File adapter for QcML files. More...

#include <OpenMS/FORMAT/QcMLFile.h>

Inheritance diagram for QcMLFile:

Classes
struct	Attachment
	Representation of an attachment. More...
struct	QualityParameter
	Representation of a quality parameter. More...
Public Member Functions
	QcMLFile ()
	Default constructor.
	~QcMLFile ()
	Destructor.
String	map2cvs (const std::map< String, std::map< String, String > > &cvs_table, const String &separator) const
String	exportIDstats (const String &filename) const
void	addRunQualityParameter (String r, QualityParameter qp)
	Just adds a qualityparameter to run by the name r.
void	addRunAttachment (String r, Attachment at)
	Just adds a attachment to run by the name r.
void	addSetQualityParameter (String r, QualityParameter qp)
	Just adds a qualityparameter to set by the name r.
void	addSetAttachment (String r, Attachment at)
	Just adds a attachment to set by the name r.
void	removeAttachment (String r, std::vector< String > &ids, String at="")
	Removes attachments referencing a id given in ids, from run/set r. All attachments if no attachment name is given with at.
void	removeAttachment (String r, String at)
	Removes attachment with cv accession at from run/set r.
void	removeAllAttachments (String at)
	Removes attachment with cv accession at from all runs/sets.
void	removeQualityParameter (String r, std::vector< String > &ids)
	Just removes qualityparameter going by one of the ID attributes given in ids.
void	merge (const QcMLFile &addendum, String setname="")
	merges the given QCFile into this one
void	collectSetParameter (const String setname, const String qp, std::vector< String > &ret)
	collects the values of given QPs (as CVid) of the given set
String	exportAttachment (const String filename, const String qpname) const
	Returns a String of a tab separated rows if found empty string else from run/set by the name filename of the qualityparameter by the name qpname.
void	getRunNames (std::vector< String > &ids) const
	Gives the names of the registered runs in the vector ids.
bool	existsRun (const String filename) const
	Returns true if the given run name is present in this file.
bool	existsSet (const String filename) const
	Returns true if the given set name is present in this file.
void	existsRunQualityParameter (const String filename, const String qpname, std::vector< String > &ids) const
	Returns the ids of the parameter name given if found in given run empty else.
void	existsSetQualityParameter (const String filename, const String qpname, std::vector< String > &ids) const
	Returns the ids of the parameter name given if found in given set, empty else.
void	store (const String &filename) const
	Store the QCFile.
void	load (const String &filename)
	Load a QCFile.
Protected Member Functions
virtual void	endElement (const XMLCh const , const XMLCh const , const XMLCh *const qname)
virtual void	startElement (const XMLCh const , const XMLCh const , const XMLCh *const qname, const xercesc::Attributes &attributes)
virtual void	characters (const XMLCh *const chars, const XMLSize_t length)
Protected Attributes
std::map< String, std::vector < QualityParameter > >	runQualityQPs_
std::map< String, std::vector < Attachment > >	runQualityAts_
std::map< String, std::vector < QualityParameter > >	setQualityQPs_
std::map< String, std::vector < Attachment > >	setQualityAts_
std::map< String, std::set < String > >	setQualityQPs_members_
String	tag_
UInt	progress_
QualityParameter	qp_
Attachment	at_
std::vector< String >	row_
std::vector< String >	header_
String	name_
std::set< String >	names_
std::vector< QualityParameter >	qps_
std::vector< Attachment >	ats_

Detailed Description

File adapter for QcML files.

This Class is supposed to internally collect the data for the qcML File

Constructor & Destructor Documentation

QcMLFile ( )

Default constructor.

~QcMLFile ( )

Destructor.

Member Function Documentation

void addRunAttachment	(	String	r,
		Attachment	at
	)

Just adds a attachment to run by the name r.

void addRunQualityParameter	(	String	r,
		QualityParameter	qp
	)

Just adds a qualityparameter to run by the name r.

void addSetAttachment	(	String	r,
		Attachment	at
	)

Just adds a attachment to set by the name r.

void addSetQualityParameter	(	String	r,
		QualityParameter	qp
	)

Just adds a qualityparameter to set by the name r.

virtual void characters	(	const XMLCh *const	chars,
		const XMLSize_t	length
	)			`[protected, virtual]`

void collectSetParameter	(	const String	setname,
		const String	qp,
		std::vector< String > &	ret
	)

collects the values of given QPs (as CVid) of the given set

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

bool existsRun ( const String filename ) const

Returns true if the given run name is present in this file.

void existsRunQualityParameter	(	const String	filename,
		const String	qpname,
		std::vector< String > &	ids
	)			const

Returns the ids of the parameter name given if found in given run empty else.

bool existsSet ( const String filename ) const

Returns true if the given set name is present in this file.

void existsSetQualityParameter	(	const String	filename,
		const String	qpname,
		std::vector< String > &	ids
	)			const

Returns the ids of the parameter name given if found in given set, empty else.

String exportAttachment	(	const String	filename,
		const String	qpname
	)			const

Returns a String of a tab separated rows if found empty string else from run/set by the name filename of the qualityparameter by the name qpname.

String exportIDstats ( const String & filename ) const

void getRunNames ( std::vector< String > & ids ) const

Gives the names of the registered runs in the vector ids.

void load ( const String & filename )

Load a QCFile.

String map2cvs	(	const std::map< String, std::map< String, String > > &	cvs_table,
		const String &	separator
	)			const

void merge	(	const QcMLFile &	addendum,
		String	setname = `""`
	)

merges the given QCFile into this one

void removeAllAttachments ( String at )

Removes attachment with cv accession at from all runs/sets.

void removeAttachment	(	String	r,
		String	at
	)

Removes attachment with cv accession at from run/set r.

void removeAttachment	(	String	r,
		std::vector< String > &	ids,
		String	at = `""`
	)

Removes attachments referencing a id given in ids, from run/set r. All attachments if no attachment name is given with at.

void removeQualityParameter	(	String	r,
		std::vector< String > &	ids
	)

Just removes qualityparameter going by one of the ID attributes given in ids.

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

void store ( const String & filename ) const

Store the QCFile.

Member Data Documentation

Attachment at_ [protected]

std::vector<Attachment> ats_ [protected]

std::vector<String> header_ [protected]

String name_ [protected]

std::set<String> names_ [protected]

UInt progress_ [protected]

QualityParameter qp_ [protected]

std::vector<QualityParameter> qps_ [protected]

std::vector<String> row_ [protected]

std::map<String, std::vector< Attachment > > runQualityAts_ [protected]

std::map<String, std::vector< QualityParameter > > runQualityQPs_ [protected]

std::map<String, std::vector< Attachment > > setQualityAts_ [protected]

std::map<String, std::vector< QualityParameter > > setQualityQPs_ [protected]

std::map<String, std::set< String > > setQualityQPs_members_ [protected]

String tag_ [protected]

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:54 using doxygen 1.7.1

QcMLFile Class Reference [File IO]

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

QcMLFile Class Reference
[File IO]