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get rid of whitespace
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antonydellavecchia committed Feb 21, 2024
1 parent 902aa47 commit af6aa79
Showing 1 changed file with 6 additions and 8 deletions.
14 changes: 6 additions & 8 deletions src/Combinatorics/PhylogeneticTrees.jl
Original file line number Diff line number Diff line change
Expand Up @@ -9,11 +9,11 @@ end
@doc raw"""
phylogenetic_tree(T::Type{<:Union{Float64, QQFieldElem}}, newick::String)
Constructs a phylogenetic tree with Newick representation `newick`. `T` indicates
Constructs a phylogenetic tree with Newick representation `newick`. `T` indicates
the numerical type of the edge lengths.
# Examples
Make a phylogenetic tree with 4 leaves from its Newick representation and print
Make a phylogenetic tree with 4 leaves from its Newick representation and print
its taxa and cophenetic matrix.
```jldoctest
julia> phylo_t = phylogenetic_tree(Float64, "((H:3,(C:1,B:1):2):1,G:4);");
Expand All @@ -38,7 +38,7 @@ function phylogenetic_tree(T::Type{<:Union{Float64, QQFieldElem}}, newick::Strin

# load graph properties
pm_ptree.ADJACENCY

return PhylogeneticTree{T}(pm_ptree)
end

Expand Down Expand Up @@ -91,9 +91,8 @@ end
@doc raw"""
adjacency_tree(ptree::PhylogeneticTree)
Returns the underlying graph of the phylogenetic tree ptree.
Returns the underlying graph of the phylogenetic tree `ptree`.
# Examples
Make a phylogenetic tree with given Newick format and print its underlying graph.
```jldoctest
Expand Down Expand Up @@ -267,9 +266,9 @@ function tropical_median_consensus(arr::Vector{PhylogeneticTree{T}}) where {T <:

phylo_type = Polymake.bigobject_type(pm_object(first(arr)))
pm_arr = Polymake.Array{Polymake.BigObject}(phylo_type, n)

pm_arr .= pm_object.(arr)

pm_cons_tree = Polymake.tropical.tropical_median_consensus(pm_arr)
return PhylogeneticTree{T}(pm_cons_tree)
end
Expand Down Expand Up @@ -301,4 +300,3 @@ julia> newick(tc)
function tropical_median_consensus(trees::Vararg{PhylogeneticTree, N}) where {N}
return tropical_median_consensus(collect(trees))
end

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