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#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
"""
DEPRECATED IN DENDROPY 4: USE `dendropy.model.discrete`.
"""
from dendropy.model import discrete
from dendropy.utility import deprecate
class SeqModel(discrete.DiscreteCharacterEvolutionModel):
def __init__(self, state_alphabet, rng=None):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.seqmodel.SeqModel' class has moved to 'dendropy.model.discrete.DiscreteCharacterEvolutionModel'.",
old_construct="from dendropy import seqmodel\nm = seqmodel.SeqModel(...)",
new_construct="from dendropy.model import discrete\nm = discrete.DiscreteCharacterEvolutionModel(...)")
discrete.DiscreteCharacterEvolutionModel.__init__(
self,
state_alphabet=state_alphabet,
rng=rng)
class Hky85SeqModel(discrete.Hky85):
def __init__(self, kappa=1.0, base_freqs=None, state_alphabet=None, rng=None):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.seqmodel.Hky85SeqModel' class has moved to 'dendropy.model.discrete.Hky85'.",
old_construct="from dendropy import seqmodel\nm = seqmodel.NucleotideSeqModel(...)",
new_construct="from dendropy.model import discrete\ndiscrete.Hky85(...)")
discrete.Hky85.__init__(
self,
kappa=kappa,
base_freqs=base_freqs,
state_alphabet=state_alphabet,
rng=rng)
class Jc69SeqModel(discrete.Jc69):
def __init__(self, state_alphabet=None, rng=None):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.seqmodel.Jc69SeqModel' class has moved to 'dendropy.model.discrete.Jc69'.",
old_construct="from dendropy import seqmodel\nm = seqmodel.NucleotideSeqModel(...)",
new_construct="from dendropy.model import discrete\ndiscrete.Jc69(...)")
discrete.Jc69.__init__(
self,
state_alphabet=state_alphabet,
rng=rng)
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