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Packages that use Ontology | |
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org.biojava.bio.program.gff3 | Support for reading and writing GFF3. |
org.biojava.bio.seq.db.biosql | General purpose Sequence storage in a relational database. |
org.biojava.ontology | A general-purpose API for ontologies. |
org.biojava.ontology.io | Tools for loading and saving ontologies. |
org.biojava.ontology.obo | |
org.biojavax.ontology | Extensions to the biojava ontology model that represent BioSQL ontology. |
Uses of Ontology in org.biojava.bio.program.gff3 |
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Methods in org.biojava.bio.program.gff3 with parameters of type Ontology | |
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protected GFF3Record |
GFF3Parser.createRecord(GFF3DocumentHandler handler,
java.util.List aList,
java.lang.String rest,
java.lang.String comment,
Ontology ontology,
Ontology fallBack)
Actually turns a list of tokens, some value string and a comment into a GFF3Record and informs handler. |
void |
GFF3Parser.parse(java.io.BufferedReader bReader,
GFF3DocumentHandler handler,
Ontology ontology)
Informs handler of each line of gff read from bReader. |
void |
GFF3Parser.parse(java.io.BufferedReader bReader,
GFF3DocumentHandler handler,
Ontology ontology,
java.lang.String locator)
Informs handler of each line of GFF read from bReader |
protected void |
GFF3Parser.parseAttribute(java.lang.String attValList,
Annotation anno,
Ontology onto,
Ontology fallBack)
Parse attValList into a Map of attributes and value lists. |
Uses of Ontology in org.biojava.bio.seq.db.biosql |
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Methods in org.biojava.bio.seq.db.biosql that return Ontology | |
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Ontology |
BioSQLSequenceDB.addOntology(Ontology onto)
Deprecated. |
Ontology |
BioSQLSequenceDB.createOntology(java.lang.String name,
java.lang.String description)
Deprecated. |
Ontology |
BioSQLSequenceDB.getOntology(java.lang.String name)
Deprecated. |
Methods in org.biojava.bio.seq.db.biosql with parameters of type Ontology | |
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Ontology |
BioSQLSequenceDB.addOntology(Ontology onto)
Deprecated. |
Uses of Ontology in org.biojava.ontology |
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Classes in org.biojava.ontology that implement Ontology | |
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class |
IntegerOntology
|
static class |
Ontology.Impl
A basic in-memory implementation of an ontology |
Methods in org.biojava.ontology that return Ontology | |
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Ontology |
OntologyFactory.createOntology(java.lang.String name,
java.lang.String description)
Creates a new Ontology |
static Ontology |
OntoTools.getCoreOntology()
Get the Ontology that defines our core "central dogma". |
Ontology |
RemoteTerm.Impl.getOntology()
|
Ontology |
OntologyTerm.getOntology()
Get the remote ontology referenced by this term |
Ontology |
OntologyTerm.Impl.getOntology()
|
Ontology |
Triple.Impl.getOntology()
|
Ontology |
IntegerOntology.IntTerm.getOntology()
|
Ontology |
Term.getOntology()
Return the ontology in which this term exists. |
Ontology |
Term.Impl.getOntology()
|
Ontology |
OntologyTerm.Impl.getTargetOntology()
|
Methods in org.biojava.ontology with parameters of type Ontology | |
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OntologyTerm |
Ontology.Impl.createOntologyTerm(Ontology o)
|
Constructors in org.biojava.ontology with parameters of type Ontology | |
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OntologyTerm.Impl(Ontology ontology,
Ontology target)
|
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OntologyTerm.Impl(Ontology ontology,
Ontology target,
java.lang.Object[] synonyms)
|
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RemoteTerm.Impl(Ontology ontology,
Term remoteTerm,
java.lang.String name)
|
|
RemoteTerm.Impl(Ontology ontology,
Term remoteTerm,
java.lang.String name,
java.lang.Object[] synonyms)
|
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Term.Impl(Ontology ontology,
java.lang.String name)
|
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Term.Impl(Ontology ontology,
java.lang.String name,
java.lang.String description)
|
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Term.Impl(Ontology ontology,
java.lang.String name,
java.lang.String description,
java.lang.Object[] synonyms)
|
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Variable.Impl(Ontology ontology,
java.lang.String name,
java.lang.String description)
|
|
Variable.Impl(Ontology ontology,
java.lang.String name,
java.lang.String description,
java.lang.Object[] synonyms)
|
Uses of Ontology in org.biojava.ontology.io |
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Methods in org.biojava.ontology.io that return Ontology | |
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Ontology |
TabDelimParser.parse(java.io.BufferedReader in,
OntologyFactory of)
Parse an ontology from a reader. |
Ontology |
GOParser.parseGO(java.io.BufferedReader goFile,
java.lang.String ontoName,
java.lang.String ontoDescription,
OntologyFactory factory)
|
Ontology |
OboParser.parseOBO(java.io.BufferedReader oboFile,
java.lang.String ontoName,
java.lang.String ontoDescription)
Parse a OBO file and return its content as a BioJava Ontology object |
Uses of Ontology in org.biojava.ontology.obo |
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Constructors in org.biojava.ontology.obo with parameters of type Ontology | |
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OboFileHandler(Ontology ontology)
|
Uses of Ontology in org.biojavax.ontology |
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Subinterfaces of Ontology in org.biojavax.ontology | |
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interface |
ComparableOntology
An Ontology that can be compared to another. |
Classes in org.biojavax.ontology that implement Ontology | |
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class |
SimpleComparableOntology
Represents an ontology that can be compared to other ontologies. |
Methods in org.biojavax.ontology that return Ontology | |
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Ontology |
SimpleComparableTriple.getOntology()
Return the ontology in which this term exists. |
Ontology |
SimpleComparableTerm.getOntology()
Return the ontology in which this term exists. |
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