Plan7
=====

.. currentmodule:: pyhmmer.plan7


.. automodule:: pyhmmer.plan7


Hidden Markov Model
-------------------

HMM
^^^

.. autoclass:: pyhmmer.plan7.HMM
   :special-members: __init__
   :members:

HMM File
^^^^^^^^

.. autoclass:: pyhmmer.plan7.HMMFile
   :special-members: __init__
   :members:


Profile
-------

Profile
^^^^^^^

.. autoclass:: pyhmmer.plan7.Profile
   :special-members: __init__
   :members:

OptimizedProfile
^^^^^^^^^^^^^^^^

.. autoclass:: pyhmmer.plan7.OptimizedProfile
   :special-members: __init__
   :members:

Background
^^^^^^^^^^

.. autoclass:: pyhmmer.plan7.Background
   :special-members: __init__
   :members:


Pipelines
---------

Pipeline
^^^^^^^^

.. autoclass:: pyhmmer.plan7.Pipeline
   :special-members: __init__
   :members:

Builder
^^^^^^^

.. autoclass:: pyhmmer.plan7.Builder
  :special-members: __init__
  :members:


Results
-------

TopHits
^^^^^^^

.. autoclass:: pyhmmer.plan7.TopHits
   :special-members: __init__
   :members:

Hit
^^^

.. autoclass:: pyhmmer.plan7.Hit
   :special-members: __init__
   :members:

Domains
^^^^^^^

.. autoclass:: pyhmmer.plan7.Domains
   :special-members: __init__
   :members:

Domain
^^^^^^

.. autoclass:: pyhmmer.plan7.Domain
   :special-members: __init__
   :members:

Alignment
^^^^^^^^^

.. autoclass:: pyhmmer.plan7.Alignment
   :special-members: __init__
   :members:


Traces
------

TraceAligner
^^^^^^^^^^^^

.. autoclass:: pyhmmer.plan7.TraceAligner
   :special-members: __init__
   :members:

Traces
^^^^^^

.. autoclass:: pyhmmer.plan7.Traces
   :special-members: __init__
   :members:

Trace
^^^^^

.. autoclass:: pyhmmer.plan7.Trace
   :special-members: __init__
   :members:


Miscellaneous
-------------

Cutoffs
^^^^^^^

.. autoclass:: pyhmmer.plan7.Cutoffs
   :members:

EvalueParameters
^^^^^^^^^^^^^^^^

.. autoclass:: pyhmmer.plan7.EvalueParameters
   :members:

Offsets
^^^^^^^

.. autoclass:: pyhmmer.plan7.Offsets
   :members: