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Package Bio :: Package SubsMat :: Class SeqMat |
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object
--+ |dict
--+ | SeqMat
Method Summary | |
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__init__(self,
data,
alphabet,
mat_type,
mat_name,
build_later)
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returns a matrix for which each entry is the multiplication product of the two matrices passed | |
returns a number which is the subtraction product of the two matrices | |
__sum__(self,
other)
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all_letters_sum(self)
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letter_sum(self,
letter)
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make_entropy(self)
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if this matrix is a log-odds matrix, return its entropy Needs the observed frequency matrix for that | |
print_full_mat(self,
f,
format,
topformat,
alphabet,
factor,
non_sym)
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Print a nice half-matrix. | |
_alphabet_from_matrix(self)
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_correct_matrix(self)
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Convert a full-matrix to a half-matrix | |
_init_zero(self)
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Inherited from dict | |
x.__cmp__(y) <==> cmp(x,y) | |
D.__contains__(k) -> True if D has a key k, else False | |
x.__delitem__(y) <==> del x[y] | |
x.__eq__(y) <==> x==y | |
x.__ge__(y) <==> x>=y | |
x.__getattribute__('name') <==> x.name | |
x.__getitem__(y) <==> x[y] | |
x.__gt__(y) <==> x>y | |
x.__hash__() <==> hash(x) | |
x.__iter__() <==> iter(x) | |
x.__le__(y) <==> x<=y | |
x.__len__() <==> len(x) | |
x.__lt__(y) <==> x<y | |
x.__ne__(y) <==> x!=y | |
T.__new__(S, ...) -> a new object with type S, a subtype of T | |
x.__repr__() <==> repr(x) | |
x.__setitem__(i, y) <==> x[i]=y | |
D.clear() -> None. | |
D.copy() -> a shallow copy of D | |
D.get(k[,d]) -> D[k] if k in D, else d. | |
D.has_key(k) -> True if D has a key k, else False | |
D.items() -> list of D's (key, value) pairs, as 2-tuples | |
D.iteritems() -> an iterator over the (key, value) items of D | |
D.iterkeys() -> an iterator over the keys of D | |
D.itervalues() -> an iterator over the values of D | |
D.keys() -> list of D's keys | |
If key is not found, d is returned if given, otherwise KeyError is raised | |
2-tuple; but raise KeyError if D is empty | |
D.setdefault(k[,d]) -> D.get(k,d), also set D[k]=d if k not in D | |
D.update(E, **F) -> None. | |
D.values() -> list of D's values | |
Inherited from object | |
x.__delattr__('name') <==> del x.name | |
helper for pickle | |
helper for pickle | |
x.__setattr__('name', value) <==> x.name = value | |
x.__str__() <==> str(x) | |
Inherited from type | |
v defaults to None. |
Method Details |
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__mul__(self, other)returns a matrix for which each entry is the multiplication product of the two matrices passed |
__sub__(self,
other)
returns a number which is the subtraction product of the two
matrices
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make_relative_entropy(self, obs_freq_mat)if this matrix is a log-odds matrix, return its entropy Needs the observed frequency matrix for that |
print_mat(self, f=None, format='%4d', bottomformat='%4s', alphabet=None, factor=1)Print a nice half-matrix. f=sys.stdout to see on the screen User may pass own alphabet, which should contain all letters in the alphabet of the matrix, but may be in a different order. This order will be the order of the letters on the axes |
_full_to_half(self)Convert a full-matrix to a half-matrix |
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