com.milaboratory.core.merger

Class MergerParameters

java.lang.Object

com.milaboratory.core.merger.MergerParameters

All Implemented Interfaces:

Serializable

public final class MergerParameters
extends Object
implements Serializable

Author:

Dmitry Bolotin, Stanislav Poslavsky

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	MergerParameters.IdentityType

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_MAX_QUALITY_VALUE

Constructor Summary

Constructors

Constructor and Description
MergerParameters(QualityMergingAlgorithm qualityMergingAlgorithm, PairedEndReadsLayout partsLayout, int minimalOverlap, Integer maxQuality, double minimalIdentity, MergerParameters.IdentityType identityType)

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(Object o)
MergerParameters.IdentityType	getIdentityType()
int	getMaxQuality()
double	getMinimalIdentity()
int	getMinimalOverlap()
PairedEndReadsLayout	getPartsLayout()
QualityMergingAlgorithm	getQualityMergingAlgorithm()
int	hashCode()
MergerParameters	overrideMinimalIdentity(double newIdentity)
MergerParameters	overrideReadsLayout(PairedEndReadsLayout partsLayout)

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_MAX_QUALITY_VALUE

public static final int DEFAULT_MAX_QUALITY_VALUE

See Also:

Constant Field Values

Constructor Detail

MergerParameters

public MergerParameters(QualityMergingAlgorithm qualityMergingAlgorithm,
                PairedEndReadsLayout partsLayout,
                int minimalOverlap,
                Integer maxQuality,
                double minimalIdentity,
                MergerParameters.IdentityType identityType)

Method Detail

getMinimalOverlap

public int getMinimalOverlap()

getMinimalIdentity

public double getMinimalIdentity()

getMaxQuality

public int getMaxQuality()

getQualityMergingAlgorithm

public QualityMergingAlgorithm getQualityMergingAlgorithm()

getPartsLayout

public PairedEndReadsLayout getPartsLayout()

getIdentityType

public MergerParameters.IdentityType getIdentityType()

overrideReadsLayout

public MergerParameters overrideReadsLayout(PairedEndReadsLayout partsLayout)

overrideMinimalIdentity

public MergerParameters overrideMinimalIdentity(double newIdentity)

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object