support AbstractTrees.jl v4

Project.toml

@@ -8,7 +8,6 @@ AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
 DataAPI = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
 
 [compat]
-AbstractTrees = "0.3"
 DataAPI = "1.6"
 julia = "1.5"
 

src/Taxonomy.jl

@@ -1,6 +1,4 @@
 module Taxonomy
-
-using AbstractTrees: isempty
 using AbstractTrees
 import DataAPI,
        DataAPI.All,
@@ -11,9 +9,7 @@ export CanonicalRank,
        Lineage,
        taxid, name, rank, parent, children, lca,
        reformat, print_lineage, isdescendant, isancestor,
-       PhyloTree,
-       topolgoy,
-       children, print_tree, Leaves,
+       children, print_tree,
        All, Between, Cols,
        From, Until
 
@@ -23,6 +19,5 @@ include("database.jl")
 include("taxon.jl")
 include("lineage.jl")
 include("lca.jl")
-include("tree.jl")
 
 end

src/lineage.jl

@@ -7,8 +7,8 @@ function Lineage(taxon::Taxon)
     line = Taxon[]
     current_taxon = taxon
     push!(line,current_taxon)
-    while parent(current_taxon) !== nothing
-        current_taxon = parent(current_taxon)
+    while AbstractTrees.parent(current_taxon) !== nothing
+        current_taxon = AbstractTrees.parent(current_taxon)
         push!(line, current_taxon)
     end
     reverse!(line)
@@ -151,13 +151,13 @@ Base.show(io::IO, lineage::Lineage) = print_lineage(io, lineage)
 
 Return true if the former taxon is a descendant of the latter taxon.
 """
-
-isdescendant(descendant::Taxon, ancestor::Taxon) = ancestor in Lineage(descendant)
+# overload because native AbstractTrees.isdescendant is too slow
+AbstractTrees.isdescendant(descendant::Taxon, ancestor::Taxon) = ancestor in Lineage(descendant)
 
 """
     isancestor(ancestor::Taxon, descendant::Taxon)
 
 Return true if the former taxon is an ancestor of the latter taxon.
 """
 
-isancestor(ancestor::Taxon, descendant::Taxon) = isdescendant(descendant, ancestor)
+isancestor(ancestor::Taxon, descendant::Taxon) = AbstractTrees.isdescendant(descendant, ancestor)

src/taxon.jl

@@ -7,9 +7,41 @@ struct Taxon <: AbstractTaxon
     db::DB
 end
 
+# define Traits
+AbstractTrees.ParentLinks(::Type{Taxon}) = StoredParents()
+AbstractTrees.ChildIndexing(::Type{Taxon}) = IndexedChildren()
+AbstractTrees.NodeType(::Type{Taxon}) = HasNodeType()
+AbstractTrees.nodetype(::Type{Taxon}) = Taxon
+
+"""
+    parent(taxon::Taxon)
+
+Return the `Taxon` object that is the parent of the given `Taxon` object.
+"""
+
+function AbstractTrees.parent(taxon::Taxon)
+   parent_taxid = get(taxon.db.parents, taxon.taxid, nothing)
+   if parent_taxid === nothing
+        return nothing
+   end
+   parent = Taxon(parent_taxid, taxon.db)
+   return parent
+end
+
+"""
+    children(taxon::Taxon)
+
+Return the vector of `Taxon` objects that are children of the given `Taxon` object.
+"""
+
+function AbstractTrees.children(taxon::Taxon)
+    children_taxid = findall(isequal(taxon.taxid), taxon.db.parents)
+    children_taxon = map(x -> Taxon(x, taxon.db), children_taxid)
+    return children_taxon
+end
+
 Base.show(io::IO, taxon::Taxon) = print(io, "$(taxon.taxid) [$(String(taxon.rank))] $(taxon.name)")
 AbstractTrees.printnode(io::IO, taxon::Taxon) = print(io, taxon)
-AbstractTrees.nodetype(::Taxon) = Taxon
 
 function Taxon(taxid::Int, db::DB)
     name = db.names[taxid]
@@ -60,33 +92,6 @@ Return the taxid of the given `Taxon` object.
 
 taxid(taxon::Taxon) = taxon.taxid
 
-"""
-    parent(taxon::Taxon)
-
-Return the `Taxon` object that is the parent of the given `Taxon` object.
-"""
-
-function Base.parent(taxon::Taxon)
-   parent_taxid = get(taxon.db.parents, taxon.taxid, nothing)
-   if parent_taxid === nothing
-        return nothing
-   end
-   parent = Taxon(parent_taxid, taxon.db)
-   return parent
-end
-
-"""
-    children(taxon::Taxon)
-
-Return the vector of `Taxon` objects that are children of the given `Taxon` object.
-"""
-
-function AbstractTrees.children(taxon::Taxon)
-    children_taxid = findall(isequal(taxon.taxid), taxon.db.parents)
-    children_taxon = map(x -> Taxon(x, taxon.db), children_taxid)
-    return children_taxon
-end
-
 struct UnclassifiedTaxon <:AbstractTaxon
     name::String
     rank::Symbol

test/runtests.jl

@@ -1,4 +1,5 @@
 using Taxonomy
+using Taxonomy.AbstractTrees
 using Test
 
 db = Taxonomy.DB("db/nodes.dmp", "db/names.dmp")
@@ -18,7 +19,7 @@ db = Taxonomy.DB("db/nodes.dmp", "db/names.dmp")
 
     @test taxid(human) == human.taxid
     @test rank(human) == human.rank
-    @test parent(human) == Taxon(9605,db)
+    @test AbstractTrees.parent(human) == Taxon(9605,db)
     @test children(human) == [Taxon(741158,db), Taxon(63221,db)]
     denisova = Taxon(741158, db)
     @test children(denisova) == Taxon[]
@@ -91,11 +92,4 @@ end
     pan = Taxon(9598, db)
     @test lca([human,gorilla]) == lca(human,gorilla) == Taxon(207598, db)
     @test lca([human,gorilla,pan]) == lca(human,gorilla,pan) == Taxon(207598, db)
-end
-
-@testset "tree.jl" begin
-    human = Taxon(9606, db)
-    gorilla = Taxon(9593, db)
-    tree = topolgoy([human, gorilla])
-    @test tree.node == Taxon(207598, db)
-end
+end