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

Inheritance diagram for TraMLHandler:

Collaboration diagram for TraMLHandler:

Public Types
typedef std::vector< ReactionMonitoringTransition::Product >	ProductListType

typedef std::vector< ReactionMonitoringTransition::Configuration >	ConfigurationListType

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
	TraMLHandler ()=delete

	TraMLHandler (const TraMLHandler &rhs)=delete

TraMLHandler &	operator= (const TraMLHandler &rhs)=delete

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...

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...

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

Constructors and destructor
const ProgressLogger &	logger_
	Progress logger. More...

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

String	tag_

TargetedExperiment *	exp_

const TargetedExperiment *	cexp_

TargetedExperiment::Publication	actual_publication_

TargetedExperiment::Contact	actual_contact_

TargetedExperiment::Instrument	actual_instrument_

TargetedExperiment::Prediction	actual_prediction_

Software	actual_software_

TargetedExperiment::Protein	actual_protein_

TargetedExperiment::RetentionTime	actual_rt_

TargetedExperiment::Peptide	actual_peptide_

TargetedExperiment::Compound	actual_compound_

ReactionMonitoringTransition	actual_transition_

IncludeExcludeTarget	actual_target_

CVTermList	actual_validation_

TargetedExperiment::Interpretation	actual_interpretation_

std::vector< ReactionMonitoringTransition::Product >	actual_intermediate_products_

ReactionMonitoringTransition::Product	actual_product_

ReactionMonitoringTransition::Configuration	actual_configuration_

SourceFile	actual_sourcefile_

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

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

	~TraMLHandler () 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 CVTerm &cv_term)
	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	writeUserParam_ (std::ostream &os, const MetaInfoInterface &meta, UInt indent) const
	Writes user terms. More...

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

void	writeCVParams_ (std::ostream &os, const CVTermList &cv_terms, UInt indent) const

void	writeCVParams_ (std::ostream &os, const CVTermListInterface &cv_terms, UInt indent) const

void	writeCVList_ (std::ostream &os, const std::map< String, std::vector< CVTerm >> &cv_terms, UInt indent) const

void	writeTarget_ (std::ostream &os, const std::vector< IncludeExcludeTarget >::const_iterator &it) const

void	writeRetentionTime_ (std::ostream &os, const TargetedExperimentHelper::RetentionTime &rt) const

void	writeProduct_ (std::ostream &os, const std::vector< ReactionMonitoringTransition::Product >::const_iterator &prod_it) const

void	writeConfiguration_ (std::ostream &os, const std::vector< ReactionMonitoringTransition::Configuration >::const_iterator &cit) const

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...

Additional Inherited Members
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...

Detailed Description

XML handler for TraMLFile.

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

Member Typedef Documentation

◆ ConfigurationListType

typedef std::vector<ReactionMonitoringTransition::Configuration> ConfigurationListType

◆ ProductListType

typedef std::vector<ReactionMonitoringTransition::Product> ProductListType

Constructor & Destructor Documentation

◆ TraMLHandler() [1/4]

TraMLHandler ( )

delete

◆ TraMLHandler() [2/4]

TraMLHandler ( const TraMLHandler & rhs )

delete

◆ TraMLHandler() [3/4]

TraMLHandler	(	const TargetedExperiment &	exp,
		const String &	filename,
		const String &	version,
		const ProgressLogger &	logger
	)

Constructor for a write-only handler.

◆ TraMLHandler() [4/4]

TraMLHandler	(	TargetedExperiment &	exp,
		const String &	filename,
		const String &	version,
		const ProgressLogger &	logger
	)

Constructor for a read-only handler.

◆ ~TraMLHandler()

~TraMLHandler ( )

override

Destructor.

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 CVTerm &	cv_term
	)

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=()

TraMLHandler& operator= ( const TraMLHandler & rhs )

delete

◆ startElement()

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

override

◆ writeConfiguration_()

void writeConfiguration_	(	std::ostream &	os,
		const std::vector< ReactionMonitoringTransition::Configuration >::const_iterator &	cit
	)		const

protected

◆ writeCVList_()

void writeCVList_	(	std::ostream &	os,
		const std::map< String, std::vector< CVTerm >> &	cv_terms,
		UInt	indent
	)		const

protected

◆ writeCVParams_() [1/2]

void writeCVParams_	(	std::ostream &	os,
		const CVTermList &	cv_terms,
		UInt	indent
	)		const

protected

◆ writeCVParams_() [2/2]

void writeCVParams_	(	std::ostream &	os,
		const CVTermListInterface &	cv_terms,
		UInt	indent
	)		const

protected

◆ writeProduct_()

void writeProduct_	(	std::ostream &	os,
		const std::vector< ReactionMonitoringTransition::Product >::const_iterator &	prod_it
	)		const

protected

◆ writeRetentionTime_()

void writeRetentionTime_	(	std::ostream &	os,
		const TargetedExperimentHelper::RetentionTime &	rt
	)		const

protected

◆ writeTarget_()

void writeTarget_	(	std::ostream &	os,
		const std::vector< IncludeExcludeTarget >::const_iterator &	it
	)		const

protected

◆ writeTo()

void writeTo ( std::ostream & )

overridevirtual

Writes the contents to a stream.

Reimplemented from XMLHandler.

◆ writeUserParam_()

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

protected

Writes user terms.

◆ writeUserParams_()

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

protected

Member Data Documentation

◆ actual_compound_

TargetedExperiment::Compound actual_compound_

protected

◆ actual_configuration_

ReactionMonitoringTransition::Configuration actual_configuration_

protected

◆ actual_contact_

TargetedExperiment::Contact actual_contact_

protected

◆ actual_instrument_

TargetedExperiment::Instrument actual_instrument_

protected

◆ actual_intermediate_products_

std::vector<ReactionMonitoringTransition::Product> actual_intermediate_products_

protected

◆ actual_interpretation_

TargetedExperiment::Interpretation actual_interpretation_

protected

◆ actual_peptide_

TargetedExperiment::Peptide actual_peptide_

protected

◆ actual_prediction_

TargetedExperiment::Prediction actual_prediction_

protected

◆ actual_product_

ReactionMonitoringTransition::Product actual_product_

protected

◆ actual_protein_

TargetedExperiment::Protein actual_protein_

protected

◆ actual_publication_

TargetedExperiment::Publication actual_publication_

protected

◆ actual_rt_

TargetedExperiment::RetentionTime actual_rt_

protected

◆ actual_software_

Software actual_software_

protected

◆ actual_sourcefile_

SourceFile actual_sourcefile_

protected

◆ actual_target_

IncludeExcludeTarget actual_target_

protected

◆ actual_transition_

ReactionMonitoringTransition actual_transition_

protected

◆ actual_validation_

CVTermList actual_validation_

protected

◆ cexp_

const TargetedExperiment* cexp_

protected

◆ cv_

ControlledVocabulary cv_

protected

Controlled vocabulary (psi-ms from OpenMS/share/OpenMS/CV/psi-ms.obo)

◆ exp_

TargetedExperiment* exp_

protected

◆ logger_

const ProgressLogger& logger_

protected

Progress logger.

◆ tag_

String tag_

protected

Public Types

Public Member Functions

Constructors and destructor

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ConfigurationListType

◆ ProductListType

Constructor & Destructor Documentation

◆ TraMLHandler() [1/4]

◆ TraMLHandler() [2/4]

◆ TraMLHandler() [3/4]

◆ TraMLHandler() [4/4]

◆ ~TraMLHandler()

Member Function Documentation

◆ characters()

◆ endElement()

◆ getChildWithName_()

◆ handleCVParam_()

◆ handleUserParam_()

◆ operator=()

◆ startElement()

◆ writeConfiguration_()

◆ writeCVList_()

◆ writeCVParams_() [1/2]

◆ writeCVParams_() [2/2]

◆ writeProduct_()

◆ writeRetentionTime_()

◆ writeTarget_()

◆ writeTo()

◆ writeUserParam_()

◆ writeUserParams_()

Member Data Documentation

◆ actual_compound_

◆ actual_configuration_

◆ actual_contact_

◆ actual_instrument_

◆ actual_intermediate_products_

◆ actual_interpretation_

◆ actual_peptide_

◆ actual_prediction_

◆ actual_product_

◆ actual_protein_

◆ actual_publication_

◆ actual_rt_

◆ actual_software_

◆ actual_sourcefile_

◆ actual_target_

◆ actual_transition_

◆ actual_validation_

◆ cexp_

◆ cv_

◆ exp_

◆ logger_

◆ tag_