1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
|
#! /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: USE `dendropy.calculate.treesum` instead.
"""
from dendropy.calculate import treesum
from dendropy.utility import deprecate
class TreeSummarizer(treesum.TreeSummarizer):
def __init__(self, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treesum.TreeSummarizer' class has moved to 'dendropy.calculate.treesum.TreeSummarizer'.",
old_construct="from dendropy import treesum\nm = treesum.TreeSummarizer(...)",
new_construct="from dendropy.calculate import treesum\nm = treesum.TreeSummarizer(...)")
treesum.TreeSummarizer.__init__(self, **kwargs)
class TopologyCounter(treesum.TopologyCounter):
def __init__(self, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treesum.TopologyCounter' class has moved to 'dendropy.calculate.treesum.TopologyCounter'.",
old_construct="from dendropy import treesum\nm = treesum.TopologyCounter(...)",
new_construct="from dendropy.calculate import treesum\nm = treesum.TopologyCounter(...)")
treesum.TopologyCounter.__init__(self, **kwargs)
|
