prolint.analysis.base
=====================

.. py:module:: prolint.analysis.base

.. autoapi-nested-parse::

   Analysis base module.

   This module provides the base classes and registry for ProLint analyses.



Classes
-------

.. autoapisummary::

   prolint.analysis.base.AnalysisResult
   prolint.analysis.base.BaseAnalysis
   prolint.analysis.base.AnalysisRegistry


Module Contents
---------------

.. py:class:: AnalysisResult

   Container for analysis results.

   The ``data`` attribute holds primary analysis data (varies by analysis type).
   The ``metadata`` attribute holds metadata about the analysis (parameters, timestamps, etc.).


   .. py:attribute:: data
      :type:  Dict[str, Any]

      Primary analysis data (varies by analysis type).


   .. py:attribute:: metadata
      :type:  Dict[str, Any]

      Metadata about the analysis (parameters, timestamps, etc.).


.. py:class:: BaseAnalysis(universe, contacts: prolint.core.contact_provider.ComputedContacts)

   Bases: :py:obj:`abc.ABC`


   Abstract base class for all ProLint analyses.

   Provides common functionality for filtering contacts, building
   residue mappings, and generating frame ranges.

   :param universe: ProLint Universe instance.
   :type universe: Universe
   :param contacts: Computed contact data to analyze.
   :type contacts: ComputedContacts

   .. seealso::

      :py:obj:`AnalysisRegistry`
          Registry for creating analyses by name
      
      :py:obj:`ComputedContacts.analyze`
          High-level interface to run analyses


   .. py:attribute:: name
      :type:  str
      :value: 'base_analysis'


      Analysis name for registry.


   .. py:attribute:: description
      :type:  str
      :value: 'Base analysis class'


      Human-readable description.


   .. py:attribute:: universe


   .. py:attribute:: contacts


   .. py:method:: run(**kwargs) -> AnalysisResult
      :abstractmethod:


      Run the analysis and return results.

      :param \*\*kwargs: Analysis-specific parameters.
      :type \*\*kwargs: dict

      :returns: Container with analysis data and metadata.
      :rtype: AnalysisResult



.. py:class:: AnalysisRegistry

   Registry for analysis types.

   Manages registration and creation of analysis classes. All built-in
   analyses are registered automatically on import.

   .. rubric:: Examples

   List available analyses:

   >>> from prolint.analysis import AnalysisRegistry
   >>> AnalysisRegistry.available()
   ['timeseries', 'database_contacts', 'kinetics', ...]

   Create an analysis:

   >>> analysis = AnalysisRegistry.create("timeseries", universe, contacts)
   >>> result = analysis.run(database_type="CHOL")


   .. py:method:: register(name: str, analysis_class: Type[BaseAnalysis])
      :classmethod:


      Register an analysis class.

      :param name: Name to register under.
      :type name: str
      :param analysis_class: Analysis class (must inherit from BaseAnalysis).
      :type analysis_class: type



   .. py:method:: create(name: str, universe, contacts: prolint.core.contact_provider.ComputedContacts, **kwargs) -> BaseAnalysis
      :classmethod:


      Create an analysis instance.

      :param name: Analysis type name.
      :type name: str
      :param universe: ProLint Universe instance.
      :type universe: Universe
      :param contacts: Computed contact data.
      :type contacts: ComputedContacts
      :param \*\*kwargs: Additional arguments for the analysis.
      :type \*\*kwargs: dict

      :returns: Initialized analysis instance.
      :rtype: BaseAnalysis



   .. py:method:: available() -> List[str]
      :classmethod:


      List available analysis types.

      :returns: Registered analysis names.
      :rtype: list of str



   .. py:method:: get_class(name: str) -> Type[BaseAnalysis]
      :classmethod:


      Get an analysis class by name.

      :param name: Analysis name.
      :type name: str

      :returns: Analysis class.
      :rtype: type