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

Constructor Summary

Constructors

Constructor	Description
SimpleFastaCmd(String fastaCmdExe)

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)
void	setBlastHome(Path blastDbHome)	Override the BLASTDB environment variable.

Methods inherited from class java.lang.Object

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

Constructor Details

SimpleFastaCmd

public SimpleFastaCmd(String fastaCmdExe)

Method Details

setBlastHome

public void setBlastHome(@Nullable
 Path blastDbHome)

Override the BLASTDB environment variable.

If null, the BLAST process will inherit the value of the environment.

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