IndexTools (biojava-legacy 1.9.5 API)

java.lang.Object
- org.biojava.bio.program.indexdb.IndexTools

```
public class IndexTools
extends Object
```
IndexTools contains static utility methods for creating flatfile indices according to the OBDA standard.

Author:

Keith James, Matthew Pocock

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method	Description
`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

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:: 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.
Throws:: FileNotFoundException - if an error occurs.; IOException - if an error occurs.; ParserException - if an error occurs.; BioException - if an error occurs.

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:

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.

Throws:

FileNotFoundException - if an error occurs.

IOException - if an error occurs.

ParserException - if an error occurs.

BioException - if an error occurs.

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:

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.

Throws:

FileNotFoundException - if an error occurs.

IOException - if an error occurs.

ParserException - if an error occurs.

BioException - if an error occurs.

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 - a File directory which will contain the indices.; seqFiles - a File [] 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.

Method Summary

Methods inherited from class java.lang.Object

Method Detail

indexFasta

indexEmbl

indexGenbank

indexSwissprot