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## de.jstacs.classifier.modelBased
Class ModelBasedClassifier

    java.lang.Object
      de.jstacs.classifier.AbstractClassifier
          de.jstacs.classifier.AbstractScoreBasedClassifier
              de.jstacs.classifier.modelBased.ModelBasedClassifier

All Implemented Interfaces:
  Storable, Cloneable

Direct Known Subclasses:
  SharedStructureClassifier

    public class ModelBasedClassifier

extends AbstractScoreBasedClassifier

This class is the main class for all model based classifiers. The score for this class is the logarithm of the joint probability `p(x,c|\lambda)`.

Author:
  Jens Keilwagen
See Also:
  `Model`

Nested Class Summary

Nested classes/interfaces inherited from class de.jstacs.classifier.AbstractScoreBasedClassifier
`AbstractScoreBasedClassifier.DoubleTableResult`

Field Summary
`protected Model[]` | `models` The internal `Model`s.

Constructor Summary
`protected` | `ModelBasedClassifier(boolean cloneModels, Model... models)` This constructor creates a new instance with the given `Model`s and clones these if necessary.
`` | `ModelBasedClassifier(Model... models)` The default constructor that creates a new instance with the given `Model`s.
`` | `ModelBasedClassifier(StringBuffer xml)` The standard constructor for the interface `Storable`.

Method Summary
`byte[]` | `classify(Sample s)` This method classifies all sequences of a sample and returns an array of indices of the classes to which the respective sequences are assigned with for each index `i` in the array `0 < i < getNumberOfClasses()`.
`ModelBasedClassifier` | `clone()`
`protected void` | `extractFurtherClassifierInfosFromXML(StringBuffer xml)` Extracts further information of a classifier from an XML representation.
`ResultSet` | `getCharacteristics()` Returns some information characterizing or describing the current instance of the classifier.
`CategoricalResult[]` | `getClassifierAnnotation()` Returns an array of `Result`s of dimension `AbstractClassifier.getNumberOfClasses()` that contains information about the classifier and for each class.
`protected StringBuffer` | `getFurtherClassifierInfos()` This method returns further information of a classifier as a `StringBuffer`.
`String` | `getInstanceName()` Returns a short description of the classifier.
`Model` | `getModel(int classIndex)` Returns a clone of the `Model` for a specified class.
`NumericalResultSet` | `getNumericalCharacteristics()` Returns the subset of numerical values that are also returned by `AbstractClassifier.getCharacteristics()`.
`static int` | `getPossibleLength(Model... models)` This method returns the possible length of a classifier that would use the given `Model`s.
`protected double` | `getScore(Sequence seq, int i, boolean check)` This method returns the score for a given `Sequence` and a given class.
`double[]` | `getScores(Sample s)` This method returns the scores of the classifier for any `Sequence` in the `Sample`.
`protected String` | `getXMLTag()` Returns the `String` that is used as tag for the XML representation of the classifier.
`boolean` | `isTrained()` This method gives information about the state of the classifier.
`boolean` | `setNewAlphabetContainerInstance(AlphabetContainer abc)` This method tries to set a new instance of an `AlphabetContainer` for the current classifier.
`void` | `train(Sample[] s, double[][] weights)` This method trains a classifier over an array of weighted `Sample` s.

Methods inherited from class de.jstacs.classifier.AbstractScoreBasedClassifier
`check, check, classify, classify, createDefaultClassWeights, getClassWeight, getClassWeights, getNumberOfClasses, getPValue, getPValue, getResults, getScore, setClassWeights, setThresholdClassWeights, test`

Methods inherited from class de.jstacs.classifier.AbstractClassifier
`evaluate, evaluateAll, getAlphabetContainer, getClassificationRate, getLength, getMeasuresForEvaluate, getMeasuresForEvaluateAll, toXML, train`

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

Field Detail

### models

    protected Model[] models

  The internal `Model`s. `Model` 0 handles class 0; `Model` 1 handles class 1 ... etc.

Constructor Detail

### ModelBasedClassifier

    protected ModelBasedClassifier(boolean cloneModels,
                                   Model... models)
                            throws IllegalArgumentException,
                                   CloneNotSupportedException,
                                   ClassDimensionException

  This constructor creates a new instance with the given `Model`s and clones these if necessary.

  Parameters:
    `cloneModels` - a switch to decide whether to clone the `Model` or not
    `models` - the `Model`s
  Throws:
    `IllegalArgumentException` - if the `Model`s do not describe a common domain of sequences
    `CloneNotSupportedException` - if at least one `Model` could not be cloned
    `ClassDimensionException` - if the number of classes is below 2
  See Also:
    `AbstractScoreBasedClassifier.AbstractScoreBasedClassifier(AlphabetContainer, int, int, double)`

### ModelBasedClassifier

    public ModelBasedClassifier(Model... models)
                         throws IllegalArgumentException,
                                CloneNotSupportedException,
                                ClassDimensionException

  The default constructor that creates a new instance with the given `Model`s.

