QcMLFile Class Reference

File adapter for QcML files used to load and store QcML files. More...

#include <OpenMS/FORMAT/QcMLFile.h>

Inheritance diagram for QcMLFile:

Collaboration diagram for QcMLFile:

Classes
class	Attachment
	Representation of an attachment. More...
class	QualityParameter
	Representation of a quality parameter. More...

Public Member Functions
	QcMLFile ()
	Default constructor.
	~QcMLFile () override
	Destructor.
std::string	map2csv (const std::map< std::string, std::map< std::string, std::string > > &cvs_table, const std::string &separator) const
std::string	exportIDstats (const std::string &filename) const
void	registerRun (const std::string &id, const std::string &name)
	Registers a run in the qcml file with the respective mappings.
void	registerSet (const std::string &id, const std::string &name, const std::set< std::string > &names)
	Registers a set in the qcml file with the respective mappings.
void	addRunQualityParameter (const std::string &r, const QualityParameter &qp)
	Just adds a qualityparameter to run by the name r.
void	addRunAttachment (const std::string &r, const Attachment &at)
	Just adds a attachment to run by the name r.
void	addSetQualityParameter (const std::string &r, const QualityParameter &qp)
	Just adds a qualityparameter to set by the name r.
void	addSetAttachment (const std::string &r, const Attachment &at)
	Just adds a attachment to set by the name r.
void	removeAttachment (const std::string &r, std::vector< std::string > &ids, const std::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 (const std::string &r, const std::string &at)
	Removes attachment with cv accession at from run/set r.
void	removeAllAttachments (const std::string &at)
	Removes attachment with cv accession at from all runs/sets.
void	removeQualityParameter (const std::string &r, std::vector< std::string > &ids)
	Just removes qualityparameter going by one of the ID attributes given in ids.
void	merge (const QcMLFile &addendum, const std::string &setname="")
	merges the given QCFile into this one
void	collectSetParameter (const std::string &setname, const std::string &qp, std::vector< std::string > &ret)
	collects the values of given QPs (as CVid) of the given set
std::string	exportAttachment (const std::string &filename, const std::string &qpname) const
	Returns a std::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.
std::string	exportQP (const std::string &filename, const std::string &qpname) const
	Returns a std::string value in quotation of a qualityparameter by the name qpname in run/set by the name filename.
std::string	exportQPs (const std::string &filename, const StringList &qpnames) const
	Returns a std::string of a tab separated qualityparameter by the name qpname in run/set by the name filename.
void	getRunIDs (std::vector< std::string > &ids) const
	Gives the ids of the registered runs in the vector ids.
void	getRunNames (std::vector< std::string > &ids) const
	Gives the names of the registered runs in the vector ids.
bool	existsRun (const std::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.
bool	existsSet (const std::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.
void	existsRunQualityParameter (const std::string &filename, const std::string &qpname, std::vector< std::string > &ids) const
	Returns the ids of the parameter name given if found in given run empty else.
void	existsSetQualityParameter (const std::string &filename, const std::string &qpname, std::vector< std::string > &ids) const
	Returns the ids of the parameter name given if found in given set, empty else.
void	collectQCData (std::vector< ProteinIdentification > &prot_ids, PeptideIdentificationList &pep_ids, const FeatureMap &feature_map, const ConsensusMap &consensus_map, const std::string &inputfile_raw, const bool remove_duplicate_features, const MSExperiment &exp)
	Calculation and collection of QC data.
void	store (const std::string &filename) const
	Store the QCFile.
void	load (const std::string &filename)
	Load a QCFile.
Public Member Functions inherited from XMLHandler
	XMLHandler (const std::string &filename, const std::string &version)
	Default constructor.
	~XMLHandler () override
	Destructor.
void	reset ()
	Release internal memory used for parsing (call.
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 std::string &msg, UInt line=0, UInt column=0) const
	Fatal error handler. Throws a ParseError exception.
void	error (ActionMode mode, const std::string &msg, UInt line=0, UInt column=0) const
	Error handler for recoverable errors.
void	warning (ActionMode mode, const std::string &msg, UInt line=0, UInt column=0) const
	Warning handler.
void	characters (const XMLCh *const chars, const XMLSize_t length) override
	Parsing method for character data.
void	startElement (const XMLCh *const uri, const XMLCh *const localname, const XMLCh *const qname, const xercesc::Attributes &attrs) override
	Parsing method for opening tags.
void	endElement (const XMLCh *const uri, const XMLCh *const localname, const XMLCh *const qname) override
	Parsing method for closing tags.
virtual void	writeTo (std::ostream &)
	Writes the contents to a stream.
virtual LOADDETAIL	getLoadDetail () const
	handler which support partial loading, implement this method
virtual void	setLoadDetail (const LOADDETAIL d)
	handler which support partial loading, implement this method
DataValue	cvParamToValue (const ControlledVocabulary &cv, const std::string &parent_tag, const std::string &accession, const std::string &name, const std::string &value, const std::string &unit_accession) const
	Convert the value of a <cvParam value=.> (as commonly found in PSI schemata) to the DataValue with the correct type (e.g. int) according to the type stored in the CV (usually PSI-MS CV), as well as set its unit.
DataValue	cvParamToValue (const ControlledVocabulary &cv, const CVTerm &raw_term) const
	Convert the value of a <cvParam value=.> (as commonly found in PSI schemata) to the DataValue with the correct type (e.g. int) according to the type stored in the CV (usually PSI-MS CV), as well as set its unit.
void	checkUniqueIdentifiers_ (const std::vector< ProteinIdentification > &prot_ids) const
Public Member Functions inherited from XMLFile
	XMLFile ()
	Construct an XMLFile without schema info; schema_location_ remains unset, so isValid cannot be used until derived-class logic initializes schema_location_ before calling isValid.
	XMLFile (const std::string &schema_location, const std::string &version)
	Construct with a schema location for later isValid calls.
virtual	~XMLFile ()
	Virtual destructor — defaulted; allows safe deletion through a base-class pointer.
bool	isValid (const std::string &filename, std::ostream &os)
	Check if filename validates against the bound XML schema.
const std::string &	getVersion () const
	Return the schema version string passed to the parameterised constructor; empty for default-constructed instances.
Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor.
virtual	~ProgressLogger ()
	Destructor.
	ProgressLogger (const ProgressLogger &other)
	Copy constructor.
ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator.
void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE!
LogType	getLogType () const
	Returns the type of progress log being used.
void	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging.
void	startProgress (SignedSize begin, SignedSize end, const std::string &label) const
	Initializes the progress display.
void	setProgress (SignedSize value) const
	Sets the current progress.
void	endProgress (UInt64 bytes_processed=0) const
void	nextProgress () const
	increment progress by 1 (according to range begin-end)

