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## de.jstacs.scoringFunctions.directedGraphicalModels
Class MutableMarkovModelScoringFunction

    java.lang.Object
      de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
          de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction
              de.jstacs.scoringFunctions.directedGraphicalModels.MutableMarkovModelScoringFunction

All Implemented Interfaces:
  InstantiableFromParameterSet, Mutable, NormalizableScoringFunction, SamplingScoringFunction, ScoringFunction, Storable, Cloneable

    public class MutableMarkovModelScoringFunction

extends BayesianNetworkScoringFunction
implements Mutable, SamplingScoringFunction

This class implements a `AbstractNormalizableScoringFunction` for an inhomogeneous Markov model. The modeled length can be modified which might be very important for de-novo motif discovery.

Author:
  Jan Grau, Jens Keilwagen

Field Summary

Fields inherited from class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction
`ess, isTrained, logNormalizationConstant, numFreePars, nums, order, parameters, plugInParameters, structureMeasure, trees`

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

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

Constructor Summary
`MutableMarkovModelScoringFunction(AlphabetContainer alphabet, int length, double ess, boolean plugInParameters, InhomogeneousMarkov structureMeasure)` This constructor creates an instance without any prior for the modeled length.
`MutableMarkovModelScoringFunction(AlphabetContainer alphabet, int length, double ess, boolean plugInParameters, InhomogeneousMarkov structureMeasure, DurationScoringFunction lengthPenalty)` This constructor creates an instance with an prior for the modeled length.
`MutableMarkovModelScoringFunction(AlphabetContainer alphabet, int length, double ess, boolean plugInParameters, int order, DurationScoringFunction lengthPenalty)` This constructor creates an instance with an prior for the modeled length.
`MutableMarkovModelScoringFunction(StringBuffer xml)` The standard constructor for the interface `Storable`.

Method Summary
`protected void` | `fromXML(StringBuffer source)` This method is called in the constructor for the `Storable` interface to create a scoring function from a `StringBuffer`.
`double` | `getLogPriorTerm()` This method computes a value that is proportional to ``NormalizableScoringFunction.getEss()` * `NormalizableScoringFunction.getLogNormalizationConstant()` + Math.log( prior )` where `prior` is the prior for the parameters of this model.
`int` | `getOrder()` Returns the order of the inhomogeneous Markov model.
`int[][]` | `getSamplingGroups(int parameterOffset)` Returns groups of indexes of parameters that shall be drawn together in a sampling procedure
`boolean` | `modify(int offsetLeft, int offsetRight)` Manually modifies the model.
`StringBuffer` | `toXML()` This method returns an XML representation as `StringBuffer` of an instance of the implementing class.

Methods inherited from class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction
`addGradientOfLogPriorTerm, clone, createTrees, getCurrentParameterSet, getCurrentParameterValues, getEss, getInstanceName, getLogNormalizationConstant, getLogPartialNormalizationConstant, getLogScore, getLogScoreAndPartialDerivation, getNumberOfParameters, getPositionDependentKMerProb, getPositionForParameter, getPWM, getSizeOfEventSpaceForRandomVariablesOfParameter, initializeFunction, initializeFunctionRandomly, isInitialized, precomputeNormalization, setParameters, setPlugInParameters, toString`

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

Constructor Detail

### MutableMarkovModelScoringFunction

    public MutableMarkovModelScoringFunction(AlphabetContainer alphabet,
                                             int length,
                                             double ess,
                                             boolean plugInParameters,
                                             int order,
                                             DurationScoringFunction lengthPenalty)
                                      throws Exception

  This constructor creates an instance with an prior for the modeled length.

  Parameters:
    `alphabet` - the `AlphabetContainer` of the `MutableMarkovModelScoringFunction`
    `length` - the initial length of the modeled sequences
    `ess` - the equivalent sample size
    `plugInParameters` - a switch whether to use plug-in parameters of not
    `order` - the order of the Markov model
    `lengthPenalty` - the prior on the modeled sequence length
  Throws:
    `Exception` - if super class constructor throws an `Exception` or if the `lengthPenalty` does not allow the initial length

### MutableMarkovModelScoringFunction

    public MutableMarkovModelScoringFunction(AlphabetContainer alphabet,
                                             int length,
                                             double ess,
                                             boolean plugInParameters,
                                             InhomogeneousMarkov structureMeasure)
                                      throws Exception

  This constructor creates an instance without any prior for the modeled length.

