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## de.jstacs.sequenceScores.differentiable.logistic
Class LogisticDiffSS

    java.lang.Object
      de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore
          de.jstacs.sequenceScores.differentiable.logistic.LogisticDiffSS

All Implemented Interfaces:
  DifferentiableSequenceScore, SequenceScore, Storable, Cloneable

    public class LogisticDiffSS

extends AbstractDifferentiableSequenceScore

This class implements a logistic function. The score is computed by the following formula

The constraints are defined by `LogisticConstraint`s.

Author:
  Jens Keilwagen

Field Summary

Fields inherited from class de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore
`alphabets, length, r`

Fields inherited from interface de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore
`UNKNOWN`

Constructor Summary
`LogisticDiffSS(AlphabetContainer con, int length, LogisticConstraint... constraint)` This is the main constructor to create `LogisticDiffSS` instance.
`LogisticDiffSS(StringBuffer xml)` This is the constructor for `Storable`.

Method Summary
`LogisticDiffSS` | `clone()` Creates a clone (deep copy) of the current `DifferentiableSequenceScore` instance.
`protected void` | `fromXML(StringBuffer xml)` This method is called in the constructor for the `Storable` interface to create a scoring function from a `StringBuffer`.
`double[]` | `getCurrentParameterValues()` Returns a `double` array of dimension `DifferentiableSequenceScore.getNumberOfParameters()` containing the current parameter values.
`String` | `getInstanceName()` Should return a short instance name such as iMM(0), BN(2), ...
`double` | `getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)` Returns the logarithmic score for a `Sequence` beginning at position `start` in the `Sequence` and fills lists with the indices and the partial derivations.
`double` | `getLogScoreFor(Sequence seq, int start)` Returns the logarithmic score for the `Sequence` `seq` beginning at position `start` in the `Sequence`.
`int` | `getNumberOfParameters()` Returns the number of parameters in this `DifferentiableSequenceScore`.
`void` | `initializeFunction(int index, boolean freeParams, DataSet[] data, double[][] weights)` This method creates the underlying structure of the `DifferentiableSequenceScore`.
`void` | `initializeFunctionRandomly(boolean freeParams)` This method initializes the `DifferentiableSequenceScore` randomly.
`boolean` | `isInitialized()` This method can be used to determine whether the instance is initialized.
`void` | `setParameters(double[] params, int start)` This method sets the internal parameters to the values of `params` between `start` and `start + `DifferentiableSequenceScore.getNumberOfParameters()` - 1`
`String` | `toString()`
`StringBuffer` | `toXML()` This method returns an XML representation as `StringBuffer` of an instance of the implementing class.

Methods inherited from class de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore
`getAlphabetContainer, getCharacteristics, getInitialClassParam, getLength, getLogScoreAndPartialDerivation, getLogScoreAndPartialDerivation, getLogScoreFor, getLogScoreFor, getLogScoreFor, getLogScoreFor, getNumberOfRecommendedStarts, getNumberOfStarts, getNumericalCharacteristics`

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

Constructor Detail

### LogisticDiffSS

    public LogisticDiffSS(AlphabetContainer con,
                          int length,
                          LogisticConstraint... constraint)
                   throws CloneNotSupportedException

  This is the main constructor to create `LogisticDiffSS` instance.

  Parameters:
    `con` - the `AlphabetContainer` of this instance
    `length` - the length of this instance, i.e. the length of the modeled sequences
    `constraint` - the constraints used in this instance
  Throws:
    `CloneNotSupportedException` - if the constraints could not be cloned

### LogisticDiffSS

    public LogisticDiffSS(StringBuffer xml)
                   throws NonParsableException

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

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

Method Detail

### clone

    public LogisticDiffSS clone()
                         throws CloneNotSupportedException

  Description copied from interface: `DifferentiableSequenceScore`
  Creates a clone (deep copy) of the current `DifferentiableSequenceScore` instance.

