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Hierarchy For Package org.biojava.bio.dp
Package Hierarchies:
All Packages
Class Hierarchy
class java.lang.Object
class org.biojava.utils.
AbstractChangeable
(implements org.biojava.utils.
Changeable
)
class org.biojava.bio.symbol.
AbstractSymbol
(implements org.biojava.bio.symbol.
Symbol
)
class org.biojava.bio.symbol.
FundamentalAtomicSymbol
(implements org.biojava.bio.symbol.
AtomicSymbol
, java.io.Serializable)
class org.biojava.bio.dp.
SimpleDotState
(implements org.biojava.bio.dp.
DotState
, java.io.Serializable)
class org.biojava.bio.dp.
SimpleModelInState
(implements org.biojava.bio.dp.
ModelInState
)
class org.biojava.bio.dp.
SimpleEmissionState
(implements org.biojava.bio.dp.
EmissionState
, java.io.Serializable)
class org.biojava.bio.dp.
MagicalState
class org.biojava.bio.dp.
SimpleMarkovModel
(implements org.biojava.bio.dp.
MarkovModel
, java.io.Serializable)
class org.biojava.bio.dp.
ProfileHMM
class org.biojava.bio.dp.
WMAsMM
(implements org.biojava.bio.dp.
MarkovModel
, java.io.Serializable)
class org.biojava.bio.dp.
AbstractTrainer
(implements org.biojava.bio.dp.
TrainingAlgorithm
)
class org.biojava.bio.dp.
BaumWelchSampler
(implements java.io.Serializable)
class org.biojava.bio.dp.
BaumWelchTrainer
(implements java.io.Serializable)
class org.biojava.bio.dp.
BackPointer
class org.biojava.utils.
ChangeForwarder
(implements org.biojava.utils.
ChangeListener
)
class org.biojava.bio.dp.
MarkovModel.DistributionForwarder
class org.biojava.bio.dp.
DP
class org.biojava.bio.dp.
DP.ReverseIterator
(implements java.util.Iterator, java.io.Serializable)
class org.biojava.bio.dp.
DPFactory.DefaultFactory
(implements org.biojava.bio.dp.
DPFactory
)
class org.biojava.bio.dp.
ScoreType.NullModel
(implements org.biojava.bio.dp.
ScoreType
)
class org.biojava.bio.dp.
ScoreType.Odds
(implements org.biojava.bio.dp.
ScoreType
)
class org.biojava.bio.dp.
ScoreType.Probability
(implements org.biojava.bio.dp.
ScoreType
)
class org.biojava.bio.dist.
SimpleDistributionTrainerContext
(implements org.biojava.bio.dist.
DistributionTrainerContext
, java.io.Serializable)
class org.biojava.bio.dp.
SimpleModelTrainer
(implements org.biojava.bio.dp.
ModelTrainer
, java.io.Serializable)
class org.biojava.bio.dp.
SimpleWeightMatrix
(implements java.io.Serializable, org.biojava.bio.dp.
WeightMatrix
)
class java.lang.Throwable (implements java.io.Serializable)
class java.lang.Exception
class org.biojava.utils.
NestedException
class org.biojava.bio.
BioException
class org.biojava.bio.dp.
IllegalTransitionException
class org.biojava.bio.dp.
TrainerTransition
(implements java.io.Serializable)
class org.biojava.bio.dp.
Transition
(implements java.io.Serializable)
class org.biojava.utils.
Unchangeable
(implements org.biojava.utils.
Changeable
)
class org.biojava.bio.dp.
SimpleStatePath
(implements java.io.Serializable, org.biojava.bio.dp.
StatePath
)
class org.biojava.bio.dp.
WeightMatrixAnnotator
(implements org.biojava.bio.seq.
SequenceAnnotator
, java.io.Serializable)
class org.biojava.bio.dp.
XmlMarkovModel
Interface Hierarchy
interface org.biojava.utils.
Changeable
interface org.biojava.bio.
Annotatable
interface org.biojava.bio.symbol.
Symbol
interface org.biojava.bio.symbol.
BasisSymbol
interface org.biojava.bio.symbol.
AtomicSymbol
interface org.biojava.bio.dp.
State
interface org.biojava.bio.dp.
DotState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
ModelInState
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.bio.dp.
State
, org.biojava.bio.dp.
Trainable
)
interface org.biojava.bio.dp.
MarkovModel
interface org.biojava.bio.symbol.
SymbolList
interface org.biojava.bio.symbol.
Alignment
interface org.biojava.bio.dp.
StatePath
interface org.biojava.bio.dist.
DistributionTrainerContext
interface org.biojava.bio.dp.
ModelTrainer
interface org.biojava.bio.dp.
DPFactory
interface org.biojava.bio.dp.
DPMatrix
interface org.biojava.bio.dp.
ScoreType
interface org.biojava.bio.dp.
StoppingCriteria
interface org.biojava.bio.dp.
Trainable
interface org.biojava.bio.dp.
EmissionState
(also extends org.biojava.utils.
Changeable
, org.biojava.bio.dp.
State
)
interface org.biojava.bio.dp.
TrainingAlgorithm
interface org.biojava.bio.dp.
TransitionTrainer
interface org.biojava.bio.dp.
WeightMatrix
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