def get_parameters_from_model(model):
"""Get all the SBML parameters from the model"""
params = outline_sbml.get_elements_from_lists_of_list("listOfParameters",
"parameter",
get_parameter_of_element,
model)
return [ p for p in params if p is not None ]
def get_assignment_rules_from_model(model):
"""Get all the assignment rules from the model"""
arules = outline_sbml.get_elements_from_lists_of_list("listOfRules",
"assignmentRule",
get_assign_rule_from_element,
model)
return arules
def params_from_param_histories(model):
"""Get all the parameter histories in the model file and parse
these into parameter descriptions suitable for creating an
init params file
"""
annotations = model.getElementsByTagName("annotation")
params = []
for annotation in annotations:
list_name = "listOfParameterHistories"
annot_params = outline_sbml.get_elements_from_lists_of_list(list_name,
"parameterHistory",
get_param_of_history,
annotation)
params += [ p for p in annot_params if p.use ]
return params
