com.milaboratory.core.alignment

Class AffineGapAlignmentScoring<S extends Sequence<S>>

java.lang.Object

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

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

Type Parameters:

S - type of sequences to be aligned using this scoring

All Implemented Interfaces:

AlignmentScoring<S>, Serializable

public final class AffineGapAlignmentScoring<S extends Sequence<S>>
extends AbstractAlignmentScoring<S>
implements Serializable

AffineGapAlignmentScoring - scoring which uses different penalties for gap opening and gap extension

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static class	AffineGapAlignmentScoring.SerializationObject

Field Summary

Fields

Modifier and Type	Field and Description
static AffineGapAlignmentScoring<NucleotideSequence>	IGBLAST_NUCLEOTIDE_SCORING Scoring as used in IgBlast for alignments of V genes
static int	IGBLAST_NUCLEOTIDE_SCORING_THRESHOLD Scoring threshold as used in IgBlast for alignments of V genes

Fields inherited from class com.milaboratory.core.alignment.AbstractAlignmentScoring

alphabet, subsMatrix, subsMatrixActual

Constructor Summary

Constructors

Constructor and Description
AffineGapAlignmentScoring(Alphabet<S> alphabet, int[] subsMatrix, int gapOpenPenalty, int gapExtensionPenalty) Creates new AffineGapScoring
AffineGapAlignmentScoring(Alphabet<S> alphabet, int match, int mismatch, int gapOpen, int gapExtension) Creates scoring with uniform match and mismatch scores
AffineGapAlignmentScoring(Alphabet<S> alphabet, com.milaboratory.core.alignment.SubstitutionMatrix subsMatrix, int gapOpenPenalty, int gapExtensionPenalty)

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(Object o)
int	getAffineGapPenalty(int l) Returns score value for a gap with length l
static AffineGapAlignmentScoring<AminoAcidSequence>	getAminoAcidBLASTScoring(BLASTMatrix matrix) Returns standard AminoAcid BLAST scoring (#gapOpenPenalty=-10, #gapExtensionPenalty=-1)
static AffineGapAlignmentScoring<AminoAcidSequence>	getAminoAcidBLASTScoring(BLASTMatrix matrix, int gapOpenPenalty, int gapExtensionPenalty) Returns AminoAcid BLAST scoring
int	getGapExtensionPenalty() Returns penalty value for extending gap
int	getGapOpenPenalty() Returns penalty value for opening gap
static AffineGapAlignmentScoring<NucleotideSequence>	getNucleotideBLASTScoring() Returns standard Nucleotide BLAST scoring (#gapOpenPenalty=-10, #gapExtensionPenalty=-1)
static AffineGapAlignmentScoring<NucleotideSequence>	getNucleotideBLASTScoring(int gapOpenPenalty, int gapExtensionPenalty) Returns Nucleotide BLAST scoring
int	hashCode()
AffineGapAlignmentScoring<S>	setGapExtensionScore(int gapExtensionPenalty)
AffineGapAlignmentScoring<S>	setGapOpenScore(int gapOpenPenalty)
AffineGapAlignmentScoring<S>	setMatchScore(int matchScore)
AffineGapAlignmentScoring<S>	setMismatchScore(int mismatchScore)
protected Object	writeReplace()

Methods inherited from class com.milaboratory.core.alignment.AbstractAlignmentScoring

getAlphabet, getMaximalMatchScore, getMaximalMismatchScore, getMinimalMatchScore, getMinimalMismatchScore, getScore, uniformBasicMatchScore

Methods inherited from class java.lang.Object

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

Field Detail

IGBLAST_NUCLEOTIDE_SCORING

public static final AffineGapAlignmentScoring<NucleotideSequence> IGBLAST_NUCLEOTIDE_SCORING

Scoring as used in IgBlast for alignments of V genes

IGBLAST_NUCLEOTIDE_SCORING_THRESHOLD

public static final int IGBLAST_NUCLEOTIDE_SCORING_THRESHOLD

Scoring threshold as used in IgBlast for alignments of V genes

See Also:

