com.milaboratory.core.alignment.benchmark

Class ChallengeProvider

java.lang.Object

com.milaboratory.core.alignment.benchmark.ChallengeProvider

All Implemented Interfaces:

cc.redberry.pipe.OutputPort<Challenge>

public final class ChallengeProvider
extends Object
implements cc.redberry.pipe.OutputPort<Challenge>

Created by dbolotin on 27/10/15.

Field Summary

Fields

Modifier and Type	Field and Description
static int	MAX_RERUNS

Constructor Summary

Constructors

Constructor and Description
ChallengeProvider(ChallengeParameters parameters, long seed)

Method Summary

Methods

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>> S	randomSequence(Alphabet<S> alphabet, org.apache.commons.math3.random.RandomDataGenerator r, int minLength, int maxLength, boolean basicLettersOnly)
static <S extends Sequence<S>> S	randomSequence(Alphabet<S> alphabet, org.apache.commons.math3.random.RandomGenerator r, int minLength, int maxLength, boolean basicLettersOnly)
Challenge	take()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

MAX_RERUNS

public static int MAX_RERUNS

Constructor Detail

ChallengeProvider

public ChallengeProvider(ChallengeParameters parameters,
                 long seed)

Method Detail

take

public Challenge take()

Specified by:

take in interface cc.redberry.pipe.OutputPort<Challenge>

generateDB

public static NucleotideSequence[] generateDB(org.apache.commons.math3.random.RandomDataGenerator generator,
                              ChallengeParameters params)

randomSequence

public static <S extends Sequence<S>> S randomSequence(Alphabet<S> alphabet,
                                       org.apache.commons.math3.random.RandomDataGenerator r,
                                       int minLength,
                                       int maxLength,
                                       boolean basicLettersOnly)

randomSequence

public static <S extends Sequence<S>> S randomSequence(Alphabet<S> alphabet,
                                       org.apache.commons.math3.random.RandomGenerator r,
                                       int minLength,
                                       int maxLength,
                                       boolean basicLettersOnly)

getParams1NoGap

public static ChallengeParameters getParams1NoGap(AffineGapAlignmentScoring<NucleotideSequence> scoring,
                                  int minAlignmentScoring,
                                  int maxAlignmentScoring,
                                  double multiplier)

getParamsOneCluster

public static ChallengeParameters getParamsOneCluster(AffineGapAlignmentScoring<NucleotideSequence> scoring,
                                      int minAlignmentScoring,
                                      int maxAlignmentScoring,
                                      double multiplier)

getParamsTwoClusters

public static ChallengeParameters getParamsTwoClusters(AffineGapAlignmentScoring<NucleotideSequence> scoring,
                                       int minAlignmentScoring,
                                       int maxAlignmentScoring,
                                       double multiplier)