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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.
##
##############################################################################
"""
Split calculation and management.
DEPRECATED IN DENDROPY 4.
"""
import dendropy
from dendropy.utility import bitprocessing
from dendropy.utility import deprecate
def tree_from_splits(splits, taxon_set, is_rooted=False):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: 'dendropy.treesplit.tree_from_splits()'.",
old_construct="from dendropy import treesplit\ntree = treesplit.tree_from_splits(...)",
new_construct="import dendropy\ntree = dendropy.Tree.from_split_bitmasks(...)")
return dendropy.Tree.from_split_bitmasks(
split_bitmasks=splits,
taxon_namespace=taxon_set,
is_rooted=is_rooted)
def split_to_list(s, mask=-1, one_based=False, ordination_in_mask=False):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: 'dendropy.treesplit.split_to_list()'.",
old_construct="from dendropy import treesplit\nd = treesplit.split_to_list(...)",
new_construct="from dendropy.utility import bitprocessing\nd = bitprocessing.indexes_of_set_bits(...)")
return bitprocessing.indexes_of_set_bits(
s=s,
fill_bitmask=mask,
one_based=one_based,
ordination_in_mask=ordination_in_mask)
def is_trivial_split(split, mask):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: 'dendropy.treesplit.is_trivial_split()'.",
old_construct="from dendropy import treesplit\nd = treesplit.is_trivial_split(...)",
new_construct="import dendropy\nd = dendropy.Bipartition.is_trivial_bitmask(...)")
return dendropy.Bipartition.is_trivial_bitmask(bitmask=split, fill_bitmask=mask)
def is_non_singleton_split(split, mask):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: 'dendropy.treesplit.is_non_singleton_split()'.",
old_construct="from dendropy import treesplit\nd = treesplit.is_non_singleton_split(...)",
new_construct="import dendropy\nd = not dendropy.Bipartition.is_trivial_bitmask(...)")
return dendropy.Bipartition.is_trivial_bitmask(bitmask=split, fill_bitmask=mask)
def split_as_string(split_mask, width, symbol1=None, symbol2=None):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: 'dendropy.treesplit.split_as_string()'.",
old_construct="from dendropy import treesplit\nd = treesplit.split_as_string(...)",
new_construct="""\
# if using a bipartition
d = bipartition.split_as_bitstring(...)
d = bipartition.leafset_as_bitstring(...)
# if a "raw" bitmask
from dendropy.utility import bitprocessing
d = bitprocessing.int_as_bitstring(...)""")
return bitprocessing.int_as_bitstring(
n=split_mask,
length=width,
symbol0=symbol1,
symbol1=symbol2,
reverse=False)
def split_as_string_rev(split_mask, width, symbol1='.', symbol2='*'):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: 'dendropy.treesplit.split_as_string_rev()'.",
old_construct="from dendropy import treesplit\nd = treesplit.split_as_string(...)",
new_construct="""\
# if using a bipartition
d = bipartition.split_as_bitstring(...)[::-1]
d = bipartition.leafset_as_bitstring(...)[::-1]
# if a "raw" bitmask
from dendropy.utility import bitprocessing
d = bitprocessing.int_as_bitstring(..., reverse=True)""")
return bitprocessing.int_as_bitstring(
mask=split_mask,
length=width,
symbol0=symbol0,
symbol1=symbol1,
reverse=True)
def find_edge_from_split(root, split_to_find, mask=-1):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: 'dendropy.treesplit.find_edge_from_split()'",
old_construct="from dendropy import treesplit\nd = treesplit.find_edge_from_split(...)",
new_construct="""\
# if using a bipartition
d = bipartition.edge
# if a "raw" bitmask
d = tree.find_edge_for_split_bitmask(...)""")
return root.find_edge_for_split_bitmask(split_to_find, fill_bitmask=mask)
def encode_splits(tree, create_dict=True, suppress_unifurcations=True):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: 'dendropy.treesplit.encode_splits()'.",
old_construct="from dendropy import treesplit\nd = treesplit.encode_splits(tree, ...)",
new_construct="bipartitions = tree.encode_bipartitions(...)\nsplit_bitmasks = tree.split_bitmask_edge_map.keys()")
return tree.encode_bipartitions(suppress_unifurcations=suppress_unifurcations)
def is_compatible(split1, split2, mask):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: 'dendropy.treesplit.is_compatible()'.",
old_construct="from dendropy import treesplit\nd = treesplit.is_compatible(...)",
new_construct="""\
# if using a bipartition
d = bipartition.is_compatible_with(other_bipartition)
# if a "raw" bitmask
d = dendropy.Bipartition.is_compatible_bitmasks(m1, m2, fill_bitmask=mask)""")
"""
Mask should have 1 for every leaf in the leaf_set
"""
# m1 = mask & split1
# m2 = mask & split2
# if 0 == (m1 & m2):
# return True
# c2 = mask ^ split2
# if 0 == (m1 & c2):
# return True
# c1 = mask ^ split1
# if 0 == (c1 & m2):
# return True
# if 0 == (c1 & c2):
# return True
# return False
return dendropy.Bipartition.is_compatible_bitmasks(split1, split2, fill_bitmask=mask)
def delete_outdegree_one(tree):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: 'dendropy.treesplit.delete_outdegree_one()'.",
old_construct="from dendropy import treesplit\nd = treesplit.delete_outdegree_one(tree)",
new_construct="tree.suppress_unifurcations()")
return tree.suppress_unifurcations()
def lowest_bit_only(s):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: 'dendropy.treesplit.lowest_bit_only()'.",
old_construct="from dendropy import treesplit\nd = treesplit.lowest_bit_only(...)",
new_construct="from dendropy.utility import bitprocessing\nd = bitprocessing.least_significant_set_bit(...)")
return bitprocessing.least_significant_set_bit(s)
def count_bits(a):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: 'dendropy.treesplit.count_bits()'.",
old_construct="from dendropy import treesplit\nd = treesplit.count_bits(...)",
new_construct="from dendropy.utility import bitprocessing\nd = bitprocessing.num_set_bits(...)")
return bitprocessing.num_set_bits(a)
class SplitDistribution(dendropy.SplitDistribution):
def __init__(self, taxon_set=None, split_set=None):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treesplit.SplitDistribution' class has moved to 'dendropy.calculate.treesplit.SplitDistribution'.",
old_construct="from dendropy import treesplit\nm = treesplit.SplitDistribution(...)",
new_construct="import dendropy\nm = dendropy.SplitDistribution(...)")
dendropy.SplitDistribution.__init__(self,
taxon_namespace=taxon_set)
if split_set:
for split in split_set:
self.add_split_count(split, count=1)
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