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from .identified import Identified
from .property import OwnedObject, URIProperty
from .validation import *
from .constants import *
class Interaction(Identified):
def __init__(self, rdf_type=SBOL_INTERACTION, uri='example', interaction_type=SBO_INTERACTION):
super().__init__(rdf_type, uri)
self.functionalComponents = OwnedObject(self, SBOL_FUNCTIONAL_COMPONENTS, '0', '*', [libsbol_rule_18])
self._types = URIProperty(self, SBOL_TYPES, '1', '*', [], interaction_type)
self.participations = OwnedObject(self, SBOL_PARTICIPATIONS, '0', '*', [])
self.measurements = OwnedObject(self, SBOL_MEASUREMENTS, '0', '*', [])
# TODO hidden properties
@property
def types(self):
return self._types.value
@types.setter
def types(self, new_types):
self._types.set(new_types)
from sbol3.identified import Identified
from sbol3.constants import *
from sbol3.property import LiteralProperty, URIProperty
from rdflib import URIRef
class Measurement(Identified):
"""The purpose of the Measure class is to link a numerical value to a unit of measure."""
def __init__(self, uri=URIRef('example'), value=0.0, unit='', version=VERSION_STRING):
super().__init__(SBOL_MEASURE, uri, version)
self._value = LiteralProperty(self, SBOL_VALUE, '1', '1', [], value)
self._unit = URIProperty(self, SBOL_UNIT, '1', '1', [], unit)
self._types = URIProperty(self, SBOL_TYPES, '0', '*', [])
@property
def value(self):
return self._value.value
@value.setter
def value(self, new_value):
self._value.set(new_value)
from .identified import Identified
from .toplevel import TopLevel
from .constants import *
from rdflib import URIRef
from .property import ReferencedObject, URIProperty, OwnedObject
class VariableComponent(Identified):
def __init__(self, type_uri=SBOL_IDENTIFIED, uri=URIRef('example'), repeat='http://sbols.org/v2#on', version=VERSION_STRING):
super().__init__(type_uri, uri, version)
self.variable = ReferencedObject(self, SBOL_VARIABLE, SBOL_COMPONENT, '0', '1', [])
self._repeat = URIProperty(self, SBOL_OPERATOR, '1', '1', [], repeat)
self.variants = ReferencedObject(self, SBOL_VARIANTS, SBOL_COMPONENT_DEFINITION, '0', '*', [])
self.variantCollections = ReferencedObject(self, SBOL_VARIANT_COLLECTIONS, SBOL_COLLECTION, '0', '*', [])
self.variantDerivations = ReferencedObject(self, SBOL_VARIANT_DERIVATIONS, SBOL_COMBINATORIAL_DERIVATION, '0', '*', [])
@property
def repeat(self):
return self._repeat.value
@repeat.setter
def repeat(self, new_repeat):
self._repeat.set(new_repeat)
from .identified import Identified
from .constants import *
from rdflib import URIRef
from .property import URIProperty, ReferencedObject, OwnedObject
class Participation(Identified):
def __init__(self, type_uri=SBOL_PARTICIPATION, uri=URIRef('example'), participant='', version=VERSION_STRING):
super().__init__(type_uri, uri, version)
self._roles = URIProperty(self, SBOL_ROLES, '0', '*', [])
self.participant = ReferencedObject(self, SBOL_PARTICIPANT, SBOL_FUNCTIONAL_COMPONENT, '1', '1', [], participant)
self.measurements = OwnedObject(self, SBOL_MEASUREMENTS, '0', '*', [])
@property
def roles(self):
return self._roles.value
@roles.setter
def roles(self, new_roles):
self._roles.set(new_roles)
def addRole(self, new_role):
from .identified import Identified
from .constants import *
from rdflib import URIRef
from .property import URIProperty, ReferencedObject
class MapsTo(Identified):
def __init__(self, type_uri=SBOL_MAPS_TO, uri=URIRef('example'), local='', remote='', refinement=SBOL_REFINEMENT_VERIFY_IDENTICAL, version=VERSION_STRING):
super().__init__(type_uri, uri, version)
self.local = ReferencedObject(self, SBOL_LOCAL, SBOL_COMPONENT, '1', '1', [], local)
self.remote = ReferencedObject(self, SBOL_REMOTE, SBOL_COMPONENT, '1', '1', [], remote)
self._refinement = URIProperty(self, SBOL_REFINEMENT, '1', '1', [], refinement)
@property
def refinement(self):
return self._refinement.value
@refinement.setter
def refinement(self, new_refinement):
self._refinement.set(new_refinement)
from .identified import Identified
from .constants import *
from .property import OwnedObject, ReferencedObject
class Module(Identified):
def __init__(self, rdf_type=SBOL_MODULE, uri='example', definition='', version=VERSION_STRING):
super().__init__(rdf_type, uri, version)
self.definition = ReferencedObject(self, SBOL_DEFINITION, SBOL_MODULE_DEFINITION, '1', '1', [], definition)
self.mapsTos = OwnedObject(self, SBOL_MAPS_TOS, '0', '*', [])
self.measurements = OwnedObject(self, SBOL_MEASUREMENTS, '0', '*', [])
from .identified import Identified
from .constants import *
from .property import OwnedObject, URIProperty
class SequenceAnnotation(Identified):
def __init__(self, uri='example', version=VERSION_STRING):
"""Construct a SequenceAnnotation
:param uri: A full URI including a scheme, namespace, and identifier.
