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# Alphabets

## `Alphabet` and `MolType`

`MolType` instances have an `Alphabet`.

    >>> from cogent import DNA, PROTEIN
    >>> print DNA.Alphabet
    ('T', 'C', 'A', 'G')
    >>> print PROTEIN.Alphabet
    ('A', 'C', 'D', 'E', ...

`Alphabet` instances have a `MolType`.

    >>> PROTEIN.Alphabet.MolType == PROTEIN
    True

## Creating tuple alphabets

You can create a tuple alphabet of, for example, dinucleotides or trinucleotides.

    >>> dinuc_alphabet = DNA.Alphabet.getWordAlphabet(2)
    >>> print dinuc_alphabet
    ('TT', 'CT', 'AT', 'GT', ...
    >>> trinuc_alphabet = DNA.Alphabet.getWordAlphabet(3)
    >>> print trinuc_alphabet
    ('TTT', 'CTT', 'ATT', ...

## Convert a sequence into integers

    >>> seq = 'TAGT'
    >>> indices = DNA.Alphabet.toIndices(seq)
    >>> indices
    [0, 2, 3, 0]

## Convert integers to a sequence

    >>> seq = DNA.Alphabet.fromIndices([0,2,3,0])
    >>> seq
    ['T', 'A', 'G', 'T']

or

    >>> seq = DNA.Alphabet.fromOrdinalsToSequence([0,2,3,0])
    >>> seq
    DnaSequence(TAGT)

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