ControlledVocabulary Class Reference

Representation of a controlled vocabulary. More...

#include <OpenMS/FORMAT/ControlledVocabulary.h>

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...
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 Map< String, CVTerm > &	getTerms () const
	returns all the terms stored in the CV More...
void	getAllChildTerms (std::set< String > &terms, const String &parent) const
	Writes all child terms recursively into terms. More...
bool	isChildOf (const String &child, const String &parent) const
	Returns if child is a child of parent. More...

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

Protected Attributes
Map< String, CVTerm >	terms_
	Map from ID to CVTerm. More...
Map< String, String >	namesToIds_
	Map from name to id. More...
String	name_
	Name set in the load method. More...

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

Detailed Description

Representation of a controlled vocabulary.

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

Constructor & Destructor Documentation

ControlledVocabulary

(

)

Constructor.

virtual ~ControlledVocabulary ( )

virtual

Destructor.

Member Function Documentation

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

protected

checks if a name corresponds to an id

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

bool exists

(

const String &

id

)

const

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

Referenced by MzMLHandler< MapType >::handleCVParam_().

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

Referenced by MzMLHandler< MapType >::getChildWithName_().

const CVTerm& getTerm

(

const String &

id

)

const

Returns a term specified by ID.

Exceptions

Exception::InvalidValue

is thrown if the term is not present

Referenced by MzMLHandler< MapType >::getChildWithName_(), MzMLHandler< MapType >::handleCVParam_(), and MzMLHandler< MapType >::writeCV_().

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

Referenced by MzMLHandler< MapType >::writeUserParam_().

const Map<String, CVTerm>& getTerms

(

)

const

returns all the terms stored in the CV

bool hasTermWithName

(

const String &

name

)

const

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

Referenced by MzMLHandler< MapType >::writeUserParam_().

bool isChildOf	(	const String &	child,
		const String &	parent
	)		const

Returns if child is a child of parent.

Exceptions

Exception::InvalidValue

is thrown if one of the terms is not present

Referenced by MzMLHandler< MapType >::handleCVParam_().

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

Referenced by MzMLHandler< MSExperiment<> >::MzMLHandler().

const String& name

(

)

const

Returns the CV name (set in the load method)

Friends And Related Function Documentation

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

friend

Print the contents to a stream.

Member Data Documentation

String name_

protected

Name set in the load method.

Map<String, String> namesToIds_

protected

Map from name to id.

Map<String, CVTerm> terms_

protected

Map from ID to CVTerm.