org.biojava.bio.program.indexdb

Interface IndexStore

All Known Implementing Classes:

BioStore

public interface IndexStore

IndexStore is an interface for indexing flatfiles according to the OBDA specification. It represents a map of Record instances by a primary ID and any number of Records associated with an ID in some seccondary namespace.

Author:

Matthew Pocock, Keith James

Method Summary

Modifier and Type	Method and Description
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.
Annotation	getMetaData() getMetaData returns a data structure which represents an OBDA "config.dat" flatfile indexing configuration file.
void	writeRecord(RAF file, long offset, int length, String id, Map secIDs) writeRecord creates and writes a new Record

Method Detail

get

Record get(String id)
    throws BioException

get returns a record specified by a primary identifier.

Parameters:

id - a String primary ID.

Returns:

a Record.

Throws:

BioException - if an error occurs or if there is no Record associated with the id

get

List get(String id,
         String namespace)
  throws BioException

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.

Parameters:

id - a String primary ID.

namespace - a String.

Returns:

a List of Records.

Throws:

BioException - if an error occurs.

getMetaData

Annotation getMetaData()

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

Returns:

an Annotation.

writeRecord

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

writeRecord creates and writes a new Record

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.