public class IndexTools
extends java.lang.Object
IndexTools
contains static utility methods for
creating flatfile indices according to the OBDA standard.Modifier and Type | Method and Description |
---|---|
static void |
indexEmbl(java.lang.String name,
java.io.File location,
java.io.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(java.lang.String name,
java.io.File location,
java.io.File[] seqFiles,
int alphabetIdentifier)
indexFasta indexes DNA, RNA or protein Fasta
format sequence files on primary identifier. |
static void |
indexGenbank(java.lang.String name,
java.io.File location,
java.io.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(java.lang.String name,
java.io.File location,
java.io.File[] seqFiles)
indexSwissprot indexes Swissprot format protein
sequence files on ID as primary identifier. |
public static void indexFasta(java.lang.String name, java.io.File location, java.io.File[] seqFiles, int alphabetIdentifier) throws java.io.FileNotFoundException, java.io.IOException, ParserException, BioException
indexFasta
indexes DNA, RNA or protein Fasta
format sequence files on primary identifier.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.java.io.FileNotFoundException
- if an error occurs.java.io.IOException
- if an error occurs.ParserException
- if an error occurs.BioException
- if an error occurs.public static void indexEmbl(java.lang.String name, java.io.File location, java.io.File[] seqFiles, int alphabetIdentifier) throws java.io.FileNotFoundException, java.io.IOException, ParserException, BioException
indexEmbl
indexes DNA, RNA or protein EMBL format
sequence files on ID as primary identifier and AC as secondary.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.java.io.FileNotFoundException
- if an error occurs.java.io.IOException
- if an error occurs.ParserException
- if an error occurs.BioException
- if an error occurs.public static void indexGenbank(java.lang.String name, java.io.File location, java.io.File[] seqFiles, int alphabetIdentifier) throws java.io.FileNotFoundException, java.io.IOException, ParserException, BioException
indexGenbank
indexes DNA, RNA or protein Genbank
format sequence files on LOCUS as primary identifier and
ACCESSION as secondary.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.java.io.FileNotFoundException
- if an error occurs.java.io.IOException
- if an error occurs.ParserException
- if an error occurs.BioException
- if an error occurs.public static void indexSwissprot(java.lang.String name, java.io.File location, java.io.File[] seqFiles) throws java.io.FileNotFoundException, java.io.IOException, ParserException, BioException
indexSwissprot
indexes Swissprot format protein
sequence files on ID as primary identifier.location
- a File
directory which will
contain the indices.seqFiles
- a File []
array of files to index.java.io.FileNotFoundException
- if an error occurs.java.io.IOException
- if an error occurs.ParserException
- if an error occurs.BioException
- if an error occurs.