From 75ecd1c0c1b6b46f54568725045382fd68b4945e Mon Sep 17 00:00:00 2001
From: Marco Matthies <marco.matthies@gmail.com>
Date: Sat, 3 Dec 2022 23:48:50 +0100
Subject: [PATCH] rename R2R.R2Rplot => R2R.Plot, r2r() => run_r2r()

---
 src/r2r.jl  | 22 +++++++++++-----------
 test/r2r.jl |  7 +++----
 2 files changed, 14 insertions(+), 15 deletions(-)

diff --git a/src/r2r.jl b/src/r2r.jl
index 351a2bd..c8a0146 100644
--- a/src/r2r.jl
+++ b/src/r2r.jl
@@ -86,35 +86,35 @@ function _runcmd(cmd::Cmd)
     return exitcode, out, err
 end
 
-struct R2Rplot
+struct Plot
     svg::String
 end
 
-function Base.showable(mime::Type{T}, p::R2Rplot) where {T <: MIME}
+function Base.showable(mime::Type{T}, p::Plot) where {T <: MIME}
     if mime === MIME"image/svg+xml"
         return true
     end
     return false
 end
 
-function Base.show(io::IO, mime::MIME"image/svg+xml", p::R2Rplot)
+function Base.show(io::IO, mime::MIME"image/svg+xml", p::Plot)
     # TODO: why doesn't the following signature work? claims there is
     #       no method to call for MIME"image/svg+xml", but
     #       MIME"image/svg+xml" <: MIME ???
-    # function Base.show(io::IO, mime::T, p::R2Rplot) where {T <: MIME}
+    # function Base.show(io::IO, mime::T, p::Plot) where {T <: MIME}
     println(io, p.svg)
 end
 
 function plot(msa::MSA; kwargs...)
-    ps, res, out, err = r2r(msa; kwargs...)
-    return R2Rplot(res)
+    ps, res, out, err = run_r2r(msa; kwargs...)
+    return Plot(res)
 end
 
-function r2r(msa::MSA;
-             GSC_weighted_consensus::Bool = true,
-             identity_levels = [0.97, 0.9, 0.75],
-             present_levels = [0.97, 0.9, 0.75, 0.5],
-             max_noncanon::Real = 0.1)
+function run_r2r(msa::MSA;
+                 GSC_weighted_consensus::Bool = true,
+                 identity_levels = [0.97, 0.9, 0.75],
+                 present_levels = [0.97, 0.9, 0.75, 0.5],
+                 max_noncanon::Real = 0.1)
     # TODO
     # - output file type: svg or pdf
     # - assertions on identity_levels, present_levels, max_noncanon
diff --git a/test/r2r.jl b/test/r2r.jl
index cca9ffb..54ace48 100644
--- a/test/r2r.jl
+++ b/test/r2r.jl
@@ -1,7 +1,6 @@
 using Test
 using PlotRNA: R2R
 using BioStockholm: MSA
-using PlotRNA.R2R: R2Rplot
 
 const R2R_MSA = [
 parse(MSA,
@@ -17,17 +16,17 @@ MSA{Char}(; seq = Dict("a" => "GAAAC", "b" => "UAAAA"),
           GC = Dict("SS_cons" => "<...>")),
 ]
 
-@testset "R2R.r2r" begin
+@testset "R2R.run_r2r" begin
     showtestset()
     Tres = Tuple{Int, String, String, String}
     for msa in R2R_MSA
-        @test R2R.r2r(msa) isa Tres
+        @test R2R.run_r2r(msa) isa Tres
     end
 end
 
 @testset "R2R.plot" begin
     showtestset()
-    Tres = R2Rplot
+    Tres = R2R.Plot
     for msa in R2R_MSA
         @test R2R.plot(msa) isa Tres
     end