Package org.biojava.nbio.core.sequence.io

Class FastaStreamer

java.lang.Object

org.biojava.nbio.core.sequence.io.FastaStreamer

public class FastaStreamer
extends Object

Read from a FASTA file (or gzipped FASTA file) and create a Java stream of ProteinSequence objects for use in a functional programming paradigm.

Since:

7.1.0

Author:

Gary Murphy

Method Summary

Modifier and Type	Method	Description
FastaStreamer	batchSize(int size)
protected ProteinSequence	createSequence(ProteinSequence sequence)	Create the sequence with the information from the header.
Iterable<ProteinSequence>	each()	Enable iteration through the proteins in the file using syntax such as:
static FastaStreamer	from(File file)
static FastaStreamer	from(Path path)
protected int	getBatchSize()
protected SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound>	getHeaderParser()
protected Path	getPath()
SequenceCreatorInterface<AminoAcidCompound>	getSequenceCreator()
Stream<ProteinSequence>	stream()	Create a stream of protein sequences from the contents of the path
FastaStreamer	withHeaderParser(SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound> headerParser)
FastaStreamer	withSequenceCreator(SequenceCreatorInterface<AminoAcidCompound> sequenceCreator)

Methods inherited from class java.lang.Object

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

Method Details

from

public static FastaStreamer from(Path path)

from

public static FastaStreamer from(File file)

withHeaderParser

public FastaStreamer withHeaderParser(SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound> headerParser)

withSequenceCreator

public FastaStreamer withSequenceCreator(SequenceCreatorInterface<AminoAcidCompound> sequenceCreator)

batchSize

public FastaStreamer batchSize(int size)

each

public Iterable<ProteinSequence> each()

Enable iteration through the proteins in the file using syntax such as:

     for(ProteinSequence sequence : FastaStreamer.from(path).each()) {
         .
         .
         .
     }
 

Returns:

an iterable suitable for an iteration loop

stream

public Stream<ProteinSequence> stream()

Create a stream of protein sequences from the contents of the path

Returns:

the stream

createSequence

protected ProteinSequence createSequence(ProteinSequence sequence)

Create the sequence with the information from the header. This implementation return the sequence as-is, but this is an opportunity for the implementer to build specific information into the user collection space of the sequence

Parameters:

sequence - the protein sequence

Returns:

the sequence

getPath

protected Path getPath()

getBatchSize

protected int getBatchSize()

getHeaderParser

protected SequenceHeaderParserInterface<ProteinSequence,AminoAcidCompound> getHeaderParser()

getSequenceCreator

public SequenceCreatorInterface<AminoAcidCompound> getSequenceCreator()