Class NucleotideTools

Method Details

• 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