Index

A B C D E F G H I K L M N O P R S T U V W X
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

AbstractAnnotation - Class in org.biojava.nbio.ontology.utils

A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.

AbstractAnnotation() - Constructor for class org.biojava.nbio.ontology.utils.AbstractAnnotation

Protected no-args constructor intended for sub-classes.

AbstractAnnotation(Map) - Constructor for class org.biojava.nbio.ontology.utils.AbstractAnnotation

Create a new Annotation by copying the key-value pairs from a map.

AbstractAnnotation(Annotation) - Constructor for class org.biojava.nbio.ontology.utils.AbstractAnnotation

Copy-constructor.

AbstractTerm - Class in org.biojava.nbio.ontology

Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.

AbstractTerm() - Constructor for class org.biojava.nbio.ontology.AbstractTerm

addOboFileEventListener(OboFileEventListener) - Method in class org.biojava.nbio.ontology.obo.OboFileParser

addSynonym(Object) - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm

addSynonym(Object) - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl

addSynonym(Object) - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl

addSynonym(Object) - Method in interface org.biojava.nbio.ontology.Term

Add a synonym for this term.

addSynonym(Object) - Method in class org.biojava.nbio.ontology.Term.Impl

addSynonym(Object) - Method in class org.biojava.nbio.ontology.Triple.Impl

AlreadyExistsException - Exception in org.biojava.nbio.ontology

Thrown to indicate that a term or triple can't be added to an ontology because it is already present.

AlreadyExistsException() - Constructor for exception org.biojava.nbio.ontology.AlreadyExistsException

AlreadyExistsException(String) - Constructor for exception org.biojava.nbio.ontology.AlreadyExistsException

ALT_ID - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

Annotatable - Interface in org.biojava.nbio.ontology.utils

Indicates that an object has an associated annotation.

Annotation - Interface in org.biojava.nbio.ontology.utils

Arbitrary annotation associated with one or more objects.

ANY - Static variable in class org.biojava.nbio.ontology.OntoTools

App - Class in org.biojava.nbio.ontology

Hello world!

App() - Constructor for class org.biojava.nbio.ontology.App

asMap() - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation

asMap() - Method in interface org.biojava.nbio.ontology.utils.Annotation

Return a map that contains the same key/values as this Annotation.

AssertionFailure - Error in org.biojava.nbio.ontology.utils

An unchecked exception representing an Assertion failure.

AssertionFailure(String) - Constructor for error org.biojava.nbio.ontology.utils.AssertionFailure

AssertionFailure(String, Throwable) - Constructor for error org.biojava.nbio.ontology.utils.AssertionFailure

AssertionFailure(Throwable) - Constructor for error org.biojava.nbio.ontology.utils.AssertionFailure

B

BROAD_SYNONYM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

BROAD_SYNONYM - Static variable in class org.biojava.nbio.ontology.Synonym

bytesRead - Variable in class org.biojava.nbio.ontology.obo.OboFileParser

C

COMMENT - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

COMPARATOR - Static variable in class org.biojava.nbio.ontology.Synonym

compareTo(Synonym) - Method in class org.biojava.nbio.ontology.Synonym

containsKey(Object) - Method in class org.biojava.nbio.ontology.utils.SmallMap

containsKey(Object) - Method in class org.biojava.nbio.ontology.utils.WeakValueHashMap

containsProperty(Object) - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation

containsProperty(Object) - Method in interface org.biojava.nbio.ontology.utils.Annotation

Returns whether there the property is defined.

containsTerm(String) - Method in class org.biojava.nbio.ontology.IntegerOntology

containsTerm(String) - Method in interface org.biojava.nbio.ontology.Ontology

Determines if this ontology currently contains a term named name

containsTerm(String) - Method in class org.biojava.nbio.ontology.Ontology.Impl

containsTriple(Term, Term, Term) - Method in class org.biojava.nbio.ontology.IntegerOntology

containsTriple(Term, Term, Term) - Method in interface org.biojava.nbio.ontology.Ontology

