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Packages that use de.jstacs.data.sequences | |
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de.jstacs.algorithms.alignment | Provides classes for alignments. |
de.jstacs.algorithms.alignment.cost | Provides classes for cost functions used in alignments. |
de.jstacs.classifiers | This package provides the framework for any classifier. |
de.jstacs.classifiers.differentiableSequenceScoreBased | Provides the classes for Classifier s that are based on SequenceScore s.It includes a sub-package for discriminative objective functions, namely conditional likelihood and supervised posterior, and a separate sub-package for the parameter priors, that can be used for the supervised posterior. |
de.jstacs.classifiers.differentiableSequenceScoreBased.sampling | Provides the classes for AbstractScoreBasedClassifier s that are based on
SamplingDifferentiableStatisticalModel s
and that sample parameters using the Metropolis-Hastings algorithm. |
de.jstacs.classifiers.trainSMBased | Provides the classes for Classifier s that are based on TrainableStatisticalModel s. |
de.jstacs.data | Provides classes for the representation of data. The base classes to represent data are Alphabet and AlphabetContainer for representing alphabets,
Sequence and its sub-classes to represent continuous and discrete sequences, and
DataSet to represent data sets comprising a set of sequences. |
de.jstacs.data.sequences | Provides classes for representing sequences. The implementations of sequences currently include DiscreteSequence s prepared for alphabets of different sizes, and ArbitrarySequence s that may
contain continuous values as well.As sub-package provides the facilities to annotate Sequence s. |
de.jstacs.data.sequences.annotation | Provides the facilities to annotate Sequence s using a number of pre-defined annotation types, or additional
implementations of the SequenceAnnotation class. |
de.jstacs.motifDiscovery | This package provides the framework including the interface for any de novo motif discoverer. |
de.jstacs.sequenceScores | Provides all SequenceScore s, which can be used to score a Sequence , typically using some model assumptions. |
de.jstacs.sequenceScores.differentiable | |
de.jstacs.sequenceScores.differentiable.logistic | |
de.jstacs.sequenceScores.statisticalModels | Provides all StatisticalModel s, which can compute a proper (i.e., normalized) likelihood over the input space of sequences.StatisticalModel s can be further differentiated into TrainableStatisticalModel s,
which can be learned from a single input DataSet , and DifferentiableStatisticalModel s,
which define a proper likelihood but can also compute gradients like DifferentiableSequenceScore s. |
de.jstacs.sequenceScores.statisticalModels.differentiable | Provides all DifferentiableStatisticalModel s, which can compute the gradient with
respect to their parameters for a given input Sequence . |
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels | Provides DifferentiableStatisticalModel s that are directed graphical models. |
de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous | Provides DifferentiableStatisticalModel s that are homogeneous, i.e. |
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture | Provides DifferentiableSequenceScore s that are mixtures of other DifferentiableSequenceScore s. |
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif | |
de.jstacs.sequenceScores.statisticalModels.trainable | Provides all TrainableStatisticalModel s, which can
be learned from a single DataSet . |
de.jstacs.sequenceScores.statisticalModels.trainable.discrete | |
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous | |
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous | This package contains various inhomogeneous models. |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm | The package provides all interfaces and classes for a hidden Markov model (HMM). |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models | The package provides different implementations of hidden Markov models based on AbstractHMM . |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states | The package provides all interfaces and classes for states used in hidden Markov models. |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions | |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous | |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete | |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions | The package provides all interfaces and classes for transitions used in hidden Markov models. |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements | |
de.jstacs.sequenceScores.statisticalModels.trainable.mixture | This package is the super package for any mixture model. |
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif | |
de.jstacs.utils | This package contains a bundle of useful classes and interfaces like ... |
Classes in de.jstacs.data.sequences used by de.jstacs.algorithms.alignment | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.algorithms.alignment.cost | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.classifiers | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.classifiers.differentiableSequenceScoreBased | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.classifiers.differentiableSequenceScoreBased.sampling | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.classifiers.trainSMBased | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.data | |
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Sequence
This is the main class for all sequences. |
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WrongSequenceTypeException
This Exception indicates that the type of the sequence (
ByteSequence , ShortSequence , ...) is not suitable for a given
AlphabetContainer . |
Classes in de.jstacs.data.sequences used by de.jstacs.data.sequences | |
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ArbitraryFloatSequence
This class is for any continuous or hybrid sequence. |
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ArbitrarySequence
This class is for any continuous or hybrid sequence. |
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ByteSequence
This class is for sequences with the alphabet symbols encoded as byte s and can therefore be used for discrete
AlphabetContainer s with alphabets that use only few symbols. |
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IntSequence
This class is for sequences with the alphabet symbols encoded as int s and can therefore be used for discrete
AlphabetContainer s with alphabets that use a huge number of symbols. |
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MappedDiscreteSequence
This class allows to map a discrete Sequence to an new Sequence using some DiscreteAlphabetMapping s. |
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MultiDimensionalArbitrarySequence
This class is for multidimensional arbitrary sequences. |
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MultiDimensionalDiscreteSequence
This class is for multidimensional discrete sequences that can be used, for instance, for phylogenetic footprinting. |
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MultiDimensionalSequence
This class is for multidimensional sequences that can be used, for instance, for phylogenetic footprinting. |
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PermutedSequence
This class is for permuted sequences. |
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Sequence
This is the main class for all sequences. |
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Sequence.RecursiveSequence
This is the main class for subsequences, composite sequences, ... |
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ShortSequence
This class is for sequences with the alphabet symbols encoded as shorts s and can therefore be used for discrete
AlphabetContainer s with alphabets that use many different symbols. |
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SimpleDiscreteSequence
This is the main class for any discrete sequence. |
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SparseSequence
This class is an implementation for sequences on one alphabet with length 4. |
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WrongSequenceTypeException
This Exception indicates that the type of the sequence (
ByteSequence , ShortSequence , ...) is not suitable for a given
AlphabetContainer . |
Classes in de.jstacs.data.sequences used by de.jstacs.data.sequences.annotation | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.motifDiscovery | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.differentiable | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.differentiable.logistic | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.differentiable | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.differentiable.mixture | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous | |
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Sequence
This is the main class for all sequences. |
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WrongSequenceTypeException
This Exception indicates that the type of the sequence (
ByteSequence , ShortSequence , ...) is not suitable for a given
AlphabetContainer . |
Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.mixture | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data.sequences used by de.jstacs.utils | |
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Sequence
This is the main class for all sequences. |
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