Protected Member Functions
void	endElement (const XMLCh *const, const XMLCh *const, const XMLCh *const qname) override
void	startElement (const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) override
void	characters (const XMLCh *const chars, const XMLSize_t length) override
Protected Member Functions inherited from XMLHandler
void	writeUserParam_ (const std::string &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const
	Writes the content of MetaInfoInterface to the file.
Int	asInt_ (const std::string &in) const
	Conversion of a std::string to an integer value.
Int	asInt_ (const XMLCh *in) const
	Conversion of a Xerces string to an integer value.
UInt	asUInt_ (const std::string &in) const
	Conversion of a std::string to an unsigned integer value.
double	asDouble_ (const std::string &in) const
	Conversion of a std::string to a double value.
float	asFloat_ (const std::string &in) const
	Conversion of a std::string to a float value.
bool	asBool_ (const std::string &in) const
	Conversion of a string to a boolean value.
DateTime	asDateTime_ (std::string date_string) const
	Conversion of a xs:datetime string to a DateTime value.
bool	equal_ (const XMLCh *a, const XMLCh *b) const
	Returns if two Xerces strings are equal.
SignedSize	cvStringToEnum_ (const Size section, const std::string &term, const char *message, const SignedSize result_on_error=0)
std::string	attributeAsString_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to a String.
Int	attributeAsInt_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to a Int.
double	attributeAsDouble_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to a double.
DoubleList	attributeAsDoubleList_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to a DoubleList.
IntList	attributeAsIntList_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to an IntList.
StringList	attributeAsStringList_ (const xercesc::Attributes &a, const char *name) const
	Converts an attribute to an StringList.
bool	optionalAttributeAsString_ (std::string &value, const xercesc::Attributes &a, const char *name) const
	Assigns the attribute content to the String value if the attribute is present.
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.
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.
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.
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.
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.
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.
std::string	attributeAsString_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a String.
Int	attributeAsInt_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a Int.
double	attributeAsDouble_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a double.
DoubleList	attributeAsDoubleList_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a DoubleList.
IntList	attributeAsIntList_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a IntList.
StringList	attributeAsStringList_ (const xercesc::Attributes &a, const XMLCh *name) const
	Converts an attribute to a StringList.
bool	optionalAttributeAsString_ (std::string &value, const xercesc::Attributes &a, const XMLCh *name) const
	Assigns the attribute content to the String value if the attribute is present.
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.
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.
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.
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.
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.
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.
Protected Member Functions inherited from XMLFile
void	parse_ (const std::string &filename, XMLHandler *handler)
	Parse the XML file at filename through handler.
void	parseBuffer_ (const std::string &buffer, XMLHandler *handler)
	Parse an in-memory XML buffer through handler.
void	save_ (const std::string &filename, XMLHandler *handler) const
	Stores the contents of the XML handler given by handler in the file given by filename.
void	enforceEncoding_ (const std::string &encoding)
	Set or clear the XML-encoding override applied to subsequent parse_ / parseBuffer_ calls.