See if a triple exists in this ontology

containsTriple(Term, Term, Term) - Method in class org.biojava.nbio.ontology.Ontology.Impl

createOntology(String, String) - Method in interface org.biojava.nbio.ontology.OntologyFactory

Creates a new Ontology

createOntologyTerm(Ontology) - Method in class org.biojava.nbio.ontology.Ontology.Impl

createTerm(String) - Method in class org.biojava.nbio.ontology.IntegerOntology

createTerm(String) - Method in interface org.biojava.nbio.ontology.Ontology

Create a new term in this ontology.

createTerm(String) - Method in class org.biojava.nbio.ontology.Ontology.Impl

createTerm(String, String) - Method in class org.biojava.nbio.ontology.IntegerOntology

createTerm(String, String) - Method in interface org.biojava.nbio.ontology.Ontology

Create a new term in this ontology.

createTerm(String, String) - Method in class org.biojava.nbio.ontology.Ontology.Impl

createTerm(String, String, Object[]) - Method in class org.biojava.nbio.ontology.IntegerOntology

createTerm(String, String, Object[]) - Method in interface org.biojava.nbio.ontology.Ontology

Create a new term in this ontology.

createTerm(String, String, Object[]) - Method in class org.biojava.nbio.ontology.Ontology.Impl

createTriple(Term, Term, Term, String, String) - Method in class org.biojava.nbio.ontology.IntegerOntology

createTriple(Term, Term, Term, String, String) - Method in interface org.biojava.nbio.ontology.Ontology

Creates a new Triple.

createTriple(Term, Term, Term, String, String) - Method in class org.biojava.nbio.ontology.Ontology.Impl

createVariable(String, String) - Method in class org.biojava.nbio.ontology.IntegerOntology

createVariable(String, String) - Method in interface org.biojava.nbio.ontology.Ontology

Create a new term in this ontology that is used as a variable.

createVariable(String, String) - Method in class org.biojava.nbio.ontology.Ontology.Impl

D

dateFormat - Variable in class org.biojava.nbio.ontology.obo.OboFileParser

DEF - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

DefaultOps - Class in org.biojava.nbio.ontology

Default implementation of OntologyOps.

DefaultOps() - Constructor for class org.biojava.nbio.ontology.DefaultOps

deleteTerm(Term) - Method in class org.biojava.nbio.ontology.IntegerOntology

deleteTerm(Term) - Method in interface org.biojava.nbio.ontology.Ontology

Remove a term from an ontology, together with all triples which refer to it.

deleteTerm(Term) - Method in class org.biojava.nbio.ontology.Ontology.Impl

demo - package demo

description - Variable in class org.biojava.nbio.ontology.AbstractTerm

DISJOINT_FROM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

documentEnd() - Method in interface org.biojava.nbio.ontology.obo.OboFileEventListener

end of parsing a new OBO file

documentEnd() - Method in class org.biojava.nbio.ontology.obo.OboFileHandler

documentStart() - Method in interface org.biojava.nbio.ontology.obo.OboFileEventListener

starting to parse a new OBO file

documentStart() - Method in class org.biojava.nbio.ontology.obo.OboFileHandler

E

EMPTY_ANNOTATION - Static variable in interface org.biojava.nbio.ontology.utils.Annotation

A really useful empty and immutable annotation object.

endIndex - Variable in class org.biojava.nbio.ontology.obo.OboFileParser.SOPair

entrySet() - Method in class org.biojava.nbio.ontology.utils.SmallMap

entrySet() - Method in class org.biojava.nbio.ontology.utils.WeakValueHashMap

equals(Object) - Method in class org.biojava.nbio.ontology.Term.Impl

equals(Object) - Method in interface org.biojava.nbio.ontology.Triple

Check to see if an object is an equivalent Triple.

equals(Object) - Method in class org.biojava.nbio.ontology.Triple.Impl

Two triples are equal if all their fields are identical.

