#'@export
#' @rdname RHermesExp-class
#' @param object An RHermesExp object
setMethod("show", "RHermesExp", function(object) {
show(object@metadata@ExpParam)
nfiles <- length(object@metadata@filenames)
if (nfiles != 0) {
message(paste0("Number of processed MS1 files: ", nfiles ))
lapply(object@metadata@filenames, function(x){message(paste0("\t", x))})
show(object@data@PL)
nsoi <- length(object@data@SOI)
if (nsoi != 0) {
show(object@data@SOI)
nMS2 <- length(object@data@MS2Exp)
if (nMS2 != 0) {
show(object@data@MS2Exp)
}
} else {
message("No SOI lists generated yet.")
}
} else {
message("No files processed yet.")
}
message("Processing Timestamps ---------------------------------------")
readTime(object)
})
#' @title setTime
#' @author Roger Gine
#' @description Adds a timestamp to the RHermesExp object with a specified
#' message. Useful for adding info to the object for reproducibility purposes.
#' @param struct The RHermesExp object you want to add the timestamp to.
#' @param message A character string to append.
#' @examples setTime(RHermesExp(), "Important info")
#' @return A copy of struct with the updated timestamp list.
#' @export
setGeneric("setTime", function(struct, message) {
standardGeneric("setTime")
})
#' @rdname setTime
setMethod("setTime", c("RHermesExp", "character"), function(struct,
message) {
validObject(struct)
struct@metadata@timestamps <- c(struct@metadata@timestamps,
paste(date(), message, sep = " - "))
return(struct)
})
#' @title readTime
#' @author Roger Gine
#' @description Prints all timestamps of a given RHermesExp object. Useful to
#' keep track of all changes made to the object (added files, generated SOI
#' lists, changed parameters, etc.)
#' @param struct The RHermesExp object you want to read the timestamps from.
#' @examples readTime(RHermesExp())
#' @return None, just prints the timestamps
#'@export
setGeneric("readTime", function(struct) {
standardGeneric("readTime")
})
#' @rdname readTime
setMethod("readTime", "RHermesExp", function(struct) {
validObject(struct)
lapply(struct@metadata@timestamps, function(m) {
message(m)
})
message("")
})
## Object getters ##
#'@title DB
#'@author Roger Gine
#'@family Getters
#'@param struct An RHermesExp object
#'@return A data.frame with all molecular formulas in struct.
#'@examples
#'\dontshow{struct <- readRDS(system.file("extdata", "exampleObject.rds",
#' package = "RHermes"))}
#'DB(struct)
#'@export
setGeneric("DB", function(struct) {
standardGeneric("DB")
})
#' @rdname DB
setMethod("DB", c("RHermesExp"), function(struct) {
validObject(struct)
struct@metadata@ExpParam@DB
})
#'@title adlist
#'@author Roger Gine
#'@family Getters
#'@param struct An RHermesExp object
#'@return The current data.frame of adducts in struct.
#'@examples
#'\dontshow{struct <- readRDS(system.file("extdata", "exampleObject.rds",
#' package = "RHermes"))}
#'adlist(struct)
#'@export
setGeneric("adlist", function(struct) {
standardGeneric("adlist")
})
#' @rdname adlist
setMethod("adlist", c("RHermesExp"), function(struct) {
validObject(struct)
struct@metadata@ExpParam@adlist
})
#'@title PL
#'@author Roger Gine
#'@family Getters
#'@param struct An RHermesExp object
#'@param id The number corresponding to the PL you want to access
#'@return The RHermes_PL object at position id.
#'@examples
#'\dontshow{struct <- readRDS(system.file("extdata", "exampleObject.rds",
#' package = "RHermes"))}
#'PL(struct, 1)
#'@export
setGeneric("PL", function(struct, id) {
standardGeneric("PL")
})
#' @rdname PL
setMethod("PL", c("RHermesExp", "numeric"), function(struct, id) {
validObject(struct)
validIds <- seq_along(struct@data@PL)
if(id %in% validIds) return(struct@data@PL[[id]])
warning(paste("You have input a wrong PL id, valid ids are:",
min(validIds), "-", max(validIds)))
})
#'@title SOI
#'@author Roger Gine
#'@family Getters
#'@param struct An RHermesExp object
#'@param id The number corresponding to the SOI list you want to access
#'@return The RHermes_SOI object at position id.
#'@examples
#'\dontshow{struct <- readRDS(system.file("extdata", "exampleObject.rds",
#' package = "RHermes"))}
#'SOI(struct, 1)
#'@export
setGeneric("SOI", function(struct, id) {
standardGeneric("SOI")
})
#' @rdname SOI
setMethod("SOI", c("RHermesExp", "numeric"), function(struct, id) {
validObject(struct)
validIds <- seq_along(struct@data@SOI)
if(id %in% validIds) return(struct@data@SOI[[id]])
warning(paste("You have input a wrong SOI id, valid ids are:",
min(validIds), "-", max(validIds)))
})
#'@title IL
#'@author Roger Gine
#'@family Getters
#'@param struct An RHermesExp object
#'@param id The number corresponding to the inclusion list you want to access
#'@return The RHermes_IL object at position id.
#'@examples
#'\dontshow{struct <- readRDS(system.file("extdata", "exampleObject.rds",
#' package = "RHermes"))}
#'IL(struct, 1)
#'@export
setGeneric("IL", function(struct, id) {
standardGeneric("IL")
})
#' @rdname IL
setMethod("IL", c("RHermesExp", "numeric"), function(struct, id) {
validObject(struct)
validIds <- seq_along(struct@data@MS2Exp)
if(id %in% validIds) return(struct@data@MS2Exp[[id]]@IL)
warning(paste("You have input a wrong IL id, valid ids are:",
min(validIds), "-", max(validIds)))
})
#'@title MS2Data
#'@author Roger Gine
#'@family Getters
#'@param struct An RHermesExp object
#'@param id The number corresponding to the inclusion list you want to access
#'@return A list of all IL entries of the RHermes_IL object at position id with
#'their corresponding MS2 scan data
#'@examples
#'\dontshow{struct <- readRDS(system.file("extdata", "exampleObject.rds",
#' package = "RHermes"))}
#'MS2Data(struct, 1)
#'@export
setGeneric("MS2Data", function(struct, id) {
standardGeneric("MS2Data")
})
#' @rdname MS2Data
setMethod("MS2Data", c("RHermesExp", "numeric"), function(struct, id) {
validObject(struct)
struct@data@MS2Exp[[id]]@MS2Data
if(length(struct@data@MS2Exp) > 0){
validIds <- seq_along(struct@data@MS2Exp)
if(id %in% validIds) return(struct@data@MS2Exp[[id]]@MS2Data)
warning(paste("You have input a wrong MS2Data id, valid ids are:",
min(validIds), "-", max(validIds)))
} else {
warning("No MS2Exp in the object")
}
})
#'@title Ident
#'@author Roger Gine
#'@family Getters
#'@param struct An RHermesExp object
#'@param id The number corresponding to the inclusion list you want to access
#'@return The identification data.frame with the RHermes_MS2Exp at position id.
#'@examples
#'\dontshow{struct <- readRDS(system.file("extdata", "exampleObject.rds",
#' package = "RHermes"))}
#'Ident(struct, 1)
#'@export
setGeneric("Ident", function(struct, id) {
standardGeneric("Ident")
})
#' @rdname Ident
setMethod("Ident", c("RHermesExp", "numeric"), function(struct, id) {
validObject(struct)
struct@data@MS2Exp[[id]]@Ident[[1]]
})
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