Made Gene mutable and added shift

Author: kdyrhage

src/GenomicAnnotations.jl

@@ -17,6 +17,7 @@ export PointLocus, SingleNucleotide, BetweenNucleotides
 export Join, Order, Complement
 export Locus
 export eachposition
+export shift, shift!
 
 export relative_position
 

src/locus.jl

@@ -76,9 +76,7 @@ Base.show(io::IO, locus::SpanLocus{OpenLeftSpan}) = print(io, string("<", locus.
 Base.show(io::IO, locus::SpanLocus{OpenRightSpan}) = print(io, string(locus.position.start, "..", ">", locus.position.stop))
 Base.show(io::IO, locus::Join) = print(io, string("join(", join(locus.loc, ","), ")"))
 Base.show(io::IO, locus::Order) = print(io, string("order(", join(locus.loc, ","), ")"))
-function Base.show(io::IO, locus::Complement)
-    print(io, "complement(", string(locus.loc), ")")
-end
+Base.show(io::IO, locus::Complement) = print(io, "complement(", string(locus.loc), ")")
 
 
 Base.:(==)(loc1::SpanLocus{ClosedSpan}, loc2::SpanLocus{ClosedSpan}) = loc1.position == loc2.position
@@ -185,6 +183,8 @@ end
 
 Shift the position of `Locus` loc by `p`.
 """
-function shift(loc, p) 
-    
-end
+shift(p::PointLocus{T}, n) where T = PointLocus(p.position + n, T)
+shift(p::SpanLocus{T}, n) where T = SpanLocus(p.position .+ n, T)
+shift(P::Join{T}, n) where T = Join(map(p -> shift(p, n), P.loc))
+shift(P::Order{T}, n) where T = Order(map(p -> shift(p, n), P.loc))
+shift(p::Complement, n) = Complement(shift(p.loc, n))

src/record.jl

@@ -31,7 +31,7 @@ end
 Record(args...) = Record{Gene}(args...)
 
 
-struct Gene <: AbstractGene
+mutable struct Gene <: AbstractGene
     parent::Record{Gene}
     index::UInt
     locus::AbstractLocus
@@ -444,4 +444,9 @@ function locus!(gene::AbstractGene, loc::AbstractLocus)
     newgene
 end
 
-Base.isless(g1::AbstractGene, g2::AbstractGene) = ((locus(g1) == locus(g2)) && (feature(g1) == "gene" && feature(g2) != "gene")) || (locus(g1) < locus(g2))
+Base.isless(g1::AbstractGene, g2::AbstractGene) = ((locus(g1) == locus(g2)) && (feature(g1) == "gene" && feature(g2) != "gene")) || (locus(g1) < locus(g2))
+
+function shift!(gene, p)
+    setfield!(gene, :locus, shift(locus(gene), p))
+    return gene
+end

test/runtests.jl

@@ -133,6 +133,7 @@ using Test
     end
 
     @testset "Locus" begin
+        @test Locus("1..2") == Locus("1..2")
         @test locus(chr.genes[2]) < locus(chr.genes[4])
         @test locus(chr.genes[2]) == locus(chr.genes[2])
         @test iscomplement(chr.genes[2]) == false
@@ -156,6 +157,23 @@ using Test
         @test iscompound(Locus("1..10")) == false
         @test iscompound(Locus("<1..>10")) == false
         @test iscompound(Locus("1^2")) == false
+
+        @test shift(Locus("1..3"), 1) == Locus("2..4")
+        @test shift(Locus("join(1..3,7..9)"), 1) == Locus("join(2..4,8..10)")
+        @test shift(Locus("order(1..3,7..9)"), 1) == Locus("order(2..4,8..10)")
+        @test shift(Locus("complement(join(1..3,7..9))"), 1) == Locus("complement(join(2..4,8..10))")
+        @test shift(Locus("join(complement(1..3),complement(7..9))"), 1) == Locus("join(complement(2..4),complement(8..10))")
+        @test shift(Locus("1..10"), 1) == Locus("2..11")
+        @test shift(Locus("1^2"), 1) == Locus("2^3")
+
+        @test begin
+            shift!(chr.genes[2], 1)
+            locus(chr.genes[2]) == Locus("4..207")
+        end
+        @test begin
+            shift!(chr.genes[2], -1)
+            locus(chr.genes[2]) == Locus("3..206")
+        end
     end
 
     seq = dna"atgtccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattgccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagctctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaagaaccgccaatagacaacatatgtaa"