ControlledVocabulary::CVTerm Struct Reference

Representation of a CV term. More...

#include <OpenMS/FORMAT/ControlledVocabulary.h>

Public Types
enum	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. More...
	CVTerm (const CVTerm &rhs)
CVTerm &	operator= (const CVTerm &rhs)
String	toXMLString (const String &ref, const String &value=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 More...
String	toXMLString (const 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 More...

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

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	Flag that indicates of the term is obsolete.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

Detailed Description

Representation of a CV term.

Member Enumeration Documentation

XRefType

enum XRefType

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 String getXRefTypeName ( XRefType  type )

static

isHigherBetterScore()

static bool isHigherBetterScore ( ControlledVocabulary::CVTerm  term )

static

operator=()

CVTerm& operator=

(

const CVTerm &

rhs

)

toXMLString() [1/2]

String toXMLString	(	const String &	ref,
		const String &	value = 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

toXMLString() [2/2]

String toXMLString	(	const 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

Member Data Documentation

children

std::set<String> children

The child IDs.

description

String description

Term description.

id

String id

Identifier.

name

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<String> parents

The parent IDs.

synonyms

StringList synonyms

List of synonyms.

units

std::set<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