DNATools (biojava-legacy 1.9.1 API)

java.lang.Object
- org.biojava.bio.seq.DNATools

```
public final class DNATools
extends Object
```
Useful functionality for processing DNA sequences.

Author:

Matthew Pocock, Keith James (docs), Mark Schreiber, David Huen, Richard Holland

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 DNA symbols.
`static SymbolList`	`createDNA(String dna)` Return a new DNA SymbolList for dna.
`static Sequence`	`createDNASequence(String dna, String name)` Return a new DNA Sequence for dna.
`static GappedSequence`	`createGappedDNASequence(String dna, String name)` Get a new dna as a GappedSequence
`static Symbol`	`d()`
`static char`	`dnaToken(Symbol sym)` Get a single-character token for a DNA symbol
`static SymbolList`	`flip(SymbolList list, StrandedFeature.Strand strand)` Returns a SymbolList that is reverse complemented if the strand is negative, and the origninal one if it is not.
`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`	`getCodonAlphabet()` Gets the (DNA x DNA x DNA) Alphabet
`static FiniteAlphabet`	`getDNA()` Return the DNA alphabet.
`static Distribution`	`getDNADistribution(double fractionGC)` return a SimpleDistribution of specified GC content.
`static FiniteAlphabet`	`getDNAxDNA()` Gets the (DNA x DNA) Alphabet
`static Distribution`	`getDNAxDNADistribution(double fractionGC0, double fractionGC1)` return a (DNA x DNA) cross-product Distribution with specified DNA contents in each component 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 Symbol`	`r()`
`static SymbolList`	`reverseComplement(SymbolList list)` Retrieve a reverse-complement view of list.
`static Symbol`	`s()`
`static AtomicSymbol`	`t()`
`static SymbolList`	`toProtein(SymbolList syms)` Convenience method that directly converts a DNA sequence to RNA then to protein.
`static SymbolList`	`toProtein(SymbolList syms, int start, int end)` Convenience method to translate a region of a DNA sequence directly into protein.
`static SymbolList`	`toRNA(SymbolList syms)` Converts a `SymbolList` from the DNA `Alphabet` to the RNA `Alphabet`.
`static SymbolList`	`transcribeToRNA(SymbolList syms)` Transcribes DNA to RNA.
`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()
```
  - n
```
public static Symbol n()
```
  - m
```
public static Symbol m()
```
  - r
```
public static Symbol r()
```
  - w
```
public static Symbol w()
```
  - s
```
public static Symbol s()
```
  - y
```
public static Symbol y()
```
  - k
```
public static Symbol k()
```
  - v
```
public static Symbol v()
```
  - h
```
public static Symbol h()
```
  - d
```
public static Symbol d()
```
  - b
```
public static Symbol b()
```
  - getDNA
```
public static FiniteAlphabet getDNA()
```
    Return the DNA alphabet.
    
    Returns:
    a flyweight version of the DNA alphabet
  - getDNAxDNA
```
public static FiniteAlphabet getDNAxDNA()
```
    Gets the (DNA x DNA) Alphabet
    
    Returns:
    a flyweight version of the (DNA x DNA) alphabet
  - getCodonAlphabet
```
public static FiniteAlphabet getCodonAlphabet()
```
    Gets the (DNA x DNA x DNA) Alphabet
    
    Returns:
    a flyweight version of the (DNA x DNA x DNA) alphabet
  - createDNA
```
public static SymbolList createDNA(String dna)
                            throws IllegalSymbolException
```
    Return a new DNA SymbolList for dna.
    
    Parameters:
    dna - a String to parse into DNA
    
    Returns:
    a SymbolList created form dna
    
    Throws:
    
    IllegalSymbolException - if dna contains any non-DNA characters
  - createDNASequence
```
public static Sequence createDNASequence(String dna,
                         String name)
                                  throws IllegalSymbolException
```
    Return a new DNA Sequence for dna.
    
    Parameters:
    dna - a String to parse into DNA
    name - a String to use as the name
    
    Returns:
    a Sequence created form dna
    
    Throws:
    
    IllegalSymbolException - if dna contains any non-DNA characters
  - createGappedDNASequence
```
public static GappedSequence createGappedDNASequence(String dna,
                                     String name)
                                              throws IllegalSymbolException
```
    Get a new dna as a GappedSequence
    
    Throws:
    
    IllegalSymbolException
  - 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 DNA 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 DNA 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 is not a valid IUB dna code
  - 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
  - flip
```
public static SymbolList flip(SymbolList list,
              StrandedFeature.Strand strand)
                       throws IllegalAlphabetException
```
