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. More...

	~QcMLFile ()
	Destructor. More...

String	map2csv (const std::map< String, std::map< String, String > > &cvs_table, const String &separator) const

String	exportIDstats (const String &filename) const

void	registerRun (const String id, const String name)
	Registers a run in the qcml file with the respective mappings. More...

void	registerSet (const String id, const String name, const std::set< String > &names)
	Registers a set in the qcml file with the respective mappings. More...

void	addRunQualityParameter (String r, QualityParameter qp)
	Just adds a qualityparameter to run by the name r. More...

void	addRunAttachment (String r, Attachment at)
	Just adds a attachment to run by the name r. More...

void	addSetQualityParameter (String r, QualityParameter qp)
	Just adds a qualityparameter to set by the name r. More...

void	addSetAttachment (String r, Attachment at)
	Just adds a attachment to set by the name r. More...

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. More...

void	removeAttachment (String r, String at)
	Removes attachment with cv accession at from run/set r. More...

void	removeAllAttachments (String at)
	Removes attachment with cv accession at from all runs/sets. More...

void	removeQualityParameter (String r, std::vector< String > &ids)
	Just removes qualityparameter going by one of the ID attributes given in ids. More...

void	merge (const QcMLFile &addendum, String setname="")
	merges the given QCFile into this one More...

void	collectSetParameter (const String setname, const String qp, std::vector< String > &ret)
	collects the values of given QPs (as CVid) of the given set More...

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. More...

String	exportQP (const String filename, const String qpname) const
	Returns a String value in quotation of a qualityparameter by the name qpname in run/set by the name filename. More...

String	exportQPs (const String filename, const StringList qpnames) const
	Returns a String of a tab separated qualityparameter by the name qpname in run/set by the name filename. More...

void	getRunIDs (std::vector< String > &ids) const
	Gives the ids of the registered runs in the vector ids. More...

void	getRunNames (std::vector< String > &ids) const
	Gives the names of the registered runs in the vector ids. More...

bool	existsRun (const String filename, bool checkname=false) const
	Returns true if the given run id is present in this file, if checkname is true it also checks the names. More...

bool	existsSet (const String filename, bool checkname=false) const
	Returns true if the given set id is present in this file, if checkname is true it also checks the names. More...

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. More...

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. More...

void	store (const String &filename) const
	Store the QCFile. More...

void	load (const String &filename)
	Load a QCFile. 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	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)

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...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

	~ProgressLogger ()
	Destructor. More...

	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...

LogType	getLogType () const
	Returns the type of progress log being used. More...

void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...

void	setProgress (SignedSize value) const
	Sets the current progress. More...

void	endProgress () const
	Ends the progress display. More...

Protected Member Functions
virtual void	endElement (const XMLCh const, const XMLCh const, const XMLCh *const qname)
	Parsing method for closing tags. More...

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

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

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_

std::map< String, String >	run_Name_ID_map_

std::map< String, String >	set_Name_ID_map_

String	tag_

UInt	progress_

QualityParameter	qp_

Attachment	at_

std::vector< String >	row_

std::vector< String >	header_

String	name_

String	run_id_

std::set< String >	names_

std::vector< QualityParameter >	qps_

std::vector< Attachment >	ats_

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...

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...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Additional Inherited Members
Public Types inherited from XMLHandler
enum	ActionMode { LOAD, STORE }
	Action to set the current mode (for error messages) More...

Public Types inherited from ProgressLogger
enum	LogType { CMD, GUI, NONE }
	Possible log types. 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 Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. More...

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

File adapter for QcML files.

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

Constructor & Destructor Documentation

◆ QcMLFile()

QcMLFile ( )

Default constructor.

◆ ~QcMLFile()

~QcMLFile ( )

Destructor.

Member Function Documentation

◆ addRunAttachment()

void addRunAttachment	(	String	r,
		Attachment	at
	)

Just adds a attachment to run by the name r.

◆ addRunQualityParameter()

void addRunQualityParameter	(	String	r,
		QualityParameter	qp
	)

Just adds a qualityparameter to run by the name r.

◆ addSetAttachment()

void addSetAttachment	(	String	r,
		Attachment	at
	)

Just adds a attachment to set by the name r.

◆ addSetQualityParameter()

void addSetQualityParameter	(	String	r,
		QualityParameter	qp
	)

Just adds a qualityparameter to set by the name r.

◆ characters()

virtual void characters	(	const XMLCh *const	chars,
		const XMLSize_t	length
	)

protectedvirtual

Parsing method for character data.

Reimplemented from XMLHandler.

