def annotate_function_with_types(f):
if hasattr(f, '_orig_arg_names'):
arg_names = f._orig_arg_names
else:
arg_names = f.func_code.co_varnames[0:f.func_code.co_argcount]
argtypes = []
for name in arg_names:
arg_type = types.get(name, 'any')
if arg_type not in VALID_ARG_TYPES:
raise ValueError(
"Argument type %s is not valid, must be one of %s, "
"for argument %s" % (arg_type, VALID_ARG_TYPES, name))
argtypes.append(arg_type)
for n in types.keys():
if n not in arg_names and n != 'result':
raise ValueError("Type specified for unknown argument " + n)
return_type = types.get('result', 'float')
if return_type not in VALID_RETURN_TYPES:
raise ValueError("Result type %s is not valid, "
"must be one of %s" %
(return_type, VALID_RETURN_TYPES))
f._arg_types = argtypes
f._return_type = return_type
f._orig_arg_names = arg_names
f._annotation_attributes = getattr(
f, '_annotation_attributes', []) + ['_arg_types', '_return_type']
return f
def resType(resCode):
"""
Classify residues as aromatic (a), charged (c) or polar (p).
@param resCode: amino acid code
@type resCode: str
@return: list of types this residue belongs to...
@rtype: a|c|p OR None
"""
types = {
'a': ['F', 'Y', 'W', 'H'], ## aromatic
'c': ['E', 'D', 'L', 'R', 'H'], ## charged
'p': ['Q', 'N', 'S']
} ## polar
result = []
for t in types.keys():
if resCode in types[t]:
result += [t]
if result == []:
result = ['u']
return result
def hexacode_types():
# We go thru the Cartesian product [0,1,2,3] x ... x [0,1,2,3] with 6 factors"""
all_words = list(cartesian(*([[0, 1, 2, 3]] * 6)))
print(
"""\nDetermine types of all words of GF(4)^6 with respect to the hexacode:
The 1st entry is the weight of the vector v. Other entries are present
if v is no hexacode word. Then the other entries are the (sorted) tuple
of the weights of all hexacode words that have minimal distance to v.""")
types = {}
samples = {}
for a in all_words:
newtype = codeword_type(a)
if not newtype in types:
types[newtype] = 0
samples[newtype] = (a, decode_cocode(a))
types[newtype] += 1
n = 0
for k in sorted(types.keys()):
if k[0] != n: print('')
print(str(k) + ':' + str(types[k]) + ',', end=' ')
n = k[0]
return types
def annotate_function_with_types(f):
if hasattr(f, '_orig_arg_names'):
arg_names = f._orig_arg_names
else:
arg_names = f.func_code.co_varnames[0:f.func_code.co_argcount]
argtypes = []
for name in arg_names:
arg_type = types.get(name, 'any')
if arg_type not in VALID_ARG_TYPES:
raise ValueError("Argument type %s is not valid, must be one of %s, "
"for argument %s" % (arg_type, VALID_ARG_TYPES, name))
argtypes.append(arg_type)
for n in types.keys():
if n not in arg_names and n!='result':
raise ValueError("Type specified for unknown argument "+n)
return_type = types.get('result', 'float')
if return_type not in VALID_RETURN_TYPES:
raise ValueError("Result type %s is not valid, "
"must be one of %s" % (return_type, VALID_RETURN_TYPES))
f._arg_types = argtypes
f._return_type = return_type
f._orig_arg_names = arg_names
f._annotation_attributes = getattr(f, '_annotation_attributes', [])+['_arg_types', '_return_type']
return f
def resType( resCode ):
"""
Classify residues as aromatic (a), charged (c) or polar (p).
@param resCode: amino acid code
@type resCode: str
@return: list of types this residue belongs to...
@rtype: a|c|p OR None
"""
types = {'a' : ['F','Y','W','H'], ## aromatic
'c' : ['E','D','L','R','H'], ## charged
'p' : ['Q','N','S'] } ## polar
result = []
for t in types.keys():
if resCode in types[t]:
result += [t]
if result == []:
result = ['u']
return result
def show_help(self):
"""Show help for the action command."""
