Changed isofine to precid.

R/api.R

@@ -335,19 +335,12 @@ extr_data <-function(m) {
 
     dpath = m$run$paths$data
 
-    cg1 = data.table(isofine=integer(0),
-                     rt=numeric(0),
-                     intensity=numeric(0),
-                     scan=character(0),
-                     key = c("isofine","rt"))
+    ## Big ms1 chromatogram table.
+    cg1 = new_ms1_cgm_table() 
     
     for (fn in fine[,unique(file)]) {
 
-        fncg1 = data.table(isofine=integer(0),
-                           rt=numeric(0),
-                           intensity=numeric(0),
-                           scan=character(0),
-                           key = c("isofine","rt"))
+        
         
         ## Read data.
         ms = read_data_file(file=file.path(dpath,fn))
@@ -356,27 +349,31 @@ extr_data <-function(m) {
         ftab = fine[.(fn),on="file"]
 
         ## Extract input data that is needed.
-        isotab = ftab[,.(iso_fine_min,iso_fine_max,rt_min,rt_max),by="isofine"]
-        isotab1 = isotab[is.na(rt_min),.(isofine,iso_fine_min,iso_fine_max)]
-        isotab2 = isotab[!is.na(rt_min),.(isofine,iso_fine_min,iso_fine_max,rt_min,rt_max)]
+        isotab = ftab[,.(iso_fine_min,iso_fine_max,rt_min,rt_max),by="precid"]
+        isotab1 = isotab[is.na(rt_min),.(precid,iso_fine_min,iso_fine_max)]
+        isotab2 = isotab[!is.na(rt_min),.(precid,iso_fine_min,iso_fine_max,rt_min,rt_max)]
                   
 
         ## Extract MS1 chromatograms.
+        fncg1 = new_ms1_cgm_table()
+
         fncg1 = extr_ms1_cgm(ms=ms,
                              isotab=isotab1,
                              qrt=F,
                              fncg1)
+        
         fncg1 = extr_ms1_cgm(ms=ms,
                              isotab=isotab2,
                              qrt=T,
                              fncg1)
         
-        cg1 = cg1[fncg1,.(isofine,
+        cg1 = cg1[fncg1,.(precid,
                           rt,
                           intensity=i.intensity,
                           scan=i.scan)]
         
     }
+    
     m$db$extr$cgm$ms1 = res
     m
 

R/data-model.R

@@ -61,7 +61,7 @@ make_db_precursors <- function(m) {
         stop('make_db_precursors: Unknown mass unit (coarse).')
     }
 
-    masses$isofine = -1L
+    masses$precid = -1L
     start = 1L
     while (start <= NROW(masses)) {
         sel = masses[start:.N]
@@ -70,7 +70,7 @@ make_db_precursors <- function(m) {
         upmz = sel[1L,mz_fine_max]
         x = sel[mz<(upmz)]
         stop = start + NROW(x) - 1L
-        masses[(start):(stop),`:=`(isofine=..id,degfine=(1L+stop-start))]
+        masses[(start):(stop),`:=`(precid=..id,degfine=(1L+stop-start))]
         start = stop + 1L
     }
 
@@ -95,8 +95,8 @@ make_db_precursors <- function(m) {
 
     masses[,`:=`(iso_fine_min=min(mz_fine_min),
                  iso_fine_max=max(mz_fine_max)),
-                 by=isofine]
-    setindex(masses,isocoarse,isofine)
+                 by=precid]
+    setindex(masses,isocoarse,precid)
     ## Add files.
     filetab = m$input$tab$mzml[m$db$cat,.(catid=i.catid,file=file),on=c("set","tag"),nomatch=NULL]
     masses[filetab,file:=i.file,on="catid"]
@@ -107,3 +107,29 @@ make_db_precursors <- function(m) {
 
 
 
+new_ms1_cgm_table <- function() {
+    ## Creates a chromatogram.
+    data.table(precid=integer(0),
+               rt=numeric(0),
+               intensity=numeric(0),
+               scan=character(0),
+               key = c("precid","rt"))
+}
+
+
+
+new_ms2_cgm_cat <- function() {
+    ## A kind of catalogue of ms2.
+    data.table(precid = integer(0),
+               an = integer(0))
+}
+
+new_ms2_cgm_table <- function() {
+    ## Creates a chromatogram.
+    data.table(precid = integer(0),
+               an = intege r(0),
+               rt = numeric(0),
+               intensity = numeric(0),
+               scan = character(0),
+               key = c("precid","an"))
+}