R/loading.r

In mariev/chromatoplotsgui: Interactive graphics and interface for chromatoplots

.load1data <- function(x, includeMSn){
  if('chromatoplots' %in% loadedNamespaces()){
    loadSample(x, includeMSn = includeMSn )
  } else{
    .loadSample(x, includeMSn)
  }
}

.loadSample <- function(x, includeMSn){
  xraw <- xcmsRaw(x, profstep = 1, profmethod = "intlin",
                  profparam = list(), includeMSn = includeMSn)
}

.poploadsamples <- function(.cguienv, fly, dir){

  if(!fly){ ## calculate data objects for all the files
    # case 1: if dir is all CDFS
    fileinfos <- file.info(dir)$isdir
    if(length(fileinfos[!fileinfos]) == length(dir) ){
      .cguienv$cpdata$loaddata <- lapply(dir, FUN = function(x){.load1data(x, .cguienv$cpdata$includeMSn)})
    } else {
      # case 2: if cur dir is all dirs
      sapply(dir, function(x){
        setwd(x)
        .cguienv$cpdata$loaddata <- c(.cguienv$cpdata$loaddata, lapply(dir(), 
                                                                       FUN = function(x){.load1data(x, .cguienv$cpdata$includeMSn)}))
        setwd('..')
      })
    }
  } else { ## calculate on the fly
    if(file.info(dir[1])$isdir){
      up <- FALSE
      setwd(dir[1])
      if(file.info(dir()[1])$isdir){
        setwd(dir()[1])
        up <- TRUE
      }
      .cguienv$cpdata$loaddata <- list(.load1data(dir()[1], .cguienv$cpdata$includeMSn))
      if(up) setwd('..')
      
      setwd('..')
    } else {
      .cguienv$cpdata$loaddata <- list(.load1data(dir()[1], .cguienv$cpdata$includeMSn))
    }
  }
  
}