equals(Object) - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation

EQUIVALENCE - Static variable in class org.biojava.nbio.ontology.OntoTools

escape(String, boolean) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser

escapeChars - Static variable in class org.biojava.nbio.ontology.obo.OboFileParser

EXACT_SYNONYM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

EXACT_SYNONYM - Static variable in class org.biojava.nbio.ontology.Synonym

F

findUnescaped(String, char) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser

findUnescaped(String, char, int, int) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser

findUnescaped(String, char, int, int, boolean) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser

G

get(Object) - Method in class org.biojava.nbio.ontology.utils.SmallMap

get(Object) - Method in class org.biojava.nbio.ontology.utils.WeakValueHashMap

getAnnotation() - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm

getAnnotation() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl

getAnnotation() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl

getAnnotation() - Method in class org.biojava.nbio.ontology.Term.Impl

getAnnotation() - Method in class org.biojava.nbio.ontology.Triple.Impl

getAnnotation() - Method in interface org.biojava.nbio.ontology.utils.Annotatable

Should return the associated annotation object.

getCategory() - Method in class org.biojava.nbio.ontology.Synonym

getCoreOntology() - Static method in class org.biojava.nbio.ontology.OntoTools

Get the Ontology that defines our core "central dogma".

getDbxrefList(String, int, int) - Method in class org.biojava.nbio.ontology.obo.OboFileParser

getDefaultFactory() - Static method in class org.biojava.nbio.ontology.OntoTools

getDescription() - Method in class org.biojava.nbio.ontology.IntegerOntology

getDescription() - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm

getDescription() - Method in interface org.biojava.nbio.ontology.Ontology

Return a human-readable description of this ontology, or the empty string if none is available

getDescription() - Method in class org.biojava.nbio.ontology.Ontology.Impl

getDescription() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl

getDescription() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl

getDescription() - Method in interface org.biojava.nbio.ontology.Term

Return a human-readable description of this term, or the empty string if none is available.

getDescription() - Method in class org.biojava.nbio.ontology.Term.Impl

getDescription() - Method in class org.biojava.nbio.ontology.Triple.Impl

getIntegerOntology() - Static method in class org.biojava.nbio.ontology.OntoTools

Get the Ontology that defines integers.

getKey() - Method in class org.biojava.nbio.ontology.utils.KeyedWeakReference

getName() - Method in class org.biojava.nbio.ontology.IntegerOntology

getName() - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm

getName() - Method in interface org.biojava.nbio.ontology.Ontology

Return the name of this ontology

getName() - Method in class org.biojava.nbio.ontology.Ontology.Impl

getName() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl

getName() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl

getName() - Method in class org.biojava.nbio.ontology.Synonym

getName() - Method in interface org.biojava.nbio.ontology.Term

Return the name of this term.

getName() - Method in class org.biojava.nbio.ontology.Term.Impl

getName() - Method in class org.biojava.nbio.ontology.Triple.Impl

getNestedValue(NestedValue, String, int) - Method in class org.biojava.nbio.ontology.obo.OboFileParser

getObject() - Method in interface org.biojava.nbio.ontology.Triple

Return the object term of this triple.

getObject() - Method in class org.biojava.nbio.ontology.Triple.Impl

getOboFileEventListener() - Method in class org.biojava.nbio.ontology.obo.OboFileParser

getOntology() - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm

getOntology() - Method in interface org.biojava.nbio.ontology.OntologyTerm

Get the remote ontology referenced by this term

getOntology() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl

getOntology() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl

getOntology() - Method in interface org.biojava.nbio.ontology.Term

Return the ontology in which this term exists.

getOntology() - Method in class org.biojava.nbio.ontology.Term.Impl

getOntology() - Method in class org.biojava.nbio.ontology.Triple.Impl

getOps() - Method in class org.biojava.nbio.ontology.IntegerOntology

getOps() - Method in interface org.biojava.nbio.ontology.Ontology

Return the associated OntologyOps.

