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## M

makeRanged() - Method in class de.jstacs.parameters.ParameterSet
  Replaces all `Parameter`s in this `ParameterSet` by their equivalents implementing the `Rangeable` interface.
MappedDiscreteSequence - Class in de.jstacs.data.sequences
  This class allows to map a discrete `Sequence` to an new `Sequence` using some `DiscreteAlphabetMapping`s.
MappedDiscreteSequence(AlphabetContainer, SequenceAnnotation[], DiscreteAlphabetMapping...) - Constructor for class de.jstacs.data.sequences.MappedDiscreteSequence
  This method allows to create an empty `MappedDiscreteSequence`.
MappedDiscreteSequence(SimpleDiscreteSequence, DiscreteAlphabetMapping...) - Constructor for class de.jstacs.data.sequences.MappedDiscreteSequence
  This method allows to create a `MappedDiscreteSequence` from a given `Sequence` and some given `DiscreteAlphabetMapping`s.
MappingClassifier - Class in de.jstacs.classifier
  This class allows the user to train the classifier on a given number of classes and to evaluate the classifier on a smaller number of classes by mapping classes together.
MappingClassifier(AbstractScoreBasedClassifier, int...) - Constructor for class de.jstacs.classifier.MappingClassifier
  Creates a new `MappingClassifier` from a given classifier and a class mapping.
MappingClassifier(StringBuffer) - Constructor for class de.jstacs.classifier.MappingClassifier
  The standard constructor for the interface `Storable`.
mapSample(Sample[]) - Method in class de.jstacs.classifier.MappingClassifier
  This method maps the given `Sample`s to the internal classes.
matches(int, Sequence) - Method in class de.jstacs.data.Sequence
  This method allows to answer the question whether there is a similar pattern find a match with a given maximal number of mismatches.
max(double[], int, int) - Static method in class de.jstacs.models.mixture.AbstractMixtureModel
  This method returns the index of a maximal entry in the array `w` between index `start` and `end`.
max - Variable in class de.jstacs.scoringFunctions.mix.motifSearch.DurationScoringFunction
  The maximal value.
max - Variable in class de.jstacs.utils.DefaultProgressUpdater
  The maximal number of steps.
max(double[]) - Static method in class de.jstacs.utils.ToolBox
  This method returns the maximum of the elements of an `array`.
max(int, int, double[]) - Static method in class de.jstacs.utils.ToolBox
  This method returns the maximum of the elements of an `array` between `start` and `end`.
MAXIMALBRANCHING - Static variable in class de.jstacs.algorithms.graphs.Chu_Liu_Edmonds
  Compute the branching yielding the maximum sum of weights.
mean(int, int) - Method in class de.jstacs.utils.DoubleList
  This method computes the mean of a part of the list.
MeanResultSet - Class in de.jstacs.results
  Class that computes the mean and the standard error of a series of `NumericalResultSet`s.
MeanResultSet(SimpleResult...) - Constructor for class de.jstacs.results.MeanResultSet
  Constructs a new `MeanResultSet` with an empty set of `NumericalResultSet`s.
MeanResultSet() - Constructor for class de.jstacs.results.MeanResultSet
  Constructs a new `MeanResultSet` with an empty set of `NumericalResultSet`s and no further information.
MeanResultSet(StringBuffer) - Constructor for class de.jstacs.results.MeanResultSet
  The standard constructor for the interface `Storable`.
MeanResultSet.AdditionImpossibleException - Exception in de.jstacs.results
  Class for the exception that is thrown if two `MeanResultSet`s should be added that do not match.
MeanResultSet.AdditionImpossibleException() - Constructor for exception de.jstacs.results.MeanResultSet.AdditionImpossibleException
  Constructs a new `MeanResultSet.AdditionImpossibleException` with an appropriate error message.
MeanResultSet.InconsistentResultNumberException - Exception in de.jstacs.results
  Class for the exception that is thrown if a `NumericalResultSet` is added to the `MeanResultSet` that has a number of results which is not equal to the number of results of the previously added results.
MeanResultSet.InconsistentResultNumberException() - Constructor for exception de.jstacs.results.MeanResultSet.InconsistentResultNumberException
  Constructs a new `MeanResultSet.InconsistentResultNumberException` with an appropriate error message.
