Update exports to file level

src/GeneFinder.jl

@@ -24,18 +24,12 @@ using FASTX: FASTAReader, FASTARecord, description, sequence
 using IterTools: takewhile, iterated
 using PrecompileTools: @setup_workload, @compile_workload
 
+include("algorithms/naivefinder.jl")
 include("types.jl")
-export ORF
-
-include("algorithms/findorfs.jl")
-export locationiterator, findorfs, get_orfs_dna, get_orfs_aa, record_orfs_fna, record_orfs_faa
-
+include("findorfs.jl")
+include("getorfs.jl")
 include("io.jl")
-export write_orfs_fna, write_orfs_faa, write_orfs_bed, write_orfs_gff
-
 include("utils.jl")
-export fasta_to_dna, hasprematurestop
-
 include("extended.jl")
 
 @setup_workload begin

src/io.jl

@@ -1,3 +1,5 @@
+export write_orfs_fna, write_orfs_faa, write_orfs_bed, write_orfs_gff
+
 """
     write_orfs_bed(input::NucleicAcidAlphabet{DNAAlphabet{N}}, output::Union{IOStream, IOBuffer}; kwargs...) where {N}
     write_orfs_bed(input::NucleicAcidAlphabet{DNAAlphabet{N}}, output::String; kwargs...) where {N}

src/types.jl

@@ -1,3 +1,5 @@
+export ORF
+
 # Structs associated with gene models 
 abstract type AbstractGene end
 
@@ -48,6 +50,7 @@ The ORF struct represents an open reading frame in a DNA sequence. It has two fi
 - `score`: is a Union{Nothing, Float64} type indicating the score of the ORF. It can be a Float64 or nothing.
 """
 struct ORF <: AbstractGene
+    #TODOs:  location might be a complex Union allowing UnitRange or a Join of ranges (e.g. 1..100, 200..300)?
     location::UnitRange{Int64}  # Note that it is also called position for gene struct in GenomicAnotations
     strand::Char
     frame::Int # Use Int64 instead of Int

src/utils.jl

@@ -1,3 +1,4 @@
+export fasta_to_dna, hasprematurestop
 # General purposes methods supporting main functions
 """
     fasta_to_dna(input::String)