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# Copyright 2014 Joe Cora.
# Revisions copyright 2017 Peter Cock.
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Objects to represent NEXUS standard data type matrix coding."""
from __future__ import print_function
import sys
from Bio._py3k import basestring
class NexusError(Exception):
pass
class StandardData(object):
"""Create a StandardData iterable object.
Each coding specifies t [type] => (std [standard], multi [multistate] or
uncer [uncertain]) and d [data]
"""
def __init__(self, data):
"""Initialize the class."""
self._data = []
self._current_pos = 0
# Enforce string data requirement
if not isinstance(data, basestring):
raise NexusError("The coding data given to a StandardData object should be a string")
# Transfer each coding to a position within a sequence
multi_coding = False
uncertain_coding = False
coding_list = {'t': 'std', 'd': []}
for pos, coding in enumerate(data):
# Check if in a multiple coded or uncertain character
if multi_coding:
# End multicoding if close parenthesis
if coding == ')':
multi_coding = False
else:
# Add current coding to list and advance to next coding
coding_list['d'].append(coding)
continue
elif uncertain_coding:
# End multicoding if close parenthesis
if coding == '}':
uncertain_coding = False
else:
# Add current coding to list and advance to next coding
coding_list['d'].append(coding)
continue
else:
# Check if a multiple coded or uncertain character is starting
if coding == '(':
multi_coding = True
coding_list['t'] = 'multi'
continue
elif coding == '{':
uncertain_coding = True
coding_list['t'] = 'uncer'
continue
elif coding in [')', '}']:
raise NexusError('Improper character "' + coding +
'" at position ' + pos +
' of a coding sequence.')
else:
coding_list['d'].append(coding)
# Add character coding to data
self._data.append(coding_list.copy())
coding_list = {'t': 'std', 'd': []}
def __len__(self):
"""Return the length of the coding, use len(my_coding)."""
return len(self._data)
def __getitem__(self, arg):
return self._data[arg]
def __iter__(self):
return self
def __next__(self):
try:
return_coding = self._data[self._current_pos]
except IndexError:
self._current_pos = 0
raise StopIteration
else:
self._current_pos += 1
return return_coding
if sys.version_info[0] < 3:
def next(self):
"""Return next item, deprecated Python 2 style alias for Python 3 style __next__ method."""
return self.__next__()
def raw(self):
"""Return the full coding as a python list."""
return self._data
def __str__(self):
"""Return the full coding as a python string, use str(my_coding)."""
str_return = ''
for coding in self._data:
if coding['t'] == 'multi':
str_return += '(' + ''.join(coding['d']) + ')'
elif coding['t'] == 'uncer':
str_return += '{' + ''.join(coding['d']) + '}'
else:
str_return += coding['d'][0]
return str_return
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