jbil.sequence
Class DNAAlphabet

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<Symbol>
          jbil.sequence.Alphabet
              jbil.sequence.DNAAlphabet

All Implemented Interfaces:

java.lang.Iterable<Symbol>, java.util.Collection<Symbol>, java.util.List<Symbol>

public class DNAAlphabet
extends Alphabet

Class representing the basic DNA nucleotide alphabet {a,g,c,t}.

Author:

Paulo G. S. da Fonseca

Field Summary

static AtomicCharSymbol	a The atomic 'a' symbol
static AtomicCharSymbol	c The atomic 'c' symbol
static java.lang.String	DNA_ALPHABET The alphabet name constant
static AtomicCharSymbol	g The atomic 'g' symbol
static AtomicCharSymbol	t The atomic 't' symbol

Constructor Summary

DNAAlphabet()
Creates a DNA {a,g,c,t} alphabet.

Method Summary

AtomicCharSymbol	a()
AtomicCharSymbol	c()
AtomicCharSymbol	g()
Symbol	get(char ch) Gets a symbol from its character representation.
AtomicCharSymbol	t()

Methods inherited from class jbil.sequence.Alphabet

add, contains, get, indexOf, intersection, isLocked, lock, remove, set, size

Methods inherited from class java.util.AbstractList

add, addAll, clear, equals, hashCode, iterator, lastIndexOf, listIterator, listIterator, subList

Methods inherited from class java.util.AbstractCollection

addAll, containsAll, isEmpty, remove, removeAll, retainAll, toArray, toArray, toString

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.List

addAll, containsAll, isEmpty, remove, removeAll, retainAll, toArray, toArray

Field Detail

DNA_ALPHABET

public static final java.lang.String DNA_ALPHABET

The alphabet name constant

See Also:

Constant Field Values

a

public static final AtomicCharSymbol a

The atomic 'a' symbol

g

public static final AtomicCharSymbol g

The atomic 'g' symbol

c

public static final AtomicCharSymbol c

The atomic 'c' symbol

t

public static final AtomicCharSymbol t

The atomic 't' symbol

Constructor Detail

DNAAlphabet

public DNAAlphabet()

Creates a DNA {a,g,c,t} alphabet.

Method Detail

a

public AtomicCharSymbol a()

Returns:

the a

c

public AtomicCharSymbol c()

Returns:

the c

g

public AtomicCharSymbol g()

Returns:

the g

t

public AtomicCharSymbol t()

Returns:

the t

get

public Symbol get(char ch)

Gets a symbol from its character representation.

Parameters:

ch - The character representation of the symbol.

Returns:

The corresponding atomic symbol or null if ch is not in {'a','g','c','t'}.