From 515c392e2d995aa63e7609b8e5f0ffbdba7656db Mon Sep 17 00:00:00 2001
From: Kevin Bonham <kevbonham@gmail.com>
Date: Tue, 14 Dec 2021 15:49:17 -0500
Subject: [PATCH] add metabolite feature (#124)

* add metabolite feature

* remove qualifier
---
 src/Microbiome.jl | 10 +++++-----
 src/features.jl   | 30 +++++++++++++++++++++++++++++-
 2 files changed, 34 insertions(+), 6 deletions(-)

diff --git a/src/Microbiome.jl b/src/Microbiome.jl
index a95f12f..48fc8f4 100644
--- a/src/Microbiome.jl
+++ b/src/Microbiome.jl
@@ -4,6 +4,7 @@ module Microbiome
 export MicrobiomeSample,
        Taxon,
        GeneFunction,
+       Metabolite,
        metadata,
        set!,
        unset!,
@@ -14,7 +15,10 @@ export MicrobiomeSample,
        hasrank,
        taxon,
        hastaxon,
-       genefunction
+       genefunction,
+       commonname,
+       masscharge,
+       retentiontime
 
 # EcoBase Translations
 export abundances,
@@ -76,10 +80,6 @@ using ReTest
 import Dictionaries: set!, unset!, insert!, delete!
 import Base: ==
 
-@testset "test" begin
-    @test true
-end
-
 include("ecobase.jl")
 include("samples.jl")
 include("features.jl")
diff --git a/src/features.jl b/src/features.jl
index 3e033d9..e326321 100644
--- a/src/features.jl
+++ b/src/features.jl
@@ -180,4 +180,32 @@ function genefunction(n::AbstractString)
     end
 end
 
-Base.string(f::AbstractFeature) = String(f)
\ No newline at end of file
+Base.string(f::AbstractFeature) = String(f)
+
+struct Metabolite <: AbstractFeature
+    name::String
+    commonname::Union{Missing, String}
+    mz::Union{Missing, Float64}
+    rt::Union{Missing, Float64}
+end
+
+Metabolite(n::AbstractString) = Metabolite(n, missing, missing, missing)
+
+name(m::Metabolite) = m.name
+commonname(m::Metabolite) = m.commonname
+masscharge(m::Metabolite) = m.mz
+retentiontime(m::Metabolite) = m.rt
+
+@testset "Metabolites" begin
+    m1 = Metabolite("name", "common", 1., 1.)
+    @test name(m1) == "name"
+    @test commonname(m1) == "common"
+    @test masscharge(m1) == 1
+    @test retentiontime(m1) == 1
+    m2 = Metabolite("name")
+    @test name(m2) == "name"
+    @test ismissing(commonname(m2))
+    @test ismissing(masscharge(m2))
+    @test ismissing(masscharge(m2))
+
+end
\ No newline at end of file