org.dishevelled.bio.tools

Class CompressFasta

java.lang.Object

org.dishevelled.bio.tools.CompressFasta

All Implemented Interfaces:

Callable<Integer>

public final class CompressFasta
extends Object
implements Callable<Integer>

Compress sequences in FASTA format to splittable bgzf or bzip2 compression codecs.

Since:

1.3

Author:

Michael Heuer

Field Summary

Fields

Modifier and Type	Field and Description
(package private) static String	DEFAULT_ALPHABET
(package private) static int	DEFAULT_LINE_WIDTH
(package private) static String	DESCRIPTION_LINE

Constructor Summary

Constructors

Constructor and Description
CompressFasta(File inputFastaFile, File outputFastaFile, int lineWidth) Compress sequences in FASTA format to splittable bgzf or bzip2 compression codecs.
CompressFasta(File inputFastaFile, File outputFastaFile, String alphabet, int lineWidth) Compress sequences in FASTA format to splittable bgzf or bzip2 compression codecs.
CompressFasta(Path inputFastaPath, File outputFastaFile, int lineWidth) Compress sequences in FASTA format to splittable bgzf or bzip2 compression codecs.
CompressFasta(Path inputFastaPath, File outputFastaFile, String alphabet, int lineWidth) Compress sequences in FASTA format to splittable bgzf or bzip2 compression codecs.

Method Summary

Modifier and Type	Method and Description
Integer	call()
(package private) static String	describeSequence(org.biojava.bio.seq.Sequence sequence)
(package private) boolean	isProteinAlphabet()
static void	main(String[] args) Main.
(package private) static void	writeSequence(org.biojava.bio.seq.Sequence sequence, int lineWidth, PrintWriter writer)

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_ALPHABET

static final String DEFAULT_ALPHABET

See Also:

Constant Field Values

DEFAULT_LINE_WIDTH

static final int DEFAULT_LINE_WIDTH

See Also:

Constant Field Values

DESCRIPTION_LINE

static final String DESCRIPTION_LINE

See Also:

Constant Field Values

Constructor Detail

CompressFasta

public CompressFasta(File inputFastaFile,
                     File outputFastaFile,
                     int lineWidth)

Compress sequences in FASTA format to splittable bgzf or bzip2 compression codecs.

Parameters:

inputFastaFile - input FASTA file, if any

outputFastaFile - output FASTA file, if any

lineWidth - line width

CompressFasta

public CompressFasta(Path inputFastaPath,
                     File outputFastaFile,
                     int lineWidth)

Compress sequences in FASTA format to splittable bgzf or bzip2 compression codecs.

Parameters:

inputFastaPath - input FASTA path, if any

outputFastaFile - output FASTA file, if any

lineWidth - line width

Since:

2.1

CompressFasta

public CompressFasta(File inputFastaFile,
                     File outputFastaFile,
                     String alphabet,
                     int lineWidth)

Compress sequences in FASTA format to splittable bgzf or bzip2 compression codecs.

Parameters:

inputFastaFile - input FASTA file, if any

outputFastaFile - output FASTA file, if any

alphabet - input FASTA file alphabet { dna, protein }, if any

lineWidth - line width

Since:

2.0

CompressFasta

public CompressFasta(Path inputFastaPath,
                     File outputFastaFile,
                     String alphabet,
                     int lineWidth)

Compress sequences in FASTA format to splittable bgzf or bzip2 compression codecs.

Parameters:

inputFastaPath - input FASTA path, if any

outputFastaFile - output FASTA file, if any

alphabet - input FASTA file alphabet { dna, protein }, if any

lineWidth - line width

Since:

2.1

Method Detail

call

public Integer call()
             throws Exception

Specified by:

call in interface Callable<Integer>

Throws:

Exception

isProteinAlphabet

boolean isProteinAlphabet()

describeSequence

static String describeSequence(org.biojava.bio.seq.Sequence sequence)

writeSequence

static void writeSequence(org.biojava.bio.seq.Sequence sequence,
                          int lineWidth,
                          PrintWriter writer)
                   throws IOException

Throws:

IOException

main

public static void main(String[] args)

Main.

Parameters:

args - command line args