org.broadinstitute.hellbender.utils.mcmc

Class ParameterizedState<T extends java.lang.Enum<T> & ParameterEnum>

java.lang.Object

org.broadinstitute.hellbender.utils.mcmc.ParameterizedState<T>

public class ParameterizedState<T extends java.lang.Enum<T> & ParameterEnum>
extends java.lang.Object

Represents a mapped collection of Parameter objects, i.e., named, ordered, enumerated keys associated with values of mixed type via a key -> key, value map. See GibbsSamplerSingleGaussianUnitTest and GibbsSamplerCopyRatioUnitTest for examples of use.

Constructor Summary

Constructors

Constructor and Description
ParameterizedState(java.util.List<Parameter<T,?>> parameters) Constructs a ParameterizedState with parameters enumerated by ParameterEnum from a List of Parameter objects with values of mixed type, checking that all parameters are present without duplicates.
ParameterizedState(ParameterizedState<T> state) Copy constructor.

Method Summary

Modifier and Type	Method and Description
protected <S extends ParameterizedState<T>> S	copy()
<U> U	get(T parameterKey, java.lang.Class<U> parameterValueClass) Returns the value of a Parameter contained in the collection held by the ParameterizedState, given the ParameterEnum key and type of the Parameter.
java.util.Set<T>	keySet() Returns a Set of the keys of the Parameter objects that are held internally as values of the parameter map.
protected <U> void	update(T parameterName, U value) Updates the value of a Parameter contained in the collection held by the ParameterizedState.
java.util.List<Parameter<T,?>>	values() Returns a List of the Parameter objects that are held internally as values of the parameter map.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ParameterizedState

public ParameterizedState(java.util.List<Parameter<T,?>> parameters)

Constructs a ParameterizedState with parameters enumerated by ParameterEnum from a List of Parameter objects with values of mixed type, checking that all parameters are present without duplicates.

Parameters:

parameters - List of Parameters

Throws:

java.lang.IllegalArgumentException - if parameters is null, empty, contains duplicate parameter names, or missing parameter names

ParameterizedState

public ParameterizedState(ParameterizedState<T> state)

Copy constructor.

Parameters:

state - state to be copied

Method Detail

keySet

public java.util.Set<T> keySet()

Returns a Set of the keys of the Parameter objects that are held internally as values of the parameter map. The order of the parameters in the set is the same as in the list passed to the constructor.

Returns:

a List of the Parameter objects held internally as values of the parameter map

values

public java.util.List<Parameter<T,?>> values()

Returns a List of the Parameter objects that are held internally as values of the parameter map. The order of the parameters in the list is the same as in the list passed to the constructor.

Returns:

a List of the Parameter objects held internally as values of the parameter map

get

public <U> U get(T parameterKey,
                 java.lang.Class<U> parameterValueClass)

Returns the value of a Parameter contained in the collection held by the ParameterizedState, given the ParameterEnum key and type of the Parameter.

Type Parameters:

U - type of Parameter value

Parameters:

parameterKey - ParameterEnum key of Parameter

parameterValueClass - class of Parameter value

Returns:

Parameter value

Throws:

java.lang.IllegalArgumentException - if parameterValueClass does not match that of the Parameter in the collection

update

protected <U> void update(T parameterName,
                          U value)

Updates the value of a Parameter contained in the collection held by the ParameterizedState.

Type Parameters:

U - type of Parameter value

Parameters:

parameterName - ParameterEnum key of Parameter to update

value - new Parameter value

Throws:

java.lang.IllegalArgumentException - if parameterName does not correspond to a Parameter in the collection

copy

protected <S extends ParameterizedState<T>> S copy()