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## de.jstacs.classifier.scoringFunctionBased.sampling
Class SamplingGenDisMixClassifierParameterSet

    java.lang.Object
      de.jstacs.parameters.ParameterSet
          de.jstacs.parameters.InstanceParameterSet
              de.jstacs.parameters.SequenceScoringParameterSet
                  de.jstacs.classifier.scoringFunctionBased.sampling.SamplingScoreBasedClassifierParameterSet
                      de.jstacs.classifier.scoringFunctionBased.sampling.SamplingGenDisMixClassifierParameterSet

All Implemented Interfaces:
  GalaxyConvertible, RangeIterator, Storable, Cloneable

    public class SamplingGenDisMixClassifierParameterSet

extends SamplingScoreBasedClassifierParameterSet

`ParameterSet` to instantiate a `SamplingGenDisMixClassifier`.

Author:
  Jan Grau

Nested Class Summary

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

Field Summary

Fields inherited from class de.jstacs.parameters.SequenceScoringParameterSet
`alphabet, length`

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

Constructor Summary
`` | `SamplingGenDisMixClassifierParameterSet(AlphabetContainer alphabet, int length, int numStarts, int testSamplings, int stationarySamplings, String outfilePrefix, int threads)` Create a new `SamplingGenDisMixClassifierParameterSet` with a grouped sampling scheme, sampling all parameters (and not only the free ones), and adaption of the variance.
`` | `SamplingGenDisMixClassifierParameterSet(AlphabetContainer alphabet, int length, int numStarts, SamplingScoreBasedClassifier.SamplingScheme scheme, int testSamplings, int stationarySamplings, boolean freeParameters, boolean adaptVariance, String outfilePrefix, int threads)` Create a new `SamplingGenDisMixClassifierParameterSet`.
`protected` | `SamplingGenDisMixClassifierParameterSet(Class<? extends SamplingScoreBasedClassifier> instanceClass, AlphabetContainer alphabet, int length, int numStarts, SamplingScoreBasedClassifier.SamplingScheme scheme, int testSamplings, int stationarySamplings, boolean freeParameters, boolean adaptVariance, String outfilePrefix, int threads)` Create a new `SamplingGenDisMixClassifierParameterSet`.

Method Summary
`String` | `getInstanceComment()` Returns a comment (a textual description) of the class that can be constructed using this `ParameterSet`.
`String` | `getInstanceName()` Returns the name of an instance of the class that can be constructed using this `ParameterSet`.
`int` | `getNumberOfThreads()` Returns the number of threads for evaluating the `LogGenDisMixFunction`
`protected void` | `loadParameters()` Loads the parameters for this `ParameterSet`.

Methods inherited from class de.jstacs.classifier.scoringFunctionBased.sampling.SamplingScoreBasedClassifierParameterSet
`clone, getAdaptVariance, getFreeParameters, getNumberOfStarts, getNumberOfStationarySamplings, getNumberOfTestSamplings, getOutfilePrefix, getSamplingScheme, setNumberOfStarts`

Methods inherited from class de.jstacs.parameters.SequenceScoringParameterSet
`equals, fromXML, getAlphabetContainer, getLength, getNumberOfParameters, getParameterAt, hasDefaultOrIsSet, replaceParametersWithRangedInstance, reset, toXML`

Methods inherited from class de.jstacs.parameters.InstanceParameterSet
`getInstance, getInstanceClass`

Methods inherited from class de.jstacs.parameters.ParameterSet
`fromGalaxy, getErrorMessage, getId, getIndex, getNumberOfValues, getParent, initParameterList, initParameterList, isAtomic, isRanged, makeRanged, next, parametersLoaded, propagateId, recieveId, resetToFirst, setParent, simplify, toGalaxy, valuesToString`

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

Constructor Detail

### SamplingGenDisMixClassifierParameterSet

    public SamplingGenDisMixClassifierParameterSet(AlphabetContainer alphabet,
                                                   int length,
                                                   int numStarts,
                                                   SamplingScoreBasedClassifier.SamplingScheme scheme,
                                                   int testSamplings,
                                                   int stationarySamplings,
                                                   boolean freeParameters,
                                                   boolean adaptVariance,
                                                   String outfilePrefix,
                                                   int threads)
                                            throws Exception

  Create a new `SamplingGenDisMixClassifierParameterSet`.

