R/zzz.R

In mar-esther23/rgriffin: Gene Regulatory Interaction Formulator For Inquiring Networks

#' Initialize jvm 
#' @keywords internal
#' 
.onLoad <- function(lib, pkg, ...) {
  initGriffin(force.init=FALSE)
}

#' Initialize the Java Virtual Machine (JVM) and create a connection with griffin
#' 
#' Initialize the Java Virtual Machine (JVM) and create a connection with griffin.
#' By default it takes the parameters from the "java/jvm-param.R" file. To change the defaults modify this file in the folder where rGriffin is instaled (~//rgriffin/int/java/jvm-param.R)
#'  
#' @param jvm.param string with parameters to initialize the jvm. 
#' @param force.init If set to TRUE JVM is re-initialized even if it is already running.
#' 
#' @example 
#' init.griffin("-XX:-UseGCOverheadLimit -Xmx2000m ") #initialize griffin with only 2GB of RAM
#' library(rGriffin)
#' 
#' @export
initGriffin <- function(jvm.param=NULL, force.init=TRUE) {
  #Load all variables
  griffin.path = paste0(system.file(package = "rGriffin"),"/java/")
  griffin.dirs = c("bin","lib")
  files = list.files(paste(griffin.path,griffin.dirs,sep=""),pattern="\\.jar$",full.names=TRUE)
  if (is.null(jvm.param)) source(paste0(griffin.path,"jvm-param.R")) #load jvm.param from conf file
  params = paste0(jvm.param, "-Dlog4j.configuration=file:",
                  griffin.path,"conf/log4j.properties")
  #JVM initialization
  rJava::.jinit(parameters=params)
  rJava::.jaddClassPath(".")
  rJava::.jaddClassPath(paste(griffin.path,"conf",sep=""))
  for(f in files){ rJava::.jaddClassPath(f) }
}


#' print query
#' @keywords internal
#' @export
print.jobjRef <- function(j.query) {
  text = .jcall(j.query,returnSig = "S","asString",evalString = TRUE)
  text = gsub('^.|.$', '', text)
  text = gsub("Gene Regulation Specification. ", "Gene Regulation Specification; ", text)
  text = gsub(" = true", "=1", text)
  text = gsub(" = false", "=0", text)
  text = gsub(";", "\n", text)
  cat(text)
}

#' setClass("gquery",contains = "jobjRef")
#' 
#' #' print query
#' #' @export
#' print.gquery <- function(j.query) {
#'   text = .jcall(j.query,returnSig = "S","asString",evalString = TRUE)
#'   text = gsub('^.|.$', '', text)
#'   text = gsub("Gene Regulation Specification. ", "Gene Regulation Specification; ", text)
#'   text = gsub(" = true", "=1", text)
#'   text = gsub(" = false", "=0", text)
#'   text = gsub(";", "\n", text)
#'   cat(text)
#' }