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# Copyright 2014 Joe Cora.
# Revisions copyright 2017 Peter Cock.
# All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause 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."""
class NexusError(Exception):
"""Provision for the management of Nexus exceptions."""
pass
class StandardData:
"""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, str):
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 %s at position %i of a coding sequence."
% (coding, pos)
)
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):
"""Pull out child by index."""
return self._data[arg]
def __iter__(self):
"""Iterate over the items."""
return self
def __next__(self):
"""Return next item."""
try:
return_coding = self._data[self._current_pos]
except IndexError:
self._current_pos = 0
raise StopIteration from None
else:
self._current_pos += 1
return return_coding
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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