isatabr: Implementation for the ISA Abstract Model

### ISA Class ----
#' S4 Class ISA, initialization method
#'
#' An S4 class to store information from an ISA-Tab data set, including an
#' investigation file, one or more study files, and one or more assay files for
#' each study file.
#'
#' @slot path A length-one character vector containing the path to the ISA-Tab
#' dataset.
#' @slot iFileName A length-one character vector containing the investigation
#' filename (by definition starting with **i_** and ending at **.txt**).
#' @slot oSR A data.frame containing the "ONTOLOGY SOURCE REFERENCE" section of
#' the investigation file.
#' @slot invest A data.frame containing the "INVESTIGATION" section of
#' the investigation file.
#' @slot iPubs A data.frame containing the "INVESTIGATION PUBLICATIONS" section
#' of the investigation file.
#' @slot iContacts A data.frame containing the "INVESTIGATION CONTACTS" section
#' of the investigation file.
#' @slot study A list of data.frames containing the "STUDY" sections of the
#' investigation file. Each study has its own section and the study identifier
#' is used to name each element in the list.
#' @slot sDD A list of data.frames containing the "STUDY DESIGN DESCRIPTORS"
#' sections of the investigation file. Each study has its own section and the
#' study identifier is used to name each element in the list.
#' @slot sPubs A list of data.frames containing the "STUDY PUBLICATIONS"
#' sections of the investigation file. Each study has its own section and the
#' study identifier is used to name each element in the list.
#' @slot sFacts A list of data.frames containing the "STUDY FACTORS" sections of
#' the investigation file. Each study has its own section and the study
#' identifier is used to name each element in the list.
#' @slot sAssays A list of data.frames containing the "STUDY ASSAYS" sections of
#' the investigation file. Each study has its own section and the study
#' identifier is used to name each element in the list.
#' @slot sProts A list of data.frames containing the "STUDY PROTOCOLS" sections
#' of the investigation file. Each study has its own section and he study
#' identifier is used to name each element in the list.
#' @slot sContacts A list of data.frames containing the "STUDY CONTACTS"
#' sections of the investigation file. Each study has its own section and the
#' study identifier is used to name each element in the list.
#' @slot sFiles A list of data.frames containing the "Study Files", containing
#' the contents of the Study Table files belonging to the studies in the
#' investigation. Each study has one Study Table file.
#' @slot aFiles A list of data.frames containing the "Assay Files", containing
#' the contents of the Assay Table files belonging to the studies in the
#' investigation. Each study can have multiple Assay Table files. Each element
#' of the list is named by the Assay File Name.
#'
#' @keywords classes
#' @rdname ISA-class
#' @exportClass ISA
ISA <- setClass(Class = "ISA",
                slots = c(
                  path = "character",
                  iFileName = "character",
                  oSR = "data.frame",
                  invest = "data.frame",
                  iPubs = "data.frame",
                  iContacts = "data.frame",
                  study = "list",
                  sDD = "list",
                  sPubs = "list",
                  sFacts = "list",
                  sAssays = "list",
                  sProts = "list",
                  sContacts = "list",
                  sFiles = "list",
                  aFiles = "list"
                )
)

### assayTab Class ----
#' S4 Class assayTab, initialization methods
#'
#' An S4 class to store information from an assay files.
#'
#' @slot path A length-one character vector containing the path to the ISA-Tab
#' data set.
#' @slot sFileName A length-one character vector containing the study
#' file name (by definition starting with **s_** and ending at **.txt**).
#' @slot sIdentifier A length-one character vector containing the study
#' identifier.
#' @slot aFileName A length-one character vector containing the assay
#' file name (by definition starting with **a_** and ending at **.txt**).
#' @slot aFile A data.frame containing the contents of the Assay Table file.
#' @slot aTechType A length-one character vector containing the assay
#' technology type.
#' @slot aMeasType A length-one character vector containing the assay
#' measurement type.
#'
#' @keywords classes
#' @rdname assayTab-class
#' @exportClass assayTab
assayTab <- setClass(Class = "assayTab",
                     slots = c(
                       path = "character",
                       sFilename = "character",
                       sIdentifier = "character",
                       aFilename = "character",
                       aFile = "data.frame",
                       aTechType = "character",
                       aMeasType = "character"
                     ),
                     prototype = list(
                       path = NA_character_,
                       sFilename = NA_character_,
                       sIdentifier = NA_character_,
                       aFilename = NA_character_,
                       aFile = data.frame(),
                       aTechType = NA_character_,
                       aMeasType = NA_character_
                     )
)

### Derived assayTab Classes ----
## Special classes for different technology types to enable different methods
## for each technology type.

#' @keywords classes
#' @rdname assayTab-class
#' @exportClass msAssayTab
msAssayTab <- setClass(Class = "msAssayTab",
                       contains = "assayTab",
                       prototype = prototype(aTechType = "mass spectrometry"))

#' @keywords classes
#' @rdname assayTab-class
#' @exportClass microarrayAssayTab
microarrayAssayTab <- setClass(Class = "microarrayAssayTab",
                       contains = "assayTab",
                       prototype = prototype(aTechType = "DNA microarray"))