NucleotideTools (biojava-legacy 1.9.5 API)

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

All Methods Static Methods Concrete Methods
Modifier and Type	Method	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

Method Summary

Methods inherited from class java.lang.Object

Method Detail

a

g

c

t

u

r

y

m

k

s

w

b

d

h

v

n

getNucleotide

createNucleotide

createNucleotideSequence

index

forIndex

complement

forSymbol

complement

reverseComplement

complementTable

nucleotideToken