Merge branch 'master' into master

BioJulia · Feb 12, 2025 · 37ecff7 · 37ecff7
2 parents 7aed458 + a2e3fa0
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diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,9 @@
 # BioStructures.jl release notes
 
+## v4.3.0 - Nov 2024
+
+* Selection strings are made much faster.
+
 ## v4.2.1 - Oct 2024
 
 * Change compatibility bounds for new MetaGraphs.jl release.

diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "BioStructures"
 uuid = "de9282ab-8554-53be-b2d6-f6c222edabfc"
 authors = ["Joe G Greener <[email protected]>"]
-version = "4.2.1"
+version = "4.3.0"
 
 [deps]
 BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea"

diff --git a/src/select.jl b/src/select.jl
@@ -436,10 +436,19 @@ allselector(el) = true
 
 # Acts as a function when used within typical julia filtering functions 
 # by converting a string selection into a query call
-struct Select <: Function
-    sel::String
+struct Select{Q} <: Function
+    query_string::String
+    query::Q
 end
-(s::Select)(at) = apply_query(parse_query(s.sel), at)
+
+function Select(query_string::AbstractString) 
+    query = parse_query(query_string)
+    return Select(query_string, query)
+end
+
+(s::Select)(at) = apply_query(s.query, at)
+
+Base.show(io::IO, ::MIME"text/plain", s::Select) = print(io, """Select("$(s.query_string)")""")
 
 #
 # Parse selection string allowing interpolation in sel macro:
@@ -467,7 +476,6 @@ macro sel_str(s)
     return esc(ex)
 end
 
-
 const operators = (
     "="  => (x, y) -> isequal(x, y),
     "<"  => (x, y) -> isless(x, y),

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -942,9 +942,14 @@ end
     @test length(collectmodels(struc, sel"model 1")) == 1
     @test length(collectmodels(struc, sel"model 2")) == 0
 
-    @test_throws ArgumentError collectatoms(struc, sel"abc") # Invalid selection syntax
-    @test_throws ArgumentError collectatoms(struc, sel"index = A") # Invalid value type
-    @test_throws ArgumentError collectatoms(struc, sel"resnum C")
+    @test_throws ArgumentError collectatoms(struc, BioStructures.Select("abc")) # Invalid selection syntax
+    @test_throws ArgumentError collectatoms(struc, BioStructures.Select("index = A")) # Invalid value type
+    @test_throws ArgumentError collectatoms(struc, BioStructures.Select("resnum C"))
+
+    # Test show method for @sel_str
+    buff = IOBuffer()
+    show(buff, MIME"text/plain"(), sel"name CA and resnum 1")
+    @test String(take!(buff)) == """Select("name CA and resnum 1")"""
 end
 
 @testset "PDB reading" begin