public abstract class SeparateLogPrior extends LogPrior implements Cloneable
SeparateGaussianLogPrior
or the
SeparateLaplaceLogPrior
.Modifier and Type | Field and Description |
---|---|
protected double[] |
classMus
The means for the class parameters, as specified by the user.
|
protected double[] |
classVars
The variances for the class parameters, as specified by the user.
|
protected boolean |
freeParameters
Indicates, if only free parameters shall be used and hence penalized.
|
protected DifferentiableStatisticalModel[] |
funs
The
DifferentiableSequenceScore s using the parameters that shall be
penalized. |
protected double[] |
vars
The base variances for the parameters of the
DifferentiableSequenceScore s of
each class, the means of the non-class parameters should be 0. |
Constructor and Description |
---|
SeparateLogPrior(double[] vars,
double[] classVars,
double[] classMus)
Creates a new
SeparateLogPrior using the class-specific base
variances vars , the variances classVars and the
means classMus for the class parameters. |
SeparateLogPrior(StringBuffer xml)
The standard constructor for the interface
Storable . |
Modifier and Type | Method and Description |
---|---|
SeparateLogPrior |
getNewInstance()
This method returns an empty new instance of the current prior.
|
void |
set(boolean freeParameters,
DifferentiableSequenceScore... funs)
Resets all pre-computed values to their initial values using the
DifferentiableSequenceScore s funs . |
StringBuffer |
toXML()
Encodes the prior as an XML representation.
|
protected abstract void |
unset()
Resets all internally pre-computed values, e.g.
|
addGradientFor, evaluateGradientOfFunction, getInstanceName
findOneDimensionalMin
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
evaluateFunction, getDimensionOfScope
protected DifferentiableStatisticalModel[] funs
DifferentiableSequenceScore
s using the parameters that shall be
penalized.protected double[] vars
DifferentiableSequenceScore
s of
each class, the means of the non-class parameters should be 0.protected double[] classVars
protected double[] classMus
protected boolean freeParameters
public SeparateLogPrior(double[] vars, double[] classVars, double[] classMus)
SeparateLogPrior
using the class-specific base
variances vars
, the variances classVars
and the
means classMus
for the class parameters.vars
- the base variances for each classclassVars
- the variances for the class parametersclassMus
- the means for the class parameterspublic SeparateLogPrior(StringBuffer xml) throws NonParsableException
Storable
.
Creates a new SeparateLogPrior
out of its XML representation.xml
- the XML representation as StringBuffer
NonParsableException
- if the SeparateLogPrior
could not be reconstructed
out of the XML representation (the StringBuffer
could
not be parsed)Storable
public void set(boolean freeParameters, DifferentiableSequenceScore... funs) throws Exception
LogPrior
DifferentiableSequenceScore
s funs
.set
in class LogPrior
freeParameters
- the switch for using only the free parameters or all
parameters in a DifferentiableSequenceScore
funs
- the DifferentiableSequenceScore
s for the priorException
- if the DifferentiableSequenceScore
s could not be setprotected abstract void unset()
public SeparateLogPrior getNewInstance() throws CloneNotSupportedException
LogPrior
DifferentiableSequenceScore
s that may be inside the instance. The DifferentiableSequenceScore
s must be
set by an invocation of the method
LogPrior.set(boolean, DifferentiableSequenceScore...)
.getNewInstance
in class LogPrior
CloneNotSupportedException
- if something went wrong while cloningLogPrior.set(boolean, DifferentiableSequenceScore...)
public StringBuffer toXML()
LogPrior
LogPrior.set(boolean, DifferentiableSequenceScore...)
has to be invoked after decoding.