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. More...

	~QcMLFile () override
	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 (const String &r, const QualityParameter &qp)
	Just adds a qualityparameter to run by the name r. More...

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

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

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

void	removeAttachment (const String &r, std::vector< String > &ids, const 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 (const String &r, const String &at)
	Removes attachment with cv accession at from run/set r. More...

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

void	removeQualityParameter (const 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, const 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	collectQCData (std::vector< ProteinIdentification > &prot_ids, std::vector< PeptideIdentification > &pep_ids, const FeatureMap &feature_map, const ConsensusMap &consensus_map, const String &inputfile_raw, const bool remove_duplicate_features, const MSExperiment &exp)
	Calculation and collection of QC data. 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...

	~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...

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...

DataValue	cvParamToValue (const ControlledVocabulary &cv, const String &parent_tag, const String &accession, const String &name, const String &value, const 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. More...

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. More...

void	checkUniqueIdentifiers_ (const std::vector< ProteinIdentification > &prot_ids) const

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...

virtual	~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	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging. 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 (UInt64 bytes_processed=0) const

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

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 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...

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)

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	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...

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 String	writeXMLEscape (const String &to_escape)
	Escapes a string and returns the escaped string. More...

static DataValue	fromXSDString (const String &type, const String &value)
	Convert an XSD type (e.g. 'xsd:double') to a DataValue. More...

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 String &	r,
		const Attachment &	at
	)

Just adds a attachment to run by the name r.

◆ addRunQualityParameter()

void addRunQualityParameter	(	const String &	r,
		const QualityParameter &	qp
	)

Just adds a qualityparameter to run by the name r.

◆ addSetAttachment()

void addSetAttachment	(	const String &	r,
		const Attachment &	at
	)

Just adds a attachment to set by the name r.

◆ addSetQualityParameter()

void addSetQualityParameter	(	const 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,
		std::vector< PeptideIdentification > &	pep_ids,
		const FeatureMap &	feature_map,
		const ConsensusMap &	consensus_map,
		const 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

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

◆ 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()

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

overrideprotected

◆ 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,
		const 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 ( const String & at )

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

◆ removeAttachment() [1/2]

void removeAttachment	(	const String &	r,
		const String &	at
	)

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

◆ removeAttachment() [2/2]

void removeAttachment	(	const String &	r,
		std::vector< String > &	ids,
		const 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 String &	r,
		std::vector< 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 String & filename ) const

Store the QCFile.

Store the qcML file

Parameters

filename qcML output file name

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()

◆ collectQCData()

◆ 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_