Package ubic.gemma.core.loader.genome

Interface FastaCmd

All Known Implementing Classes:

SimpleFastaCmd

public interface FastaCmd

Interface representing a class that can retrieve sequences from Blast databases. (In later versions of BLAST this is known as Blastdbcmd)

Author:

pavlidis

Method Summary

Modifier and Type	Method	Description
Collection<BioSequence>	getBatchAccessions(Collection<String> accessions, String database)
Collection<BioSequence>	getBatchIdentifiers(Collection<Integer> identifiers, String database)
BioSequence	getByAccession(String accession, String database)
BioSequence	getByIdentifier(int identifier, String database)

Method Details

getByAccession

BioSequence getByAccession(String accession,
 String database)

getByIdentifier

BioSequence getByIdentifier(int identifier,
 String database)

getBatchAccessions

Collection<BioSequence> getBatchAccessions(Collection<String> accessions,
 String database)

getBatchIdentifiers

Collection<BioSequence> getBatchIdentifiers(Collection<Integer> identifiers,
 String database)