getOps() - Method in class org.biojava.nbio.ontology.Ontology.Impl

getPredicate() - Method in interface org.biojava.nbio.ontology.Triple

Return a Term which defines the type of relationship between the subject and object terms.

getPredicate() - Method in class org.biojava.nbio.ontology.Triple.Impl

getProperties() - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation

Implement this to return the Map delegate.

getProperties() - Method in class org.biojava.nbio.ontology.utils.SmallAnnotation

getProperty(Object) - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation

getProperty(Object) - Method in interface org.biojava.nbio.ontology.utils.Annotation

Retrieve the value of a property by key.

getRemoteTerm() - Method in interface org.biojava.nbio.ontology.RemoteTerm

Return the imported term

getRemoteTerm() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl

getRemoteTerms() - Method in interface org.biojava.nbio.ontology.OntologyOps

Get the set of all remote terms.

getScope() - Method in class org.biojava.nbio.ontology.Synonym

getSubject() - Method in interface org.biojava.nbio.ontology.Triple

Return the subject term of this triple

getSubject() - Method in class org.biojava.nbio.ontology.Triple.Impl

getSynonyms() - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm

getSynonyms() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl

getSynonyms() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl

getSynonyms() - Method in interface org.biojava.nbio.ontology.Term

Return the synonyms for this term.

getSynonyms() - Method in class org.biojava.nbio.ontology.Term.Impl

getSynonyms() - Method in class org.biojava.nbio.ontology.Triple.Impl

getTargetOntology() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl

getTempBuffer() - Method in class org.biojava.nbio.ontology.obo.OboFileParser

getTerm(String) - Method in class org.biojava.nbio.ontology.IntegerOntology

getTerm(String) - Method in interface org.biojava.nbio.ontology.Ontology

Fetch the term with the specified name.

getTerm(String) - Method in class org.biojava.nbio.ontology.Ontology.Impl

getTerms() - Method in class org.biojava.nbio.ontology.IntegerOntology

getTerms() - Method in interface org.biojava.nbio.ontology.Ontology

Return all the terms in this ontology

getTerms() - Method in class org.biojava.nbio.ontology.Ontology.Impl

getTriples(Term, Term, Term) - Method in class org.biojava.nbio.ontology.IntegerOntology

getTriples(Term, Term, Term) - Method in interface org.biojava.nbio.ontology.Ontology

Return all triples from this ontology which match the supplied pattern.

getTriples(Term, Term, Term) - Method in class org.biojava.nbio.ontology.Ontology.Impl

GOParser - Class in org.biojava.nbio.ontology.io

Simple parser for the Gene Ontology (GO) flatfile format.

GOParser() - Constructor for class org.biojava.nbio.ontology.io.GOParser

H

hashCode() - Method in class org.biojava.nbio.ontology.Term.Impl

hashCode() - Method in interface org.biojava.nbio.ontology.Triple

The hashcode for a Triple.

hashCode() - Method in class org.biojava.nbio.ontology.Triple.Impl

hashCode() - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation

I

ID_KEY - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

Impl(String, String) - Constructor for class org.biojava.nbio.ontology.Ontology.Impl

Impl(Ontology, String) - Constructor for class org.biojava.nbio.ontology.Term.Impl

Impl(Ontology, String, String) - Constructor for class org.biojava.nbio.ontology.Term.Impl

Impl(Ontology, String, String) - Constructor for class org.biojava.nbio.ontology.Variable.Impl

Impl(Ontology, String, String, Object[]) - Constructor for class org.biojava.nbio.ontology.Term.Impl

Impl(Ontology, String, String, Object[]) - Constructor for class org.biojava.nbio.ontology.Variable.Impl

Impl(Ontology, Ontology) - Constructor for class org.biojava.nbio.ontology.OntologyTerm.Impl

Impl(Ontology, Ontology, Object[]) - Constructor for class org.biojava.nbio.ontology.OntologyTerm.Impl

Impl(Ontology, Term, String) - Constructor for class org.biojava.nbio.ontology.RemoteTerm.Impl

Impl(Ontology, Term, String, Object[]) - Constructor for class org.biojava.nbio.ontology.RemoteTerm.Impl

Impl(Term, Term, Term) - Constructor for class org.biojava.nbio.ontology.Triple.Impl

Impl(Term, Term, Term, Object[]) - Constructor for class org.biojava.nbio.ontology.Triple.Impl

Impl(Term, Term, Term, String, String) - Constructor for class org.biojava.nbio.ontology.Triple.Impl

Impl(Term, Term, Term, String, String, Object[]) - Constructor for class org.biojava.nbio.ontology.Triple.Impl

importTerm(Term, String) - Method in class org.biojava.nbio.ontology.IntegerOntology

importTerm(Term, String) - Method in class org.biojava.nbio.ontology.Ontology.Impl

importTerm(Term, String) - Method in interface org.biojava.nbio.ontology.Ontology

Create a view of a term from another ontology.

index - Variable in class org.biojava.nbio.ontology.obo.OboFileParser.SOPair

IntegerOntology - Class in org.biojava.nbio.ontology

IntegerOntology.IntTerm - Class in org.biojava.nbio.ontology

INTERSECTION_OF - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

IntTerm(int) - Constructor for class org.biojava.nbio.ontology.IntegerOntology.IntTerm

IntTerm(int, Object[]) - Constructor for class org.biojava.nbio.ontology.IntegerOntology.IntTerm

intValue() - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm

InvalidTermException - Exception in org.biojava.nbio.ontology

Thrown to indicate that an ontology term is not acceptable or appropriate in a given context

InvalidTermException() - Constructor for exception org.biojava.nbio.ontology.InvalidTermException

InvalidTermException(String) - Constructor for exception org.biojava.nbio.ontology.InvalidTermException

InvalidTermException(String, Throwable) - Constructor for exception org.biojava.nbio.ontology.InvalidTermException

InvalidTermException(Throwable) - Constructor for exception org.biojava.nbio.ontology.InvalidTermException

IS_A - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

IS_A - Static variable in class org.biojava.nbio.ontology.OntoTools

IS_OBSOLETE - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

isEscapeStarter(char) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser

isQuote(char) - Static method in class org.biojava.nbio.ontology.obo.OboFileParser

K

KeyedWeakReference - Class in org.biojava.nbio.ontology.utils

Subclass of WeakReference which includes and extra field (the key) which can be used to help cleanup once this reference has been enqueued.

KeyedWeakReference(Object, Object) - Constructor for class org.biojava.nbio.ontology.utils.KeyedWeakReference

KeyedWeakReference(Object, Object, ReferenceQueue) - Constructor for class org.biojava.nbio.ontology.utils.KeyedWeakReference

keys() - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation

keys() - Method in interface org.biojava.nbio.ontology.utils.Annotation

Get a set of key objects.

keySet() - Method in class org.biojava.nbio.ontology.utils.SmallMap

L

line - Variable in class org.biojava.nbio.ontology.obo.OboFileParser

linenum - Variable in class org.biojava.nbio.ontology.obo.OboFileParser

M

main(String[]) - Static method in class demo.ParseGO

Parses Biosapiens OBO file and logs name/description at INFO level

main(String[]) - Static method in class org.biojava.nbio.ontology.App

N

NAME - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

NAMESPACE - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

NARROW_SYNONYM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

NARROW_SYNONYM - Static variable in class org.biojava.nbio.ontology.Synonym

newKey(String, String) - Method in interface org.biojava.nbio.ontology.obo.OboFileEventListener

found a new key in the file

newKey(String, String) - Method in class org.biojava.nbio.ontology.obo.OboFileHandler

newOboFileHeader() - Method in interface org.biojava.nbio.ontology.obo.OboFileEventListener

parsed a new OBO file header

newOboFileHeader() - Method in class org.biojava.nbio.ontology.obo.OboFileHandler

newStanza(String) - Method in interface org.biojava.nbio.ontology.obo.OboFileEventListener

parsed a new stanza in the file

newStanza(String) - Method in class org.biojava.nbio.ontology.obo.OboFileHandler

newSynonym(Synonym) - Method in interface org.biojava.nbio.ontology.obo.OboFileEventListener

a new synonym has been found

newSynonym(Synonym) - Method in class org.biojava.nbio.ontology.obo.OboFileHandler

