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

  • Method Summary

    Modifier and Type
    Method
    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 Details

    • 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 Details

    • 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.