Measure - Class in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures
  Class for structure measures that derive an optimal structure with respect to some criterion within a class of possible structures from data.
Measure() - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.Measure
MeasureParameters - Class in de.jstacs.classifier
  This class holds the parameters for the `evaluate`-methods of a classifier.
MeasureParameters(boolean) - Constructor for class de.jstacs.classifier.MeasureParameters
  Creates a new empty instance of `MeasureParameters`.
MeasureParameters(boolean, double, double, double) - Constructor for class de.jstacs.classifier.MeasureParameters
  Creates a new instance of `MeasureParameters`.
MeasureParameters(boolean, double, double, double, double, double, int, RangeParameter.Scale) - Constructor for class de.jstacs.classifier.MeasureParameters
  Creates a new instance of `MeasureParameters`.
MeasureParameters(StringBuffer) - Constructor for class de.jstacs.classifier.MeasureParameters
  The standard constructor for the interface `Storable`.
MeasureParameters.Measure - Enum in de.jstacs.classifier
  This `enum` defines all measures that are currently implemented in Jstacs.
median(int, int) - Method in class de.jstacs.utils.DoubleList
  This method computes the median of a part of the list.
MEMConstraint - Class in de.jstacs.models.discrete.inhomogeneous
  This constraint can be used for any maximum entropy model (MEM) application.
MEMConstraint(int[], int[]) - Constructor for class de.jstacs.models.discrete.inhomogeneous.MEMConstraint
  Creates a `MEMConstraint` as part of a (whole) model.
MEMConstraint(int[], int[], int[]) - Constructor for class de.jstacs.models.discrete.inhomogeneous.MEMConstraint
  Creates a `MEMConstraint` as part of a model.
MEMConstraint(StringBuffer) - Constructor for class de.jstacs.models.discrete.inhomogeneous.MEMConstraint
  The standard constructor for the interface `Storable`.
merge(Hashtable<Sequence, BitSet[]>, int, boolean) - Static method in class de.jstacs.motifDiscovery.KMereStatistic
  This method allows to merge the statistics of k-mers by allowing mismatches.
min - Variable in class de.jstacs.scoringFunctions.mix.motifSearch.DurationScoringFunction
  The minimal value.
min(double[]) - Static method in class de.jstacs.utils.ToolBox
  This method returns the minimum of the elements of an `array`.
min(int, int, double[]) - Static method in class de.jstacs.utils.ToolBox
  This method returns the minimum of the elements of an `array` between `start` and `end`.
MINIMALBRANCHING - Static variable in class de.jstacs.algorithms.graphs.Chu_Liu_Edmonds
  Compute the branching yielding the minimum sum of weights.
MixtureDuration - Class in de.jstacs.scoringFunctions.mix.motifSearch
  This class implements a mixture of `DurationScoringFunction`s.
MixtureDuration(int, DurationScoringFunction...) - Constructor for class de.jstacs.scoringFunctions.mix.motifSearch.MixtureDuration
  The main constructor of a `MixtureDuration`.
MixtureDuration(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.mix.motifSearch.MixtureDuration
  This is the constructor for `Storable`.
MixtureModel - Class in de.jstacs.models.mixture
  The class for a mixture model of any `Model`s.
MixtureModel(int, Model[], int, boolean, double[], double[], AbstractMixtureModel.Algorithm, double, TerminationCondition, AbstractMixtureModel.Parameterization, int, int, BurnInTest) - Constructor for class de.jstacs.models.mixture.MixtureModel
  Creates a new `MixtureModel`.
MixtureModel(int, Model[], int, double[], double, TerminationCondition, AbstractMixtureModel.Parameterization) - Constructor for class de.jstacs.models.mixture.MixtureModel
  Creates an instance using EM and estimating the component probabilities.
MixtureModel(int, Model[], double[], int, double, TerminationCondition, AbstractMixtureModel.Parameterization) - Constructor for class de.jstacs.models.mixture.MixtureModel
  Creates an instance using EM and fixed component probabilities.
MixtureModel(int, Model[], int, double[], int, int, BurnInTest) - Constructor for class de.jstacs.models.mixture.MixtureModel
  Creates an instance using Gibbs Sampling and sampling the component probabilities.
MixtureModel(int, Model[], double[], int, int, int, BurnInTest) - Constructor for class de.jstacs.models.mixture.MixtureModel
  Creates an instance using Gibbs Sampling and fixed component probabilities.
MixtureModel(StringBuffer) - Constructor for class de.jstacs.models.mixture.MixtureModel
  The constructor for the interface `Storable`.
MixtureScoringFunction - Class in de.jstacs.scoringFunctions.mix
  This class implements a real mixture model.
MixtureScoringFunction(int, boolean, NormalizableScoringFunction...) - Constructor for class de.jstacs.scoringFunctions.mix.MixtureScoringFunction
  This constructor creates a new `MixtureScoringFunction`.
MixtureScoringFunction(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.mix.MixtureScoringFunction
  This is the constructor for the interface `Storable`.
model - Variable in class de.jstacs.models.mixture.AbstractMixtureModel
  The model for the sequences.
Model - Interface in de.jstacs.models
  This interface defines all methods for a probabilistic model.
ModelBasedClassifier - Class in de.jstacs.classifier.modelBased
  This class is the main class for all model based classifiers.
ModelBasedClassifier(boolean, Model...) - Constructor for class de.jstacs.classifier.modelBased.ModelBasedClassifier
  This constructor creates a new instance with the given `Model`s and clones these if necessary.
ModelBasedClassifier(Model...) - Constructor for class de.jstacs.classifier.modelBased.ModelBasedClassifier
  The default constructor that creates a new instance with the given `Model`s.
ModelBasedClassifier(StringBuffer) - Constructor for class de.jstacs.classifier.modelBased.ModelBasedClassifier
  The standard constructor for the interface `Storable`.
models - Variable in class de.jstacs.classifier.modelBased.ModelBasedClassifier
  The internal `Model`s.
models - Variable in class de.jstacs.models.CompositeModel
  The models for the components
ModelTester - Class in de.jstacs.models.utils
  This class is useful for some test for any (discrete) models.
ModelTester() - Constructor for class de.jstacs.models.utils.ModelTester
modify(double[], double[], int, int) - Method in class de.jstacs.models.mixture.motif.SingleHiddenMotifMixture
  This method modifies the computed weights for one sequence and returns the score.
modify(int, int) - Method in interface de.jstacs.motifDiscovery.Mutable
  Manually modifies the model.
modify(int, int) - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.MutableMarkovModelScoringFunction
modify(int) - Method in class de.jstacs.scoringFunctions.mix.motifSearch.DurationScoringFunction
  This method modifies the underlying `AlphabetContainer`.
modify(int) - Method in class de.jstacs.scoringFunctions.mix.motifSearch.MixtureDuration
modify(int) - Method in class de.jstacs.scoringFunctions.mix.motifSearch.SkewNormalLikeScoringFunction
modify(int, int) - Method in class de.jstacs.scoringFunctions.mix.StrandScoringFunction
modify(int, int) - Method in class de.jstacs.scoringFunctions.NormalizedScoringFunction
modifyMotif(int, int, int) - Method in interface de.jstacs.motifDiscovery.MutableMotifDiscoverer
  Manually modifies the motif model with index `motifIndex`.
modifyMotif(int, int, int) - Method in class de.jstacs.scoringFunctions.IndependentProductScoringFunction
modifyMotif(int, int, int) - Method in class de.jstacs.scoringFunctions.mix.MixtureScoringFunction
modifyMotif(int, int, int) - Method in class de.jstacs.scoringFunctions.mix.motifSearch.HiddenMotifsMixture
modifyWeights(double[]) - Method in class de.jstacs.models.mixture.AbstractMixtureModel
  This method modifies the computed weights for one sequence and returns the score.
MotifAnnotation - Class in de.jstacs.data.sequences.annotation
  Class for a `StrandedLocatedSequenceAnnotationWithLength` that is a motif.
MotifAnnotation(String, int, int, StrandedLocatedSequenceAnnotationWithLength.Strand, Result...) - Constructor for class de.jstacs.data.sequences.annotation.MotifAnnotation
  Creates a new `MotifAnnotation` of type `type` with identifier `identifier` and additional annotation (that does not fit the `SequenceAnnotation` definitions) given as an array of `Result`s `additionalAnnotation`.
