Uses of Class
org.jaga.individualRepresentation.proteinLocation.AminoAcid

Packages that use AminoAcid

org.jaga.individualRepresentation.proteinLocation
org.jaga.reproduction.proteinLocation

Uses of AminoAcid in org.jaga.individualRepresentation.proteinLocation

Fields in org.jaga.individualRepresentation.proteinLocation declared as AminoAcid

private static AminoAcid[]	SubstitutionScoringMatrix.allAcids
private AminoAcid[]	Protein.sequence
private static AminoAcid[]	AminoAcidFactory.allAminoAcids
private static AminoAcid[]	AminoAcidFactory.smallAminoAcids
private static AminoAcid[]	AminoAcidFactory.hydrophobicAminoAcids
private static AminoAcid[]	AminoAcidFactory.polarAminoAcids
private static AminoAcid[]	AminoAcidFactory.positiveAminoAcids
private static AminoAcid[]	AminoAcidFactory.negativeAminoAcids
private static AminoAcid[]	AminoAcidFactory.tinyAminoAcids
private static AminoAcid[]	AminoAcidFactory.aliphaticAminoAcids
private static AminoAcid[]	AminoAcidFactory.aromaticAminoAcids

Methods in org.jaga.individualRepresentation.proteinLocation that return AminoAcid

AminoAcid	SubstitutionScoringMatrix.chooseProbabalisticMutation(AminoAcid aminoAcid, GAParameterSet params)
AminoAcid	SubstitutionScoringMatrix.chooseProbabalisticMutation(java.lang.String aminoAcid, GAParameterSet params)
AminoAcid[]	Protein.getSequence()
AminoAcid[]	Protein.getSequenceReferencePerformanceHack()
AminoAcid	Protein.getResidue(int index)
AminoAcid	AminoAcidGroup.getResidue(int index)
AminoAcid	AminoAcidGroup.removeResidue(int index)
static AminoAcid	AminoAcidFactory.getResidueByCode(java.lang.String code)
static AminoAcid	AminoAcidFactory.getRandomResidueByProperty(int property, GAParameterSet params)
static AminoAcid	AminoAcidFactory.getRandomResidue(GAParameterSet params)
private static AminoAcid	AminoAcidFactory.getRandomAcid(AminoAcid[] list, RandomGenerator rnd)

Methods in org.jaga.individualRepresentation.proteinLocation with parameters of type AminoAcid

abstract int	SubstitutionScoringMatrix.getLogScore(AminoAcid aminoAcid1, AminoAcid aminoAcid2)
abstract double	SubstitutionScoringMatrix.getActualScore(AminoAcid aminoAcid1, AminoAcid aminoAcid2)
AminoAcid	SubstitutionScoringMatrix.chooseProbabalisticMutation(AminoAcid aminoAcid, GAParameterSet params)
boolean	SingleGap.doesntMatch(AminoAcid aminoAcid)
abstract boolean	PolypeptidePatternItem.doesntMatch(AminoAcid aminoAcid)
boolean	PolypeptidePattern.matchesPerformanceHack(AminoAcid[] sequence, int fromLocation)
int	Blosum62.getLogScore(AminoAcid aminoAcid1, AminoAcid aminoAcid2)
double	Blosum62.getActualScore(AminoAcid aminoAcid1, AminoAcid aminoAcid2)
boolean	AminoAcidProperty.doesntMatch(AminoAcid aminoAcid)
boolean	AminoAcidGroup.doesntMatch(AminoAcid aminoAcid)
void	AminoAcidGroup.swapResidue(int index, AminoAcid newAminoAcid)
void	AminoAcidGroup.addResidue(AminoAcid aminoAcid)
private void	AminoAcidGroup.addAcidToStats(AminoAcid aminoAcid)
private void	AminoAcidGroup.removeAcidFromStats(AminoAcid aminoAcid)
private static AminoAcid	AminoAcidFactory.getRandomAcid(AminoAcid[] list, RandomGenerator rnd)
boolean	AminoAcid.doesntMatch(AminoAcid aminoAcid)

Constructors in org.jaga.individualRepresentation.proteinLocation with parameters of type AminoAcid

Protein(java.lang.String name, AminoAcid[] sequence)

Uses of AminoAcid in org.jaga.reproduction.proteinLocation

Methods in org.jaga.reproduction.proteinLocation with parameters of type AminoAcid

private PolypeptidePatternItem[]

PolypeptidePatternMutation.mutateItem(AminoAcid aAcid, GAParameterSet params)