Package fr.ens.biologie.genomique.aozan.fastqc

Class OverrepresentedSequencesBlast

java.lang.Object

fr.ens.biologie.genomique.aozan.fastqc.OverrepresentedSequencesBlast

public class OverrepresentedSequencesBlast
extends Object

This class launches blastn on one sequence query and parses xml result file to identify the best hit.

Since:

1.2

Author:

Sandrine Perrin

Method Summary

Modifier and Type	Method	Description
void	clear()	Clear sequences.
void	configure(CollectorConfiguration conf, String dockerConnectionString)	Configure and check that Blastn can be launched.
int	getAnalyzedSequenceCount()	Get the number of analyzed sequences
static OverrepresentedSequencesBlast	getInstance()	Get the singleton instance.
fr.ens.biologie.genomique.aozan.fastqc.BlastResultHit	getResult(String sequence)	Get the blast result of a sequence
int	getSubmittedSequenceCount()	Get the number of submitted sequences
void	submitSequence(String sequence)	Submit a sequence to blast

Methods inherited from class java.lang.Object

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

Method Detail

configure

public void configure(CollectorConfiguration conf,
                      String dockerConnectionString)

Configure and check that Blastn can be launched.

Parameters:

conf - object with the collector configuration

dockerConnectionString - Docker connection URI

submitSequence

public void submitSequence(String sequence)

Submit a sequence to blast

Parameters:

sequence - the sequence to blast

getSubmittedSequenceCount

public int getSubmittedSequenceCount()

Get the number of submitted sequences

Returns:

the number of submitted sequences

getAnalyzedSequenceCount

public int getAnalyzedSequenceCount()

Get the number of analyzed sequences

Returns:

the number of analyzed sequences

clear

public void clear()

Clear sequences.

getResult

public fr.ens.biologie.genomique.aozan.fastqc.BlastResultHit getResult(String sequence)
                                                                throws IOException,
                                                                       AozanException

Get the blast result of a sequence

Parameters:

sequence - the sequence to blast

Returns:

the result as BlastResultHit object

Throws:

IOException - if an error occurs while blasting sequences

AozanException - if an error occurs while blasting sequences

getInstance

public static final OverrepresentedSequencesBlast getInstance()

Get the singleton instance.

Returns:

the unique instance of the class