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Packages that use org.biojava.ontology | |
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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.db.biosql | General purpose Sequence storage in a relational database. |
org.biojava.bio.seq.impl | Standard in-memory implementations of Sequence and
Feature . |
org.biojava.ontology | A general-purpose API for ontologies. |
org.biojava.ontology.io | Tools for loading and saving 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. |
Classes in org.biojava.ontology used by org.biojava.bio.program.gff3 | |
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Ontology
An ontology. |
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Term
A term in an ontology. |
Classes in org.biojava.ontology used by org.biojava.bio.seq | |
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InvalidTermException
Thrown to indicate that an ontology term is not acceptable or appropriate in a given context |
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Term
A term in an ontology. |
Classes in org.biojava.ontology used by org.biojava.bio.seq.db.biosql | |
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Ontology
An ontology. |
Classes in org.biojava.ontology used by org.biojava.bio.seq.impl | |
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Term
A term in an ontology. |
Classes in org.biojava.ontology used by org.biojava.ontology | |
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AbstractTerm
Abstract implementation of term |
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AlreadyExistsException
Thrown to indicate that a term or triple can't be added to an ontology because it is already present. |
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IntegerOntology
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IntegerOntology.IntTerm
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Ontology
An ontology. |
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OntologyException
Thrown to indicate an error in an Ontology object |
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OntologyFactory
A factory for Ontology instances. |
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OntologyOps
This is an interface for optimizing ontology operators. |
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OntologyTerm
A term in an ontology which identifies another ontology. |
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RemoteTerm
A term in another ontology. |
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Term
A term in an ontology. |
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Term.Impl
Simple in-memory implementation of an ontology term. |
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Triple
A triple in an ontology. |
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Variable
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Classes in org.biojava.ontology used by org.biojava.ontology.io | |
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Ontology
An ontology. |
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OntologyException
Thrown to indicate an error in an Ontology object |
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OntologyFactory
A factory for Ontology instances. |
Classes in org.biojava.ontology used by org.biojavax.bio.seq | |
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InvalidTermException
Thrown to indicate that an ontology term is not acceptable or appropriate in a given context |
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Term
A term in an ontology. |
Classes in org.biojava.ontology used by org.biojavax.ontology | |
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AlreadyExistsException
Thrown to indicate that a term or triple can't be added to an ontology because it is already present. |
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Ontology
An ontology. |
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OntologyOps
This is an interface for optimizing ontology operators. |
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Term
A term in an ontology. |
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Triple
A triple in an ontology. |
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Variable
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