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, PeptideIdentificationList &identifications, const std::string &filename, std::map< std::string, std::vector< AASequence > > &peptides, const SpectrumMetaDataLookup &lookup)
	Constructor.

	~MascotXMLHandler () override
	Destructor.

void	onEndElement (const char16_t *qname) override
	Parsing method for closing tags.

void	onStartElement (const char16_t *qname, const XMLAttributes &attributes) override
	Parsing method for opening tags.

void	onCharacters (const char16_t *chars, Size) override
	Parsing method for character data.

Public Member Functions inherited from XMLHandler
	XMLHandler (const std::string &filename, const std::string &version)
	Default constructor.

virtual	~XMLHandler ()
	Destructor.

void	reset ()
	Release internal memory used for parsing (call.

void	fatalError (ActionMode mode, const std::string &msg, UInt line=0, UInt column=0) const
	Fatal error handler. Throws a ParseError exception.

void	error (ActionMode mode, const std::string &msg, UInt line=0, UInt column=0) const
	Error handler for recoverable errors.

void	warning (ActionMode mode, const std::string &msg, UInt line=0, UInt column=0) const
	Warning handler.

virtual void	writeTo (std::ostream &)
	Writes the contents to a stream.

virtual LOADDETAIL	getLoadDetail () const
	handler which support partial loading, implement this method

virtual void	setLoadDetail (const LOADDETAIL d)
	handler which support partial loading, implement this method

DataValue	cvParamToValue (const ControlledVocabulary &cv, const std::string &parent_tag, const std::string &accession, const std::string &name, const std::string &value, const std::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.

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.

void	checkUniqueIdentifiers_ (const std::vector< ProteinIdentification > &prot_ids) const

Static Public Member Functions
static std::vector< std::string >	splitModificationBySpecifiedAA (const std::string &mod)
	Split modification search parameter if for more than one amino acid specified e.g. Phospho (ST)

Static Public Member Functions inherited from XMLHandler
static std::string	writeXMLEscape (const std::string &to_escape)
	Escapes a string and returns the escaped string.

static DataValue	fromXSDString (const std::string &type, const std::string &value)
	Convert an XSD type (e.g. 'xsd:double') to a DataValue.

Private Attributes
ProteinIdentification &	protein_identification_
	the protein identifications

PeptideIdentificationList &	id_data_
	the identifications (storing the peptide hits)

ProteinHit	actual_protein_hit_

PeptideHit	actual_peptide_hit_

PeptideEvidence	actual_peptide_evidence_

UInt	peptide_identification_index_

std::string	tag_

DateTime	date_

std::string	date_time_string_

UInt	actual_query_

ProteinIdentification::SearchParameters	search_parameters_

std::string	identifier_

std::string	actual_title_

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

StringList	tags_open_
	tracking the current XML tree

std::string	character_buffer_
	filled by MascotXMLHandler::characters

std::string	major_version_

std::string	minor_version_

std::vector< std::string >	remove_fixed_mods_

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

bool	no_rt_error_
	Error for missing RT information already reported?

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 std::string &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const
	Writes the content of MetaInfoInterface to the file.

Int	asInt_ (const std::string &in) const
	Conversion of a std::string to an integer value.

Int	asInt_ (const char16_t *in) const
	Conversion of a Xerces string to an integer value.

UInt	asUInt_ (const std::string &in) const
	Conversion of a std::string to an unsigned integer value.

double	asDouble_ (const std::string &in) const
	Conversion of a std::string to a double value.

float	asFloat_ (const std::string &in) const
	Conversion of a std::string to a float value.

bool	asBool_ (const std::string &in) const
	Conversion of a string to a boolean value.

DateTime	asDateTime_ (std::string date_string) const
	Conversion of a xs:datetime string to a DateTime value.

bool	equal_ (const char16_t a, const char16_t b) const
	Returns if two Xerces strings are equal.

SignedSize	cvStringToEnum_ (const Size section, const std::string &term, const char *message, const SignedSize result_on_error=0)

std::string	attributeAsString_ (const XMLAttributes &a, const char *name) const
	Converts an attribute to a String.

Int	attributeAsInt_ (const XMLAttributes &a, const char *name) const
	Converts an attribute to a Int.

double	attributeAsDouble_ (const XMLAttributes &a, const char *name) const
	Converts an attribute to a double.

DoubleList	attributeAsDoubleList_ (const XMLAttributes &a, const char *name) const
	Converts an attribute to a DoubleList.

IntList	attributeAsIntList_ (const XMLAttributes &a, const char *name) const
	Converts an attribute to an IntList.

