Package org.biojava.bio.program.indexdb
Class IndexTools
java.lang.Object
org.biojava.bio.program.indexdb.IndexTools
IndexTools
contains static utility methods for
creating flatfile indices according to the OBDA standard.- Author:
- Keith James, Matthew Pocock
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Method Summary
Modifier and TypeMethodDescriptionstatic void
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.
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Method Details
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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:
name
- aString
arbitrary database name.location
- aFile
directory which will contain the indices.seqFiles
- aFile []
array of files to index.alphabetIdentifier
- anint
indicating the type of sequence to be indexed. May be one ofSeqIOConstants.DNA SeqIOConstants.RNA SeqIOConstants.AA
.- Throws:
FileNotFoundException
- if an error occurs.IOException
- if an error occurs.ParserException
- if an error occurs.BioException
- if an error occurs.
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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:
name
- aString
arbitrary database name.location
- aFile
directory which will contain the indices.seqFiles
- aFile []
array of files to index.alphabetIdentifier
- anint
indicating the type of sequence to be indexed. May be one ofSeqIOConstants.DNA SeqIOConstants.RNA SeqIOConstants.AA
.- Throws:
FileNotFoundException
- if an error occurs.IOException
- if an error occurs.ParserException
- if an error occurs.BioException
- if an error occurs.
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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:
name
- aString
arbitrary database name.location
- aFile
directory which will contain the indices.seqFiles
- aFile []
array of files to index.alphabetIdentifier
- anint
indicating the type of sequence to be indexed. May be one ofSeqIOConstants.DNA SeqIOConstants.RNA SeqIOConstants.AA
.- Throws:
FileNotFoundException
- if an error occurs.IOException
- if an error occurs.ParserException
- if an error occurs.BioException
- if an error occurs.
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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
- aFile
directory which will contain the indices.seqFiles
- aFile []
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.
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