NONE - Static variable in class org.biojava.nbio.ontology.OntoTools

O

OboFileEventListener - Interface in org.biojava.nbio.ontology.obo

an interface for events that occur during parsing of .obo files

OboFileHandler - Class in org.biojava.nbio.ontology.obo

A file handler for .obo files

OboFileHandler(Ontology) - Constructor for class org.biojava.nbio.ontology.obo.OboFileHandler

OboFileParser - Class in org.biojava.nbio.ontology.obo

A class to parse the content of an OBO file.

OboFileParser() - Constructor for class org.biojava.nbio.ontology.obo.OboFileParser

OboFileParser.SOPair - Class in org.biojava.nbio.ontology.obo

OboParser - Class in org.biojava.nbio.ontology.io

Parses an OBO file.

OboParser() - Constructor for class org.biojava.nbio.ontology.io.OboParser

Ontology - Interface in org.biojava.nbio.ontology

An ontology.

ONTOLOGY - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

Ontology.Impl - Class in org.biojava.nbio.ontology

A basic in-memory implementation of an ontology

OntologyException - Exception in org.biojava.nbio.ontology

Thrown to indicate an error in an Ontology object

OntologyException() - Constructor for exception org.biojava.nbio.ontology.OntologyException

OntologyException(String) - Constructor for exception org.biojava.nbio.ontology.OntologyException

OntologyException(String, Throwable) - Constructor for exception org.biojava.nbio.ontology.OntologyException

OntologyException(Throwable) - Constructor for exception org.biojava.nbio.ontology.OntologyException

OntologyFactory - Interface in org.biojava.nbio.ontology

A factory for Ontology instances.

OntologyOps - Interface in org.biojava.nbio.ontology

This is an interface for optimizing ontology operators.

OntologyTerm - Interface in org.biojava.nbio.ontology

A term in an ontology which identifies another ontology.

OntologyTerm.Impl - Class in org.biojava.nbio.ontology

Simple in-memory implementation of a remote ontology term.

OntoTools - Class in org.biojava.nbio.ontology

Tools for manipulating ontologies.

org.biojava.nbio.ontology - package org.biojava.nbio.ontology

org.biojava.nbio.ontology.io - package org.biojava.nbio.ontology.io

org.biojava.nbio.ontology.obo - package org.biojava.nbio.ontology.obo

org.biojava.nbio.ontology.utils - package org.biojava.nbio.ontology.utils

P

parse(BufferedReader, OntologyFactory) - Method in class org.biojava.nbio.ontology.io.TabDelimParser

Parse an ontology from a reader.

parseGO(BufferedReader, String, String, OntologyFactory) - Method in class org.biojava.nbio.ontology.io.GOParser

ParseGO - Class in demo

ParseGO() - Constructor for class demo.ParseGO

parseOBO(BufferedReader) - Method in class org.biojava.nbio.ontology.obo.OboFileParser

parse an ontology file

parseOBO(BufferedReader, String, String) - Method in class org.biojava.nbio.ontology.io.OboParser

Parse a OBO file and return its content as a BioJava Ontology object

parseXref(String, int, int) - Method in class org.biojava.nbio.ontology.obo.OboFileParser

PART_OF - Static variable in class org.biojava.nbio.ontology.OntoTools

PARTIAL_ORDER - Static variable in class org.biojava.nbio.ontology.OntoTools

propertiesAllocated() - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation

