Merge pull request #2 from alyst/tuple_closure

Allow tuples in ascendants()/descendants()
maximsch2 · May 11, 2017 · 3960f66 · 3960f66
2 parents 7c33e1e + aac461d
commit 3960f66
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Showing 2 changed files with 18 additions and 8 deletions.
diff --git a/src/ontology.jl b/src/ontology.jl
@@ -39,9 +39,14 @@ Base.length(ontology::Ontology) = length(ontology.terms)
 parents(ontology::Ontology, term::Term, rel::Symbol = :is_a) = ontology[relationship(term, rel)]
 children(ontology::Ontology, term::Term, rel::Symbol = :is_a) = ontology[rev_relationship(term, rel)]
 
+# FIXME use const when 0.5 compatibility is dropped
+typealias VecOrTuple{T} Union{Vector{T}, Tuple{Vararg{T}}}
+
 # return the set of all nodes of the ontology DAG that could be visited from `term`
-# node when traveling along `rel` edges using `rev` direction
-function transitive_closure{T}(ontology::Ontology, term::Term, rels::Vector{Symbol}, rev::Type{Val{T}} = Val{false})
+# node when traveling along `rels` edges using `rev` direction
+function transitive_closure{T}(ontology::Ontology, term::Term,
+                               rels::VecOrTuple{Symbol},
+                               rev::Type{Val{T}} = Val{false})
     # TODO: check if transitive & non-cyclical before doing so?
     res = Set{TermId}()
     frontier_ids = Set{TermId}((term.id,))
@@ -59,10 +64,10 @@ function transitive_closure{T}(ontology::Ontology, term::Term, rels::Vector{Symb
     return res
 end
 
-descendants(ontology::Ontology, term::Term, rels::Vector{Symbol}) = ontology[transitive_closure(ontology, term, rels, Val{true})]
-descendants(ontology::Ontology, term::Term, rel::Symbol = :is_a) = descendants(ontology, term, [rel]) 
-ancestors(ontology::Ontology, term::Term, rels::Vector{Symbol}) = ontology[transitive_closure(ontology, term, rels, Val{false})]
-ancestors(ontology::Ontology, term::Term, rel::Symbol = :is_a) = ancestors(ontology, term, [rel])
+descendants(ontology::Ontology, term::Term, rels::VecOrTuple{Symbol}) = ontology[transitive_closure(ontology, term, rels, Val{true})]
+descendants(ontology::Ontology, term::Term, rel::Symbol = :is_a) = descendants(ontology, term, (rel,))
+ancestors(ontology::Ontology, term::Term, rels::VecOrTuple{Symbol}) = ontology[transitive_closure(ontology, term, rels, Val{false})]
+ancestors(ontology::Ontology, term::Term, rel::Symbol = :is_a) = ancestors(ontology, term, (rel,))
 
 function satisfies(ontology::Ontology, term1::Term, rel::Symbol, term2::Term)
     (term1 == term2) && return true # TODO: should check if relationship is is_reflexive

diff --git a/test/test_graph.jl b/test/test_graph.jl
@@ -3,7 +3,7 @@ function test_isa(onto, term1, term2)
     @test !is_a(onto, term2, term1)
 end
 
-@testset "is_a relationship tests" begin
+@testset "relationship tests" begin
     GO = OBOParse.load("$testdir/data/go_mini.obo", "GO")
 
     term1 = gettermbyid(GO, 1)
@@ -32,9 +32,14 @@ end
 
     @test ancestors(GO, term1) == [term2]
     @test Set(ancestors(GO, term5)) == Set([term2, term4])
+    @test Set(ancestors(GO, term6, :part_of)) == Set([term5])
+    @test Set(ancestors(GO, term6, (:is_a, :part_of))) == Set([term2, term4, term5])
+    @test Set(ancestors(GO, term6, [:is_a, :part_of])) == Set([term2, term4, term5])
 
     @test Set(descendants(GO, term2)) == Set([term1, term4, term5])
     @test descendants(GO, term5) == []
-
+
+    @test Set(descendants(GO, term5, :part_of)) == Set([term6])
+    @test Set(descendants(GO, term2, (:is_a, :part_of))) == Set([term1, term4, term5, term6])
     @test Set(descendants(GO, term2, [:is_a, :part_of])) == Set([term1, term4, term5, term6])
 end