Rename abstract types

scripts/custom_modules_example.jl

@@ -17,15 +17,15 @@ fitness_dict = Dict([
     (['A', 'D', 'A', 'A'], 3.0),
     (['A', 'E', 'A', 'A'], 0.0),
 ])
-struct DummyScreening <: DESilico.Screening end
+struct DummyScreening <: DESilico.AbstractScreening end
 (::DummyScreening)(sequence::Vector{Char}) = fitness_dict[sequence]
 (s::DummyScreening)(sequences::AbstractVector{Vector{Char}}) = map(sequence -> s(sequence), sequences)
 
 # We define a custom SelectionStrategy.
 # A custom `SelectionStrategy` structure should implement a method with signature
 # `(::CustomSelectionStrategy)(sequence_fitness_pairs::AbstractVector{Variant})`
 # which returns a vector of the selected sequences as a subtype of `AbstractVector{Vector{Char}}`.
-struct DummySelectionStrategy <: DESilico.SelectionStrategy end
+struct DummySelectionStrategy <: DESilico.AbstractSelectionStrategy end
 function (::DummySelectionStrategy)(variants::Vector{Variant})
     [variants[1].sequence]
 end
@@ -34,7 +34,7 @@ end
 # A custom `Mutagenesis` structure should implement a method with signature
 # `(::CustomMutagenesis)(parents::AbstractVector{Vector{Char}})`
 # which returns a vector of the created sequences as a subtype of `AbstractVector{Vector{Char}}`.
-struct DummyMutagenesis <: DESilico.Mutagenesis end
+struct DummyMutagenesis <: DESilico.AbstractMutagenesis end
 function (::DummyMutagenesis)(parents::Vector{Vector{Char}})
     new_parent = copy(parents[1])
     new_parent[2] = new_parent[2] + 1

scripts/de_sandbox.jl

@@ -1,8 +1,8 @@
 """
 A simple de!() sandbox.
 
-Select different DE modules (Screening, SelectionStrategy, Mutagenesis) and `initial_population`
-to try different modules.
+Select different DE modules (`AbstractScreening`, `AbstractSelectionStrategy`, `AbstractMutagenesis` implementations)
+and `initial_population` to try different modules.
 """
 
 # GB1 data from

scripts/profiling.jl

@@ -3,8 +3,8 @@ include("de_sandbox.jl")
 """
 A simple function for profiling `de!()`.
 
-Select different DE modules (`Screening`, `SelectionStrategy`, `Mutagenesis`) and `initial_population`
-in `de_sandbox.jl` to profile different modules.
+Select different DE modules (`AbstractScreening`, `AbstractSelectionStrategy`, `AbstractMutagenesis` implementations)
+and `initial_population` in `de_sandbox.jl` to profile different modules.
 """
 function run_de(n::Int)
     for _ in 1:n
@@ -22,8 +22,8 @@ end
 """
 A simple function for profiling `de_evaluation()`.
 
-Select different DE modules (`Screening`, `SelectionStrategy`, `Mutagenesis`) and `initial_population`
-in `de_sandbox.jl` to profile different modules.
+Select different DE modules (`AbstractScreening`, `AbstractSelectionStrategy`, `AbstractMutagenesis` implementations)
+and `initial_population` in `de_sandbox.jl` to profile different modules.
 """
 function run_de_evaluation(n::Int)
     de_evaluation(

src/de.jl

@@ -7,9 +7,9 @@ Perform directed `n_iterations` of directed evolution and save results into `seq
 - `sequence_space::SequenceSpace`: Maintains the current population of mutants and library of screened variants.
 
 # Keywords
-- `screening::Screening`: Assigns fitness value to a sequence.
-- `selection_strategy::SelectionStrategy`: Defines the algorithm used to select new parents from a pool of screened variants.
-- `mutagenesis:Mutagenesis`: Defines the algorithm used to create new mutants from current population.
+- `screening::AbstractScreening`: Assigns fitness value to a sequence.
+- `selection_strategy::AbstractSelectionStrategy`: Defines the algorithm used to select new parents from a pool of screened variants.
+- `mutagenesis::AbstractMutagenesis`: Defines the algorithm used to create new mutants from current population.
 - `n_iterations::Integer=1`: Specifies the number of iteration of DE. Has to be greater than 0.
 
 # Examples
@@ -19,9 +19,9 @@ See 'https://github.com/soldamatlab/DESilico.jl/blob/master/scripts/custom_modul
 """
 function de!(
     sequence_space::SequenceSpace;
-    screening::Screening,
-    selection_strategy::SelectionStrategy,
-    mutagenesis::Mutagenesis,
+    screening::AbstractScreening,
+    selection_strategy::AbstractSelectionStrategy,
+    mutagenesis::AbstractMutagenesis,
     n_iterations::Int=1,
 )
     @assert n_iterations > 0
@@ -33,7 +33,7 @@ function de!(
     end
 end
 
-function screeen_mutants(sequences::AbstractVector{Vector{Char}}, screening::Screening)
+function screeen_mutants(sequences::AbstractVector{Vector{Char}}, screening::AbstractScreening)
     fitness = screening(sequences)
     map((s, f) -> Variant(s, f), sequences, fitness)
 end

src/de_evaluation.jl

@@ -9,18 +9,18 @@ Returns the top fitness obtained in each run as a `Vector{Float64}`.
 - `runs::Int`: Number of times `de!()` will be called.
 
