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Expand on documentation for compatbits #63

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Jan 15, 2024
Merged

Expand on documentation for compatbits #63

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13 changes: 13 additions & 0 deletions src/aminoacid.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -198,6 +198,11 @@ gap(::Type{AminoAcid}) = AA_Gap
compatbits(aa::AminoAcid)

Return the compatibility bits of `aa` as `UInt32`.
The resulting `UInt32` has one bit set per amino acid
it is compatible with.

For example, `J` is compatible with `I` (bit 10) and `L` (bit 11),
and so is `0x00000600`.

Examples
--------
Expand All @@ -206,9 +211,17 @@ Examples
julia> compatbits(AA_A)
0x00000001

julia> compatbits(AA_E)
0x00000040

julia> compatbits(AA_J)
0x00000600

julia> compatbits(AA_X)
0x003fffff

julia> compatbits(AA_Gap)
0x00000000
```
"""
compatbits(aa::AminoAcid) = @inbounds compatbits_aa[encoded_data(aa) + 1]
10 changes: 10 additions & 0 deletions src/nucleicacid.jl
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Expand Up @@ -460,6 +460,11 @@ end
compatbits(nt::NucleicAcid)

Return the compatibility bits of `nt` as `UInt8`.
The resulting `UInt8` has the lower four bits set
if `nt` is compatible with `A`, `C`, `G` and `T/U`, respectively.

Hence, `RNA_Gap` is `0x00` (not compatible with any nucleotide),
and `DNA_W` is `0x09` (compatible with `A` and `T`)

Examples
--------
Expand All @@ -474,6 +479,11 @@ julia> compatbits(DNA_C)
julia> compatbits(DNA_N)
0x0f

julia> compatbits(DNA_W)
0x09

julia> compatbits(RNA_Gap)
0x00
```
"""
@inline function compatbits(nt::NucleicAcid)
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