org.biojava.app
Class BioFlatIndex
java.lang.Object
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 |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
BioFlatIndex
public BioFlatIndex()
main
public static void main(String[] argv)
throws Exception
- Throws:
Exception