org.biojava.bio.seq

Class NucleotideTools

java.lang.Object

org.biojava.bio.seq.NucleotideTools

public final class NucleotideTools
extends Object

Useful functionality for processing nucleotide sequences.

Author:

Matthew Pocock, Keith James (docs)

Method Summary

Methods

Modifier and Type	Method and Description
static AtomicSymbol	a()
static Symbol	b()
static AtomicSymbol	c()
static Symbol	complement(Symbol sym) Complement the symbol.
static SymbolList	complement(SymbolList list) Retrieve a complement view of list.
static ReversibleTranslationTable	complementTable() Get a translation table for complementing Nucleotide symbols.
static SymbolList	createNucleotide(String nucleotide) Return a new Nucleotide SymbolList for nucleotide.
static Sequence	createNucleotideSequence(String nucleotide, String name) Return a new Nucleotide Sequence for nucleotide.
static Symbol	d()
static Symbol	forIndex(int index) Return the symbol for an index - compatible with index.
static Symbol	forSymbol(char token) Retrieve the symbol for a symbol.
static AtomicSymbol	g()
static FiniteAlphabet	getNucleotide() Return the Nucleotide alphabet.
static Symbol	h()
static int	index(Symbol sym) Return an integer index for a symbol - compatible with forIndex.
static Symbol	k()
static Symbol	m()
static Symbol	n()
static char	nucleotideToken(Symbol sym) Get a single-character token for a Nucleotide symbol
static Symbol	r()
static SymbolList	reverseComplement(SymbolList list) Retrieve a reverse-complement view of list.
static Symbol	s()
static AtomicSymbol	t()
static AtomicSymbol	u()
static Symbol	v()
static Symbol	w()
static Symbol	y()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

a

public static AtomicSymbol a()

g

public static AtomicSymbol g()

c

public static AtomicSymbol c()

t

public static AtomicSymbol t()

u

public static AtomicSymbol u()

r

public static Symbol r()

y

public static Symbol y()

m

public static Symbol m()

k

public static Symbol k()

s

public static Symbol s()

w

public static Symbol w()

b

public static Symbol b()

d

public static Symbol d()

h

public static Symbol h()

v

public static Symbol v()

n

public static Symbol n()

getNucleotide

public static FiniteAlphabet getNucleotide()

Return the Nucleotide alphabet.

Returns:

a flyweight version of the Nucleotide alphabet

createNucleotide

public static SymbolList createNucleotide(String nucleotide)
                                   throws IllegalSymbolException

Return a new Nucleotide SymbolList for nucleotide.

Parameters:

nucleotide - a String to parse into Nucleotide

Returns:

a SymbolList created form nucleotide

Throws:

IllegalSymbolException - if nucleotide contains any non-Nucleotide characters

createNucleotideSequence

public static Sequence createNucleotideSequence(String nucleotide,
                                String name)
                                         throws IllegalSymbolException

Return a new Nucleotide Sequence for nucleotide.

Parameters:

nucleotide - a String to parse into Nucleotide

name - a String to use as the name

Returns:

a Sequence created form nucleotide

Throws:

IllegalSymbolException - if nucleotide contains any non-Nucleotide characters

index

public static int index(Symbol sym)
                 throws IllegalSymbolException

Return an integer index for a symbol - compatible with forIndex.

The index for a symbol is stable accross virtual machines & invocations.

Parameters:

sym - the Symbol to index

Returns:

the index for that symbol

Throws:

IllegalSymbolException - if sym is not a member of the Nucleotide alphabet

forIndex

public static Symbol forIndex(int index)
                       throws IndexOutOfBoundsException

Return the symbol for an index - compatible with index.

The index for a symbol is stable accross virtual machines & invocations.

Parameters:

index - the index to look up

Returns:

the symbol at that index

Throws:

IndexOutOfBoundsException - if index is not between 0 and 3

complement

public static Symbol complement(Symbol sym)
                         throws IllegalSymbolException

Complement the symbol.

Parameters:

sym - the symbol to complement

Returns:

a Symbol that is the complement of sym

Throws:

IllegalSymbolException - if sym is not a member of the Nucleotide alphabet

forSymbol

public static Symbol forSymbol(char token)
                        throws IllegalSymbolException

Retrieve the symbol for a symbol.

Parameters:

token - the char to look up

Returns:

the symbol for that char

Throws:

IllegalSymbolException - if the char does not belong to {a, g, c, t, u}

complement

public static SymbolList complement(SymbolList list)
                             throws IllegalAlphabetException

Retrieve a complement view of list.

Parameters:

list - the SymbolList to complement

Returns:

a SymbolList that is the complement

Throws:

IllegalAlphabetException - if list is not a complementable alphabet

reverseComplement

public static SymbolList reverseComplement(SymbolList list)
                                    throws IllegalAlphabetException

Retrieve a reverse-complement view of list.

Parameters:

list - the SymbolList to complement

Returns:

a SymbolList that is the complement

Throws:

IllegalAlphabetException - if list is not a complementable alphabet

complementTable

public static ReversibleTranslationTable complementTable()

Get a translation table for complementing Nucleotide symbols.

Since:

1.1

nucleotideToken

public static char nucleotideToken(Symbol sym)
                            throws IllegalSymbolException

Get a single-character token for a Nucleotide symbol

Throws:

IllegalSymbolException - if sym is not a member of the Nucleotide alphabet