Uses of Package
org.biojava.bio.dp

Packages that use org.biojava.bio.dp
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
ModelTrainer
          Encapsulates the training of an entire model.
 

Classes in org.biojava.bio.dp used by org.biojava.bio.dp
AbstractTrainer
          An abstract implementation of TrainingAlgorithm that provides a framework for plugging in per-cycle code for parameter optimization.
BackPointer
          A backpointer.
DotState
           A Dot state.
DP
           Objects that can perform dymamic programming operations upon sequences with HMMs.
DPFactory
          The interface for objects that can generate a DP object for a MarkovModel.
DPMatrix
           
EmissionState
           A state in a markov process that has an emission spectrum.
HMMTrainer
          interface implemented by objects that train HMMs.
IllegalTransitionException
          This exception indicates that there is no transition between two states.
MagicalState
          Start/end state for HMMs.
MarkovModel
          A markov model.
ModelInState
          A state that contains an entire sub-model.
ModelTrainer
          Encapsulates the training of an entire model.
ScoreType
          This class computes the score that is used to be used in a DP optimisation.
SimpleEmissionState
           
SimpleMarkovModel
           
State
          A state in a markov process.
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.
StoppingCriteria
          A callback that is invoked during the training of an HMM.
Trainable
          Flags an object as being able to register itself with a model trainer.
TrainingAlgorithm
           
TransitionTrainer
          An object that can be used to train the transitions within a MarkovModel.
WeightMatrix
          A log odds weight matrix.
 

Classes in org.biojava.bio.dp used by org.biojava.bio.dp.onehead
DP
           Objects that can perform dymamic programming operations upon sequences with HMMs.
DPMatrix
           
IllegalTransitionException
          This exception indicates that there is no transition between two states.
MarkovModel
          A markov model.
ScoreType
          This class computes the score that is used to be used in a DP optimisation.
State
          A state in a markov process.
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
BackPointer
          A backpointer.
DP
           Objects that can perform dymamic programming operations upon sequences with HMMs.
DPMatrix
           
IllegalTransitionException
          This exception indicates that there is no transition between two states.
MarkovModel
          A markov model.
ScoreType
          This class computes the score that is used to be used in a DP optimisation.
State
          A state in a markov process.
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
EmissionState
           A state in a markov process that has an emission spectrum.
IllegalTransitionException
          This exception indicates that there is no transition between two states.
MarkovModel
          A markov model.
ModelInState
          A state that contains an entire sub-model.
ProfileHMM
           
SimpleEmissionState
           
SimpleMarkovModel
           
State
          A state in a markov process.
Trainable
          Flags an object as being able to register itself with a model trainer.