uni.bielefeld.cmg.reflexiv.util

Class DefaultParam

java.lang.Object

uni.bielefeld.cmg.reflexiv.util.DefaultParam

All Implemented Interfaces:

java.io.Serializable

public class DefaultParam
extends java.lang.Object
implements java.io.Serializable

A data structure class that stores all default parameters.

See Also:

, Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
boolean	bubble
boolean	cache
int	endClip
int	frontClip
java.lang.String	inputContigPath
java.lang.String	inputFaPath
java.lang.String	inputFqPath
java.lang.String	inputKmerPath
int	kmerBits
int	kmerOverlap
int	kmerSize
int	maximumIteration
int	maxKmerCoverage
java.lang.String	mightyName
int	minContig
int	minErrorCoverage
int	minimumIteration
int	minKmerCoverage
int	minReadSize
java.lang.String	outputPath
int	partitions
int	subKmerSize

Constructor Summary

Constructors

Constructor and Description
DefaultParam() A constructor that construct an object of DefaultParam class.

Method Summary

Methods

Modifier and Type	Method and Description
void	setKmerOverlap(int o) This method initiates the overlap between k-mers.
void	setKmerSize(int k) This method initiates the K-mer size parameter.
void	setMinErrorCoverage(int s) This method initiates the minimal coverage for error correction.
void	setSubKmerSize(int s) This method initiates the sub K-mer size parameter.

Methods inherited from class java.lang.Object

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

Field Detail

mightyName

public java.lang.String mightyName

inputFqPath

public java.lang.String inputFqPath

inputKmerPath

public java.lang.String inputKmerPath

inputFaPath

public java.lang.String inputFaPath

inputContigPath

public java.lang.String inputContigPath

outputPath

public java.lang.String outputPath

kmerSize

public int kmerSize

subKmerSize

public int subKmerSize

kmerBits

public int kmerBits

kmerOverlap

public int kmerOverlap

minReadSize

public int minReadSize

minKmerCoverage

public int minKmerCoverage

maxKmerCoverage

public int maxKmerCoverage

minErrorCoverage

public int minErrorCoverage

minContig

public int minContig

bubble

public boolean bubble

cache

public boolean cache

partitions

public int partitions

maximumIteration

public int maximumIteration

minimumIteration

public int minimumIteration

frontClip

public int frontClip

endClip

public int endClip

Constructor Detail

DefaultParam

public DefaultParam()

A constructor that construct an object of DefaultParam class.

Method Detail

setKmerSize

public void setKmerSize(int k)

This method initiates the K-mer size parameter.

Parameters:

k - the size of the k-mer.

setSubKmerSize

public void setSubKmerSize(int s)

This method initiates the sub K-mer size parameter.

Parameters:

s - the size of the sub k-mer.

setMinErrorCoverage

public void setMinErrorCoverage(int s)

This method initiates the minimal coverage for error correction.

Parameters:

s - the minimal size for error correction.

setKmerOverlap

public void setKmerOverlap(int o)

This method initiates the overlap between k-mers.

Parameters:

o - the size of the overlap between k-mers.