Package org.biojava.bio.program.indexdb

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

Method Detail

indexFasta

public static void indexFasta(String name,
                              File location,
                              File[] seqFiles,
                              int alphabetIdentifier)
                       throws FileNotFoundException,
                              IOException,
                              ParserException,
                              BioException

indexFasta indexes DNA, RNA or protein Fasta format sequence files on primary identifier.

Parameters:

location - a File directory which will contain the indices.

seqFiles - a File [] array of files to index.

alphabetIdentifier - an int indicating the type of sequence to be indexed. May be one of SeqIOConstants.DNA SeqIOConstants.RNA SeqIOConstants.AA.

name - a String arbitrary database name.

Throws:

FileNotFoundException - if an error occurs.

IOException - if an error occurs.

ParserException - if an error occurs.

BioException - if an error occurs.

indexEmbl

public static void indexEmbl(String name,
                             File location,
                             File[] seqFiles,
                             int alphabetIdentifier)
                      throws FileNotFoundException,
                             IOException,
                             ParserException,
                             BioException

indexEmbl indexes DNA, RNA or protein EMBL format sequence files on ID as primary identifier and AC as secondary.

Parameters:

location - a File directory which will contain the indices.

seqFiles - a File [] array of files to index.

alphabetIdentifier - an int indicating the type of sequence to be indexed. May be one of SeqIOConstants.DNA SeqIOConstants.RNA SeqIOConstants.AA.

name - a String arbitrary database name.

Throws:

FileNotFoundException - if an error occurs.

IOException - if an error occurs.

ParserException - if an error occurs.

BioException - if an error occurs.

indexGenbank

public static void indexGenbank(String name,
                                File location,
                                File[] seqFiles,
                                int alphabetIdentifier)
                         throws FileNotFoundException,
                                IOException,
                                ParserException,
                                BioException

indexGenbank indexes DNA, RNA or protein Genbank format sequence files on LOCUS as primary identifier and ACCESSION as secondary.

Parameters:

location - a File directory which will contain the indices.

seqFiles - a File [] array of files to index.

alphabetIdentifier - an int indicating the type of sequence to be indexed. May be one of SeqIOConstants.DNA SeqIOConstants.RNA SeqIOConstants.AA.

name - a String arbitrary database name.

Throws:

FileNotFoundException - if an error occurs.

IOException - if an error occurs.

ParserException - if an error occurs.

BioException - if an error occurs.

indexSwissprot

public static void indexSwissprot(String name,
                                  File location,
                                  File[] seqFiles)
                           throws FileNotFoundException,
                                  IOException,
                                  ParserException,
                                  BioException

indexSwissprot indexes Swissprot format protein sequence files on ID as primary identifier.

Parameters:

location - a File directory which will contain the indices.

seqFiles - a File [] array of files to index.

Throws:

FileNotFoundException - if an error occurs.

IOException - if an error occurs.

ParserException - if an error occurs.

BioException - if an error occurs.