|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES All Classes | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectde.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.SimpleState
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.SimpleSamplingState
public class SimpleSamplingState
This class implements a state that can be used for a HMM that obtains its parameters from sampling.
Field Summary |
---|
Fields inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.SimpleState |
---|
e, forward, name |
Constructor Summary | |
---|---|
SimpleSamplingState(SamplingEmission e,
String name,
boolean forward)
This constructor creates a state that can be used in a HMM that obtains its parameters from sampling. |
Method Summary | |
---|---|
void |
acceptParameters()
This methods accepts the drawn parameters. |
void |
drawParametersFromStatistic()
This method draws the parameters using a sufficient statistic representing a posteriori density. |
void |
extendSampling(int sampling,
boolean append)
This method allows to extend a sampling. |
double |
getLogGammaScoreForCurrentStatistic()
This method calculates a score for the current statistics, which is independent from the current parameters In general the gamma-score is a product of gamma-functions parameterized with the current statistics |
double |
getLogPosteriorFromStatistic()
This method calculates the a-posteriori probability for the current statistics |
void |
initForSampling(int starts)
This method initializes the instance for the sampling. |
boolean |
isInSamplingMode()
This method returns true if the object is currently used in
a sampling, otherwise false . |
boolean |
parseNextParameterSet()
This method allows the user to parse the next set of parameters (from a file). |
boolean |
parseParameterSet(int sampling,
int n)
This method allows the user to parse the set of parameters with index n of a certain sampling (from a file). |
void |
samplingStopped()
This method is the opposite of the method SamplingComponent.extendSampling(int, boolean) . |
Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.SimpleState |
---|
addToStatistic, getGraphvizNodeOptions, getLogScoreFor, isSilent, toString |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.TrainableState |
---|
addToStatistic |
Methods inherited from interface de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.State |
---|
getGraphvizNodeOptions, getLogScoreFor, isSilent |
Constructor Detail |
---|
public SimpleSamplingState(SamplingEmission e, String name, boolean forward)
e
- the emissionname
- the name of the emission (e.g. for the Graphviz representation)forward
- a switch whether to use the forward or the reverse strandMethod Detail |
---|
public void drawParametersFromStatistic() throws Exception
SamplingFromStatistic
SamplingComponent.acceptParameters()
so that they can later be parsed using the
methods of the interface.
SamplingComponent.initForSampling(int)
should be
called.
drawParametersFromStatistic
in interface SamplingFromStatistic
Exception
- if there is a problem with drawing the parameters, the initialization, ...SamplingComponent.initForSampling(int)
,
SamplingComponent.acceptParameters()
public void extendSampling(int sampling, boolean append) throws IOException
SamplingComponent
extendSampling
in interface SamplingComponent
sampling
- the index of the samplingappend
- whether to append the sampled parameters to an existing file
or to overwrite the file
IOException
- if the file could not be handled correctlypublic void initForSampling(int starts) throws IOException
SamplingComponent
initForSampling
in interface SamplingComponent
starts
- the number of different sampling starts that will be done
IOException
- if something went wrongFile.createTempFile(String, String, java.io.File )
public boolean isInSamplingMode()
SamplingComponent
true
if the object is currently used in
a sampling, otherwise false
.
isInSamplingMode
in interface SamplingComponent
true
if the object is currently used in a sampling,
otherwise false
public boolean parseNextParameterSet()
SamplingComponent
parseNextParameterSet
in interface SamplingComponent
true
if the parameters could be parsed, otherwise
false
SamplingComponent.parseParameterSet(int, int)
public boolean parseParameterSet(int sampling, int n) throws Exception
SamplingComponent
n
of a certain sampling
(from a file). The
internal numbering should start with 0. The parameter set with index 0 is
the initial (random) parameter set. It is recommended that a series of
parameter sets is accessed by the following lines:
for( sampling = 0; sampling < numSampling; sampling++ )
{
boolean b = parseParameterSet( sampling, n );
while( b )
{
//do something
b = parseNextParameterSet();
}
}
parseParameterSet
in interface SamplingComponent
sampling
- the index of the samplingn
- the index of the parameter set
true
if the parameter set could be parsed
Exception
- if there is a problem with parsing the parametersSamplingComponent.parseNextParameterSet()
public void samplingStopped() throws IOException
SamplingComponent
SamplingComponent.extendSampling(int, boolean)
. It can be
used for closing any streams of writer, ...
samplingStopped
in interface SamplingComponent
IOException
- if something went wrongSamplingComponent.extendSampling(int, boolean)
public void acceptParameters() throws IOException
SamplingComponent
acceptParameters
in interface SamplingComponent
IOException
- if the file could not be handled correctlypublic double getLogGammaScoreForCurrentStatistic()
SamplingState
getLogGammaScoreForCurrentStatistic
in interface SamplingState
public double getLogPosteriorFromStatistic()
SamplingFromStatistic
getLogPosteriorFromStatistic
in interface SamplingFromStatistic
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES All Classes | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |