com.milaboratory.core.alignment

Class LinearGapAlignmentScoring<S extends Sequence<S>>

java.lang.Object

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

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

All Implemented Interfaces:

AlignmentScoring<S>, Serializable

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

LinearGapAlignmentScoring - scoring system which uses penalty for gap

See Also:

Serialized Form

Nested Class Summary

Nested Classes

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

Field Summary

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

alphabet, subsMatrix, subsMatrixActual

Constructor Summary

Constructors

Constructor and Description
LinearGapAlignmentScoring(Alphabet<S> alphabet, int[] subsMatrix, int gapPenalty) Creates new LinearGapAlignmentScoring
LinearGapAlignmentScoring(Alphabet<S> alphabet, int match, int mismatch, int gap) Returns scoring with uniform match and mismatch scores
LinearGapAlignmentScoring(Alphabet<S> alphabet, com.milaboratory.core.alignment.SubstitutionMatrix subsMatrix, int gapPenalty)

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(Object o)
static LinearGapAlignmentScoring<AminoAcidSequence>	getAminoAcidBLASTScoring(BLASTMatrix matrix) Returns standard amino acid BLAST scoring with #gapPenalty=5
static LinearGapAlignmentScoring<AminoAcidSequence>	getAminoAcidBLASTScoring(BLASTMatrix matrix, int gapPenalty) Returns standard amino acid BLAST scoring
int	getGapPenalty() Returns penalty score for gap
static LinearGapAlignmentScoring<NucleotideSequence>	getNucleotideBLASTScoring() Returns standard Nucleotide BLAST scoring with #gapPenalty=5
static LinearGapAlignmentScoring<NucleotideSequence>	getNucleotideBLASTScoring(int gapPenalty) Returns standard Nucleotide BLAST scoring
int	hashCode()
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

Constructor Detail

LinearGapAlignmentScoring

public LinearGapAlignmentScoring(Alphabet<S> alphabet,
                         com.milaboratory.core.alignment.SubstitutionMatrix subsMatrix,
                         int gapPenalty)

LinearGapAlignmentScoring

public LinearGapAlignmentScoring(Alphabet<S> alphabet,
                         int[] subsMatrix,
                         int gapPenalty)

Creates new LinearGapAlignmentScoring

Parameters:

alphabet - alphabet to be used

subsMatrix - substitution matrix to be used

gapPenalty - penalty for gap, must be < 0

LinearGapAlignmentScoring

public LinearGapAlignmentScoring(Alphabet<S> alphabet,
                         int match,
                         int mismatch,
                         int gap)

Returns scoring with uniform match and mismatch scores

Parameters:

alphabet - alphabet

match - match score > 0

mismatch - mismatch score < 0

gap - gap penalty < 0

Method Detail

getGapPenalty

public int getGapPenalty()

Returns penalty score for gap

Returns:

penalty score for gap

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 LinearGapAlignmentScoring<NucleotideSequence> getNucleotideBLASTScoring()

Returns standard Nucleotide BLAST scoring with #gapPenalty=5

Returns:

standard Nucleotide BLAST Scoring

getNucleotideBLASTScoring

public static LinearGapAlignmentScoring<NucleotideSequence> getNucleotideBLASTScoring(int gapPenalty)

Returns standard Nucleotide BLAST scoring

Parameters:

gapPenalty - penalty for gap value

Returns:

standard Nucleotide BLAST scoring

getAminoAcidBLASTScoring

public static LinearGapAlignmentScoring<AminoAcidSequence> getAminoAcidBLASTScoring(BLASTMatrix matrix)

Returns standard amino acid BLAST scoring with #gapPenalty=5

Parameters:

matrix - BLAST substitution matrix

Returns:

standard amino acid BLAST scoring

getAminoAcidBLASTScoring

public static LinearGapAlignmentScoring<AminoAcidSequence> getAminoAcidBLASTScoring(BLASTMatrix matrix,
                                                                    int gapPenalty)

Returns standard amino acid BLAST scoring

Parameters:

matrix - BLAST substitution matrix

gapPenalty - penalty for gap, must be < 0

Returns:

standard amino acid BLAST scoring

writeReplace

protected Object writeReplace()
                       throws ObjectStreamException

Throws:

ObjectStreamException