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

Inheritance diagram for MzQuantMLHandler:

Collaboration diagram for MzQuantMLHandler:

Constructors and destructor
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_

std::map< String, std::vector< ExperimentalSettings > >	current_files_
	1.rawfilesgroup_ref 2.inputfiles for each assay as ExperimentalSettings More...

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_

	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...

	~MzQuantMLHandler () override
	Destructor. More...

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

void	startElement (const XMLCh const, const XMLCh const, 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
	Writes the contents to a stream. More...

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...

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

	MzQuantMLHandler (const MzQuantMLHandler &rhs)

MzQuantMLHandler &	operator= (const MzQuantMLHandler &rhs)

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...

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

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

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

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

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

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()

~MzQuantMLHandler ( )

override

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()

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

override

◆ endElement()

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

override

◆ 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()

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

override

◆ 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()

void writeTo ( std::ostream & )

overridevirtual

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

1.rawfilesgroup_ref 2.inputfiles for each assay as ExperimentalSettings

◆ 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

Constructors and destructor

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_