If SBOLCompliance configuration is enabled, then this argument is simply
the displayId for the new object and a full URI will automatically be constructed.
:param version: An arbitrary version string. If SBOLCompliance is enabled,
this should be a Maven version string of the form "major.minor.patch".
"""
super().__init__(SBOL_SEQUENCE_ANNOTATION, uri, version)
self.component = None # TODO support ReferencedObject
self.locations = OwnedObject(self, SBOL_LOCATIONS, '0', '*', [])
self._roles = URIProperty(self, SBOL_ROLES, '0', '*', [])
@property
def roles(self):
from .constants import *
from .identified import Identified
from rdflib import URIRef
from .property import URIProperty, ReferencedObject
class SequenceConstraint(Identified):
def __init__(self, type_uri=SBOL_SEQUENCE_CONSTRAINT, uri=URIRef('example'), subject='', object='', restriction=SBOL_RESTRICTION_PRECEDES, version=VERSION_STRING):
super().__init__(type_uri, uri, version)
self.subject = ReferencedObject(self, SBOL_SUBJECT, SBOL_COMPONENT, '1', '1', [], subject)
self.object = ReferencedObject(self, SBOL_OBJECT, SBOL_COMPONENT, '1', '1', [], object)
self._restriction = URIProperty(self, SBOL_RESTRICTION, '1', '1', [], restriction)
@property
def restriction(self):
return self._restriction.value
@restriction.setter
def restriction(self, new_restriction):
self._restriction.set(new_restriction)
from .identified import Identified
from .constants import *
from .property import URIProperty, ReferencedObject, LiteralProperty
from rdflib import URIRef
class Location(Identified):
"""The Location class specifies the strand orientation of a Component."""
def __init__(self, type_uri=SBOL_LOCATION, uri=URIRef('example'), orientation=SBOL_ORIENTATION_INLINE):
super().__init__(type_uri, uri)
self._orientation = URIProperty(self, SBOL_ORIENTATION, '1', '1', [], orientation)
self.sequence = ReferencedObject(self, SBOL_SEQUENCE_PROPERTY, SBOL_SEQUENCE, '0', '1', [])
@property
def orientation(self):
return self._orientation.value
@orientation.setter
def orientation(self, new_orientation):
self._orientation.set(new_orientation)
class Range(Location):
from .identified import Identified
from .property import URIProperty, OwnedObject, ReferencedObject
from .constants import *
class ComponentInstance(Identified):
def __init__(self, rdf_type, uri, definition, access, version):
super().__init__(rdf_type, uri, version)
self.definition = ReferencedObject(self, SBOL_DEFINITION, SBOL_COMPONENT_DEFINITION, '1', '1', [], definition)
self._access = URIProperty(self, SBOL_ACCESS, '0', '1', [], access)
self.mapsTos = OwnedObject(self, SBOL_MAPS_TOS, '0', '*', [])
self.measurements = OwnedObject(self, SBOL_MEASUREMENTS, '0', '*', [])
@property
def access(self):
return self._access.value
@access.setter
def access(self, new_access):
self._access.set(new_access)