MotifAnnotation(StringBuffer) - Constructor for class de.jstacs.data.sequences.annotation.MotifAnnotation
  The standard constructor for the interface `Storable`.
MotifDiscoverer - Interface in de.jstacs.motifDiscovery
  This is the interface that any tool for de-novo motif discovery should implement.
MotifDiscoverer.KindOfProfile - Enum in de.jstacs.motifDiscovery
  This `enum` can be used to determine which kind of profile should be returned.
MotifDiscovererToolBox - Class in de.jstacs.motifDiscovery
  This class contains static methods for the `MotifDiscoverer`.
MotifDiscovererToolBox() - Constructor for class de.jstacs.motifDiscovery.MotifDiscovererToolBox
MotifDiscoveryAssessment - Class in de.jstacs.motifDiscovery
  This class enables the user to assess the prediction of motif occurrences
MotifDiscoveryAssessment() - Constructor for class de.jstacs.motifDiscovery.MotifDiscoveryAssessment
motifLength - Variable in class de.jstacs.models.mixture.motif.positionprior.PositionPrior
  The length of the motif.
MRFScoringFunction - Class in de.jstacs.scoringFunctions
  This class implements the scoring function for any MRF (Markov Random Field).
MRFScoringFunction(AlphabetContainer, int, String) - Constructor for class de.jstacs.scoringFunctions.MRFScoringFunction
  This constructor creates an instance of a `MRFScoringFunction` with equivalent sample size (ess) 0.
MRFScoringFunction(AlphabetContainer, int, double, String) - Constructor for class de.jstacs.scoringFunctions.MRFScoringFunction
  This is the main constructor that creates an instance of a `MRFScoringFunction`.
MRFScoringFunction(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.MRFScoringFunction
  This is the constructor for the interface `Storable`.
MRGParams - Class in de.jstacs.utils.random
  The super container for parameter of multivariate random generators.
MRGParams() - Constructor for class de.jstacs.utils.random.MRGParams
MSPClassifier - Class in de.jstacs.classifier.scoringFunctionBased.msp
  This class implements a classifier that allows the training via MCL or MSP principle.
MSPClassifier(GenDisMixClassifierParameterSet, ScoringFunction...) - Constructor for class de.jstacs.classifier.scoringFunctionBased.msp.MSPClassifier
  This convenience constructor creates an `MSPClassifier` that used MCL principle for training.
MSPClassifier(GenDisMixClassifierParameterSet, LogPrior, ScoringFunction...) - Constructor for class de.jstacs.classifier.scoringFunctionBased.msp.MSPClassifier
  The default constructor that creates a new `MSPClassifier` from a given parameter set, a prior and `ScoringFunction`s for the classes.
MSPClassifier(GenDisMixClassifierParameterSet, LogPrior, double, ScoringFunction...) - Constructor for class de.jstacs.classifier.scoringFunctionBased.msp.MSPClassifier
  This constructor that creates a new `MSPClassifier` from a given parameter set, a prior and `ScoringFunction`s for the classes.
MSPClassifier(StringBuffer) - Constructor for class de.jstacs.classifier.scoringFunctionBased.msp.MSPClassifier
  This is the constructor for `Storable`.
MST - Class in de.jstacs.algorithms.graphs
  This class enables you to compute the maximal spanning forest for an undirected, weighted graph.
MST() - Constructor for class de.jstacs.algorithms.graphs.MST
MultiDimensionalDiscreteSequence - Class in de.jstacs.data.sequences
  This class is for multidimensional sequences that can be used, for instance, for phylogenetic footprinting.
MultiDimensionalDiscreteSequence(SequenceAnnotation[], SimpleDiscreteSequence...) - Constructor for class de.jstacs.data.sequences.MultiDimensionalDiscreteSequence
  This constructor creates an `MultiDimensionalDiscreteSequence` from a set of individual `SimpleDiscreteSequence`s.
multiply(int, int, double) - Method in class de.jstacs.utils.DoubleList
  Multiplies all values in the list from index `start` to `end` with the value `factor`.
multiplyExpLambdaWith(int, double) - Method in class de.jstacs.models.discrete.inhomogeneous.MEMConstraint
  Multiplies the exponential value of with the factor `val`: .
