OpenMS  2.7.0
Public Types | Public Member Functions | Static Public Member Functions | Public Attributes | List of all members
ControlledVocabulary::CVTerm Struct Reference

Representation of a CV term. More...

#include <OpenMS/FORMAT/ControlledVocabulary.h>

Collaboration diagram for ControlledVocabulary::CVTerm:
[legend]

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)
 
CVTermoperator= (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< Stringparents
 The parent IDs. More...
 
std::set< Stringchildren
 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 Flag that indicates of the term is obsolete.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< Stringunits
 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 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]

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

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