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## de.jstacs.data.alphabets
Class ComplementableDiscreteAlphabet

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

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

Direct Known Subclasses:
  DNAAlphabet, GenericComplementableDiscreteAlphabet

    public abstract class ComplementableDiscreteAlphabet

extends DiscreteAlphabet

This abstract class indicates that an alphabet can be used to compute the complement. The most important method is `getComplementaryCode(int)`.

Author:
  Jan Grau, Jens Keilwagen

Nested Class Summary

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
`protected` | `ComplementableDiscreteAlphabet(boolean caseInsensitive, String... alphabet)` Creates a new `ComplementableDiscreteAlphabet` from a given array of symbols.
`protected` | `ComplementableDiscreteAlphabet(DiscreteAlphabet.DiscreteAlphabetParameterSet parameters)` The constructor for the `InstantiableFromParameterSet` interface.
`protected` | `ComplementableDiscreteAlphabet(StringBuffer representation)` The standard constructor for the interface `Storable`.

Method Summary
`abstract int` | `getComplementaryCode(int code)` This method returns the code of the symbol that is the complement of the symbol encoded by `code`.
`abstract 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

### ComplementableDiscreteAlphabet

    protected ComplementableDiscreteAlphabet(DiscreteAlphabet.DiscreteAlphabetParameterSet parameters)
                                      throws IllegalArgumentException,
                                             DoubleSymbolException

  The constructor for the `InstantiableFromParameterSet` interface. Creates a new `ComplementableDiscreteAlphabet` from a given set of parameters.

  Parameters:
    `parameters` - the parameter set for the `ComplementableDiscreteAlphabet`
  Throws:
    `IllegalArgumentException` - if space or tab will be used as symbols
    `DoubleSymbolException` - if one of the symbols occurred more than once
  See Also:
    `InstantiableFromParameterSet`

### ComplementableDiscreteAlphabet

    protected ComplementableDiscreteAlphabet(StringBuffer representation)
                                      throws NonParsableException

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

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

### ComplementableDiscreteAlphabet

    protected ComplementableDiscreteAlphabet(boolean caseInsensitive,
                                             String... alphabet)
                                      throws DoubleSymbolException,
                                             IllegalArgumentException

  Creates a new `ComplementableDiscreteAlphabet` from a given array of symbols.

  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)
  Throws:
    `DoubleSymbolException` - if a symbol occurs more than once in the alphabet
    `IllegalArgumentException` - if one of the symbols is either empty or a white-space character
  See Also:
    `DiscreteAlphabet.DiscreteAlphabet(boolean, String...)`

Method Detail

### getCurrentParameterSet

    public abstract 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`
  Overrides:
    `getCurrentParameterSet` in class `DiscreteAlphabet`
  Returns:
    the current `InstanceParameterSet`
  Throws:
    `Exception` - if the `InstanceParameterSet` could not be returned

### getComplementaryCode

    public abstract int getComplementaryCode(int code)

  This method returns the code of the symbol that is the complement of the symbol encoded by `code`.

  Parameters:
    `code` - the encoded symbol
  Returns:
    the code of the complement

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