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## de.jstacs.scoringFunctions.mix
Class VariableLengthMixtureScoringFunction

    java.lang.Object
      de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
          de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
              de.jstacs.scoringFunctions.mix.MixtureScoringFunction
                  de.jstacs.scoringFunctions.mix.VariableLengthMixtureScoringFunction

All Implemented Interfaces:
  MotifDiscoverer, MutableMotifDiscoverer, NormalizableScoringFunction, ScoringFunction, VariableLengthScoringFunction, Storable, Cloneable

    public class VariableLengthMixtureScoringFunction

extends MixtureScoringFunction
implements VariableLengthScoringFunction

This class implements a mixture of `VariableLengthScoringFunction` by extending `MixtureScoringFunction` and implementing the methods of `VariableLengthScoringFunction`.

Author:
  Jens Keilwagen

Nested Class Summary

Nested classes/interfaces inherited from interface de.jstacs.motifDiscovery.MotifDiscoverer
`MotifDiscoverer.KindOfProfile`

Field Summary

Fields inherited from class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
`componentScore, dList, freeParams, function, hiddenParameter, hiddenPotential, iList, logGammaSum, logHiddenNorm, logHiddenPotential, norm, optimizeHidden, paramRef, partNorm`

Fields inherited from class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
`alphabets, length, r`

Fields inherited from interface de.jstacs.scoringFunctions.ScoringFunction
`UNKNOWN`

Constructor Summary
`VariableLengthMixtureScoringFunction(int starts, boolean plugIn, VariableLengthScoringFunction... component)` This constructor creates a new `VariableLengthMixtureScoringFunction`.
`VariableLengthMixtureScoringFunction(StringBuffer xml)` This is the constructor for the interface `Storable`.

Method Summary
`double` | `getLogNormalizationConstant(int length)` This method returns the logarithm of the normalization constant for a given sequence length.
`double` | `getLogPartialNormalizationConstant(int parameterIndex, int length)` This method returns the logarithm of the partial normalization constant for a given parameter index and a sequence length.
`double` | `getLogScore(Sequence seq, int start, int length)` This method computes the logarithm of the score for a given subsequence.
`double` | `getLogScoreAndPartialDerivation(Sequence seq, int start, int length, IntList indices, DoubleList partialDer)` This method computes the logarithm of the score and the partial derivations for a given subsequence.
`void` | `setStatisticForHyperparameters(int[] length, double[] weight)` This method sets the hyperparameters for the model parameters by evaluating the given statistic.

Methods inherited from class de.jstacs.scoringFunctions.mix.MixtureScoringFunction
`adjustHiddenParameters, clone, fillComponentScores, getEss, getGlobalIndexOfMotifInComponent, getHyperparameterForHiddenParameter, getIndexOfMaximalComponentFor, getInstanceName, getLogNormalizationConstantForComponent, getLogPartialNormalizationConstant, getLogScoreAndPartialDerivation, getMotifLength, getNumberOfMotifs, getNumberOfMotifsInComponent, getProfileOfScoresFor, getStrandFor, initializeMotif, initializeMotifRandomly, initializeUsingPlugIn, modifyMotif, toString`

Methods inherited from class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
`addGradientOfLogPriorTerm, cloneFunctions, computeHiddenParameter, computeLogGammaSum, determineIsNormalized, extractFurtherInformation, fromXML, getCurrentParameterValues, getFunction, getFunctions, getFurtherInformation, getIndexOfMaximalComponentFor, getIndices, getLogNormalizationConstant, getLogPriorTerm, getLogScore, getMaxIndex, getNumberOfComponents, getNumberOfParameters, getNumberOfRecommendedStarts, getProbsForComponent, getScoringFunctions, getSizeOfEventSpaceForRandomVariablesOfParameter, getXMLTag, init, initializeFunction, initializeFunctionRandomly, initializeHiddenPotentialRandomly, initializeHiddenUniformly, initWithLength, isInitialized, isNormalized, precomputeNorm, setHiddenParameters, setParameters, setParametersForFunction, toXML`

Methods inherited from class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
`getAlphabetContainer, getInitialClassParam, getLength, getLogScore, getLogScoreAndPartialDerivation, getNumberOfStarts, isNormalized`

Methods inherited from class java.lang.Object
`equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait`

Methods inherited from interface de.jstacs.scoringFunctions.NormalizableScoringFunction
`addGradientOfLogPriorTerm, getEss, getInitialClassParam, getLogNormalizationConstant, getLogPartialNormalizationConstant, getLogPriorTerm, getSizeOfEventSpaceForRandomVariablesOfParameter, isNormalized`

Methods inherited from interface de.jstacs.scoringFunctions.ScoringFunction
`clone, getAlphabetContainer, getCurrentParameterValues, getInstanceName, getLength, getLogScore, getLogScore, getLogScoreAndPartialDerivation, getLogScoreAndPartialDerivation, getNumberOfParameters, getNumberOfRecommendedStarts, initializeFunction, initializeFunctionRandomly, isInitialized, setParameters`

Methods inherited from interface de.jstacs.Storable
`toXML`

Methods inherited from interface de.jstacs.motifDiscovery.MotifDiscoverer
`getNumberOfComponents`

Constructor Detail

### VariableLengthMixtureScoringFunction

    public VariableLengthMixtureScoringFunction(int starts,
                                                boolean plugIn,
                                                VariableLengthScoringFunction... component)
                                         throws CloneNotSupportedException

  This constructor creates a new `VariableLengthMixtureScoringFunction`.

