From 9f9d0899bdff26f936bc90e2b99ec2b395bf5071 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Fri, 30 Dec 2022 14:43:55 -0600
Subject: [PATCH] Move Insertion-related code to edits/Insertion.jl

---
 src/Edit.jl            | 32 +-------------------------------
 src/edits/Insertion.jl | 31 +++++++++++++++++++++++++++++++
 2 files changed, 32 insertions(+), 31 deletions(-)
 create mode 100644 src/edits/Insertion.jl

diff --git a/src/Edit.jl b/src/Edit.jl
index 654b6d5..9ac2012 100644
--- a/src/Edit.jl
+++ b/src/Edit.jl
@@ -1,24 +1,6 @@
 include("edits/Substitution.jl")
 include("edits/Deletion.jl")
-
-"""
-    Insertion{S <: BioSequence}
-
-Represents the insertion of a `S` into a sequence. The location of the insertion
-is stored outside the struct.
-"""
-struct Insertion{S<:BioSequence}
-    seq::S
-
-    function Insertion{S}(x::S) where {S<:BioSequence}
-        isempty(x) && error("Insertion must be at least 1 symbol")
-        return new(x)
-    end
-end
-Insertion(s::BioSequence) = Insertion{typeof(s)}(s)
-Base.length(x::Insertion) = length(x.seq)
-Base.:(==)(x::Insertion, y::Insertion) = x.seq == y.seq
-Base.hash(x::Insertion, h::UInt) = hash(Insertion, hash(x.seq, h))
+include("edits/Insertion.jl")
 
 """
     Edit{S <: BioSequence, T <: BioSymbol}
@@ -77,15 +59,3 @@ function lendiff(edit::Edit)
     x = edit.x
     return x isa Substitution ? 0 : (x isa Deletion ? -length(x) : length(x.x))
 end
-
-function _refbases(i::Insertion, reference::S, pos::UInt) where {S<:BioSequence}
-    return S([reference[pos]])
-end
-
-function _altbases(i::Insertion, reference::S, pos::UInt) where {S<:BioSequence}
-    if pos == 1
-        return S([i.seq..., reference[pos]])
-    else
-        return S([reference[pos], i.seq...])
-    end
-end
diff --git a/src/edits/Insertion.jl b/src/edits/Insertion.jl
new file mode 100644
index 0000000..bba1b25
--- /dev/null
+++ b/src/edits/Insertion.jl
@@ -0,0 +1,31 @@
+"""
+    Insertion{S <: BioSequence}
+
+Represents the insertion of a `S` into a sequence. The location of the insertion
+is stored outside the struct.
+"""
+struct Insertion{S<:BioSequence}
+    seq::S
+
+    function Insertion{S}(x::S) where {S<:BioSequence}
+        isempty(x) && error("Insertion must be at least 1 symbol")
+        return new(x)
+    end
+end
+Insertion(s::BioSequence) = Insertion{typeof(s)}(s)
+
+Base.length(x::Insertion) = length(x.seq)
+Base.:(==)(x::Insertion, y::Insertion) = x.seq == y.seq
+Base.hash(x::Insertion, h::UInt) = hash(Insertion, hash(x.seq, h))
+
+function _refbases(i::Insertion, reference::S, pos::UInt) where {S<:BioSequence}
+    return S([reference[pos]])
+end
+
+function _altbases(i::Insertion, reference::S, pos::UInt) where {S<:BioSequence}
+    if pos == 1
+        return S([i.seq..., reference[pos]])
+    else
+        return S([reference[pos], i.seq...])
+    end
+end