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## de.jstacs.data
Class AlphabetContainerParameterSet.AlphabetArrayParameterSet

    java.lang.Object
      de.jstacs.parameters.ParameterSet
          de.jstacs.parameters.ExpandableParameterSet
              de.jstacs.parameters.ArrayParameterSet
                  de.jstacs.data.AlphabetContainerParameterSet.AlphabetArrayParameterSet

All Implemented Interfaces:
  GalaxyConvertible, RangeIterator, Storable, Cloneable

Enclosing class:
  AlphabetContainerParameterSet

    public static class AlphabetContainerParameterSet.AlphabetArrayParameterSet

extends ArrayParameterSet

Class for the parameters of an array of `Alphabet`s of defined length.

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.ExpandableParameterSet
`commentTemplate, nameTemplate, template`

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

Constructor Summary
`AlphabetContainerParameterSet.AlphabetArrayParameterSet(Alphabet[] alphabets, AlphabetContainer.AlphabetContainerType type)` Creates a new `AlphabetContainerParameterSet.AlphabetArrayParameterSet` from an array of `Alphabet`s and the information about the `type` of the `Alphabet`s.
`AlphabetContainerParameterSet.AlphabetArrayParameterSet(AlphabetContainer.AlphabetContainerType type)` Creates a new `AlphabetContainerParameterSet.AlphabetArrayParameterSet` from the information about the `type` of the `Alphabet`s, e.g. if the array shall contain only the parameters for discrete `Alphabet` s.
`AlphabetContainerParameterSet.AlphabetArrayParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable` .

Method Summary
`AlphabetContainerParameterSet.AlphabetArrayParameterSet` | `clone()` Creates a full clone (deep copy) of this `ParameterSet`.
`void` | `fromXML(StringBuffer representation)` Parses the instance fields of a `ParameterSet` from the XML representation as returned by `ParameterSet.toXML()`.
`String` | `getInstanceComment()` Returns a descriptive comment on this `AlphabetContainerParameterSet.AlphabetArrayParameterSet`.
`String` | `getInstanceName()` Returns a descriptive name for this `AlphabetContainerParameterSet.AlphabetArrayParameterSet` .
`StringBuffer` | `toXML()` This method returns an XML representation as `StringBuffer` of an instance of the implementing class.

Methods inherited from class de.jstacs.parameters.ArrayParameterSet
`getNumberOfParameters, getParameterAt, hasDefaultOrIsSet, loadParameters`

Methods inherited from class de.jstacs.parameters.ExpandableParameterSet
`addParameterToSet, fromGalaxy, parameterRemovable, removeParameterFromSet, replaceContentWith, replaceParametersWithRangedInstance, toGalaxy`

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

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

Constructor Detail

### AlphabetContainerParameterSet.AlphabetArrayParameterSet

    public AlphabetContainerParameterSet.AlphabetArrayParameterSet(AlphabetContainer.AlphabetContainerType type)
                                                            throws Exception

  Creates a new `AlphabetContainerParameterSet.AlphabetArrayParameterSet` from the information about the `type` of the `Alphabet`s, e.g. if the array shall contain only the parameters for discrete `Alphabet` s.

  Parameters:
    `type` - the type of the `Alphabet`(s)
  Throws:
    `Exception` - if the `AlphabetContainerParameterSet.AlphabetArrayParameterSet` could not be created
  See Also:
    `ArrayParameterSet.ArrayParameterSet(ParameterSet, String, String)`

### AlphabetContainerParameterSet.AlphabetArrayParameterSet

    public AlphabetContainerParameterSet.AlphabetArrayParameterSet(StringBuffer representation)
                                                            throws NonParsableException

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

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

### AlphabetContainerParameterSet.AlphabetArrayParameterSet

    public AlphabetContainerParameterSet.AlphabetArrayParameterSet(Alphabet[] alphabets,
                                                                   AlphabetContainer.AlphabetContainerType type)
                                                            throws Exception

  Creates a new `AlphabetContainerParameterSet.AlphabetArrayParameterSet` from an array of `Alphabet`s and the information about the `type` of the `Alphabet`s.

  Parameters:
    `alphabets` - the `Alphabet`s
    `type` - the type of the `AlphabetContainer`
  Throws:
    `Exception` - if the `AlphabetContainerParameterSet.AlphabetArrayParameterSet` could not be created

Method Detail

### clone

    public AlphabetContainerParameterSet.AlphabetArrayParameterSet clone()
                                                                  throws CloneNotSupportedException

  Description copied from class: `ParameterSet`
  Creates a full clone (deep copy) of this `ParameterSet`. As a convenience-method the user can use `fillWithStandardFieldsForClone(ParameterSet)` on a newly created instance of a subclass of `ParameterSet` to obtain a clone/copy of all standard member variables (those already defined in `ParameterSet`) in the passed `ParameterSet`. Using this method, the cloning process becomes merely three-step:
  - Create a new instance of your subclass of `ParameterSet`, most likely with an empty constructor or the one taking just the instance class.
  - Call `this.fillWithStandardFieldsForClone` on this instance.
  - Return the instance.
  This method fulfills the conventions of `Object`'s method `Object.clone()`.

  Overrides:
    `clone` in class `ExpandableParameterSet`
  Returns:
    a deep clone/copy of this `ParameterSet`
  Throws:
    `CloneNotSupportedException`

### toXML

    public StringBuffer toXML()

  Description copied from interface: `Storable`
  This method returns an XML representation as `StringBuffer` of an instance of the implementing class.

  Specified by:
    `toXML` in interface `Storable`
  Overrides:
    `toXML` in class `ArrayParameterSet`
  Returns:
    the XML representation

### fromXML

    public void fromXML(StringBuffer representation)
                 throws NonParsableException

  Description copied from class: `ParameterSet`
  Parses the instance fields of a `ParameterSet` from the XML representation as returned by `ParameterSet.toXML()`.

  Overrides:
    `fromXML` in class `ArrayParameterSet`
  Parameters:
    `representation` - the XML representation as `StringBuffer`
  Throws:
    `NonParsableException` - if the XML code could not be parsed
  See Also:
    `ParameterSet.toXML()`

### getInstanceName

    public String getInstanceName()

  Returns a descriptive name for this `AlphabetContainerParameterSet.AlphabetArrayParameterSet` .

  Returns:
    the descriptive name

### getInstanceComment

    public String getInstanceComment()

  Returns a descriptive comment on this `AlphabetContainerParameterSet.AlphabetArrayParameterSet`.

  Returns:
    the descriptive comment

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