=============
Documentation
=============

Core Functionality
------------------

.. automodule:: protein_inference.problem_network
        :members:

.. automodule:: protein_inference.network_grapher
        :members:

.. automodule:: protein_inference.protein_inference_runner
        :members:

.. automodule:: protein_inference.table_maker
        :members:

Processing
----------

.. automodule:: protein_inference.processing.processed_psms
        :members:

.. automodule:: protein_inference.processing.psms_preprocessor
        :members:

.. automodule:: protein_inference.processing.psms_network_splitter
        :members:

.. automodule:: protein_inference.processing.psms_network_generator
        :members:

Inference
----------

.. automodule:: protein_inference.inference.false_discovery_rate_calculator
        :members:

.. automodule:: protein_inference.inference.protein_merger
        :members:

.. automodule:: protein_inference.inference.scorers
        :members: