uni.bielefeld.cmg.sparkhit.pipeline

Class OnePipe

java.lang.Object

uni.bielefeld.cmg.sparkhit.pipeline.OnePipe

All Implemented Interfaces:

java.lang.Runnable, Pipeline

public class OnePipe
extends java.lang.Object
implements Pipeline, java.lang.Runnable

Returns an object for managing one thread of the pipeline. This class is used in local mode only. For cluster mode, Spark RDD is used to parallelize the tasks.

See Also:

Field Summary

Fields

Modifier and Type	Field and Description
FastqUnitBuffer	inputBufferedFastqUnit
java.io.BufferedReader	inputBufferedReader
java.io.BufferedWriter	outputBufferedWriter
DefaultParam	param
readInfo	read

Constructor Summary

Constructors

Constructor and Description
OnePipe(java.lang.String threadName) A constructor that construct an object of OnePipe class.

Method Summary

Methods

Modifier and Type	Method and Description
void	join() wait util all threads finish.
void	run() This method runs the fragment recruitment pipeline within this thread.
void	setInput(java.io.BufferedReader InputRead) This method sets the buffer for loading input data.
void	setInputFastqUnitBuffer(FastqUnitBuffer inputBufferedFastqUnit) This method sets the buffer for loading fastq units.
void	setMatrix(ScoreMatrix matrix) This method sets the scoring matrix for sequence alignment.
void	setOutput(java.io.BufferedWriter OutputWrite) This method sets the buffer for writing output data.
void	setParameter(DefaultParam param) This method sets the input parameters.
void	setStruct(RefStructBuilder ref) This method sets the reference index.
void	start() the pipeline starts by calling the thread start() function

Methods inherited from class java.lang.Object

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

Field Detail

param

public DefaultParam param

inputBufferedReader

public java.io.BufferedReader inputBufferedReader

outputBufferedWriter

public java.io.BufferedWriter outputBufferedWriter

inputBufferedFastqUnit

public FastqUnitBuffer inputBufferedFastqUnit

read

public readInfo read

Constructor Detail

OnePipe

public OnePipe(java.lang.String threadName)

A constructor that construct an object of OnePipe class.

Parameters:

threadName - the index of this thread.

Method Detail

start

public void start()

the pipeline starts by calling the thread start() function

join

public void join()

wait util all threads finish.

run

public void run()

This method runs the fragment recruitment pipeline within this thread.

Specified by:

run in interface java.lang.Runnable

setInputFastqUnitBuffer

public void setInputFastqUnitBuffer(FastqUnitBuffer inputBufferedFastqUnit)

This method sets the buffer for loading fastq units.

Parameters:

inputBufferedFastqUnit -

setMatrix

public void setMatrix(ScoreMatrix matrix)

This method sets the scoring matrix for sequence alignment.

Parameters:

matrix - ScoreMatrix.

setStruct

public void setStruct(RefStructBuilder ref)

This method sets the reference index.

Parameters:

ref - RefStructBuilder the reference index.

setParameter

public void setParameter(DefaultParam param)

This method sets the input parameters.

Specified by:

setParameter in interface Pipeline

Parameters:

param - DefaultParam is the object for command line parameters.

setInput

public void setInput(java.io.BufferedReader InputRead)

This method sets the buffer for loading input data.

Specified by:

setInput in interface Pipeline

Parameters:

InputRead - a BufferedReader to read input data.

setOutput

public void setOutput(java.io.BufferedWriter OutputWrite)

This method sets the buffer for writing output data.

Specified by:

setOutput in interface Pipeline

Parameters:

OutputWrite - a BufferedWriter to write to an output file.