ControlledVocabulary Class Reference

#include <OpenMS/FORMAT/ControlledVocabulary.h>

Collaboration diagram for ControlledVocabulary:

Classes
struct	CVTerm
	Representation of a CV term. More...
struct	FNV1aHasher
	ensure same hash on all platforms (for reproducibility)- More...

Public Member Functions
	ControlledVocabulary ()
	Constructor.
virtual	~ControlledVocabulary ()
	Destructor.
const std::string &	name () const
	Returns the CV name (set in the load method)
const std::string &	label () const
	Returns the CV label (set in the load method)
const std::string &	version () const
	Returns the CV version (set in the load method)
const std::string &	url () const
	Returns the CV url (set in the load method)
void	loadFromOBO (const std::string &name, const std::string &filename)
	Loads the CV from an OBO file.
bool	exists (const std::string &id) const
	Returns true if the term is in the CV. Returns false otherwise.
bool	hasTermWithName (const std::string &name) const
	Returns true if a term with the given name is in the CV. Returns false otherwise.
const CVTerm &	getTerm (const std::string &id) const
	Returns a term specified by ID.
const CVTerm &	getTermByName (const std::string &name, const std::string &desc="") const
	Returns a term specified by name.
const std::map< std::string, CVTerm > &	getTerms () const
	returns all the terms stored in the CV
void	getAllChildTerms (std::set< std::string > &terms, const std::string &parent_id) const
	Writes all child terms recursively into terms.
void	addAllChildTerms (std::set< std::string > &terms, const std::string &parent_id) const
	Writes the parent term and all descendant term IDs into terms.
template<class LAMBDA >
bool	iterateAllChildren (const std::string &parent_id, LAMBDA lbd) const
	Iterates over all children (incl. subchildren etc) of parent recursively, i.e. the whole subtree.
const ControlledVocabulary::CVTerm *	checkAndGetTermByName (const std::string &name) const
	Searches the existing terms for the given name.
bool	isChildOf (const std::string &child_id, const std::string &parent_id) const
	Returns if child is a child of parent.

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.

Protected Member Functions
bool	checkName_ (const std::string &id, const std::string &name, bool ignore_case=true) const
	checks if a name corresponds to an id

Protected Attributes
std::map< std::string, CVTerm >	terms_
	Map from ID to CVTerm.
std::map< std::string, std::string >	namesToIds_
	Map from name to id.
std::string	name_
	Name set in the load method.
std::string	label_
	CV label.
std::string	version_
	CV version.
std::string	url_
	CV URL.

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

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

addAllChildTerms()

void addAllChildTerms	(	std::set< std::string > &	terms,
		const std::string &	parent_id
	)		const

Writes the parent term and all descendant term IDs into terms.

Parameters

[in,out]	terms	Output set extended with parent_id and all descendants
[in]	parent_id	The parent term ID

Exceptions

Exception::InvalidValue

is thrown if the term is not present

checkAndGetTermByName()

const ControlledVocabulary::CVTerm * checkAndGetTermByName

(

const std::string &

name

)

const

Searches the existing terms for the given name.

Parameters

[in]

name

The term name to search for

Returns

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

checkName_()

bool checkName_ ( const std::string &  id, const std::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 std::string &

id

)

const

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

getAllChildTerms()

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

Writes all child terms recursively into terms.

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

Parameters

[out]	terms	Output set of child term IDs
[in]	parent_id	The parent term ID

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 std::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 std::string &	name,
		const std::string &	desc = ""
	)		const

Returns a term specified by name.

Exceptions

Exception::InvalidValue

is thrown if the term is not present

getTerms()

const std::map< std::string, CVTerm > & getTerms

(

)

const

returns all the terms stored in the CV

hasTermWithName()

bool hasTermWithName

(

const std::string &

name

)

const

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

isChildOf()

bool isChildOf	(	const std::string &	child_id,
		const std::string &	parent_id
	)		const

Returns if child is a child of parent.

Parameters

[in]	child_id	The child term ID
[in]	parent_id	The parent term ID

Exceptions

Exception::InvalidValue

is thrown if one of the terms is not present

iterateAllChildren()

template<class LAMBDA >

bool iterateAllChildren ( const std::string &  parent_id, LAMBDA  lbd  ) const

inline

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

Parameters

[in]	parent_id	Id of parent (to be passed to getTerm(), to obtain its children).
[in]	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 std::string & label

(

)

const

Returns the CV label (set in the load method)

loadFromOBO()

void loadFromOBO	(	const std::string &	name,
		const std::string &	filename
	)

Loads the CV from an OBO file.

Parameters

[in]	name	The CV name
[in]	filename	The OBO file path

Exceptions

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

name()

const std::string & name

(

)

const

Returns the CV name (set in the load method)

url()

const std::string & url

(

)

const

Returns the CV url (set in the load method)

version()

const std::string & version

(

)

const

Returns the CV version (set in the load method)

Friends And Related Symbol Documentation

operator<<

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

friend

Print the contents to a stream.

Member Data Documentation

label_

std::string label_

protected

CV label.

name_

std::string name_

protected

Name set in the load method.

namesToIds_

std::map<std::string, std::string> namesToIds_

protected

Map from name to id.

terms_

std::map<std::string, CVTerm> terms_

protected

Map from ID to CVTerm.

url_

std::string url_

protected

CV URL.

version_

std::string version_

protected

CV version.