#include <OpenMS/FORMAT/ControlledVocabulary.h>

Collaboration diagram for ControlledVocabulary:

Classes
struct	CVTerm
	Representation of a CV term. More...

Public Member Functions
	ControlledVocabulary ()
	Constructor. More...

virtual	~ControlledVocabulary ()
	Destructor. More...

const String &	name () const
	Returns the CV name (set in the load method) More...

const String &	label () const
	Returns the CV label (set in the load method) More...

const String &	version () const
	Returns the CV version (set in the load method) More...

const String &	url () const
	Returns the CV url (set in the load method) More...

void	loadFromOBO (const String &name, const String &filename)
	Loads the CV from an OBO file. More...

bool	exists (const String &id) const
	Returns true if the term is in the CV. Returns false otherwise. More...

bool	hasTermWithName (const String &name) const
	Returns true if a term with the given name is in the CV. Returns false otherwise. More...

const CVTerm &	getTerm (const String &id) const
	Returns a term specified by ID. More...

const CVTerm &	getTermByName (const String &name, const String &desc="") const
	Returns a term specified by name. More...

const std::map< String, CVTerm > &	getTerms () const
	returns all the terms stored in the CV More...

void	getAllChildTerms (std::set< String > &terms, const String &parent_id) const
	Writes all child terms recursively into terms. More...

template<class LAMBDA >
bool	iterateAllChildren (const String &parent_id, LAMBDA lbd) const
	Iterates over all children (incl. subchildren etc) of parent recursively, i.e. the whole subtree. More...

const ControlledVocabulary::CVTerm *	checkAndGetTermByName (const OpenMS::String &name) const
	Searches the existing terms for the given `name`. More...

bool	isChildOf (const String &child_id, const String &parent_id) const
	Returns if `child` is a child of `parent`. More...

Static Public Member Functions
static const ControlledVocabulary &	getPSIMSCV ()
	Returns a CV for parsing/storing PSI-MS related data, e.g. mzML, or handle accessions/ids in datastructures. More...

Protected Member Functions
bool	checkName_ (const String &id, const String &name, bool ignore_case=true) const
	checks if a name corresponds to an id More...

Protected Attributes
std::map< String, CVTerm >	terms_
	Map from ID to CVTerm. More...

std::map< String, String >	namesToIds_
	Map from name to id. More...

String	name_
	Name set in the load method. More...

String	label_
	CV label. More...

String	version_
	CV version. More...

String	url_
	CV URL. More...

Friends
std::ostream &	operator<< (std::ostream &os, const ControlledVocabulary &cv)
	Print the contents to a stream. More...

Detailed Description

@brief Representation of a controlled vocabulary.

This representation only contains the information used for parsing and validation.
All other lines are stored in the @em unparsed member of the CVTerm struct.

Constructor & Destructor Documentation

◆ ControlledVocabulary()

ControlledVocabulary ( )

Constructor.

◆ ~ControlledVocabulary()

virtual ~ControlledVocabulary ( )

virtual

Destructor.

Member Function Documentation

◆ checkAndGetTermByName()

const ControlledVocabulary::CVTerm* checkAndGetTermByName ( const OpenMS::String & name ) const

Searches the existing terms for the given name.

Returns: const Pointer to found term. When term is not found, returns nullptr

◆ checkName_()

bool checkName_	(	const String &	id,
		const String &	name,
		bool	ignore_case = `true`
	)		const

protected

checks if a name corresponds to an id

If the term is not known, 'true' is returned!

◆ exists()

bool exists ( const String & id ) const

Returns true if the term is in the CV. Returns false otherwise.

◆ getAllChildTerms()

void getAllChildTerms	(	std::set< String > &	terms,
		const String &	parent_id
	)		const

Writes all child terms recursively into terms.

If parent has child this method writes them recursively into the term object

Exceptions

Exception::InvalidValue is thrown if the term is not present

◆ getPSIMSCV()

static const ControlledVocabulary& getPSIMSCV ( )

static

Returns a CV for parsing/storing PSI-MS related data, e.g. mzML, or handle accessions/ids in datastructures.

The CV will be initialized on first access. Repeated access is therefor cheap.

It consists of the following CVs:

PSI-MS (psi-ms.obo)
PATO (quality.obo)
UO (unit.obo)
BTO (CV/brenda.obo)
GO (goslim_goa.obo)

◆ getTerm()

const CVTerm& getTerm ( const String & id ) const

Returns a term specified by ID.

Exceptions

Exception::InvalidValue is thrown if the term is not present

◆ getTermByName()

const CVTerm& getTermByName	(	const String &	name,
		const String &	desc = `""`
	)		const

Returns a term specified by name.

Exceptions

Exception::InvalidValue is thrown if the term is not present

◆ getTerms()

const std::map<String, CVTerm>& getTerms ( ) const

returns all the terms stored in the CV

◆ hasTermWithName()

bool hasTermWithName ( const String & name ) const

Returns true if a term with the given name is in the CV. Returns false otherwise.

◆ isChildOf()

bool isChildOf	(	const String &	child_id,
		const String &	parent_id
	)		const

Returns if child is a child of parent.

Exceptions

Exception::InvalidValue is thrown if one of the terms is not present

◆ iterateAllChildren()

bool iterateAllChildren	(	const String &	parent_id,
		LAMBDA	lbd
	)		const

inline

Iterates over all children (incl. subchildren etc) of parent recursively, i.e. the whole subtree.

Parameters

parent_id	Id of parent (to be passed to getTerm(), to obtain its children).
lbd	Function that gets the child-Ids passed. Must return bool. Used for comparisons and / or to set captured variables. If the lambda returns true, the iteration is exited prematurely. E.g. if you have found your search, you don't need to continue searching. Otherwise, if you want to go through the whole tree (e.g. to fill a vector) you can just return false always to not quit early.

◆ label()

const String& label ( ) const

Returns the CV label (set in the load method)

◆ loadFromOBO()

void loadFromOBO	(	const String &	name,
		const String &	filename
	)

Loads the CV from an OBO file.

Exceptions

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

◆ name()

const String& name ( ) const

Returns the CV name (set in the load method)

◆ url()

const String& url ( ) const

Returns the CV url (set in the load method)

◆ version()

const String& version ( ) const

Returns the CV version (set in the load method)

Friends And Related Function Documentation

◆ operator<<

std::ostream& operator<<	(	std::ostream &	os,
		const ControlledVocabulary &	cv
	)

friend

Print the contents to a stream.

Member Data Documentation

◆ label_

String label_

protected

CV label.

◆ name_

String name_

protected

Name set in the load method.

◆ namesToIds_

std::map<String, String> namesToIds_

protected

Map from name to id.

◆ terms_

std::map<String, CVTerm> terms_

protected

Map from ID to CVTerm.

◆ url_

String url_

protected

CV URL.

◆ version_

String version_

protected

CV version.

Classes

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ ControlledVocabulary()

◆ ~ControlledVocabulary()

Member Function Documentation

◆ checkAndGetTermByName()

◆ checkName_()

◆ exists()

◆ getAllChildTerms()

◆ getPSIMSCV()

◆ getTerm()

◆ getTermByName()

◆ getTerms()

◆ hasTermWithName()

◆ isChildOf()

◆ iterateAllChildren()

◆ label()

◆ loadFromOBO()

◆ name()

◆ url()

◆ version()

Friends And Related Function Documentation

◆ operator<<

Member Data Documentation

◆ label_

◆ name_

◆ namesToIds_

◆ terms_

◆ url_

◆ version_