struct VossEncoder{A<:NucleicAcidAlphabet, B<:BitMatrix}

The VossEncoder struct represents a binary matrix encoding a sequence of nucleic acids. This is also called the Voss representation of a sequence.

Fields

• alphabet::A: The nucleic acid alphabet used for encoding.
• bitmatrix::B: The binary matrix representing the encoded sequence.

Constructors

• VossEncoder(sequence::SeqOrView{A}): Constructs a VossEncoder from a sequence of nucleic acids.

Arguments

• sequence::SeqOrView{A}: The sequence of nucleic acids to be encoded.

vossmatrix(VossEncoder::VossEncoder{A, B}) where {A <: NucleicAcidAlphabet, B <: BitMatrix}
vossmatrix(sequence::NucleicSeqOrView{A}) where {A <: NucleicAcidAlphabet}
vossmatrix(sequence::SeqOrView{AminoAcidAlphabet}) where {A <: AminoAcidAlphabet}

Create a binary sequence matrix from a given nucleic acid sequence.

Arguments

• sequence: A nucleic acid sequence.

Returns

The binary sequence matrix.

Examples

julia> vossmatrix(aa"IANRMWRDTIED")

    20×12 BitMatrix:
    0  1  0  0  0  0  0  0  0  0  0  0
    0  0  0  0  0  0  0  0  0  0  0  0
    0  0  0  0  0  0  0  1  0  0  0  1
    0  0  0  0  0  0  0  0  0  0  1  0
    0  0  0  0  0  0  0  0  0  0  0  0
    0  0  0  0  0  0  0  0  0  0  0  0
    0  0  0  0  0  0  0  0  0  0  0  0
    1  0  0  0  0  0  0  0  0  1  0  0
    0  0  0  0  0  0  0  0  0  0  0  0
    0  0  0  0  0  0  0  0  0  0  0  0
    0  0  0  0  1  0  0  0  0  0  0  0
    0  0  1  0  0  0  0  0  0  0  0  0
    0  0  0  0  0  0  0  0  0  0  0  0
    0  0  0  0  0  0  0  0  0  0  0  0
    0  0  0  1  0  0  1  0  0  0  0  0
    0  0  0  0  0  0  0  0  0  0  0  0
    0  0  0  0  0  0  0  0  1  0  0  0
    0  0  0  0  0  0  0  0  0  0  0  0
    0  0  0  0  0  1  0  0  0  0  0  0
    0  0  0  0  0  0  0  0  0  0  0  0

vossvector(sequence::NucleicSeqOrView{A}, molecule::T) where {A <: NucleicAcidAlphabet, T <: BioSymbol}
vossvector(sequence::SeqOrView{AminoAcidAlphabet}, molecule::T) where {T <: BioSymbol}
vossvector(sequence::SeqOrView{A}, molecules::Tuple{Vararg{T}}) where {A <: Alphabet, T <: BioSymbol}

Converts a sequence of nucleotides into a binary representation.

Arguments

• sequence::SeqOrView{A}: The input sequence of nucleotides.
• molecule::BioSymbol: The nucleotide to be encoded as 1, while others are encoded as 0.
• molecules::Tuple{Vararg{T}}: The nucleotides to be encoded as 1, while others are encoded as 0.

Returns

A BitVector representing the binary encoding of the input sequence, where 1 indicates the presence of the specified nucleotide and 0 indicates the absence in the ith position of the sequence.

Examples

julia> vossvector(dna"ACGT", DNA_A)

    4-element view(::BitMatrix, 1, :) with eltype Bool:
     1
     0
     0
     0