MzIdentMLDOMHandler Class Reference

XML DOM handler for MzIdentMLFile. More...

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

Classes
struct	AnalysisSoftware
	Struct to hold the used analysis software for that file. More...
struct	DatabaseInput
	Struct to hold the information from the DatabaseInput xml tag. More...
struct	DBSequence
	Struct to hold the information from the DBSequence xml tag. More...
struct	ModificationParam
	Struct to hold the information from the ModificationParam xml tag. More...
struct	PeptideEvidence
	Struct to hold the PeptideEvidence information. More...
struct	SpectrumIdentification
	Struct to hold the information from the SpectrumIdentification xml tag. More...
struct	SpectrumIdentificationProtocol
	Struct to hold the information from the SpectrumIdentificationProtocol xml tag. More...

Public Member Functions
void	readMzIdentMLFile (const std::string &mzid_file)
	Provides the functionality of reading a mzid with a handler object. More...
void	writeMzIdentMLFile (const std::string &mzid_file)
	Provides the functionality to write a mzid with a handler object. More...
Constructors and destructor
	MzIdentMLDOMHandler (const std::vector< ProteinIdentification > &pro_id, const std::vector< PeptideIdentification > &pep_id, const String &version, const ProgressLogger &logger)
	Constructor for a write-only handler for internal identification structures. More...
	MzIdentMLDOMHandler (std::vector< ProteinIdentification > &pro_id, std::vector< PeptideIdentification > &pep_id, const String &version, const ProgressLogger &logger)
	Constructor for a read-only handler for internal identification structures. More...
virtual	~MzIdentMLDOMHandler ()
	Destructor. More...

Protected Member Functions
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...
Helper functions to build a DOM tree from the internal id structures
void	buildCvList_ (xercesc::DOMElement *cvElements)
void	buildAnalysisSoftwareList_ (xercesc::DOMElement *analysisSoftwareElements)
void	buildSequenceCollection_ (xercesc::DOMElement *sequenceCollectionElements)
void	buildAnalysisCollection_ (xercesc::DOMElement *analysisCollectionElements)
void	buildAnalysisProtocolCollection_ (xercesc::DOMElement *protocolElements)
void	buildInputDataCollection_ (xercesc::DOMElement *inputElements)
void	buildEnclosedCV_ (xercesc::DOMElement *parentElement, String encel, String acc, String name, String cvref)
void	buildAnalysisDataCollection_ (xercesc::DOMElement *analysisElements)

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...
std::vector< ProteinIdentification > *	pro_id_
	Internal +w Identification Item for proteins. More...
std::vector< PeptideIdentification > *	pep_id_
	Internal +w Identification Item for peptides. More...
const std::vector< ProteinIdentification > *	cpro_id_
	Internal -w Identification Item for proteins. More...
const std::vector< PeptideIdentification > *	cpep_id_
	Internal -w Identification Item for peptides. More...
const String	schema_version_
	Internal version keeping. More...

Private Member Functions
	MzIdentMLDOMHandler ()
	MzIdentMLDOMHandler (const MzIdentMLDOMHandler &rhs)
MzIdentMLDOMHandler &	operator= (const MzIdentMLDOMHandler &rhs)

Private Attributes
XMLCh *	xml_root_tag_ptr_
XMLCh *	xml_cvparam_tag_ptr_
XMLCh *	xml_name_attr_ptr_
xercesc::XercesDOMParser	mzid_parser_
String	search_engine_
String	search_engine_version_
std::map< String, AnalysisSoftware >	as_map_
std::map< String, String >	sr_map_
std::map< String, String >	sd_map_
std::map< String, DatabaseInput >	db_map_
std::map< String, SpectrumIdentification >	si_map_
std::map< String, size_t >	si_pro_map_
std::map< String, SpectrumIdentificationProtocol >	sp_map_
std::map< String, AASequence >	pep_map_
std::map< String, PeptideEvidence >	pe_ev_map_
std::map< String, String >	pv_db_map_
std::multimap< String, String >	p_pv_map_
std::map< String, DBSequence >	db_sq_map_
std::list< std::list< String > >	hit_pev_
bool	xl_ms_search_
std::map< String, String >	xl_id_donor_map_
std::map< String, String >	xl_id_acceptor_map_
std::map< String, SignedSize >	xl_donor_pos_map_
std::map< String, SignedSize >	xl_acceptor_pos_map_
std::map< String, double >	xl_mass_map_
std::map< String, String >	xl_mod_map_

