Package org.biojava.bio.program.indexdb

package org.biojava.bio.program.indexdb
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.

  • Class
    Description
    BioStore
    BioStores represent directory and file structures which index flat files according to the OBDA specification.
    BioStoreFactory
    BioStoreFactory creates BioStore instances.
    IndexStore
    IndexStore is an interface for indexing flatfiles according to the OBDA specification.
    IndexTools
    IndexTools contains static utility methods for creating flatfile indices according to the OBDA standard.
    Record
    Record represents a record within an indexed flat file databank as defined by the OBDA standard.
    Record.Impl
    Impl is the default implementation of Record.