lint

tools/isolib/isolib.R

@@ -10,29 +10,29 @@ main <- function() {
 
   args <- commandArgs(trailingOnly = TRUE)
   compound_table <- read.delim(args[1], stringsAsFactors = FALSE)
-  adducts_to_use <- c(unlist(strsplit(args[2], ',', fixed = TRUE)))
+  adducts_to_use <- c(unlist(strsplit(args[2], ",", fixed = TRUE)))
 
   chemforms <- compound_table$formula
   chemforms <- check_chemform(isotopes, chemforms)[, 2]
-  
+
   spectra <- data.frame()
 
   for (current in adducts_to_use) {
-    adduct <- adducts[adducts$Name == current,]
+    adduct <- adducts[adducts$Name == current, ]
     multiplied_chemforms <- multiform(chemforms, adduct$Mult)
 
-    if(adduct$Ion_mode == "negative") {
+    if (adduct$Ion_mode == "negative") {
       merged_chemforms <- subform(multiplied_chemforms, adduct$Formula_ded)
     } else {
       merged_chemforms <- mergeform(multiplied_chemforms, adduct$Formula_add)
     }
 
-    charge_string <- paste0(if(adduct$Charge > 0) "+" else "-", if(abs(adduct$Charge) > 1) abs(adduct$Charge) else "")
+    charge_string <- paste0(if (adduct$Charge > 0) "+" else "-", if (abs(adduct$Charge) > 1) abs(adduct$Charge) else "")
     adduct_string <- paste0("[", adduct$Name, "]", charge_string)
     precursor_mz <- calculateMass(multiplied_chemforms) + adduct$Mass
 
     if (args[4] == TRUE) {
-      names <- paste(compound_table$name, paste0("(", adduct$Name, ")"), sep=" ")
+      names <- paste(compound_table$name, paste0("(", adduct$Name, ")"), sep = " ")
     } else {
       names <- compound_table$name
     }
@@ -64,12 +64,12 @@ main <- function() {
       mzs <- append(mzs, list(patterns[[i]][, 1]))
       intensities <- append(intensities, list(patterns[[i]][, 2]))
     }
-  
+
     spectra_df$mz <- mzs
     spectra_df$intensity <- intensities
     spectra <- rbind(spectra, spectra_df)
   }
-  
+
   sps <- Spectra(spectra)
   export(sps, MsBackendMsp(), file = args[5])
 }