 # Keywords
-- `screening::Screening`: Assigns fitness value to a sequence.
-- `selection_strategy::SelectionStrategy`: Defines the algorithm used to select new parents from a pool of screened variants.
-- `mutagenesis:Mutagenesis`: Defines the algorithm used to create new mutants from current population.
+- `screening::AbstractScreening`: Assigns fitness value to a sequence.
+- `selection_strategy::AbstractSelectionStrategy`: Defines the algorithm used to select new parents from a pool of screened variants.
+- `mutagenesis::AbstractMutagenesis`: Defines the algorithm used to create new mutants from current population.
 - `n_iterations::Integer`: Specifies the number of iteration of `de!()`.
 - `parallel::Bool=false`: If true, the calls of `de!()` will be run in parallel.
 """
 function de_evaluation(
     sequence_space::SequenceSpace,
     runs::Int;
-    screening::Screening,
-    selection_strategy::SelectionStrategy,
-    mutagenesis::Mutagenesis,
+    screening::AbstractScreening,
+    selection_strategy::AbstractSelectionStrategy,
+    mutagenesis::AbstractMutagenesis,
     n_iterations::Int,
     parallel::Bool=false,
 )
@@ -45,17 +45,17 @@ Returns the top fitness obtained in each run as a `Vector{Float64}`.
 - `starting_variants::AbstractVector{Variant}`: Each of the `starting_variants` will be used as the sole initial parent in one run of `de!()`.
 
 # Keywords
-- `screening::Screening`: Assigns fitness value to a sequence.
-- `selection_strategy::SelectionStrategy`: Defines the algorithm used to select new parents from a pool of screened variants.
-- `mutagenesis:Mutagenesis`: Defines the algorithm used to create new mutants from current population.
+- `screening::AbstractScreening`: Assigns fitness value to a sequence.
+- `selection_strategy::AbstractSelectionStrategy`: Defines the algorithm used to select new parents from a pool of screened variants.
+- `mutagenesis::AbstractMutagenesis`: Defines the algorithm used to create new mutants from current population.
 - `n_iterations::Integer`: Specifies the number of iteration of `de!()`.
 - `parallel::Bool=false`: If true, the calls of `de!()` will be run in parallel.
 """
 function de_evaluation(
     starting_variants::AbstractVector{Variant};
-    screening::Screening,
-    selection_strategy::SelectionStrategy,
-    mutagenesis::Mutagenesis,
+    screening::AbstractScreening,
+    selection_strategy::AbstractSelectionStrategy,
+    mutagenesis::AbstractMutagenesis,
     n_iterations::Int,
     parallel::Bool=false,
 )
@@ -74,9 +74,9 @@ function _run_de_sequential!(
     results::Vector{Float64},
     get_sequence_space::Function,
     runs::Int;
-    screening::Screening,
-    selection_strategy::SelectionStrategy,
-    mutagenesis::Mutagenesis,
+    screening::AbstractScreening,
+    selection_strategy::AbstractSelectionStrategy,
+    mutagenesis::AbstractMutagenesis,
     n_iterations::Int,
 )
     for r = 1:runs
@@ -96,9 +96,9 @@ function _run_de_parallel!(
     results::Vector{Float64},
     get_sequence_space::Function,
     runs::Int;
-    screening::Screening,
-    selection_strategy::SelectionStrategy,
-    mutagenesis::Mutagenesis,
+    screening::AbstractScreening,
+    selection_strategy::AbstractSelectionStrategy,
+    mutagenesis::AbstractMutagenesis,
     n_iterations::Int,
 )
     Threads.@threads :static for r = 1:runs

src/mutagenesis/recombination.jl

@@ -3,7 +3,7 @@ Creates all recombinations of parents sequences.
 
