de.jstacs.data.alphabets

Class GenericComplementableDiscreteAlphabet

java.lang.Object

de.jstacs.data.alphabets.Alphabet

de.jstacs.data.alphabets.DiscreteAlphabet

de.jstacs.data.alphabets.ComplementableDiscreteAlphabet

de.jstacs.data.alphabets.GenericComplementableDiscreteAlphabet

All Implemented Interfaces:

InstantiableFromParameterSet, Storable, Comparable<Alphabet>

public class GenericComplementableDiscreteAlphabet
extends ComplementableDiscreteAlphabet

This class implements an generic complementable discrete alphabet. The complement is determined in the constructor, where the user has to specify for each symbol the index of the complement symbol.

Author:

Jens Keilwagen

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet This class is used as container for the parameters of a GenericComplementableDiscreteAlphabet.

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

Constructor and Description
GenericComplementableDiscreteAlphabet(boolean caseInsensitive, String[] alphabet, int[] revComp) The main constructor.
GenericComplementableDiscreteAlphabet(GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet parameters) This constructor creates a GenericComplementableDiscreteAlphabet from a parameter set.
GenericComplementableDiscreteAlphabet(StringBuffer representation) The standard constructor for the interface Storable.

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.
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.alphabets.Alphabet

checkConsistency

Methods inherited from class java.lang.Object

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

Constructor Detail

GenericComplementableDiscreteAlphabet

public GenericComplementableDiscreteAlphabet(StringBuffer representation)
                                      throws NonParsableException

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

Parameters:

representation - the XML representation as StringBuffer

Throws:

NonParsableException - if the GenericComplementableDiscreteAlphabet could not be reconstructed out of the XML representation (the StringBuffer representation could not be parsed)

See Also:

Storable

GenericComplementableDiscreteAlphabet

public GenericComplementableDiscreteAlphabet(GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet parameters)
                                      throws IllegalArgumentException,
                                             DoubleSymbolException

This constructor creates a GenericComplementableDiscreteAlphabet from a parameter set.

Parameters:

parameters - the set of parameters needed to create a GenericComplementableDiscreteAlphabet

Throws:

IllegalArgumentException - if space or tab will be used as symbols

DoubleSymbolException - if one of the symbols occurred more than once

GenericComplementableDiscreteAlphabet

public GenericComplementableDiscreteAlphabet(boolean caseInsensitive,
                                             String[] alphabet,
                                             int[] revComp)
                                      throws DoubleSymbolException,
                                             IllegalArgumentException

The main constructor.

Parameters:

alphabet - the array of symbols

caseInsensitive - indicates if there will be no difference between lower case and upper case letters/symbols in the alphabet (no case sensitivity)

revComp - the array is used to provide the complementarity, revComp[i] contains the index of the complement of the i-th symbol

Throws:

IllegalArgumentException - if space or tab will be used as symbols

DoubleSymbolException - if one of the symbols occurred more than once

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

getCurrentParameterSet

public 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