Add PSSM computation

src/Information/Information.jl

@@ -93,6 +93,16 @@ export  # MIToS.MSA
     # CorrectedMutualInformation
     buslje09,
     BLMI,
+    # PSSM
+    AbstractPositionSpecificMatrix,
+    PositionFrequencyMatrix,
+    position_frequency_matrix,
+    PositionSpecificProbabilityMatrix,
+    position_specific_probability_matrix,
+    PositionSpecificScoringMatrix,
+    position_specific_scoring_matrix,
+    ProfileScore,
+    score_sequence,
     # Gaps
     gap_union_percentage,
     gap_intersection_percentage,
@@ -119,5 +129,6 @@ include("Corrections.jl")
 include("CorrectedMutualInformation.jl")
 include("Gaps.jl")
 include("Externals.jl")
+include("PSSM.jl")
 
 end

src/Information/InformationMeasures.jl

@@ -191,11 +191,11 @@ function _gettablearray(
     gettablearray(table)
 end
 
-_gettablearray(table::Array{T,N}) where {T,N} = table
+_gettablearray(table::AbstractArray{T,N}) where {T,N} = table
 
 const _DOC_KL_KARG = """
 You can use the keyword argument `background` to set the background distribution. This 
-argument can take an `Array`, `Probabilities`, or `ContingencyTable` object. The background 
+argument can take an `AbstractArray`, `Probabilities`, or `ContingencyTable` object. The background 
 distribution must have the same size and alphabet as the probabilities. The default is the 
 `BLOSUM62_Pi` table. $_DOC_LOG_BASE
 """
@@ -234,9 +234,10 @@ end
 # Kullback-Leibler for MSA
 
 """
-    kullback_leibler(msa::AbstractArray{Residue}; background::Union{Array{T,N}, Probabilities{T,N,A}, ContingencyTable{T,N,A}}=BLOSUM62_Pi, base::Number=ℯ, kargs...)
+    kullback_leibler(msa::AbstractArray{Residue}; background::AbstractArray=BLOSUM62_Pi, base::Number=ℯ, rank::Int=1, kargs...)
 
 It calculates the Kullback-Leibler (KL) divergence from a multiple sequence alignment (MSA).
+Currently, `rank` must be `1`.
 $_DOC_KL_KARG The other keyword arguments are passed to the [`mapfreq`](@ref) function.
 """
 function kullback_leibler(