com.milaboratory.core.io.sequence.fastq

Class SingleFastqIndexer

java.lang.Object

com.milaboratory.core.io.sequence.fastq.SingleFastqIndexer

All Implemented Interfaces:

cc.redberry.pipe.OutputPort<SingleRead>, cc.redberry.pipe.OutputPortCloseable<SingleRead>, SequenceReader<SingleRead>, SequenceReaderCloseable<SingleRead>, SingleReader, CanReportProgress, AutoCloseable

public class SingleFastqIndexer
extends Object
implements SingleReader, CanReportProgress, cc.redberry.pipe.OutputPortCloseable<SingleRead>

Constructor Summary

Constructors

Constructor and Description
SingleFastqIndexer(SingleFastqReader reader, long step)

Method Summary

Methods

Modifier and Type	Method and Description
void	close()
FileIndex	createIndex()
long	getNumberOfReads() For sequential readers returns the number of reads read till this moment, after reader is exhausted returns total number of reads.
double	getProgress()
boolean	isFinished()
SingleFastqIndexer	readToEnd()
SingleFastqReader	setTotalSize(long totalSize)
SingleRead	take()

Methods inherited from class java.lang.Object

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

Constructor Detail

SingleFastqIndexer

public SingleFastqIndexer(SingleFastqReader reader,
                  long step)

Method Detail

setTotalSize

public SingleFastqReader setTotalSize(long totalSize)

getProgress

public double getProgress()

Specified by:

getProgress in interface CanReportProgress

isFinished

public boolean isFinished()

Specified by:

isFinished in interface CanReportProgress

take

public SingleRead take()

Specified by:

take in interface cc.redberry.pipe.OutputPort<SingleRead>

getNumberOfReads

public long getNumberOfReads()

Description copied from interface: SequenceReader

For sequential readers returns the number of reads read till this moment, after reader is exhausted returns total number of reads. For random access readers returns total number of reads.

This method is thread-safe.

Specified by:

getNumberOfReads in interface SequenceReader<SingleRead>

Returns:

number of reads read till this moment for sequential readers and total number of reads for random access readers

close

public void close()

Specified by:

close in interface cc.redberry.pipe.OutputPortCloseable<SingleRead>

Specified by:

close in interface AutoCloseable

createIndex

public FileIndex createIndex()

readToEnd

public SingleFastqIndexer readToEnd()