Used to load and store PepXML files. More...

#include <OpenMS/FORMAT/PepXMLFile.h>

Inheritance diagram for PepXMLFile:

Collaboration diagram for PepXMLFile:

Classes
struct	AminoAcidModification

Public Member Functions
	PepXMLFile ()
	Constructor. More...

	~PepXMLFile () override
	Destructor. More...

void	load (const String &filename, std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides, const String &experiment_name, const SpectrumMetaDataLookup &lookup)
	Loads peptide sequences with modifications out of a PepXML file. More...

void	load (const String &filename, std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides, const String &experiment_name="")
	load function with empty defaults for some parameters (see above) More...

void	store (const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids, const String &mz_file="", const String &mz_name="", bool peptideprophet_analyzed=false, double rt_tolerance=0.01)
	Stores idXML as PepXML file. More...

void	keepNativeSpectrumName (bool keep)
	Whether we should keep the native spectrum name of the pepXML. More...

void	setPreferredFixedModifications (const std::vector< const ResidueModification * > &mods)
	sets the preferred fixed modifications More...

void	setPreferredVariableModifications (const std::vector< const ResidueModification * > &mods)
	sets the preferred variable modifications More...

Public Member Functions inherited from XMLFile
	XMLFile ()
	Default constructor. More...

	XMLFile (const String &schema_location, const String &version)
	Constructor that sets the schema location. More...

virtual	~XMLFile ()
	Destructor. More...

bool	isValid (const String &filename, std::ostream &os)
	Checks if a file validates against the XML schema. More...

const String &	getVersion () const
	return the version of the schema More...

Protected Member Functions
void	endElement (const XMLCh const, const XMLCh const, const XMLCh *const qname) override
	Docu in base class. More...

void	startElement (const XMLCh const, const XMLCh const, const XMLCh *const qname, const xercesc::Attributes &attributes) override
	Docu in base class. More...

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...

	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...

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)

Protected Member Functions inherited from XMLFile
void	parse_ (const String &filename, XMLHandler *handler)
	Parses the XML file given by `filename` using the handler given by `handler`. More...

void	parseBuffer_ (const std::string &buffer, XMLHandler *handler)
	Parses the in-memory buffer given by `buffer` using the handler given by `handler`. More...

void	save_ (const String &filename, XMLHandler *handler) const
	Stores the contents of the XML handler given by `handler` in the file given by `filename`. More...

void	enforceEncoding_ (const String &encoding)

	XMLFile ()
	Default constructor. More...

	XMLFile (const String &schema_location, const String &version)
	Constructor that sets the schema location. More...

virtual	~XMLFile ()
	Destructor. More...

bool	isValid (const String &filename, std::ostream &os)
	Checks if a file validates against the XML schema. More...

const String &	getVersion () const
	return the version of the schema More...

Private Member Functions
void	makeScanMap_ ()
	Fill `scan_map_`. More...

void	readRTMZCharge_ (const xercesc::Attributes &attributes)
	Read RT, m/z, charge information from attributes of "spectrum_query". More...

bool	lookupAddFromHeader_ (double modification_mass, Size modification_position, std::vector< AminoAcidModification > const &header_mods)

Private Attributes
std::vector< ProteinIdentification > *	proteins_
	Pointer to the list of identified proteins. More...

std::vector< PeptideIdentification > *	peptides_
	Pointer to the list of identified peptides. More...

const SpectrumMetaDataLookup *	lookup_
	Pointer to wrapper for looking up spectrum meta data. More...

String	exp_name_
	Name of the associated experiment (filename of the data file, extension will be removed) More...

String	search_engine_
	Set name of search engine. More...

String	native_spectrum_name_
	Several optional attributes of spectrum_query. More...

String	experiment_label_

String	swath_assay_

String	status_

bool	use_precursor_data_ {}
	Get RT and m/z for peptide ID from precursor scan (should only matter for RT)? More...

std::map< Size, Size >	scan_map_
	Mapping between scan number in the pepXML file and index in the corresponding MSExperiment. More...

