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## de.jstacs.scoringFunctions.mix.motifSearch
Class HiddenMotifsMixture

    java.lang.Object
      de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
          de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
              de.jstacs.scoringFunctions.mix.motifSearch.HiddenMotifsMixture

All Implemented Interfaces:
  MotifDiscoverer, MutableMotifDiscoverer, NormalizableScoringFunction, ScoringFunction, Storable, Cloneable

    public class HiddenMotifsMixture

extends AbstractMixtureScoringFunction
implements MutableMotifDiscoverer

This class handles mixtures with at least one hidden motif.

Author:
  Jens Keilwagen

Nested Class Summary

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

Field Summary
`static boolean` | `CONTAINS_ALWAYS_A_MOTIF` This constant indicates that in each sequence has one binding site of a motif instance (similar to OOPS).
`static boolean` | `CONTAINS_SOMETIMES_A_MOTIF` This constant indicates that a sequence possibly has one binding site of a motif instance (similar to ZOOPS).

Fields inherited from class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
`componentScore, dList, freeParams, function, hiddenParameter, hiddenPotential, iList, logGammaSum, logHiddenNorm, logHiddenPotential, norm, optimizeHidden, paramRef, partNorm`

Fields inherited from class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
`alphabets, length, r`

Fields inherited from interface de.jstacs.scoringFunctions.ScoringFunction
`UNKNOWN`

Constructor Summary
`HiddenMotifsMixture(boolean type, int length, int starts, boolean plugIn, HomogeneousScoringFunction bg, NormalizableScoringFunction[] motif, DurationScoringFunction[] posPrior, boolean plugInBg)` This constructor creates an instance of `HiddenMotifsMixture` that allows to have one site of the specified motifs in a `Sequence`.
`HiddenMotifsMixture(boolean type, int length, int starts, boolean plugIn, HomogeneousScoringFunction bg, NormalizableScoringFunction motif, DurationScoringFunction posPrior, boolean plugInBg)` This constructor creates an instance of `HiddenMotifsMixture` that is either an OOPS or a ZOOPS model depending on the chosen `type`.
`HiddenMotifsMixture(StringBuffer source)` This is the constructor for the interface `Storable`.

Method Summary
`void` | `adjustHiddenParameters(int classIndex, Sample[] data, double[][] dataWeights)` Adjusts all hidden parameters including duration and mixture parameters according to the current values of the remaining parameters.
`HiddenMotifsMixture` | `clone()` Creates a clone (deep copy) of the current `ScoringFunction` instance.
`protected void` | `extractFurtherInformation(StringBuffer xml)` This method is the opposite of `AbstractMixtureScoringFunction.getFurtherInformation()`.
`protected int` | `fillComponentScoreOf(int i, Sequence seq, int start)` This method fills an internal array with the partial scores.
`protected void` | `fillComponentScores(Sequence seq, int start)` Fills the internal array `AbstractMixtureScoringFunction.componentScore` with the logarithmic scores of the components given a `Sequence`.
`double` | `getEss()` Returns the equivalent sample size (ess) of this model, i.e. the equivalent sample size for the class or component that is represented by this model.
`protected StringBuffer` | `getFurtherInformation()` This method is used to append further information of the instance to the XML representation.
`int` | `getGlobalIndexOfMotifInComponent(int component, int motif)` Returns the global index of the `motif` used in `component`.
`double` | `getHyperparameterForHiddenParameter(int index)` This method returns the hyperparameter for the hidden parameter with index `index`.
`int` | `getIndexOfMaximalComponentFor(Sequence sequence)` Returns the index of the component with the maximal score for the sequence `sequence`.
`String` | `getInstanceName()` Returns a short instance name.
`protected double` | `getLogNormalizationConstantForComponent(int i)` Computes the logarithm of the normalization constant for the component `i`.
`double` | `getLogPartialNormalizationConstant(int parameterIndex)` Returns the logarithm of the partial normalization constant for the parameter with index `parameterIndex`.
`double` | `getLogScore(Sequence seq, int start)` Returns the logarithmic score for the `Sequence` `seq` beginning at position `start` in the `Sequence`.
`double` | `getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)` Returns the logarithmic score for a `Sequence` beginning at position `start` in the `Sequence` and fills lists with the indices and the partial derivations.
`int` | `getMotifLength(int motif)` This method returns the length of the motif with index `motif` .
`int` | `getNumberOfMotifs()` Returns the number of motifs for this `MotifDiscoverer`.
`int` | `getNumberOfMotifsInComponent(int component)` Returns the number of motifs that are used in the component `component` of this `MotifDiscoverer`.
`double[]` | `getProfileOfScoresFor(int component, int motif, Sequence sequence, int startpos, MotifDiscoverer.KindOfProfile dist)` Returns the profile of the scores for component `component` and motif `motif` at all possible start positions of the motif in the sequence `sequence` beginning at `startpos`.
`StrandedLocatedSequenceAnnotationWithLength.Strand` | `getStrandFor(int component, int motif, Sequence sequence, int startpos)` This method returns the strand for a given subsequence if it is considered as site of the motif model in a specific component.
`void` | `initializeFunctionRandomly(boolean freeParams)` This method initializes the `ScoringFunction` randomly.
`void` | `initializeMotif(int motif, 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)`.
`protected void` | `initializeUsingPlugIn(int index, boolean freeParams, Sample[] data, double[][] weights)` This method initializes the functions using the data in some way.
`boolean` | `modifyMotif(int motif, int offsetLeft, int offsetRight)` Manually modifies the motif model with index `motifIndex`.
`String` | `toString()`

