XML STREAM handler for MzIdentMLFile. More...

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

Inheritance diagram for MzIdentMLHandler:

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
	MzIdentMLHandler (const Identification &id, const String &filename, const String &version, const ProgressLogger &logger)
	Constructor for a write-only handler. More...

	MzIdentMLHandler (const std::vector< ProteinIdentification > &pro_id, const std::vector< PeptideIdentification > &pep_id, const String &filename, const String &version, const ProgressLogger &logger)
	Constructor for a write-only handler for internal identification structures. More...

	MzIdentMLHandler (Identification &id, const String &filename, const String &version, const ProgressLogger &logger)
	Constructor for a read-only handler. More...

	MzIdentMLHandler (std::vector< ProteinIdentification > &pro_id, std::vector< PeptideIdentification > &pep_id, const String &filename, const String &version, const ProgressLogger &logger)
	Constructor for a read-only handler for internal identification structures. More...

virtual	~MzIdentMLHandler ()
	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 xercesc::Attributes &attributes, const String &cv_ref)
	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	writeMetaInfos_ (String &s, const MetaInfoInterface &meta, UInt indent) const
	Writes user terms. More...

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	writeEnzyme_ (String &s, Enzyme enzy, UInt miss, UInt indent) const
	Helper method that writes a source file. More...

void	writeModParam_ (String &s, const std::vector< String > &mod_names, bool fixed, UInt indent) const
	Helper method that writes the modification search params (fixed or variable) More...

void	writeFragmentAnnotations_ (String &s, const std::vector< PeptideHit::PeakAnnotation > &annotations, UInt indent, bool is_ppxl) const
	Helper method that writes the FragmentAnnotations section of a spectrum identification. More...

String	trimOpenMSfileURI (const String file) const
	Convenience method to remove the [] from OpenMS internal file uri representation. 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...

ControlledVocabulary	unimod_
	Controlled vocabulary for modifications (unimod from OpenMS/share/OpenMS/CV/unimod.obo) More...

String	tag_
	XML tag parse element. More...

Identification *	id_
	Identification Item. More...

std::vector< ProteinIdentification > *	pro_id_
	internal Identification Item for proteins More...

std::vector< PeptideIdentification > *	pep_id_
	Identification Item for peptides. More...

const Identification *	cid_

const std::vector< ProteinIdentification > *	cpro_id_

const std::vector< PeptideIdentification > *	cpep_id_

SpectrumIdentification	current_spectrum_id_
	SpectrumIdentification Item. More...

IdentificationHit	current_id_hit_
	IdentificationHit Item. 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...

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
	MzIdentMLHandler ()

	MzIdentMLHandler (const MzIdentMLHandler &rhs)

MzIdentMLHandler &	operator= (const MzIdentMLHandler &rhs)

Private Attributes
Map< String, AASequence >	pep_sequences_

std::map< String, String >	pp_identifier_2_sil_

std::map< String, String >	sil_2_sdb_

std::map< String, String >	sil_2_sdat_

std::map< String, String >	ph_2_sdat_

std::map< String, String >	sil_2_sip_

AASequence	actual_peptide_

Int	current_mod_location_

ProteinHit	actual_protein_

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 STREAM handler for MzIdentMLFile.

In read-mode, this class will parse an MzIdentML XML file and append the input identifications to the provided PeptideIdentifications and ProteinIdentifications.

Note: Do not use this class. It is only needed in MzIdentMLFile.; DOM and STREAM handler for MzIdentML have the same interface for legacy id structures.

Constructor & Destructor Documentation

◆ MzIdentMLHandler() [1/6]

MzIdentMLHandler	(	const Identification &	id,
		const String &	filename,
		const String &	version,
		const ProgressLogger &	logger
	)

Constructor for a write-only handler.

◆ MzIdentMLHandler() [2/6]

MzIdentMLHandler	(	const std::vector< ProteinIdentification > &	pro_id,
		const std::vector< PeptideIdentification > &	pep_id,
		const String &	filename,
		const String &	version,
		const ProgressLogger &	logger
	)

Constructor for a write-only handler for internal identification structures.

◆ MzIdentMLHandler() [3/6]

MzIdentMLHandler	(	Identification &	id,
		const String &	filename,
		const String &	version,
		const ProgressLogger &	logger
	)

Constructor for a read-only handler.

◆ MzIdentMLHandler() [4/6]

MzIdentMLHandler	(	std::vector< ProteinIdentification > &	pro_id,
		std::vector< PeptideIdentification > &	pep_id,
		const String &	filename,
		const String &	version,
		const ProgressLogger &	logger
	)

Constructor for a read-only handler for internal identification structures.

◆ ~MzIdentMLHandler()

virtual ~MzIdentMLHandler ( )

virtual

Destructor.

◆ MzIdentMLHandler() [5/6]

MzIdentMLHandler ( )

private

◆ MzIdentMLHandler() [6/6]

MzIdentMLHandler ( const MzIdentMLHandler & 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 xercesc::Attributes &	attributes,
		const String &	cv_ref
	)

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=()

MzIdentMLHandler& operator= ( const MzIdentMLHandler & 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.

◆ trimOpenMSfileURI()

String trimOpenMSfileURI ( const String file ) const

protected

Convenience method to remove the [] from OpenMS internal file uri representation.

◆ writeEnzyme_()

void writeEnzyme_	(	String &	s,
		Enzyme	enzy,
		UInt	miss,
		UInt	indent
	)		const

protected

Helper method that writes a source file.

Helper method that writes the Enzymes

◆ writeFragmentAnnotations_()

void writeFragmentAnnotations_	(	String &	s,
		const std::vector< PeptideHit::PeakAnnotation > &	annotations,
		UInt	indent,
		bool	is_ppxl
	)		const

protected

Helper method that writes the FragmentAnnotations section of a spectrum identification.

◆ writeMetaInfos_()

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

protected

Writes user terms.

◆ writeModParam_()

void writeModParam_	(	String &	s,
		const std::vector< String > &	mod_names,
		bool	fixed,
		UInt	indent
	)		const

protected

Helper method that writes the modification search params (fixed or variable)

◆ writeTo()

virtual void writeTo ( std::ostream & )

virtual

Writes the contents to a stream.

Reimplemented from XMLHandler.

Member Data Documentation

◆ actual_peptide_

AASequence actual_peptide_

private

◆ actual_protein_

ProteinHit actual_protein_

private

◆ cid_

const Identification* cid_

protected

◆ cpep_id_

const std::vector<PeptideIdentification>* cpep_id_

protected

◆ cpro_id_

const std::vector<ProteinIdentification>* cpro_id_

protected

◆ current_id_hit_

IdentificationHit current_id_hit_

protected

IdentificationHit Item.

◆ current_mod_location_

Int current_mod_location_

private

◆ current_spectrum_id_

SpectrumIdentification current_spectrum_id_

protected

SpectrumIdentification Item.

◆ cv_

ControlledVocabulary cv_

protected

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

◆ id_

Identification* id_

protected

Identification Item.

◆ logger_

const ProgressLogger& logger_

protected

Progress logger.

◆ pep_id_

std::vector<PeptideIdentification>* pep_id_

protected

Identification Item for peptides.

◆ pep_sequences_

Map<String, AASequence> pep_sequences_

private

◆ ph_2_sdat_

std::map<String, String> ph_2_sdat_

private

◆ pp_identifier_2_sil_

std::map<String, String> pp_identifier_2_sil_

private

◆ pro_id_

std::vector<ProteinIdentification>* pro_id_

protected

internal Identification Item for proteins

◆ sil_2_sdat_

std::map<String, String> sil_2_sdat_

private

◆ sil_2_sdb_

std::map<String, String> sil_2_sdb_

private

◆ sil_2_sip_

std::map<String, String> sil_2_sip_

private

◆ tag_

String tag_

protected

XML tag parse element.

◆ unimod_

ControlledVocabulary unimod_

protected

Controlled vocabulary for modifications (unimod from OpenMS/share/OpenMS/CV/unimod.obo)

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MzIdentMLHandler() [1/6]

◆ MzIdentMLHandler() [2/6]

◆ MzIdentMLHandler() [3/6]

◆ MzIdentMLHandler() [4/6]

◆ ~MzIdentMLHandler()

◆ MzIdentMLHandler() [5/6]

◆ MzIdentMLHandler() [6/6]

Member Function Documentation

◆ characters()

◆ endElement()

◆ getChildWithName_()

◆ handleCVParam_()

◆ handleUserParam_()

◆ operator=()

◆ startElement()

◆ trimOpenMSfileURI()

◆ writeEnzyme_()

◆ writeFragmentAnnotations_()

◆ writeMetaInfos_()

◆ writeModParam_()

◆ writeTo()

Member Data Documentation

◆ actual_peptide_

◆ actual_protein_

◆ cid_

◆ cpep_id_

◆ cpro_id_

◆ current_id_hit_

◆ current_mod_location_

◆ current_spectrum_id_

◆ cv_

◆ id_

◆ logger_

◆ pep_id_

◆ pep_sequences_

◆ ph_2_sdat_

◆ pp_identifier_2_sil_

◆ pro_id_

◆ sil_2_sdat_

◆ sil_2_sdb_

◆ sil_2_sip_

◆ tag_

◆ unimod_