Package transsys :: Module optim :: Class TranssysTypedParameterTransformer
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Class TranssysTypedParameterTransformer

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          object --+    
                   |    
ParameterTransformer --+
                       |
                      TranssysTypedParameterTransformer

Parameter transformer differentiating decay, diffusibility, constitutive, aspec, amax, rspec and rmax nodes.

This class is intended for transsys programs with constant values (i.e. ExpressionNodeValue instances) for decay, diffusibility, constitutive, aspec, amax, rspec and rmax. Use with transsys programs that do not have this standard, basic structure has undefined effects and may be disabled in the future.

Instance Methods [hide private]
 
__init__(self, decayTransformation=None, diffusibilityTransformation=None, constitutiveTransformation=None, aspecTransformation=None, amaxTransformation=None, rspecTransformation=None, rmaxTransformation=None)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
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__str__(self)
str(x)
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setAllTransformations(self, transformation)
Set all transformations to transformation.
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setConstrainedTransformations(self)
Configure transformer to be equivalent to the abandoned ConstrainedTransformer.
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parse_variables(self, f)
Parse instance variables from file f.
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setTranssysProgram(self, transsys_program, factor_name_list, gene_name_list)
Set the transsys program on which the transformer is to operate.
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clipParameters(self)
Clip the parameters in transsys_program to the range required by the respective transformer.
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getParameters(self)
Get unconstrained parameters from a transsys program.
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setParameters(self, parameter_list)
Set values in a transsys program based on a list of unconstrained parameters.
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Inherited from ParameterTransformer: check_savefile_magic, parse, randomiseParametersUniform

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__

Class Variables [hide private]
  savefile_magic = 'TranssysTypedParameterTransformer'
Instance Variables [hide private]
TransformationFunction amaxTransformation
transformation function for amax values.
TransformationFunction aspecTransformation
transformation function for aspec values.
TransformationFunction constitutiveTransformation
transformation function for constitutive values.
TransformationFunction decayTransformation
transformation function for decay values.
TransformationFunction diffusibilityTransformation
transformation function for diffusibility values.
TransformationFunction rmaxTransformation
transformation function for rmax values.
TransformationFunction rspecTransformation
transformation function for rspec values.

Inherited from ParameterTransformer: factor_name_list, gene_name_list, target_node_list, transsys_program

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, decayTransformation=None, diffusibilityTransformation=None, constitutiveTransformation=None, aspecTransformation=None, amaxTransformation=None, rspecTransformation=None, rmaxTransformation=None)
(Constructor)

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x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__
(inherited documentation)

__str__(self)
(Informal representation operator)

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str(x)

Overrides: object.__str__
(inherited documentation)

setAllTransformations(self, transformation)

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Set all transformations to transformation.

Parameters:

setConstrainedTransformations(self)

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Configure transformer to be equivalent to the abandoned ConstrainedTransformer.

Deprecated: assemble transformers manually, by assigning to instance variables.

parse_variables(self, f)

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Parse instance variables from file f.

Parameters:
  • f (a file object (file object emulators should generally work too)) - the file to read from
Overrides: ParameterTransformer.parse_variables

setTranssysProgram(self, transsys_program, factor_name_list, gene_name_list)

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Set the transsys program on which the transformer is to operate.

Passing None as factor name list selects all factor-related parameters for optimisation, and likewise, passing None as gene name list selects all gene-related parameters for optimisation.

Parameters:
  • transsys_program - the transsys program
  • factor_name_list - factors for which parameters are to be optimised
  • gene_name_list - genes for which parameters are to be optimised
Overrides: ParameterTransformer.setTranssysProgram
(inherited documentation)

clipParameters(self)

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Clip the parameters in transsys_program to the range required by the respective transformer.

Overrides: ParameterTransformer.clipParameters
(inherited documentation)

getParameters(self)

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Get unconstrained parameters from a transsys program.

Returns:
a list of the unconstrained parameters
Overrides: ParameterTransformer.getParameters

setParameters(self, parameter_list)

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Set values in a transsys program based on a list of unconstrained parameters.

Notice that the parameter list must have the same length as that obtained by getParameters.

Raises:
  • StandardError - if the parameter list is too long or too short
Overrides: ParameterTransformer.setParameters