================================
Low-level binding of C++ library
================================

Besides sequence storage classes :class:`~egglib.Container` and
:class:`~egglib.Align`,
the wrapped C++ library available through the :mod:`egglib` egglib-py
module contains several classes that might be of use for Python scripts.
Still, they are a priori not intended to be used directly and this page
only provides automated documentation. The user is prompted to refer to
the doxygen documentation of the C++ library for a more comprehensive
documentation of these tools.


Data holders
------------

.. autoclass:: egglib.egglib_binding.Align
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.CharMatrix
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.Container
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.DataMatrix
   :members:
   :inherited-members:

Conversion and parsing
----------------------

.. autoclass:: egglib.egglib_binding.Consensus
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.Convert
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.Fasta
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.Ms
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.Staden
   :members:
   :inherited-members:

Analysis of polymorphism
------------------------

.. autoclass:: egglib.egglib_binding.BaseDiversity
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.BppDiversity
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.FStatistics
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.HFStatistics
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.HaplotypeDiversity
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.LinkageDisequilibrium
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.MicrosatelliteDiversity
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.NucleotideDiversity
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.SitePolymorphism
   :members:
   :inherited-members:

Coalescent simulator
--------------------

.. autoclass:: egglib.egglib_binding.AllMigrationRateChange
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.AllPopulationSizeChange
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.Arg
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.Bottleneck
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.Change
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.Controller
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.Current
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.Edge
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.GrowthRateChange
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.Mutator
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.ParamSet
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.PopulationBottleneck
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.PopulationFusion
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.PopulationGrowthRateChange
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.PopulationParamChange
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.PopulationSplit
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.SelfingRateChange
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.SingleMigrationRateChange
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.SingleParamChange
   :members:
   :inherited-members:

.. autoclass:: egglib.egglib_binding.SinglePopulationSizeChange
   :members:
   :inherited-members:

Approximate Bayesian Computation
--------------------------------

.. autoclass:: egglib.egglib_binding.ABC
   :members:
   :inherited-members:

Random number generator
-----------------------

.. autoclass:: egglib.egglib_binding.Random
   :members:
   :inherited-members: