Modify write_conf and read_conf

* R/api.R(read_conf): The call of vrfy_conf removed due to some
  conflicts. Reinstate verification somewhere else.

* R/api.R(write_conf): Substitute conf with m argument.

(read_conf): Conflicts with the one in R/aip.R, so removed.

R/api.R

@@ -107,12 +107,15 @@ mk_comp_tab <- function(m) {
 }
 
 ##' @export
-read_conf <- function(fn_conf) {
-    assert(file.exists(fn_conf),msg=paste("Unable to read the configuration file:", fn_conf))
-    conf <- yaml::yaml.load_file(fn_conf)
-    conf <- vrfy_conf(conf)
-    conf
+read_conf <- function(fn) {
+    yaml::yaml.load_file(fn)
 }
+## read_conf <- function(fn_conf) {
+##     assert(file.exists(fn_conf),msg=paste("Unable to read the configuration file:", fn_conf))
+##     conf <- yaml::yaml.load_file(fn_conf)
+##     conf <- vrfy_conf(conf)
+##     conf
+## }
 
 ##' @export
 vrfy_conf <- function(conf) {

R/mix.R

@@ -596,12 +596,16 @@ read_setid <- function(fn,known,unk) {
 }
 
 
-write_conf <- function(conf,fn) {
-    yaml::write_yaml(x=conf,file=fn)
+write_conf <- function(m,fn) {
+    m$conf$data <- file.path(m$conf$project,FN_DATA_TAB)
+    yaml::write_yaml(x=m$conf,file=fn)
+    
+    
+    
 }
-
-read_conf <- function(fn) {
-    yaml::yaml.load_file(fn)
+write_state <- function(m,fn_conf) {
+    write_conf(m,fn_conf)
+    tab2file(tab=m$input$tab$mzml,file=file.path(m$conf$project,FN_DATA_TAB))
 }
 
 new_state <- function(conf,GUI) {