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

Nested Classes

Modifier and Type	Class and Description
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

Fields

Modifier and Type	Field and Description
static DNAAlphabet	SINGLETON The only instance of this class.

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

alphabet, caseInsensitive, parameters

Method Summary

Modifier and Type	Method and Description
int	getCode(String symbol) Returns the code of a given symbol.
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, 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

getCode

public final int getCode(String symbol)
                  throws WrongAlphabetException

Description copied from class: DiscreteAlphabet

Returns the code of a given symbol.

Overrides:

getCode in class DiscreteAlphabet

Parameters:

symbol - the given symbol

Returns:

the code of a given symbol

Throws:

WrongAlphabetException - if the symbol is not defined in the alphabet