Delete AbstractQuantData

Project.toml

@@ -1,7 +1,7 @@
 name = "SphingolipidsID"
 uuid = "c1ebf20f-b457-45e9-b029-ffb3f0746310"
 authors = ["Yu-Fong Peng <[email protected]"]
-version = "0.3.0"
+version = "0.4.0"
 
 [deps]
 AnovaBase = "946dddda-6a23-4b48-8e70-8e60d9b8d680"

src/SphingolipidsID.jl

@@ -35,8 +35,8 @@ export SPDB, LIBRARY_POS, FRAGMENT_POS, ADDUCTCODE, CLASSDB,
  LossCH2O, AddO, AddC2H2O, LossCH8NO, LossC2H8NO, AddC3H5NO, AddC2H5NO, LossCH3,
 
  # Core Data structures
- CompoundSP, AnalyteSP,
- PreIS, MRM, QuantData, QCData, SerialDilution, Quantification, Project, Query,
+ CompoundSP, AnalyteSP, TransitionID,
+ PreIS, MRM, MRM!, qtMRM, qtMRM!, Quantification, Project, Query,
  # Create library/rule
  library, rule,
  # Data inputs
@@ -54,9 +54,8 @@ export SPDB, LIBRARY_POS, FRAGMENT_POS, ADDUCTCODE, CLASSDB,
  analytetable_mrm, transitiontable, concurrent_transition, write_transition, 
  read_transition, union_transition!, union_transition, diff_transition!, diff_transition,
  # Quantification
- quantification_mrm, set_quantification_mrm!, set_qcdata_mrm!, qcdata_mrm, qcdata_mrm!, 
- set_serialdilution_mrm!, serialdilution_mrm, serialdilution_mrm!, qualitytable, 
- set_quantdata_mrm!, quantdata_mrm, quantdata_mrm!,
+ quantification_mrm, set_quantification_mrm!, match, match!, quantify, quantify!, set_qc_id!, qctable, set_serialdilution!, run_serialdilution, 
+ run_serialdilution!, serialdilutiontable,
  # Utils/Query
  q!, qand, qor, qnot, spid, analyteid, transitionid, lcb, acyl, acylα, acylβ, reuse,
  new_project, allow_unknown, only_known, ncb, ndb, nox, ndbox, compound_formula, 
@@ -71,7 +70,7 @@ export SPDB, LIBRARY_POS, FRAGMENT_POS, ADDUCTCODE, CLASSDB,
  plot_rt_mw, plotlyjs, gr, histogram_transition
 
 import Base: getproperty, propertynames, show, print, isless, isequal, isempty, keys, length, iterate, getindex, view, firstindex, lastindex, sort, sort!, in,
- union, union!, intersect, setdiff, deleteat!, delete!, push!, pop!, popat!, popfirst!, reverse, reverse!, getproperty, copy, convert
+ union, union!, intersect, setdiff, deleteat!, delete!, push!, pop!, popat!, popfirst!, reverse, reverse!, getproperty, copy, convert, match
 
 """
  const SPDB
@@ -231,17 +230,13 @@ struct TransitionID
 end
 """
  AbstractData
- AbstractRawData <: AbstractData
- AbstractQuantData{T} <: AbstractData
 
 Abstract type for LC-MS data.
 """
 abstract type AbstractData end
-abstract type AbstractRawData <: AbstractData end
-abstract type AbstractQuantData{T} <: AbstractData end
 # precursor/product, ion => name, ms/mz => m/z, mw => molecular weight
 """
- PreIS <: AbstractRawData
+ PreIS <: AbstractData
 
 Precursor ion scan data.
 
@@ -269,15 +264,15 @@ Precursor ion scan data.
  * `:n`: `Int`. Minimal number of detection.
  * `:other_fn`: `Dictionary`. Stores functions for calculating other signal information.
 """
-struct PreIS <: AbstractRawData
+struct PreIS <: AbstractData
  table::Table # id, mz1, mz2_id, height, area, collision_energy, FWHM, symmetry, error, isf
  range::Vector{RealIntervals}
  mz2::Vector{Float64}
  polarity::Bool
  config::Dictionary
 end
 """
- MRM <: AbstractRawData
+ MRM <: AbstractData
 
 Multiple reaction monitoring data.
 
