com.milaboratory.core.alignment

Class AbstractAlignmentScoring<S extends Sequence<S>>

java.lang.Object

com.milaboratory.core.alignment.AbstractAlignmentScoring<S>

Type Parameters:

S - type of sequences to be aligned using scoring system

All Implemented Interfaces:

AlignmentScoring<S>, Serializable

Direct Known Subclasses:

AffineGapAlignmentScoring, LinearGapAlignmentScoring

public class AbstractAlignmentScoring<S extends Sequence<S>>
extends Object
implements AlignmentScoring<S>

AbstractAlignmentScoring - abstract scoring system class used for alignment procedure.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected Alphabet<S>	alphabet Link to alphabet
protected com.milaboratory.core.alignment.SubstitutionMatrix	subsMatrix Stores information about how the object was created.
protected int[]	subsMatrixActual Actual substitution matrix

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractAlignmentScoring(Alphabet<S> alphabet, com.milaboratory.core.alignment.SubstitutionMatrix subsMatrix) Abstract class constructor.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(Object o)
Alphabet<S>	getAlphabet() Returns alphabet
int	getMaximalMatchScore()
int	getMaximalMismatchScore()
int	getMinimalMatchScore()
int	getMinimalMismatchScore()
int	getScore(byte from, byte to) Returns score value for specified alphabet letter codes
int	hashCode()
boolean	uniformBasicMatchScore() Returns @code{true} if @code{getScore(i, i)} returns the same score for all basic letters values of @code{i}.

Methods inherited from class java.lang.Object

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

Field Detail

alphabet

protected final Alphabet<S extends Sequence<S>> alphabet

Link to alphabet

subsMatrix

protected final com.milaboratory.core.alignment.SubstitutionMatrix subsMatrix

Stores information about how the object was created. subsMatrixActual used for actual calculations

subsMatrixActual

protected final int[] subsMatrixActual

Actual substitution matrix

Constructor Detail

AbstractAlignmentScoring

protected AbstractAlignmentScoring(Alphabet<S> alphabet,
                        com.milaboratory.core.alignment.SubstitutionMatrix subsMatrix)

Abstract class constructor. Used in deserialization.

Initializes substitution matrix to null and uniformBasicMatch to true

Parameters:

alphabet - alphabet to be used by scoring system

Method Detail

getScore

public int getScore(byte from,
           byte to)

Returns score value for specified alphabet letter codes

Specified by:

getScore in interface AlignmentScoring<S extends Sequence<S>>

Parameters:

from - code of letter which is to be replaced

to - code of letter which is replacing

Returns:

score value

getAlphabet

public Alphabet<S> getAlphabet()

Returns alphabet

Specified by:

getAlphabet in interface AlignmentScoring<S extends Sequence<S>>

Returns:

alphabet

uniformBasicMatchScore

public boolean uniformBasicMatchScore()

Returns @code{true} if @code{getScore(i, i)} returns the same score for all basic letters values of @code{i}.

Returns:

@code{true} if @code{getScore(i, i)} returns the same score for all basic letters values of @code{i}

getMinimalMatchScore

public int getMinimalMatchScore()

Specified by:

getMinimalMatchScore in interface AlignmentScoring<S extends Sequence<S>>

getMaximalMatchScore

public int getMaximalMatchScore()

Specified by:

getMaximalMatchScore in interface AlignmentScoring<S extends Sequence<S>>

getMinimalMismatchScore

public int getMinimalMismatchScore()

Specified by:

getMinimalMismatchScore in interface AlignmentScoring<S extends Sequence<S>>

getMaximalMismatchScore

public int getMaximalMismatchScore()

Specified by:

getMaximalMismatchScore in interface AlignmentScoring<S extends Sequence<S>>

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object