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## de.jstacs.classifier
Class AbstractScoreBasedClassifier

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

All Implemented Interfaces:
  Storable, Cloneable

Direct Known Subclasses:
  MappingClassifier, ModelBasedClassifier, SamplingScoreBasedClassifier, ScoreClassifier

    public abstract class AbstractScoreBasedClassifier

extends AbstractClassifier

This class is the main class for all score based classifiers. Score based classifiers enable you to compute many different measures easily. For instance one can use the package "ROCR" in R to compute or plot many of them.

Author:
  Jens Keilwagen, Jan Grau, Andre Gohr

Nested Class Summary
`static class` | `AbstractScoreBasedClassifier.DoubleTableResult` This class is for `Result`s given as a table of `double` s.

Constructor Summary
`AbstractScoreBasedClassifier(AlphabetContainer abc, int classes)` The constructor for a homogeneous classifier.
`AbstractScoreBasedClassifier(AlphabetContainer abc, int classes, double classWeight)` The constructor for a homogeneous classifier.
`AbstractScoreBasedClassifier(AlphabetContainer abc, int length, int classes)` The constructor for an inhomogeneous classifier.
`AbstractScoreBasedClassifier(AlphabetContainer abc, int length, int classes, double classWeight)` The constructor for an inhomogeneous classifier.
`AbstractScoreBasedClassifier(StringBuffer xml)` The standard constructor for the interface `Storable`.

Method Summary
`protected void` | `check(Sample s)` This method checks if the given `Sample` can be used.
`protected void` | `check(Sequence seq)` This method checks if the given `Sequence` can be used.
`byte` | `classify(Sequence seq)` This method classifies a sequence and returns the index `i` of the class to which the sequence is assigned with `0 < i < getNumberOfClasses()`.
`protected byte` | `classify(Sequence seq, boolean check)` This method classifies a `Sequence`.
`AbstractScoreBasedClassifier` | `clone()`
`protected void` | `createDefaultClassWeights(int classes, double val)` This method creates new class weights.
`protected void` | `extractFurtherClassifierInfosFromXML(StringBuffer xml)` Extracts further information of a classifier from an XML representation.
`protected double` | `getClassWeight(int index)` Returns the class weight for the class with a given `index`.
`double[]` | `getClassWeights()` Returns the specific class weights of a `AbstractScoreBasedClassifier`.
`protected StringBuffer` | `getFurtherClassifierInfos()` This method returns further information of a classifier as a `StringBuffer`.
`int` | `getNumberOfClasses()` Returns the number of classes that can be distinguished.
`double[]` | `getPValue(Sample candidates, Sample bg)` Returns the p-values for all `Sequence`s in the `Sample` `candidates` with respect to a given background `Sample` .
`double` | `getPValue(Sequence candidate, Sample bg)` Returns the p-value for a `Sequence` `candidate` with respect to a given background `Sample`.
`protected LinkedList<? extends Result>` | `getResults(Sample[] s, MeasureParameters params, boolean exceptionIfNotComputeable, boolean all)` This method computes the results for any evaluation of the classifier.
`double` | `getScore(Sequence seq, int i)` This method returns the score for a given `Sequence` and a given class.
`protected abstract 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`.
`void` | `setClassWeights(boolean add, double... weights)` Sets new class weights.
`protected void` | `setClassWeights(boolean add, double[] weights, int start)` Sets new class weights.
`void` | `setThresholdClassWeights(boolean add, double t)` Sets a new threshold for 2-class-classifiers.
`ConfusionMatrix` | `test(Sample... testData)` This method computes the confusion matrix for a given array of test data.

Methods inherited from class de.jstacs.classifier.AbstractClassifier
`classify, evaluate, evaluateAll, getAlphabetContainer, getCharacteristics, getClassificationRate, getClassifierAnnotation, getInstanceName, getLength, getMeasuresForEvaluate, getMeasuresForEvaluateAll, getNumericalCharacteristics, getXMLTag, isTrained, setNewAlphabetContainerInstance, toXML, train, train`

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

Constructor Detail

### AbstractScoreBasedClassifier

    public AbstractScoreBasedClassifier(AlphabetContainer abc,
                                        int classes)

  The constructor for a homogeneous classifier. Such a classifier can handle sequences of arbitrary length. The class weights are set initially to `0`.

  Parameters:
    `abc` - the alphabets that are used
    `classes` - the number of different classes
  See Also:
    `AbstractScoreBasedClassifier(AlphabetContainer, int, int, double)`

### AbstractScoreBasedClassifier

    public AbstractScoreBasedClassifier(AlphabetContainer abc,
                                        int classes,
                                        double classWeight)

  The constructor for a homogeneous classifier. Such a classifier can handle sequences of arbitrary length. The class weights are set initially to `classWeight`.

