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Packages that use Term | |
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org.biojava.bio.program.gff3 | Support for reading and writing GFF3. |
org.biojava.bio.seq | Classes and interfaces for defining biological sequences and informatics objects. |
org.biojava.bio.seq.impl | Standard in-memory implementations of Sequence and
Feature . |
org.biojava.ontology | A general-purpose API for ontologies. |
org.biojavax.bio.seq | Rich implementations of Sequences, Locations and Features. |
org.biojavax.ontology | Extensions to the biojava ontology model that represent BioSQL ontology. |
Uses of Term in org.biojava.bio.program.gff3 |
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Methods in org.biojava.bio.program.gff3 that return Term | |
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Term |
GFF3Record.getSource()
|
Term |
GFF3Record.Impl.getSource()
|
Term |
GFF3Record.getType()
|
Term |
GFF3Record.Impl.getType()
|
Methods in org.biojava.bio.program.gff3 with parameters of type Term | |
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void |
GFF3Record.Impl.setSource(Term source)
|
void |
GFF3Record.Impl.setType(Term type)
|
Uses of Term in org.biojava.bio.seq |
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Fields in org.biojava.bio.seq declared as Term | |
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Term |
Feature.Template.sourceTerm
|
Term |
Feature.Template.typeTerm
|
Methods in org.biojava.bio.seq that return Term | |
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Term |
Feature.getSourceTerm()
An ontology term defining the source of this feature. |
Term |
Feature.getTypeTerm()
An ontology term defining the type of feature. |
Methods in org.biojava.bio.seq with parameters of type Term | |
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void |
Feature.setSourceTerm(Term t)
Set the source ontology-term for this feature. |
void |
Feature.setTypeTerm(Term t)
Set the type ontology-term for this feature. |
Uses of Term in org.biojava.bio.seq.impl |
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Methods in org.biojava.bio.seq.impl that return Term | |
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Term |
SimpleFeature.getSourceTerm()
|
Term |
SimpleFeature.getTypeTerm()
|
Methods in org.biojava.bio.seq.impl with parameters of type Term | |
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void |
SimpleFeature.setSourceTerm(Term t)
|
void |
SimpleFeature.setTypeTerm(Term t)
|
Uses of Term in org.biojava.ontology |
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Subinterfaces of Term in org.biojava.ontology | |
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interface |
OntologyTerm
A term in an ontology which identifies another ontology. |
interface |
RemoteTerm
A term in another ontology. |
interface |
Triple
A triple in an ontology. |
interface |
Variable
|
Classes in org.biojava.ontology that implement Term | |
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class |
AbstractTerm
Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties. |
class |
IntegerOntology.IntTerm
|
static class |
OntologyTerm.Impl
Simple in-memory implementation of a remote ontology term. |
static class |
RemoteTerm.Impl
Simple in-memory implementation of a remote ontology term. |
static class |
Term.Impl
Simple in-memory implementation of an ontology term. |
static class |
Triple.Impl
Basic in-memory implementation of a Triple in an ontology This can be used to implement Ontology.createTriple |
static class |
Variable.Impl
|
Fields in org.biojava.ontology declared as Term | |
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static Term |
OntoTools.ANY
|
static Term |
OntoTools.EQUIVALENCE
|
static Term |
OntoTools.IS_A
|
static Term |
OntoTools.NONE
|
static Term |
OntoTools.PART_OF
|
static Term |
OntoTools.PARTIAL_ORDER
|
static Term |
OntoTools.REFLEXIVE
|
static Term |
OntoTools.RELATION
|
static Term |
OntoTools.SYMMETRIC
|
static Term |
OntoTools.TRANSITIVE
|
Methods in org.biojava.ontology that return Term | |
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Term |
IntegerOntology.createTerm(String name)
|
Term |
Ontology.createTerm(String name)
Create a new term in this ontology. |
Term |
Ontology.Impl.createTerm(String name)
|
Term |
IntegerOntology.createTerm(String name,
String description)
|
Term |
Ontology.createTerm(String name,
String description)
Create a new term in this ontology. |
Term |
Ontology.Impl.createTerm(String name,
String description)
|
Term |
IntegerOntology.createTerm(String name,
String description,
Object[] synonyms)
|
Term |
Ontology.createTerm(String name,
String description,
Object[] synonyms)
Create a new term in this ontology. |
Term |
Ontology.Impl.createTerm(String name,
String description,
Object[] synonyms)
|
Term |
Triple.getObject()
Return the object term of this triple. |
Term |
Triple.Impl.getObject()
|
Term |
Triple.getPredicate()
Return a Term which defines the type of relationship between the subject and object terms. |
Term |
Triple.Impl.getPredicate()
|
Term |
RemoteTerm.getRemoteTerm()
Return the imported term |
Term |
RemoteTerm.Impl.getRemoteTerm()
|
Term |
Triple.getSubject()
Return the subject term of this triple |
Term |
Triple.Impl.getSubject()
|
Term |
IntegerOntology.getTerm(String s)
|
Term |
Ontology.getTerm(String name)
Fetch the term with the specified name. |
Term |
Ontology.Impl.getTerm(String name)
|
Term |
IntegerOntology.importTerm(Term t,
String name)
|
Term |
Ontology.importTerm(Term t,
String localName)
Create a view of a term from another ontology. |
Term |
Ontology.Impl.importTerm(Term t,
String name)
|
Methods in org.biojava.ontology that return types with arguments of type Term | |
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Set<Term> |
Ontology.getTerms()
Return all the terms in this ontology |
Set<Term> |
