From 629973d8175d3d3b0c75d1a488cfc83261c578f4 Mon Sep 17 00:00:00 2001
From: tpoisseau <22891227+tpoisseau@users.noreply.github.com>
Date: Thu, 19 Dec 2024 11:27:52 +0100
Subject: [PATCH] fix(mf-utilities): types returned by preprocessIonizations
 (#258)

migrate to ts

Closes: https://github.com/cheminfo/mass-tools/issues/243
---
 packages/mf-parser/src/util/flatten.js        |  7 ++++
 .../mf-utilities/src/{index.js => index.ts}   |  0
 .../mf-utilities/src/preprocessIonizations.js | 25 -------------
 .../mf-utilities/src/preprocessIonizations.ts | 35 +++++++++++++++++++
 4 files changed, 42 insertions(+), 25 deletions(-)
 rename packages/mf-utilities/src/{index.js => index.ts} (100%)
 delete mode 100644 packages/mf-utilities/src/preprocessIonizations.js
 create mode 100644 packages/mf-utilities/src/preprocessIonizations.ts

diff --git a/packages/mf-parser/src/util/flatten.js b/packages/mf-parser/src/util/flatten.js
index 1fd037f8..37c5502c 100644
--- a/packages/mf-parser/src/util/flatten.js
+++ b/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) {
diff --git a/packages/mf-utilities/src/index.js b/packages/mf-utilities/src/index.ts
similarity index 100%
rename from packages/mf-utilities/src/index.js
rename to packages/mf-utilities/src/index.ts
diff --git a/packages/mf-utilities/src/preprocessIonizations.js b/packages/mf-utilities/src/preprocessIonizations.js
deleted file mode 100644
index d62c1789..00000000
--- a/packages/mf-utilities/src/preprocessIonizations.js
+++ /dev/null
@@ -1,25 +0,0 @@
-import { MF } from 'mf-parser';
-
-export function preprocessIonizations(ionizationsString = '') {
-  if (Array.isArray(ionizationsString)) return ionizationsString;
-  let ionizations = ionizationsString.split(/ *[\t\n\r,.;]+ */);
-
-  // it is allowed to have ranges in Ionizations. We need to explode them.
-
-  let results = [];
-
-  for (let ionization of ionizations) {
-    let parts = new MF(ionization).flatten();
-    for (let part of parts) {
-      let info = new MF(part).getInfo();
-      results.push({
-        mf: part,
-        em: info.monoisotopicMass,
-        charge: info.charge,
-        atoms: info.atoms,
-      });
-    }
-  }
-
-  return results;
-}
diff --git a/packages/mf-utilities/src/preprocessIonizations.ts b/packages/mf-utilities/src/preprocessIonizations.ts
new file mode 100644
index 00000000..b18577ee
--- /dev/null
+++ b/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;
+}