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## de.jstacs.models
Class NormalizableScoringFunctionModel

    java.lang.Object
      de.jstacs.models.AbstractModel
          de.jstacs.models.NormalizableScoringFunctionModel

All Implemented Interfaces:
  Model, Storable, Cloneable

    public class NormalizableScoringFunctionModel

extends AbstractModel

This model can be used to use a NormalizableScoringFunction as model. It enables the user to train the NormalizableScoringFunction in a generative way.

Author:
  Jens Keilwagen
See Also:
  `NormalizableScoringFunction`, `LogGenDisMixFunction`

Field Summary

Fields inherited from class de.jstacs.models.AbstractModel
`alphabets, length`

Constructor Summary
`NormalizableScoringFunctionModel(NormalizableScoringFunction nsf, int threads, byte algo, double eps, double lineps, double startD)` The main constructor that creates an instance with the user given parameters.
`NormalizableScoringFunctionModel(StringBuffer stringBuff)` The standard constructor for the interface `Storable`.

Method Summary
`NormalizableScoringFunctionModel` | `clone()` Follows the conventions of `Object`'s `clone()`-method.
`protected void` | `fromXML(StringBuffer xml)` This method should only be used by the constructor that works on a `StringBuffer`.
`NormalizableScoringFunction` | `getFunction()` Returns a copy of the internally used `NormalizableScoringFunction`.
`String` | `getInstanceName()` Should return a short instance name such as iMM(0), BN(2), ...
`double` | `getLogPriorTerm()` Returns a value that is proportional to the log of the prior.
`double` | `getLogProbFor(Sequence sequence, int startpos, int endpos)` Returns the logarithm of the probability of (a part of) the given sequence given the model.
`NumericalResultSet` | `getNumericalCharacteristics()` Returns the subset of numerical values that are also returned by `Model.getCharacteristics()`.
`double` | `getProbFor(Sequence sequence, int startpos, int endpos)` Returns the probability of (a part of) the given sequence given the model.
`boolean` | `isTrained()` Returns `true` if the model has been trained successfully, `false` otherwise.
`void` | `setOutputStream(OutputStream o)` Sets the OutputStream that is used e.g. for writing information while training.
`String` | `toString()` Should give a simple representation (text) of the model as `String` .
`StringBuffer` | `toXML()` This method returns an XML representation as `StringBuffer` of an instance of the implementing class.
`void` | `train(Sample data, double[] weights)` Trains the `Model` object given the data as `Sample` using the specified weights.

Methods inherited from class de.jstacs.models.AbstractModel
`emitSample, getAlphabetContainer, getCharacteristics, getLength, getLogProbFor, getLogProbFor, getLogProbFor, getLogProbFor, getMaximalMarkovOrder, getPriorTerm, getProbFor, getProbFor, set, setNewAlphabetContainerInstance, train`

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

Constructor Detail

### NormalizableScoringFunctionModel

    public NormalizableScoringFunctionModel(NormalizableScoringFunction nsf,
                                            int threads,
                                            byte algo,
                                            double eps,
                                            double lineps,
                                            double startD)
                                     throws CloneNotSupportedException

  The main constructor that creates an instance with the user given parameters.

  Parameters:
    `nsf` - the `NormalizableScoringFunction` that should be used
    `threads` - the number of threads that should be used for optimization
    `algo` - the algorithm that should be used for the optimization
    `eps` - the epsilon for stopping the optimization
    `lineps` - the line epsilon for stopping the line search in the optimization
    `startD` - the start distance that should be used initially
  Throws:
    `CloneNotSupportedException` - if `nsf` can not be cloned

### NormalizableScoringFunctionModel

    public NormalizableScoringFunctionModel(StringBuffer stringBuff)
                                     throws NonParsableException

  The standard constructor for the interface `Storable`. Creates a new `NormalizableScoringFunctionModel` out of a `StringBuffer`.

  Parameters:
    `stringBuff` - the `StringBuffer` to be parsed
  Throws:
    `NonParsableException` - is thrown if the `StringBuffer` could not be parsed

Method Detail

### clone

    public NormalizableScoringFunctionModel clone()
                                           throws CloneNotSupportedException

  Description copied from class: `AbstractModel`
  Follows the conventions of `Object`'s `clone()`-method.

  Specified by:
    `clone` in interface `Model`
  Overrides:
    `clone` in class `AbstractModel`
  Returns:
    an object, that is a copy of the current `AbstractModel` (the member-`AlphabetContainer` isn't deeply cloned since it is assumed to be immutable). The type of the returned object is defined by the class `X` directly inherited from `AbstractModel`. Hence `X`'s `clone()`-method should work as:
    1. `Object o = (X)super.clone();`
    2. all additional member variables of `o` defined by `X` that are not of simple data-types like `int`, `double`, ... have to be deeply copied
    3. `return o`
  Throws:
    `CloneNotSupportedException` - if something went wrong while cloning

### train

    public void train(Sample data,
                      double[] weights)
               throws Exception

  Description copied from interface: `Model`
  Trains the `Model` object given the data as `Sample` using the specified weights. The weight at position i belongs to the element at position i. So the array `weight` should have the number of sequences in the sample as dimension. (Optionally it is possible to use `weight == null` if all weights have the value one.)
  This method should work non-incrementally. That means the result of the following series: `train(data1)`; `train(data2)` should be a fully trained model over `data2` and not over `data1+data2`. All parameters of the model were given by the call of the constructor.