Element	hydrogen_
	Hydrogen data (for mass types) More...

bool	analysis_summary_
	Are we currently in an "analysis_summary" element (should be skipped)? More...

bool	keep_native_name_
	Whether we should keep the native spectrum name of the pepXML. More...

bool	search_score_summary_
	Are we currently in an "search_score_summary" element (should be skipped)? More...

bool	search_summary_ {}
	Are we currently in an "search_summary" element (should be skipped)? More...

bool	wrong_experiment_ {}
	Do current entries belong to the experiment of interest (for pepXML files that bundle results from different experiments)? More...

bool	seen_experiment_ {}
	Have we seen the experiment of interest at all? More...

bool	checked_base_name_ {}
	Have we checked the "base_name" attribute in the "msms_run_summary" element? More...

bool	has_decoys_ {}
	Does the file have decoys (e.g. from Comet's internal decoy search) More...

String	decoy_prefix_
	In case it has decoys, what is the prefix? More...

String	current_base_name_
	current base name More...

std::vector< std::vector< ProteinIdentification >::iterator >	current_proteins_
	References to currently active ProteinIdentifications. More...

ProteinIdentification::SearchParameters	params_
	Search parameters of the current identification run. More...

String	enzyme_
	Enzyme name associated with the current identification run. More...

String	enzyme_cuttingsite_

PeptideIdentification	current_peptide_
	PeptideIdentification instance currently being processed. More...

PeptideHit::PepXMLAnalysisResult	current_analysis_result_
	Analysis result instance currently being processed. More...

PeptideHit	peptide_hit_
	PeptideHit instance currently being processed. More...

String	current_sequence_
	Sequence of the current peptide hit. More...

double	rt_ {}
	RT and m/z of current PeptideIdentification. More...

double	mz_ {}

Int	charge_ {}
	Precursor ion charge. More...

UInt	search_id_ {}
	ID of current search result. More...

String	prot_id_
	Identifier linking PeptideIdentifications and ProteinIdentifications. More...

DateTime	date_
	Date the pepXML file was generated. More...

double	hydrogen_mass_ {}
	Mass of a hydrogen atom (monoisotopic/average depending on case) More...

std::vector< std::pair< const ResidueModification *, Size > >	current_modifications_
	The modifications of the current peptide hit (position is 1-based) More...

std::vector< AminoAcidModification >	fixed_modifications_
	Fixed aminoacid modifications as parsed from the header. More...

std::vector< AminoAcidModification >	variable_modifications_
	Variable aminoacid modifications as parsed from the header. More...

std::vector< const ResidueModification * >	preferred_fixed_modifications_

std::vector< const ResidueModification * >	preferred_variable_modifications_

Static Private Attributes
static const double	mod_tol_

static const double	xtandem_artificial_mod_tol_

Additional Inherited Members
Protected 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 }

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

Protected Attributes inherited from XMLFile
String	schema_location_
	XML schema file location. More...

String	schema_version_
	Version string. More...

String	enforced_encoding_
	Encoding string that replaces the encoding (system dependent or specified in the XML). Disabled if empty. Used as a workaround for XTandem output xml. More...

Detailed Description

Used to load and store PepXML files.

This class is used to load and store documents that implement the schema of PepXML files.

A documented schema for this format comes with the TPP and can also be found at https://github.com/OpenMS/OpenMS/tree/develop/share/OpenMS/SCHEMAS

Constructor & Destructor Documentation

◆ PepXMLFile()

PepXMLFile ( )

Constructor.

◆ ~PepXMLFile()

~PepXMLFile ( )

override

Destructor.

Member Function Documentation

◆ endElement()

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

overrideprotected

Docu in base class.

◆ keepNativeSpectrumName()

void keepNativeSpectrumName ( bool keep )

inline

Whether we should keep the native spectrum name of the pepXML.

Note: This will lead to a "pepxml_spectrum_name" meta value being added to each PeptideIdentification containing the original name of the spectrum in TPP format.

◆ load() [1/2]

void load	(	const String &	filename,
		std::vector< ProteinIdentification > &	proteins,
		std::vector< PeptideIdentification > &	peptides,
		const String &	experiment_name,
		const SpectrumMetaDataLookup &	lookup
	)

Loads peptide sequences with modifications out of a PepXML file.

Parameters

filename	PepXML file to load
proteins	Protein identification output
peptides	Peptide identification output
experiment_name	Experiment file name, which is used to extract the corresponding search results from the PepXML file.
lookup	Helper for looking up retention times (PepXML may contain only scan numbers).

