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## org.biojava.bio.dist
Class DistributionTools

    java.lang.Object
      org.biojava.bio.dist.DistributionTools

    public final class DistributionTools

extends Object

A class to hold static methods for calculations and manipulations using Distributions.

Since:
  1.2
Author:
  Mark Schreiber, Matthew Pocock

Method Summary
`static boolean` | `areEmissionSpectraEqual(Distribution[] a, Distribution[] b)` Compares the emission spectra of two distribution arrays.
`static boolean` | `areEmissionSpectraEqual(Distribution a, Distribution b)` Compares the emission spectra of two distributions.
`static Distribution` | `average(Distribution[] dists)` Averages two or more distributions.
`static double` | `bitsOfInformation(Distribution observed)` Calculates the total bits of information for a distribution.
`static Distribution` | `countToDistribution(Count c)` Make a distribution from a count.
`static Distribution[]` | `distOverAlignment(Alignment a)` Equivalent to distOverAlignment(a, false, 0.0).
`static Distribution[]` | `distOverAlignment(Alignment a, boolean countGaps)` Creates an array of distributions, one for each column of the alignment.
`static Distribution[]` | `distOverAlignment(Alignment a, boolean countGaps, double nullWeight)` Creates an array of distributions, one for each column of the alignment.
`protected static Sequence` | `generateOrderNSequence(String name, OrderNDistribution d, int length)` Deprecated. use generateSequence() or generateSymbolList() instead.
`static Sequence` | `generateSequence(String name, Distribution d, int length)` Produces a sequence by randomly sampling the Distribution.
`static SymbolList` | `generateSymbolList(Distribution d, int length)` Produces a `SymbolList` by randomly sampling a Distribution.
`static Distribution` | `jointDistOverAlignment(Alignment a, boolean countGaps, double nullWeight, int[] cols)` Creates a joint distribution.
`static HashMap` | `KLDistance(Distribution observed, Distribution expected, double logBase)` A method to calculate the Kullback-Liebler Distance (relative entropy).
`static void` | `randomizeDistribution(Distribution d)` Randomizes the weights of a `Distribution`.
`static Distribution` | `readFromXML(InputStream is)` Read a distribution from XML.
`static HashMap` | `shannonEntropy(Distribution observed, double logBase)` A method to calculate the Shannon Entropy for a Distribution.
`static double` | `totalEntropy(Distribution observed)` Calculates the total Entropy for a Distribution.
`static void` | `writeToXML(Distribution d, OutputStream os)` Writes a Distribution to XML that can be read with the readFromXML method.

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

Method Detail

### writeToXML

    public static void writeToXML(Distribution d,
                                  OutputStream os)
                           throws IOException

  Writes a Distribution to XML that can be read with the readFromXML method.

  Parameters:
    `d` - the Distribution to write.
    `os` - where to write it to.
  Throws:
    `IOException` - if writing fails

### readFromXML

    public static Distribution readFromXML(InputStream is)
                                    throws IOException,
                                           SAXException

  Read a distribution from XML.

  Parameters:
    `is` - an InputStream to read from
  Returns:
    a Distribution parameterised by the xml in is
  Throws:
    `IOException` - if is failed
    `SAXException` - if is could not be processed as XML

### randomizeDistribution

    public static void randomizeDistribution(Distribution d)
                                      throws ChangeVetoException

  Randomizes the weights of a `Distribution`.

  Parameters:
    `d` - the `Distribution` to randomize
  Throws:
    `ChangeVetoException` - if the Distribution is locked

### countToDistribution

    public static Distribution countToDistribution(Count c)

  Make a distribution from a count.

  Parameters:
    `c` - the count
  Returns:
    a Distrubution over the same `FiniteAlphabet` as `c` and trained with the counts of `c`

### areEmissionSpectraEqual

    public static final boolean areEmissionSpectraEqual(Distribution a,
                                                        Distribution b)
                                                 throws BioException

  Compares the emission spectra of two distributions.

  Parameters:
    `a` - A `Distribution` with the same `Alphabet` as `b`
    `b` - A `Distribution` with the same `Alphabet` as `a`
  Returns:
    true if alphabets and symbol weights are equal for the two distributions.
  Throws:
    `BioException` - if one or both of the Distributions are over infinite alphabets.
  Since:
    1.2

### areEmissionSpectraEqual

    public static final boolean areEmissionSpectraEqual(Distribution[] a,
                                                        Distribution[] b)
                                                 throws BioException

  Compares the emission spectra of two distribution arrays.

  Parameters:
    `a` - A `Distribution[]` consisting of `Distributions` over a `FiniteAlphabet`
    `b` - A `Distribution[]` consisting of `Distributions` over a `FiniteAlphabet`
  Returns:
    true if alphabets and symbol weights are equal for each pair of distributions. Will return false if the arrays are of unequal length.
  Throws:
    `BioException` - if one of the Distributions is over an infinite alphabet.
  Since:
    1.3

### KLDistance

    public static final HashMap KLDistance(Distribution observed,
                                           Distribution expected,
                                           double logBase)

  A method to calculate the Kullback-Liebler Distance (relative entropy).

  Parameters:
    `logBase` - - the log base for the entropy calculation. 2 is standard.
    `observed` - - the observed frequence of `Symbols` .
    `expected` - - the excpected or background frequency.
  Returns:
    - A HashMap mapping Symbol to `(Double)` relative entropy.
  Since:
    1.2

### shannonEntropy

    public static final HashMap shannonEntropy(Distribution observed,
                                               double logBase)

  A method to calculate the Shannon Entropy for a Distribution.

