Package org.biojava.nbio.ontology
Class IntegerOntology
- java.lang.Object
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- org.biojava.nbio.ontology.IntegerOntology
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- All Implemented Interfaces:
Ontology
public class IntegerOntology extends Object implements Ontology
- Author:
- Matthew Pocock
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Nested Class Summary
Nested Classes Modifier and Type Class Description class
IntegerOntology.IntTerm
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Nested classes/interfaces inherited from interface org.biojava.nbio.ontology.Ontology
Ontology.Impl
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
containsTerm(String name)
Determines if this ontology currently contains a term namedname
boolean
containsTriple(Term subject, Term object, Term predicate)
See if a triple exists in this ontologyTerm
createTerm(String name)
Create a new term in this ontology.Term
createTerm(String name, String description)
Create a new term in this ontology.Term
createTerm(String name, String description, Object[] synonyms)
Create a new term in this ontology.Triple
createTriple(Term subject, Term object, Term predicate, String name, String description)
Creates a new Triple.Variable
createVariable(String name, String description)
Create a new term in this ontology that is used as a variable.void
deleteTerm(Term t)
Remove a term from an ontology, together with all triples which refer to it.String
getDescription()
Return a human-readable description of this ontology, or the empty string if none is availableString
getName()
Return the name of this ontologyOntologyOps
getOps()
Return the associated OntologyOps.Term
getTerm(String s)
Fetch the term with the specified name.Set
getTerms()
Return all the terms in this ontologySet
getTriples(Term subject, Term object, Term predicate)
Return all triples from this ontology which match the supplied pattern.Term
importTerm(Term t, String name)
Create a view of a term from another ontology.IntegerOntology.IntTerm
resolveInt(int val)
void
setDescription(String description)
set the description of this ontologyvoid
setName(String name)
Set the name for this ontology
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Method Detail
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getName
public String getName()
Description copied from interface:Ontology
Return the name of this ontology
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getDescription
public String getDescription()
Description copied from interface:Ontology
Return a human-readable description of this ontology, or the empty string if none is available- Specified by:
getDescription
in interfaceOntology
- Returns:
- the description of the term
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setDescription
public void setDescription(String description)
Description copied from interface:Ontology
set the description of this ontology- Specified by:
setDescription
in interfaceOntology
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getTerms
public Set getTerms()
Description copied from interface:Ontology
Return all the terms in this ontology
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getTerm
public Term getTerm(String s) throws NoSuchElementException
Description copied from interface:Ontology
Fetch the term with the specified name.- Specified by:
getTerm
in interfaceOntology
- Parameters:
s
- the name of the term- Returns:
- The term named
name
- Throws:
NoSuchElementException
- if no term exists with that name
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getTriples
public Set getTriples(Term subject, Term object, Term predicate)
Description copied from interface:Ontology
Return all triples from this ontology which match the supplied pattern. If any of the parameters of this method arenull
, they are treated as wildcards.- Specified by:
getTriples
in interfaceOntology
- Parameters:
subject
- The subject to search for, ornull
object
- The object to search for, ornull
predicate
- The relationship to search for, ornull
.- Returns:
- a Set of triples
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getOps
public OntologyOps getOps()
Description copied from interface:Ontology
Return the associated OntologyOps. This method should be implemented by ontology implementors to allow OntoTools to get optimized access to some usefull ontology operations. It is not intended that users will ever invoke this. A sensible dumb implementation of this would return a per-ontology instance of DefaultOps.
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createTerm
public Term createTerm(String name) throws AlreadyExistsException, IllegalArgumentException
Description copied from interface:Ontology
Create a new term in this ontology.- Specified by:
createTerm
in interfaceOntology
- Parameters:
name
- The name of the term (must be unique))- Returns:
- The newly created term.
- Throws:
AlreadyExistsException
- if a term of this name already existsIllegalArgumentException
- if eithername
ordescription
isnull
, or violates some other constraint of this implementation.
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createTerm
public Term createTerm(String name, String description) throws AlreadyExistsException, IllegalArgumentException
Description copied from interface:Ontology
Create a new term in this ontology.- Specified by:
createTerm
in interfaceOntology
- Parameters:
name
- The name of the term (must be unique)description
- A human-readable description (may be empty)- Returns:
- The newly created term.
- Throws:
AlreadyExistsException
- if a term of this name already existsIllegalArgumentException
- if eithername
ordescription
isnull
, or violates some other constraint of this implementation.
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createTerm
public Term createTerm(String name, String description, Object[] synonyms) throws AlreadyExistsException, IllegalArgumentException
Description copied from interface:Ontology
Create a new term in this ontology.- Specified by:
createTerm
in interfaceOntology
- Parameters:
name
- The name of the term (must be unique)description
- A human-readable description (may be empty)synonyms
- Some synonyms for this term.- Returns:
- The newly created term.
- Throws:
AlreadyExistsException
- if a term of this name already existsIllegalArgumentException
- if eithername
ordescription
isnull
, or violates some other constraint of this implementation.
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createVariable
public Variable createVariable(String name, String description) throws AlreadyExistsException, IllegalArgumentException
Description copied from interface:Ontology
Create a new term in this ontology that is used as a variable.- Specified by:
createVariable
in interfaceOntology
- Parameters:
name
- The name of the term (must be unique)description
- A human-readable description (may be empty)- Returns:
- The newly created term.
- Throws:
AlreadyExistsException
- if a term of this name already existsIllegalArgumentException
- if eithername
ordescription
isnull
, or violates some other constraint of this implementation.
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importTerm
public Term importTerm(Term t, String name)
Description copied from interface:Ontology
Create a view of a term from another ontology. If the requested term has already been imported under that name, this method returns the existing RemoteTerm object. If the term that is being imported is itself a RemoteTerm instance then first unwrap the term back to the orriginal term it represents and then produce a RemoteTerm from that. If the term being imported orriginated from this ontology, then return that term unaltered.- Specified by:
importTerm
in interfaceOntology
- Parameters:
t
- the Term to importname
- the local name to import it under, optionally null- Returns:
- a Term
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createTriple
public Triple createTriple(Term subject, Term object, Term predicate, String name, String description) throws AlreadyExistsException
Description copied from interface:Ontology
Creates a new Triple.- Specified by:
createTriple
in interfaceOntology
- Parameters:
subject
- the subject Termobject
- the object Termpredicate
- the predicate Termname
- the name of the triple, or nulldescription
- the description of the triple, or null- Returns:
- a new Triple over these three terms
- Throws:
AlreadyExistsException
- if a triple already exists with the same subject, object and predicate, regardless of the name and description
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containsTriple
public boolean containsTriple(Term subject, Term object, Term predicate)
Description copied from interface:Ontology
See if a triple exists in this ontology- Specified by:
containsTriple
in interfaceOntology
- Returns:
- true if contained
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deleteTerm
public void deleteTerm(Term t)
Description copied from interface:Ontology
Remove a term from an ontology, together with all triples which refer to it.- Specified by:
deleteTerm
in interfaceOntology
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containsTerm
public boolean containsTerm(String name)
Description copied from interface:Ontology
Determines if this ontology currently contains a term namedname
- Specified by:
containsTerm
in interfaceOntology
- Returns:
- true is contained
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resolveInt
public IntegerOntology.IntTerm resolveInt(int val)
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