Helper functions to build the internal id structures from the DOM tree
std::pair< CVTermList, std::map< String, DataValue > >	parseParamGroup_ (xercesc::DOMNodeList *paramGroup)
CVTerm	parseCvParam_ (xercesc::DOMElement *param)
std::pair< String, DataValue >	parseUserParam_ (xercesc::DOMElement *param)
void	parseAnalysisSoftwareList_ (xercesc::DOMNodeList *analysisSoftwareElements)
void	parseDBSequenceElements_ (xercesc::DOMNodeList *dbSequenceElements)
void	parsePeptideElements_ (xercesc::DOMNodeList *peptideElements)
AASequence	parsePeptideSiblings_ (xercesc::DOMElement *peptide)
void	parsePeptideEvidenceElements_ (xercesc::DOMNodeList *peptideEvidenceElements)
void	parseSpectrumIdentificationElements_ (xercesc::DOMNodeList *spectrumIdentificationElements)
void	parseSpectrumIdentificationProtocolElements_ (xercesc::DOMNodeList *spectrumIdentificationProtocolElements)
void	parseInputElements_ (xercesc::DOMNodeList *inputElements)
void	parseSpectrumIdentificationListElements_ (xercesc::DOMNodeList *spectrumIdentificationListElements)
void	parseSpectrumIdentificationItemSetXLMS (std::set< String >::const_iterator set_it, std::multimap< String, int > xl_val_map, xercesc::DOMElement *element_res, String spectrumID)
void	parseSpectrumIdentificationItemElement_ (xercesc::DOMElement *spectrumIdentificationItemElement, PeptideIdentification &spectrum_identification, String &spectrumIdentificationList_ref)
void	parseProteinDetectionHypothesisElement_ (xercesc::DOMElement *proteinDetectionHypothesisElement, ProteinIdentification &protein_identification)
void	parseProteinAmbiguityGroupElement_ (xercesc::DOMElement *proteinAmbiguityGroupElement, ProteinIdentification &protein_identification)
void	parseProteinDetectionListElements_ (xercesc::DOMNodeList *proteinDetectionListElements)
static ProteinIdentification::SearchParameters	findSearchParameters_ (std::pair< CVTermList, std::map< String, DataValue > > as_params)

Detailed Description

XML DOM 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.

Only upon destruction of this class it can be guaranteed that all data has been appended to the appropriate containers. Do not try to access the data before that.

Constructor & Destructor Documentation

MzIdentMLDOMHandler() [1/4]

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

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

MzIdentMLDOMHandler() [2/4]

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

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

~MzIdentMLDOMHandler()

virtual ~MzIdentMLDOMHandler ( )

virtual

Destructor.

MzIdentMLDOMHandler() [3/4]

MzIdentMLDOMHandler ( )

private

MzIdentMLDOMHandler() [4/4]

MzIdentMLDOMHandler ( const MzIdentMLDOMHandler &  rhs )

private

Member Function Documentation

buildAnalysisCollection_()

void buildAnalysisCollection_ ( xercesc::DOMElement *  analysisCollectionElements )

protected

buildAnalysisDataCollection_()

void buildAnalysisDataCollection_ ( xercesc::DOMElement *  analysisElements )

protected

buildAnalysisProtocolCollection_()

void buildAnalysisProtocolCollection_ ( xercesc::DOMElement *  protocolElements )

protected

buildAnalysisSoftwareList_()

void buildAnalysisSoftwareList_ ( xercesc::DOMElement *  analysisSoftwareElements )

protected

buildCvList_()

void buildCvList_ ( xercesc::DOMElement *  cvElements )

protected

buildEnclosedCV_()

void buildEnclosedCV_ ( xercesc::DOMElement *  parentElement, String  encel, String  acc, String  name, String  cvref  )

protected

buildInputDataCollection_()

void buildInputDataCollection_ ( xercesc::DOMElement *  inputElements )

protected

buildSequenceCollection_()

void buildSequenceCollection_ ( xercesc::DOMElement *  sequenceCollectionElements )

protected

findSearchParameters_()

static ProteinIdentification::SearchParameters findSearchParameters_ ( std::pair< CVTermList, std::map< String, DataValue > >  as_params )

staticprotected

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.

operator=()

MzIdentMLDOMHandler& operator= ( const MzIdentMLDOMHandler &  rhs )

private

parseAnalysisSoftwareList_()

void parseAnalysisSoftwareList_ ( xercesc::DOMNodeList *  analysisSoftwareElements )

protected

parseCvParam_()

CVTerm parseCvParam_ ( xercesc::DOMElement *  param )

protected

parseDBSequenceElements_()

void parseDBSequenceElements_ ( xercesc::DOMNodeList *  dbSequenceElements )

protected

parseInputElements_()

void parseInputElements_ ( xercesc::DOMNodeList *  inputElements )

protected

parseParamGroup_()

std::pair<CVTermList, std::map<String, DataValue> > parseParamGroup_ ( xercesc::DOMNodeList *  paramGroup )

protected

parsePeptideElements_()

void parsePeptideElements_ ( xercesc::DOMNodeList *  peptideElements )

protected

parsePeptideEvidenceElements_()

void parsePeptideEvidenceElements_ ( xercesc::DOMNodeList *  peptideEvidenceElements )

protected

parsePeptideSiblings_()

