org.biojava.bio.program.indexdb

Class BioStore

java.lang.Object

org.biojava.bio.program.indexdb.BioStore

All Implemented Interfaces:

IndexStore

public class BioStore
extends Object
implements IndexStore

BioStores represent directory and file structures which index flat files according to the OBDA specification. The preferred method of constructing new instances is to use BioStoreFactory.

Author:

Matthew Pocock, Keith James

Constructor Summary

Constructors

Constructor and Description
BioStore(File location, boolean cache) Creates a new BioStore flatfile index at the specified location with the specified caching behaviour.

Method Summary

Methods

Modifier and Type	Method and Description
void	commit() commit writes an index to disk.
Record	get(String id) get returns a record specified by a primary identifier.
List	get(String id, String namespace) get returns a list of Records by searching against the primary identifiers if the namespace argument is equal to the primary namespace or otherwise by searching the secondary namespaces.
File	getLocation() getLocation returns the directory where the index is located.
Annotation	getMetaData() getMetaData returns a data structure which represents an OBDA "config.dat" flatfile indexing configuration file.
String	getName() The name of this store or null if the name has not been set.
List	getRecordList() getRecordList returns all the Records in the index.
void	writeRecord(RAF file, long offset, int length, String id, Map secIDs) writeRecord creates and writes a new Record

Methods inherited from class java.lang.Object

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

Constructor Detail

BioStore

public BioStore(File location,
        boolean cache)
         throws IOException,
                BioException

Creates a new BioStore flatfile index at the specified location with the specified caching behaviour.

Parameters:

location - a File indicating the index directory.

cache - a boolean indicating whether the implementation should cache its state.

Throws:

IOException - if an error occurs.

BioException - if an error occurs.

Method Detail

getName

public String getName()

The name of this store or null if the name has not been set.

getLocation

public File getLocation()

getLocation returns the directory where the index is located.

Returns:

a File.

getMetaData

public Annotation getMetaData()

Description copied from interface: IndexStore

getMetaData returns a data structure which represents an OBDA "config.dat" flatfile indexing configuration file.

Specified by:

getMetaData in interface IndexStore

Returns:

an Annotation.

get

public Record get(String id)

Description copied from interface: IndexStore

get returns a record specified by a primary identifier.

Specified by:

get in interface IndexStore

Parameters:

id - a String primary ID.

Returns:

a Record.

get

public List get(String id,
       String namespace)
         throws BioException

Description copied from interface: IndexStore

get returns a list of Records by searching against the primary identifiers if the namespace argument is equal to the primary namespace or otherwise by searching the secondary namespaces. The list of Record instances retuned may be empty, but is never null.

Specified by:

get in interface IndexStore

Parameters:

id - a String primary ID.

namespace - a String.

Returns:

a List of Records.

Throws:

BioException - if an error occurs.

writeRecord

public void writeRecord(RAF file,
               long offset,
               int length,
               String id,
               Map secIDs)

Description copied from interface: IndexStore

writeRecord creates and writes a new Record

Specified by:

writeRecord in interface IndexStore

Parameters:

file - a RAF file.

offset - a long byte offset.

length - an int byte record length.

id - a String primary ID.

secIDs - a Map of primary ID to a List of secondary IDs.

getRecordList

public List getRecordList()

getRecordList returns all the Records in the index.

Returns:

a List of Records.

commit

public void commit()
            throws CommitFailure

commit writes an index to disk.

Throws:

CommitFailure - if an error occurs.