de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous
Class HomogeneousDiffSM
java.lang.Object
de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore
de.jstacs.sequenceScores.statisticalModels.differentiable.AbstractDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.AbstractVariableLengthDiffSM
de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous.HomogeneousDiffSM
- All Implemented Interfaces:
- DifferentiableSequenceScore, SequenceScore, DifferentiableStatisticalModel, SamplingDifferentiableStatisticalModel, VariableLengthDiffSM, StatisticalModel, Storable, Cloneable
- Direct Known Subclasses:
- HomogeneousMM0DiffSM, HomogeneousMMDiffSM, UniformHomogeneousDiffSM
public abstract class HomogeneousDiffSM
- extends AbstractVariableLengthDiffSM
- implements SamplingDifferentiableStatisticalModel
This is the main class for all homogeneous DifferentiableSequenceScore
s.
- Author:
- Jens Keilwagen
Method Summary |
abstract byte |
getMaximalMarkovOrder()
Returns the maximal used markov oder. |
abstract void |
initializeUniformly(boolean freeParams)
This method allows to initialize the instance with an uniform distribution. |
Methods inherited from interface de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore |
clone, getCurrentParameterValues, getInitialClassParam, getLogScoreAndPartialDerivation, getLogScoreAndPartialDerivation, getLogScoreAndPartialDerivation, getNumberOfParameters, getNumberOfRecommendedStarts, initializeFunction, initializeFunctionRandomly, setParameters |
Methods inherited from interface de.jstacs.sequenceScores.SequenceScore |
getAlphabetContainer, getCharacteristics, getInstanceName, getLength, getLogScoreFor, getLogScoreFor, getLogScoreFor, getLogScoreFor, getLogScoreFor, getNumericalCharacteristics, isInitialized, toString |
HomogeneousDiffSM
protected HomogeneousDiffSM(AlphabetContainer alphabets)
- This is the main constructor that creates an instance of a
HomogeneousDiffSM
that models sequences of arbitrary
length.
- Parameters:
alphabets
- the AlphabetContainer
HomogeneousDiffSM
protected HomogeneousDiffSM(AlphabetContainer alphabets,
int length)
- This is the main constructor that creates an instance of a
HomogeneousDiffSM
that models sequences of a given
length.
- Parameters:
alphabets
- the AlphabetContainer
length
- the length of the modeled sequences
HomogeneousDiffSM
protected HomogeneousDiffSM(StringBuffer source)
throws NonParsableException
- This is the constructor for
Storable
. Creates a new
HomogeneousDiffSM
out of its XML representation.
- Parameters:
source
- the XML representation as StringBuffer
- Throws:
NonParsableException
- if the XML representation could not be parsed
getMaximalMarkovOrder
public abstract byte getMaximalMarkovOrder()
- Returns the maximal used markov oder.
- Specified by:
getMaximalMarkovOrder
in interface StatisticalModel
- Overrides:
getMaximalMarkovOrder
in class AbstractDifferentiableStatisticalModel
- Returns:
- the maximal used markov oder
initializeUniformly
public abstract void initializeUniformly(boolean freeParams)
- This method allows to initialize the instance with an uniform distribution.
- Parameters:
freeParams
- a switch whether to take only free parameters or to take all