Handler that is used for parsing MascotXML data. More...

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

Inheritance diagram for MascotXMLHandler:

Collaboration diagram for MascotXMLHandler:

Public Member Functions
	MascotXMLHandler (ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &identifications, const String &filename, std::map< String, std::vector< AASequence > > &peptides, const SpectrumMetaDataLookup &lookup)
	Constructor. More...

	~MascotXMLHandler () 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) override

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 void	writeTo (std::ostream &)
	Writes the contents to a stream. 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
static std::vector< String >	splitModificationBySpecifiedAA (const String &mod)
	Split modification search parameter if for more than one amino acid specified e.g. Phospho (ST) More...

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...

Private Attributes
ProteinIdentification &	protein_identification_
	the protein identifications More...

std::vector< PeptideIdentification > &	id_data_
	the identifications (storing the peptide hits) More...

ProteinHit	actual_protein_hit_

PeptideHit	actual_peptide_hit_

PeptideEvidence	actual_peptide_evidence_

UInt	peptide_identification_index_

String	tag_

DateTime	date_

String	date_time_string_

UInt	actual_query_

ProteinIdentification::SearchParameters	search_parameters_

String	identifier_

String	actual_title_

std::map< String, std::vector< AASequence > > &	modified_peptides_

StringList	tags_open_
	tracking the current XML tree More...

String	character_buffer_
	filled by MascotXMLHandler::characters More...

String	major_version_

String	minor_version_

std::vector< String >	remove_fixed_mods_

const SpectrumMetaDataLookup &	lookup_
	Helper object for looking up RT information. More...

bool	no_rt_error_
	Error for missing RT information already reported? More...

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 }

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

Handler that is used for parsing MascotXML data.

Constructor & Destructor Documentation

◆ MascotXMLHandler()

MascotXMLHandler	(	ProteinIdentification &	protein_identification,
		std::vector< PeptideIdentification > &	identifications,
		const String &	filename,
		std::map< String, std::vector< AASequence > > &	peptides,
		const SpectrumMetaDataLookup &	lookup
	)

Constructor.

◆ ~MascotXMLHandler()

~MascotXMLHandler ( )

override

Destructor.

Member Function Documentation

◆ characters()

void characters	(	const XMLCh *const	chars,
		const	XMLSize_t
	)

override

◆ endElement()

void endElement	(	const XMLCh * const	,
		const XMLCh * const	,
		const XMLCh *const	qname
	)

override

◆ splitModificationBySpecifiedAA()

static std::vector<String> splitModificationBySpecifiedAA ( const String & mod )

static

Split modification search parameter if for more than one amino acid specified e.g. Phospho (ST)

◆ startElement()

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

override

Member Data Documentation

◆ actual_peptide_evidence_

PeptideEvidence actual_peptide_evidence_

private

◆ actual_peptide_hit_

PeptideHit actual_peptide_hit_

private

◆ actual_protein_hit_

ProteinHit actual_protein_hit_

private

◆ actual_query_

UInt actual_query_

private

◆ actual_title_

String actual_title_

private

◆ character_buffer_

String character_buffer_

private

filled by MascotXMLHandler::characters

◆ date_

DateTime date_

private

◆ date_time_string_

String date_time_string_

private

◆ id_data_

std::vector<PeptideIdentification>& id_data_

private

the identifications (storing the peptide hits)

◆ identifier_

String identifier_

private

◆ lookup_

const SpectrumMetaDataLookup& lookup_

private

Helper object for looking up RT information.

◆ major_version_

String major_version_

private

◆ minor_version_

String minor_version_

private

◆ modified_peptides_

std::map<String, std::vector<AASequence> >& modified_peptides_

private

◆ no_rt_error_

bool no_rt_error_

private

Error for missing RT information already reported?

◆ peptide_identification_index_

UInt peptide_identification_index_

private

◆ protein_identification_

ProteinIdentification& protein_identification_

private

the protein identifications

◆ remove_fixed_mods_

std::vector<String> remove_fixed_mods_

private

◆ search_parameters_

ProteinIdentification::SearchParameters search_parameters_

private

◆ tag_

String tag_

private

◆ tags_open_

StringList tags_open_

private

tracking the current XML tree

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MascotXMLHandler()

◆ ~MascotXMLHandler()

Member Function Documentation

◆ characters()

◆ endElement()

◆ splitModificationBySpecifiedAA()

◆ startElement()

Member Data Documentation

◆ actual_peptide_evidence_

◆ actual_peptide_hit_

◆ actual_protein_hit_

◆ actual_query_

◆ actual_title_

◆ character_buffer_

◆ date_

◆ date_time_string_

◆ id_data_

◆ identifier_

◆ lookup_

◆ major_version_

◆ minor_version_

◆ modified_peptides_

◆ no_rt_error_

◆ peptide_identification_index_

◆ protein_identification_

◆ remove_fixed_mods_

◆ search_parameters_

◆ tag_

◆ tags_open_