Exceptions

Exception::FileNotFound	is thrown if the file could not be opened
Exception::ParseError	is thrown if an error occurs during parsing

◆ load() [2/2]

void load	(	const String &	filename,
		std::vector< ProteinIdentification > &	proteins,
		std::vector< PeptideIdentification > &	peptides,
		const String &	experiment_name = `""`
	)

load function with empty defaults for some parameters (see above)

Exceptions

Exception::FileNotFound	is thrown if the file could not be opened
Exception::ParseError	is thrown if an error occurs during parsing

◆ lookupAddFromHeader_()

bool lookupAddFromHeader_	(	double	modification_mass,
		Size	modification_position,
		std::vector< AminoAcidModification > const &	header_mods
	)

private

looks up modification by modification_mass and aminoacid of current_sequence_[ modification_position ] and adds it to the current_modifications_

◆ makeScanMap_()

void makeScanMap_ ( )

private

Fill scan_map_.

◆ readRTMZCharge_()

void readRTMZCharge_ ( const xercesc::Attributes & attributes )

private

Read RT, m/z, charge information from attributes of "spectrum_query".

◆ setPreferredFixedModifications()

void setPreferredFixedModifications ( const std::vector< const ResidueModification * > & mods )

sets the preferred fixed modifications

◆ setPreferredVariableModifications()

void setPreferredVariableModifications ( const std::vector< const ResidueModification * > & mods )

sets the preferred variable modifications

◆ startElement()

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

overrideprotected

Docu in base class.

◆ store()

void store	(	const String &	filename,
		std::vector< ProteinIdentification > &	protein_ids,
		std::vector< PeptideIdentification > &	peptide_ids,
		const String &	mz_file = `""`,
		const String &	mz_name = `""`,
		bool	peptideprophet_analyzed = `false`,
		double	rt_tolerance = `0.01`
	)

Stores idXML as PepXML file.

Exceptions

Exception::UnableToCreateFile is thrown if the file could not be opened for writing

Member Data Documentation

◆ analysis_summary_

bool analysis_summary_

private

Are we currently in an "analysis_summary" element (should be skipped)?

◆ charge_

Int charge_ {}

private

Precursor ion charge.

◆ checked_base_name_

bool checked_base_name_ {}

private

Have we checked the "base_name" attribute in the "msms_run_summary" element?

◆ current_analysis_result_

PeptideHit::PepXMLAnalysisResult current_analysis_result_

private

Analysis result instance currently being processed.

◆ current_base_name_

String current_base_name_

private

current base name

◆ current_modifications_

std::vector<std::pair<const ResidueModification*, Size> > current_modifications_

private

The modifications of the current peptide hit (position is 1-based)

◆ current_peptide_

PeptideIdentification current_peptide_

private

PeptideIdentification instance currently being processed.

◆ current_proteins_

std::vector<std::vector<ProteinIdentification>::iterator> current_proteins_

private

References to currently active ProteinIdentifications.

◆ current_sequence_

String current_sequence_

private

Sequence of the current peptide hit.

◆ date_

DateTime date_

private

Date the pepXML file was generated.

◆ decoy_prefix_

String decoy_prefix_

private

In case it has decoys, what is the prefix?

◆ enzyme_

String enzyme_

private

Enzyme name associated with the current identification run.

◆ enzyme_cuttingsite_

String enzyme_cuttingsite_

private

◆ exp_name_

String exp_name_

private

Name of the associated experiment (filename of the data file, extension will be removed)

◆ experiment_label_

String experiment_label_

private

◆ fixed_modifications_

std::vector<AminoAcidModification> fixed_modifications_

private

Fixed aminoacid modifications as parsed from the header.

◆ has_decoys_

bool has_decoys_ {}

private

Does the file have decoys (e.g. from Comet's internal decoy search)

◆ hydrogen_

Element hydrogen_

private

Hydrogen data (for mass types)

◆ hydrogen_mass_

double hydrogen_mass_ {}

private

Mass of a hydrogen atom (monoisotopic/average depending on case)

◆ keep_native_name_

bool keep_native_name_

private

Whether we should keep the native spectrum name of the pepXML.

