Merge pull request #28 from LCSB-BioCore/mk-associations

src/readsbml.jl

@@ -51,6 +51,38 @@ getNotes(x::VPtr)::Maybe{String} = getOptionalString(x, :SBase_getNotesString)
 getAnnotation(x::VPtr)::Maybe{String} = getOptionalString(x, :SBase_getAnnotationString)
 
 """
+    function getAssociation(x::VPtr)::GeneProductAssociation
+
+Convert a pointer to SBML `FbcAssociation_t` to the `GeneProductAssociation`
+tree structure.
+"""
+function getAssociation(x::VPtr)::GeneProductAssociation
+    # libsbml C API is currently missing functions to check this in a normal
+    # way, so we use a bit of a hack.
+    typecode = ccall(sbml(:SBase_getTypeCode), Cint, (VPtr,), x)
+    if typecode == 808 # SBML_FBC_GENEPRODUCTREF
+        return GPARef(
+            unsafe_string(ccall(sbml(:GeneProductRef_getGeneProduct), Cstring, (VPtr,), x)),
+        )
+    elseif typecode == 809 # SBML_FBC_AND
+        return GPAAnd([
+            getAssociation(
+                ccall(sbml(:FbcAnd_getAssociation), VPtr, (VPtr, Cuint), x, i - 1),
+            ) for i = 1:ccall(sbml(:FbcAnd_getNumAssociations), Cuint, (VPtr,), x)
+        ])
+    elseif typecode == 810 # SBML_FBC_OR
+        return GPAOr([
+            getAssociation(
+                ccall(sbml(:FbcOr_getAssociation), VPtr, (VPtr, Cuint), x, i - 1),
+            ) for i = 1:ccall(sbml(:FbcOr_getNumAssociations), Cuint, (VPtr,), x)
+        ])
+    else
+        throw(ErrorException("Unsupported FbcAssociation type"))
+    end
+end
+
+
+""""
     function extractModel(mdl::VPtr)::Model
 
 Take the `SBMLModel_t` pointer and extract all information required to make a
@@ -152,7 +184,6 @@ function extractModel(mdl::VPtr)::Model
                 mdl_fbc,
                 i - 1,
             )
-
             for j = 1:ccall(sbml(:Objective_getNumFluxObjectives), Cuint, (VPtr,), o)
                 fo = ccall(sbml(:Objective_getFluxObjective), VPtr, (VPtr, Cuint), o, j - 1)
                 objectives_fbc[unsafe_string(
@@ -231,12 +262,28 @@ function extractModel(mdl::VPtr)::Model
             add_stoi(sr, 1)
         end
 
+        association = nothing
+        if re_fbc != C_NULL
+            gpa = ccall(
+                sbml(:FbcReactionPlugin_getGeneProductAssociation),
+                VPtr,
+                (VPtr,),
+                re_fbc,
+            )
+            if gpa != C_NULL
+                a = ccall(sbml(:GeneProductAssociation_getAssociation), VPtr, (VPtr,), gpa)
+                a != C_NULL
+                association = getAssociation(a)
+            end
+        end
+
         reid = unsafe_string(ccall(sbml(:Reaction_getId), Cstring, (VPtr,), re))
         reactions[reid] = Reaction(
             stoi,
             lb,
             ub,
             haskey(objectives_fbc, reid) ? objectives_fbc[reid] : oc,
+            association,
             getNotes(re),
             getAnnotation(re),
         )

src/structs.jl

@@ -28,6 +28,34 @@ struct UnitPart
     UnitPart(k, e, s, m) = new(k, e, s, m)
 end
 
+
+"""
+Abstract type for all kinds of gene product associations
+"""
+abstract type GeneProductAssociation end
+
+"""
+Gene product reference in the association expression
+"""
+struct GPARef <: GeneProductAssociation
+    gene_product::String
+end
+
+"""
+Boolean binary "and" in the association expression
+"""
+struct GPAAnd <: GeneProductAssociation
+    terms::Vector{GeneProductAssociation}
+end
+
+"""
+Boolean binary "or" in the association expression
+"""
+struct GPAOr <: GeneProductAssociation
+    terms::Vector{GeneProductAssociation}
+end
+
+
 """
 Reaction with stoichiometry that assigns reactants and products their relative
 consumption/production rates (accessible in field `stoichiometry`), lower/upper
@@ -39,9 +67,10 @@ struct Reaction
     lb::Tuple{Float64,String}
     ub::Tuple{Float64,String}
     oc::Float64
+    gene_product_association::Maybe{GeneProductAssociation}
     notes::Maybe{String}
     annotation::Maybe{String}
-    Reaction(s, l, u, o, n = nothing, a = nothing) = new(s, l, u, o, n, a)
+    Reaction(s, l, u, o, as, n = nothing, an = nothing) = new(s, l, u, o, as, n, an)
 end
 
 """