frozenleaves/biopython
1
0
Fork 0
mirror of https://github.com/biopython/biopython.git synced 2025-10-20 13:43:47 +08:00
Code Issues Packages Projects Releases Wiki Activity

Phylo: rename reprstr to as_string; repr(Clade) is OK

Browse Source
This commit is contained in:
Eric Talevich
2014-12-08 08:52:09 -08:00
parent ecb10aa76d
commit 7c1b492cc9
1 changed files with 8 additions and 11 deletions
Download Patch File Download Diff File Expand all files Collapse all files

19
Bio/Phylo/BaseTree.py
View File

@ -10,10 +10,7 @@ classes in order to use the common methods defined on them.
"""
__docformat__ = "restructuredtext en"
from Bio._py3k import zip
from Bio._py3k import filter
from Bio._py3k import basestring
from Bio._py3k import unicode
from Bio._py3k import basestring, filter, unicode, zip
import collections
import copy
@ -28,12 +25,12 @@ from Bio import _utils
# unicode. On Python 3, it's the opposite. Horrible.
import sys
if sys.version_info[0] < 3:
def reprstr(s):
def as_string(s):
if isinstance(s, unicode):
return s.encode('utf-8')
return str(s)
else:
reprstr = str
as_string = str
# General tree-traversal algorithms
@ -107,7 +104,7 @@ def _string_matcher(target):
if isinstance(node, (Clade, Tree)):
# Avoid triggering specialized or recursive magic methods
return node.name == target
return reprstr(node) == target
return as_string(node) == target
return match
@ -247,7 +244,7 @@ class TreeElement(object):
def pair_as_kwarg_string(key, val):
if isinstance(val, basestring):
return ("%s='%s'"
% (key, _utils.trim_str(reprstr(val), 60, '...')))
% (key, _utils.trim_str(as_string(val), 60, '...')))
return "%s=%s" % (key, val)
return ('%s(%s)'
% (self.__class__.__name__,
@ -966,11 +963,11 @@ class Tree(TreeElement, TreeMixin):
This closes over textlines and modifies it in-place.
"""
if isinstance(obj, Tree):
# Avoid infinite recursion from str()
if isinstance(obj, (Tree, Clade)):
# Avoid infinite recursion or special formatting from str()
objstr = repr(obj)
else:
objstr = reprstr(obj)
objstr = as_string(obj)
textlines.append(TAB * indent + objstr)
indent += 1
for attr in obj.__dict__: