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

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

Inheritance diagram for XQuestResultXMLHandler:

Collaboration diagram for XQuestResultXMLHandler:

Public Member Functions
	XQuestResultXMLHandler (const String &filename, std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids)
	Constructor for a read-only handler for internal identification structures. More...

	XQuestResultXMLHandler (const std::vector< ProteinIdentification > &pro_id, const std::vector< PeptideIdentification > &pep_id, const String &filename, const String &version)
	Constructor for a write-only handler for internal identification structures. More...

	~XQuestResultXMLHandler () override

void	endElement (const XMLCh const uri, const XMLCh const local_name, const XMLCh *const qname) override

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

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...

void	writeTo (std::ostream &os) override
	Writes the contents to a stream. More...

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...

String	errorString ()
	Returns the last error description. 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...

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

Static Public Member Functions
static StringList	splitByNth (const String &input, const char separator, const Size n)
	splits the @input string at the nth occurrence of the @separator More...

static StringList	splitByMiddle (const String &input, const char separator)
	counts occurrences of the @separator and splits the @input string into two at the middle 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...

Static Public Attributes
static std::map< Size, String >	enzymes
	Maps enzyme_num in xQuest result file to the enzyme name used by OpenMS. More...

static std::map< String, UInt >	months
	Maps String encoding month to the numeric value. More...

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

void	addMetaValues_ (MetaInfoInterface &meta_info_interface)
	Assigns 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...

Private Attributes
String	decoy_string_ = "decoy_"

int	spectrum_index_light_

int	spectrum_index_heavy_

String	cross_linker_name_

std::vector< PeptideIdentification > *	pep_ids_

std::vector< ProteinIdentification > *	prot_ids_

const std::vector< ProteinIdentification > *	cpro_id_

const std::vector< PeptideIdentification > *	cpep_id_

UInt	n_hits_
	Total no. of hits found in the result XML file. More...

double	min_score_

double	max_score_

bool	is_openpepxl_
	Whether or not current xquest result tag comes from OpenPepXL (xQuest otherwise) More...

std::set< String >	accessions_
	Set of all protein accessions that are within the ProteinHits. More...

ProteaseDB *	enzymes_db_
	The enzyme database for enzyme lookup. More...

std::set< UInt >	charges_
	Keeps track of the charges of the hits. More...

UInt	min_precursor_charge_

UInt	max_precursor_charge_

double	rt_light_

double	rt_heavy_

double	mz_light_

double	mz_heavy_

StringList	ms_run_path_

String	spectrum_input_file_

std::vector< PeptideIdentification >	current_spectrum_search_
	The current spectrum search. More...

std::map< String, DataValue >	peptide_id_meta_values_
	Stores the attributes of a record (peptide identification) 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	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...

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

XMLHandler for the result files of XQuest.

Constructor & Destructor Documentation

◆ XQuestResultXMLHandler() [1/2]

XQuestResultXMLHandler	(	const String &	filename,
		std::vector< PeptideIdentification > &	pep_ids,
		std::vector< ProteinIdentification > &	prot_ids
	)

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

◆ XQuestResultXMLHandler() [2/2]

XQuestResultXMLHandler	(	const std::vector< ProteinIdentification > &	pro_id,
		const std::vector< PeptideIdentification > &	pep_id,
		const String &	filename,
		const String &	version
	)

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

◆ ~XQuestResultXMLHandler()

~XQuestResultXMLHandler ( )

override

Member Function Documentation

◆ addMetaValues_()

void addMetaValues_ ( MetaInfoInterface & meta_info_interface )

private

Assigns 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	local_name,
		const XMLCh *const	qname
	)

override

◆ extractDateTime_()

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

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.

◆ 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.

◆ splitByMiddle()

static StringList splitByMiddle	(	const String &	input,
		const char	separator
	)

static

counts occurrences of the @separator and splits the @input string into two at the middle

If the separator occurs 5 times in the input string, the string will be split at the 3rd occurrence. If 7 times, then at the 4th. The separator has to occur in the string an uneven number of times. If the separator occurs once, the string will be split at this one instance. If this one occurrence is at the beginning or end, one of the result strings will be empty.