args = self.arguments
opts = self.options
types = TypeHelper.get_actionable_types(expendNestedTypes=True,
groupOptions=True)
subst = {}
if not args or self.is_supported_type(types.keys(), args[0]):
if len(args) == 2 and len(opts) == 2:
helptext = self.helptext1
subst['type'] = args[0]
subst['id'] = args[1]
base = self.resolve_base(self.options)
obj = self.get_object(args[0],
args[1],
base,
context_variants=types[args[0]])
if obj is None:
self.error(Messages.Error.NO_SUCH_OBJECT %
(args[1], args[1]))
actions = self._get_action_methods(obj)
subst['actions'] = self.format_list(actions)
if len(args) == 3 and len(opts) == 2:
helptext = self.helptext1
subst['type'] = args[0]
subst['id'] = args[1]
subst['action'] = args[0]
base = self.resolve_base(self.options)
obj = self.get_object(args[1],
args[2],
base,
context_variants=types[args[0]])
if obj is None:
self.error(Messages.Error.NO_SUCH_OBJECT %
(args[0], args[1]))
actions = self._get_action_methods(obj)
if args[0] not in actions:
self.error(Messages.Error.NO_SUCH_ACTION % args[2])
options = self.get_options(method=args[0],
resource=obj,
context_variants=types[args[0]])
subst['actions'] = self.format_list(actions)
subst['options'] = self.format_list(options,
bullet='',
sort=False)
elif len(args) == 1:
helptext = self.helptext0
subst['types'] = self.format_map({args[0]: types[args[0]]})
subst['type'] = args[0]
elif len(args) == 2:
helptext = self.helptext1
subst['type'] = args[0]
subst['id'] = args[1]
base = self.resolve_base(opts)
obj = self.get_object(args[0],
args[1],
base,
context_variants=types[args[0]])
if obj is None:
self.error(Messages.Error.NO_SUCH_OBJECT %
(args[0], args[1]))
actions = self._get_action_methods(obj)
subst['actions'] = self.format_list(actions)
elif len(args) == 3:
helptext = self.helptext1
subst['type'] = args[0]
subst['id'] = args[1]
subst['action'] = args[2]
base = self.resolve_base(self.options)
obj = self.get_object(args[0],
args[1],
base,
context_variants=types[args[0]])
if obj is None:
self.error(Messages.Error.NO_SUCH_OBJECT %
(args[0], args[1]))
actions = self._get_action_methods(obj)
if args[2] not in actions:
self.error(Messages.Error.NO_SUCH_ACTION % args[2])
options = self.get_options(method=args[2],
resource=obj,
sub_resource=base,
context_variants=types[args[0]])
subst['actions'] = self.format_list(actions)
subst['options'] = self.format_list(options,
bullet='',
sort=False)
else:
helptext = self.helptext0
subst['types'] = self.format_map(types)
# scope = '%s:%s' % (type(obj).__name__, args[2])
statuses = self.get_statuses()
subst['statuses'] = self.format_list(statuses)
helptext = self.format_help(helptext, subst)
self.write(helptext)
def show_help(self):
"""Show help for the action command."""
args = self.arguments
opts = self.options
types = TypeHelper.get_actionable_types(
expendNestedTypes=True,
groupOptions=True
)
subst = {}
if not args or self.is_supported_type(types.keys(), args[0]):
if len(args) == 2 and len(opts) == 2:
helptext = self.helptext1
subst['type'] = args[0]
subst['id'] = args[1]
base = self.resolve_base(self.options)
obj = self.get_object(
args[0],
args[1],
base,
context_variants=types[args[0]]
)
if obj is None:
self.error(
Messages.Error.NO_SUCH_OBJECT % (args[1], args[1])
)
actions = self._get_action_methods(obj)
subst['actions'] = self.format_list(actions)
if len(args) == 3 and len(opts) == 2:
helptext = self.helptext1
subst['type'] = args[0]
subst['id'] = args[1]
subst['action'] = args[0]
base = self.resolve_base(self.options)
obj = self.get_object(
args[1],
args[2],
base,
context_variants=types[args[0]]
)
if obj is None:
self.error(
Messages.Error.NO_SUCH_OBJECT % (args[0], args[1])
)
actions = self._get_action_methods(obj)
if args[0] not in actions:
self.error(
Messages.Error.NO_SUCH_ACTION % args[2]
)
options = self.get_options(
method=args[0],
resource=obj,
context_variants=types[args[0]]
)
subst['actions'] = self.format_list(actions)
subst['options'] = self.format_list(options, bullet='', sort=False)
elif len(args) == 1:
helptext = self.helptext0
subst['types'] = self.format_map({args[0]:types[args[0]]})
subst['type'] = args[0]
elif len(args) == 2:
helptext = self.helptext1
subst['type'] = args[0]
subst['id'] = args[1]
base = self.resolve_base(opts)
obj = self.get_object(
args[0],
args[1],
base,
context_variants=types[args[0]]
)
if obj is None:
self.error(
Messages.Error.NO_SUCH_OBJECT % (args[0], args[1])
)
actions = self._get_action_methods(obj)
subst['actions'] = self.format_list(actions)
elif len(args) == 3:
helptext = self.helptext1
subst['type'] = args[0]
subst['id'] = args[1]
subst['action'] = args[2]
base = self.resolve_base(self.options)
obj = self.get_object(
args[0],
args[1],
base,
context_variants=types[args[0]]
)
if obj is None:
self.error(
Messages.Error.NO_SUCH_OBJECT % (args[0], args[1])
)
actions = self._get_action_methods(obj)
if args[2] not in actions:
self.error(Messages.Error.NO_SUCH_ACTION % args[2])
options = self.get_options(
method=args[2],
resource=obj,
sub_resource=base,
context_variants=types[args[0]]
)
subst['actions'] = self.format_list(actions)
subst['options'] = self.format_list(options, bullet='', sort=False)
else:
helptext = self.helptext0
subst['types'] = self.format_map(types)
# scope = '%s:%s' % (type(obj).__name__, args[2])
statuses = self.get_statuses()
subst['statuses'] = self.format_list(statuses)
helptext = self.format_help(helptext, subst)
self.write(helptext)
