de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states
Class SimpleSamplingState

java.lang.Object
  de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.SimpleState
      de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.SimpleSamplingState

All Implemented Interfaces:

SamplingComponent, SamplingFromStatistic, SamplingState, State, TrainableState

public class SimpleSamplingState
extends SimpleState
implements SamplingState

This class implements a state that can be used for a HMM that obtains its parameters from sampling.

Author:

Jens Keilwagen

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

SimpleSamplingState

public 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.

Parameters:

e - the emission

name - the name of the emission (e.g. for the Graphviz representation)

forward - a switch whether to use the forward or the reverse strand

Method Detail

drawParametersFromStatistic

public void drawParametersFromStatistic()
                                 throws Exception

Description copied from interface: SamplingFromStatistic

This method draws the parameters using a sufficient statistic representing a posteriori density. It is recommended to write the parameters to a specific file using SamplingComponent.acceptParameters() so that they can later be parsed using the methods of the interface.

Before using this method the method SamplingComponent.initForSampling(int) should be called.

Specified by:

drawParametersFromStatistic in interface SamplingFromStatistic

Throws:

Exception - if there is a problem with drawing the parameters, the initialization, ...

See Also:

SamplingComponent.initForSampling(int), SamplingComponent.acceptParameters()

extendSampling

public void extendSampling(int sampling,
                           boolean append)
                    throws IOException

Description copied from interface: SamplingComponent

This method allows to extend a sampling.

Specified by:

extendSampling in interface SamplingComponent

Parameters:

sampling - the index of the sampling

append - whether to append the sampled parameters to an existing file or to overwrite the file

Throws:

IOException - if the file could not be handled correctly

initForSampling

public void initForSampling(int starts)
                     throws IOException

Description copied from interface: SamplingComponent

This method initializes the instance for the sampling. For instance this method can be used to create new files where all parameter sets are stored.

Specified by:

initForSampling in interface SamplingComponent

Parameters:

starts - the number of different sampling starts that will be done

Throws:

IOException - if something went wrong

See Also:

File.createTempFile(String, String, java.io.File )

isInSamplingMode

public boolean isInSamplingMode()

Description copied from interface: SamplingComponent

This method returns true if the object is currently used in a sampling, otherwise false.

Specified by:

isInSamplingMode in interface SamplingComponent

Returns:

true if the object is currently used in a sampling, otherwise false

parseNextParameterSet

public boolean parseNextParameterSet()

Description copied from interface: SamplingComponent

This method allows the user to parse the next set of parameters (from a file).

Specified by:

parseNextParameterSet in interface SamplingComponent

Returns:

true if the parameters could be parsed, otherwise false

See Also:

SamplingComponent.parseParameterSet(int, int)

parseParameterSet

public boolean parseParameterSet(int sampling,
                                 int n)
                          throws Exception

Description copied from interface: SamplingComponent

This method allows the user to parse the set of parameters with index 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();
} }


Specified by:

parseParameterSet in interface SamplingComponent

Parameters:

sampling - the index of the sampling

n - the index of the parameter set

Returns:

true if the parameter set could be parsed

Throws:

Exception - if there is a problem with parsing the parameters

See Also:

SamplingComponent.parseNextParameterSet()

samplingStopped

public void samplingStopped()
                     throws IOException

Description copied from interface: SamplingComponent

This method is the opposite of the method SamplingComponent.extendSampling(int, boolean). It can be used for closing any streams of writer, ...

Specified by:

samplingStopped in interface SamplingComponent

Throws:

IOException - if something went wrong

See Also:

SamplingComponent.extendSampling(int, boolean)

acceptParameters

public void acceptParameters()
                      throws IOException

Description copied from interface: SamplingComponent

This methods accepts the drawn parameters. Internally the drawn parameters should be saved (to a file).

Specified by:

acceptParameters in interface SamplingComponent

Throws:

IOException - if the file could not be handled correctly

getLogGammaScoreForCurrentStatistic

public double getLogGammaScoreForCurrentStatistic()

Description copied from interface: SamplingState

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

Specified by:

getLogGammaScoreForCurrentStatistic in interface SamplingState

Returns:

the logarithm of the gamma-score for the current statistics

getLogPosteriorFromStatistic

public double getLogPosteriorFromStatistic()

Description copied from interface: SamplingFromStatistic

This method calculates the a-posteriori probability for the current statistics

Specified by:

getLogPosteriorFromStatistic in interface SamplingFromStatistic

Returns:

the logarithm of the a-posteriori probability