first attempts at writing the serializers for the new types PhylogeneticModel and GroupBasedPhylogeneticModel

experimental/AlgebraicStatistics/src/AlgebraicStatistics.jl

@@ -6,6 +6,8 @@ include("PhylogeneticModels.jl")
 include("PhylogeneticAuxiliary.jl")
 include("PhylogeneticParametrization.jl")
 
+include("serialization.jl")
+
 #export models
 export cavender_farris_neyman_model
 export jukes_cantor_model

experimental/AlgebraicStatistics/src/serialization.jl

@@ -0,0 +1,58 @@
+@register_serialization_type PhylogeneticModel uses_params 
+@register_serialization_type GroupBasedPhylogeneticModel uses_params 
+
+function save_object(s::SerializerState, pm::PhylogeneticModel)
+    save_data_dict(s) do 
+        save_object(s, pm.graph, :tree) # already implemented 
+        save_object(s, pm.n_states, :states) # already implemented 
+        save_object(s, pm.prob_ring, :probability_ring) # already implemented
+        save_object(s, pm.root_distr, :root_distribution) # needs to be implemented, or we change the entry type to QQFieldElem
+        save_object(s, pm.trans_matrices, :transition_matrices) # needs to be implemented
+    end
+end
+
+function save_object(s::SerializerState, pm::GroupBasedPhylogeneticModel)
+    save_data_dict(s) do
+        save_object(s,pm.phylo_model,:phylomodel) # details see above
+        save_object(s, pm.fourier_ring, :fourier_ring) # already implemented
+        save_object(s,pm.fourier_params,:fourier_params) # needs to be implemented
+        save_object(s,pm.group,:group) # already implemented
+    end
+end
+
+
+function load_object(s::DeserializerState, ::Type{<: PhylogeneticModel})
+    graph = load_object(s, Graph{Directed}, :tree)
+    n_states = load_object(s, Int64, :states)
+    prob_ring = load_object(s, QQMPolyRing, :probability_ring)
+    root_distr = load_object(s, Vector{Any}, :root_distribution)
+    trans_matrices = load_object(s, Dict{Edge, MatElem{QQMPolyRingElem}}, :trans_matrices)
+
+    return PhylogeneticModel(graph, n_states, prob_ring, root_distr, trans_matrices)
+end 
+
+function load_object(s::DeserializerState, ::Type{<: GroupBasedPhylogeneticModel})
+    phylomodel = load_object(s, PhylogeneticModel, :phylomodel)
+    fourier_ring = load_object(s, QQMPolyRing, :fourier_ring)
+    fourier_params = load_object(s, Dict{Edge, Vector{QQMPolyRingElem}} , :fourier_params)
+    group = load_object(s, Vector{FinGenAbGroupElem}, :group)
+
+    return GroupBasedPhylogeneticModel(phylomodel, fourier_ring, fourier_params, group)
+end
+
+### Structure of both Types: ###
+
+#= struct PhylogeneticModel
+  graph::Graph{Directed}
+  n_states::Int
+  prob_ring::MPolyRing{QQFieldElem}
+  root_distr::Vector{Any}
+  trans_matrices::Dict{Edge, MatElem{QQMPolyRingElem}}
+end
+
+struct GroupBasedPhylogeneticModel
+  phylo_model::PhylogeneticModel
+  fourier_ring::MPolyRing{QQFieldElem}
+  fourier_params::Dict{Edge, Vector{QQMPolyRingElem}}
+  group::Vector{FinGenAbGroupElem}
+end =#