data-model: make_db_precursors: Group "fine" and "coarse" isobars.

R/data-model.R

@@ -28,28 +28,69 @@ make_db_precursors <- function(m) {
     cat = m$db$cat
     masses = m$out$tab$comp[cat,.(catid=catid,mz=mz),on=key(cat)]
     setkey(masses,mz)
+    
+    ## Fine error.
     if (ms1unit == "ppm") {
-        masses[,`:=`(mz_min=mz-ms1tol*mz*1e-6,mz_max=mz+ms1tol*mz*1e-6)]
+        masses[,`:=`(mz_fine_min=mz-ms1tol*mz*1e-6,mz_fine_max=mz+ms1tol*mz*1e-6)]
     } else if (ms1unit == "Da") {
-        masses[,`:=`(mz_min=mz-ms1tol,mz_max=mz+ms1tol)]
+        masses[,`:=`(mz_fine_min=mz-ms1tol,mz_fine_max=mz+ms1tol)]
     } else {
-        stop('make_db_precursors: Unknown mass unit.')
+        stop('make_db_precursors: Unknown mass unit (fine).')
     }
-    masses$isobar = -1L
-    ## masses[,isobar := fifelse(isobar==-1L & mz_min < themz & themz < mz_max,..id,catid)]
 
+
+    ## Coarse error.
+    tmp = get_val_unit(m$conf$tolerance[['ms1 coarse']])
+    ms1tol = as.numeric(tmp[['val']])
+    ms1unit = tmp[['unit']]
+    if (ms1unit == "ppm") {
+        masses[,`:=`(mz_coarse_min=mz-ms1tol*mz*1e-6,mz_coarse_max=mz+ms1tol*mz*1e-6)]
+    } else if (ms1unit == "Da") {
+        masses[,`:=`(mz_coarse_min=mz-ms1tol,mz_coarse_max=mz+ms1tol)]
+    } else {
+        stop('make_db_precursors: Unknown mass unit (coarse).')
+    }
+
+    masses$isofine = -1L
     start = 1L
     while (start <= NROW(masses)) {
         sel = masses[start:.N]
         themz = sel[1L,mz]
         id = sel[1L,catid]
-        upmz = sel[1L,mz_max]
+        upmz = sel[1L,mz_fine_max]
         x = sel[mz<(upmz)]
         stop = start + NROW(x) - 1L
-        message('a',start,'o',stop)
-        masses[(start):(stop),`:=`(isobar=..id,deg=(1L+stop-start))]
+        masses[(start):(stop),`:=`(isofine=..id,degfine=(1L+stop-start))]
         start = stop + 1L
     }
+
+    masses$isocoarse = -1L
+    start = 1L
+    while (start <= NROW(masses)) {
+        sel = masses[start:.N]
+        themz = sel[1L,mz]
+        id = sel[1L,catid]
+        upmz = sel[1L,mz_coarse_max]
+        x = sel[mz<(upmz)]
+        stop = start + NROW(x) - 1L
+        masses[(start):(stop),`:=`(isocoarse=..id,degcoarse=(1L+stop-start))]
+        start = stop + 1L
+    }
+
+    
+
+    masses[,`:=`(iso_coarse_min=min(mz_coarse_min),
+                 iso_coarse_max=max(mz_coarse_max)),
+                 by=isocoarse]
+
+    masses[,`:=`(iso_fine_min=min(mz_fine_min),
+                 iso_fine_max=max(mz_fine_max)),
+                 by=isofine]
+    setindex(masses,isocoarse,isofine)
     m$db$precursors = masses
     m
 }
+
+
+
+

R/extraction.R

@@ -607,3 +607,7 @@ gen_ms2_spec_blk <- function(spectra) {
                                                           CE = row[["CE"]],
                                                           an = row[["an"]])))
 }
+
+
+
+## NEW FUNCTIONS.

tests/testthat/test-integration.R

@@ -10,5 +10,8 @@ test_that("Extraction returns what is needed.",{
                 phase=c("setup","comptab","db"))
 
     cat = m$db$cat
+
+    m = run(envopts=eo,m=m,phase="extract")
+    
     expect_true(1==1)
 })