
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.


r"""

.. currentmodule:: pyemma.msm

User Functions
==============
For most users, the following high-level functions are sufficient to estimate msm models from data.
Expert users may want to construct Estimators or Models (see below) directly.

.. autosummary::
   :toctree: generated/

   markov_model
   timescales_msm
   its
   estimate_markov_model
   bayesian_markov_model
   tpt
   timescales_hmsm
   estimate_hidden_markov_model
   bayesian_hidden_markov_model

MSM classes
===========

**Estimators** to generate models from data. If you are not an expert user,
use the API functions above.

.. autosummary::
   :toctree: generated/

   ImpliedTimescales
   ChapmanKolmogorovValidator
   MaximumLikelihoodMSM
   BayesianMSM
   OOMReweightedMSM
   MaximumLikelihoodHMSM
   BayesianHMSM


**Models** of the kinetics or stationary properties of the data. 
If you are not an expert user, use the API functions above.

.. autosummary::
   :toctree: generated/

   MSM
   SampledMSM
   HMSM
   SampledHMSM
   ReactiveFlux
   PCCA


MSM functions (low-level API)
=============================
Low-level functions for estimation and analysis of transition matrices and io have been moved to `MSMTools
<https://msmtools.readthedocs.io/>`_.


"""
from __future__ import absolute_import as _

######################################################
from msmtools.analysis.dense.pcca import PCCA

#####################################################
# Estimators and models
from .estimators import MaximumLikelihoodMSM, BayesianMSM
from .estimators import MaximumLikelihoodHMSM, BayesianHMSM
from .estimators import OOMReweightedMSM
from .estimators import AugmentedMarkovModel 
from .estimators import ImpliedTimescales
from .estimators import ChapmanKolmogorovValidator

from .models import MSM, HMSM, SampledMSM, SampledHMSM, ReactiveFlux

# high-level api
from .api import *