  Parameters:
    `starts` - the number of starts that should be done in an optimization
    `plugIn` - indicates whether the initial parameters for an optimization should be related to the data or randomly drawn
    `component` - the `VariableLengthScoringFunction`s
  Throws:
    `CloneNotSupportedException` - if an element of `component` could not be cloned

### VariableLengthMixtureScoringFunction

    public VariableLengthMixtureScoringFunction(StringBuffer xml)
                                         throws NonParsableException

  This is the constructor for the interface `Storable`. Creates a new `VariableLengthMixtureScoringFunction` out of a `StringBuffer`.

  Parameters:
    `xml` - the XML representation as `StringBuffer`
  Throws:
    `NonParsableException` - if the XML representation could not be parsed

Method Detail

### getLogScore

    public double getLogScore(Sequence seq,
                              int start,
                              int length)

  Description copied from interface: `VariableLengthScoringFunction`
  This method computes the logarithm of the score for a given subsequence.

  Specified by:
    `getLogScore` in interface `VariableLengthScoringFunction`
  Parameters:
    `seq` - the `Sequence`
    `start` - the start index in the `Sequence`
    `length` - the length of the `Sequence` beginning at `start`
  Returns:
    the logarithm of the score for the subsequence
  See Also:
    `ScoringFunction.getLogScore(Sequence, int)`

### getLogScoreAndPartialDerivation

    public double getLogScoreAndPartialDerivation(Sequence seq,
                                                  int start,
                                                  int length,
                                                  IntList indices,
                                                  DoubleList partialDer)

  Description copied from interface: `VariableLengthScoringFunction`
  This method computes the logarithm of the score and the partial derivations for a given subsequence.

  Specified by:
    `getLogScoreAndPartialDerivation` in interface `VariableLengthScoringFunction`
  Parameters:
    `seq` - the `Sequence`
    `start` - the start index in the `Sequence`
    `length` - the end index in the `Sequence`
    `indices` - an `IntList` of indices, after method invocation the list should contain the indices i where is not zero
    `partialDer` - a `DoubleList` of partial derivations, after method invocation the list should contain the corresponding that are not zero
  Returns:
    the logarithm of the score
  See Also:
    `ScoringFunction.getLogScoreAndPartialDerivation(Sequence, int, IntList, DoubleList)`

### getLogNormalizationConstant

    public double getLogNormalizationConstant(int length)

  Description copied from interface: `VariableLengthScoringFunction`
  This method returns the logarithm of the normalization constant for a given sequence length.

  Specified by:
    `getLogNormalizationConstant` in interface `VariableLengthScoringFunction`
  Parameters:
    `length` - the sequence length
  Returns:
    the logarithm of the normalization constant
  See Also:
    `NormalizableScoringFunction.getLogNormalizationConstant()`

### getLogPartialNormalizationConstant

    public double getLogPartialNormalizationConstant(int parameterIndex,
                                                     int length)
                                              throws Exception

  Description copied from interface: `VariableLengthScoringFunction`
  This method returns the logarithm of the partial normalization constant for a given parameter index and a sequence length.

  Specified by:
    `getLogPartialNormalizationConstant` in interface `VariableLengthScoringFunction`
  Parameters:
    `parameterIndex` - the index of the parameter
    `length` - the sequence length
  Returns:
    the logarithm of the partial normalization constant
  Throws:
    `Exception` - if something went wrong
  See Also:
    `NormalizableScoringFunction.getLogPartialNormalizationConstant(int)`

### setStatisticForHyperparameters

    public void setStatisticForHyperparameters(int[] length,
                                               double[] weight)
                                        throws Exception

  Description copied from interface: `VariableLengthScoringFunction`
  This method sets the hyperparameters for the model parameters by evaluating the given statistic. The statistic can be interpreted as follows: The model has seen a number of sequences. From these sequences it is only known how long (`length`) and how often ( `weight`) they have been seen.

  Specified by:
    `setStatisticForHyperparameters` in interface `VariableLengthScoringFunction`
  Parameters:
    `length` - the non-negative lengths of the sequences
    `weight` - the non-negative weight for the corresponding sequence
  Throws:
    `Exception` - if something went wrong
  See Also:
    `Mutable`

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