Protected Attributes
std::map< std::string, std::vector< QualityParameter > >	runQualityQPs_
std::map< std::string, std::vector< Attachment > >	runQualityAts_
std::map< std::string, std::vector< QualityParameter > >	setQualityQPs_
std::map< std::string, std::vector< Attachment > >	setQualityAts_
std::map< std::string, std::set< std::string > >	setQualityQPs_members_
std::map< std::string, std::string >	run_Name_ID_map_
std::map< std::string, std::string >	set_Name_ID_map_
std::string	tag_
UInt	progress_
QualityParameter	qp_
Attachment	at_
std::vector< std::string >	row_
std::vector< std::string >	header_
std::string	name_
std::string	run_id_
std::set< std::string >	names_
std::vector< QualityParameter >	qps_
std::vector< Attachment >	ats_
Protected Attributes inherited from XMLHandler
std::string	file_
	File name.
std::string	version_
	Schema version.
StringManager	sm_
	Helper class for string conversion.
std::vector< std::string >	open_tags_
	Stack of open XML tags.
LOADDETAIL	load_detail_
	parse only until total number of scans and chroms have been determined from attributes
std::vector< std::vector< std::string > >	cv_terms_
	Array of CV term lists (one sublist denotes one term and it's children)
Protected Attributes inherited from XMLFile
std::string	schema_location_
	Path of the XML schema for validation; empty when the default constructor was used (isValid then throws NotImplemented).
std::string	schema_version_
	Schema version string returned by getVersion.
std::string	enforced_encoding_
	Optional XML encoding override applied to the InputSource in parse_ and parseBuffer_; empty disables the override. Used as a workaround for XTandem output XML which carries an encoding the parser otherwise stumbles on.
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...
enum	LOADDETAIL { LD_ALLDATA , LD_RAWCOUNTS , LD_COUNTS_WITHOPTIONS }
Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...
Static Public Member Functions inherited from XMLHandler
static std::string	writeXMLEscape (const std::string &to_escape)
	Escapes a string and returns the escaped string.
static DataValue	fromXSDString (const std::string &type, const std::string &value)
	Convert an XSD type (e.g. 'xsd:double') to a DataValue.
Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

File adapter for QcML files used to load and store QcML files.

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

A documented schema for this format can be found at https://github.com/OpenMS/OpenMS/tree/develop/share/OpenMS/SCHEMAS

Constructor & Destructor Documentation

QcMLFile()

QcMLFile

(

)

Default constructor.

~QcMLFile()

~QcMLFile ( )

override

Destructor.

