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## de.jstacs.motifDiscovery
Class MotifDiscoveryAssessment

    java.lang.Object
      de.jstacs.motifDiscovery.MotifDiscoveryAssessment

    public class MotifDiscoveryAssessment

extends Object

This class enables the user to assess the prediction of motif occurrences

Author:
  Jan Grau, Jens Keilwagen

Constructor Summary
`MotifDiscoveryAssessment()`

Method Summary
`static ListResult` | `assess(Sample truth, Sample prediction, int maxDiff)` This method computes the nucleotide and site measures.
`static double[][]` | `getSorted1MinusPValuesForMotifAndFlanking(Sample data, double[][] pValues, String identifier)` This method provides some score arrays that can be used in `ScoreBasedPerformanceMeasureDefinitions` to determine some curves or area under curves based on the `p`-values of the predictions.

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

Constructor Detail

### MotifDiscoveryAssessment

    public MotifDiscoveryAssessment()

Method Detail

### assess

    public static ListResult assess(Sample truth,
                                    Sample prediction,
                                    int maxDiff)
                             throws Exception

  This method computes the nucleotide and site measures.

  Parameters:
    `truth` - the `Sample` annotated with the true annotation
    `prediction` - annotated with the predicted annotation
    `maxDiff` - the maximal difference between predicted and true start position; this value is used to determine the site measures
  Returns:
    a `ListResult` containing all `NumericalResultSet`s
  Throws:
    `Exception` - if something went wrong

### getSorted1MinusPValuesForMotifAndFlanking

    public static double[][] getSorted1MinusPValuesForMotifAndFlanking(Sample data,
                                                                       double[][] pValues,
                                                                       String identifier)
                                                                throws Exception

  This method provides some score arrays that can be used in `ScoreBasedPerformanceMeasureDefinitions` to determine some curves or area under curves based on the `p`-values of the predictions.

  Parameters:
    `data` - the data
    `pValues` - the p-value
    `identifier` - the identifier of the annotation of the positive class
  Returns:
    two arrays containing 1-`p`-value; the first contains the values for the positive class, the second contains the values for the negative class
  Throws:
    `Exception`
  See Also:
    `SequenceAnnotation.getIdentifier()`

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