de.jstacs.data.alphabets
Class DNAAlphabet

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

All Implemented Interfaces:

InstantiableFromParameterSet, Storable, Comparable<Alphabet>

public final class DNAAlphabet
extends ComplementableDiscreteAlphabet

This class implements the alphabet that is used for DNA.

Author:

Jan Grau, Jens Keilwagen

Nested Class Summary

static class

DNAAlphabet.DNAAlphabetParameterSet The parameter set for an DNA alphabet.

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

DNAAlphabet()
The main constructor.

DNAAlphabet(DNAAlphabet.DNAAlphabetParameterSet parameters)
The constructor for the InstantiableFromParameterSet interface.

DNAAlphabet(StringBuffer representation)
The constructor for the Storable interface.

Method Summary

int	getComplementaryCode(int code) This method returns the code of the symbol the is the complement of the symbol encoded by code
Alphabet.AlphabetParameterSet	getCurrentParameterSet() Returns the ParameterSet 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

DNAAlphabet

public DNAAlphabet(StringBuffer representation)
            throws NonParsableException

The constructor for the Storable interface.

Parameters:

representation - the xml representation

Throws:

NonParsableException - if the stream is not parsable

DNAAlphabet

public DNAAlphabet(DNAAlphabet.DNAAlphabetParameterSet parameters)
            throws IllegalArgumentException,
                   DoubleSymbolException

The constructor for the InstantiableFromParameterSet interface.

Parameters:

parameters - the ParameterSet

Throws:

IllegalArgumentException - is thrown if space or tab will be used as symbols

DoubleSymbolException - is thrown if one of the symbols occurred more than once

DNAAlphabet

public DNAAlphabet()
            throws DoubleSymbolException,
                   IllegalArgumentException

The main constructor.

Throws:

DoubleSymbolException - is thrown if one of the symbols occurred more than once

IllegalArgumentException - is thrown if space or tab will be used as symbols

Method Detail

getComplementaryCode

public int getComplementaryCode(int code)

Description copied from class: ComplementableDiscreteAlphabet

This method returns the code of the symbol the 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 ParameterSet that has been used to instantiate the current instance of the implementing class. If the current instance was not created using a ParameterSet, an equivalent ParameterSet should be returned, such that an instance created using this ParameterSet would be in principle equal to the current instance.

Specified by:

getCurrentParameterSet in interface InstantiableFromParameterSet

Specified by:

getCurrentParameterSet in class ComplementableDiscreteAlphabet

Returns:

the current ParameterSet

Throws:

Exception - is thrown if the ParameterSet could not be returned