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

#include <OpenMS/FORMAT/PepXMLFile.h>

Inheritance diagram for PepXMLFile:

Classes
struct	AminoAcidModification
Public Member Functions
	PepXMLFile ()
	Constructor.
virtual	~PepXMLFile ()
	Destructor.
void	load (const String &filename, std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides, const String &experiment_name, const MSExperiment<> &experiment, bool use_precursor_data=false)
	Loads peptide sequences with modifications out of a PepXML file.
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)
void	store (const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
	Stores idXML as PepXML file.
Protected Member Functions
virtual void	endElement (const XMLCh const , const XMLCh const , const XMLCh *const qname)
	Docu in base class.
virtual void	startElement (const XMLCh const , const XMLCh const , const XMLCh *const qname, const xercesc::Attributes &attributes)
	Docu in base class.
Private Member Functions
void	makeScanMap_ ()
	Fill `scan_map_`.
void	readRTMZCharge_ (const xercesc::Attributes &attributes)
	Read RT, m/z, charge information from attributes of "spectrum_query".
void	matchModification_ (const DoubleReal mass, const String &origin, String &modification_description)
	find modification name given a modified AA mass
Private Attributes
std::vector < ProteinIdentification > *	proteins_
	Pointer to the list of identified proteins.
std::vector < PeptideIdentification > *	peptides_
	Pointer to the list of identified peptides.
const MSExperiment *	experiment_
	Pointer to the experiment from which the pepXML file was generated.
String	exp_name_
	Name of the associated experiment (filename of the data file, extension will be removed).
String	search_engine_
	Set name of search engine.
bool	use_precursor_data_
	Get RT and m/z for peptide ID from precursor scan (should only matter for RT)?
std::map< Size, Size >	scan_map_
	Mapping between scan number in the pepXML file and index in the corresponding MSExperiment.
DoubleReal	rt_tol_
	Retention time and mass-to-charge tolerance.
DoubleReal	mz_tol_
Element	hydrogen_
	Hydrogen data (for mass types).
bool	wrong_experiment_
	Do current entries belong to the experiment of interest (for pepXML files that bundle results from different experiments)?
bool	seen_experiment_
	Have we seen the experiment of interest at all?
std::vector< std::vector < ProteinIdentification > ::iterator >	current_proteins_
	References to currently active ProteinIdentifications.
ProteinIdentification::SearchParameters	params_
	Search parameters of the current identification run.
ProteinIdentification::DigestionEnzyme	enzyme_
	Enyzme associated with the current identification run.
PeptideIdentification	current_peptide_
	PeptideIdentification instance currently being processed.
PeptideHit	peptide_hit_
	PeptideHit instance currently being processed.
String	current_sequence_
	Sequence of the current peptide hit.
DoubleReal	rt_
	RT and m/z of current PeptideIdentification.
DoubleReal	mz_
Int	charge_
	Precursor ion charge.
UInt	search_id_
	ID of current search result.
String	prot_id_
	Identifier linking PeptideIdentifications and ProteinIdentifications.
DateTime	date_
	Date the pepXML file was generated.
DoubleReal	hydrogen_mass_
	Mass of a hydrogen atom (monoisotopic/average depending on case).
std::vector< std::pair< String, Size > >	current_modifications_
	The modifications of the current peptide hit (position is 1-based).
std::vector < AminoAcidModification >	fixed_modifications_
	Fixed aminoacid modifications.
std::vector < AminoAcidModification >	variable_modifications_
	Variable aminoacid modifications.

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.

Constructor & Destructor Documentation

PepXMLFile ( )

Constructor.

virtual ~PepXMLFile ( ) [virtual]

Destructor.

Member Function Documentation

virtual void endElement	(	const XMLCh *	const,
		const XMLCh *	const,
		const XMLCh *const	qname
	)			`[protected, virtual]`

Docu in base class.

void load	(	const String &	filename,
		std::vector< ProteinIdentification > &	proteins,
		std::vector< PeptideIdentification > &	peptides,
		const String &	experiment_name,
		const MSExperiment<> &	experiment,
		bool	use_precursor_data = `false`
	)

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.
	experiment	MS run to extract the retention times from (PepXML may contain only scan numbers).
	use_precursor_data	Use m/z and RT of the precursor (instead of the RT of the MS2 spectrum) for the peptide?

Exceptions:

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

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

void makeScanMap_ ( ) [private]

Fill scan_map_.

void matchModification_	(	const DoubleReal	mass,
		const String &	origin,
		String &	modification_description
	)			`[private]`

find modification name given a modified AA mass

Matches a mass of a modified AA to a mod in our modification db For ambigious mods, the first (arbitrary) is returned If no mod is found an error is issued and the return string is empty

Note:: A duplicate of this function is also used in ProtXMLFile

Parameters:

	mass	Modified AA's mass
	origin	AA one letter code
	modification_description	[out] Name of the modification, e.g. 'Carboxymethyl (C)'

void readRTMZCharge_ ( const xercesc::Attributes & attributes ) [private]

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

virtual void startElement	(	const XMLCh *	const,
		const XMLCh *	const,
		const XMLCh *const	qname,
		const xercesc::Attributes &	attributes
	)			`[protected, virtual]`