Package org.biojava.bio.annodb

Class MergingAnnotationDB

java.lang.Object

org.biojava.bio.annodb.MergingAnnotationDB

All Implemented Interfaces:

AnnotationDB

public class MergingAnnotationDB
extends Object
implements AnnotationDB

An AnnotationDB that provides a merged view of a list of underlying DBs.

Since:

1.3

Author:

Matthew Pocock

Field Summary

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

EMPTY

Constructor Summary

Constructors

Constructor	Description
MergingAnnotationDB(String name)	Create a new MergingAnnotationDB with a name and no DBs to merge.
MergingAnnotationDB(String name, List merged)	Create a new MergingAnnotationDB with a name and a list of DBs to merge.

Method Summary

Modifier and Type	Method	Description
void	addAnnotationDB(AnnotationDB toAdd)	Add a DB to be merged in this view.
AnnotationDB	filter(AnnotationType at)	Find all Annotation instances in this DB that are of a particular type.
List	getMerged()	Return a list of merged DBs.
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.
void	removeAnnotationDB(AnnotationDB toRemove)	Remove a DB from this view.
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

MergingAnnotationDB

public MergingAnnotationDB(String name)

Create a new MergingAnnotationDB with a name and no DBs to merge.

Parameters:

name - the name of this DB

MergingAnnotationDB

public MergingAnnotationDB(String name,
                           List merged)

Create a new MergingAnnotationDB with a name and a list of DBs to merge.

Parameters:

name - the name of this DB

merged - a list of DBs to merge

Method Detail

addAnnotationDB

public void addAnnotationDB(AnnotationDB toAdd)

Add a DB to be merged in this view.

Parameters:

toAdd - the AnnotationDB to add

removeAnnotationDB

public void removeAnnotationDB(AnnotationDB toRemove)

Remove a DB from this view.

Parameters:

toRemove - the AnnotationDB to remove

getMerged

public List getMerged()

Return a list of merged DBs. This can be modified independantly of this DB.

Returns:

a List of merged DBs

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

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

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

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