org.dishevelled.bio.tools

Class SplitFasta

java.lang.Object

org.dishevelled.bio.tools.AbstractSplit

org.dishevelled.bio.tools.SplitFasta

All Implemented Interfaces:

Callable<Integer>

public final class SplitFasta
extends AbstractSplit

Split FASTA files.

Author:

Michael Heuer

Nested Class Summary

Nested classes/interfaces inherited from class org.dishevelled.bio.tools.AbstractSplit

AbstractSplit.CountingWriter

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

Fields inherited from class org.dishevelled.bio.tools.AbstractSplit

bytes, inputPath, records

Constructor Summary

Constructors

Constructor and Description
SplitFasta(File inputFile, Long bytes, Long records, String prefix, int leftPad, String suffix, int lineWidth) Split FASTA files.
SplitFasta(File inputFile, Long bytes, Long records, String prefix, String suffix, int lineWidth) Split FASTA files.
SplitFasta(File inputFile, String alphabet, Long bytes, Long records, String prefix, int leftPad, String suffix, int lineWidth) Split FASTA files.
SplitFasta(Path inputPath, Long bytes, Long records, String prefix, int leftPad, String suffix, int lineWidth) Split FASTA files.
SplitFasta(Path inputPath, Long bytes, Long records, String prefix, String suffix, int lineWidth) Split FASTA files.
SplitFasta(Path inputPath, String alphabet, Long bytes, Long records, String prefix, int leftPad, String suffix, int lineWidth) Split FASTA files.

Method Summary

Modifier and Type	Method and Description
Integer	call()
(package private) static String	describeSequence(org.biojava.bio.seq.Sequence sequence)
(package private) static String	getBaseName(Path path)
(package private) static String	getFileExtensions(Path path)
(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 org.dishevelled.bio.tools.AbstractSplit

closeWriters, createCountingWriter, getFileExtension, getNameWithoutExtension, leftPad, toBytes

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

SplitFasta

public SplitFasta(File inputFile,
                  Long bytes,
                  Long records,
                  String prefix,
                  String suffix,
                  int lineWidth)

Split FASTA files.

Parameters:

inputFile - input file, if any

bytes - split the input file at next record after each n bytes, if any

records - split the input file after each n records, if any

prefix - output file prefix, must not be null

suffix - output file suffix, must not be null

lineWidth - line width

SplitFasta

public SplitFasta(Path inputPath,
                  Long bytes,
                  Long records,
                  String prefix,
                  String suffix,
                  int lineWidth)

Split FASTA files.

Parameters:

inputPath - input path, if any

bytes - split the input path at next record after each n bytes, if any

records - split the input path after each n records, if any

prefix - output file prefix, must not be null

suffix - output file suffix, must not be null

lineWidth - line width

Since:

2.1

SplitFasta

public SplitFasta(File inputFile,
                  Long bytes,
                  Long records,
                  String prefix,
                  int leftPad,
                  String suffix,
                  int lineWidth)

Split FASTA files.

Parameters:

inputFile - input file, if any

bytes - split the input file at next record after each n bytes, if any

records - split the input file after each n records, if any

prefix - output file prefix, must not be null

leftPad - left pad split index in output file name

suffix - output file suffix, must not be null

lineWidth - line width

Since:

1.3.2

SplitFasta

public SplitFasta(Path inputPath,
                  Long bytes,
                  Long records,
                  String prefix,
                  int leftPad,
                  String suffix,
                  int lineWidth)

Split FASTA files.

Parameters:

inputPath - input path, if any

bytes - split the input path at next record after each n bytes, if any

records - split the input path after each n records, if any

prefix - output file prefix, must not be null

leftPad - left pad split index in output file name

suffix - output file suffix, must not be null

lineWidth - line width

Since:

2.1

SplitFasta

public SplitFasta(File inputFile,
                  String alphabet,
                  Long bytes,
                  Long records,
                  String prefix,
                  int leftPad,
                  String suffix,
                  int lineWidth)

Split FASTA files.

Parameters:

inputFile - input file, if any

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

bytes - split the input file at next record after each n bytes, if any

records - split the input file after each n records, if any

prefix - output file prefix, must not be null

leftPad - left pad split index in output file name

suffix - output file suffix, must not be null

lineWidth - line width

Since:

2.0

SplitFasta

public SplitFasta(Path inputPath,
                  String alphabet,
                  Long bytes,
                  Long records,
                  String prefix,
                  int leftPad,
                  String suffix,
                  int lineWidth)

Split FASTA files.

Parameters:

inputPath - input path, if any

alphabet - input path alphabet { dna, protein }, if any

bytes - split the input path at next record after each n bytes, if any

records - split the input path after each n records, if any

prefix - output file prefix, must not be null

leftPad - left pad split index in output file name

suffix - output file suffix, must not be null

lineWidth - line width

Since:

2.1

Method Detail

call

public Integer call()
             throws Exception

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)

getBaseName

static String getBaseName(Path path)

getFileExtensions

static String getFileExtensions(Path path)

main

public static void main(String[] args)

Main.

Parameters:

args - command line args