api, envopts, errors: Add max_proc parameter to envopts.

DESCRIPTION

 Package: shinyscreen
 Title: Pre-screening of Mass Spectrometry Data 
-Version: 1.2.9006
+Version: 1.2.9007
 Author: Todor Kondić
 Maintainer: Todor Kondić <todor.kondic@uni.lu>
 Authors@R: 

R/api.R

@@ -862,9 +862,13 @@ report <- function(m) {
 #' @inheritParams envopts
 #' @return Nothing.
 #' @author Todor Kondić
-init <- function(metfrag_db_dir="",metfrag_jar="",java_bin=Sys.which("java")) {
+init <- function(metfrag_db_dir="",
+                 metfrag_jar="",
+                 java_bin=Sys.which("java"),
+                 metfrag_max_proc=parallel::detectCores()) {
     e = envopts(metfrag_db_dir=metfrag_db_dir,
                 metfrag_jar=metfrag_jar,
-                java_bin=java_bin)
+                java_bin=java_bin,
+                metfrag_max_proc=metfrag_max_proc)
     save_envopts(o=e)
 }

R/envopts.R

@@ -30,9 +30,14 @@
 #'     pipeline.
 #' @param metfrag_db_dir `character(1)`, a path to the directory which contains MetFrag databases
 #' @param metfrag_jar  `character(1)`, a path to MetFrag JAR file
+#' @param metfrag_max_proc `integer(1)`, maximum number of CPU cores
+#'     available for MetFrag.
 #' @return An `envopts` object.
 #' @author Todor Kondić
-envopts <- function(metfrag_db_dir="",metfrag_jar="",java_bin=Sys.which("java")) {
+envopts <- function(metfrag_db_dir="",
+                    metfrag_jar="",
+                    java_bin=Sys.which("java"),
+                    metfrag_max_proc = parallel::detectCores()) {
     res = list(metfrag=list())
     class(res) = c("envopts","list") #Just to officially make it an
                                      #object.
@@ -41,8 +46,12 @@ envopts <- function(metfrag_db_dir="",metfrag_jar="",java_bin=Sys.which("java"))
     res$metfrag$db_dir = norm_path(metfrag_db_dir)
 
     check_file_absent(metfrag_jar,what="mf-jar")
-    res$metfrag$jar = norm_path(metfrag_jar)
 
+    check_not_integer(value=metfrag_max_proc,
+                      what="metfrag_max_proc")
+    
+    res$metfrag$jar = norm_path(metfrag_jar)
+    res$metfrag$max_proc = metfrag_max_proc
     if (nchar(res$metfrag$jar)>0L) {
         check_file_absent(java_bin,"java-bin")
         res$metfrag$java_bin = java_bin

R/errors.R

@@ -38,6 +38,10 @@ check_extension <- function(extfileval,what) {
                                                               class = paste0(what,'-no-ext-found')))
 }
 
+check_not_integer <- function(value,what) {
+    if (!is.integer(value)) stop(errorCondition(paste0("The value of `", what,"' must be an integer.")),
+                                 class = paste0(what,'-not-an-int'))
+}
 
 check_key_absent <- function(keys,l,what) {
     nms = names(l)

man/envopts.Rd

@@ -4,12 +4,20 @@
 \alias{envopts}
 \title{Create a \code{envopts} Object}
 \usage{
-envopts(metfrag_db_dir = "", metfrag_jar = "", java_bin = Sys.which("java"))
+envopts(
+  metfrag_db_dir = "",
+  metfrag_jar = "",
+  java_bin = Sys.which("java"),
+  metfrag_max_proc = parallel::detectCores()
+)
 }
 \arguments{
 \item{metfrag_db_dir}{\code{character(1)}, a path to the directory which contains MetFrag databases}
 
 \item{metfrag_jar}{\code{character(1)}, a path to MetFrag JAR file}
+
+\item{metfrag_max_proc}{\code{integer(1)}, maximum number of CPU cores
+available for MetFrag.}
 }
 \value{
 An \code{envopts} object.

man/init.Rd

@@ -4,12 +4,20 @@
 \alias{init}
 \title{Initialise Shinyscreen Configuration}
 \usage{
-init(metfrag_db_dir = "", metfrag_jar = "", java_bin = Sys.which("java"))
+init(
+  metfrag_db_dir = "",
+  metfrag_jar = "",
+  java_bin = Sys.which("java"),
+  metfrag_max_proc = parallel::detectCores()
+)
 }
 \arguments{
 \item{metfrag_db_dir}{\code{character(1)}, a path to the directory which contains MetFrag databases}
 
 \item{metfrag_jar}{\code{character(1)}, a path to MetFrag JAR file}
+
+\item{metfrag_max_proc}{\code{integer(1)}, maximum number of CPU cores
+available for MetFrag.}
 }
 \value{
 Nothing.