◆ lookup_

const SpectrumMetaDataLookup* lookup_

private

Pointer to wrapper for looking up spectrum meta data.

◆ mod_tol_

const double mod_tol_

staticprivate

◆ mz_

double mz_ {}

private

◆ native_spectrum_name_

String native_spectrum_name_

private

Several optional attributes of spectrum_query.

◆ params_

ProteinIdentification::SearchParameters params_

private

Search parameters of the current identification run.

◆ peptide_hit_

PeptideHit peptide_hit_

private

PeptideHit instance currently being processed.

◆ peptides_

std::vector<PeptideIdentification>* peptides_

private

Pointer to the list of identified peptides.

◆ preferred_fixed_modifications_

std::vector<const ResidueModification*> preferred_fixed_modifications_

private

Fixed modifications that should be preferred when parsing the header (e.g. when pepXML was produced through an adapter)

◆ preferred_variable_modifications_

std::vector<const ResidueModification*> preferred_variable_modifications_

private

Variable modifications that should be preferred when parsing the header (e.g. when pepXML was produced through an adapter)

◆ prot_id_

String prot_id_

private

Identifier linking PeptideIdentifications and ProteinIdentifications.

◆ proteins_

std::vector<ProteinIdentification>* proteins_

private

Pointer to the list of identified proteins.

◆ rt_

double rt_ {}

private

RT and m/z of current PeptideIdentification.

◆ scan_map_

std::map<Size, Size> scan_map_

private

Mapping between scan number in the pepXML file and index in the corresponding MSExperiment.

◆ search_engine_

String search_engine_

private

Set name of search engine.

◆ search_id_

UInt search_id_ {}

private

ID of current search result.

◆ search_score_summary_

bool search_score_summary_

private

Are we currently in an "search_score_summary" element (should be skipped)?

◆ search_summary_

bool search_summary_ {}

private

Are we currently in an "search_summary" element (should be skipped)?

◆ seen_experiment_

bool seen_experiment_ {}

private

Have we seen the experiment of interest at all?

◆ status_

String status_

private

◆ swath_assay_

String swath_assay_

private

◆ use_precursor_data_

bool use_precursor_data_ {}

private

Get RT and m/z for peptide ID from precursor scan (should only matter for RT)?

◆ variable_modifications_

std::vector<AminoAcidModification> variable_modifications_

private

Variable aminoacid modifications as parsed from the header.

◆ wrong_experiment_

bool wrong_experiment_ {}

private

Do current entries belong to the experiment of interest (for pepXML files that bundle results from different experiments)?

◆ xtandem_artificial_mod_tol_

const double xtandem_artificial_mod_tol_

staticprivate

Classes

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ PepXMLFile()

◆ ~PepXMLFile()

Member Function Documentation

◆ endElement()

◆ keepNativeSpectrumName()

◆ load() [1/2]

◆ load() [2/2]

◆ lookupAddFromHeader_()

◆ makeScanMap_()

◆ readRTMZCharge_()

◆ setPreferredFixedModifications()

◆ setPreferredVariableModifications()

◆ startElement()

◆ store()

Member Data Documentation

◆ analysis_summary_

◆ charge_

◆ checked_base_name_

◆ current_analysis_result_

◆ current_base_name_

◆ current_modifications_

◆ current_peptide_

◆ current_proteins_

◆ current_sequence_

◆ date_

◆ decoy_prefix_

◆ enzyme_

◆ enzyme_cuttingsite_

◆ exp_name_

◆ experiment_label_

◆ fixed_modifications_

◆ has_decoys_

◆ hydrogen_

◆ hydrogen_mass_

◆ keep_native_name_

◆ lookup_

◆ mod_tol_

◆ mz_

◆ native_spectrum_name_

◆ params_

◆ peptide_hit_

◆ peptides_

◆ preferred_fixed_modifications_

◆ preferred_variable_modifications_

◆ prot_id_

◆ proteins_

◆ rt_

◆ scan_map_

◆ search_engine_

◆ search_id_

◆ search_score_summary_

◆ search_summary_

◆ seen_experiment_

◆ status_

◆ swath_assay_

◆ use_precursor_data_

◆ variable_modifications_

◆ wrong_experiment_

◆ xtandem_artificial_mod_tol_