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## 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
`Record` | `get(String id)` `get` returns a record specified by a primary identifier.
`List` | `get(String id, String namespace)` `get` returns a list of `Record`s 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 `Record`s 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 `Record`s.
  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.

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