Class IndexTools

java.lang.Object
org.biojava.bio.program.indexdb.IndexTools

public class IndexTools extends Object
IndexTools contains static utility methods for creating flatfile indices according to the OBDA standard.
Author:
Keith James, Matthew Pocock
  • Method Summary

    Modifier and Type
    Method
    Description
    static void
    indexEmbl(String name, File location, File[] seqFiles, int alphabetIdentifier)
    indexEmbl indexes DNA, RNA or protein EMBL format sequence files on ID as primary identifier and AC as secondary.
    static void
    indexFasta(String name, File location, File[] seqFiles, int alphabetIdentifier)
    indexFasta indexes DNA, RNA or protein Fasta format sequence files on primary identifier.
    static void
    indexGenbank(String name, File location, File[] seqFiles, int alphabetIdentifier)
    indexGenbank indexes DNA, RNA or protein Genbank format sequence files on LOCUS as primary identifier and ACCESSION as secondary.
    static void
    indexSwissprot(String name, File location, File[] seqFiles)
    indexSwissprot indexes Swissprot format protein sequence files on ID as primary identifier.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait