Uses of Interface
org.biojava.bio.AnnotationType

Packages that use AnnotationType

Package	Description
org.biojava.bio	The core classes that will be used throughout the bio packages.
org.biojava.bio.annodb	Databases of generic structured data (annotation) objects.
org.biojava.bio.program.formats	Experimental parsers using the tagvalue framework.
org.biojava.bio.program.indexdb	A flat-file ascii index of ascii flat files as per the OBDA specification.
org.biojava.bio.program.tagvalue	Process files as streams of records, each with tags with values.
org.biojava.bio.program.unigene	Objects for representing Unigene clusters.
org.biojava.bio.seq	Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.io.filterxml	Tools for reading and writing an XML representation of BioJava's FeatureFilter language.

Uses of AnnotationType in org.biojava.bio

Classes in org.biojava.bio that implement AnnotationType

Modifier and Type	Class and Description
static class	AnnotationType.Abstract An abstract base class useful for implementing AnnotationType instances.
static class	AnnotationType.Impl An implementation of AnnotationType.

Fields in org.biojava.bio declared as AnnotationType

Modifier and Type	Field and Description
static AnnotationType	AnnotationType.ANY The type that accepts all annotations and is the supertype of all other annotations.
static AnnotationType	AnnotationType.NONE The type that accepts no annotations at all and is the subtype of all other annotations.

Methods in org.biojava.bio that return AnnotationType

Modifier and Type	Method and Description
AnnotationType	PropertyConstraint.ByAnnotationType.getAnnotationType() Get the AnnotationType used as a constraint.
static AnnotationType	AnnotationTools.intersection(AnnotationType ann1, AnnotationType ann2) Calculate an AnnotationType that matches all Annotation instances matched by both types.
static AnnotationType	AnnotationTools.union(AnnotationType ann1, AnnotationType ann2) Create an AnnotationType that matches all Anntotations that are accepted by two others.

Methods in org.biojava.bio with parameters of type AnnotationType

Modifier and Type	Method and Description
static Annotation	AnnotationTools.allIn(Annotation annotation, AnnotationType annType) Destructive down-cast an annotation to a type.
static Annotation	AnnotationTools.allOut(Annotation annotation, AnnotationType annType) allOut returns a new Annotation containing only those values in the Annotation argument which are not of a type specified by the AnnotationType.
static AnnotationType	AnnotationTools.intersection(AnnotationType ann1, AnnotationType ann2) Calculate an AnnotationType that matches all Annotation instances matched by both types.
static Set	AnnotationTools.searchAnnotation(Annotation ann, AnnotationType query) Scans an Annotation with an AnnotationType and returns all Annotation instances matching a Type.
boolean	AnnotationType.subTypeOf(AnnotationType subType) See if an AnnotationType is a specialisation of this type.
boolean	AnnotationType.Abstract.subTypeOf(AnnotationType subType)
static AnnotationType	AnnotationTools.union(AnnotationType ann1, AnnotationType ann2) Create an AnnotationType that matches all Anntotations that are accepted by two others.

Constructors in org.biojava.bio with parameters of type AnnotationType

Constructor and Description
PropertyConstraint.ByAnnotationType(AnnotationType annType) Create a new constraint by type.

Uses of AnnotationType in org.biojava.bio.annodb

Methods in org.biojava.bio.annodb that return AnnotationType

Modifier and Type	Method and Description
AnnotationType	SimpleAnnotationDB.getSchema()
AnnotationType	MergingAnnotationDB.getSchema()
AnnotationType	LazySearchedAnnotationDB.getSchema()
AnnotationType	LazyFilteredAnnotationDB.getSchema()
AnnotationType	IndexedAnnotationDB.getSchema()
AnnotationType	AnnotationDB.getSchema() Get an AnnotationType that accepts all Annotation instances in this DB.

Methods in org.biojava.bio.annodb with parameters of type AnnotationType

Modifier and Type	Method and Description
AnnotationDB	SimpleAnnotationDB.filter(AnnotationType at)
AnnotationDB	MergingAnnotationDB.filter(AnnotationType at)
AnnotationDB	LazySearchedAnnotationDB.filter(AnnotationType at)
AnnotationDB	LazyFilteredAnnotationDB.filter(AnnotationType at)
AnnotationDB	IndexedAnnotationDB.filter(AnnotationType at)
AnnotationDB	AnnotationDB.filter(AnnotationType at) Find all Annotation instances in this DB that are of a particular type.
AnnotationDB	SimpleAnnotationDB.search(AnnotationType at)
AnnotationDB	MergingAnnotationDB.search(AnnotationType at)
AnnotationDB	LazySearchedAnnotationDB.search(AnnotationType at)
AnnotationDB	LazyFilteredAnnotationDB.search(AnnotationType at)
AnnotationDB	IndexedAnnotationDB.search(AnnotationType at)
AnnotationDB	AnnotationDB.search(AnnotationType at) Find all Annotation instances in this DB and any Annotations that are child properties of these that match an AnnotationType.

Constructors in org.biojava.bio.annodb with parameters of type AnnotationType

Constructor and Description
IndexedAnnotationDB(String dbName, File storeLoc, Index2Model model, List toIndex, int maxKeyLen, AnnotationType schema, IndexedAnnotationDB.ParserListenerFactory plFactory) Create a new IndexedAnnotationDB.
LazyFilteredAnnotationDB(String name, AnnotationDB source, AnnotationType schema) Create a new DB by wrapping another with a schema.
LazySearchedAnnotationDB(String name, AnnotationDB source, AnnotationType schema) Create a new DB from an old one by applying a schema.
SimpleAnnotationDB(String name, Set anns, AnnotationType schema) Create a no-frills AnnotationDB instancec.

Uses of AnnotationType in org.biojava.bio.program.formats

Methods in org.biojava.bio.program.formats that return AnnotationType

Modifier and Type	Method and Description
AnnotationType	Swissprot.getType()
AnnotationType	Ligand.Enzyme.getType()
AnnotationType	Ligand.Reaction.getType()
AnnotationType	Ligand.Compound.getType()
AnnotationType	Format.getType() Get the AnnotationType that constrains the events that will be fired.
AnnotationType	Enzyme.getType()
AnnotationType	Embl.getType()

Uses of AnnotationType in org.biojava.bio.program.indexdb

Fields in org.biojava.bio.program.indexdb declared as AnnotationType

Modifier and Type	Field and Description
static AnnotationType	BioStoreFactory.META_DATA_TYPE AnnotationType that all meta-data files should fit.

Uses of AnnotationType in org.biojava.bio.program.tagvalue

Fields in org.biojava.bio.program.tagvalue declared as AnnotationType

Modifier and Type	Field and Description
static AnnotationType	Formats.EMBL_GENBANK_FEATURE_TABLE_TYPE
static AnnotationType	Formats.EMBL_TYPE
static AnnotationType	Formats.SWISSPROT_TYPE

Constructors in org.biojava.bio.program.tagvalue with parameters of type AnnotationType

Constructor and Description
AnnotationBuilder(AnnotationType type) Make a new AnnotationBuilder that will build Annotation instances of a given type.

Uses of AnnotationType in org.biojava.bio.program.unigene

Fields in org.biojava.bio.program.unigene declared as AnnotationType

Modifier and Type	Field and Description
static AnnotationType	UnigeneTools.LIBRARY_ANNOTATION Annotation schema for all Unigene libraries.
static AnnotationType	UnigeneTools.UNIGENE_ANNOTATION Annotation schema for all UnigeneCluster instances.

Uses of AnnotationType in org.biojava.bio.seq

Methods in org.biojava.bio.seq that return AnnotationType

Modifier and Type	Method and Description
AnnotationType	FeatureFilter.ByAnnotationType.getType()

Methods in org.biojava.bio.seq with parameters of type AnnotationType

Modifier and Type	Method and Description
static FeatureFilter	FilterUtils.byAnnotationType(AnnotationType type) Match features with annotations matching the specified AnnotationType
protected void	FeatureFilter.ByAnnotationType.setType(AnnotationType type)

Constructors in org.biojava.bio.seq with parameters of type AnnotationType

Constructor and Description
FeatureFilter.ByAnnotationType(AnnotationType type)

Uses of AnnotationType in org.biojava.bio.seq.io.filterxml

Methods in org.biojava.bio.seq.io.filterxml that return AnnotationType

Modifier and Type	Method and Description
AnnotationType	XMLAnnotationTypeHandler.getAnnotationType() Return the AnnotationType built by this handler

Methods in org.biojava.bio.seq.io.filterxml with parameters of type AnnotationType

Modifier and Type	Method and Description
void	XMLAnnotationTypeWriter.writeAnnotationType(AnnotationType at, XMLWriter xw) Write an AnnotationType to the specified XMLWriter.