fix(mf-utilities): types returned by preprocessIonizations (#258)

migrate to ts

Closes: #243

packages/mf-parser/src/util/flatten.js

@@ -1,3 +1,8 @@
+/**
+ * @param parsed
+ * @param options
+ * @return {string[]}
+ */
 export function flatten(parsed, options = {}) {
   const { groupIdentical = false, limit = 100000 } = options;
   if (parsed.length === 0) return [''];
@@ -114,6 +119,8 @@ function createMFs(parts, comment, limit) {
   for (let i = 0; i < currents.length; i++) {
     currents[i] = parts[i].min;
   }
+
+  /** @type {string[]} */
   const mfs = [];
   let position = 0;
   while (position < currents.length) {

packages/mf-utilities/src/preprocessIonizations.ts

@@ -0,0 +1,35 @@
+import { MF } from 'mf-parser';
+import type { AtomsMap } from 'mf-parser';
+
+export interface Ionization {
+  mf: string;
+  em: number;
+  charge: number;
+  atoms: AtomsMap;
+}
+
+export function preprocessIonizations(
+  ionizationsString: string | Ionization[] = '',
+): Ionization[] {
+  if (Array.isArray(ionizationsString)) return ionizationsString;
+  const ionizations = ionizationsString.split(/ *[\t\n\r,.;]+ */);
+
+  // it is allowed to have ranges in Ionizations. We need to explode them.
+
+  const results: Ionization[] = [];
+
+  for (const ionization of ionizations) {
+    const parts = new MF(ionization).flatten();
+    for (const part of parts) {
+      const info = new MF(part).getInfo();
+      results.push({
+        mf: part,
+        em: info.monoisotopicMass,
+        charge: info.charge,
+        atoms: info.atoms,
+      });
+    }
+  }
+
+  return results;
+}