@@ -305,86 +300,13 @@ Multiple reaction monitoring data.
  * `:n`: `Int`. Minimal number of detection.
  * `:other_fn`: `Dictionary`. Stores functions for calculating other signal information.
 """
-struct MRM <: AbstractRawData
+struct MRM <: AbstractData
  table::Table
  mz2::Vector{Float64}
  polarity::Bool
  config::Dictionary
 end
 
-"""
- QuantData{T} <: AbstractQuantData{T}
-
-Type containing raw data and tables related to quantification. 
-
-* `raw`: raw data.
-* `table`: `AnalysisTable`, data for quantification (`table.area` or `table.height`), and quantification result (`table.estimated_concentration`).
-* `config`: `Dictionary` containing config information.
-"""
-struct QuantData{T} <: AbstractQuantData{T}
- raw::T
- table::AnalysisTable
- config::Dictionary
-end
-
-function getproperty(dt::QuantData, p::Symbol)
- if !in(p, fieldnames(QuantData)) && in(p, propertynames(getfield(dt, :table))) 
- getproperty(getfield(dt, :table), p)
- else
- getfield(dt, p)
- end
-end
-propertynames(dt::QuantData) = Tuple(unique((:raw, :table, :config, propertynames(getfield(dt, :table))...)))
-
-"""
- QCData{T} <: AbstractQuantData{T}
-
-Type for QC samples containing raw data and tables related to quantification. 
-
-* `raw`: raw data.
-* `table`: `AnalysisTable`, data for quantification (`table.area` or `table.height`), and quantification result (`table.estimated_concentration`).
-* `config`: `Dictionary` containing config information.
-"""
-struct QCData{T} <: AbstractQuantData{T}
- raw::T
- table::AnalysisTable # id, analyte, FWHM, symmetry, estimate, error, raw_id
- config::Dictionary
-end
-
-function getproperty(qc::QCData, p::Symbol)
- if !in(p, fieldnames(QCData)) && in(p, propertynames(getfield(qc, :table))) 
- getproperty(getfield(qc, :table), p)
- else
- getfield(qc, p)
- end
-end
-propertynames(qc::QCData) = Tuple(unique((:raw, :table, :config, propertynames(getfield(qc, :table))...)))
-#QCData(raw::T, table::Table, config::Dictionary) where {T <: Data} = QCData{T}(raw, table, config)
-"""
- SerialDilution{T} <: AbstractQuantData{T}
-
-Type for serial dilution samples containing raw data and calibration data. 
-
-* `raw`: raw data.
-* `batch`: `Batch` containg analyte settings and calibration curves.
-* `config`: `Dictionary` containing config information.
-"""
-struct SerialDilution{T} <: AbstractQuantData{T}
- raw::T
- batch::Batch
- config::Dictionary
-end
-
-function getproperty(sd::SerialDilution, p::Symbol)
- if p in propertynames(getfield(sd, :batch)) 
- getproperty(getfield(sd, :batch), p)
- else
- getfield(sd, p)
- end
-end
-propertynames(sd::SerialDilution) = Tuple(unique((:raw, :batch, :config, propertynames(getfield(sd, :batch))...)))
-#SerialDilution(raw::T, table::Table, level::Vector, config::Dictionary) where {T <: Data} = SerialDilution{T}(raw, table, level, config)
-
 """
  Quantification{A}
 
@@ -422,7 +344,7 @@ Type holding rt data and regression line for correcting rt from new batch (data
 This is a callable object taking a class and rt or vector of class and a vector of rt as input, and returning new rt or a vector of new rt. If the class is not in `fn`, it will return the original rt. 
 """
 struct RTCorrection
- data::AbstractRawData
+ data::AbstractData
  table::Table
  model::Dictionary
  config::Dictionary
@@ -456,7 +378,7 @@ This type is considered as `Vector{AnalyteSP}` and it supports iteration and mos
 mutable struct Project <: AbstractProject
  analyte::Vector{AnalyteSP}
  data::Vector{AbstractData}
- quantification::Quantification
+ quantification::Union{Quantification, Nothing}
  appendix::Dictionary
 end
 """
@@ -468,7 +390,7 @@ function Project(; kwargs...)
  appendix = Dictionary{Symbol, Any}(kwargs)
  get!(appendix, :anion, :acetate)
  get!(appendix, :signal, :area)
- Project(AnalyteSP[], AbstractData[], Quantification(), appendix)
+ Project(AnalyteSP[], AbstractData[], nothing, appendix)
 end
 """
  Project(qt::Quantification; kwargs...)