From 5ca0a4d817f750684f07d32c12f1bf3cc9dd364b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Camilo=20Garc=C3=ADa?= <ca.garcia2@uniandes.edu.co>
Date: Tue, 30 Jul 2024 09:35:00 -0500
Subject: [PATCH] Housekeep and clean files

---
 src/types.jl | 45 +++++++++++++++++++++------------------------
 src/utils.jl |  6 +++---
 2 files changed, 24 insertions(+), 27 deletions(-)

diff --git a/src/types.jl b/src/types.jl
index 5518f36..a535cad 100644
--- a/src/types.jl
+++ b/src/types.jl
@@ -1,27 +1,9 @@
 import GenomicFeatures: first, last, length, strand, groupname, metadata
 
-export RBS, ORF
+export ORF
 export features, sequence, source
 export groupname, finder, frame, score, strand, STRAND_BOTH, STRAND_NEG, STRAND_POS, STRAND_NA
 
-# #### Ribosome Binding Site (RBS) struct ####
-
-struct RBS
-    motif::BioRegex{DNA}
-    offset::UnitRange{Int64} # offset
-    score::Float64
-
-    function RBS(motif::BioRegex{DNA}, offset::UnitRange{Int64}, score::Float64)
-        return new(motif, offset, score)
-    end
-    # rbsinst = RBS(biore"RRR"dna, 3:4, 1.0)
-end
-
-# seq[orf.first-bin01.offset.start:orf.first-1]
-
-# motifs = [dna"GGA", dna"GAG", dna"AGG"]
-
-####### End of RBS struct #######
 
 """
     struct ORF{N,F} <: GenomicFeatures.AbstractGenomicInterval{F}
@@ -183,10 +165,6 @@ function frame(i::ORF{N,F}) where {N,F}
     return i.frame
 end
 
-function score(i::ORF{N,F}) where {N,F}
-    return i.features[:score]
-end
-
 function strand(i::ORF{N,F}) where {N,F}
     return i.strand
 end
@@ -211,4 +189,23 @@ end
 #     orf::ORF
 #     coding::Bool
 #     join::Bool
-# end
\ No newline at end of file
+# end
+
+# #### Ribosome Binding Site (RBS) struct ####
+
+# struct RBS
+#     motif::BioRegex{DNA}
+#     offset::UnitRange{Int64} # offset
+#     score::Float64
+
+#     function RBS(motif::BioRegex{DNA}, offset::UnitRange{Int64}, score::Float64)
+#         return new(motif, offset, score)
+#     end
+#     # rbsinst = RBS(biore"RRR"dna, 3:4, 1.0)
+# end
+
+# seq[orf.first-bin01.offset.start:orf.first-1]
+
+# motifs = [dna"GGA", dna"GAG", dna"AGG"]
+
+####### End of RBS struct #######
\ No newline at end of file
diff --git a/src/utils.jl b/src/utils.jl
index d46cfed..5aab583 100644
--- a/src/utils.jl
+++ b/src/utils.jl
@@ -1,6 +1,6 @@
-export hasprematurestop, _varname, _varsymbol, _orfseq #fasta2bioseq
+export _hasprematurestop, _varname, _varsymbol, _orfseq #fasta2bioseq
 
-# General purposes methods supporting main functions
+# General purposes private methods supporting main functions
 
 """
     hasprematurestop(seq::LongNucOrView{4})::Bool
@@ -9,7 +9,7 @@ Determine whether the `sequence` of type `LongSequence{DNAAlphabet{4}}` contains
 
 Returns a boolean indicating whether the `sequence` has more than one stop codon.
 """
-function hasprematurestop(seq::NucleicSeqOrView{DNAAlphabet{N}})::Bool where {N}
+function _hasprematurestop(seq::NucleicSeqOrView{DNAAlphabet{N}})::Bool where {N}
     
     stopcodons = [LongDNA{4}("TAA"), LongDNA{4}("TAG"), LongDNA{4}("TGA")]  # Create a set of stop codons
     length(seq) % 3 == 0 || error("The sequence is not divisible by 3")