de.jstacs.data.alphabets
Class DNAAlphabet

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

All Implemented Interfaces:

InstantiableFromParameterSet, Singleton, Storable, Comparable<Alphabet>

public final class DNAAlphabet
extends ComplementableDiscreteAlphabet
implements Singleton

This class implements the discrete alphabet that is used for DNA.

Author:

Jan Grau, Jens Keilwagen

Nested Class Summary

static class

DNAAlphabet.DNAAlphabetParameterSet The parameter set for a DNAAlphabet.

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

DiscreteAlphabet.DiscreteAlphabetParameterSet

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

Alphabet.AlphabetParameterSet<T extends Alphabet>

Nested classes/interfaces inherited from interface de.jstacs.Singleton

Singleton.SingletonHandler

Field Summary

static DNAAlphabet

SINGLETON The only instance of this class.

Fields inherited from class de.jstacs.data.alphabets.DiscreteAlphabet

alphabet, caseInsensitive, parameters

Method Summary

int	getComplementaryCode(int code) This method returns the code of the symbol that is the complement of the symbol encoded by code.

Methods inherited from class de.jstacs.data.alphabets.DiscreteAlphabet

compareTo, getCode, getCurrentParameterSet, getMaximalSymbolLength, getMin, getSymbolAt, ignoresCase, isEncodedSymbol, isSymbol, length, toString, toXML

Methods inherited from class de.jstacs.data.alphabets.Alphabet

checkConsistency

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

SINGLETON

public static final DNAAlphabet SINGLETON

The only instance of this class.

See Also:

Singleton

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