Methods inherited from class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
`addGradientOfLogPriorTerm, cloneFunctions, computeHiddenParameter, computeLogGammaSum, determineIsNormalized, fromXML, getCurrentParameterValues, getFunction, getFunctions, getIndexOfMaximalComponentFor, getIndices, getLogNormalizationConstant, getLogPriorTerm, getMaxIndex, getNumberOfComponents, getNumberOfParameters, getNumberOfRecommendedStarts, getProbsForComponent, getScoringFunctions, getSizeOfEventSpaceForRandomVariablesOfParameter, getXMLTag, init, initializeFunction, initializeHiddenPotentialRandomly, initializeHiddenUniformly, initWithLength, isInitialized, isNormalized, precomputeNorm, setHiddenParameters, setParameters, setParametersForFunction, toXML`

Methods inherited from class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
`getAlphabetContainer, getInitialClassParam, getLength, getLogScore, getLogScoreAndPartialDerivation, getNumberOfStarts, isNormalized`

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

Methods inherited from interface de.jstacs.motifDiscovery.MotifDiscoverer
`getNumberOfComponents`

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

Field Detail

### CONTAINS_ALWAYS_A_MOTIF

    public static final boolean CONTAINS_ALWAYS_A_MOTIF

  This constant indicates that in each sequence has one binding site of a motif instance (similar to OOPS).

  See Also:
    Constant Field Values

### CONTAINS_SOMETIMES_A_MOTIF

    public static final boolean CONTAINS_SOMETIMES_A_MOTIF

  This constant indicates that a sequence possibly has one binding site of a motif instance (similar to ZOOPS).

  See Also:
    Constant Field Values

Constructor Detail

### HiddenMotifsMixture

    public HiddenMotifsMixture(boolean type,
                               int length,
                               int starts,
                               boolean plugIn,
                               HomogeneousScoringFunction bg,
                               NormalizableScoringFunction motif,
                               DurationScoringFunction posPrior,
                               boolean plugInBg)
                        throws Exception

  This constructor creates an instance of `HiddenMotifsMixture` that is either an OOPS or a ZOOPS model depending on the chosen `type`.

  Parameters:
    `type` - the type of hidden motifs, either `CONTAINS_ALWAYS_A_MOTIF` or `CONTAINS_SOMETIMES_A_MOTIF`
    `length` - the length of the modeled sequences (e.g. 500)
    `starts` - the number of recommended starts
    `plugIn` - a switch whether to use plug-in or randomly chosen parameter when using `ScoringFunction.initializeFunction(int, boolean, Sample[], double[][])`
    `bg` - the `ScoringFunction` for the overall background (i.e. flanking sequence that does not contain a motif)
    `motif` - the `ScoringFunction` for the motif
    `posPrior` - the `ScoringFunction` for the position
    `plugInBg` - a switch whether to plug in the (old = last) parameters of the background model, if `false` the background model is initialized again
  Throws:
    `Exception` - if something went wrong (e.g. the `AlphabetContainer` is not simple, ...)

### HiddenMotifsMixture

    public HiddenMotifsMixture(boolean type,
                               int length,
                               int starts,
                               boolean plugIn,
                               HomogeneousScoringFunction bg,
                               NormalizableScoringFunction[] motif,
                               DurationScoringFunction[] posPrior,
                               boolean plugInBg)
                        throws Exception

  This constructor creates an instance of `HiddenMotifsMixture` that allows to have one site of the specified motifs in a `Sequence`.