  Parameters:
    `logBase` - - the log base for the entropy calculation. 2 is standard.
    `observed` - - the observed frequence of `Symbols` .
  Returns:
    - A HashMap mapping Symbol to `(Double)` entropy.
  Since:
    1.2

### totalEntropy

    public static double totalEntropy(Distribution observed)

  Calculates the total Entropy for a Distribution. Entropies for individual `Symbols` are weighted by their probability of occurence.

  Parameters:
    `observed` - the observed frequence of `Symbols` .
  Returns:
    the total entropy of the `Distribution` .

### bitsOfInformation

    public static final double bitsOfInformation(Distribution observed)

  Calculates the total bits of information for a distribution.

  Parameters:
    `observed` - - the observed frequence of `Symbols` .
  Returns:
    the total information content of the `Distribution` .
  Since:
    1.2

### distOverAlignment

    public static Distribution[] distOverAlignment(Alignment a)
                                            throws IllegalAlphabetException

  Equivalent to distOverAlignment(a, false, 0.0).

  Parameters:
    `a` - the Alignment
  Returns:
    an array of Distribution instances representing columns of the alignment
  Throws:
    `IllegalAlphabetException` - if the alignment alphabet is not compattible

### jointDistOverAlignment

    public static final Distribution jointDistOverAlignment(Alignment a,
                                                            boolean countGaps,
                                                            double nullWeight,
                                                            int[] cols)
                                                     throws IllegalAlphabetException

  Creates a joint distribution.

  Parameters:
    `a` - the `Alignment` to build the `Distribution[]` over.
    `countGaps` - if true gaps will be included in the distributions (NOT YET IMPLEMENTED!!, CURRENTLY EITHER OPTION WILL PRODUCE THE SAME RESULT)
    `nullWeight` - the number of pseudo counts to add to each distribution
    `cols` - a list of positions in the alignment to include in the joint distribution
  Returns:
    a `Distribution`
  Throws:
    `IllegalAlphabetException` - if all sequences don't use the same alphabet
  Since:
    1.2

### distOverAlignment

    public static final Distribution[] distOverAlignment(Alignment a,
                                                         boolean countGaps,
                                                         double nullWeight)
                                                  throws IllegalAlphabetException

  Creates an array of distributions, one for each column of the alignment.

  Parameters:
    `a` - the `Alignment` to build the `Distribution[]` over.
    `countGaps` - if true gaps will be included in the distributions
    `nullWeight` - the number of pseudo counts to add to each distribution, pseudo counts will not affect gaps, no gaps, no gap counts.
  Returns:
    a `Distribution[]` where each member of the array is a `Distribution` of the `Symbols` found at that position of the `Alignment` .
  Throws:
    `IllegalAlphabetException` - if all sequences don't use the same alphabet
  Since:
    1.2

### distOverAlignment

    public static final Distribution[] distOverAlignment(Alignment a,
                                                         boolean countGaps)
                                                  throws IllegalAlphabetException

  Creates an array of distributions, one for each column of the alignment. No pseudo counts are used.

  Parameters:
    `countGaps` - if true gaps will be included in the distributions
    `a` - the `Alignment` to build the `Distribution[]` over.
  Returns:
    a `Distribution[]` where each member of the array is a `Distribution` of the `Symbols` found at that position of the `Alignment` .
  Throws:
    `IllegalAlphabetException` - if the alignment is not composed from sequences all with the same alphabet
  Since:
    1.2

### average

    public static final Distribution average(Distribution[] dists)

  Averages two or more distributions. NOTE the current implementation ignore the null model.

  Parameters:
    `dists` - the `Distributions` to average
  Returns:
    a `Distribution` were the weight of each `Symbol` is the average of the weights of that `Symbol` in each `Distribution` .
  Since:
    1.2

### generateSequence

    public static final Sequence generateSequence(String name,
                                                  Distribution d,
                                                  int length)

  Produces a sequence by randomly sampling the Distribution.

  Parameters:
    `name` - the name for the sequence
    `d` - the distribution to sample. If this distribution is of order N a seed sequence is generated allowed to 'burn in' for 1000 iterations and used to produce a sequence over the conditioned alphabet.
    `length` - the number of symbols in the sequence.
  Returns:
    a Sequence with name and urn = to name and an Empty Annotation.

### generateSymbolList

    public static final SymbolList generateSymbolList(Distribution d,
                                                      int length)

  Produces a `SymbolList` by randomly sampling a Distribution.

  Parameters:
    `d` - the distribution to sample. If this distribution is of order N a seed sequence is generated allowed to 'burn in' for 1000 iterations and used to produce a sequence over the conditioned alphabet.
    `length` - the number of symbols in the sequence.
  Returns:
    a SymbolList or length `length`

### generateOrderNSequence

    protected static final Sequence generateOrderNSequence(String name,
                                                           OrderNDistribution d,
                                                           int length)

  Deprecated. use generateSequence() or generateSymbolList() instead.

  Generate a sequence by sampling a distribution.

  Parameters:
    `name` - the name of the sequence
    `d` - the distribution to sample
    `length` - the length of the sequence
  Returns:
    a new sequence with the required composition

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