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Packages that use org.biojava.bio.dp | |
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org.biojava.bio.dist | Probability distributions over Alphabets. |
org.biojava.bio.dp | HMM and Dynamic Programming Algorithms. |
org.biojava.bio.dp.onehead | |
org.biojava.bio.dp.twohead | |
org.biojava.bio.program.hmmer | Tools for working with profile Hidden Markov Models from the HMMer package. |
Classes in org.biojava.bio.dp used by org.biojava.bio.dist | |
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ModelTrainer
Encapsulates the training of an entire model. |
Classes in org.biojava.bio.dp used by org.biojava.bio.dp | |
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AbstractTrainer
An abstract implementation of TrainingAlgorithm that provides a framework for plugging in per-cycle code for parameter optimization. |
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BackPointer
A backpointer. |
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DotState
A Dot state. |
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DP
Objects that can perform dymamic programming operations upon sequences with HMMs. |
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DPFactory
The interface for objects that can generate a DP object for a MarkovModel. |
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DPMatrix
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EmissionState
A state in a markov process that has an emission spectrum. |
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HMMTrainer
interface implemented by objects that train HMMs. |
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IllegalTransitionException
This exception indicates that there is no transition between two states. |
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MagicalState
Start/end state for HMMs. |
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MarkovModel
A markov model. |
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ModelInState
A state that contains an entire sub-model. |
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ModelTrainer
Encapsulates the training of an entire model. |
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ScoreType
This class computes the score that is used to be used in a DP optimisation. |
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SimpleEmissionState
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SimpleMarkovModel
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State
A state in a markov process. |
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StatePath
Extends the Alignment interface so that it is explicitly used to represent a state path through an HMM, and the associated emitted sequence and likelihoods. |
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StoppingCriteria
A callback that is invoked during the training of an HMM. |
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Trainable
Flags an object as being able to register itself with a model trainer. |
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TrainingAlgorithm
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TransitionTrainer
An object that can be used to train the transitions within a MarkovModel. |
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WeightMatrix
A log odds weight matrix. |
Classes in org.biojava.bio.dp used by org.biojava.bio.dp.onehead | |
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DP
Objects that can perform dymamic programming operations upon sequences with HMMs. |
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DPMatrix
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IllegalTransitionException
This exception indicates that there is no transition between two states. |
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MarkovModel
A markov model. |
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ScoreType
This class computes the score that is used to be used in a DP optimisation. |
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State
A state in a markov process. |
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StatePath
Extends the Alignment interface so that it is explicitly used to represent a state path through an HMM, and the associated emitted sequence and likelihoods. |
Classes in org.biojava.bio.dp used by org.biojava.bio.dp.twohead | |
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BackPointer
A backpointer. |
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DP
Objects that can perform dymamic programming operations upon sequences with HMMs. |
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DPMatrix
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IllegalTransitionException
This exception indicates that there is no transition between two states. |
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MarkovModel
A markov model. |
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ScoreType
This class computes the score that is used to be used in a DP optimisation. |
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State
A state in a markov process. |
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StatePath
Extends the Alignment interface so that it is explicitly used to represent a state path through an HMM, and the associated emitted sequence and likelihoods. |
Classes in org.biojava.bio.dp used by org.biojava.bio.program.hmmer | |
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EmissionState
A state in a markov process that has an emission spectrum. |
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IllegalTransitionException
This exception indicates that there is no transition between two states. |
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MarkovModel
A markov model. |
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ModelInState
A state that contains an entire sub-model. |
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ProfileHMM
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SimpleEmissionState
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SimpleMarkovModel
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State
A state in a markov process. |
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Trainable
Flags an object as being able to register itself with a model trainer. |
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