Plan7
=====

.. currentmodule:: pyhmmer.plan7


.. automodule:: pyhmmer.plan7


Profile HMMs
------------

HMM
^^^

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

Profile
^^^^^^^

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

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

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


OptimizedProfileBlock
^^^^^^^^^^^^^^^^^^^^^

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


HMM Files
---------

HMMFile
^^^^^^^

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

HMMPressedFile
^^^^^^^^^^^^^^

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


Pipelines
---------

Pipeline
^^^^^^^^

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

LongTargetsPipeline
^^^^^^^^^^^^^^^^^^^

.. autoclass:: pyhmmer.plan7.LongTargetsPipeline(Pipeline)
  :special-members: __init__
  :members:


Builder
^^^^^^^

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


Background
^^^^^^^^^^

.. autoclass:: pyhmmer.plan7.Background
   :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:


Iterative Searches
------------------

IterativeSearch
^^^^^^^^^^^^^^^

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


IterationResult
^^^^^^^^^^^^^^^

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


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

Cutoffs
^^^^^^^

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

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

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

Offsets
^^^^^^^

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


Transitions
^^^^^^^^^^^

.. autoclass:: pyhmmer.plan7.Transitions(enum.IntEnum)

   .. autoattribute:: MM

   .. autoattribute:: MI

   .. autoattribute:: MD

   .. autoattribute:: IM

   .. autoattribute:: II

   .. autoattribute:: DM

   .. autoattribute:: DD