org.biojava.bio.annodb

Class SimpleAnnotationDB

java.lang.Object

org.biojava.bio.annodb.SimpleAnnotationDB

All Implemented Interfaces:

AnnotationDB

public class SimpleAnnotationDB
extends Object
implements AnnotationDB

A no-frills implementation of AnnotationDB.

Since:

1.3

Author:

Matthew Pocock

Field Summary

Fields inherited from interface org.biojava.bio.annodb.AnnotationDB

EMPTY

Constructor Summary

Constructors

Constructor and Description
SimpleAnnotationDB(String name, Set anns, AnnotationType schema) Create a no-frills AnnotationDB instancec.

Method Summary

Methods

Modifier and Type	Method and Description
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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SimpleAnnotationDB

public SimpleAnnotationDB(String name,
                  Set anns,
                  AnnotationType schema)

Create a no-frills AnnotationDB instancec.

Parameters:

name - the name of this Annotation DB

anns - a Set of Annotation instances it contains

schema - an AnnotationType schema that applies to them

Method Detail

getName

public String getName()

Description copied from interface: AnnotationDB

The name of this AnnotationDB.

Specified by:

getName in interface AnnotationDB

Returns:

the name of this AnnotationDB

size

public int size()

Description copied from interface: AnnotationDB

The number of Annotation instances in the DB.

Specified by:

size in interface AnnotationDB

Returns:

the size of this DB

getSchema

public AnnotationType getSchema()

Description copied from interface: AnnotationDB

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.

Specified by:

getSchema in interface AnnotationDB

Returns:

the schema AnnotationType

iterator

public Iterator iterator()

Description copied from interface: AnnotationDB

Loop over each Annotation in this db.

Specified by:

iterator in interface AnnotationDB

Returns:

an Iterator over each item in the DB

filter

public AnnotationDB filter(AnnotationType at)

Description copied from interface: AnnotationDB

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

Specified by:

filter in interface AnnotationDB

Parameters:

at - the AnnotationType to match

Returns:

an AnnotationDB with all matching Annotation instances

search

public AnnotationDB search(AnnotationType at)

Description copied from interface: AnnotationDB

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

Specified by:

search in interface AnnotationDB

Parameters:

at - the AnnotationType to search with

Returns:

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