jbil.sequence
Class ExtendedDNAAlphabet

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

All Implemented Interfaces:

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

public class ExtendedDNAAlphabet
extends Alphabet

Class representing the extended DNA nucleotide alphabet.

Author:

Paulo G. S. da Fonseca

Field Summary

static AtomicCharSymbol	a The atomic 'a' symbol
static HighOrderCharSymbol	b The high order b={g,c,t} symbol
static AtomicCharSymbol	c The atomic 'a' symbol
static HighOrderCharSymbol	d The high order d={a,g,t} symbol
static java.lang.String	EXTENDED_DNA_ALPHABET The alphabet name constant
static AtomicCharSymbol	g The atomic 'a' symbol
static HighOrderCharSymbol	h The high order h={a,c,t} symbol
static HighOrderCharSymbol	k The high order k={g,t} symbol
static HighOrderCharSymbol	m The high order m={a,c} symbol
static HighOrderCharSymbol	n The high order n={a,g,c,t} symbol
static HighOrderCharSymbol	r The high order r={a,g} symbol
static HighOrderCharSymbol	s The high order s={g,c} symbol
static AtomicCharSymbol	t The atomic 'a' symbol
static HighOrderCharSymbol	v The high order v={a,g,c} symbol
static HighOrderCharSymbol	w The high order w={a,t} symbol
static HighOrderCharSymbol	y The high order y={c,t} symbol

Constructor Summary

ExtendedDNAAlphabet()
Creates an extended DNA alphabet {a,g,c,t,r,y,k,m,s,w,b,d,h,v,n}.

Method Summary

AtomicCharSymbol	a()
HighOrderCharSymbol	b()
AtomicCharSymbol	c()
HighOrderCharSymbol	d()
AtomicCharSymbol	g()
Symbol	get(char ch) Gets a symbol from its character representation.
HighOrderCharSymbol	h()
HighOrderCharSymbol	k()
HighOrderCharSymbol	m()
HighOrderCharSymbol	n()
HighOrderCharSymbol	r()
HighOrderCharSymbol	s()
AtomicCharSymbol	t()
HighOrderCharSymbol	v()
HighOrderCharSymbol	w()
HighOrderCharSymbol	y()

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

EXTENDED_DNA_ALPHABET

public static final java.lang.String EXTENDED_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 'a' symbol

c

public static final AtomicCharSymbol c

The atomic 'a' symbol

t

public static final AtomicCharSymbol t

The atomic 'a' symbol

r

public static final HighOrderCharSymbol r

The high order r={a,g} symbol

y

public static final HighOrderCharSymbol y

The high order y={c,t} symbol

k

public static final HighOrderCharSymbol k

The high order k={g,t} symbol

m

public static final HighOrderCharSymbol m

The high order m={a,c} symbol

s

public static final HighOrderCharSymbol s

The high order s={g,c} symbol

w

public static final HighOrderCharSymbol w

The high order w={a,t} symbol

b

public static final HighOrderCharSymbol b

The high order b={g,c,t} symbol

d

public static final HighOrderCharSymbol d

The high order d={a,g,t} symbol

h

public static final HighOrderCharSymbol h

The high order h={a,c,t} symbol

v

public static final HighOrderCharSymbol v

The high order v={a,g,c} symbol

n

public static final HighOrderCharSymbol n

The high order n={a,g,c,t} symbol

Constructor Detail

ExtendedDNAAlphabet

public ExtendedDNAAlphabet()

Creates an extended DNA alphabet {a,g,c,t,r,y,k,m,s,w,b,d,h,v,n}.

Method Detail

a

public AtomicCharSymbol a()

Returns:

the a

b

public HighOrderCharSymbol b()

Returns:

the b

c

public AtomicCharSymbol c()

Returns:

the c

d

public HighOrderCharSymbol d()

Returns:

the d

g

public AtomicCharSymbol g()

Returns:

the g

h

public HighOrderCharSymbol h()

Returns:

the h

k

public HighOrderCharSymbol k()

Returns:

the k

m

public HighOrderCharSymbol m()

Returns:

the m

n

public HighOrderCharSymbol n()

Returns:

the n

r

public HighOrderCharSymbol r()

Returns:

the r

s

public HighOrderCharSymbol s()

Returns:

the s

t

public AtomicCharSymbol t()

Returns:

the t

v

public HighOrderCharSymbol v()

Returns:

the v

w

public HighOrderCharSymbol w()

Returns:

the w

y

public HighOrderCharSymbol y()

Returns:

the y

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,r,y,k,m,s,w,b,d,h,v,n}.