  Parameters:
    `type` - the type of hidden motifs, either `CONTAINS_ALWAYS_A_MOTIF` or `CONTAINS_SOMETIMES_A_MOTIF`
    `length` - the length of the modeled sequences (e.g. 500)
    `starts` - the number of recommended starts
    `plugIn` - a switch whether to use plug-in or randomly chosen parameter when using `ScoringFunction.initializeFunction(int, boolean, Sample[], double[][])`
    `bg` - the `ScoringFunction` for the overall background (i.e. flanking sequence that does not contain a motif)
    `motif` - the `ScoringFunction`s for the sequence motif
    `posPrior` - the `ScoringFunction`s for the position of the the sequence motifs
    `plugInBg` - a switch whether to plug in the parameters of the background model in some way, if `false` the background model is initialized uniformly
  Throws:
    `Exception` - if something went wrong (e.g. the `AlphabetContainer` is not simple, ...)

### HiddenMotifsMixture

    public HiddenMotifsMixture(StringBuffer source)
                        throws NonParsableException

  This is the constructor for the interface `Storable`. Recreates a new `HiddenMotifsMixture` out of a `StringBuffer` as returned by `AbstractMixtureScoringFunction.toXML()`.

  Parameters:
    `source` - the XML representation as `StringBuffer`
  Throws:
    `NonParsableException` - if the representation could not be parsed

Method Detail

### clone

    public HiddenMotifsMixture clone()
                              throws CloneNotSupportedException

  Description copied from interface: `ScoringFunction`
  Creates a clone (deep copy) of the current `ScoringFunction` instance.

  Specified by:
    `clone` in interface `ScoringFunction`
  Overrides:
    `clone` in class `AbstractMixtureScoringFunction`
  Returns:
    the cloned instance of the current `ScoringFunction`
  Throws:
    `CloneNotSupportedException` - if something went wrong while cloning the `ScoringFunction`

### getHyperparameterForHiddenParameter

    public double getHyperparameterForHiddenParameter(int index)

  Description copied from class: `AbstractMixtureScoringFunction`
  This method returns the hyperparameter for the hidden parameter with index `index`.

  Specified by:
    `getHyperparameterForHiddenParameter` in class `AbstractMixtureScoringFunction`
  Parameters:
    `index` - the index of the hidden parameter
  Returns:
    the hyperparameter for the hidden parameter

### getLogNormalizationConstantForComponent

    protected double getLogNormalizationConstantForComponent(int i)

  Description copied from class: `AbstractMixtureScoringFunction`
  Computes the logarithm of the normalization constant for the component `i`.

  Specified by:
    `getLogNormalizationConstantForComponent` in class `AbstractMixtureScoringFunction`
  Parameters:
    `i` - the index of the component
  Returns:
    the logarithm of the normalization constant of the component

### getLogPartialNormalizationConstant

    public double getLogPartialNormalizationConstant(int parameterIndex)
                                              throws Exception

  Description copied from interface: `NormalizableScoringFunction`
  Returns the logarithm of the partial normalization constant for the parameter with index `parameterIndex`. This is the logarithm of the partial derivation of the normalization constant for the parameter with index `parameterIndex`,
  .

  Specified by:
    `getLogPartialNormalizationConstant` in interface `NormalizableScoringFunction`
  Parameters:
    `parameterIndex` - the index of the parameter
  Returns:
    the logarithm of the partial normalization constant
  Throws:
    `Exception` - if something went wrong with the normalization
  See Also:
    `NormalizableScoringFunction.getLogNormalizationConstant()`

### getEss

    public double getEss()

  Description copied from interface: `NormalizableScoringFunction`
  Returns the equivalent sample size (ess) of this model, i.e. the equivalent sample size for the class or component that is represented by this model.

  Specified by:
    `getEss` in interface `NormalizableScoringFunction`
  Returns:
    the equivalent sample size.

### initializeFunctionRandomly

    public void initializeFunctionRandomly(boolean freeParams)
                                    throws Exception

  Description copied from interface: `ScoringFunction`
  This method initializes the `ScoringFunction` randomly. It has to create the underlying structure of the `ScoringFunction`.

  Specified by:
    `initializeFunctionRandomly` in interface `ScoringFunction`
  Overrides:
    `initializeFunctionRandomly` in class `AbstractMixtureScoringFunction`
  Parameters:
    `freeParams` - indicates whether the (reduced) parameterization is used
  Throws:
    `Exception` - if something went wrong

### getInstanceName

    public String getInstanceName()

  Description copied from interface: `ScoringFunction`
  Returns a short instance name.

