Uses of Interface
org.biojava.bio.annodb.AnnotationDB

Packages that use AnnotationDB

Package	Description
org.biojava.bio.annodb	Databases of generic structured data (annotation) objects.

Uses of AnnotationDB in org.biojava.bio.annodb

Classes in org.biojava.bio.annodb that implement AnnotationDB

Modifier and Type	Class and Description
class	IndexedAnnotationDB A database of Annotation instances backed by an indexed file set.
class	LazyFilteredAnnotationDB An implementation of AnnotationDB that lazily applies a filter.
class	LazySearchedAnnotationDB An implementation of AnnotationDB that does a JIT search on another set.
class	MergingAnnotationDB An AnnotationDB that provides a merged view of a list of underlying DBs.
class	SimpleAnnotationDB A no-frills implementation of AnnotationDB.

Fields in org.biojava.bio.annodb declared as AnnotationDB

Modifier and Type	Field and Description
static AnnotationDB	AnnotationDB.EMPTY An AnnotationDB that is always empty.

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

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.

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

Modifier and Type	Method and Description
void	MergingAnnotationDB.addAnnotationDB(AnnotationDB toAdd) Add a DB to be merged in this view.
void	MergingAnnotationDB.removeAnnotationDB(AnnotationDB toRemove) Remove a DB from this view.

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

Constructor and Description
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.