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first attempts at writing the serializers for the new types PhylogeneticModel and GroupBasedPhylogeneticModel #4010

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first attempts at writing the serializers for the new types PhylogeneticModel and GroupBasedPhylogeneticModel #4010

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bf3f0b2
first attempts at writing the serializers for the new types Phylogene…
mariusneu Aug 13, 2024
7f08d36
include serialization functions from AlgebraicStatistics
antonydellavecchia Aug 14, 2024
d630180
Removed used_params for both types, save_object uses functions instea…
mariusneu Aug 16, 2024
66a6681
Added functions to serialize edges of graphs
mariusneu Aug 16, 2024
6e91a31
Changed indentation from 4 to 2
mariusneu Aug 16, 2024
18bbc4d
Apply suggestions from code review: Save all polynomial rings as type…
mariusneu Aug 16, 2024
637aad8
Changed tpye of root_distribution to Vector. Dirty workaround to allo…
mariusneu Aug 16, 2024
458e28e
Resolved conflicts
mariusneu Aug 16, 2024
b3be37e
Changed serialization of Edges to a more efficient way
mariusneu Aug 21, 2024
b7ece5d
saving loading working
antonydellavecchia Aug 21, 2024
715d3d0
Some more changes in the serialization file as well as in the seriali…
mariusneu Sep 6, 2024
7ebdb16
jukes cantor model saving and loading
antonydellavecchia Sep 9, 2024
fdb6a0b
Changed documentation, removed unneccessary comments
mariusneu Sep 9, 2024
4f6cfeb
Wrote first mini test
mariusneu Sep 19, 2024
8723fc9
Wrote tests to verify serialization on object-identity level
mariusneu Sep 20, 2024
dd43585
Changed type of root_distribution entries to QQ in all models. Made t…
mariusneu Sep 27, 2024
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2 changes: 2 additions & 0 deletions experimental/AlgebraicStatistics/src/AlgebraicStatistics.jl
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Expand Up @@ -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
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41 changes: 41 additions & 0 deletions experimental/AlgebraicStatistics/src/serialization.jl
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@@ -0,0 +1,41 @@
@register_serialization_type PhylogeneticModel
@register_serialization_type GroupBasedPhylogeneticModel

function save_object(s::SerializerState, pm::PhylogeneticModel)
save_data_dict(s) do
save_object(s, graph(pm), :tree) # already implemented
save_object(s, number_states(pm), :states) # already implemented
save_object(s, probability_ring(pm), :probability_ring) # already implemented
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save_object(s, root_distribution(pm), :root_distribution) # needs to be implemented, or we change the entry type to QQFieldElem
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you can using save_typed_object here if the type isn't always know, or if your using a vector any because not all entries are the same type you'll need to use a tuple

save_object(s, transition_matrices(pm), :transition_matrices) # needs to be implemented
end
end

function save_object(s::SerializerState, pm::GroupBasedPhylogeneticModel)
save_data_dict(s) do
save_object(s, phylogenetic_model(pm), :phylomodel) # details see above
save_object(s, fourier_ring(pm), :fourier_ring) # already implemented
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save_object(s, fourier_parameters(pm), :fourier_params) # needs to be implemented
save_object(s,group_of_model(pm), :group) # already implemented
end
end


function load_object(s::DeserializerState, ::Type{<: PhylogeneticModel})
graph = load_object(s, Graph{Directed}, :tree)
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here you would need to use

Suggested change
graph = load_object(s, Graph{Directed}, :tree)
graph = load_typed_object(s, :tree)

n_states = load_object(s, Int64, :states)
prob_ring = load_object(s, QQMPolyRing, :probability_ring)
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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)
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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
14 changes: 14 additions & 0 deletions src/Serialization/Combinatorics.jl
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Expand Up @@ -5,6 +5,7 @@ using JSON
###############################################################################
@register_serialization_type Graph{Directed} "Graph{Directed}"
@register_serialization_type Graph{Undirected} "Graph{Undirected}"
@register_serialization_type Edge "Edge"

function save_object(s::SerializerState, g::Graph{T}) where T <: Union{Directed, Undirected}
smallobject = pm_object(g)
Expand All @@ -19,6 +20,19 @@ function load_object(s::DeserializerState, g::Type{Graph{T}}) where T <: Union{D
return g(smallobj)
end

function save_object(s::SerializerState, e::Edge)
save_data_dict(s) do
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this can be done using save_data_array instead, it'll make file sizes smaller

save_object(s, src(e), :source)
save_object(s, dst(e), :target)
end
end

function load_object(s::DeserializerState, e::Type{Edge})
source = load_object(s, Int64, :source)
target = load_object(s, Int64, :target)
return Edge(source, target)
end

###############################################################################
## Matroid
###############################################################################
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