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## de.jstacs.motifDiscovery
Interface MutableMotifDiscoverer

All Superinterfaces:
  Cloneable, MotifDiscoverer, Storable

All Known Implementing Classes:
  HiddenMotifsMixture, IndependentProductScoringFunction, MixtureScoringFunction, VariableLengthMixtureScoringFunction

    public interface MutableMotifDiscoverer

extends MotifDiscoverer

This is the interface that any tool for de-novo motif discovery should implement that allows any modify-operations like shift, shrink and expand. These operations are possible if the motif is mutable.

Author:
  Jan Grau, Jens Keilwagen
See Also:
  `Mutable`

Nested Class Summary

Nested classes/interfaces inherited from interface de.jstacs.motifDiscovery.MotifDiscoverer
`MotifDiscoverer.KindOfProfile`

Method Summary
`void` | `adjustHiddenParameters(int index, Sample[] data, double[][] weights)` Adjusts all hidden parameters including duration and mixture parameters according to the current values of the remaining parameters.
`void` | `initializeMotif(int motifIndex, Sample data, double[] weights)` This method allows to initialize the model of a motif manually using a weighted sample.
`void` | `initializeMotifRandomly(int motif)` This method initializes the motif with index `motif` randomly using for instance `ScoringFunction.initializeFunctionRandomly(boolean)`.
`boolean` | `modifyMotif(int motifIndex, int offsetLeft, int offsetRight)` Manually modifies the motif model with index `motifIndex`.

Methods inherited from interface de.jstacs.motifDiscovery.MotifDiscoverer
`clone, getGlobalIndexOfMotifInComponent, getIndexOfMaximalComponentFor, getMotifLength, getNumberOfComponents, getNumberOfMotifs, getNumberOfMotifsInComponent, getProfileOfScoresFor, getStrandProbabilitiesFor`

Methods inherited from interface de.jstacs.Storable
`toXML`

Method Detail

### modifyMotif

    boolean modifyMotif(int motifIndex,
                        int offsetLeft,
                        int offsetRight)
                        throws Exception

  Manually modifies the motif model with index `motifIndex`. The two offsets `offsetLeft` and `offsetRight` define how many positions the left or right border positions shall be moved. Negative numbers indicate moves to the left while positive numbers correspond to moves to the right. The distribution for sequences to the left and right side of the motif shall be computed internally.

  Parameters:
    `motifIndex` - the index of the motif in the motif discoverer
    `offsetLeft` - the offset on the left side
    `offsetRight` - the offset on the right side
  Returns:
    `true` if the motif model was modified otherwise `false`
  Throws:
    `Exception` - if some unexpected error occurred during the modification
  See Also:
    `modifyMotif(int, int, int)`, `Mutable.modify(int, int)`

### initializeMotif

    void initializeMotif(int motifIndex,
                         Sample data,
                         double[] weights)
                         throws Exception

  This method allows to initialize the model of a motif manually using a weighted sample.

  Parameters:
    `motifIndex` - the index of the motif in the motif discoverer
    `data` - the sample of sequences
    `weights` - either `null` or an array of length `data.getNumberofElements()` with non-negative weights.
  Throws:
    `Exception` - if initialize was not possible

### initializeMotifRandomly

    void initializeMotifRandomly(int motif)
                                 throws Exception

  This method initializes the motif with index `motif` randomly using for instance `ScoringFunction.initializeFunctionRandomly(boolean)`. Furthermore, if available, it also initializes the positional distribution.

  Parameters:
    `motif` - the index of the motif
  Throws:
    `Exception` - either if the index is wrong or if it is thrown by the method `ScoringFunction.initializeFunctionRandomly(boolean)`

### adjustHiddenParameters

    void adjustHiddenParameters(int index,
                                Sample[] data,
                                double[][] weights)
                                throws Exception

  Adjusts all hidden parameters including duration and mixture parameters according to the current values of the remaining parameters.

  Parameters:
    `index` - the index of the class of this `MutableMotifDiscoverer`
    `data` - the array of data for all classes
    `weights` - the weights for all sequences in data
  Throws:
    `Exception` - thrown if the hidden parameters could not be adjusted

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