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WIP: Add all the noop 2bit methods
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src/biosequence/find.jl

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -46,12 +46,16 @@ end
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# N.B: The isgap and isambiguous have identical definitions but are separate methods to avoid
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# ambiguity errors.
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_findnext(::typeof(isambiguous), ::BioSequence{<:NucleicAcidAlphabet{2}}, ::Int) = nothing
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_findnext(::typeof(isgap), ::BioSequence{<:NucleicAcidAlphabet{2}}, ::Int) = nothing
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_findprev(::typeof(isambiguous), ::BioSequence{<:NucleicAcidAlphabet{2}}, ::Int) = nothing
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_findnext(::typeof(isgap), ::BioSequence{<:NucleicAcidAlphabet{2}}, ::Int) = nothing
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_findprev(::typeof(isgap), ::BioSequence{<:NucleicAcidAlphabet{2}}, ::Int) = nothing
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_findnext(::typeof(iscertain), seq::BioSequence{<:NucleicAcidAlphabet{2}}, from::Int) = from
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_findprev(::typeof(iscertain), seq::BioSequence{<:NucleicAcidAlphabet{2}}, from::Int) = from
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_findnext(::typeof(!isambiguous), seq::BioSequence{<:NucleicAcidAlphabet{2}}, from::Int) = from
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_findprev(::typeof(!isambiguous), seq::BioSequence{<:NucleicAcidAlphabet{2}}, from::Int) = from
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_findnext(::typeof(!isgap), seq::BioSequence{<:NucleicAcidAlphabet{2}}, from::Int) = from
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_findprev(::typeof(!isgap), seq::BioSequence{<:NucleicAcidAlphabet{2}}, from::Int) = from
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# Finding specific symbols
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Base.findnext(x::DNA, seq::BioSequence{<:DNAAlphabet}, start::Integer) = findnext(isequal(x), seq, start)

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