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 discrete alphabet that is used for DNA.

Author:

Jan Grau, Jens Keilwagen

Nested Class Summary

static class

DNAAlphabet.DNAAlphabetParameterSet The parameter set for a DNAAlphabet.

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

alphabet, caseInsensitive, parameters

Constructor Summary

DNAAlphabet()
The main constructor.

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

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

Method Summary

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

Parameters:

representation - the XML representation as StringBuffer

Throws:

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

See Also:

ComplementableDiscreteAlphabet.ComplementableDiscreteAlphabet(StringBuffer), Storable

DNAAlphabet

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

The constructor for the InstantiableFromParameterSet interface. Creates a new DNAAlphabet from a given parameter set.

Parameters:

parameters - the given set of parameters

Throws:

IllegalArgumentException - if space or tab will be used as symbols

DoubleSymbolException - if one of the symbols occurred more than once

See Also:

DNAAlphabet()

DNAAlphabet

public DNAAlphabet()
            throws DoubleSymbolException,
                   IllegalArgumentException

The main constructor. Creates a new DNAAlphabet with the standard DNA-alphabet ("A", "C", "G", "T").

Throws:

DoubleSymbolException - if one of the symbols occurred more than once

IllegalArgumentException - if space or tab will be used as symbols

See Also:

ComplementableDiscreteAlphabet.ComplementableDiscreteAlphabet(boolean, String...)

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

Specified by:

getCurrentParameterSet in class ComplementableDiscreteAlphabet

Returns:

the current InstanceParameterSet

Throws:

Exception - if the InstanceParameterSet could not be returned