de.jstacs.data.alphabets
Class DNAAlphabet

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