  Parameters:
    `data` - the given sequences as `Sample`
    `weights` - the weights of the elements, each weight should be non-negative
  Throws:
    `Exception` - if the training did not succeed (e.g. the dimension of `weights` and the number of sequences in the sample do not match)
  See Also:
    `Sample.getElementAt(int)`, `Sample.ElementEnumerator`

### getProbFor

    public double getProbFor(Sequence sequence,
                             int startpos,
                             int endpos)
                      throws NotTrainedException,
                             Exception

  Description copied from interface: `Model`
  Returns the probability of (a part of) the given sequence given the model. If at least one random variable is continuous the value of density function is returned.
  It extends the possibility given by the method `Model.getProbFor(Sequence, int)` by the fact, that the model could be e.g. homogeneous and therefore the length of the sequences, whose probability should be returned, is not fixed. Additionally the end position of the part of the given sequence is given and the probability of the part from position `startpos` to `endpos` (inclusive) should be returned.
  The `length` and the `alphabets` define the type of data that can be modeled and therefore both has to be checked.

  Parameters:
    `sequence` - the given sequence
    `startpos` - the start position within the given sequence
    `endpos` - the last position to be taken into account
  Returns:
    the probability or the value of the density function of (the part of) the given sequence given the model
  Throws:
    `NotTrainedException` - if the model is not trained yet
    `Exception` - if the sequence could not be handled (e.g. `startpos > endpos`, `endpos > sequence.length`, ...) by the model

### getLogProbFor

    public double getLogProbFor(Sequence sequence,
                                int startpos,
                                int endpos)
                         throws NotTrainedException,
                                Exception

  Description copied from interface: `Model`
  Returns the logarithm of the probability of (a part of) the given sequence given the model. If at least one random variable is continuous the value of density function is returned.
  For more details see `Model.getProbFor(Sequence, int, int)`

  Specified by:
    `getLogProbFor` in interface `Model`
  Overrides:
    `getLogProbFor` in class `AbstractModel`
  Parameters:
    `sequence` - the given sequence
    `startpos` - the start position within the given sequence
    `endpos` - the last position to be taken into account
  Returns:
    the logarithm of the probability or the value of the density function of (the part of) the given sequence given the model
  Throws:
    `NotTrainedException` - if the model is not trained yet
    `Exception` - if the sequence could not be handled (e.g. `startpos >` , `endpos > sequence.length`, ...) by the model
  See Also:
    `Model.getProbFor(Sequence, int, int)`

### getLogPriorTerm

    public double getLogPriorTerm()
                           throws Exception

  Description copied from interface: `Model`
  Returns a value that is proportional to the log of the prior. For ML 0 should be returned.

  Returns:
    a value that is proportional to the log of the prior
  Throws:
    `Exception` - if something went wrong
  See Also:
    `Model.getPriorTerm()`

### getInstanceName

    public String getInstanceName()

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

  Returns:
    a short instance name

### isTrained

    public boolean isTrained()

  Description copied from interface: `Model`
  Returns `true` if the model has been trained successfully, `false` otherwise.

  Returns:
    `true` if the model has been trained successfully, `false` otherwise

### getNumericalCharacteristics

    public NumericalResultSet getNumericalCharacteristics()
                                                   throws Exception

  Description copied from interface: `Model`
  Returns the subset of numerical values that are also returned by `Model.getCharacteristics()`.

  Returns:
    the numerical characteristics of the current instance of the model
  Throws:
    `Exception` - if some of the characteristics could not be defined

### toString

    public String toString()

  Description copied from interface: `Model`
  Should give a simple representation (text) of the model as `String` .

  Specified by:
    `toString` in interface `Model`
  Overrides:
    `toString` in class `Object`
  Returns:
    the representation as `String`

### fromXML

    protected void fromXML(StringBuffer xml)
                    throws NonParsableException

  Description copied from class: `AbstractModel`
  This method should only be used by the constructor that works on a `StringBuffer`. It is the counter part of `Storable.toXML()`.

  Specified by:
    `fromXML` in class `AbstractModel`
  Parameters:
    `xml` - the XML representation of the model
  Throws:
    `NonParsableException` - if the `StringBuffer` is not parsable or the representation is conflicting
  See Also:
    `AbstractModel.AbstractModel(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.

  Returns:
    the XML representation

### setOutputStream

    public final void setOutputStream(OutputStream o)

  Sets the OutputStream that is used e.g. for writing information while training. It is possible to set `o=null`, than nothing will be written.

  Parameters:
    `o` - the OutputStream

### getFunction

    public NormalizableScoringFunction getFunction()
                                            throws CloneNotSupportedException

  Returns a copy of the internally used `NormalizableScoringFunction`.

  Returns:
    a copy of the internally used `NormalizableScoringFunction`
  Throws:
    `CloneNotSupportedException` - if the internal instance could not be cloned

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