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## de.jstacs.data.alphabets
Class GenericComplementableDiscreteAlphabet

    java.lang.Object
      de.jstacs.data.Alphabet
          de.jstacs.data.alphabets.DiscreteAlphabet
              de.jstacs.data.alphabets.ComplementableDiscreteAlphabet
                  de.jstacs.data.alphabets.GenericComplementableDiscreteAlphabet

All Implemented Interfaces:
  InstantiableFromParameterSet, Storable, Comparable<Alphabet>

    public class GenericComplementableDiscreteAlphabet

extends ComplementableDiscreteAlphabet

This class implements an generic complementable discrete alphabet. The complement is determined in the constructor, where the user has to specify for each symbol the index of the complement symbol.

Author:
  Jens Keilwagen

Nested Class Summary
`static class` | `GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet` This class is used as container for the parameters of a `GenericComplementableDiscreteAlphabet`.

Nested classes/interfaces inherited from class de.jstacs.data.alphabets.DiscreteAlphabet
`DiscreteAlphabet.DiscreteAlphabetParameterSet`

Nested classes/interfaces inherited from class de.jstacs.data.Alphabet
`Alphabet.AlphabetParameterSet`

Field Summary

Fields inherited from class de.jstacs.data.alphabets.DiscreteAlphabet
`alphabet, caseInsensitive, parameters`

Constructor Summary
`GenericComplementableDiscreteAlphabet(boolean caseInsensitive, String[] alphabet, int[] revComp)` The main constructor.
`GenericComplementableDiscreteAlphabet(GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet parameters)` This constructor creates a `GenericComplementableDiscreteAlphabet` from a parameter set.
`GenericComplementableDiscreteAlphabet(StringBuffer representation)` The standard constructor for the interface `Storable`.

Method Summary
`int` | `getComplementaryCode(int code)` This method returns the code of the symbol that is the complement of the symbol encoded by `code`.
`Alphabet.AlphabetParameterSet` | `getCurrentParameterSet()` Returns the `InstanceParameterSet` that has been used to instantiate the current instance of the implementing class.

Methods inherited from class de.jstacs.data.alphabets.DiscreteAlphabet
`compareTo, getCode, getMaximalSymbolLength, getMin, getSymbolAt, ignoresCase, isEncodedSymbol, isSymbol, length, toString, toXML`

Methods inherited from class de.jstacs.data.Alphabet
`checkConsistency`

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

Constructor Detail

### GenericComplementableDiscreteAlphabet

    public GenericComplementableDiscreteAlphabet(StringBuffer representation)
                                          throws NonParsableException

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

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

### GenericComplementableDiscreteAlphabet

    public GenericComplementableDiscreteAlphabet(GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet parameters)
                                          throws IllegalArgumentException,
                                                 DoubleSymbolException

  This constructor creates a `GenericComplementableDiscreteAlphabet` from a parameter set.

  Parameters:
    `parameters` - the set of parameters needed to create a `GenericComplementableDiscreteAlphabet`
  Throws:
    `IllegalArgumentException` - if space or tab will be used as symbols
    `DoubleSymbolException` - if one of the symbols occurred more than once

### GenericComplementableDiscreteAlphabet

    public GenericComplementableDiscreteAlphabet(boolean caseInsensitive,
                                                 String[] alphabet,
                                                 int[] revComp)
                                          throws DoubleSymbolException,
                                                 IllegalArgumentException

  The main constructor.

  Parameters:
    `alphabet` - the array of symbols
    `caseInsensitive` - indicates if there will be no difference between lowercase and uppercase letters/symbols in the alphabet (no case sensitivity)
    `revComp` - the array is used to provide the complementarity, `revComp[i]` contains the index of the complement of the i-th symbol
  Throws:
    `IllegalArgumentException` - if space or tab will be used as symbols
    `DoubleSymbolException` - if one of the symbols occurred more than once

Method Detail

### getComplementaryCode

    public int getComplementaryCode(int code)

  Description copied from class: `ComplementableDiscreteAlphabet`
  This method returns the code of the symbol that is the complement of the symbol encoded by `code`.

  Specified by:
    `getComplementaryCode` in class `ComplementableDiscreteAlphabet`
  Parameters:
    `code` - the encoded symbol
  Returns:
    the code of the complement

### getCurrentParameterSet

    public Alphabet.AlphabetParameterSet getCurrentParameterSet()
                                                         throws Exception

  Description copied from interface: `InstantiableFromParameterSet`
  Returns the `InstanceParameterSet` that has been used to instantiate the current instance of the implementing class. If the current instance was not created using an `InstanceParameterSet`, an equivalent `InstanceParameterSet` should be returned, so that an instance created using this `InstanceParameterSet` would be in principle equal to the current instance.

  Specified by:
    `getCurrentParameterSet` in interface `InstantiableFromParameterSet`
  Specified by:
    `getCurrentParameterSet` in class `ComplementableDiscreteAlphabet`
  Returns:
    the current `InstanceParameterSet`
  Throws:
    `Exception` - if the `InstanceParameterSet` could not be returned

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