public class Parameter
extends java.lang.Object
implements java.io.Serializable
Modifier and Type | Class and Description |
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static class |
Parameter.FormatException
Exception thrown when the format of a parameter string is incorrect
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Modifier and Type | Method and Description |
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Parameter |
clone() |
boolean |
getEstimate()
Returns whether this paramater is a parameter that should be estimated
|
double |
getLowerBound()
Gets the lower bound of a parameter
|
java.lang.String |
getName()
Gets the name of the parameter
|
double |
getUpperBound()
Gets the upper bound of a parameter
|
double |
getValue()
Gets the value of the parameter
|
boolean |
matrix()
Whether this parameter is in a rate matrix.
|
static Parameter |
newEstimatedBoundedParameter(java.lang.String name,
double lbound,
double ubound)
Creates a new bounded parameter that is estimated.
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static Parameter |
newEstimatedBoundedParameter(java.lang.String name,
double lbound,
double ubound,
boolean matrix)
Creates a new bounded paramater that is estimated and is optionally in a
rate matrix
|
static Parameter |
newEstimatedParameter(java.lang.String name)
Creates a new (unbounded) paramater that is estimated.
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static Parameter |
newEstimatedParameter(java.lang.String name,
boolean matrix)
Creates a new unbounded parameter that is estimated and is optionally in
a rate matrix.
|
static Parameter |
newEstimatedPositiveParameter(java.lang.String name)
Creates a new parameter that has to be positive and is estimated.
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static Parameter |
newEstimatedPositiveParameter(java.lang.String name,
boolean matrix)
Creates a new positive parameter that is estimated and is optionally in
a rate matrix.
|
static Parameter |
newFixedParameter(java.lang.String name,
double value)
Creates a new fixed parameter (i.e.
|
java.lang.String |
toString() |
public Parameter clone()
clone
in class java.lang.Object
public java.lang.String getName()
public double getValue()
public double getLowerBound()
public double getUpperBound()
public boolean getEstimate()
public boolean matrix()
public java.lang.String toString()
toString
in class java.lang.Object
public static Parameter newEstimatedPositiveParameter(java.lang.String name)
name
- The name of the parameterpublic static Parameter newEstimatedParameter(java.lang.String name)
name
- The name of the parameterpublic static Parameter newEstimatedBoundedParameter(java.lang.String name, double lbound, double ubound)
name
- The name of the parameterlbound
- The lower bound of the value the parameter can takeubound
- The upper bound of the value the parameter cantakepublic static Parameter newFixedParameter(java.lang.String name, double value)
name
- The parameters namevalue
- The value of the parameterpublic static Parameter newEstimatedPositiveParameter(java.lang.String name, boolean matrix)
name
- The name of the parametermatrix
- Whether the parameter is in a rate matrixpublic static Parameter newEstimatedParameter(java.lang.String name, boolean matrix)
name
- The name if the parametermatrix
- Whether the parameter is in a rate matrixpublic static Parameter newEstimatedBoundedParameter(java.lang.String name, double lbound, double ubound, boolean matrix)
name
- The name of the parameterlbound
- The lower bound of the value the parameter can takeubound
- The upper bound of the value the parameter cantakematrix
- Whether the parameter is in a rate matrix