From 1bbb85153c176ff1fb4c909136b0e8ea8369de9e Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Wed, 20 Jul 2022 17:13:06 -0500
Subject: [PATCH] Add constructor for Variant based on Variations

A Variant is a collection of Variations, right? Unfortunately there was no
way to convert a collection of Variations into a Variant, so I added one.
---
 src/SequenceVariation.jl | 7 +++++++
 test/runtests.jl         | 7 +++++++
 2 files changed, 14 insertions(+)

diff --git a/src/SequenceVariation.jl b/src/SequenceVariation.jl
index 0237a15..fb752c8 100644
--- a/src/SequenceVariation.jl
+++ b/src/SequenceVariation.jl
@@ -211,6 +211,8 @@ function Variant(ref::S, edits::Vector{Edit{S, T}}) where {S<:BioSequence, T<:Bi
     Variant{S, T}(ref, edits)
 end
 
+
+
 function Base.show(io::IO, x::Variant)
     n = length(x.edits)
     print(io, summary(x), " with $n edit$(n > 1 ? "s" : ""):")
@@ -367,6 +369,11 @@ function Variation(ref::S, edit::AbstractString) where {S<:BioSequence}
     return Variation{S,T}(ref, e)
 end
 
+function Variant(ref::S, vars::Vector{Variation{S,T}}) where {S<:BioSequence, T<:BioSymbol}
+    edits = edit.(vars)
+    return Variant{S, T}(ref, edits)
+end
+
 reference(v::Variation) = v.ref
 edit(v::Variation) = v.edit
 mutation(v::Variation) = mutation(edit(v))
diff --git a/test/runtests.jl b/test/runtests.jl
index 9982a55..c1eeb37 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -35,6 +35,13 @@ seq1 = ungap!(dna"--ATGCGTGTTAGCAAC--TTATCGCG")
 seq2 = ungap!(dna"TGATGCGTGT-AGCAACACTTATAGCG")
 var = Variant(align(seq1, seq2))
 
+@testset "VariantRoundtrip" begin
+    for v in variations(var)
+        @test v in var
+        @test v in Variant(seq2, [v])
+    end
+end
+
 @testset "VariationPosition" begin
     refseq = dna"ACAACTTTATCT"
     mutseq = dna"ACATCTTTATCT"