| Modifier and Type | Field and Description |
|---|---|
static int |
MAX_RERUNS |
| Constructor and Description |
|---|
ChallengeProvider(ChallengeParameters parameters,
long seed) |
| Modifier and Type | Method and Description |
|---|---|
static NucleotideSequence[] |
generateDB(org.apache.commons.math3.random.RandomDataGenerator generator,
ChallengeParameters params) |
static ChallengeParameters |
getParams1NoGap(AffineGapAlignmentScoring<NucleotideSequence> scoring,
int minAlignmentScoring,
int maxAlignmentScoring,
double multiplier) |
static ChallengeParameters |
getParamsOneCluster(AffineGapAlignmentScoring<NucleotideSequence> scoring,
int minAlignmentScoring,
int maxAlignmentScoring,
double multiplier) |
static ChallengeParameters |
getParamsTwoClusters(AffineGapAlignmentScoring<NucleotideSequence> scoring,
int minAlignmentScoring,
int maxAlignmentScoring,
double multiplier) |
static <S extends Sequence<S>> |
randomSequence(Alphabet<S> alphabet,
org.apache.commons.math3.random.RandomDataGenerator r,
int minLength,
int maxLength,
boolean basicLettersOnly) |
static <S extends Sequence<S>> |
randomSequence(Alphabet<S> alphabet,
org.apache.commons.math3.random.RandomGenerator r,
int minLength,
int maxLength,
boolean basicLettersOnly) |
Challenge |
take() |
public ChallengeProvider(ChallengeParameters parameters, long seed)
public static NucleotideSequence[] generateDB(org.apache.commons.math3.random.RandomDataGenerator generator, ChallengeParameters params)
public static <S extends Sequence<S>> S randomSequence(Alphabet<S> alphabet, org.apache.commons.math3.random.RandomDataGenerator r, int minLength, int maxLength, boolean basicLettersOnly)
public static <S extends Sequence<S>> S randomSequence(Alphabet<S> alphabet, org.apache.commons.math3.random.RandomGenerator r, int minLength, int maxLength, boolean basicLettersOnly)
public static ChallengeParameters getParams1NoGap(AffineGapAlignmentScoring<NucleotideSequence> scoring, int minAlignmentScoring, int maxAlignmentScoring, double multiplier)
public static ChallengeParameters getParamsOneCluster(AffineGapAlignmentScoring<NucleotideSequence> scoring, int minAlignmentScoring, int maxAlignmentScoring, double multiplier)
public static ChallengeParameters getParamsTwoClusters(AffineGapAlignmentScoring<NucleotideSequence> scoring, int minAlignmentScoring, int maxAlignmentScoring, double multiplier)
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