#! /usr/bin/env python # -*- coding: utf-8 -*- ############################################################################## ## 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)