Package org.biojava.bio.annodb

Class IndexedAnnotationDB

java.lang.Object

org.biojava.bio.annodb.IndexedAnnotationDB

All Implemented Interfaces:

AnnotationDB

public class IndexedAnnotationDB
extends Object
implements AnnotationDB

A database of Annotation instances backed by an indexed file set.

Since:

1.3

Author:

Matthew Pocock

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static interface	IndexedAnnotationDB.ParserListenerFactory	A factory for retrieving parsers and listeners.
static class	IndexedAnnotationDB.StaticMethodRPFactory	An implementation of ParserListenerFactory that uses a static method.

Field Summary

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

EMPTY

Constructor Summary

Constructors

Constructor	Description
IndexedAnnotationDB(String dbName, File storeLoc, Index2Model model, List toIndex, int maxKeyLen, AnnotationType schema, IndexedAnnotationDB.ParserListenerFactory plFactory)	Create a new IndexedAnnotationDB.
IndexedAnnotationDB(BioStore store)	Initialise the db from a store.

Method Summary

Modifier and Type	Method	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.
IndexedAnnotationDB.ParserListenerFactory	getParserListenerFactory()	Get the ParserListenerFactory used by this IndexedAnnotationDB.
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

IndexedAnnotationDB

public IndexedAnnotationDB(String dbName,
                           File storeLoc,
                           Index2Model model,
                           List toIndex,
                           int maxKeyLen,
                           AnnotationType schema,
                           IndexedAnnotationDB.ParserListenerFactory plFactory)
                    throws BioException,
                           CommitFailure,
                           IOException,
                           ParserException

Create a new IndexedAnnotationDB.

Parameters:

dbName -

storeLoc -

model -

toIndex -

maxKeyLen -

schema -

plFactory -

Throws:

BioException

CommitFailure

IOException

ParserException

IndexedAnnotationDB

public IndexedAnnotationDB(BioStore store)
                    throws IOException,
                           SAXException

Initialise the db from a store.

Parameters:

store - the BioStore to initalise from

Throws:

IOException - if there was an IO fault accessing the store

SAXException - if the XML configuration file is corrupted

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

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

getParserListenerFactory

public IndexedAnnotationDB.ParserListenerFactory getParserListenerFactory()

Get the ParserListenerFactory used by this IndexedAnnotationDB.

Returns:

the ParserListenerFactory