StringList	attributeAsStringList_ (const XMLAttributes &a, const char *name) const
	Converts an attribute to an StringList.

bool	optionalAttributeAsString_ (std::string &value, const XMLAttributes &a, const char *name) const
	Assigns the attribute content to the String value if the attribute is present.

bool	optionalAttributeAsInt_ (Int &value, const XMLAttributes &a, const char *name) const
	Assigns the attribute content to the Int value if the attribute is present.

bool	optionalAttributeAsUInt_ (UInt &value, const XMLAttributes &a, const char *name) const
	Assigns the attribute content to the UInt value if the attribute is present.

bool	optionalAttributeAsDouble_ (double &value, const XMLAttributes &a, const char *name) const
	Assigns the attribute content to the double value if the attribute is present.

bool	optionalAttributeAsDoubleList_ (DoubleList &value, const XMLAttributes &a, const char *name) const
	Assigns the attribute content to the DoubleList value if the attribute is present.

bool	optionalAttributeAsStringList_ (StringList &value, const XMLAttributes &a, const char *name) const
	Assigns the attribute content to the StringList value if the attribute is present.

bool	optionalAttributeAsIntList_ (IntList &value, const XMLAttributes &a, const char *name) const
	Assigns the attribute content to the IntList value if the attribute is present.

std::string	attributeAsString_ (const XMLAttributes &a, const char16_t *name) const
	Converts an attribute to a String.

Int	attributeAsInt_ (const XMLAttributes &a, const char16_t *name) const
	Converts an attribute to a Int.

double	attributeAsDouble_ (const XMLAttributes &a, const char16_t *name) const
	Converts an attribute to a double.

DoubleList	attributeAsDoubleList_ (const XMLAttributes &a, const char16_t *name) const
	Converts an attribute to a DoubleList.

IntList	attributeAsIntList_ (const XMLAttributes &a, const char16_t *name) const
	Converts an attribute to a IntList.

StringList	attributeAsStringList_ (const XMLAttributes &a, const char16_t *name) const
	Converts an attribute to a StringList.

bool	optionalAttributeAsString_ (std::string &value, const XMLAttributes &a, const char16_t *name) const
	Assigns the attribute content to the String value if the attribute is present.

bool	optionalAttributeAsInt_ (Int &value, const XMLAttributes &a, const char16_t *name) const
	Assigns the attribute content to the Int value if the attribute is present.

bool	optionalAttributeAsUInt_ (UInt &value, const XMLAttributes &a, const char16_t *name) const
	Assigns the attribute content to the UInt value if the attribute is present.

bool	optionalAttributeAsDouble_ (double &value, const XMLAttributes &a, const char16_t *name) const
	Assigns the attribute content to the double value if the attribute is present.

bool	optionalAttributeAsDoubleList_ (DoubleList &value, const XMLAttributes &a, const char16_t *name) const
	Assigns the attribute content to the DoubleList value if the attribute is present.

bool	optionalAttributeAsIntList_ (IntList &value, const XMLAttributes &a, const char16_t *name) const
	Assigns the attribute content to the IntList value if the attribute is present.

bool	optionalAttributeAsStringList_ (StringList &value, const XMLAttributes &a, const char16_t *name) const
	Assigns the attribute content to the StringList value if the attribute is present.

Protected Attributes inherited from XMLHandler
std::string	file_
	File name.

std::string	version_
	Schema version.

StringManager	sm_
	Helper class for string conversion.

std::vector< std::string >	open_tags_
	Stack of open XML tags.

LOADDETAIL	load_detail_
	parse only until total number of scans and chroms have been determined from attributes

std::vector< std::vector< std::string > >	cv_terms_
	Array of CV term lists (one sublist denotes one term and it's children)

Detailed Description

Handler that is used for parsing MascotXML data.

Constructor & Destructor Documentation

◆ MascotXMLHandler()

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

Constructor.

◆ ~MascotXMLHandler()

~MascotXMLHandler ( )

override

Destructor.

Member Function Documentation

◆ onCharacters()

void onCharacters	(	const char16_t *	chars,
		Size	length
	)

overridevirtual

Parsing method for character data.

Reimplemented from XMLHandler.

◆ onEndElement()

void onEndElement ( const char16_t * qname )

overridevirtual

Parsing method for closing tags.

Reimplemented from XMLHandler.

◆ onStartElement()

void onStartElement	(	const char16_t *	qname,
		const XMLAttributes &	attributes
	)

overridevirtual

Parsing method for opening tags.

Reimplemented from XMLHandler.

◆ splitModificationBySpecifiedAA()

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

static

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

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_

std::string actual_title_

private

◆ character_buffer_

std::string character_buffer_

private

filled by MascotXMLHandler::characters

◆ date_

DateTime date_

private

◆ date_time_string_

std::string date_time_string_

private

◆ id_data_

PeptideIdentificationList& id_data_

private

the identifications (storing the peptide hits)

◆ identifier_

std::string identifier_

private

◆ lookup_

const SpectrumMetaDataLookup& lookup_

private

Helper object for looking up RT information.

◆ major_version_

std::string major_version_

private

◆ minor_version_

std::string minor_version_

private

◆ modified_peptides_

std::map<std::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<std::string> remove_fixed_mods_

private

◆ search_parameters_

ProteinIdentification::SearchParameters search_parameters_

private

◆ tag_

std::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

◆ onCharacters()

◆ onEndElement()

◆ onStartElement()

◆ splitModificationBySpecifiedAA()

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_