org.biojava.bio.annodb
Interface AnnotationDB

All Known Implementing Classes:

IndexedAnnotationDB, LazyFilteredAnnotationDB, LazySearchedAnnotationDB, MergingAnnotationDB, SimpleAnnotationDB

public interface AnnotationDB

A database of Annotation instances.

It is often a pain to provide explicit API for a particular file format, but it is still necisary to present it as some collection of structured objects. Annotation, together with AnnotationType are capable of representing structured data and the tag-value parser API is uniquely suited to creating these from structured text files. AnnotationDB is provided as a way to wrap up a whole collection of Annotation instances so that they can be queried and handled as a unit.

Since:

1.3

Author:

Matthew Pocock

Field Summary

static AnnotationDB

EMPTY An AnnotationDB that is always empty.

Method Summary

AnnotationDB	filter(AnnotationType at) Find all Annotation instances in this DB that are of a particular type.
String	getName() The name of this AnnotationDB.
AnnotationType	getSchema() Get an AnnotationType that accepts all Annotation instances in this DB.
Iterator	iterator() Loop over each Annotation in this db.
AnnotationDB	search(AnnotationType at) Find all Annotation instances in this DB and any Annotations that are child properties of these that match an AnnotationType.
int	size() The number of Annotation instances in the DB.

Field Detail

EMPTY

static final AnnotationDB EMPTY

An AnnotationDB that is always empty.

Method Detail

getName

String getName()

The name of this AnnotationDB.

Returns:

the name of this AnnotationDB

getSchema

AnnotationType getSchema()

Get an AnnotationType that accepts all Annotation instances in this DB.

The schema should accept all Annotations in the DB. However, it may hit other Annotations. So, AnnotationType.ALL is always a valid schema. Obviously, the more retrictive it is, the more usefull it becomes for introspection.

Returns:

the schema AnnotationType

iterator

Iterator iterator()

Loop over each Annotation in this db.

Returns:

an Iterator over each item in the DB

size

int size()

The number of Annotation instances in the DB.

Returns:

the size of this DB

filter

AnnotationDB filter(AnnotationType at)

Find all Annotation instances in this DB that are of a particular type.

Parameters:

at - the AnnotationType to match

Returns:

an AnnotationDB with all matching Annotation instances

search

AnnotationDB search(AnnotationType at)

Find all Annotation instances in this DB and any Annotations that are child properties of these that match an AnnotationType.

Parameters:

at - the AnnotationType to search with

Returns:

an AnnotationDB with all matching Annotation instances, irregardless of how deep in the hieracy they are