<filename>dendropy/legacy/seqsim.py
#! /usr/bin/env python

##############################################################################
##  DendroPy Phylogenetic Computing Library.
##
##  Copyright 2010-2015 <NAME> and <NAME>.
##  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:
##
##     <NAME>. and <NAME>. 2010. DendroPy: a Python library
##     for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################

"""
DEPRECATED IN DENDROPY 4: USE `dendropy.simulate.charsim`.
"""

import dendropy
from dendropy.simulate import charsim
from dendropy.utility import deprecate

def generate_hky_dataset(seq_len,
                         tree_model,
                         mutation_rate=1.0,
                         kappa=1.0,
                         base_freqs=[0.25, 0.25, 0.25, 0.25],
                         root_states=None,
                         dataset=None,
                         rng=None):
    deprecate.dendropy_deprecation_warning(
            preamble="Deprecated since DendroPy 4: The 'dendropy.seqsim.generate_hky_dataset()' function has been replaced with 'dendropy.simulate.charsim.hky85_chars()'.",
            old_construct="from dendropy import seqsim\ndataset = seqsim.generate_hky_dataset(...)",
            new_construct="import dendropy\nfrom dendropy.simulate import charsim\ndataset = dendropy.DataSet()\nchar_matrix = charsim.hky85_chars(...)\ndataset.add_char_matrix(char_matrix)")
    if dataset is None:
        dataset = dendropy.DataSet()
    char_matrix = dataset.new_char_matrix(char_matrix_type="dna", taxon_namespace=tree_model.taxon_namespace)
    charsim.hky85_chars(
            seq_len=seq_len,
            tree_model=tree_model,
            mutation_rate=mutation_rate,
            kappa=kappa,
            base_freqs=base_freqs,
            root_states=root_states,
            char_matrix=char_matrix,
            rng=rng)
    return dataset

def generate_hky_characters(seq_len,
                            tree_model,
                            mutation_rate=1.0,
                            kappa=1.0,
                            base_freqs=[0.25, 0.25, 0.25, 0.25],
                            root_states=None,
                            char_matrix=None,
                            rng=None):
    deprecate.dendropy_deprecation_warning(
            preamble="Deprecated since DendroPy 4: The 'dendropy.seqsim.generate_hky_characters()' function has been replaced with 'dendropy.simulate.charsim.hky85_chars()'.",
            old_construct="from dendropy import seqsim\nchar_matrix = seqsim.generate_hky_characters(...)",
            new_construct="from dendropy.simulate import charsim\nchar_matrix = charsim.hky85_chars(...)")
    return charsim.hky85_chars(
            seq_len=seq_len,
            tree_model=tree_model,
            mutation_rate=mutation_rate,
            kappa=kappa,
            base_freqs=base_freqs,
            root_states=root_states,
            char_matrix=char_matrix,
            rng=rng)

# def generate_dataset(seq_len,
#                      tree_model,
#                      seq_model,
#                      mutation_rate=1.0,
#                      root_states=None,
#                      dataset=None,
#                      rng=None):
#     deprecate.dendropy_deprecation_warning(
#             preamble="Deprecated since DendroPy 4: The 'dendropy.seqsim.generate_hky_characters()' function has been replaced with 'dendropy.simulate.charsim.hky85_chars()'.",
#             old_construct="from dendropy import seqsim\nchar_matrix = seqsim.generate_hky_characters(...)",
#             new_construct="from dendropy.simulate import charsim\nchar_matrix = discrete.hky85_chars(...)")

# def generate_char_matrix(seq_len,
#                         tree_model,
#                         seq_model,
#                         mutation_rate=1.0,
#                         root_states=None,
#                         char_matrix=None,
#                         rng=None):

#     pass

# class SeqEvolver(object):
#     def __init__(self,
#      seq_model=None,
#      mutation_rate=None,
#      seq_attr='sequences',
#      seq_model_attr="seq_model",
#      edge_length_attr="length",
#      edge_rate_attr="mutation_rate",
#      seq_label_attr='taxon'):
#         pass


<filename>dendropy/legacy/seqsim.py
#! /usr/bin/env python

##############################################################################
##  DendroPy Phylogenetic Computing Library.
##
##  Copyright 2010-2015 <NAME> and <NAME>.
##  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:
##
##     <NAME>. and <NAME>. 2010. DendroPy: a Python library
##     for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################

