ControlledVocabulary::CVTerm Struct Reference

Representation of a CV term. More...

#include <OpenMS/FORMAT/ControlledVocabulary.h>

Collaboration diagram for ControlledVocabulary::CVTerm:

Public Types
enum class	XRefType {   XSD_STRING = 0 , XSD_INTEGER , XSD_DECIMAL , XSD_NEGATIVE_INTEGER ,   XSD_POSITIVE_INTEGER , XSD_NON_NEGATIVE_INTEGER , XSD_NON_POSITIVE_INTEGER , XSD_BOOLEAN ,   XSD_DATE , XSD_ANYURI , NONE }
	define xsd types allowed in cv term to specify their value-type More...

Public Member Functions
	CVTerm ()
	Default constructor.
	CVTerm (const CVTerm &rhs)
CVTerm &	operator= (const CVTerm &rhs)
std::string	toXMLString (const std::string &ref, const std::string &value=std::string("")) const
	get mzidentml formatted string. i.e. a cvparam xml element, ref should be the name of the ControlledVocabulary (i.e. cv.name()) containing the CVTerm (e.g. PSI-MS for the psi-ms.obo - gets loaded in all cases like that??), value can be empty if not available
std::string	toXMLString (const std::string &ref, const DataValue &value) const
	get mzidentml formatted string. i.e. a cvparam xml element, ref should be the name of the ControlledVocabulary (i.e. cv.name()) containing the CVTerm (e.g. PSI-MS for the psi-ms.obo - gets loaded in all cases like that??), value can be empty if not available

Static Public Member Functions
static std::string	getXRefTypeName (XRefType type)
static bool	isHigherBetterScore (ControlledVocabulary::CVTerm term)

Public Attributes
std::string	name
	if it is a score type, lookup has_order
std::string	id
	Identifier.
std::set< std::string >	parents
	The parent IDs.
std::set< std::string >	children
	The child IDs.
bool	obsolete
	Flag that indicates of the term is obsolete.
std::string	description
	Term description.
StringList	synonyms
	List of synonyms.
StringList	unparsed
	Unparsed lines from the definition file.
XRefType	xref_type
	xref value-type for the CV-term
StringList	xref_binary
	xref binary-data-type for the CV-term (list of all allowed data value types for the current binary data array)
std::set< std::string >	units
	unit accession ids, defined by relationship has units

Detailed Description

Representation of a CV term.

Member Enumeration Documentation

XRefType

enum class XRefType

strong

define xsd types allowed in cv term to specify their value-type

Enumerator
XSD_STRING
XSD_INTEGER
XSD_DECIMAL
XSD_NEGATIVE_INTEGER
XSD_POSITIVE_INTEGER
XSD_NON_NEGATIVE_INTEGER
XSD_NON_POSITIVE_INTEGER
XSD_BOOLEAN
XSD_DATE
XSD_ANYURI
NONE

Constructor & Destructor Documentation

CVTerm() [1/2]

CVTerm

(

)

Default constructor.

CVTerm() [2/2]

CVTerm

(

const CVTerm &

rhs

)

Member Function Documentation

getXRefTypeName()

static std::string getXRefTypeName ( XRefType  type )

static

isHigherBetterScore()

static bool isHigherBetterScore ( ControlledVocabulary::CVTerm  term )

static

operator=()

CVTerm & operator=

(

const CVTerm &

rhs

)

toXMLString() [1/2]

std::string toXMLString	(	const std::string &	ref,
		const DataValue &	value
	)		const

get mzidentml formatted string. i.e. a cvparam xml element, ref should be the name of the ControlledVocabulary (i.e. cv.name()) containing the CVTerm (e.g. PSI-MS for the psi-ms.obo - gets loaded in all cases like that??), value can be empty if not available

toXMLString() [2/2]

std::string toXMLString	(	const std::string &	ref,
		const std::string &	value = std::string("")
	)		const

get mzidentml formatted string. i.e. a cvparam xml element, ref should be the name of the ControlledVocabulary (i.e. cv.name()) containing the CVTerm (e.g. PSI-MS for the psi-ms.obo - gets loaded in all cases like that??), value can be empty if not available

Member Data Documentation

children

std::set<std::string> children

The child IDs.

description

std::string description

Term description.

id

std::string id

Identifier.

name

std::string name

if it is a score type, lookup has_order

Text name

obsolete

bool obsolete

Flag that indicates of the term is obsolete.

parents

std::set<std::string> parents

The parent IDs.

synonyms

StringList synonyms

List of synonyms.

units

std::set<std::string> units

unit accession ids, defined by relationship has units

unparsed

StringList unparsed

Unparsed lines from the definition file.

xref_binary

StringList xref_binary

xref binary-data-type for the CV-term (list of all allowed data value types for the current binary data array)

xref_type

XRefType xref_type

xref value-type for the CV-term