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## de.jstacs.sequenceScores.statisticalModels.trainable.discrete
Class ConstraintManager

    java.lang.Object
      de.jstacs.sequenceScores.statisticalModels.trainable.discrete.ConstraintManager

    public class ConstraintManager

extends Object

This class manipulates and manages some constraints.

Author:
  Jens Keilwagen

Method Summary
`static void` | `computeFreqs(double ess, Constraint... constr)` This method computes the (smoothed) relative frequencies.
`static double` | `countInhomogeneous(AlphabetContainer alphabets, int length, DataSet data, double[] weights, boolean reset, Constraint... constr)` Fills the (inhomogeneous) `Constraint` `constr` with the weighted absolute frequencies of the `DataSet` `data`.
`static MEMConstraint[]` | `createConstraints(AbstractList<int[]> list, int[] alphabetLength)` Creates the constraints of a model.
`static MEMConstraint[]` | `createConstraints(AbstractList<int[]> list, int[] alphabetLength, int[] indices)` Creates the constraints for a part of a model.
`static void` | `drawFreqs(double ess, InhCondProb... constr)` This method draws relative frequencies for the constraints in `constr`.
`static ArrayList<int[]>` | `extract(int length, String encoded)` Extracts the constraints of a `String` and returns an `ArrayList` of `int[]`.
`static double` | `getEntropy(Constraint c)` Tries to compute the entropy of a `Constraint` as exact as possible.
`static double` | `getLogGammaSum(Constraint c, double ess)` Computes the sum of the differences between the logarithmic values of the prior knowledge and all counts of a `Constraint` `c`.
`static void` | `reduce(AbstractList<int[]> list)` This method tries to find and remove subconstraints that are already fulfilled by a bigger one.

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

Method Detail

### computeFreqs

    public static void computeFreqs(double ess,
                                    Constraint... constr)
                             throws IllegalArgumentException

  This method computes the (smoothed) relative frequencies. If the ess (equivalent sample size) is zero no smoothing is done.

  Parameters:
    `ess` - the ess (equivalent sample size), if the ess is zero then MLE (maximum likelihood estimation) otherwise MAPE (maximum a posteriori estimation)
    `constr` - the constraints, should be filled with absolute frequencies
  Throws:
    `IllegalArgumentException` - if the ess is negative

### countInhomogeneous

    public static double countInhomogeneous(AlphabetContainer alphabets,
                                            int length,
                                            DataSet data,
                                            double[] weights,
                                            boolean reset,
                                            Constraint... constr)
                                     throws WrongAlphabetException,
                                            IllegalArgumentException

  Fills the (inhomogeneous) `Constraint` `constr` with the weighted absolute frequencies of the `DataSet` `data`. The relative frequencies will not be computed, for this task use `computeFreqs(double, Constraint...)`

  Parameters:
    `alphabets` - the alphabets over which the constraints are defined
    `length` - the length for which the constraints are defined
    `data` - the `DataSet`
    `weights` - the weights for the `Sequence`s in the `DataSet`:
    1. `weights == null` or
    2. `weights.length = data.getNumberOfElements()`, for all `i`: `weights[i] >= 0`
    `reset` - indicates whether the constraints should be reseted
    `constr` - the (inhomogeneous) constraints to be filled
  Returns:
    the sum of the weights
  Throws:
    `WrongAlphabetException` - if the alphabet of the data is not correct
    `IllegalArgumentException` - if the weights array has wrong dimension or the element length of the data is not correct

### drawFreqs

    public static void drawFreqs(double ess,
                                 InhCondProb... constr)
                          throws IllegalArgumentException

  This method draws relative frequencies for the constraints in `constr`.

  Parameters:
    `ess` - the ess (equivalent sample size, additional pseudocount)
    `constr` - the constraints (can be filled with absolute frequencies)
  Throws:
    `IllegalArgumentException` - if the ess is negative
  See Also:
    `InhCondProb.drawParameters(double)`

### extract

    public static ArrayList<int[]> extract(int length,
                                           String encoded)
                                    throws IllegalArgumentException

  Extracts the constraints of a `String` and returns an `ArrayList` of `int[]`. This can be used to create constraints.

  Parameters:
    `length` - the sequence/model length
    `encoded` - constraints encoded in a `String`
    - items are separated by ";"
    - short notation for sets of constraints, e.g. "m2sx"
    - or each constraint as list of positions e.g. "0,1,2;"
  Returns:
    an `ArrayList` of `int[]`
  Throws:
    `IllegalArgumentException` - if something is wrong with the `length` or the encoded `String`

### getEntropy

    public static double getEntropy(Constraint c)

  Tries to compute the entropy of a `Constraint` as exact as possible.

  Parameters:
    `c` - the constraint
  Returns:
    the entropy of the constraint as exact as possible

### getLogGammaSum

    public static double getLogGammaSum(Constraint c,
                                        double ess)

  Computes the sum of the differences between the logarithmic values of the prior knowledge and all counts of a `Constraint` `c`.

  Parameters:
    `c` - the constraint
    `ess` - the ess (equivalent sample size)
  Returns:
    the sum of the differences

### reduce

    public static void reduce(AbstractList<int[]> list)

  This method tries to find and remove subconstraints that are already fulfilled by a bigger one. The method only looks for the positions, so it is recommended to use this method before any learning step.

  Parameters:
    `list` - the list of all constraints

### createConstraints

    public static MEMConstraint[] createConstraints(AbstractList<int[]> list,
                                                    int[] alphabetLength,
                                                    int[] indices)

  Creates the constraints for a part of a model.

  Parameters:
    `list` - the list of all cliques, each clique is used for one constraint
    `alphabetLength` - the array of alphabet lengths for each position
    `indices` - the positions used in this part of the model
  Returns:
    the array of constraints
  See Also:
    `extract(int, String)`, `createConstraints(AbstractList, int[])`

### createConstraints

    public static MEMConstraint[] createConstraints(AbstractList<int[]> list,
                                                    int[] alphabetLength)

  Creates the constraints of a model.

  Parameters:
    `list` - the list of all cliques, each clique is used for one constraint
    `alphabetLength` - the array of alphabet lengths for each position
  Returns:
    the array of constraints
  See Also:
    `extract(int, String)`, `createConstraints(AbstractList, int[], int[])`

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