  Parameters:
    `models` - the `Model`s
  Throws:
    `IllegalArgumentException` - if the `Model`s do not describe a common domain of sequences
    `CloneNotSupportedException` - if at least one `Model` could not be cloned
    `ClassDimensionException` - if the number of classes is below 2
  See Also:
    `ModelBasedClassifier(boolean, Model...)`

### ModelBasedClassifier

    public ModelBasedClassifier(StringBuffer xml)
                         throws NonParsableException

  The standard constructor for the interface `Storable`. Constructs a `ModelBasedClassifier` out of its XML representation.

  Parameters:
    `xml` - the XML representation as `StringBuffer`
  Throws:
    `NonParsableException` - if the `ModelBasedClassifier` could not be reconstructed out of the XML representation (the `StringBuffer` could not be parsed)
  See Also:
    `AbstractScoreBasedClassifier.AbstractScoreBasedClassifier(StringBuffer)`, `Storable`

Method Detail

### getPossibleLength

    public static int getPossibleLength(Model... models)
                                 throws IllegalArgumentException

  This method returns the possible length of a classifier that would use the given `Model`s.

  Parameters:
    `models` - the `Model`s that will be tested
  Returns:
    the length of a classifier that would use the given models
  Throws:
    `IllegalArgumentException` - if no classifier could be created since the `Model`s have incompatible lengths

### clone

    public ModelBasedClassifier clone()
                               throws CloneNotSupportedException

  Overrides:
    `clone` in class `AbstractScoreBasedClassifier`
  Throws:
    `CloneNotSupportedException`

### getCharacteristics

    public ResultSet getCharacteristics()
                                 throws Exception

  Description copied from class: `AbstractClassifier`
  Returns some information characterizing or describing the current instance of the classifier. This could be for instance the number of edges for a Bayesian network or an image showing some representation of the model of a class. The set of characteristics should always include the XML representation of the classifier. The corresponding result type is `StorableResult`.

  Overrides:
    `getCharacteristics` in class `AbstractClassifier`
  Returns:
    the characteristics of the current instance of the classifier
  Throws:
    `Exception` - if some of the characteristics could not be defined
  See Also:
    `StorableResult`, `AbstractClassifier.getNumericalCharacteristics()`, `ResultSet.ResultSet(de.jstacs.results.Result[][])`

### getInstanceName

    public String getInstanceName()

  Description copied from class: `AbstractClassifier`
  Returns a short description of the classifier.

  Specified by:
    `getInstanceName` in class `AbstractClassifier`
  Returns:
    a short description of the classifier

### getModel

    public Model getModel(int classIndex)
                   throws CloneNotSupportedException

  Returns a clone of the `Model` for a specified class.

  Parameters:
    `classIndex` - the index of the specified class
  Returns:
    a clone of the `Model` of the specified class
  Throws:
    `CloneNotSupportedException` - if the `Model` could not be cloned
  See Also:
    `Model.clone()`

### getNumericalCharacteristics

    public NumericalResultSet getNumericalCharacteristics()
                                                   throws Exception

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

  Specified by:
    `getNumericalCharacteristics` in class `AbstractClassifier`
  Returns:
    the numerical characteristics
  Throws:
    `Exception` - if some of the characteristics could not be defined

### isTrained

    public boolean isTrained()

  Description copied from class: `AbstractClassifier`
  This method gives information about the state of the classifier.

  Specified by:
    `isTrained` in class `AbstractClassifier`
  Returns:
    `true` if the classifier is trained and therefore able to classify sequences, otherwise `false`

### setNewAlphabetContainerInstance

    public final boolean setNewAlphabetContainerInstance(AlphabetContainer abc)

  Description copied from class: `AbstractClassifier`
  This method tries to set a new instance of an `AlphabetContainer` for the current classifier.
  This instance has to be consistent with the underlying instance of an `AlphabetContainer`.
  This method can be very useful to save time.

  Overrides:
    `setNewAlphabetContainerInstance` in class `AbstractClassifier`
  Parameters:
    `abc` - the alphabets
  Returns:
    `true` if the new `AlphabetContainer` could be set, `false` otherwise
  See Also:
    `AbstractClassifier.getAlphabetContainer()`, `AlphabetContainer.checkConsistency(AlphabetContainer)`

### train

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

  Description copied from class: `AbstractClassifier`
  This method trains a classifier over an array of weighted `Sample` s. That is why the following has to be fulfilled:
  - `s.length == weights.length`
  - and for all i: `weights[i] == null || s[i].getNumberOfElements() == weights[i].length`.
  This method should work non-incrementally as the method `AbstractClassifier.train(Sample...)`.
  This method should check that the `Sample`s are defined over the underlying alphabet and length.

