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## org.biojava.bio.seq
Class RNATools

    java.lang.Object
      org.biojava.bio.seq.RNATools

    public final class RNATools

extends Object

Useful functionality for processing DNA and RNA sequences.

Author:
  Matthew Pocock, Keith James (docs), Thomas Down, Greg Cox, Mark Schreiber, David Huen (refactoring), gwaldon (update genetic code translation tables)

Method Summary
`static AtomicSymbol` | `a()`
`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` | `createRNA(String rna)` Return a new RNA SymbolList for rna.
`static Sequence` | `createRNASequence(String rna, String name)` Return a new RNA Sequence for rna.
`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 (RNA x RNA x RNA) Alphabet
`static ManyToOneTranslationTable` | `getGeneticCode(int table_num)` Retrieve a TranslationTable by number.
`static ManyToOneTranslationTable` | `getGeneticCode(String name)` Retrieve a TranslationTable by name.
`static Set` | `getGeneticCodeNames()` Retrieve a Set containing the name of each genetic code.
`static FiniteAlphabet` | `getRNA()` Return the RNA alphabet.
`static int` | `index(Symbol sym)` Return an integer index for a symbol - compatible with forIndex.
`static Symbol` | `n()`
`static SymbolList` | `reverseComplement(SymbolList list)` Retrieve a reverse-complement view of list.
`static SymbolList` | `transcribe(SymbolList list)` Deprecated. The naming of this method is confusing and inconsistent use either DNATools.toRNA(SymbolList list) or DNATools.transcribeToRNA(SymbolList list) depending on the desired behaivour.
`static ReversibleTranslationTable` | `transcriptionTable()` Get a translation table for converting DNA to RNA.
`static SymbolList` | `translate(SymbolList syms)` Translate RNA into protein (with termination symbols).
`static AtomicSymbol` | `u()`

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()

### u

    public static AtomicSymbol u()

### n

    public static Symbol n()

### getRNA

    public static FiniteAlphabet getRNA()

  Return the RNA alphabet.

  Returns:
    a flyweight version of the RNA alphabet

### getCodonAlphabet

    public static FiniteAlphabet getCodonAlphabet()

  Gets the (RNA x RNA x RNA) Alphabet

  Returns:
    a flyweight version of the (RNA x RNA x RNA) alphabet

### createRNA

    public static SymbolList createRNA(String rna)
                                throws IllegalSymbolException

  Return a new RNA SymbolList for rna.

  Parameters:
    `rna` - a String to parse into RNA
  Returns:
    a SymbolList created form rna
  Throws:
    `IllegalSymbolException` - if rna contains any non-RNA characters

### createRNASequence

    public static Sequence createRNASequence(String rna,
                                             String name)
                                      throws IllegalSymbolException

  Return a new RNA Sequence for rna.

  Parameters:
    `rna` - a String to parse into RNA
    `name` - a String to use as the name
  Returns:
    a Sequence created form dna
  Throws:
    `IllegalSymbolException` - if rna contains any non-DNA 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 across 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 RNA 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 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

### transcribe

    public static SymbolList transcribe(SymbolList list)
                                 throws IllegalAlphabetException

  Deprecated. The naming of this method is confusing and inconsistent use either DNATools.toRNA(SymbolList list) or DNATools.transcribeToRNA(SymbolList list) depending on the desired behaivour.

  Transcribe DNA into RNA.

  Parameters:
    `list` - the SymbolList to transcribe
  Returns:
    a SymbolList that is the transcribed view
  Throws:
    `IllegalAlphabetException` - if the list is not DNA

### complementTable

    public static ReversibleTranslationTable complementTable()

  Get a translation table for complementing DNA symbols.

  Since:
    1.1

### transcriptionTable

    public static ReversibleTranslationTable transcriptionTable()

  Get a translation table for converting DNA to RNA.

  Since:
    1.1

### getGeneticCode

    public static ManyToOneTranslationTable getGeneticCode(String name)

  Retrieve a TranslationTable by name. The valid names are:
  - "UNIVERSAL"
  - "VERTEBRATE_MITOCHONDRIAL"
  - "YEAST_MITOCHONDRIAL"
  - "MOLD_MITOCHONDRIAL"
  - "INVERTEBRATE_MITOCHONDRIAL"
  - "CILIATE_NUCLEAR"
  - "ECHINODERM_MITOCHONDRIAL"
  - "EUPLOTID_NUCLEAR"
  - "BACTERIAL"
  - "ALTERNATIVE_YEAST_NUCLEAR"
  - "ASCIDIAN_MITOCHONDRIAL"
  - "FLATWORM_MITOCHONDRIAL"
  - "BLEPHARISMA_MACRONUCLEAR"
  - "CHLOROPHYCEAN_MITOCHONDRIAL"
  - "TREMATODE_MITOCHONDRIAL"
  - "SCENEDESMUS_MITOCHONDRIAL"
  There are public static final fields in the TranslationTable interface which contain these values. One of these should be used as the argument for this method.

  You can now get the reverse translation of the residue back to its (usually several) codons too.

  Since:
    1.1

### getGeneticCode

    public static ManyToOneTranslationTable getGeneticCode(int table_num)

  Retrieve a TranslationTable by number. These numbers correspond to the transl_table qualifier in the DDBJ/EMBL/GenBank Feature Table (Version 6.5 Apr 2006): transl_table defines the genetic code table used if other than the universal genetic code table. Tables are described in appendix V, section 7.5.5:
  - " 1 - UNIVERSAL"
  - " 2 - VERTEBRATE_MITOCHONDRIAL"
  - " 3 - YEAST_MITOCHONDRIAL"
  - " 4 - MOLD_MITOCHONDRIAL"
  - " 5 - INVERTEBRATE_MITOCHONDRIAL"
  - " 6 - CILIATE_NUCLEAR"
  - " 9 - ECHINODERM_MITOCHONDRIAL"
  - "10 - EUPLOTID_NUCLEAR"
  - "11 - BACTERIAL"
  - "12 - ALTERNATIVE_YEAST_NUCLEAR"
  - "13 - ASCIDIAN_MITOCHONDRIAL"
  - "14 - FLATWORM_MITOCHONDRIAL"
  - "15 - BLEPHARISMA_MACRONUCLEAR"
  - "16 - 2CHLOROPHYCEAN_MITOCHONDRIAL"
  - "21 - TREMATODE_MITOCHONDRIAL"
  - "23 - SCENEDESMUS_MITOCHONDRIAL"

  Throws:
    `IllegalArgumentException` - if there is no table with that number.
  Since:
    1.5

### getGeneticCodeNames

    public static Set getGeneticCodeNames()

  Retrieve a Set containing the name of each genetic code.

  Since:
    1.1

### translate

    public static SymbolList translate(SymbolList syms)
                                throws IllegalAlphabetException

  Translate RNA into protein (with termination symbols). For compatibility with BioJava 1.1, this will also handle sequences which are already expressed in the (RNA x RNA x RNA) (codon) alphabet.

  Throws:
    `IllegalAlphabetException`
  Since:
    1.1

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