Package 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

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method 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.