XMLHandler for the result files of XQuest. More...

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

Inheritance diagram for XQuestResultXMLHandler:

Public Member Functions
	XQuestResultXMLHandler (const String &filename, std::vector< std::vector< PeptideIdentification > > &csms, std::vector< ProteinIdentification > &prot_ids, Size min_n_ions_per_spectrum, bool load_to_peptideHit_)

virtual	~XQuestResultXMLHandler ()

void	endElement (const XMLCh const uri, const XMLCh const local_name, const XMLCh *const qname)
	Parsing method for closing tags. More...

void	startElement (const XMLCh const uri, const XMLCh const local_name, const XMLCh *const qname, const xercesc::Attributes &attributes)
	Parsing method for opening tags. More...

double	getMinScore () const
	Returns the minimum score encountered in the file. More...

double	getMaxScore () const
	Returns the maximum score encountered in the file. More...

UInt	getNumberOfHits () const
	Returns the total number of hits in the file. 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...

virtual void	characters (const XMLCh *const chars, const XMLSize_t length)
	Parsing method for character data. More...

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

Static Public Attributes
static std::map< Size, String >	enzymes

static std::map< String, UInt >	months

static const String	decoy_string

Private Member Functions
void	extractDateTime_ (const String &xquest_datetime_string, DateTime &date_time)
	Extracts the DateTime from datetime string from xQuest. More...

void	addMetaValues_ (MetaInfoInterface &meta_info_interface)
	Assignes all meta values stored in the peptide_id_attributes member to an meta info interface. More...

void	getLinkPosition_ (const xercesc::Attributes &attributes, std::pair< SignedSize, SignedSize > &pair)
	Gets the link location of a xQuest xlinkPositionString. More...

void	setPeptideEvidence_ (const String &prot_string, PeptideHit &pep_hit)
	Sets the peptide evidence for Alpha and Beta. More...

void	setMetaValue_ (const String &key, const DataValue &datavalue, PeptideIdentification &pep_id, PeptideHit &alpha)
	Sets the meta value of the peptide identification for alpha hit. More...

void	setMetaValue_ (const String &key, const DataValue &datavalue, PeptideIdentification &pep_id, PeptideHit &alpha, PeptideHit &beta)
	Sets the meta value of the peptide identification for alpha hit. More...

Private Attributes
std::vector< std::vector< PeptideIdentification > > &	csms_

std::vector< ProteinIdentification > &	prot_ids_

UInt	n_hits_

double	min_score_

double	max_score_

Size	min_n_ions_per_spectrum_

bool	load_to_peptideHit_

bool	is_openproxl_

std::set< String >	accessions_

EnzymesDB *	enzymes_db_

std::set< UInt >	charges_

UInt	min_precursor_charge_

UInt	max_precursor_charge_

double	rt_light_

std::set< double >	monolinks_masses_

std::vector< PeptideIdentification >	current_spectrum_search_

std::map< String, DataValue >	peptide_id_meta_values_

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...

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 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...

Detailed Description

XMLHandler for the result files of XQuest.

Constructor & Destructor Documentation

◆ XQuestResultXMLHandler()

XQuestResultXMLHandler	(	const String &	filename,
		std::vector< std::vector< PeptideIdentification > > &	csms,
		std::vector< ProteinIdentification > &	prot_ids,
		Size	min_n_ions_per_spectrum,
		bool	load_to_peptideHit_
	)

◆ ~XQuestResultXMLHandler()

virtual ~XQuestResultXMLHandler ( )

virtual

Member Function Documentation

◆ addMetaValues_()

void addMetaValues_ ( MetaInfoInterface & meta_info_interface )

private

Assignes all meta values stored in the peptide_id_attributes member to an meta info interface.

Parameters

meta_info_interface Where the meta values from the peptide_id_attributes member should be assigned to

◆ endElement()

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

virtual

Parsing method for closing tags.

Reimplemented from XMLHandler.

◆ extractDateTime_()

void extractDateTime_	(	const String &	xquest_datetime_string,
		DateTime &	date_time
	)

inlineprivate

Extracts the DateTime from datetime string from xQuest.

Parameters

xquest_datetime_string	The DateTime String to be processed
date_time	DateTime that reflects the value given in the `xquest_datetime_string`

◆ getLinkPosition_()

void getLinkPosition_	(	const xercesc::Attributes &	attributes,
		std::pair< SignedSize, SignedSize > &	pair
	)

private

Gets the link location of a xQuest xlinkPositionString.

Parameters

attributes	XML attributes of Xerces.
pair	Pair to be populated with the xlinkposition in xQuest.

◆ getMaxScore()

double getMaxScore ( ) const

Returns the maximum score encountered in the file.

Returns: Maximum score encountered in the file.

◆ getMinScore()

double getMinScore ( ) const

Returns the minimum score encountered in the file.

Returns: Minimum score encountered in the file.

◆ getNumberOfHits()

UInt getNumberOfHits ( ) const

Returns the total number of hits in the file.

Returns: Total number of hits in the file.

◆ setMetaValue_() [1/2]

void setMetaValue_	(	const String &	key,
		const DataValue &	datavalue,
		PeptideIdentification &	pep_id,
		PeptideHit &	alpha
	)

private

Sets the meta value of the peptide identification for alpha hit.

Parameters

key	Which meta value to set
datavalue	Value to be set
pep_id	For which peptide identification the meta value should be set.
alpha	Alpha peptide hit for which the meta value should be set.

◆ setMetaValue_() [2/2]

void setMetaValue_	(	const String &	key,
		const DataValue &	datavalue,
		PeptideIdentification &	pep_id,
		PeptideHit &	alpha,
		PeptideHit &	beta
	)

private

Sets the meta value of the peptide identification for alpha hit.

Parameters

key	Which meta value to set
datavalue	Value to be set
pep_id	For which peptide identification the meta value should be set.
alpha	Alpha peptide hit for which the meta value should be set.
beta	Beta peptide hit for which the meta value should be set.

◆ setPeptideEvidence_()

void setPeptideEvidence_	(	const String &	prot_string,
		PeptideHit &	pep_hit
	)

private

Sets the peptide evidence for Alpha and Beta.

Parameters

prot_string	Protein string of the xquest file the peptide evidence should be populated from.
pep_hit	For which peptide hit the peptide evidence should be set.

◆ startElement()

void startElement	(	const XMLCh *const	uri,
		const XMLCh *const	localname,
		const XMLCh *const	qname,
		const xercesc::Attributes &	attrs
	)

virtual

Parsing method for opening tags.

Reimplemented from XMLHandler.

Member Data Documentation

◆ accessions_

std::set< String > accessions_

private

◆ charges_

std::set< UInt > charges_

private

◆ csms_

std::vector< std::vector< PeptideIdentification > >& csms_

private

◆ current_spectrum_search_

std::vector< PeptideIdentification > current_spectrum_search_

private

◆ decoy_string

const String decoy_string

static

◆ enzymes

std::map< Size, String > enzymes

static

◆ enzymes_db_

EnzymesDB* enzymes_db_

private

◆ is_openproxl_

bool is_openproxl_

private

◆ load_to_peptideHit_

bool load_to_peptideHit_

private

◆ max_precursor_charge_

UInt max_precursor_charge_

private

◆ max_score_

double max_score_

private

◆ min_n_ions_per_spectrum_

Size min_n_ions_per_spectrum_

private

◆ min_precursor_charge_

UInt min_precursor_charge_

private

◆ min_score_

double min_score_

private

◆ monolinks_masses_

std::set< double > monolinks_masses_

private

◆ months

std::map<String, UInt> months

static

◆ n_hits_

UInt n_hits_

private

◆ peptide_id_meta_values_

std::map<String, DataValue> peptide_id_meta_values_

private

◆ prot_ids_

std::vector< ProteinIdentification >& prot_ids_

private

◆ rt_light_

double rt_light_

private

Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ XQuestResultXMLHandler()

◆ ~XQuestResultXMLHandler()

Member Function Documentation

◆ addMetaValues_()

◆ endElement()

◆ extractDateTime_()

◆ getLinkPosition_()

◆ getMaxScore()

◆ getMinScore()

◆ getNumberOfHits()

◆ setMetaValue_() [1/2]

◆ setMetaValue_() [2/2]

◆ setPeptideEvidence_()

◆ startElement()

Member Data Documentation

◆ accessions_

◆ charges_

◆ csms_

◆ current_spectrum_search_

◆ decoy_string

◆ enzymes

◆ enzymes_db_

◆ is_openproxl_

◆ load_to_peptideHit_

◆ max_precursor_charge_

◆ max_score_

◆ min_n_ions_per_spectrum_

◆ min_precursor_charge_

◆ min_score_

◆ monolinks_masses_

◆ months

◆ n_hits_

◆ peptide_id_meta_values_

◆ prot_ids_

◆ rt_light_