Uses of Interface
com.milaboratory.core.mutations.generator.NucleotideMutationModel

Packages that use NucleotideMutationModel

Package	Description
com.milaboratory.core.alignment.benchmark
com.milaboratory.core.mutations.generator

Uses of NucleotideMutationModel in com.milaboratory.core.alignment.benchmark

Constructors in com.milaboratory.core.alignment.benchmark with parameters of type NucleotideMutationModel

Constructor and Description

ChallengeParameters(int dbSize, int dbMinSeqLength, int dbMaxSeqLength, int queryCount, int falseCount, int minClusters, int maxClusters, int minClusterLength, int maxClusterLength, int minIndelLength, int maxIndelLength, double insertionProbability, double deletionProbability, double boundaryInsertProbability, NucleotideMutationModel mutationModel, int minAlignmentScoring, int maxAlignmentScoring, AffineGapAlignmentScoring<NucleotideSequence> scoring)

Uses of NucleotideMutationModel in com.milaboratory.core.mutations.generator

Classes in com.milaboratory.core.mutations.generator that implement NucleotideMutationModel

Modifier and Type	Class and Description
class	GenericNucleotideMutationModel

Methods in com.milaboratory.core.mutations.generator that return NucleotideMutationModel

Modifier and Type	Method and Description
NucleotideMutationModel	NucleotideMutationModel.clone() Clones only parameters, the state is generated randomly.
NucleotideMutationModel	GenericNucleotideMutationModel.clone()
static NucleotideMutationModel	MutationModels.getEmpiricalNucleotideMutationModel()
static NucleotideMutationModel	MutationModels.getEmpiricalNucleotideMutationModelWithNoise(org.apache.commons.math3.random.RandomGenerator rd, double minFactor, double maxFactor)
NucleotideMutationModel	NucleotideMutationModel.multiplyProbabilities(double factor)

Methods in com.milaboratory.core.mutations.generator with parameters of type NucleotideMutationModel

Modifier and Type	Method and Description
static Mutations<NucleotideSequence>	MutationsGenerator.generateMutations(NucleotideSequence sequence, NucleotideMutationModel model)
static Mutations<NucleotideSequence>	MutationsGenerator.generateMutations(NucleotideSequence sequence, NucleotideMutationModel model, int from, int to)
static Mutations<NucleotideSequence>	MutationsGenerator.generateMutations(NucleotideSequence sequence, NucleotideMutationModel model, Range range)