Constant Field Values

Constructor Detail

AffineGapAlignmentScoring

public AffineGapAlignmentScoring(Alphabet<S> alphabet,
                         com.milaboratory.core.alignment.SubstitutionMatrix subsMatrix,
                         int gapOpenPenalty,
                         int gapExtensionPenalty)

AffineGapAlignmentScoring

public AffineGapAlignmentScoring(Alphabet<S> alphabet,
                         int[] subsMatrix,
                         int gapOpenPenalty,
                         int gapExtensionPenalty)

Creates new AffineGapScoring

Parameters:

alphabet - alphabet to be used

subsMatrix - substitution matrix to be used

gapOpenPenalty - penalty for opening gap

gapExtensionPenalty - penalty for extending gap

AffineGapAlignmentScoring

public AffineGapAlignmentScoring(Alphabet<S> alphabet,
                         int match,
                         int mismatch,
                         int gapOpen,
                         int gapExtension)

Creates scoring with uniform match and mismatch scores

Parameters:

alphabet - alphabet

match - match score > 0

mismatch - mismatch score < 0

gapOpen - gap open score < 0

gapExtension - gap extend score < 0

Method Detail

getAffineGapPenalty

public int getAffineGapPenalty(int l)

Returns score value for a gap with length l

Parameters:

l - lenth of gap

Returns:

score value

getGapOpenPenalty

public int getGapOpenPenalty()

Returns penalty value for opening gap

Returns:

penalty value for opening gap

getGapExtensionPenalty

public int getGapExtensionPenalty()

Returns penalty value for extending gap

Returns:

penalty value for extending gap

setMatchScore

public AffineGapAlignmentScoring<S> setMatchScore(int matchScore)

setMismatchScore

public AffineGapAlignmentScoring<S> setMismatchScore(int mismatchScore)

setGapOpenScore

public AffineGapAlignmentScoring<S> setGapOpenScore(int gapOpenPenalty)

setGapExtensionScore

public AffineGapAlignmentScoring<S> setGapExtensionScore(int gapExtensionPenalty)

equals

public boolean equals(Object o)

Overrides:

equals in class AbstractAlignmentScoring<S extends Sequence<S>>

hashCode

public int hashCode()

Overrides:

hashCode in class AbstractAlignmentScoring<S extends Sequence<S>>

getNucleotideBLASTScoring

public static AffineGapAlignmentScoring<NucleotideSequence> getNucleotideBLASTScoring()

Returns standard Nucleotide BLAST scoring (#gapOpenPenalty=-10, #gapExtensionPenalty=-1)

Returns:

standard Nucleotide BLAST scoring

getNucleotideBLASTScoring

public static AffineGapAlignmentScoring<NucleotideSequence> getNucleotideBLASTScoring(int gapOpenPenalty,
                                                                      int gapExtensionPenalty)

Returns Nucleotide BLAST scoring

Parameters:

gapOpenPenalty - penalty for opening gap to be used in system

gapExtensionPenalty - penalty for extending gap to be used in system

Returns:

Nucleotide BLAST scoring

getAminoAcidBLASTScoring

public static AffineGapAlignmentScoring<AminoAcidSequence> getAminoAcidBLASTScoring(BLASTMatrix matrix)

Returns standard AminoAcid BLAST scoring (#gapOpenPenalty=-10, #gapExtensionPenalty=-1)

Parameters:

matrix - BLAST substitution matrix to be used

Returns:

standard AminoAcid BLAST scoring

getAminoAcidBLASTScoring

public static AffineGapAlignmentScoring<AminoAcidSequence> getAminoAcidBLASTScoring(BLASTMatrix matrix,
                                                                    int gapOpenPenalty,
                                                                    int gapExtensionPenalty)

Returns AminoAcid BLAST scoring

Parameters:

matrix - BLAST substitution matrix to be used

gapOpenPenalty - penalty for opening gap to be used in system

gapExtensionPenalty - penalty for extending gap to be used in system

Returns:

AminoAcid BLAST scoring

writeReplace

protected Object writeReplace()
                       throws ObjectStreamException

Throws:

ObjectStreamException