api: prescreen creates new m$out$tab members, ms1_spec, ms2_spec, summ

* R/api.R(prescreen): Split the qa$ms table into three: one to hold
ms1 spectra (ms1_spec), one for ms2 spectra (ms2_spec) and a summary
table (former ftable, now summ). This was done due to mismatch in the
number of entries between MS1 and MS2 spectra and in order to keep
summ table lightweight (no complex objects such as other tables).

* R/resources.R(MS2_SPEC_COLS, MS1_SPEC_COLS, DEF_ORDER_SPECTRA):
Constants COLS define the columns of ms?_spec and DEF_ORDER_SPECTRA
lost set as uninteresting column.

R/api.R

@@ -333,14 +333,54 @@ conf_trans <- function(conf) {
 ##' @export
 prescreen <- function(m) {
     ## Top-level auto prescreening function.
+
+
+    ## TODO need to fix max spec intensity
+    gen_ms2_spec_tab <- function(ms) {data.table::rbindlist(lapply(1:nrow(ms), function (nr) {
+        adduct <- ms$adduct[[nr]]
+        ID <- ms$ID[[nr]]
+        Files <- ms$Files[[nr]]
+        spec <- ms$spec[[nr]]
+        dt <- if (length(spec[[1]]) < 3)
+                  dtable(CE=NA_real_,
+                                       rt=NA_real_,
+                                       spec=list(dtable(mz=NA_real_,intensity=NA_real_))) else {
+                                                                                                            dtable(
+                                                                                                                              CE=sapply(spec,
+                                                                                                                                        function (x) x$CE),
+                                                                                                                              rt=sapply(spec,
+                                                                                                                                        function (x) x$rt),
+                                                                                                                              spec=lapply(spec,
+                                                                                                                                          function (x) x$spec))
+                                                                                                        }
+        dt$Files <- Files
+        dt$ID <- ID
+        dt$adduct <- adduct
+        dt[,ms2_max_int := .(sapply(spec,function (sp) sp[,max(intensity)]))] 
+        dt
+    }))}
+
+    gen_ms1_spec_tab <- function(ms) {
+        cols <- MS1_SPEC_COLS
+        ms[,..cols]
+    }
+
+
     m$qa <- create_qa_table(m$extr$ms,m$conf$prescreen)
     mms1 <- assess_ms1(m)
     m <- assess_ms2(mms1)
-    fields <- c("Files","adduct","ID",QA_COLS,SPEC_DATA_COLS)
+    fields <- c("Files","adduct","ID",QA_COLS)
+    m$out$tab$ms2_spec <- gen_ms2_spec_tab(m$qa$ms)
+    data.table::setkeyv(m$out$tab$ms2_spec,c("adduct","Files","ID"))
+    m$out$tab$ms1_spec <- gen_ms1_spec_tab(m$qa$ms)
+    data.table::setkeyv(m$out$tab$ms1_spec,c("adduct","Files","ID"))
     m$out$tab$summ <- merge(m$out$tab$comp,m$qa$ms[,..fields],by=c("Files","adduct","ID"))
     m
 }
 
+
+
+
 ##' @export
 sort_spectra <- function(m) {
     ## Sorts the summary table (summ) in order specified either in

R/resources.R

@@ -183,7 +183,10 @@ QA_NUM_INT <- c("ms2_sel","ms1_rt_ind")
 
 QA_COLS <- c(QA_FLAGS,QA_NUM_REAL,QA_NUM_INT)
 
-SPEC_DATA_COLS <- c("eicMS1")
+## MS2 spectral table columns
+MS2_SPEC_COLS <- c("adduct","ID","CE","rt","Files","spec","ms2_max_int")
 
+## MS1 spectral table columns
+MS1_SPEC_COLS <- c("adduct","Files","ID","eicMS1","ms1_int","ms1_rt","ms1_mean")
 ## Default order of spectra in summary table
-DEF_ORDER_SPECTRA <- c("set","qa_pass","ms1_int","adduct","mz","tag")
+DEF_ORDER_SPECTRA <- c("qa_pass","ms1_int","adduct","mz","tag")