Class RNATools

Method Details

• 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