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## de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training
Class SamplingHMMTrainingParameterSet

    java.lang.Object
      de.jstacs.parameters.ParameterSet
          de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.HMMTrainingParameterSet
              de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.SamplingHMMTrainingParameterSet

All Implemented Interfaces:
  GalaxyConvertible, Storable, Cloneable

    public class SamplingHMMTrainingParameterSet

extends HMMTrainingParameterSet

This class contains the parameters for training training an `AbstractHMM` using a sampling strategy.

Author:
  Michael Scharfe, Jens Keilwagen

Nested Class Summary

Nested classes/interfaces inherited from class de.jstacs.parameters.ParameterSet
`ParameterSet.ParameterList`

Field Summary

Fields inherited from class de.jstacs.parameters.ParameterSet
`errorMessage, parameters, parent`

Constructor Summary
`SamplingHMMTrainingParameterSet()` This is the empty constructor that can be used to fill the parameters after creation.
`SamplingHMMTrainingParameterSet(int starts, int stepsPerIteration, int stationarySteps, AbstractBurnInTestParameterSet burnInTestParameters)` This is the main constructor creating an already filled parameter set for training an `AbstractHMM` using a sampling strategy.
`SamplingHMMTrainingParameterSet(StringBuffer xml)` The standard constructor for the interface `Storable`.

Method Summary
`AbstractBurnInTest` | `getBurnInTest()` This method return the burn in test to be used during sampling.
`int` | `getNumberOfStepsInStationaryPhase()` The method returns the number of steps to be done in the stationary phase.
`int` | `getNumberOfStepsPerIteration()` This method returns the number of steps to be done in each start before testing for the end of the burn in phase (again).

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.HMMTrainingParameterSet
`getNumberOfStarts`

Methods inherited from class de.jstacs.parameters.ParameterSet
`clone, fromGalaxy, fromXML, getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getNumberOfParameters, getParameterAt, getParameterForName, getParent, hasDefaultOrIsSet, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, reset, setParent, toGalaxy, toXML`

Methods inherited from class java.lang.Object
`equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Constructor Detail

### SamplingHMMTrainingParameterSet

    public SamplingHMMTrainingParameterSet()

  This is the empty constructor that can be used to fill the parameters after creation.

### SamplingHMMTrainingParameterSet

    public SamplingHMMTrainingParameterSet(int starts,
                                           int stepsPerIteration,
                                           int stationarySteps,
                                           AbstractBurnInTestParameterSet burnInTestParameters)
                                    throws SimpleParameter.IllegalValueException

  This is the main constructor creating an already filled parameter set for training an `AbstractHMM` using a sampling strategy.

  Parameters:
    `starts` - the number of independent starts
    `stepsPerIteration` - the number of steps to be done for each start before testing for the end of the burn in phase
    `stationarySteps` - the number of steps in the stationary phase
    `burnInTestParameters` - the parameter set for the `BurnInTest`
  Throws:
    `SimpleParameter.IllegalValueException` - if some parameter is not permitted

### SamplingHMMTrainingParameterSet

    public SamplingHMMTrainingParameterSet(StringBuffer xml)
                                    throws NonParsableException

  The standard constructor for the interface `Storable`. Constructs a `SamplingHMMTrainingParameterSet` out of an XML representation.

  Parameters:
    `xml` - the XML representation as `StringBuffer`
  Throws:
    `NonParsableException` - if the `SamplingHMMTrainingParameterSet` could not be reconstructed out of the `StringBuffer` `xml`

Method Detail

### getNumberOfStepsPerIteration

    public int getNumberOfStepsPerIteration()

  This method returns the number of steps to be done in each start before testing for the end of the burn in phase (again).

  Returns:
    the number of steps to be done in each start before testing for the end of the burn in phase (again)

### getNumberOfStepsInStationaryPhase

    public int getNumberOfStepsInStationaryPhase()

  The method returns the number of steps to be done in the stationary phase.

  Returns:
    the number of steps to be done in the stationary phase

### getBurnInTest

    public AbstractBurnInTest getBurnInTest()
                                     throws ParameterSetParser.NotInstantiableException

  This method return the burn in test to be used during sampling.

  Returns:
    the burn in test to be used
  Throws:
    `ParameterSetParser.NotInstantiableException` - if the burn in test could not be created

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