     Recombination()
 """
-struct Recombination <: Mutagenesis end
+struct Recombination <: AbstractMutagenesis end
 
 function (m::Recombination)(parents::AbstractVector{Vector{Char}})
     @assert DESilico.same_length_sequences(parents)

src/mutagenesis/single_mutation.jl

@@ -6,7 +6,7 @@ Creates all single-symbol mutants for each parent sequence.
 # Arguments
 `alphabet::Set{Char}`: Contains the characters which will be used to create mutants.
 """
-struct SingleMutation <: Mutagenesis
+struct SingleMutation <: AbstractMutagenesis
     alphabet::Set{Char}
 end
 

src/screening/dict_screening.jl

@@ -30,7 +30,7 @@ Constructs `DictScreening` from a '.xlsx' file.
 - `fitness_column::String`: Label in the first row of the column containing the fitness values. Default is "Fitness".
 - `default::Float64`: If present, the constructor returns `DictScreeningWithDefault` instead.
 """
-struct DictScreening <: Screening
+struct DictScreening <: AbstractScreening
     fitness_dict::Dict{Vector{Char},Float64}
 end
 
@@ -84,7 +84,7 @@ Constructs `DictScreeningWithDefault` via `DictScreening` constructors by adding
     `default::Float64`: Default fitness value returned for sequences not present in `fitness_dict`.
     See `DictScreening`.
 """
-struct DictScreeningWithDefault <: Screening
+struct DictScreeningWithDefault <: AbstractScreening
     fitness_dict::Dict{Vector{Char},Float64}
     default::Float64
 end

src/selection_strategy/sampling_select.jl

@@ -11,7 +11,7 @@ Randomly selects `k` sequences.
 # Keywords
 - `weighting::Float64`: Adding this argument to the constructer returns a `WeightedSamplingSelect` instead.
 """
-struct SamplingSelect <: SelectionStrategy
+struct SamplingSelect <: AbstractSelectionStrategy
     k::Int
 
     SamplingSelect(k::Int) = k > 0 ? new(k) : throw(ArgumentError("`k` needs to be greater than 0"))
@@ -40,7 +40,7 @@ or via `SamplingSelect` constructor by providing the `weighting` keyword:
 
 - `weighting::Float64`: Defines the influence of fitness values on the weighted probabilities on scale <0,1).
 """
-struct WeightedSamplingSelect <: SelectionStrategy
+struct WeightedSamplingSelect <: AbstractSelectionStrategy
     k::Int
     weighting::Real
 

src/selection_strategy/top_k.jl

@@ -6,7 +6,7 @@ Selects `k` sequences with the highest fitness.
 # Arguments
 - `k::Int`: Defines the number of sequences which will be selected.
 """
-struct TopK <: SelectionStrategy
+struct TopK <: AbstractSelectionStrategy
     k::Int
     TopK(k::Int) = k > 0 ? new(k) : throw(ArgumentError("`k` needs to be greater than 0"))
 end

src/types/types.jl

@@ -7,9 +7,9 @@ Structures derived from this type have to implement the following method:
 This method should return vector of selected sequences as a subtype of `AbstractVector{Vector{Char}}`.
 
 Structures derived from this type can have a parameter `k` which specifies the number of sequences that should be selected.
-This can be useful with some Mutagenesis implementations that require a specific amount of selected sequences as input.
+This can be useful with some AbstractMutagenesis implementations that require a specific amount of selected sequences as input.
 """
-abstract type SelectionStrategy end
+abstract type AbstractSelectionStrategy end
 
 """
 Specifies the algorithm used to create new sequences from a library of parent sequences.
@@ -25,7 +25,7 @@ This can be useful with some SelectionStrategy implementations that require a sp
 
 Structures derived from this type can have a parameter `alphabet` which specifies the allowed characters in the sequences.
 """
-abstract type Mutagenesis end
+abstract type AbstractMutagenesis end
 
 """
 Specifies the oracle used to evaluate fitness of a sequence.
@@ -34,4 +34,4 @@ Structures derived from this type have to implement the following method:
 `(::CustomScreening)(sequences::AbstractVector{Vector{Char}})`
 This method should return the sequences' fitness values as a subtype of `AbstarctVector{Float64}`.
 """
-abstract type Screening end
+abstract type AbstractScreening end

test/unit/de.jl

@@ -9,18 +9,18 @@
         (['A', 'D', 'A', 'A'], 3.0),
         (['A', 'E', 'A', 'A'], 0.0),
     ])
-    struct DummyScreening <: DESilico.Screening end
+    struct DummyScreening <: DESilico.AbstractScreening end
     (::DummyScreening)(sequence::Vector{Char}) = fitness_dict[sequence]
     (s::DummyScreening)(sequences::AbstractVector{Vector{Char}}) = map(sequence -> s(sequence), sequences)
 
     # Define a custom SelectionStrategy
-    struct DummySelectionStrategy <: DESilico.SelectionStrategy end
+    struct DummySelectionStrategy <: DESilico.AbstractSelectionStrategy end
     function (::DummySelectionStrategy)(variants::Vector{Variant})
         [variants[1].sequence]
     end
 
     # Define a custom Mutagenesis
-    struct DummyMutagenesis <: DESilico.Mutagenesis end
+    struct DummyMutagenesis <: DESilico.AbstractMutagenesis end
     function (::DummyMutagenesis)(parents::Vector{Vector{Char}})
         new_parent = copy(parents[1])
         new_parent[2] = new_parent[2] + 1