com.milaboratory.core.io.sequence

Interface SequenceReader<S extends SequenceRead>

All Superinterfaces:

cc.redberry.pipe.OutputPort<S>

All Known Subinterfaces:

SequenceReaderCloseable<S>, SingleReader

All Known Implementing Classes:

AbstractMultiReader, AbstractSequenceReader, FastaSequenceReaderWrapper, MultiReader, PairedFastqReader, PairedReader, RandomAccessFastqReader, RandomAccessPairedFastqReader, SingleFastqIndexer, SingleFastqReader

public interface SequenceReader<S extends SequenceRead>
extends cc.redberry.pipe.OutputPort<S>

If this reader has some system resources associated with it (like opened file or network streams) implement OutputPortCloseable interface along with this interface.

Author:

Dmitry Bolotin, Stanislav Poslavsky

Method Summary

Methods

Modifier and Type	Method and Description
long	getNumberOfReads() For sequential readers returns the number of reads read till this moment, after reader is exhausted returns total number of reads.

Methods inherited from interface cc.redberry.pipe.OutputPort

take

Method Detail

getNumberOfReads

long getNumberOfReads()

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.

Returns:

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