de.jstacs.data.alphabets

Class ComplementableDiscreteAlphabet

java.lang.Object

de.jstacs.data.alphabets.Alphabet

de.jstacs.data.alphabets.DiscreteAlphabet

de.jstacs.data.alphabets.ComplementableDiscreteAlphabet

All Implemented Interfaces:

InstantiableFromParameterSet, Storable, Comparable<Alphabet>

Direct Known Subclasses:

DNAAlphabet, GenericComplementableDiscreteAlphabet, IUPACDNAAlphabet

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.alphabets.Alphabet

Alphabet.AlphabetParameterSet<T extends Alphabet>

Field Summary

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

alphabet, caseInsensitive, parameters

Constructor Summary

Constructors

Modifier	Constructor and Description
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

Modifier and Type	Method and Description
abstract 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

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

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