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## de.jstacs.classifier.scoringFunctionBased
Class ScoreClassifierParameterSet

    java.lang.Object
      de.jstacs.parameters.ParameterSet
          de.jstacs.parameters.InstanceParameterSet
              de.jstacs.parameters.SequenceScoringParameterSet
                  de.jstacs.classifier.scoringFunctionBased.ScoreClassifierParameterSet

All Implemented Interfaces:
  GalaxyConvertible, RangeIterator, Storable, Cloneable

Direct Known Subclasses:
  GenDisMixClassifierParameterSet

    public class ScoreClassifierParameterSet

extends SequenceScoringParameterSet

A set of `Parameter`s for any `ScoreClassifier`.

Author:
  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.SequenceScoringParameterSet
`alphabet, length`

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

Constructor Summary
`ScoreClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass, AlphabetContainer alphabet, int length, byte algo, double eps, double lineps, double startD, boolean free, OptimizableFunction.KindOfParameter kind)` The constructor for a simple, instantiated parameter set.
`ScoreClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass, boolean simple, AlphabetContainer.AlphabetContainerType type, boolean variableLength)` Creates a new `ScoreClassifierParameterSet` with empty parameter values.
`ScoreClassifierParameterSet(StringBuffer xml)` The standard constructor for the interface `Storable`.

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`.
`protected void` | `loadParameters()` Loads the parameters for this `ParameterSet`.
`boolean` | `useOnlyFreeParameter()` This method indicates if only the free parameters shall be used.

Methods inherited from class de.jstacs.parameters.SequenceScoringParameterSet
`clone, 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

### ScoreClassifierParameterSet

    public ScoreClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass,
                                       boolean simple,
                                       AlphabetContainer.AlphabetContainerType type,
                                       boolean variableLength)

  Creates a new `ScoreClassifierParameterSet` with empty parameter values.

  Parameters:
    `instanceClass` - the class of the instance
    `simple` - indicates whether the `AlphabetContainer` shall be simple
    `type` - the type of the `AlphabetContainer`
    `variableLength` - indicates whether the corresponding classifier can handle sequences of arbitrary length
  See Also:
    `SequenceScoringParameterSet.SequenceScoringParameterSet(Class, de.jstacs.data.AlphabetContainer.AlphabetContainerType, boolean, boolean)`

### ScoreClassifierParameterSet

    public ScoreClassifierParameterSet(StringBuffer xml)
                                throws NonParsableException

  The standard constructor for the interface `Storable`. Creates a new `ScoreClassifierParameterSet` out of its XML representation.

  Parameters:
    `xml` - the XML representation as `StringBuffer`
  Throws:
    `NonParsableException` - if the `ScoreClassifierParameterSet` could not be reconstructed out of the XML representation (the `StringBuffer` could not be parsed)
  See Also:
    `SequenceScoringParameterSet.SequenceScoringParameterSet(StringBuffer)`, `Storable`

### ScoreClassifierParameterSet

    public ScoreClassifierParameterSet(Class<? extends ScoreClassifier> instanceClass,
                                       AlphabetContainer alphabet,
                                       int length,
                                       byte algo,
                                       double eps,
                                       double lineps,
                                       double startD,
                                       boolean free,
                                       OptimizableFunction.KindOfParameter kind)
                                throws Exception

  The constructor for a simple, instantiated parameter set.

  Parameters:
    `instanceClass` - the class of the instance
    `alphabet` - the alphabet
    `length` - the length of the sequences, 0 for homogeneous
    `algo` - the choice of algorithm
    `eps` - the threshold for stopping the algorithm
    `lineps` - the threshold for stopping the line search in the algorithm
    `startD` - the start distance for the line search in the algorithm
    `free` - indicates whether only the free parameters or all parameters should be used
    `kind` - indicates the kind of class parameter initialization
  Throws:
    `Exception` - if something went wrong
  See Also:
    `SequenceScoringParameterSet.SequenceScoringParameterSet(Class, AlphabetContainer, int, boolean)`

Method Detail

### 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`.

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

### useOnlyFreeParameter

    public boolean useOnlyFreeParameter()

  This method indicates if only the free parameters shall be used.

  Returns:
    `true` if only the free parameters shall be used, `false` otherwise

### 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

### 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

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