AASequence parsePeptideSiblings_ ( xercesc::DOMElement *  peptide )

protected

parseProteinAmbiguityGroupElement_()

void parseProteinAmbiguityGroupElement_ ( xercesc::DOMElement *  proteinAmbiguityGroupElement, ProteinIdentification &  protein_identification  )

protected

parseProteinDetectionHypothesisElement_()

void parseProteinDetectionHypothesisElement_ ( xercesc::DOMElement *  proteinDetectionHypothesisElement, ProteinIdentification &  protein_identification  )

protected

parseProteinDetectionListElements_()

void parseProteinDetectionListElements_ ( xercesc::DOMNodeList *  proteinDetectionListElements )

protected

parseSpectrumIdentificationElements_()

void parseSpectrumIdentificationElements_ ( xercesc::DOMNodeList *  spectrumIdentificationElements )

protected

parseSpectrumIdentificationItemElement_()

void parseSpectrumIdentificationItemElement_ ( xercesc::DOMElement *  spectrumIdentificationItemElement, PeptideIdentification &  spectrum_identification, String &  spectrumIdentificationList_ref  )

protected

parseSpectrumIdentificationItemSetXLMS()

void parseSpectrumIdentificationItemSetXLMS ( std::set< String >::const_iterator  set_it, std::multimap< String, int >  xl_val_map, xercesc::DOMElement *  element_res, String  spectrumID  )

protected

parseSpectrumIdentificationListElements_()

void parseSpectrumIdentificationListElements_ ( xercesc::DOMNodeList *  spectrumIdentificationListElements )

protected

parseSpectrumIdentificationProtocolElements_()

void parseSpectrumIdentificationProtocolElements_ ( xercesc::DOMNodeList *  spectrumIdentificationProtocolElements )

protected

parseUserParam_()

std::pair<String, DataValue> parseUserParam_ ( xercesc::DOMElement *  param )

protected

readMzIdentMLFile()

void readMzIdentMLFile

(

const std::string &

mzid_file

)

Provides the functionality of reading a mzid with a handler object.

writeMzIdentMLFile()

void writeMzIdentMLFile

(

const std::string &

mzid_file

)

Provides the functionality to write a mzid with a handler object.

Member Data Documentation

as_map_

std::map<String, AnalysisSoftware> as_map_

private

cpep_id_

const std::vector<PeptideIdentification>* cpep_id_

protected

Internal -w Identification Item for peptides.

cpro_id_

const std::vector<ProteinIdentification>* cpro_id_

protected

Internal -w Identification Item for proteins.

cv_

ControlledVocabulary cv_

protected

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

db_map_

std::map<String, DatabaseInput> db_map_

private

db_sq_map_

std::map<String, DBSequence> db_sq_map_

private

hit_pev_

std::list<std::list<String> > hit_pev_

private

logger_

const ProgressLogger& logger_

protected

Progress logger.

mzid_parser_

xercesc::XercesDOMParser mzid_parser_

private

p_pv_map_

std::multimap<String, String> p_pv_map_

private

pe_ev_map_

std::map<String, PeptideEvidence> pe_ev_map_

private

pep_id_

std::vector<PeptideIdentification>* pep_id_

protected

Internal +w Identification Item for peptides.

pep_map_

std::map<String, AASequence> pep_map_

private

pro_id_

std::vector<ProteinIdentification>* pro_id_

protected

Internal +w Identification Item for proteins.

pv_db_map_

std::map<String, String> pv_db_map_

private

schema_version_

const String schema_version_

protected

Internal version keeping.

sd_map_

std::map<String, String> sd_map_

private

search_engine_

String search_engine_

private

search_engine_version_

String search_engine_version_

private

si_map_

std::map<String, SpectrumIdentification> si_map_

private

si_pro_map_

std::map<String, size_t> si_pro_map_

private

sp_map_

std::map<String, SpectrumIdentificationProtocol> sp_map_

private

sr_map_

std::map<String, String> sr_map_

private

unimod_

ControlledVocabulary unimod_

protected

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

xl_acceptor_pos_map_

std::map<String, SignedSize> xl_acceptor_pos_map_

private

xl_donor_pos_map_

std::map<String, SignedSize> xl_donor_pos_map_

private

xl_id_acceptor_map_

std::map<String, String> xl_id_acceptor_map_

private

xl_id_donor_map_

std::map<String, String> xl_id_donor_map_

private

xl_mass_map_

std::map<String, double> xl_mass_map_

private

xl_mod_map_

std::map<String, String> xl_mod_map_

private

xl_ms_search_

bool xl_ms_search_

private

xml_cvparam_tag_ptr_

XMLCh* xml_cvparam_tag_ptr_

private

xml_name_attr_ptr_

XMLCh* xml_name_attr_ptr_

private

xml_root_tag_ptr_

XMLCh* xml_root_tag_ptr_

private