    Returns a SymbolList that is reverse complemented if the strand is negative, and the origninal one if it is not.
    
    Parameters:
    list - the SymbolList to view
    strand - the Strand to use
    
    Returns:
    the apropreate view of the SymbolList
    
    Throws:
    
    IllegalAlphabetException - if list is not a complementable alphabet
  - complementTable
```
public static ReversibleTranslationTable complementTable()
```
    Get a translation table for complementing DNA symbols.
    
    Since:
    
    1.1
  - dnaToken
```
public static char dnaToken(Symbol sym)
                     throws IllegalSymbolException
```
    Get a single-character token for a DNA symbol
    
    Throws:
    
    IllegalSymbolException - if sym is not a member of the DNA alphabet
  - getDNADistribution
```
public static Distribution getDNADistribution(double fractionGC)
```
    return a SimpleDistribution of specified GC content.
    
    Parameters:
    fractionGC - (G+C) content as a fraction.
  - getDNAxDNADistribution
```
public static Distribution getDNAxDNADistribution(double fractionGC0,
                                  double fractionGC1)
```
    return a (DNA x DNA) cross-product Distribution with specified DNA contents in each component Alphabet.
    
    Parameters:
    fractionGC0 - (G+C) content of first sequence as a fraction.
    fractionGC1 - (G+C) content of second sequence as a fraction.
  - toRNA
```
public static SymbolList toRNA(SymbolList syms)
                        throws IllegalAlphabetException
```
    Converts a SymbolList from the DNA Alphabet to the RNA Alphabet.
    
    Parameters:
    syms - the SymbolList to convert to RNA
    
    Returns:
    a view on syms where Symbols have been converted to RNA. Most significantly t's are now u's. The 5' to 3' order of the Symbols is conserved.
    
    Throws:
    
    IllegalAlphabetException - if syms is not DNA.
    Since:
    
    1.4
  - transcribeToRNA
```
public static SymbolList transcribeToRNA(SymbolList syms)
                                  throws IllegalAlphabetException
```
    Transcribes DNA to RNA. The method more closely represents the biological reality than toRNA(SymbolList syms) does. The presented DNA SymbolList is assumed to be the template strand in the 5' to 3' orientation. The resulting RNA is transcribed from this template effectively a reverse complement in the RNA alphabet. The method is equivalent to calling reverseComplement() and toRNA() in sequence.
    If you are dealing with cDNA sequences that you want converted to RNA you would be better off calling toRNA(SymbolList syms)
    
    Parameters:
    syms - the SymbolList to convert to RNA
    
    Returns:
    a view on syms where Symbols have been converted to RNA.
    
    Throws:
    
    IllegalAlphabetException - if syms is not DNA.
    Since:
    
    1.4
  - toProtein
```
public static SymbolList toProtein(SymbolList syms)
                            throws IllegalAlphabetException
```
    Convenience method that directly converts a DNA sequence to RNA then to protein. The translated protein is from the +1 reading frame of the SymbolList. The whole SymbolList is translated although up to 2 DNA residues may be truncated if full codons cannot be formed.
    
    Parameters:
    syms - the sequence to be translated.
    
    Returns:
    the translated protein sequence.
    
    Throws:
    
    IllegalAlphabetException - if syms is not from the DNA alphabet.
    Since:
    
    1.5.1
  - toProtein
```
public static SymbolList toProtein(SymbolList syms,
                   int start,
                   int end)
                            throws IllegalAlphabetException
```
    Convenience method to translate a region of a DNA sequence directly into protein. While the start and end can be specified if the length of the specified region is not evenly divisible by three then the translated region will be truncated until a full terminal codon can be formed.
    
    Parameters:
    syms - the DNA sequence to be translated.
    start - the location to begin translation.
    end - the end of the translated region.
    
    Returns:
    the translated protein sequence.
    
    Throws:
    
    IllegalAlphabetException - if syms is not from the DNA alphabet.
    Since:
    
    1.5.1

Class DNATools

Method Summary

Methods inherited from class java.lang.Object

Method Detail

a

g

c

t

n

m

r

w

s

y

k

v

h

d

b

getDNA

getDNAxDNA

getCodonAlphabet

createDNA

createDNASequence

createGappedDNASequence

index

forIndex

complement

forSymbol

complement

reverseComplement

flip

complementTable

dnaToken

getDNADistribution

getDNAxDNADistribution

toRNA

transcribeToRNA

toProtein

toProtein