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java.lang.Objectorg.biojava.bio.program.indexdb.IndexTools
public class IndexTools
IndexTools
contains static utility methods for
creating flatfile indices according to the OBDA standard.
Method Summary | |
---|---|
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 |
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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.
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.
FileNotFoundException
- if an error occurs.
IOException
- if an error occurs.
ParserException
- if an error occurs.
BioException
- if an error occurs.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.
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.
FileNotFoundException
- if an error occurs.
IOException
- if an error occurs.
ParserException
- if an error occurs.
BioException
- if an error occurs.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.
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.
FileNotFoundException
- if an error occurs.
IOException
- if an error occurs.
ParserException
- if an error occurs.
BioException
- if an error occurs.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.
location
- a File
directory which will
contain the indices.seqFiles
- a File []
array of files to index.
FileNotFoundException
- if an error occurs.
IOException
- if an error occurs.
ParserException
- if an error occurs.
BioException
- if an error occurs.
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