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 Details
- 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.

Class IndexTools

Method Summary

Methods inherited from class java.lang.Object

Method Details

indexFasta

indexEmbl

indexGenbank

indexSwissprot