DataStructures - Alignment
============

:mod:`Run` Module
-------------------

Run
^^^^^^^^^^^^^^

.. autoclass:: msproteomicstoolslib.data_structures.Run.Run
    :members:
    :undoc-members:
    :show-inheritance:

:mod:`PrecursorGroup` Module
----------------------------

PrecursorGroup
^^^^^^^^^^^^^^

.. autoclass:: msproteomicstoolslib.data_structures.PrecursorGroup.PrecursorGroup
    :members:
    :undoc-members:
    :show-inheritance:

:mod:`Precursor` Module
------------------------

PrecursorBase
^^^^^^^^^^^^^

.. autoclass:: msproteomicstoolslib.data_structures.Precursor.PrecursorBase
    :members:
    :undoc-members:
    :show-inheritance:

GeneralPrecursor
^^^^^^^^^^^^^^^^

.. autoclass:: msproteomicstoolslib.data_structures.Precursor.GeneralPrecursor
    :members:
    :undoc-members:
    :show-inheritance:

Precursor
^^^^^^^^^

.. autoclass:: msproteomicstoolslib.data_structures.Precursor.Precursor
    :members:
    :undoc-members:
    :show-inheritance:

:mod:`PeakGroup` Module
-----------------------

PeakGroupBase
^^^^^^^^^^^^^^

.. autoclass:: msproteomicstoolslib.data_structures.PeakGroup.PeakGroupBase
    :members:
    :undoc-members:
    :show-inheritance:

MinimalPeakGroup
^^^^^^^^^^^^^^

.. autoclass:: msproteomicstoolslib.data_structures.PeakGroup.MinimalPeakGroup
    :members:
    :undoc-members:
    :show-inheritance:

GuiPeakGroup
^^^^^^^^^^^^^^

.. autoclass:: msproteomicstoolslib.data_structures.PeakGroup.GuiPeakGroup
    :members:
    :undoc-members:
    :show-inheritance:

GeneralPeakGroup
^^^^^^^^^^^^^^^^

.. autoclass:: msproteomicstoolslib.data_structures.PeakGroup.GeneralPeakGroup
    :members:
    :undoc-members:
    :show-inheritance:

DataStructures - Basic
=====================

:mod:`Aminoacides` Module
-------------------

Aminoacid
^^^^^^^^^^^^^^

.. autoclass:: msproteomicstoolslib.data_structures.aminoacides.Aminoacid
    :members:
    :undoc-members:
    :show-inheritance:


Aminoacides
^^^^^^^^^^^^^^

.. autoclass:: msproteomicstoolslib.data_structures.aminoacides.Aminoacides
    :members:
    :undoc-members:
    :show-inheritance:


:mod:`Modifications` Module
-------------------

Modification
^^^^^^^^^^^^^^

.. autoclass:: msproteomicstoolslib.data_structures.modifications.Modification
    :members:
    :undoc-members:
    :show-inheritance:


Modifications
^^^^^^^^^^^^^^

.. autoclass:: msproteomicstoolslib.data_structures.modifications.Modifications
    :members:
    :undoc-members:
    :show-inheritance:

:mod:`Peak` Module
-------------------

Peak
^^^^^^^^^^^^^^

.. autoclass:: msproteomicstoolslib.data_structures.peak.Peak
    :members:
    :undoc-members:
    :show-inheritance:


:mod:`Peptide` Module
-------------------

Peptide
^^^^^^^^^^^^^^

.. autoclass:: msproteomicstoolslib.data_structures.peptide.Peptide
    :members:
    :undoc-members:
    :show-inheritance:

:mod:`Residues` Module
-------------------

Residues
^^^^^^^^^^^^^^

.. autoclass:: msproteomicstoolslib.data_structures.Residues.Residues
    :show-inheritance:

:mod:`DDB` Module
-------------------

DDB
^^^^^^^^^^^^^^

Abstraction layer to the `2DDB <http://sourceforge.net/projects/twoddb/>`_  software framework.