ControlledVocabulary::CVTerm Struct Reference

Representation of a CV term. More...

#include <OpenMS/FORMAT/ControlledVocabulary.h>

List of all members.

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.
	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
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
Static Public Member Functions
static String	getXRefTypeName (XRefType type)
Public Attributes
String	name
	Text name.
String	id
	Identifier.
std::set< String >	parents
	The parent IDs.
std::set< String >	children
	The child IDs.
bool	obsolete
	Flag that indicates of the term is obsolete.
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< String >	units
	unit accession ids, defined by relationship has units

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Detailed Description

Representation of a CV term.

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Member Enumeration Documentation

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

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Constructor & Destructor Documentation

CVTerm

(

)

Default constructor.

CVTerm

(

const CVTerm &

rhs

)

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Member Function Documentation

static String getXRefTypeName

(

XRefType

type

)

[static]

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

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

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

std::set<String> children

The child IDs.

String description

Term description.

String id

Identifier.

Referenced by MzMLHandler< MapType >::handleCVParam_(), MzMLHandler< MapType >::validateCV_(), MzMLHandler< MapType >::writeCV_(), MzMLHandler< MapType >::writeSoftware_(), MzMLHandler< MapType >::writeSourceFile_(), and MzMLHandler< MapType >::writeTo().

String name

Text name.

Referenced by MzMLHandler< MapType >::handleCVParam_(), MzMLHandler< MapType >::validateCV_(), MzMLHandler< MapType >::writeCV_(), MzMLHandler< MapType >::writeSoftware_(), MzMLHandler< MapType >::writeSourceFile_(), and MzMLHandler< MapType >::writeTo().

bool obsolete

Flag that indicates of the term is obsolete.

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

std::set<String> parents

The parent IDs.

StringList synonyms

List of synonyms.

std::set<String> units

unit accession ids, defined by relationship has units

StringList unparsed

Unparsed lines from the definition file.

StringList xref_binary

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

XRefType xref_type

xref value-type for the CV-term

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