Member Function Documentation

addRunAttachment()

void addRunAttachment	(	const std::string &	r,
		const Attachment &	at
	)

Just adds a attachment to run by the name r.

addRunQualityParameter()

void addRunQualityParameter	(	const std::string &	r,
		const QualityParameter &	qp
	)

Just adds a qualityparameter to run by the name r.

addSetAttachment()

void addSetAttachment	(	const std::string &	r,
		const Attachment &	at
	)

Just adds a attachment to set by the name r.

addSetQualityParameter()

void addSetQualityParameter	(	const std::string &	r,
		const QualityParameter &	qp
	)

Just adds a qualityparameter to set by the name r.

characters()

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

overrideprotected

collectQCData()

void collectQCData	(	std::vector< ProteinIdentification > &	prot_ids,
		PeptideIdentificationList &	pep_ids,
		const FeatureMap &	feature_map,
		const ConsensusMap &	consensus_map,
		const std::string &	inputfile_raw,
		const bool	remove_duplicate_features,
		const MSExperiment &	exp
	)

Calculation and collection of QC data.

Collects QC data in qualityParameters and qualityAttachments

Parameters

[in]	prot_ids	protein identifications from ID file
[in]	pep_ids	peptide identifications
[in]	feature_map	FeatureMap from feature file (featureXML)
[in]	consensus_map	ConsensusMap from consensus file (consensusXML)
[in]	inputfile_raw	mzML input file name
[in]	remove_duplicate_features	removes duplicates in a set of merged features
[in]	exp	MSExperiment to extract QC data from, prior sortSpectra() and updateRanges() required

collectSetParameter()

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

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

endElement()

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

overrideprotected

existsRun()

bool existsRun	(	const std::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 std::string &	filename,
		const std::string &	qpname,
		std::vector< std::string > &	ids
	)		const

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

existsSet()

bool existsSet	(	const std::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 std::string &	filename,
		const std::string &	qpname,
		std::vector< std::string > &	ids
	)		const

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

exportAttachment()

std::string exportAttachment	(	const std::string &	filename,
		const std::string &	qpname
	)		const

Returns a std::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()

std::string exportIDstats

(

const std::string &

filename

)

const

exportQP()

std::string exportQP	(	const std::string &	filename,
		const std::string &	qpname
	)		const

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

exportQPs()

std::string exportQPs	(	const std::string &	filename,
		const StringList &	qpnames
	)		const

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

getRunIDs()

void getRunIDs

(

std::vector< std::string > &

ids

)

const

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

getRunNames()

void getRunNames

(

std::vector< std::string > &

ids

)

const

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

load()

void load

(

const std::string &

filename

)

Load a QCFile.

map2csv()

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

merge()

void merge	(	const QcMLFile &	addendum,
		const std::string &	setname = ""
	)

merges the given QCFile into this one

registerRun()

void registerRun	(	const std::string &	id,
		const std::string &	name
	)

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

registerSet()

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

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

removeAllAttachments()

void removeAllAttachments

(

const std::string &

at

)

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

removeAttachment() [1/2]

void removeAttachment	(	const std::string &	r,
		const std::string &	at
	)

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

removeAttachment() [2/2]

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

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

removeQualityParameter()

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

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

startElement()

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

overrideprotected

store()

void store

(

const std::string &

filename

)

const

Store the QCFile.

Store the qcML file

Parameters

[out]

filename

qcML output file name

Member Data Documentation

at_

Attachment at_

protected

ats_

std::vector<Attachment> ats_

protected

header_

std::vector<std::string> header_

protected

name_

std::string name_

protected

names_

std::set<std::string> names_

protected

progress_

UInt progress_

protected

qp_

QualityParameter qp_

protected

qps_

std::vector<QualityParameter> qps_

protected

row_

std::vector<std::string> row_

protected

run_id_

std::string run_id_

protected

run_Name_ID_map_

std::map<std::string, std::string > run_Name_ID_map_

protected

runQualityAts_

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

protected

runQualityQPs_

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

protected

set_Name_ID_map_

std::map<std::string, std::string > set_Name_ID_map_

protected

setQualityAts_

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

protected

setQualityQPs_

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

protected

setQualityQPs_members_

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

protected

tag_

std::string tag_

protected