  Specified by:
    `getInstanceName` in interface `ScoringFunction`
  Returns:
    a short instance name

### fillComponentScoreOf

    protected int fillComponentScoreOf(int i,
                                       Sequence seq,
                                       int start)

  This method fills an internal array with the partial scores.

  Parameters:
    `i` - the index of the component
    `seq` - the `Sequence`
    `start` - the start position
  Returns:
    the number of computed partial scores

### fillComponentScores

    protected void fillComponentScores(Sequence seq,
                                       int start)

  Description copied from class: `AbstractMixtureScoringFunction`
  Fills the internal array `AbstractMixtureScoringFunction.componentScore` with the logarithmic scores of the components given a `Sequence`.

  Specified by:
    `fillComponentScores` in class `AbstractMixtureScoringFunction`
  Parameters:
    `seq` - the sequence
    `start` - the start position in `seq`

### getLogScore

    public double getLogScore(Sequence seq,
                              int start)

  Description copied from interface: `ScoringFunction`
  Returns the logarithmic score for the `Sequence` `seq` beginning at position `start` in the `Sequence`.

  Specified by:
    `getLogScore` in interface `ScoringFunction`
  Overrides:
    `getLogScore` in class `AbstractMixtureScoringFunction`
  Parameters:
    `seq` - the `Sequence`
    `start` - the start position in the `Sequence`
  Returns:
    the logarithmic score for the `Sequence`

### getLogScoreAndPartialDerivation

    public double getLogScoreAndPartialDerivation(Sequence seq,
                                                  int start,
                                                  IntList indices,
                                                  DoubleList partialDer)

  Description copied from interface: `ScoringFunction`
  Returns the logarithmic score for a `Sequence` beginning at position `start` in the `Sequence` and fills lists with the indices and the partial derivations.

  Specified by:
    `getLogScoreAndPartialDerivation` in interface `ScoringFunction`
  Parameters:
    `seq` - the `Sequence`
    `start` - the start position in the `Sequence`
    `indices` - an `IntList` of indices, after method invocation the list should contain the indices i where is not zero
    `partialDer` - a `DoubleList` of partial derivations, after method invocation the list should contain the corresponding that are not zero
  Returns:
    the logarithmic score for the `Sequence`

### toString

    public String toString()

  Overrides:
    `toString` in class `Object`

### getFurtherInformation

    protected StringBuffer getFurtherInformation()

  Description copied from class: `AbstractMixtureScoringFunction`
  This method is used to append further information of the instance to the XML representation. This method is designed to allow subclasses to add information to the XML representation.

  Overrides:
    `getFurtherInformation` in class `AbstractMixtureScoringFunction`
  Returns:
    the further information as XML code in a `StringBuffer`
  See Also:
    `AbstractMixtureScoringFunction.extractFurtherInformation(StringBuffer)`

### extractFurtherInformation

    protected void extractFurtherInformation(StringBuffer xml)
                                      throws NonParsableException

  Description copied from class: `AbstractMixtureScoringFunction`
  This method is the opposite of `AbstractMixtureScoringFunction.getFurtherInformation()`. It extracts further information of the instance from a XML representation.

  Overrides:
    `extractFurtherInformation` in class `AbstractMixtureScoringFunction`
  Parameters:
    `xml` - the `StringBuffer` containing the information to be extracted as XML code
  Throws:
    `NonParsableException` - if the `StringBuffer` could not be parsed
  See Also:
    `AbstractMixtureScoringFunction.getFurtherInformation()`

### modifyMotif

    public boolean modifyMotif(int motif,
                               int offsetLeft,
                               int offsetRight)
                        throws Exception

  Description copied from interface: `MutableMotifDiscoverer`
  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.

  Specified by:
    `modifyMotif` in interface `MutableMotifDiscoverer`
  Parameters:
    `motif` - 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:
    `MutableMotifDiscoverer.modifyMotif(int, int, int)`, `Mutable.modify(int, int)`

### initializeMotif

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

  Description copied from interface: `MutableMotifDiscoverer`
  This method allows to initialize the model of a motif manually using a weighted sample.

  Specified by:
    `initializeMotif` in interface `MutableMotifDiscoverer`
  Parameters:
    `motif` - 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

    public void initializeMotifRandomly(int motif)
                                 throws Exception

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

  Specified by:
    `initializeMotifRandomly` in interface `MutableMotifDiscoverer`
  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)`

### getNumberOfMotifs

    public int getNumberOfMotifs()

  Description copied from interface: `MotifDiscoverer`
  Returns the number of motifs for this `MotifDiscoverer`.