"""
DEPRECATED IN DENDROPY 4: USE `dendropy.simulate.charsim`.
"""

import dendropy
from dendropy.simulate import charsim
from dendropy.utility import deprecate

def generate_hky_dataset(seq_len,
                         tree_model,
                         mutation_rate=1.0,
                         kappa=1.0,
                         base_freqs=[0.25, 0.25, 0.25, 0.25],
                         root_states=None,
                         dataset=None,
                         rng=None):
    deprecate.dendropy_deprecation_warning(
            preamble="Deprecated since DendroPy 4: The 'dendropy.seqsim.generate_hky_dataset()' function has been replaced with 'dendropy.simulate.charsim.hky85_chars()'.",
            old_construct="from dendropy import seqsim\ndataset = seqsim.generate_hky_dataset(...)",
            new_construct="import dendropy\nfrom dendropy.simulate import charsim\ndataset = dendropy.DataSet()\nchar_matrix = charsim.hky85_chars(...)\ndataset.add_char_matrix(char_matrix)")
    if dataset is None:
        dataset = dendropy.DataSet()
    char_matrix = dataset.new_char_matrix(char_matrix_type="dna", taxon_namespace=tree_model.taxon_namespace)
    charsim.hky85_chars(
            seq_len=seq_len,
            tree_model=tree_model,
            mutation_rate=mutation_rate,
            kappa=kappa,
            base_freqs=base_freqs,
            root_states=root_states,
            char_matrix=char_matrix,
            rng=rng)
    return dataset

def generate_hky_characters(seq_len,
                            tree_model,
                            mutation_rate=1.0,
                            kappa=1.0,
                            base_freqs=[0.25, 0.25, 0.25, 0.25],
                            root_states=None,
                            char_matrix=None,
                            rng=None):
    deprecate.dendropy_deprecation_warning(
            preamble="Deprecated since DendroPy 4: The 'dendropy.seqsim.generate_hky_characters()' function has been replaced with 'dendropy.simulate.charsim.hky85_chars()'.",
            old_construct="from dendropy import seqsim\nchar_matrix = seqsim.generate_hky_characters(...)",
            new_construct="from dendropy.simulate import charsim\nchar_matrix = charsim.hky85_chars(...)")
    return charsim.hky85_chars(
            seq_len=seq_len,
            tree_model=tree_model,
            mutation_rate=mutation_rate,
            kappa=kappa,
            base_freqs=base_freqs,
            root_states=root_states,
            char_matrix=char_matrix,
            rng=rng)

# def generate_dataset(seq_len,
#                      tree_model,
#                      seq_model,
#                      mutation_rate=1.0,
#                      root_states=None,
#                      dataset=None,
#                      rng=None):
#     deprecate.dendropy_deprecation_warning(
#             preamble="Deprecated since DendroPy 4: The 'dendropy.seqsim.generate_hky_characters()' function has been replaced with 'dendropy.simulate.charsim.hky85_chars()'.",
#             old_construct="from dendropy import seqsim\nchar_matrix = seqsim.generate_hky_characters(...)",
#             new_construct="from dendropy.simulate import charsim\nchar_matrix = discrete.hky85_chars(...)")

# def generate_char_matrix(seq_len,
#                         tree_model,
#                         seq_model,
#                         mutation_rate=1.0,
#                         root_states=None,
#                         char_matrix=None,
#                         rng=None):

#     pass

# class SeqEvolver(object):
#     def __init__(self,
#      seq_model=None,
#      mutation_rate=None,
#      seq_attr='sequences',
#      seq_model_attr="seq_model",
#      edge_length_attr="length",
#      edge_rate_attr="mutation_rate",
#      seq_label_attr='taxon'):
#         pass


#! /usr/bin/env python ############################################################################## ##  DendroPy Phylogenetic Computing Library. ## ##  Copyright 2010-2015 <NAME> and <NAME>. ##  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: ## ##     <NAME>. and <NAME>. 2010. DendroPy: a Python library ##     for phylogenetic computing. Bioinformatics 26: 1569-1571. ## ############################################################################## DEPRECATED IN DENDROPY 4: USE `dendropy.simulate.charsim`. # def generate_dataset(seq_len, #                      tree_model, #                      seq_model, #                      mutation_rate=1.0, #                      root_states=None, #                      dataset=None, #                      rng=None): #     deprecate.dendropy_deprecation_warning( #             preamble="Deprecated since DendroPy 4: The 'dendropy.seqsim.generate_hky_characters()' function has been replaced with 'dendropy.simulate.charsim.hky85_chars()'.", #             old_construct="from dendropy import seqsim\nchar_matrix = seqsim.generate_hky_characters(...)", #             new_construct="from dendropy.simulate import charsim\nchar_matrix = discrete.hky85_chars(...)") # def generate_char_matrix(seq_len, #                         tree_model, #                         seq_model, #                         mutation_rate=1.0, #                         root_states=None, #                         char_matrix=None, #                         rng=None): #     pass # class SeqEvolver(object): #     def __init__(self, #      seq_model=None, #      mutation_rate=None, #      seq_attr='sequences', #      seq_model_attr="seq_model", #      edge_length_attr="length", #      edge_rate_attr="mutation_rate", #      seq_label_attr='taxon'): #         pass