Exceptions

Exception::IllegalArgument is thrown if the @separator does not occur in the @input string an uneven number of times and at least once

Returns: StringList with two elements, the two halves of the input without the middle separator

◆ splitByNth()

static StringList splitByNth	(	const String &	input,
		const char	separator,
		const Size	n
	)

static

splits the @input string at the nth occurrence of the @separator

If the separator does not occur in the input string n times, then the first output string will be the entire input string and the second one will be empty.

Returns: StringList with two elements, the two parts of the input without the nth separator

◆ startElement()

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

override

◆ writeTo()

void writeTo ( std::ostream & )

overridevirtual

Writes the contents to a stream.

Reimplemented from XMLHandler.

Member Data Documentation

◆ accessions_

std::set< String > accessions_

private

Set of all protein accessions that are within the ProteinHits.

◆ charges_

std::set< UInt > charges_

private

Keeps track of the charges of the hits.

◆ cpep_id_

const std::vector<PeptideIdentification>* cpep_id_

private

◆ cpro_id_

const std::vector<ProteinIdentification>* cpro_id_

private

◆ cross_linker_name_

String cross_linker_name_

private

◆ current_spectrum_search_

std::vector< PeptideIdentification > current_spectrum_search_

private

The current spectrum search.

◆ decoy_string_

String decoy_string_ = "decoy_"

private

◆ enzymes

std::map< Size, String > enzymes

static

Maps enzyme_num in xQuest result file to the enzyme name used by OpenMS.

◆ enzymes_db_

ProteaseDB* enzymes_db_

private

The enzyme database for enzyme lookup.

◆ is_openpepxl_

bool is_openpepxl_

private

Whether or not current xquest result tag comes from OpenPepXL (xQuest otherwise)

◆ max_precursor_charge_

UInt max_precursor_charge_

private

◆ max_score_

double max_score_

private

◆ min_precursor_charge_

UInt min_precursor_charge_

private

◆ min_score_

double min_score_

private

◆ months

std::map<String, UInt> months

static

Maps String encoding month to the numeric value.

◆ ms_run_path_

StringList ms_run_path_

private

◆ mz_heavy_

double mz_heavy_

private

◆ mz_light_

double mz_light_

private

◆ n_hits_

UInt n_hits_

private

Total no. of hits found in the result XML file.

◆ pep_ids_

std::vector< PeptideIdentification >* pep_ids_

private

◆ peptide_id_meta_values_

std::map<String, DataValue> peptide_id_meta_values_

private

Stores the attributes of a record (peptide identification)

◆ prot_ids_

std::vector< ProteinIdentification >* prot_ids_

private

◆ rt_heavy_

double rt_heavy_

private

◆ rt_light_

double rt_light_

private

◆ spectrum_index_heavy_

int spectrum_index_heavy_

private

◆ spectrum_index_light_

int spectrum_index_light_

private

◆ spectrum_input_file_

String spectrum_input_file_

private

Public Member Functions

Static Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ XQuestResultXMLHandler() [1/2]

◆ XQuestResultXMLHandler() [2/2]

◆ ~XQuestResultXMLHandler()

Member Function Documentation

◆ addMetaValues_()

◆ endElement()

◆ extractDateTime_()

◆ getLinkPosition_()

◆ getMaxScore()

◆ getMinScore()

◆ getNumberOfHits()

◆ setPeptideEvidence_()

◆ splitByMiddle()

◆ splitByNth()

◆ startElement()

◆ writeTo()

Member Data Documentation

◆ accessions_

◆ charges_

◆ cpep_id_

◆ cpro_id_

◆ cross_linker_name_

◆ current_spectrum_search_

◆ decoy_string_

◆ enzymes

◆ enzymes_db_

◆ is_openpepxl_

◆ max_precursor_charge_

◆ max_score_

◆ min_precursor_charge_

◆ min_score_

◆ months

◆ ms_run_path_

◆ mz_heavy_

◆ mz_light_

◆ n_hits_

◆ pep_ids_

◆ peptide_id_meta_values_

◆ prot_ids_

◆ rt_heavy_

◆ rt_light_

◆ spectrum_index_heavy_

◆ spectrum_index_light_

◆ spectrum_input_file_