  Specified by:
    `getNumberOfMotifs` in interface `MotifDiscoverer`
  Returns:
    the number of motifs

### getNumberOfMotifsInComponent

    public int getNumberOfMotifsInComponent(int component)

  Description copied from interface: `MotifDiscoverer`
  Returns the number of motifs that are used in the component `component` of this `MotifDiscoverer`.

  Specified by:
    `getNumberOfMotifsInComponent` in interface `MotifDiscoverer`
  Parameters:
    `component` - the component of the `MotifDiscoverer`
  Returns:
    the number of motifs

### getIndexOfMaximalComponentFor

    public int getIndexOfMaximalComponentFor(Sequence sequence)

  Description copied from interface: `MotifDiscoverer`
  Returns the index of the component with the maximal score for the sequence `sequence`.

  Specified by:
    `getIndexOfMaximalComponentFor` in interface `MotifDiscoverer`
  Parameters:
    `sequence` - the given sequence
  Returns:
    the index of the component with the maximal score for the given sequence

### getGlobalIndexOfMotifInComponent

    public int getGlobalIndexOfMotifInComponent(int component,
                                                int motif)

  Description copied from interface: `MotifDiscoverer`
  Returns the global index of the `motif` used in `component`. The index returned must be at least 0 and less than `MotifDiscoverer.getNumberOfMotifs()`.

  Specified by:
    `getGlobalIndexOfMotifInComponent` in interface `MotifDiscoverer`
  Parameters:
    `component` - the component index
    `motif` - the motif index in the component
  Returns:
    the global index of the `motif`in `component```

### getProfileOfScoresFor

    public double[] getProfileOfScoresFor(int component,
                                          int motif,
                                          Sequence sequence,
                                          int startpos,
                                          MotifDiscoverer.KindOfProfile dist)
                                   throws WrongLengthException

  Description copied from interface: `MotifDiscoverer`
  Returns the profile of the scores for component `component` and motif `motif` at all possible start positions of the motif in the sequence `sequence` beginning at `startpos`. This array should be of length
  `sequence.length() - startpos - motifs[motif].length() + 1`.
  A high score should encode for a probable start position.

  Specified by:
    `getProfileOfScoresFor` in interface `MotifDiscoverer`
  Parameters:
    `component` - the component index
    `motif` - the index of the motif in the component
    `sequence` - the given sequence
    `startpos` - the start position in the sequence
    `dist` - indicates the kind of profile
  Returns:
    the profile of scores
  Throws:
    `WrongLengthException`

### getMotifLength

    public int getMotifLength(int motif)

  Description copied from interface: `MotifDiscoverer`
  This method returns the length of the motif with index `motif` .

  Specified by:
    `getMotifLength` in interface `MotifDiscoverer`
  Parameters:
    `motif` - the index of the motif
  Returns:
    the length of the motif with index `motif`

### adjustHiddenParameters

    public void adjustHiddenParameters(int classIndex,
                                       Sample[] data,
                                       double[][] dataWeights)
                                throws Exception

  Description copied from interface: `MutableMotifDiscoverer`
  Adjusts all hidden parameters including duration and mixture parameters according to the current values of the remaining parameters.

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

### initializeUsingPlugIn

    protected void initializeUsingPlugIn(int index,
                                         boolean freeParams,
                                         Sample[] data,
                                         double[][] weights)
                                  throws Exception

  Description copied from class: `AbstractMixtureScoringFunction`
  This method initializes the functions using the data in some way.

  Specified by:
    `initializeUsingPlugIn` in class `AbstractMixtureScoringFunction`
  Parameters:
    `index` - the class index
    `freeParams` - if `true`, the (reduced) parameterization is used``
    `data` - the data
    `weights` - the weights for the data
  Throws:
    `Exception` - if the initialization could not be done
  See Also:
    `ScoringFunction.initializeFunction(int, boolean, Sample[], double[][])`

### getStrandFor

    public StrandedLocatedSequenceAnnotationWithLength.Strand getStrandFor(int component,
                                                                           int motif,
                                                                           Sequence sequence,
                                                                           int startpos)
                                                                    throws Exception

  Description copied from interface: `MotifDiscoverer`
  This method returns the strand for a given subsequence if it is considered as site of the motif model in a specific component.

  Specified by:
    `getStrandFor` in interface `MotifDiscoverer`
  Parameters:
    `component` - the component index
    `motif` - the index of the motif in the component
    `sequence` - the given sequence
    `startpos` - the start position in the sequence
  Returns:
    the predicted strand annotation
  Throws:
    `Exception` - if the strand could not be computed for any reasons

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