com.milaboratory.core.io.sequence.fasta

Class FastaReader<S extends Sequence<S>>

java.lang.Object

com.milaboratory.core.io.sequence.fasta.FastaReader<S>

Type Parameters:

S - sequence type

All Implemented Interfaces:

cc.redberry.pipe.OutputPort<FastaRecord<S>>, cc.redberry.pipe.OutputPortCloseable<FastaRecord<S>>, CanReportProgress, AutoCloseable

public class FastaReader<S extends Sequence<S>>
extends Object
implements CanReportProgress, cc.redberry.pipe.OutputPortCloseable<FastaRecord<S>>, AutoCloseable

Reads amino acid or nucleotide sequence from FASTA formatted file

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	FastaReader.RawFastaRecord Used internally

Constructor Summary

Constructors

Constructor and Description
FastaReader(File file, Alphabet<S> alphabet) Creates FASTA reader for file
FastaReader(InputStream inputStream, Alphabet<S> alphabet) Creates reader for stream with unknown size.
FastaReader(InputStream inputStream, Alphabet<S> alphabet, long size) Creates reader from the specified input stream.
FastaReader(String file, Alphabet<S> alphabet) Creates FASTA reader for file

Method Summary

Methods

Modifier and Type	Method and Description
cc.redberry.pipe.OutputPortCloseable<FastaReader.RawFastaRecord>	asRawRecordsPort() Returns output port of raw records.
void	close() Closes the reader
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()
FastaRecord<S>	take() Return next FASTA record or null if end of stream is reached.
FastaReader.RawFastaRecord	takeRawRecord() Return next raw FASTA record or null if end of stream is reached.

Methods inherited from class java.lang.Object

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

Constructor Detail

FastaReader

public FastaReader(InputStream inputStream,
           Alphabet<S> alphabet,
           long size)

Creates reader from the specified input stream.

Parameters:

inputStream - input stream

size - file size

FastaReader

public FastaReader(InputStream inputStream,
           Alphabet<S> alphabet)

Creates reader for stream with unknown size.

Parameters:

inputStream - input stream

alphabet - alphabet

FastaReader

public FastaReader(String file,
           Alphabet<S> alphabet)
            throws FileNotFoundException

Creates FASTA reader for file

Parameters:

file - file name

alphabet - alphabet

Throws:

FileNotFoundException

FastaReader

public FastaReader(File file,
           Alphabet<S> alphabet)
            throws FileNotFoundException

Creates FASTA reader for file

Parameters:

file - file

alphabet - alphabet

Throws:

FileNotFoundException

Method Detail

getProgress

public double getProgress()

Specified by:

getProgress in interface CanReportProgress

isFinished

public boolean isFinished()

Specified by:

isFinished in interface CanReportProgress

take

public FastaRecord<S> take()

Return next FASTA record or null if end of stream is reached.

This method is thread-safe.

Specified by:

take in interface cc.redberry.pipe.OutputPort<FastaRecord<S extends Sequence<S>>>

Returns:

next FASTA record or null if end of stream is reached

takeRawRecord

public FastaReader.RawFastaRecord takeRawRecord()

Return next raw FASTA record or null if end of stream is reached.

This method is thread-safe.

Returns:

next raw FASTA record or null if end of stream is reached

asRawRecordsPort

public cc.redberry.pipe.OutputPortCloseable<FastaReader.RawFastaRecord> asRawRecordsPort()

Returns output port of raw records.

Returns:

output port of raw records

close

public void close()

Closes the reader

Specified by:

close in interface cc.redberry.pipe.OutputPortCloseable<FastaRecord<S extends Sequence<S>>>

Specified by:

close in interface AutoCloseable

getNumberOfReads

public long getNumberOfReads()

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

This method is thread-safe.

Returns:

number of reads read till this moment for sequential readers