◆ collectSetParameter()

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

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

◆ endElement()

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

protectedvirtual

Parsing method for closing tags.

Reimplemented from XMLHandler.

◆ existsRun()

bool existsRun	(	const String	filename,
		bool	checkname = `false`
	)		const

Returns true if the given run id is present in this file, if checkname is true it also checks the names.

◆ existsRunQualityParameter()

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.

◆ existsSet()

bool existsSet	(	const String	filename,
		bool	checkname = `false`
	)		const

Returns true if the given set id is present in this file, if checkname is true it also checks the names.

◆ existsSetQualityParameter()

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.

◆ exportAttachment()

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.

◆ exportIDstats()

String exportIDstats ( const String & filename ) const

◆ exportQP()

String exportQP	(	const String	filename,
		const String	qpname
	)		const

Returns a String value in quotation of a qualityparameter by the name qpname in run/set by the name filename.

◆ exportQPs()

String exportQPs	(	const String	filename,
		const StringList	qpnames
	)		const

Returns a String of a tab separated qualityparameter by the name qpname in run/set by the name filename.

◆ getRunIDs()

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

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

◆ getRunNames()

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

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

◆ load()

void load ( const String & filename )

Load a QCFile.

◆ map2csv()

String map2csv	(	const std::map< String, std::map< String, String > > &	cvs_table,
		const String &	separator
	)		const

◆ merge()

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

merges the given QCFile into this one

◆ registerRun()

void registerRun	(	const String	id,
		const String	name
	)

Registers a run in the qcml file with the respective mappings.

◆ registerSet()

void registerSet	(	const String	id,
		const String	name,
		const std::set< String > &	names
	)

Registers a set in the qcml file with the respective mappings.

◆ removeAllAttachments()

void removeAllAttachments ( String at )

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

◆ removeAttachment() [1/2]

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.

◆ removeAttachment() [2/2]

void removeAttachment	(	String	r,
		String	at
	)

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

◆ removeQualityParameter()

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

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

◆ startElement()

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

protectedvirtual

Parsing method for opening tags.

Reimplemented from XMLHandler.

◆ store()

void store ( const String & filename ) const

Store the QCFile.

Member Data Documentation

◆ at_

Attachment at_

protected

◆ ats_

std::vector<Attachment> ats_

protected

◆ header_

std::vector<String> header_

protected

◆ name_

String name_

protected

◆ names_

std::set<String> names_

protected

◆ progress_

UInt progress_

protected

◆ qp_

QualityParameter qp_

protected

◆ qps_

std::vector<QualityParameter> qps_

protected

◆ row_

std::vector<String> row_

protected

◆ run_id_

String run_id_

protected

◆ run_Name_ID_map_

std::map<String, String > run_Name_ID_map_

protected

◆ runQualityAts_

std::map<String, std::vector< Attachment > > runQualityAts_

protected

◆ runQualityQPs_

std::map<String, std::vector< QualityParameter > > runQualityQPs_

protected

◆ set_Name_ID_map_

std::map<String, String > set_Name_ID_map_

protected

◆ setQualityAts_

std::map<String, std::vector< Attachment > > setQualityAts_

protected

◆ setQualityQPs_

std::map<String, std::vector< QualityParameter > > setQualityQPs_

protected

◆ setQualityQPs_members_

std::map<String, std::set< String > > setQualityQPs_members_

protected

◆ tag_

String tag_

protected

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ QcMLFile()

◆ ~QcMLFile()

Member Function Documentation

◆ addRunAttachment()

◆ addRunQualityParameter()

◆ addSetAttachment()

◆ addSetQualityParameter()

◆ characters()

◆ collectSetParameter()

◆ endElement()

◆ existsRun()

◆ existsRunQualityParameter()

◆ existsSet()

◆ existsSetQualityParameter()

◆ exportAttachment()

◆ exportIDstats()

◆ exportQP()

◆ exportQPs()

◆ getRunIDs()

◆ getRunNames()

◆ load()

◆ map2csv()

◆ merge()

◆ registerRun()

◆ registerSet()

◆ removeAllAttachments()

◆ removeAttachment() [1/2]

◆ removeAttachment() [2/2]

◆ removeQualityParameter()

◆ startElement()

◆ store()

Member Data Documentation

◆ at_

◆ ats_

◆ header_

◆ name_

◆ names_

◆ progress_

◆ qp_

◆ qps_

◆ row_

◆ run_id_

◆ run_Name_ID_map_

◆ runQualityAts_

◆ runQualityQPs_

◆ set_Name_ID_map_

◆ setQualityAts_

◆ setQualityQPs_

◆ setQualityQPs_members_

◆ tag_