def __init__(self, in_dict, dict_type, alphabet=None):
self.alphabet = alphabet
if dict_type == COUNT:
self.count = in_dict
self._freq_from_count()
elif dict_type == FREQ:
self.count = {}
self.update(in_dict)
else:
raise ValueError("bad dict_type")
if not alphabet:
self.alphabet = Alphabet.Alphabet()
self.alphabet.letters = self._alphabet_from_input()
def __init__(self, data=None, alphabet=None, mat_name='', build_later=0):
# User may supply:
# data: matrix itself
# mat_name: its name. See below.
# alphabet: an instance of Bio.Alphabet, or a subclass. If not
# supplied, constructor builds its own from that matrix.
# build_later: skip the matrix size assertion. User will build the
# matrix after creating the instance. Constructor builds a half matrix
# filled with zeroes.
assert isinstance(mat_name, str)
# "data" may be:
# 1) None --> then self.data is an empty dictionary
# 2) type({}) --> then self takes the items in data
# 3) An instance of SeqMat
# This whole creation-during-execution is done to avoid changing
# default values, the way Python does because default values are
# created when the function is defined, not when it is created.
if data:
try:
self.update(data)
except ValueError:
raise ValueError("Failed to store data in a dictionary")
if alphabet is None:
alphabet = Alphabet.Alphabet()
assert Alphabet.generic_alphabet.contains(alphabet)
self.alphabet = alphabet
# If passed alphabet is empty, use the letters in the matrix itself
if not self.alphabet.letters:
self._alphabet_from_matrix()
# Assert matrix size: half or full
if not build_later:
N = len(self.alphabet.letters)
assert len(self) == N**2 or len(self) == N*(N+1)/2
self.ab_list = list(self.alphabet.letters)
self.ab_list.sort()
# Names: a string like "BLOSUM62" or "PAM250"
self.mat_name = mat_name
if build_later:
self._init_zero()
else:
# Convert full to half
self._full_to_half()
self._correct_matrix()
self.sum_letters = {}
self.relative_entropy = 0
