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

Inheritance 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...

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
	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...

virtual	~TraMLHandler ()
	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 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

template<typename CVTList >
void	writeCVParams_ (std::ostream &os, const CVTList &cv_terms, UInt indent) const

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

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 (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_

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

	TraMLHandler (const TraMLHandler &rhs)

TraMLHandler &	operator= (const TraMLHandler &rhs)

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...

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

Constructor for a write-only handler.

◆ TraMLHandler() [2/4]

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

Constructor for a read-only handler.

◆ ~TraMLHandler()

virtual ~TraMLHandler ( )

virtual

Destructor.

◆ TraMLHandler() [3/4]

TraMLHandler ( )

private

Helper method that writes a source file.

◆ TraMLHandler() [4/4]

TraMLHandler ( const TraMLHandler & 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 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 )

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.

◆ writeConfiguration_()

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

protected

◆ writeCVParams_()

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

inlineprotected

◆ writeProduct_()

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

protected

◆ writeTarget_()

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

protected

◆ writeTo()

virtual void writeTo ( std::ostream & )

virtual

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

Protected Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ConfigurationListType

◆ ProductListType

Constructor & Destructor Documentation

◆ TraMLHandler() [1/4]

◆ TraMLHandler() [2/4]

◆ ~TraMLHandler()

◆ TraMLHandler() [3/4]

◆ TraMLHandler() [4/4]

Member Function Documentation

◆ characters()

◆ endElement()

◆ getChildWithName_()

◆ handleCVParam_()

◆ handleUserParam_()

◆ operator=()

◆ startElement()

◆ writeConfiguration_()

◆ writeCVParams_()

◆ writeProduct_()

◆ 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_