MultiSelectionCollectionParameter - Class in de.jstacs.parameters
  Class for a `Parameter` that provides a collection of possible values.
MultiSelectionCollectionParameter(DataType, String[], Object[], String, String, boolean) - Constructor for class de.jstacs.parameters.MultiSelectionCollectionParameter
  Constructor for a `MultiSelectionCollectionParameter`.
MultiSelectionCollectionParameter(DataType, String[], Object[], String[], String, String, boolean) - Constructor for class de.jstacs.parameters.MultiSelectionCollectionParameter
  Constructor for a `MultiSelectionCollectionParameter`.
MultiSelectionCollectionParameter(ParameterSet[], String[], String[], String, String, boolean) - Constructor for class de.jstacs.parameters.MultiSelectionCollectionParameter
  Creates a new `MultiSelectionCollectionParameter` from an array of `ParameterSet`s.
MultiSelectionCollectionParameter(InstanceParameterSet[], String, String, boolean) - Constructor for class de.jstacs.parameters.MultiSelectionCollectionParameter
  Creates a new `MultiSelectionCollectionParameter` from an array of `ParameterSet`s.
MultiSelectionCollectionParameter(StringBuffer) - Constructor for class de.jstacs.parameters.MultiSelectionCollectionParameter
  The standard constructor for the interface `Storable`.
MultiSelectionCollectionParameter(ParameterSet, boolean[], boolean[], boolean, String, String, boolean, DataType, String, int, boolean) - Constructor for class de.jstacs.parameters.MultiSelectionCollectionParameter
  Creates a new `MultiSelectionCollectionParameter` from the necessary field.
MultivariateRandomGenerator - Class in de.jstacs.utils.random
  This class is the abstract super class for any multivariate random generator (MRG).
MultivariateRandomGenerator() - Constructor for class de.jstacs.utils.random.MultivariateRandomGenerator
Mutable - Interface in de.jstacs.motifDiscovery
  This interface allows to modify a motif model.
MutableMarkovModelScoringFunction - Class in de.jstacs.scoringFunctions.directedGraphicalModels
  This class implements a `AbstractNormalizableScoringFunction` for an inhomogeneous Markov model.
MutableMarkovModelScoringFunction(AlphabetContainer, int, double, boolean, int, DurationScoringFunction) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.MutableMarkovModelScoringFunction
  This constructor creates an instance with an prior for the modeled length.
MutableMarkovModelScoringFunction(AlphabetContainer, int, double, boolean, InhomogeneousMarkov) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.MutableMarkovModelScoringFunction
  This constructor creates an instance without any prior for the modeled length.
MutableMarkovModelScoringFunction(AlphabetContainer, int, double, boolean, InhomogeneousMarkov, DurationScoringFunction) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.MutableMarkovModelScoringFunction
  This constructor creates an instance with an prior for the modeled length.
MutableMarkovModelScoringFunction(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.MutableMarkovModelScoringFunction
  The standard constructor for the interface `Storable`.
MutableMotifDiscoverer - Interface in de.jstacs.motifDiscovery
  This is the interface that any tool for de-novo motif discovery should implement that allows any modify-operations like shift, shrink and expand.
MutableMotifDiscovererToolbox - Class in de.jstacs.motifDiscovery
  This class contains some important methods for the initiation and optimization of `MutableMotifDiscoverer`.
MutableMotifDiscovererToolbox() - Constructor for class de.jstacs.motifDiscovery.MutableMotifDiscovererToolbox
MutableMotifDiscovererToolbox.InitMethodForScoringFunction - Enum in de.jstacs.motifDiscovery
  This enum defines some constants for the method `MutableMotifDiscovererToolbox.getSortedInitialParameters(ScoringFunction[], InitMethodForScoringFunction[], SFBasedOptimizableFunction, int, OutputStream, int)`.
myAbstractClassifier - Variable in class de.jstacs.classifier.assessment.ClassifierAssessment
  This array contains the internal used classifiers.
myModel - Variable in class de.jstacs.classifier.assessment.ClassifierAssessment
  This array contains for each class the internal used models.
myTempMeanResultSets - Variable in class de.jstacs.classifier.assessment.ClassifierAssessment
  The temporary result set.

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