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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.calculate.treecompare`,`dendropy.calculate.treemeasure`,
or `dendropy.calculate.treescore`,
"""
import dendropy
from dendropy.calculate import treecompare
from dendropy.calculate import treemeasure
from dendropy.calculate import treescore
from dendropy.utility import deprecate
##############################################################################
## dendropy.calculate.treemeasure
class PhylogeneticDistanceMatrix(dendropy.PhylogeneticDistanceMatrix):
def __init__(self, tree=None):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treecalc.PhylogeneticDistanceMatrix' class has moved to 'dendropy.PhylogeneticDistanceMatrix'.",
old_construct="from dendropy import treecalc\npdm = treecalc.PhylogeneticDistanceMatrix(...)",
new_construct="import dendropy\npdm = dendropy.PhylogeneticDistanceMatrix(...)")
dendropy.PhylogeneticDistanceMatrix.__init__(self, tree=tree)
def patristic_distance(tree, taxon1, taxon2):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treecalc.patristic_distance()' function has moved to 'dendropy.calculate.treemeasure.patristic_distance()'.",
old_construct="from dendropy import treecalc\npdm = treecalc.patristic_distance(...)",
new_construct="from dendropy.calculate import treemeasure\npdm = treemeasure.patristic_distance(...)")
return treemeasure.patristic_distance(
tree=tree,
taxon1=taxon1,
taxon2=taxon2)
##############################################################################
## dendropy.calculate.treecompare
def robinson_foulds_distance(tree1,
tree2,
edge_length_attr="length"):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treecalc.robinson_foulds_distance()' function has moved to 'dendropy.calculate.treecompare.weighted_robinson_foulds_distance()'.",
old_construct="from dendropy import treecalc\nd = treecalc.robinson_foulds_distance(...)",
new_construct="from dendropy.calculate import treecompare\nd = treecompare.weighted_robinson_foulds_distance(...)")
return treecompare.weighted_robinson_foulds_distance(
tree1=tree1,
tree2=tree2,
edge_weight_attr=edge_length_attr)
def euclidean_distance(tree1,
tree2,
edge_length_attr="length",
value_type=float):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treecalc.euclidean_distance()' function has moved to 'dendropy.calculate.treecompare.euclidean_distance()'.",
old_construct="from dendropy import treecalc\nd = treecalc.euclidean_distance(...)",
new_construct="from dendropy.calculate import treecompare\nd = treecompare.euclidean_distance(...)")
return treecompare.euclidean_distance(
tree1=tree1,
tree2=tree2,
edge_weight_attr=edge_length_attr,
value_type=value_type)
def false_positives_and_negatives(reference_tree, test_tree):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treecalc.false_positives_and_negatives()' function has moved to 'dendropy.calculate.treecompare.false_positives_and_negatives()'.",
old_construct="from dendropy import treecalc\nd = treecalc.false_positives_and_negatives(...)",
new_construct="from dendropy.calculate import treecompare\nd = treecompare.false_positives_and_negatives(...)")
return treecompare.false_positives_and_negatives(
reference_tree=reference_tree,
comparison_tree=test_tree)
def symmetric_difference(tree1, tree2):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treecalc.symmetric_difference()' function has moved to 'dendropy.calculate.treecompare.symmetric_difference()'.",
old_construct="from dendropy import treecalc\nd = treecalc.symmetric_difference(...)",
new_construct="from dendropy.calculate import treecompare\nd = treecompare.symmetric_difference(...)")
return treecompare.symmetric_difference(
tree1=tree1,
tree2=tree2)
def find_missing_splits(reference_tree, test_tree):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treecalc.find_missing_splits()' function has moved to 'dendropy.calculate.treecompare.find_missing_splits()'.",
old_construct="from dendropy import treecalc\nd = treecalc.find_missing_splits(...)",
new_construct="from dendropy.calculate import treecompare\nd = treecompare.find_missing_splits(...)")
return treecompare.find_missing_splits(
reference_tree=reference_tree,
comparison_tree=test_tree)
##############################################################################
## dendropy.calculate.treescore
# def fitch_up_pass(preorder_node_list, attr_name="state_sets", taxa_to_state_set_map=None):
# deprecate.dendropy_deprecation_warning(
# preamble="Deprecated since DendroPy 4: The 'dendropy.treecalc.euclidean_distance()' function has moved to 'dendropy.calculate.treecompare.euclidean_distance()'.",
# old_construct="from dendropy import treecalc\nd = treecalc.euclidean_distance(...)",
# new_construct="from dendropy.calculate import treecompare\nd = treecompare.euclidean_distance(...)")
# return treecompare.euclidean_distance(
# tree1=tree1,
# tree2=tree2,
# edge_weight_attr=edge_length_attr,
# value_type=value_type)
# def fitch_down_pass(postorder_node_list, attr_name="state_sets", weight_list=None, taxa_to_state_set_map=None):
# deprecate.dendropy_deprecation_warning(
# preamble="Deprecated since DendroPy 4: The 'dendropy.treecalc.euclidean_distance()' function has moved to 'dendropy.calculate.treecompare.euclidean_distance()'.",
# old_construct="from dendropy import treecalc\nd = treecalc.euclidean_distance(...)",
# new_construct="from dendropy.calculate import treecompare\nd = treecompare.euclidean_distance(...)")
# return treecompare.euclidean_distance(
# tree1=tree1,
# tree2=tree2,
# edge_weight_attr=edge_length_attr,
# value_type=value_type)
# def mason_gamer_kellogg_score(tree1, tree2):
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