Parameter Handling

Parameter handling in OpenMS and pyOpenMS is usually implemented through inheritance from DefaultParamHandler and allow access to parameters through the Param object. This means, the classes implement the methods getDefaults, getParameters, setParameters which allows access to the default parameters, the current parameters and allows to set the parameters.

The Param object that is returned can be manipulated through the setValue and getValue methods (the exists method can be used to check for existence of a key). Using the getDescription method, it is possible to get a help-text for each parameter value in an interactive session without consulting the documentation.

from pyopenms import *
p = Param()
p.setValue("param1", 4.0, "This is value 1")
p.setValue("param2", 5.0, "This is value 2")
print( p[b"param1"] )
p[b"param1"] += 3 # add three to the parameter value
print( p[b"param1"] )

The parameters can then be accessed as

>>> p.asDict()
{'param2': 4.0, 'param1': 7.0}
>>> p.values()
[4.0, 7.0]
>>> p.keys()
['param1', 'param2']
>>> p.items()
[('param1', 7.0), ('param2', 4.0)]
>>> p.exists("param1")
True