org.dishevelled.bio.tools

Class AbstractSplit

java.lang.Object

org.dishevelled.bio.tools.AbstractSplit

All Implemented Interfaces:

Callable<Integer>

Direct Known Subclasses:

SplitBed, SplitFasta, SplitFastq, SplitGaf, SplitGff3, SplitInterleavedFastq, SplitPaf, SplitSam, SplitVcf

abstract class AbstractSplit
extends Object
implements Callable<Integer>

Abstract split callable.

Author:

Michael Heuer

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static class	AbstractSplit.CountingWriter Counting writer.

Field Summary

Fields

Modifier and Type	Field and Description
protected long	bytes Split the input path at the next record after each n bytes, if any.
protected Path	inputPath Input path, if any.
protected long	records Split the input path after each n records, if any.

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractSplit(Path inputPath, Long bytes, Long records, String prefix, int leftPad, String suffix) Abstract split callable.

Method Summary

Modifier and Type	Method and Description
protected void	closeWriters() Attempt to close writers created by createCountingWriter.
protected AbstractSplit.CountingWriter	createCountingWriter(int n) Create and return a new CountingWriter for a file name consisting of prefix + n + suffix.
(package private) static String	getFileExtension(Path path)
(package private) static String	getNameWithoutExtension(Path path)
protected String	leftPad(int n) Left pad the specified split index.
(package private) static long	toBytes(String b) Parse the specified byte string (e.g.

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.concurrent.Callable

call

Field Detail

inputPath

protected final Path inputPath

Input path, if any.

bytes

protected final long bytes

Split the input path at the next record after each n bytes, if any.

records

protected final long records

Split the input path after each n records, if any.

Constructor Detail

AbstractSplit

protected AbstractSplit(Path inputPath,
                        Long bytes,
                        Long records,
                        String prefix,
                        int leftPad,
                        String suffix)

Abstract split callable.

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

Method Detail

closeWriters

protected final void closeWriters()

Attempt to close writers created by createCountingWriter.

leftPad

protected final String leftPad(int n)

Left pad the specified split index.

Parameters:

n - split index to left pad

Returns:

the specified index left padded by zeros

createCountingWriter

protected final AbstractSplit.CountingWriter createCountingWriter(int n)

Create and return a new CountingWriter for a file name consisting of prefix + n + suffix.

Parameters:

n - n

Returns:

a new CountingWriter for a file name consisting of prefix + n + suffix

toBytes

static long toBytes(String b)

Parse the specified byte string (e.g. 100gb) into a long number of bytes.

Parameters:

b - byte string to parse, must not be null or empty

Returns:

the specified byte string parsed into a long number of bytes

getNameWithoutExtension

static String getNameWithoutExtension(Path path)

getFileExtension

static String getFileExtension(Path path)