Package | Description |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
Ontology |
BioSQLSequenceDB.addOntology(Ontology onto)
Deprecated.
|
Modifier and Type | Class and Description |
---|---|
class |
IntegerOntology |
static class |
Ontology.Impl
A basic in-memory implementation of an ontology
|
Modifier and Type | Method and Description |
---|---|
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 |
Triple.Impl.getOntology() |
Ontology |
OntologyTerm.getOntology()
Get the remote ontology referenced by this term
|
Ontology |
OntologyTerm.Impl.getOntology() |
Ontology |
IntegerOntology.IntTerm.getOntology() |
Ontology |
Term.getOntology()
Return the ontology in which this term exists.
|
Ontology |
Term.Impl.getOntology() |
Ontology |
RemoteTerm.Impl.getOntology() |
Ontology |
OntologyTerm.Impl.getTargetOntology() |
Modifier and Type | Method and Description |
---|---|
OntologyTerm |
Ontology.Impl.createOntologyTerm(Ontology o) |
Constructor and Description |
---|
Impl(Ontology ontology,
Ontology target) |
Impl(Ontology ontology,
Ontology target,
java.lang.Object[] synonyms) |
Impl(Ontology ontology,
java.lang.String name) |
Impl(Ontology ontology,
java.lang.String name,
java.lang.String description) |
Impl(Ontology ontology,
java.lang.String name,
java.lang.String description) |
Impl(Ontology ontology,
java.lang.String name,
java.lang.String description,
java.lang.Object[] synonyms) |
Impl(Ontology ontology,
java.lang.String name,
java.lang.String description,
java.lang.Object[] synonyms) |
Impl(Ontology ontology,
Term remoteTerm,
java.lang.String name) |
Impl(Ontology ontology,
Term remoteTerm,
java.lang.String name,
java.lang.Object[] synonyms) |
Modifier and Type | Method and Description |
---|---|
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
|
Constructor and Description |
---|
OboFileHandler(Ontology ontology) |
Modifier and Type | Interface and Description |
---|---|
interface |
ComparableOntology
An Ontology that can be compared to another.
|
Modifier and Type | Class and Description |
---|---|
class |
SimpleComparableOntology
Represents an ontology that can be compared to other ontologies.
|
Modifier and Type | Method and Description |
---|---|
Ontology |
SimpleComparableTerm.getOntology()
Return the ontology in which this term exists.
|
Ontology |
SimpleComparableTriple.getOntology()
Return the ontology in which this term exists.
|