| Package | Description |
|---|---|
| com.milaboratory.core.alignment.benchmark | |
| com.milaboratory.core.mutations.generator |
| 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) |
| Modifier and Type | Class and Description |
|---|---|
class |
GenericNucleotideMutationModel |
| 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) |
| 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) |
Copyright © 2018. All rights reserved.