  Parameters:
    `alphabet` - the alphabet of the classifier
    `length` - the length of the sequences that can be classified
    `numStarts` - the number of independent samplings
    `scheme` - the sampling scheme
    `testSamplings` - the number of samplings between checks for the lenght of the burn-in phase
    `stationarySamplings` - the number of samplings in the stationary phase
    `freeParameters` - if only free parameters shall be used
    `adaptVariance` - if the variance shall be adapted to the size of the event space of a random variable
    `outfilePrefix` - the prefix of the temporary files for storing the parameters
    `threads` - the number of threads for evaluating the `LogGenDisMixFunction`
  Throws:
    `Exception` - if the parameters could not be created

### SamplingGenDisMixClassifierParameterSet

    protected SamplingGenDisMixClassifierParameterSet(Class<? extends SamplingScoreBasedClassifier> instanceClass,
                                                      AlphabetContainer alphabet,
                                                      int length,
                                                      int numStarts,
                                                      SamplingScoreBasedClassifier.SamplingScheme scheme,
                                                      int testSamplings,
                                                      int stationarySamplings,
                                                      boolean freeParameters,
                                                      boolean adaptVariance,
                                                      String outfilePrefix,
                                                      int threads)
                                               throws Exception

  Create a new `SamplingGenDisMixClassifierParameterSet`.

  Parameters:
    `instanceClass` - the class, which must be a subclass of `SamplingScoreBasedClassifier`
    `alphabet` - the alphabet of the classifier
    `length` - the length of the sequences that can be classified
    `numStarts` - the number of independent samplings
    `scheme` - the sampling scheme
    `testSamplings` - the number of samplings between checks for the lenght of the burn-in phase
    `stationarySamplings` - the number of samplings in the stationary phase
    `freeParameters` - if only free parameters shall be used
    `adaptVariance` - if the variance shall be adapted to the size of the event space of a random variable
    `outfilePrefix` - the prefix of the temporary files for storing the parameters
    `threads` - the number of threads for evaluating the `LogGenDisMixFunction`
  Throws:
    `Exception` - if the parameters could not be created

### SamplingGenDisMixClassifierParameterSet

    public SamplingGenDisMixClassifierParameterSet(AlphabetContainer alphabet,
                                                   int length,
                                                   int numStarts,
                                                   int testSamplings,
                                                   int stationarySamplings,
                                                   String outfilePrefix,
                                                   int threads)
                                            throws Exception

  Create a new `SamplingGenDisMixClassifierParameterSet` with a grouped sampling scheme, sampling all parameters (and not only the free ones), and adaption of the variance.

  Parameters:
    `alphabet` - the alphabet of the classifier
    `length` - the length of the sequences that can be classified
    `numStarts` - the number of independent samplings
    `testSamplings` - the number of samplings between checks for the lenght of the burn-in phase
    `stationarySamplings` - the number of samplings in the stationary phase
    `outfilePrefix` - the prefix of the temporary files for storing the parameters
    `threads` - the number of threads for evaluating the `LogGenDisMixFunction`
  Throws:
    `Exception` - if the parameters could not be created

Method Detail

### getInstanceComment

    public String getInstanceComment()

  Description copied from class: `InstanceParameterSet`
  Returns a comment (a textual description) of the class that can be constructed using this `ParameterSet`.

  Specified by:
    `getInstanceComment` in class `InstanceParameterSet`
  Returns:
    the comment of the class

### getInstanceName

    public String getInstanceName()

  Description copied from class: `InstanceParameterSet`
  Returns the name of an instance of the class that can be constructed using this `ParameterSet`.

  Specified by:
    `getInstanceName` in class `InstanceParameterSet`
  Returns:
    the name of the class

### loadParameters

    protected void loadParameters()
                           throws Exception

  Description copied from class: `ParameterSet`
  Loads the parameters for this `ParameterSet`. This is in most cases done by calling `ParameterSet.initParameterList()` or `ParameterSet.initParameterList(int)` to initialize `ParameterSet.parameters` and afterwards filling `ParameterSet.parameters` with instances of subclasses of `Parameter`.

  Overrides:
    `loadParameters` in class `SamplingScoreBasedClassifierParameterSet`
  Throws:
    `Exception` - if the parameters could not be loaded
  See Also:
    `Parameter`, `ParameterSet.parameters`, `ParameterSet.initParameterList()`, `ParameterSet.initParameterList(int)`

### getNumberOfThreads

    public int getNumberOfThreads()

  Returns the number of threads for evaluating the `LogGenDisMixFunction`

  Returns:
    the number of threads

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