A convenience method to see if we have allocated the properties Map.

propertiesAllocated() - Method in class org.biojava.nbio.ontology.utils.SmallAnnotation

put(Object, Object) - Method in class org.biojava.nbio.ontology.utils.SmallMap

put(Object, Object) - Method in class org.biojava.nbio.ontology.utils.WeakValueHashMap

R

readQuotedString(String, int, int, char, boolean, boolean) - Method in class org.biojava.nbio.ontology.obo.OboFileParser

readResolve() - Method in class org.biojava.nbio.ontology.utils.StaticMemberPlaceHolder

REFLEXIVE - Static variable in class org.biojava.nbio.ontology.OntoTools

REL_SYNONYM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

RELATED_SYNONYM - Static variable in class org.biojava.nbio.ontology.Synonym

RELATION - Static variable in class org.biojava.nbio.ontology.OntoTools

RELATIONSHIP - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

RemoteTerm - Interface in org.biojava.nbio.ontology

A term in another ontology.

RemoteTerm.Impl - Class in org.biojava.nbio.ontology

Simple in-memory implementation of a remote ontology term.

removeProperty(Object) - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation

removeProperty(Object) - Method in interface org.biojava.nbio.ontology.utils.Annotation

Delete a property.

removeSynonym(Object) - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm

removeSynonym(Object) - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl

removeSynonym(Object) - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl

removeSynonym(Object) - Method in class org.biojava.nbio.ontology.Term.Impl

removeSynonym(Object) - Method in interface org.biojava.nbio.ontology.Term

Remove a synonym for this term.

removeSynonym(Object) - Method in class org.biojava.nbio.ontology.Triple.Impl

REPLACED_BY - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

resolveInt(int) - Method in class org.biojava.nbio.ontology.IntegerOntology

S

setAnnotation(Annotation) - Method in class org.biojava.nbio.ontology.Term.Impl

setCategory(String) - Method in class org.biojava.nbio.ontology.Synonym

setDescription(String) - Method in class org.biojava.nbio.ontology.AbstractTerm

setDescription(String) - Method in class org.biojava.nbio.ontology.IntegerOntology.IntTerm

setDescription(String) - Method in class org.biojava.nbio.ontology.IntegerOntology

setDescription(String) - Method in class org.biojava.nbio.ontology.Ontology.Impl

setDescription(String) - Method in interface org.biojava.nbio.ontology.Ontology

set the description of this ontology

setDescription(String) - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl

setDescription(String) - Method in interface org.biojava.nbio.ontology.Term

set the description of the term;

setDescription(String) - Method in class org.biojava.nbio.ontology.Triple.Impl

setName(String) - Method in class org.biojava.nbio.ontology.IntegerOntology

setName(String) - Method in class org.biojava.nbio.ontology.Ontology.Impl

setName(String) - Method in interface org.biojava.nbio.ontology.Ontology

Set the name for this ontology

setName(String) - Method in class org.biojava.nbio.ontology.Synonym

setProperty(Object, Object) - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation

setProperty(Object, Object) - Method in interface org.biojava.nbio.ontology.utils.Annotation

Set the value of a property.

setScope(int) - Method in class org.biojava.nbio.ontology.Synonym

setSynonyms(Set<Object>) - Method in class org.biojava.nbio.ontology.Term.Impl

size() - Method in class org.biojava.nbio.ontology.utils.SmallMap

SmallAnnotation - Class in org.biojava.nbio.ontology.utils

Annotation that is optimized for memory usage.

SmallAnnotation() - Constructor for class org.biojava.nbio.ontology.utils.SmallAnnotation

Return a new SmallAnnotation optimised for small sets of properties.

SmallAnnotation(Map) - Constructor for class org.biojava.nbio.ontology.utils.SmallAnnotation

Return a new SmallAnnotation that copies all values from a Map.

SmallAnnotation(Annotation) - Constructor for class org.biojava.nbio.ontology.utils.SmallAnnotation

Return a new SmallAnnotation that copies all values from another annoation.

SmallMap - Class in org.biojava.nbio.ontology.utils

Lightweight implementation of Map which uses little memory to store a small number of mappings, at the expense of scalability.

SmallMap() - Constructor for class org.biojava.nbio.ontology.utils.SmallMap

SmallMap(int) - Constructor for class org.biojava.nbio.ontology.utils.SmallMap

SmallMap(Map) - Constructor for class org.biojava.nbio.ontology.utils.SmallMap

SOPair(String, int) - Constructor for class org.biojava.nbio.ontology.obo.OboFileParser.SOPair

SOPair(String, int, int) - Constructor for class org.biojava.nbio.ontology.obo.OboFileParser.SOPair

StaticMemberPlaceHolder - Class in org.biojava.nbio.ontology.utils

StaticMemberPlaceHolder() - Constructor for class org.biojava.nbio.ontology.utils.StaticMemberPlaceHolder

StaticMemberPlaceHolder(Field) - Constructor for class org.biojava.nbio.ontology.utils.StaticMemberPlaceHolder

str - Variable in class org.biojava.nbio.ontology.obo.OboFileParser.SOPair

SUBSET - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

SYMMETRIC - Static variable in class org.biojava.nbio.ontology.OntoTools

Synonym - Class in org.biojava.nbio.ontology

Synonym() - Constructor for class org.biojava.nbio.ontology.Synonym

SYNONYM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

T

TabDelimParser - Class in org.biojava.nbio.ontology.io

Parse tab-delimited ontology files into Ontology objects.

TabDelimParser() - Constructor for class org.biojava.nbio.ontology.io.TabDelimParser

tempBuffer - Variable in class org.biojava.nbio.ontology.obo.OboFileParser

Term - Interface in org.biojava.nbio.ontology

A term in an ontology.

TERM - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

Term.Impl - Class in org.biojava.nbio.ontology

Simple in-memory implementation of an ontology term.

toString() - Method in class org.biojava.nbio.ontology.Ontology.Impl

toString() - Method in class org.biojava.nbio.ontology.OntologyTerm.Impl

toString() - Method in class org.biojava.nbio.ontology.RemoteTerm.Impl

toString() - Method in class org.biojava.nbio.ontology.Synonym

toString() - Method in class org.biojava.nbio.ontology.Term.Impl

toString() - Method in class org.biojava.nbio.ontology.Triple.Impl

toString() - Method in class org.biojava.nbio.ontology.utils.AbstractAnnotation

totalSize - Variable in class org.biojava.nbio.ontology.obo.OboFileParser

TRANSITIVE - Static variable in class org.biojava.nbio.ontology.OntoTools

Triple - Interface in org.biojava.nbio.ontology

A triple in an ontology.

Triple.Impl - Class in org.biojava.nbio.ontology

Basic in-memory implementation of a Triple in an ontology This can be used to implement Ontology.createTriple

TYPEDEF - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

U

unescape(String) - Method in class org.biojava.nbio.ontology.obo.OboFileParser

unescape(String, char, int, boolean) - Method in class org.biojava.nbio.ontology.obo.OboFileParser

unescape(String, char, int, int, boolean) - Method in class org.biojava.nbio.ontology.obo.OboFileParser

unescapeChars - Static variable in class org.biojava.nbio.ontology.obo.OboFileParser

UNKNOWN_SCOPE - Static variable in class org.biojava.nbio.ontology.Synonym

V

Variable - Interface in org.biojava.nbio.ontology

Variable.Impl - Class in org.biojava.nbio.ontology

W

WeakValueHashMap - Class in org.biojava.nbio.ontology.utils

Map implementation which keeps weak references to values.

WeakValueHashMap() - Constructor for class org.biojava.nbio.ontology.utils.WeakValueHashMap

X

XREF_ANALOG - Static variable in class org.biojava.nbio.ontology.obo.OboFileHandler

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