de.jstacs.data.alphabets
Class ComplementableDiscreteAlphabet

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

All Implemented Interfaces:

InstantiableFromParameterSet, Storable, Comparable<Alphabet>

Direct Known Subclasses:

DNAAlphabet

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.Alphabet

Alphabet.AlphabetParameterSet

Field Summary

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

parameters

Constructor Summary

protected	ComplementableDiscreteAlphabet(String[] alphabet, boolean caseInsensitive) The main constructor.
protected	ComplementableDiscreteAlphabet(StringBuffer representation) The constructor for the Storable interface.

Method Summary

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

checkConsistency

Methods inherited from class java.lang.Object

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

Constructor Detail

ComplementableDiscreteAlphabet

protected ComplementableDiscreteAlphabet(StringBuffer representation)
                                  throws NonParsableException

The constructor for the Storable interface.

Parameters:

representation - the XML representation

Throws:

NonParsableException - if the stream is not parsable

ComplementableDiscreteAlphabet

protected ComplementableDiscreteAlphabet(String[] alphabet,
                                         boolean caseInsensitive)
                                  throws DoubleSymbolException,
                                         IllegalArgumentException

The main constructor.

Parameters:

alphabet - the array of symbols

caseInsensitive - if true then there will be no difference between lowercase and uppercase letters/symbols in the alphabet (no case sensivity)

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

Method Detail

getCurrentParameterSet

public abstract 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 a InstanceParameterSet, an equivalent InstanceParameterSet should be returned, such 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 - is thrown if the InstanceParameterSet could not be returned

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