Package ubic.gemma.core.loader.genome

Class SimpleFastaCmd

java.lang.Object

ubic.gemma.core.loader.genome.SimpleFastaCmd

All Implemented Interfaces:

FastaCmd

public class SimpleFastaCmd
extends Object
implements FastaCmd

Simple implementation of methods for fetching sequences from blast-formatted databases, using blastdbcmd (aka fastacmd)

Author:

pavlidis

Field Summary

Fields

Modifier and Type	Field	Description
static String	FASTA_CMD_ENV_VAR

Constructor Summary

Constructors

Constructor	Description
SimpleFastaCmd()

Method Summary

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

FASTA_CMD_ENV_VAR

public static final String FASTA_CMD_ENV_VAR

See Also:

Constant Field Values

Constructor Detail

SimpleFastaCmd

public SimpleFastaCmd()

Method Detail

getByAccession

public BioSequence getByAccession(String accession,
                                  String database)

Specified by:

getByAccession in interface FastaCmd

getByIdentifier

public BioSequence getByIdentifier(int identifier,
                                   String database)

Specified by:

getByIdentifier in interface FastaCmd

getBatchAccessions

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

Specified by:

getBatchAccessions in interface FastaCmd

getBatchIdentifiers

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

Specified by:

getBatchIdentifiers in interface FastaCmd

getByAccession

public BioSequence getByAccession(String accession,
                                  String database,
                                  String blastHome)

Specified by:

getByAccession in interface FastaCmd

getByIdentifier

public BioSequence getByIdentifier(int identifier,
                                   String database,
                                   String blastHome)

Specified by:

getByIdentifier in interface FastaCmd

getBatchAccessions

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

Specified by:

getBatchAccessions in interface FastaCmd

getBatchIdentifiers

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

Specified by:

getBatchIdentifiers in interface FastaCmd