def get_composition(self, obj):
try:
composition = obj.glycan_composition
except AttributeError:
composition = HashableGlycanComposition.parse(obj)
composition = symbolic_expression.GlycanSymbolContext(composition)
return composition
def handle_node_line(self, line):
try:
index, composition, score = line.replace("\n", "").split("\t")
score = float(score)
except ValueError:
index, composition = line.replace("\n", "").split("\t")
score = 0.
index = int(index)
composition = HashableGlycanComposition.parse(composition)
node = CompositionGraphNode(composition, index, score)
node.internal_score = score
self.network.nodes.append(node)
self.network.node_map[str(node.composition)] = node
def handle_node_line(self, line):
try:
index, composition, score = line.replace("\n", "").split("\t")
score = float(score)
except ValueError:
index, composition = line.replace("\n", "").split("\t")
score = 0.
index = int(index)
composition = HashableGlycanComposition.parse(composition)
node = CompositionGraphNode(composition, index, score)
node.internal_score = score
self.network.nodes.append(node)
self.network.node_map[str(node.composition)] = node
def symbolic_composition(obj):
"""Extract the glycan composition from *obj* and converts it
into an instance of :class:`.GlycanSymbolContext`
The extraction process first attempts to access *obj.glycan_composition*
but on an :class:`AttributeError` calls :meth:`.HashableGlycanComposition.parse`
on *obj*. The resulting :class:`.GlycanComposition` object is then passed
to :class:`.GlycanSymbolContext`
Parameters
----------
obj : object
The object to convert
Returns
-------
GlycanSymbolContext
"""
try:
composition = obj.glycan_composition
except AttributeError:
composition = HashableGlycanComposition.parse(obj)
composition = symbolic_expression.GlycanSymbolContext(composition)
return composition
def symbolic_composition(obj):
"""Extract the glycan composition from *obj* and converts it
into an instance of :class:`.GlycanSymbolContext`
The extraction process first attempts to access *obj.glycan_composition*
but on an :class:`AttributeError` calls :meth:`.HashableGlycanComposition.parse`
on *obj*. The resulting :class:`.GlycanComposition` object is then passed
to :class:`.GlycanSymbolContext`
Parameters
----------
obj : object
The object to convert
Returns
-------
GlycanSymbolContext
"""
try:
composition = obj.glycan_composition
except AttributeError:
composition = HashableGlycanComposition.parse(obj)
composition = symbolic_expression.GlycanSymbolContext(composition)
return composition
def _normalize_key(self, key):
if isinstance(key, basestring):
key = HashableGlycanComposition.parse(key)
key = symbolic_expression.GlycanSymbolContext(key)
return HashableGlycanComposition.parse(key.serialize())
def _normalize_key(self, key):
if isinstance(key, basestring):
key = HashableGlycanComposition.parse(key)
key = symbolic_expression.GlycanSymbolContext(key)
return HashableGlycanComposition.parse(key.serialize())
def keys(self):
if self._glycan_composition is None:
self._glycan_composition = HashableGlycanComposition.parse(
self.composition)
return self._glycan_composition.keys()
def __getitem__(self, key):
if self._glycan_composition is None:
self._glycan_composition = HashableGlycanComposition.parse(
self.composition)
return self._glycan_composition[key]
def convert(self):
inst = HashableGlycanComposition.parse(self.composition)
inst.id = self.id
return inst
def keys(self):
if self._glycan_composition is None:
self._glycan_composition = HashableGlycanComposition.parse(self.composition)
return self._glycan_composition.keys()
def __getitem__(self, key):
if self._glycan_composition is None:
self._glycan_composition = HashableGlycanComposition.parse(self.composition)
return self._glycan_composition[key]
def convert(self):
inst = HashableGlycanComposition.parse(self.composition)
inst.id = self.id
return inst