com.milaboratory.core.io.sequence.fasta

Class FastaWriter<S extends Sequence<S>>

java.lang.Object

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

Type Parameters:

S - sequence type

All Implemented Interfaces:

AutoCloseable

public final class FastaWriter<S extends Sequence<S>>
extends Object
implements AutoCloseable

Writer of FASTA files.

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_MAX_LENGTH

Constructor Summary

Constructors

Constructor and Description
FastaWriter(File file) Creates FASTA writer
FastaWriter(File file, int maxLength) Creates FASTA writer
FastaWriter(OutputStream outputStream) Creates FASTA writer
FastaWriter(OutputStream outputStream, int maxLength) Creates FASTA writer
FastaWriter(String fileName) Creates FASTA writer

Method Summary

Methods

Modifier and Type	Method and Description
void	close() Close writer.
void	flush() Flush underlying stream.
void	write(FastaRecord<S> record)
void	write(String description, S sequence)

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_MAX_LENGTH

public static final int DEFAULT_MAX_LENGTH

See Also:

Constant Field Values

Constructor Detail

FastaWriter

public FastaWriter(String fileName)
            throws FileNotFoundException

Creates FASTA writer

Parameters:

fileName - file to be created

Throws:

FileNotFoundException

FastaWriter

public FastaWriter(File file)
            throws FileNotFoundException

Creates FASTA writer

Parameters:

file - output file

Throws:

FileNotFoundException

FastaWriter

public FastaWriter(File file,
           int maxLength)
            throws FileNotFoundException

Creates FASTA writer

Parameters:

file - output file

maxLength - line length limit after which sequence will be split into several lines

Throws:

FileNotFoundException

FastaWriter

public FastaWriter(OutputStream outputStream)

Creates FASTA writer

Parameters:

outputStream - output stream

FastaWriter

public FastaWriter(OutputStream outputStream,
           int maxLength)

Creates FASTA writer

Parameters:

outputStream - output stream

maxLength - line length limit after which sequence will be split into several lines

Method Detail

write

public void write(FastaRecord<S> record)

write

public void write(String description,
         S sequence)

flush

public void flush()

Flush underlying stream.

close

public void close()

Close writer.

Specified by:

close in interface AutoCloseable