Package org.biojava.bio.program.indexdb
Class IndexTools
- java.lang.Object
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- org.biojava.bio.program.indexdb.IndexTools
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public class IndexTools extends java.lang.Object
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
All Methods Static Methods Concrete Methods Modifier and Type Method 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.
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Method Detail
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indexFasta
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.- Parameters:
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
.name
- aString
arbitrary database name.- Throws:
java.io.FileNotFoundException
- if an error occurs.java.io.IOException
- if an error occurs.ParserException
- if an error occurs.BioException
- if an error occurs.
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indexEmbl
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.- Parameters:
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
.name
- aString
arbitrary database name.- Throws:
java.io.FileNotFoundException
- if an error occurs.java.io.IOException
- if an error occurs.ParserException
- if an error occurs.BioException
- if an error occurs.
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indexGenbank
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.- Parameters:
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
.name
- aString
arbitrary database name.- Throws:
java.io.FileNotFoundException
- if an error occurs.java.io.IOException
- if an error occurs.ParserException
- if an error occurs.BioException
- if an error occurs.
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indexSwissprot
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.- Parameters:
location
- aFile
directory which will contain the indices.seqFiles
- aFile []
array of files to index.- Throws:
java.io.FileNotFoundException
- if an error occurs.java.io.IOException
- if an error occurs.ParserException
- if an error occurs.BioException
- if an error occurs.
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