com.milaboratory.core.io.sequence.fasta

Class FastaSequenceReaderWrapper

java.lang.Object

com.milaboratory.core.io.sequence.fasta.FastaSequenceReaderWrapper

All Implemented Interfaces:

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

public class FastaSequenceReaderWrapper
extends Object
implements SingleReader, CanReportProgress

Converts FastaReader<NucleotideSequence> to SingleReader.

Constructor Summary

Constructors

Constructor and Description
FastaSequenceReaderWrapper(FastaReader<NucleotideSequence> internalReader)
FastaSequenceReaderWrapper(FastaReader<NucleotideSequence> internalReader, boolean replaceWildcards)

Method Summary

Methods

Modifier and Type	Method and Description
void	close()
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()
SingleRead	take()

Methods inherited from class java.lang.Object

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

Constructor Detail

FastaSequenceReaderWrapper

public FastaSequenceReaderWrapper(FastaReader<NucleotideSequence> internalReader)

FastaSequenceReaderWrapper

public FastaSequenceReaderWrapper(FastaReader<NucleotideSequence> internalReader,
                          boolean replaceWildcards)

Method Detail

getProgress

public double getProgress()

Specified by:

getProgress in interface CanReportProgress

isFinished

public boolean isFinished()

Specified by:

isFinished in interface CanReportProgress

close

public void close()

Specified by:

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

Specified by:

close in interface AutoCloseable

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

take

public SingleRead take()

Specified by:

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