Merge pull request #522 from LCSB-BioCore/mk-grr-naming

naming & tests for grr vector function
LCSB-BioCore · Nov 22, 2021 · 94c4361 · 94c4361
2 parents 87a7db0 + cfc1b5d
commit 94c4361
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Showing 3 changed files with 20 additions and 6 deletions.
diff --git a/src/base/types/CoreModel.jl b/src/base/types/CoreModel.jl
@@ -103,11 +103,12 @@ reaction_stoichiometry(m::CoreModel, ridx)::Dict{String,Float64} =
     Dict(m.mets[k] => v for (k, v) in zip(findnz(m.S[:, ridx])...))
 
 """
-    grrs(a::CoreModel)::Vector{Maybe{GeneAssociation}}
+    reaction_gene_association_vec(model::CoreModel)::Vector{Maybe{GeneAssociation}}
 
-Get the gene associations in a [`CoreModel`](@ref).
+Retrieve a vector of all gene associations in a [`CoreModel`](@ref), in the
+same order as `reactions(model)`.
 """
-grrs(a::CoreModel)::Vector{Maybe{GeneAssociation}} = a.grrs
+reaction_gene_association_vec(model::CoreModel)::Vector{Maybe{GeneAssociation}} = model.grrs
 
 """
     reaction_gene_association(model::CoreModel, ridx::Int)::Maybe{GeneAssociation}

diff --git a/src/base/types/CoreModelCoupled.jl b/src/base/types/CoreModelCoupled.jl
@@ -109,11 +109,13 @@ function reaction_stoichiometry(m::CoreModelCoupled, ridx)::Dict{String,Float64}
 end
 
 """
-    grrs(a::CoreModelCoupled)::Vector{Maybe{GeneAssociation}}
+    reaction_gene_association_vec(model::CoreModelCoupled)::Vector{Maybe{GeneAssociation}}
 
-Get the gene associations in a [`CoreModelCoupled`](@ref).
+Retrieve a vector of gene associations in a [`CoreModelCoupled`](@ref), in the
+same order as `reactions(model)`.
 """
-grrs(a::CoreModelCoupled)::Vector{Maybe{GeneAssociation}} = a.lm.grrs
+reaction_gene_association_vec(model::CoreModelCoupled)::Vector{Maybe{GeneAssociation}} =
+    reaction_gene_association_vec(model.lm)
 
 """
     reaction_gene_association(model::CoreModelCoupled, ridx::Int)::Maybe{GeneAssociation}

diff --git a/test/base/types/CoreModelCoupled.jl b/test/base/types/CoreModelCoupled.jl
@@ -17,4 +17,15 @@ end
 
     @test reaction_gene_association(sm, reactions(sm)[1]) ==
           reaction_gene_association(cm, reactions(sm)[1])
+
+    @test reaction_gene_association_vec(cm)[1:3] == [
+        [["b3916"], ["b1723"]],
+        [
+            ["b0902", "b0903", "b2579"],
+            ["b0902", "b0903"],
+            ["b0902", "b3114"],
+            ["b3951", "b3952"],
+        ],
+        [["b4025"]],
+    ]
 end