  Parameters:
    `abc` - the alphabets that are used
    `classes` - the number of different classes
    `classWeight` - the value of all class weights
  See Also:
    `AbstractScoreBasedClassifier(AlphabetContainer, int, int, double)`

### AbstractScoreBasedClassifier

    public AbstractScoreBasedClassifier(AlphabetContainer abc,
                                        int length,
                                        int classes)

  The constructor for an inhomogeneous classifier. Such a classifier can handle sequences of fixed length. The class weights are set initially to `0`.

  Parameters:
    `abc` - the alphabets that are used
    `length` - the length of the sequences that can be classified
    `classes` - the number of different classes
  See Also:
    `AbstractScoreBasedClassifier(AlphabetContainer, int, int, double)`

### AbstractScoreBasedClassifier

    public AbstractScoreBasedClassifier(AlphabetContainer abc,
                                        int length,
                                        int classes,
                                        double classWeight)
                                 throws IllegalArgumentException

  The constructor for an inhomogeneous classifier. Such a classifier can handle sequences of fixed length. The class weights are set initially to `classWeight`.

  Parameters:
    `abc` - the alphabets that are used
    `length` - the length of the sequences that can be classified
    `classes` - the number of different classes
    `classWeight` - the value of all class weights
  Throws:
    `IllegalArgumentException` - if the length and the possible length of the `AlphabetContainer` does not match or the number of classes is less than 2
  See Also:
    `AbstractClassifier.AbstractClassifier(AlphabetContainer, int)`

### AbstractScoreBasedClassifier

    public AbstractScoreBasedClassifier(StringBuffer xml)
                                 throws NonParsableException

  The standard constructor for the interface `Storable`. Creates a new `AbstractScoreBasedClassifier` out of its XML representation.

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

Method Detail

### clone

    public AbstractScoreBasedClassifier clone()
                                       throws CloneNotSupportedException

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

### classify

    public byte classify(Sequence seq)
                  throws Exception

  Description copied from class: `AbstractClassifier`
  This method classifies a sequence and returns the index `i` of the class to which the sequence is assigned with `0 < i < getNumberOfClasses()`.
  This method should check that the sequence is defined over the underlying alphabet and length.

  Specified by:
    `classify` in class `AbstractClassifier`
  Parameters:
    `seq` - the sequence to be classified
  Returns:
    the index of the class to which the sequence is assigned
  Throws:
    `Exception` - if the classifier is not trained or something is wrong with the sequence

### getResults

    protected LinkedList<? extends Result> getResults(Sample[] s,
                                                      MeasureParameters params,
                                                      boolean exceptionIfNotComputeable,
                                                      boolean all)
                                               throws Exception

  Description copied from class: `AbstractClassifier`
  This method computes the results for any evaluation of the classifier.

  Overrides:
    `getResults` in class `AbstractClassifier`
  Parameters:
    `s` - the array of `Sample`s
    `params` - the current parameters
    `exceptionIfNotComputeable` - indicates the method throws an `Exception` if a measure could not be computed
    `all` - indicates the method computes all results or only the numerical results
  Returns:
    a list of results
  Throws:
    `Exception` - if something went wrong
  See Also:
    `AbstractClassifier.evaluate(MeasureParameters, boolean, Sample...)`, `AbstractClassifier.evaluateAll(MeasureParameters, boolean, Sample...)`

### getClassWeights

    public double[] getClassWeights()

  Returns the specific class weights of a `AbstractScoreBasedClassifier`.

  Returns:
    the class weights of the classifier

### getNumberOfClasses

    public int getNumberOfClasses()

  Description copied from class: `AbstractClassifier`
  Returns the number of classes that can be distinguished. For example if distinguishing between foreground and background this method should return 2, even if you use a mixture model for either foreground or background.

  Specified by:
    `getNumberOfClasses` in class `AbstractClassifier`
  Returns:
    the number of classes that can be distinguished

### getScore

    public double getScore(Sequence seq,
                           int i)
                    throws Exception

  This method returns the score for a given `Sequence` and a given class.

  Parameters:
    `seq` - the given `Sequence`
    `i` - the index of the class
  Returns:
    the score for a given `Sequence` and a given class
  Throws:
    `Exception` - if something went wrong
  See Also:
    `getScore(Sequence, int, boolean)`

### setClassWeights

    public final void setClassWeights(boolean add,
                                      double... weights)
                               throws ClassDimensionException

  Sets new class weights.
  The logarithmic probabilities of an item `i` given class 0 to class `n` are computed to classify this item into a class. The class weights are added to each of these logarithmic probabilities. As higher (relational) the class weight of class `j`, as more probable it becomes, that any item is classified into this class.
  Class weights do not have to be logarithmic probabilities. If , the class weights may be interpreted as logarithmic class-a-priori-probabilities.

  Parameters:
    `add` - indicates if the class weights are added to the current class weights
    `weights` - the array of weights, for each class the weight that is added in a classification
  Throws:
    `ClassDimensionException` - if something is wrong with the number of classes

### setClassWeights

    protected final void setClassWeights(boolean add,
                                         double[] weights,
                                         int start)

  Sets new class weights.
  Only for internal use.

  Parameters:
    `add` - indicates if the class weights are added to the current class weights
    `weights` - an array of weights that might have more entries than the classifier has classes
    `start` - the start index
  See Also:
    `setClassWeights(boolean, double...)`

### setThresholdClassWeights

    public final void setThresholdClassWeights(boolean add,
                                               double t)
                                        throws OperationNotSupportedException

  Sets a new threshold for 2-class-classifiers.
  Only available if this `AbstractScoreBasedClassifier` distinguishes between 2 classes 0 and 1. In this case, `t` will be interpreted as . A large `t` (greater than 0) makes the classifier to decide more often for class 1. A small `t` (smaller than 0) makes the classifier to decide more often for class 0.

  Parameters:
    `add` - indicates if the class weights are added to the current class weights
    `t` - the new threshold
  Throws:
    `OperationNotSupportedException` - if the classifier is no 2-class-classifier

### test

    public ConfusionMatrix test(Sample... testData)
                         throws Exception

  Description copied from class: `AbstractClassifier`
  This method computes the confusion matrix for a given array of test data.

  Overrides:
    `test` in class `AbstractClassifier`
  Parameters:
    `testData` - the given array of test data
  Returns:
    the confusion matrix
  Throws:
    `ClassDimensionException` - if the number of `Sample`s is incorrect
    `Exception` - if something else went wrong

### 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.

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

### check

    protected void check(Sample s)
                  throws NotTrainedException,
                         IllegalArgumentException

  This method checks if the given `Sample` can be used.

  Parameters:
    `s` - the `Sample` to be checked
  Throws:
    `NotTrainedException` - if the classifier is not trained
    `IllegalArgumentException` - if something is wrong with the `Sample` `s`
  See Also:
    `AbstractClassifier.setNewAlphabetContainerInstance(AlphabetContainer)`

### check

    protected void check(Sequence seq)
                  throws NotTrainedException,
                         IllegalArgumentException

  This method checks if the given `Sequence` can be used.

  Parameters:
    `seq` - the `Sequence` to be checked
  Throws:
    `NotTrainedException` - if the classifier is not trained
    `IllegalArgumentException` - if something is wrong with the `Sequence` `seq`

### classify

    protected byte classify(Sequence seq,
                            boolean check)
                     throws Exception

  This method classifies a `Sequence`. It enables you to check the constraints (`alphabets`, `length`, `AbstractClassifier.isTrained()` ).

  Parameters:
    `seq` - the `Sequence`
    `check` - indicates if the constraints will be checked
  Returns:
    the index of the class the `Sequence` is assigned to
  Throws:
    `Exception` - if something went wrong
  See Also:
    `check(Sequence)`

### createDefaultClassWeights

    protected void createDefaultClassWeights(int classes,
                                             double val)
                                      throws IllegalArgumentException

  This method creates new class weights. Each class weight has the same value `val`. So the class weights do not have any influence on the classification.

  Parameters:
    `classes` - the number of different classes
    `val` - the value that is used for all classes
  Throws:
    `IllegalArgumentException` - if the number of classes is below 2

### 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.

  Specified by:
    `extractFurtherClassifierInfosFromXML` in class `AbstractClassifier`
  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)`

### getClassWeight

    protected double getClassWeight(int index)

  Returns the class weight for the class with a given `index`.

  Parameters:
    `index` - the given index of the class
  Returns:
    the class weight

### getScore

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

  This method returns the score for a given `Sequence` and a given class.

  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

  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.

  Parameters:
    `s` - the `Sample`
  Returns:
    the array of scores
  Throws:
    `Exception` - if something went wrong

### getPValue

    public double getPValue(Sequence candidate,
                            Sample bg)
                     throws Exception

  Returns the p-value for a `Sequence` `candidate` with respect to a given background `Sample`.
  The p-value is the percentage of background `Sequence`s that have a score that is at least as high as the score for the `candidate`.
  It is not recommended to use this method in a `for`-loop. In such cases one should use the method that works on two `Sample`s.

  Parameters:
    `candidate` - the candidate `Sequence`
    `bg` - the background `Sample`
  Returns:
    the p-value for the `Sequence` `candidate`
  Throws:
    `Exception` - if something went wrong
  See Also:
    `getPValue(Sample, Sample)`, `PValueComputation.getPValue(double[], double)`

### getPValue

    public double[] getPValue(Sample candidates,
                              Sample bg)
                       throws Exception

  Returns the p-values for all `Sequence`s in the `Sample` `candidates` with respect to a given background `Sample` .
  The p-value is the percentage of background `Sequence`s that have a score that is at least as high as the score for a `Sequence` in `candidates`.

  Parameters:
    `candidates` - the `Sample` with candidate sequences
    `bg` - the background sample
  Returns:
    the p-values for all sequences in `candidates`
  Throws:
    `Exception` - if something went wrong
  See Also:
    `getPValue(Sequence, Sample)`, `PValueComputation.getPValue(double[], double)`

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