def __init__(self, data=None, RowOrder=None, ColOrder=None, Default=None,
Pad=None, RowConstructor=None, info=None):
""" Init dict with pre-exisitng data: dict of dicts
Usage:
data = distance matrix in form acceptable by Dict2D class
RowOrder = list of 'interesting keys', default is the set of
all amino acids
ColOrder = list of 'interesting keys', default is the set of
all amino acids
Default = value to set padded elements to
Pad = boolean describing whether to fill object to hold all
possible elements based on RowOrder and ColOrder
RowConstructor = constructor to use when building inner
objects, default dict
info = the AAIndexRecord object
Power = Power the original matrix has been raised to yield current
matrix
"""
if RowOrder is not None:
self.RowOrder = RowOrder
if ColOrder is not None:
self.ColOrder = ColOrder
if Pad is not None:
self.Pad = Pad
# Initialize super class attributes
Dict2D.__init__(self, data=data, RowOrder=self.RowOrder,\
ColOrder=self.ColOrder, Default=Default, Pad=self.Pad,\
RowConstructor=RowConstructor)
Delegator.__init__(self, info)
# The power to which the original data has been raised to give
# the current data, starts at 1., modified by elementPow()
# accessed as self.Power
self.__dict__['Power'] = 1.
def __init__(self, data=None, RowOrder=None, ColOrder=None, Default=None,
Pad=None, RowConstructor=None, info=None):
""" Init dict with pre-exisitng data: dict of dicts
Usage:
data = distance matrix in form acceptable by Dict2D class
RowOrder = list of 'interesting keys', default is the set of
all amino acids
ColOrder = list of 'interesting keys', default is the set of
all amino acids
Default = value to set padded elements to
Pad = boolean describing whether to fill object to hold all
possible elements based on RowOrder and ColOrder
RowConstructor = constructor to use when building inner
objects, default dict
info = the AAIndexRecord object
Power = Power the original matrix has been raised to yield current
matrix
"""
if RowOrder is not None:
self.RowOrder = RowOrder
if ColOrder is not None:
self.ColOrder = ColOrder
if Pad is not None:
self.Pad = Pad
# Initialize super class attributes
Dict2D.__init__(self, data=data, RowOrder=self.RowOrder,\
ColOrder=self.ColOrder, Default=Default, Pad=self.Pad,\
RowConstructor=RowConstructor)
Delegator.__init__(self, info)
# The power to which the original data has been raised to give
# the current data, starts at 1., modified by elementPow()
# accessed as self.Power
self.__dict__['Power'] = 1.
def __init__(self, items='', length=None):
"""Initializes the Bitvector class, storing data in long _vector.
Items can be any sequence with members that evaluate to True or False.
Private data:
_vector: long representing the bitvector
_string: string representation of the vector
_is_current: boolean indicating whether the string is known to
match the long data
"""
Delegator.__init__(self, None)
self.replace(items, length)
def __init__(self, items='', length=None):
"""Initializes the Bitvector class, storing data in long _vector.
Items can be any sequence with members that evaluate to True or False.
Private data:
_vector: long representing the bitvector
_string: string representation of the vector
_is_current: boolean indicating whether the string is known to
match the long data
"""
Delegator.__init__(self, None)
self.replace(items, length)
def __init__(self, data=None, Info=None, **kwargs):
"""Intializes BaseUsage with data, either sequence or dict of freqs.
Ignores additional kwargs (e.g. to support copy).
Makes the _handler for delegator accessible with the name Info.
"""
if Info is None:
if hasattr(data, 'Info'):
Info = data.Info
else:
Info = InfoClass()
Delegator.__init__(self, Info)
Freqs.__init__(self, data or [], **kwargs)
def __init__(self, data=None, Info=None, **kwargs):
"""Intializes BaseUsage with data, either sequence or dict of freqs.
Ignores additional kwargs (e.g. to support copy).
Makes the _handler for delegator accessible with the name Info.
"""
if Info is None:
if hasattr(data, 'Info'):
Info = data.Info
else:
Info = InfoClass()
Delegator.__init__(self, Info)
Freqs.__init__(self, data or [], **kwargs)
def __init__(self, *args, **kwargs):
"""Returns new Info object. Creates DbRefs if necessary."""
temp = dict(*args, **kwargs)
if 'Refs' in temp:
refs = temp['Refs']
if not isinstance(refs, DbRefs):
refs = DbRefs(refs)
else:
refs = DbRefs()
#move keys into refs if they belong there: allows init from flat dict
for key, val in temp.items():
if key in KnownDatabases:
refs[key] = val
del temp[key]
Delegator.__init__(self, refs)
self['Refs'] = refs
MappedRecord.__init__(self, temp)
def __init__(self, *args, **kwargs):
"""Returns new Info object. Creates DbRefs if necessary."""
temp = dict(*args, **kwargs)
if 'Refs' in temp:
refs = temp['Refs']
if not isinstance(refs, DbRefs):
refs = DbRefs(refs)
else:
refs = DbRefs()
#move keys into refs if they belong there: allows init from flat dict
for key, val in temp.items():
if key in KnownDatabases:
refs[key] = val
del temp[key]
Delegator.__init__(self, refs)
self['Refs'] = refs
MappedRecord.__init__(self, temp)
def __init__(self, data, *args):
Delegator.__init__(self, *args)
self.__dict__['Info'] = self._handler
str.__init__(data)
def __init__(self, First=None, Second=None, Third=None, Info=None):
"""Returns new PositionalBaseUsage with values for the 3 positions."""
Delegator.__init__(self, Info)
self.__dict__['First'] = First or BaseUsage()
self.__dict__['Second'] = Second or BaseUsage()
self.__dict__['Third'] = Third or BaseUsage()
def __init__(self, First=None, Second=None, Third=None, Info=None):
"""Returns new PositionalBaseUsage with values for the 3 positions."""
Delegator.__init__(self, Info)
self.__dict__['First'] = First or BaseUsage()
self.__dict__['Second'] = Second or BaseUsage()
self.__dict__['Third'] = Third or BaseUsage()
def __init__(self, data, *args):
Delegator.__init__(self, *args)
self.__dict__['Info'] = self._handler
str.__init__(data)