XML STREAM handler for MzIdentMLFile. More...

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

Inheritance diagram for MzIdentMLHandler:

Collaboration diagram for MzIdentMLHandler:

Constructors and destructor
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...

std::map< String, AASequence >	pep_sequences_

std::map< String, String >	pp_identifier_2_sil_
	mapping peptide/proteinidentification identifier_ to spectrumidentificationlist More...

std::map< String, String >	sil_2_sdb_
	mapping spectrumidentificationlist to the search data bases More...

std::map< String, String >	sil_2_sdat_
	mapping spectrumidentificationlist to the search input More...

std::map< String, String >	ph_2_sdat_
	mapping identification runs (mapping PeptideIdentifications and ProteinIdentifications via .getIdentifier()) to spectra data More...

std::map< String, String >	sil_2_sip_
	mapping spectrumidentificationlist to the search protocol (where the params are at) More...

AASequence	actual_peptide_

Int	current_mod_location_

ProteinHit	actual_protein_

	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 (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...

	~MzIdentMLHandler () 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 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, const DigestionEnzymeProtein &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...

void	writePeptideHit (const PeptideHit &hit, std::vector< PeptideIdentification >::const_iterator &it, std::map< String, String > &pep_ids, const String &cv_ns, std::set< String > &sen_set, std::map< String, String > &sen_ids, std::map< String, std::vector< String > > &pep_evis, std::map< String, double > &pp_identifier_2_thresh, String &sidres)
	Abstraction of PeptideHit loop for most PeptideHits. More...

void	writeXLMSPeptideHit (const PeptideHit &hit, std::vector< PeptideIdentification >::const_iterator &it, const String &ppxl_linkid, std::map< String, String > &pep_ids, const String &cv_ns, std::set< String > &sen_set, std::map< String, String > &sen_ids, std::map< String, std::vector< String > > &pep_evis, std::map< String, double > &pp_identifier_2_thresh, double ppxl_crosslink_mass, std::map< String, String > &ppxl_specref_2_element, String &sid, bool alpha_peptide)
	Abstraction of PeptideHit loop for XL-MS data from OpenPepXL. More...

	MzIdentMLHandler ()

	MzIdentMLHandler (const MzIdentMLHandler &rhs)

MzIdentMLHandler &	operator= (const MzIdentMLHandler &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...

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

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 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() [1/4]

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() [2/4]

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()

~MzIdentMLHandler ( )

override

Destructor.

◆ MzIdentMLHandler() [3/4]

MzIdentMLHandler ( )

private

◆ MzIdentMLHandler() [4/4]

MzIdentMLHandler ( const MzIdentMLHandler & 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 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()

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

override

◆ trimOpenMSfileURI()

String trimOpenMSfileURI ( const String & file ) const

protected

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

◆ writeEnzyme_()

void writeEnzyme_	(	String &	s,
		const DigestionEnzymeProtein &	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)

◆ writePeptideHit()

void writePeptideHit	(	const PeptideHit &	hit,
		std::vector< PeptideIdentification >::const_iterator &	it,
		std::map< String, String > &	pep_ids,
		const String &	cv_ns,
		std::set< String > &	sen_set,
		std::map< String, String > &	sen_ids,
		std::map< String, std::vector< String > > &	pep_evis,
		std::map< String, double > &	pp_identifier_2_thresh,
		String &	sidres
	)

protected

Abstraction of PeptideHit loop for most PeptideHits.

◆ writeTo()

void writeTo ( std::ostream & )

overridevirtual

Writes the contents to a stream.

Reimplemented from XMLHandler.

◆ writeXLMSPeptideHit()

void writeXLMSPeptideHit	(	const PeptideHit &	hit,
		std::vector< PeptideIdentification >::const_iterator &	it,
		const String &	ppxl_linkid,
		std::map< String, String > &	pep_ids,
		const String &	cv_ns,
		std::set< String > &	sen_set,
		std::map< String, String > &	sen_ids,
		std::map< String, std::vector< String > > &	pep_evis,
		std::map< String, double > &	pp_identifier_2_thresh,
		double	ppxl_crosslink_mass,
		std::map< String, String > &	ppxl_specref_2_element,
		String &	sid,
		bool	alpha_peptide
	)

protected

Abstraction of PeptideHit loop for XL-MS data from OpenPepXL.

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_

std::map<String, AASequence> pep_sequences_

private

◆ ph_2_sdat_

std::map<String, String> ph_2_sdat_

private

mapping identification runs (mapping PeptideIdentifications and ProteinIdentifications via .getIdentifier()) to spectra data

◆ pp_identifier_2_sil_

std::map<String, String> pp_identifier_2_sil_

private

mapping peptide/proteinidentification identifier_ to spectrumidentificationlist

◆ pro_id_

std::vector<ProteinIdentification>* pro_id_

protected

internal Identification Item for proteins

◆ sil_2_sdat_

std::map<String, String> sil_2_sdat_

private

mapping spectrumidentificationlist to the search input

◆ sil_2_sdb_

std::map<String, String> sil_2_sdb_

private

mapping spectrumidentificationlist to the search data bases

◆ sil_2_sip_

std::map<String, String> sil_2_sip_

private

mapping spectrumidentificationlist to the search protocol (where the params are at)

◆ tag_

String tag_

protected

XML tag parse element.

◆ unimod_

ControlledVocabulary unimod_

protected

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

Constructors and destructor

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MzIdentMLHandler() [1/4]

◆ MzIdentMLHandler() [2/4]

◆ ~MzIdentMLHandler()

◆ MzIdentMLHandler() [3/4]

◆ MzIdentMLHandler() [4/4]

Member Function Documentation

◆ characters()

◆ endElement()

◆ getChildWithName_()

◆ handleCVParam_()

◆ handleUserParam_()

◆ operator=()

◆ startElement()

◆ trimOpenMSfileURI()

◆ writeEnzyme_()

◆ writeFragmentAnnotations_()

◆ writeMetaInfos_()

◆ writeModParam_()

◆ writePeptideHit()

◆ writeTo()

◆ writeXLMSPeptideHit()

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_