writeUserParams_() [1/2]

◆ writeUserParams_() [2/2]

Member Data Documentation

◆ cf_cf_obj_

◆ cm_cf_ids_

◆ cmsq_

◆ current_assay_

◆ current_cf_id_

◆ current_col_types_

◆ current_count_

◆ current_dm_values_

◆ current_dp_

◆ current_files_

◆ current_id_

◆ current_orderedps_

◆ current_pas_

◆ current_row_

◆ current_sws_

◆ cv_

◆ cvp_stack_

◆ f_cf_ids_

◆ f_f_obj_

◆ logger_

◆ msq_

◆ numden_r_ids_

◆ r_r_obj_

◆ r_rtemp_

◆ tag_

◆ up_stack_