  Parameters:
    `alphabet` - the `AlphabetContainer` of the `MutableMarkovModelScoringFunction`
    `length` - the initial length of the modeled sequences
    `ess` - the equivalent sample size
    `plugInParameters` - a switch whether to use plug-in parameters of not
    `structureMeasure` - an `InhomogeneousMarkov` `Measure` for the structure
  Throws:
    `Exception` - if super class constructor throws an `Exception`

### MutableMarkovModelScoringFunction

    public MutableMarkovModelScoringFunction(AlphabetContainer alphabet,
                                             int length,
                                             double ess,
                                             boolean plugInParameters,
                                             InhomogeneousMarkov structureMeasure,
                                             DurationScoringFunction lengthPenalty)
                                      throws Exception

  This constructor creates an instance with an prior for the modeled length.

  Parameters:
    `alphabet` - the `AlphabetContainer` of the `MutableMarkovModelScoringFunction`
    `length` - the initial length of the modeled sequences
    `ess` - the equivalent sample size
    `plugInParameters` - a switch whether to use plug-in parameters of not
    `structureMeasure` - a `InhomogeneousMarkov` `Measure` for the structure
    `lengthPenalty` - the prior on the modeled sequence length
  Throws:
    `Exception` - if super class constructor throws an `Exception` or if the `lengthPenalty` does not allow the initial length

### MutableMarkovModelScoringFunction

    public MutableMarkovModelScoringFunction(StringBuffer xml)
                                      throws NonParsableException

  The standard constructor for the interface `Storable`. Recreates a `MutableMarkovModelScoringFunction` from its XML representation as saved by the method `toXML()`.

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

Method Detail

### fromXML

    protected void fromXML(StringBuffer source)
                    throws NonParsableException

  Description copied from class: `AbstractNormalizableScoringFunction`
  This method is called in the constructor for the `Storable` interface to create a scoring function from a `StringBuffer`.

  Overrides:
    `fromXML` in class `BayesianNetworkScoringFunction`
  Parameters:
    `source` - the XML representation as `StringBuffer`
  Throws:
    `NonParsableException` - if the `StringBuffer` could not be parsed
  See Also:
    `AbstractNormalizableScoringFunction.AbstractNormalizableScoringFunction(StringBuffer)`

### toXML

    public StringBuffer toXML()

  Description copied from interface: `Storable`
  This method returns an XML representation as `StringBuffer` of an instance of the implementing class.

  Specified by:
    `toXML` in interface `Storable`
  Overrides:
    `toXML` in class `BayesianNetworkScoringFunction`
  Returns:
    the XML representation

### getLogPriorTerm

    public double getLogPriorTerm()

  Description copied from interface: `NormalizableScoringFunction`
  This method computes a value that is proportional to

  ``NormalizableScoringFunction.getEss()` * `NormalizableScoringFunction.getLogNormalizationConstant()` + Math.log( prior )`

  where `prior` is the prior for the parameters of this model.

  Specified by:
    `getLogPriorTerm` in interface `NormalizableScoringFunction`
  Overrides:
    `getLogPriorTerm` in class `BayesianNetworkScoringFunction`
  Returns:
    a value that is proportional to ``NormalizableScoringFunction.getEss()` * `NormalizableScoringFunction.getLogNormalizationConstant()` + Math.log( prior ).`
  See Also:
    `NormalizableScoringFunction.getEss()`, `NormalizableScoringFunction.getLogNormalizationConstant()`

### getOrder

    public int getOrder()

  Returns the order of the inhomogeneous Markov model.

  Returns:
    the order

### modify

    public boolean modify(int offsetLeft,
                          int offsetRight)

  Description copied from interface: `Mutable`
  Manually modifies the model. The two offsets `offsetLeft` and `offsetRight` define how many positions the left or right border positions shall be moved. Negative numbers indicate moves to the left while positive numbers correspond to moves to the right.

  Specified by:
    `modify` in interface `Mutable`
  Parameters:
    `offsetLeft` - the offset on the left side
    `offsetRight` - the offset on the right side
  Returns:
    `true` if the motif model was modified otherwise `false`

### getSamplingGroups

    public int[][] getSamplingGroups(int parameterOffset)

  Description copied from interface: `SamplingScoringFunction`
  Returns groups of indexes of parameters that shall be drawn together in a sampling procedure

  Specified by:
    `getSamplingGroups` in interface `SamplingScoringFunction`
  Parameters:
    `parameterOffset` - a global offset on the parameter indexes
  Returns:
    the groups of indexes. The first dimension represents the different groups while the second dimension contains the parameters that shall be sampled together. Internal parameter indexes need to be increased by `parameterOffset`.

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