R/api.R, R/mix.R: Save extracted data

* R/mix.R(new_state): Add new conf field, m$extr$fn, to hold the name
  of the file where the extracted data is saved.

* R/api.R(extr_data): Save extracted data.

R/api.R

@@ -283,10 +283,13 @@ extr_data <- function(m) {
 
     })
     m$extr$ms1 <- data.table::rbindlist(lapply(m$extr$tmp, function (e) e$ms1))
-    m$extr$ms2 <- data.table::rbindlist(lapply(m$extr$tmp, function (e) e$ms2)) 
+    m$extr$ms2 <- data.table::rbindlist(lapply(m$extr$tmp, function (e) e$ms2))
+
+    message('Saving extracted date to ', m$extr$fn)
+    saveRDS(object = m$extr, file = m$extr$fn)
+    message('Done saving extracted data.')
     
     m$extr$tmp <- NULL
-    
     m
     
 }

R/mix.R

@@ -722,6 +722,7 @@ new_state <- function(conf=NULL,fn_conf="",GUI=F) {
     m <- list()
     m$conf <- if (!is.null(conf)) conf else read_conf(fn_conf)
     if (is.null(m$conf$debug)) m$conf$debug <- F
+    m$extr$fn <- file.path(m$conf$project,"extracted.rds")
     m$GUI <- GUI
     m$out$tab <- list()
     m$input$tab$mzml <- EMPTY_MZML