Ontology.Impl.getTerms()
|
Methods in org.biojava.ontology with parameters of type Term | |
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boolean |
IntegerOntology.containsTriple(Term subject,
Term object,
Term predicate)
|
boolean |
Ontology.containsTriple(Term subject,
Term object,
Term predicate)
See if a triple exists in this ontology |
boolean |
Ontology.Impl.containsTriple(Term subject,
Term object,
Term predicate)
|
Triple |
IntegerOntology.createTriple(Term subject,
Term object,
Term predicate,
String name,
String description)
|
Triple |
Ontology.createTriple(Term subject,
Term object,
Term predicate,
String name,
String description)
Creates a new Triple. |
Triple |
Ontology.Impl.createTriple(Term subject,
Term object,
Term predicate,
String name,
String description)
|
void |
IntegerOntology.deleteTerm(Term t)
|
void |
Ontology.deleteTerm(Term t)
Remove a term from an ontology, together with all triples which refer to it. |
void |
Ontology.Impl.deleteTerm(Term t)
|
Set |
IntegerOntology.getTriples(Term subject,
Term object,
Term predicate)
|
Set<Triple> |
Ontology.getTriples(Term subject,
Term object,
Term predicate)
Return all triples from this ontology which match the supplied pattern. |
Set<Triple> |
Ontology.Impl.getTriples(Term subject,
Term object,
Term predicate)
|
Term |
IntegerOntology.importTerm(Term t,
String name)
|
Term |
Ontology.importTerm(Term t,
String localName)
Create a view of a term from another ontology. |
Term |
Ontology.Impl.importTerm(Term t,
String name)
|
Constructors in org.biojava.ontology with parameters of type Term | |
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RemoteTerm.Impl(Ontology ontology,
Term remoteTerm,
String name)
|
|
RemoteTerm.Impl(Ontology ontology,
Term remoteTerm,
String name,
Object[] synonyms)
|
|
Triple.Impl(Term subject,
Term object,
Term predicate)
|
|
Triple.Impl(Term subject,
Term object,
Term predicate,
Object[] synonyms)
|
|
Triple.Impl(Term subject,
Term object,
Term predicate,
String name,
String description)
|
|
Triple.Impl(Term subject,
Term object,
Term predicate,
String name,
String description,
Object[] synonyms)
|
Uses of Term in org.biojavax.bio.seq |
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Methods in org.biojavax.bio.seq that return Term | |
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Term |
SimpleRichFeature.getSourceTerm()
An ontology term defining the source of this feature. |
Term |
SimpleRichFeature.getTypeTerm()
An ontology term defining the type of feature. |
Methods in org.biojavax.bio.seq with parameters of type Term | |
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void |
SimpleRichFeature.setSourceTerm(Term t)
Set the source ontology-term for this feature. |
void |
SimpleRichFeature.setTypeTerm(Term t)
Set the type ontology-term for this feature. |
Uses of Term in org.biojavax.ontology |
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Subinterfaces of Term in org.biojavax.ontology | |
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interface |
ComparableTerm
Makes Term objects comparable properly and adds some extra features to them. |
interface |
ComparableTriple
Comparable triples, obviously. |
Classes in org.biojavax.ontology that implement Term | |
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class |
SimpleComparableTerm
A Term object that can be compared and thus sorted. |
class |
SimpleComparableTriple
Basic comparable triple, BioSQL style. |
Methods in org.biojavax.ontology that return Term | |
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Term |
SimpleComparableOntology.createTerm(String name)
Create a new term in this ontology. |
Term |
SimpleComparableOntology.createTerm(String name,
String description)
Create a new term in this ontology. |
Term |
SimpleComparableOntology.createTerm(String name,
String description,
Object[] synonyms)
Create a new term in this ontology. |
Term |
SimpleComparableTriple.getObject()
Return the object term of this triple. |
Term |
SimpleComparableTriple.getPredicate()
Return a Term which defines the type of relationship between the subject and object terms. |
Term |
SimpleComparableTriple.getSubject()
Return the subject term of this triple |
Term |
SimpleComparableOntology.getTerm(String s)
Fetch the term with the specified name. |
Term |
SimpleComparableOntology.importTerm(Term t,
String localName)
Create a view of a term from another ontology. |
Methods in org.biojavax.ontology with parameters of type Term | |
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boolean |
SimpleComparableOntology.containsTriple(Term subject,
Term object,
Term predicate)
See if a triple exists in this ontology |
Triple |
SimpleComparableOntology.createTriple(Term subject,
Term object,
Term predicate,
String name,
String description)
Creates a new Triple. |
void |
SimpleComparableOntology.deleteTerm(Term t)
Remove a term from an ontology, together with all triples which refer to it. |
ComparableTriple |
SimpleComparableOntology.getOrCreateTriple(Term subject,
Term object,
Term predicate)
Looks for a triple with the given subject object and predicate and returns it. |
ComparableTriple |
ComparableOntology.getOrCreateTriple(Term subject,
Term object,
Term predicate)
Looks for a triple with the given subject object and predicate and returns it. |
ComparableTerm |
SimpleComparableOntology.getOrImportTerm(Term term)
Looks for a term with the same name as the given term and returns it. |
ComparableTerm |
ComparableOntology.getOrImportTerm(Term term)
Looks for a term with the same name as the given term and returns it. |
Set |
SimpleComparableOntology.getTriples(Term subject,
Term object,
Term predicate)
Return all triples from this ontology which match the supplied pattern. |
Term |
SimpleComparableOntology.importTerm(Term t,
String localName)
Create a view of a term from another ontology. |
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