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## de.jstacs.motifDiscovery
Class SignificantMotifOccurrencesFinder

    java.lang.Object
      de.jstacs.motifDiscovery.SignificantMotifOccurrencesFinder

    public class SignificantMotifOccurrencesFinder

extends Object

This class enables the user to predict motif occurrences given a specific significance level.

Author:
  Jan Grau, Jens Keilwagen

Nested Class Summary
`static class` | `SignificantMotifOccurrencesFinder.RandomSeqType`

Constructor Summary
`SignificantMotifOccurrencesFinder(MotifDiscoverer disc, Sample bg, double sign)` This constructor creates an instance of `SignificantMotifOccurrencesFinder` that uses a `Sample` to determine the siginificance level.
`SignificantMotifOccurrencesFinder(MotifDiscoverer disc, SignificantMotifOccurrencesFinder.RandomSeqType type, int numSequences, double sign)` This constructor creates an instance of `SignificantMotifOccurrencesFinder` that uses the given `SignificantMotifOccurrencesFinder.RandomSeqType` to determine the siginificance level.

Method Summary
`Sample` | `annotateMotifs(int startPos, Sample data)` This method annotates a `Sample` starting in each sequence at `startPos`.
`Sample` | `annotateMotifs(int startPos, Sample data, int addMax)` This method annotates a `Sample` starting in each sequence at `startPos`.
`Sample` | `annotateMotifs(Sample data)` This method annotates a `Sample`.
`Sample` | `annotateMotifs(Sample data, int addMax)` This method annotates a `Sample`.
`MotifAnnotation[]` | `findSignificantMotifOccurrences(int motif, Sequence seq, int start)` This method finds the significant motif occurrences in the sequence.
`double[][]` | `getPValuesForEachNucleotide(Sample data, int component, int motif, boolean addOnlyBest)` This method determines the p-value for each symbol to be annotated at least in one motif occurrence of the motif with index `index` in the component `component`.

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

Constructor Detail

### SignificantMotifOccurrencesFinder

    public SignificantMotifOccurrencesFinder(MotifDiscoverer disc,
                                             SignificantMotifOccurrencesFinder.RandomSeqType type,
                                             int numSequences,
                                             double sign)

  This constructor creates an instance of `SignificantMotifOccurrencesFinder` that uses the given `SignificantMotifOccurrencesFinder.RandomSeqType` to determine the siginificance level.

  Parameters:
    `disc` - the `MotifDiscoverer` for the prediction
    `type` - the type that determines how the significance level is determined
    `numSequences` - the number of sampled sequence instances used to determine the significance level
    `sign` - the significance level

### SignificantMotifOccurrencesFinder

    public SignificantMotifOccurrencesFinder(MotifDiscoverer disc,
                                             Sample bg,
                                             double sign)

  This constructor creates an instance of `SignificantMotifOccurrencesFinder` that uses a `Sample` to determine the siginificance level.

  Parameters:
    `disc` - the `MotifDiscoverer` for the prediction
    `bg` - the background data set
    `sign` - the significance level

Method Detail

### findSignificantMotifOccurrences

    public MotifAnnotation[] findSignificantMotifOccurrences(int motif,
                                                             Sequence seq,
                                                             int start)
                                                      throws Exception

  This method finds the significant motif occurrences in the sequence.

  Parameters:
    `motif` - the motif index
    `seq` - the sequence
    `start` - the start position
  Returns:
    an array of `MotifAnnotation` for the sequence
  Throws:
    `Exception`

### annotateMotifs

    public Sample annotateMotifs(int startPos,
                                 Sample data)
                          throws Exception

  This method annotates a `Sample` starting in each sequence at `startPos`.

  Parameters:
    `startPos` - the start position used for all sequences
    `data` - the `Sample`
  Returns:
    an annotated `Sample`
  Throws:
    `Exception` - if something went wrong
  See Also:
    `annotateMotifs(int, Sample, int)`

### annotateMotifs

    public Sample annotateMotifs(Sample data)
                          throws Exception

  This method annotates a `Sample`.

  Parameters:
    `data` - the `Sample`
  Returns:
    an annotated `Sample`
  Throws:
    `Exception` - if something went wrong
  See Also:
    `annotateMotifs(int, Sample, int)`

### annotateMotifs

    public Sample annotateMotifs(Sample data,
                                 int addMax)
                          throws Exception

  This method annotates a `Sample`. At most, `addMax` motif occurrences of each motif instance will be annotated.

  Parameters:
    `data` - the `Sample`
    `addMax` - the number of motif occurrences that can at most be annotated for each motif instance
  Returns:
    an annotated `Sample`
  Throws:
    `Exception` - if something went wrong
  See Also:
    `annotateMotifs(int, Sample, int)`

### annotateMotifs

    public Sample annotateMotifs(int startPos,
                                 Sample data,
                                 int addMax)
                          throws Exception

  This method annotates a `Sample` starting in each sequence at `startPos`. At most, `addMax` motif occurrences of each motif instance will be annotated.

  Parameters:
    `startPos` - the start position used for all sequences
    `data` - the `Sample`
    `addMax` - the number of motif occurrences that can at most be annotated for each motif instance
  Returns:
    an annotated `Sample`
  Throws:
    `Exception` - if something went wrong
  See Also:
    `annotateMotifs(int, Sample, int)`

### getPValuesForEachNucleotide

    public double[][] getPValuesForEachNucleotide(Sample data,
                                                  int component,
                                                  int motif,
                                                  boolean addOnlyBest)
                                           throws Exception

  This method determines the p-value for each symbol to be annotated at least in one motif occurrence of the motif with index `index` in the component `component`.

  Parameters:
    `data` - the `Sample`
    `component` - the component index
    `motif` - the motif index
    `addOnlyBest` - a switch whether to add only the best
  Returns:
    an array containing for each sequence an array with the `p`-value for each symbol in the sequence
  Throws:
    `Exception` - if something went wrong
  See Also:
    `MotifDiscoveryAssessment.getSorted1MinusPValuesForMotifAndFlanking(Sample, double[][], String)`

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