  Specified by:
    `train` in class `AbstractClassifier`
  Parameters:
    `s` - an array of `Sample`s
    `weights` - the weights for the `Sample`s
  Throws:
    `Exception` - if the weights are incorrect or the training did not succeed
  See Also:
    `AbstractClassifier.train(Sample...)`

### getFurtherClassifierInfos

    protected StringBuffer getFurtherClassifierInfos()

  Description copied from class: `AbstractClassifier`
  This method returns further information of a classifier as a `StringBuffer`. This method is used by the method `AbstractClassifier.toXML()` and should not be made public.

  Overrides:
    `getFurtherClassifierInfos` in class `AbstractScoreBasedClassifier`
  Returns:
    further information of a classifier as a `StringBuffer`
  See Also:
    `AbstractClassifier.toXML()`

### getScore

    protected double getScore(Sequence seq,
                              int i,
                              boolean check)
                       throws Exception

  Description copied from class: `AbstractScoreBasedClassifier`
  This method returns the score for a given `Sequence` and a given class.

  Specified by:
    `getScore` in class `AbstractScoreBasedClassifier`
  Parameters:
    `seq` - the `Sequence`
    `i` - the index of the class
    `check` - the switch to decide whether to check `AlphabetContainer` and the length of the `Sequence` or not
  Returns:
    the score for a given `Sequence` and a given class
  Throws:
    `NotTrainedException` - if the classifier is not trained
    `IllegalArgumentException` - if something is wrong with the `Sequence` `seq`
    `Exception` - if something went wrong

### getScores

    public double[] getScores(Sample s)
                       throws Exception

  Description copied from class: `AbstractScoreBasedClassifier`
  This method returns the scores of the classifier for any `Sequence` in the `Sample`. The scores are stored in the array according to the index of the `Sequence` in the `Sample`.
  Only for 2-class-classifiers.

  Overrides:
    `getScores` in class `AbstractScoreBasedClassifier`
  Parameters:
    `s` - the `Sample`
  Returns:
    the array of scores
  Throws:
    `Exception` - if something went wrong

### classify

    public byte[] classify(Sample s)
                    throws Exception

  Description copied from class: `AbstractClassifier`
  This method classifies all sequences of a sample and returns an array of indices of the classes to which the respective sequences are assigned with for each index `i` in the array `0 < i < getNumberOfClasses()`.

  Overrides:
    `classify` in class `AbstractClassifier`
  Parameters:
    `s` - the sample to be classified
  Returns:
    an array of class assignments
  Throws:
    `Exception` - if something went wrong during the classification

### getXMLTag

    protected String getXMLTag()

  Description copied from class: `AbstractClassifier`
  Returns the `String` that is used as tag for the XML representation of the classifier. This method is used by the methods `AbstractClassifier.fromXML(StringBuffer)` and `AbstractClassifier.toXML()`.

  Specified by:
    `getXMLTag` in class `AbstractClassifier`
  Returns:
    the `String` that is used as tag for the XML representation of the classifier

### extractFurtherClassifierInfosFromXML

    protected void extractFurtherClassifierInfosFromXML(StringBuffer xml)
                                                 throws NonParsableException

  Description copied from class: `AbstractClassifier`
  Extracts further information of a classifier from an XML representation. This method is used by the method `AbstractClassifier.fromXML(StringBuffer)` and should not be made public.

  Overrides:
    `extractFurtherClassifierInfosFromXML` in class `AbstractScoreBasedClassifier`
  Parameters:
    `xml` - the XML representation as `StringBuffer`
  Throws:
    `NonParsableException` - if the information could not be parsed out of the XML representation (the `StringBuffer` could not be parsed)
  See Also:
    `AbstractClassifier.fromXML(StringBuffer)`

### getClassifierAnnotation

    public CategoricalResult[] getClassifierAnnotation()

  Description copied from class: `AbstractClassifier`
  Returns an array of `Result`s of dimension `AbstractClassifier.getNumberOfClasses()` that contains information about the classifier and for each class.
  `res[0] = new CategoricalResult( "classifier", "the kind of classifier", getInstanceName() );
  res[1] = new CategoricalResult( "class info 0", "some information about the class", "info0" );
  res[2] = new CategoricalResult( "class info 1", "some information about the class", "info1" );
  ...`

  Specified by:
    `getClassifierAnnotation` in class `AbstractClassifier`
  Returns:
    an array of `Result`s that contains information about the classifier

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