de.jstacs.data.alphabets

Class IUPACDNAAlphabet

java.lang.Object

de.jstacs.data.alphabets.Alphabet

de.jstacs.data.alphabets.DiscreteAlphabet

de.jstacs.data.alphabets.ComplementableDiscreteAlphabet

de.jstacs.data.alphabets.IUPACDNAAlphabet

All Implemented Interfaces:

InstantiableFromParameterSet, Singleton, Storable, Comparable<Alphabet>

public final class IUPACDNAAlphabet
extends ComplementableDiscreteAlphabet
implements Singleton

This class implements a discrete alphabet for the IUPAC DNA code.

Author:

Jan Grau, Jens Keilwagen

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	IUPACDNAAlphabet.IUPACDNAAlphabetParameterSet The parameter set for a IUPACDNAAlphabet.

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 IUPACDNAAlphabet	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	getComplementaryCode(int code) This method returns the code of the symbol that is the complement of the symbol encoded by code.
boolean	isPart(int query, int code) Indicates if query is contained in code according to the IUPAC DNA alphabet.
boolean	isPart(String query, String code) Indicates if query is contained in code according to the IUPAC DNA alphabet.

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 IUPACDNAAlphabet 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

isPart

public boolean isPart(String query,
                      String code)
               throws WrongAlphabetException

Indicates if query is contained in code according to the IUPAC DNA alphabet.

Parameters:

query - the query symbol

code - the reference symbol

Returns:

if query is contained in code

Throws:

WrongAlphabetException - if either of the arguments is not defined in the IUPAC alphabet

isPart

public boolean isPart(int query,
                      int code)

Indicates if query is contained in code according to the IUPAC DNA alphabet.

Parameters:

query - the code of the query symbol

code - the code of the reference symbol

Returns:

if query is contained in code