org.biojava.bio.program.indexdb (BioJava-1.5-beta API)
Keywords: org.biojava.bio.program.indexdb package

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## Package org.biojava.bio.program.indexdb

A flat-file ascii index of ascii flat files as per the OBDA specification.

See:
Description

Interface Summary
IndexStore | `IndexStore` is an interface for indexing flatfiles according to the OBDA specification.
Record | `Record` represents a record within an indexed flat file databank as defined by the OBDA standard.

Class Summary
BioStore | `BioStore`s represent directory and file structures which index flat files according to the OBDA specification.
BioStoreFactory | `BioStoreFactory` creates `BioStore` instances.
IndexTools | `IndexTools` contains static utility methods for creating flatfile indices according to the OBDA standard.
Record.Impl | `Impl` is the default implementation of Record.

## Package org.biojava.bio.program.indexdb Description

A flat-file ascii index of ascii flat files as per the OBDA specification.

The OBDA flat file indexing specification adresses the need to provide a cross-platform indexing scheim for flat files that are reccord based. Typically these files have a primary ID per entry and potentially multiple secondary IDs in potentially multiple namespaces. Different entries will all have different primary IDs, but may shair seccondary IDs in a given namespace.

This package provides an API for managing these ID associations and retrieving blocks of files accordingly. Where ever possible, a sensible choice is made between linear scans and binary searches over ID. All index files use fixed-length reccords to make the binary searches as fast as is feasable.

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