refactor: simplify delta mass extraction

rformassspectrometry · Dec 27, 2024 · 4a167ea · 4a167ea
1 parent 08eadfc
commit 4a167ea
Showing 1 changed file with 11 additions and 23 deletions.
diff --git a/R/proforma-parser.R b/R/proforma-parser.R
@@ -37,36 +37,24 @@
 #' )
 .proforma_delta_masses <- function(x) {
     rx <- gregexpr(
-        pattern = "(?<=\\[)[GMURX]?:?[+-][0-9.]+(?=\\])",
+        pattern =
+            "(?<AA>[A-Z])(?:\\[[GMURX]?:?)?(?<DeltaMass>[+-][0-9.]+)?(?:\\])?",
         text = x,
         perl = TRUE
     )
-    mapply(function(sequence, start, matched_length, n) {
-        if (any(matched_length < 0))
-            return(double(n))
 
-        # add 2 for the surrounding "[" and "]"
-        matched_length2 <- matched_length + 2L
-        n_clean <- n - sum(matched_length2, na.rm = TRUE)
-        masses <- double(n_clean)
-
-        # subtract 2 for the "[" and the previous amino acid position
-        masses[
-            (start -
-             cumsum(c(2L, matched_length2[-length(matched_length2)]) ))
-        ] <- as.double(
-            gsub(
-                "^[GMURX]:",
-                "",
-                substring(sequence, start, start + matched_length - 1L)
-            )
+    mapply(function(sequence, start, matched_length) {
+        mod <- as.double(
+            substring(sequence, start, start + matched_length - 1L)
         )
-        masses
+        mod[is.na(mod)] <- 0
+        mod
     },
         sequence = x,
-        start = rx,
-        matched_length = lapply(rx, attr, "match.length"),
-        n = nchar(x),
+        start =
+            lapply(rx, function(r)attr(r, "capture.start")[, "DeltaMass"]),
+        matched_length =
+            lapply(rx, function(r)attr(r, "capture.length")[, "DeltaMass"]),
         SIMPLIFY = FALSE, USE.NAMES = FALSE
     )
 }