org.biojava.app
Class BioFlatIndex

java.lang.Object
  extended by org.biojava.app.BioFlatIndex

public class BioFlatIndex
extends Object

BioFlatIndex is a user application for performing sequence flat file indexing according to the Open Bioinformatics Database Access (OBDA) indexing standard. It may be used to create a new index or to update an existing index with new files. When creating a new index the sequence file format (currently one of 'fasta', 'swissprot', 'embl' or 'genbank', case-insensitive) and alphabet ('dna', 'rna', 'aa', case-insensitive) must be indicated. This information is stored in the index and is used by the sequence retrieval code to determine how to treat the indexed file(s). See the FLAT-DATABASES-HOWTO for more information.

Author:
Keith James, Matthew Pocock
Useage:
java org.biojava.app.BioFlatIndex-c -a alphabet -d dbName -f format [-i indexScheme -l indexRoot] seqFileList
java org.biojava.app.BioFlatIndex-d [-l] seqFileList
java org.biojava.app.BioFlatIndex-h
Option:
-a, --alphabet Source file alphabet {@biojava.values dna rna aa}
-c, --create Create a new index
-d, --dbname Specify the symbolic database name (used as the index root directory name)
-f, --format Specifies the source file format
-h, --help Command line help
-i, --index Specify the indexing scheme {@biojava.default flat}
-l, --location Path to the index root directory {@biojava.default `cwd`}
Argument:
seqFileList Any number of sequence file names of the apropreate format

Constructor Summary
BioFlatIndex()
           
 
Method Summary
static void main(String[] argv)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

BioFlatIndex

public BioFlatIndex()
Method Detail

main

public static void main(String[] argv)
                 throws Exception
Throws:
Exception