  Specified by:
    `clone` in interface `DifferentiableSequenceScore`
  Specified by:
    `clone` in interface `SequenceScore`
  Overrides:
    `clone` in class `AbstractDifferentiableSequenceScore`
  Returns:
    the cloned instance of the current `DifferentiableSequenceScore`
  Throws:
    `CloneNotSupportedException` - if something went wrong while cloning the `DifferentiableSequenceScore`

### getCurrentParameterValues

    public double[] getCurrentParameterValues()
                                       throws Exception

  Description copied from interface: `DifferentiableSequenceScore`
  Returns a `double` array of dimension `DifferentiableSequenceScore.getNumberOfParameters()` containing the current parameter values. If one likes to use these parameters to start an optimization it is highly recommended to invoke `DifferentiableSequenceScore.initializeFunction(int, boolean, DataSet[], double[][])` before. After an optimization this method can be used to get the current parameter values.

  Returns:
    the current parameter values
  Throws:
    `Exception` - if no parameters exist (yet)

### getInstanceName

    public String getInstanceName()

  Description copied from interface: `SequenceScore`
  Should return a short instance name such as iMM(0), BN(2), ...

  Returns:
    a short instance name

### getLogScoreFor

    public double getLogScoreFor(Sequence seq,
                                 int start)

  Description copied from interface: `SequenceScore`
  Returns the logarithmic score for the `Sequence` `seq` beginning at position `start` in the `Sequence`.

  Parameters:
    `seq` - the `Sequence`
    `start` - the start position in the `Sequence`
  Returns:
    the logarithmic score for the `Sequence`

### getLogScoreAndPartialDerivation

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

  Description copied from interface: `DifferentiableSequenceScore`
  Returns the logarithmic score for a `Sequence` beginning at position `start` in the `Sequence` and fills lists with the indices and the partial derivations.

  Parameters:
    `seq` - the `Sequence`
    `start` - the start position 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 logarithmic score for the `Sequence`

### getNumberOfParameters

    public int getNumberOfParameters()

  Description copied from interface: `DifferentiableSequenceScore`
  Returns the number of parameters in this `DifferentiableSequenceScore`. If the number of parameters is not known yet, the method returns `DifferentiableSequenceScore.UNKNOWN`.

  Returns:
    the number of parameters in this `DifferentiableSequenceScore`
  See Also:
    `DifferentiableSequenceScore.UNKNOWN`

### initializeFunction

    public void initializeFunction(int index,
                                   boolean freeParams,
                                   DataSet[] data,
                                   double[][] weights)
                            throws Exception

  Description copied from interface: `DifferentiableSequenceScore`
  This method creates the underlying structure of the `DifferentiableSequenceScore`.

  Parameters:
    `index` - the index of the class the `DifferentiableSequenceScore` models
    `freeParams` - indicates whether the (reduced) parameterization is used
    `data` - the samples
    `weights` - the weights of the sequences in the samples
  Throws:
    `Exception` - if something went wrong

### initializeFunctionRandomly

    public void initializeFunctionRandomly(boolean freeParams)
                                    throws Exception

  Description copied from interface: `DifferentiableSequenceScore`
  This method initializes the `DifferentiableSequenceScore` randomly. It has to create the underlying structure of the `DifferentiableSequenceScore`.

  Parameters:
    `freeParams` - indicates whether the (reduced) parameterization is used
  Throws:
    `Exception` - if something went wrong

### isInitialized

    public boolean isInitialized()

  Description copied from interface: `SequenceScore`
  This method can be used to determine whether the instance is initialized. If the instance is initialized you should be able to invoke `SequenceScore.getLogScoreFor(Sequence)`.

  Returns:
    `true` if the instance is initialized, `false` otherwise

### setParameters

    public void setParameters(double[] params,
                              int start)

  Description copied from interface: `DifferentiableSequenceScore`
  This method sets the internal parameters to the values of `params` between `start` and `start + `DifferentiableSequenceScore.getNumberOfParameters()` - 1`

  Parameters:
    `params` - the new parameters
    `start` - the start index in `params`

### toXML

    public StringBuffer toXML()

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

  Returns:
    the XML representation

### fromXML

    protected void fromXML(StringBuffer xml)
                    throws NonParsableException

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

  Specified by:
    `fromXML` in class `AbstractDifferentiableSequenceScore`
  Parameters:
    `xml` - the XML representation as `StringBuffer`
  Throws:
    `NonParsableException` - if the `StringBuffer` could not be parsed
  See Also:
    `AbstractDifferentiableSequenceScore.AbstractDifferentiableSequenceScore(StringBuffer)`

### toString

    public String toString()

  Overrides:
    `toString` in class `Object`

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