feat(ms-spectrum): export fromMonoisotopicMass (#260)

* feat(ms-spectrum): export `fromMonoisotopicMass` moved from `emdb` package to remove circular dependency between `emdb` and `ms-spectrum` it was internal, method was accessible through `EMDB.prototype.fromMonoisotopicMass` closes: #70 * test: add `numberMFs` test case for coverage
cheminfo · Dec 22, 2024 · dd8d2a4 · dd8d2a4
1 parent 629973d
commit dd8d2a4
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Showing 10 changed files with 199 additions and 15 deletions.
diff --git a/eslint.config.mjs b/eslint.config.mjs
@@ -9,6 +9,7 @@ import globals from 'globals';
 export default [
   {
     ignores: [
+      'packages/*/coverage',
       'packages/*/dist',
       'packages/*/docs',
       'packages/*/examples',

diff --git a/packages/emdb/src/index.js b/packages/emdb/src/index.js
@@ -1,9 +1,8 @@
-import { Spectrum } from 'ms-spectrum';
+import { Spectrum, fromMonoisotopicMass } from 'ms-spectrum';
 
 import { appendFragmentsInfo } from './append/appendFragmentsInfo.js';
 import { fromArray } from './from/fromArray.js';
 import { fromMolecules } from './from/fromMolecules.js';
-import { fromMonoisotopicMass } from './from/fromMonoisotopicMass.js';
 import { fromNucleicSequence } from './from/fromNucleicSequence.js';
 import { fromPeptidicSequence } from './from/fromPeptidicSequence.js';
 import { fromRange } from './from/fromRange.js';

diff --git a/packages/ms-spectrum/package.json b/packages/ms-spectrum/package.json
@@ -20,8 +20,8 @@
   "homepage": "https://github.com/cheminfo/mass-tools/tree/main/packages/emdb#readme",
   "dependencies": {
     "cheminfo-types": "^1.8.1",
-    "emdb": "^3.3.17",
     "is-any-array": "^2.0.1",
+    "mf-finder": "^3.4.11",
     "mf-parser": "^3.3.0",
     "mf-utilities": "^3.3.4",
     "ml-gsd": "^12.1.8",

diff --git a/packages/ms-spectrum/src/from/__tests__/fromMonoisotopicMass.test.js b/packages/ms-spectrum/src/from/__tests__/fromMonoisotopicMass.test.js
@@ -0,0 +1,50 @@
+import { expect, test } from 'vitest';
+
+import { fromMonoisotopicMass } from '../..';
+
+test('fromMonoisotopicMass', async () => {
+  const { mfs } = await fromMonoisotopicMass(120, {
+    allowNeutral: true,
+  });
+  expect(mfs).toHaveLength(8);
+});
+
+test('fromMonoisotopicMass string', async () => {
+  const { mfs } = await fromMonoisotopicMass('120,60', {
+    allowNeutral: true,
+  });
+  expect(mfs).toHaveLength(10);
+});
+
+test('fromMonoisotopicMass array', async () => {
+  const { mfs } = await fromMonoisotopicMass([60, 120], {
+    allowNeutral: true,
+  });
+  expect(mfs).toHaveLength(10);
+});
+
+test('fromMonoisotopicMass with ionizations', async () => {
+  const { mfs } = await fromMonoisotopicMass(120, {
+    allowNeutral: false,
+    ionizations: ', H+, K+',
+    precision: 100,
+  });
+  expect(mfs).toHaveLength(9);
+});
+
+test('fromMonoisotopicMass large database', async () => {
+  const { mfs } = await fromMonoisotopicMass(1000, {
+    ranges: 'C0-100 H0-100 N0-100 O0-100',
+    filter: {
+      unsaturation: {
+        min: 0,
+        max: 100,
+        onlyInteger: true,
+      },
+    },
+    precision: 100,
+    allowNeutral: true,
+    limit: 10000,
+  });
+  expect(mfs).toHaveLength(1407);
+});
diff --git a/...ges/emdb/src/from/fromMonoisotopicMass.js → ...spectrum/src/from/fromMonoisotopicMass.js b/...ges/emdb/src/from/fromMonoisotopicMass.js → ...spectrum/src/from/fromMonoisotopicMass.js
diff --git a/packages/ms-spectrum/src/getFragmentPeaks.js b/packages/ms-spectrum/src/getFragmentPeaks.js
@@ -1,6 +1,6 @@
-import { EMDB } from 'emdb';
 import { MF } from 'mf-parser';
 
+import { fromMonoisotopicMass } from './from/fromMonoisotopicMass';
 import { getPeaks } from './getPeaks.js';
 
 /**
@@ -18,8 +18,6 @@ import { getPeaks } from './getPeaks.js';
  */
 
 export async function getFragmentPeaks(peaks, mf, options = {}) {
-  const emdb = new EMDB();
-
   const { ionizations = '', precision } = options;
 
   const mfInfo = new MF(mf).getInfo();
@@ -28,7 +26,7 @@ export async function getFragmentPeaks(peaks, mf, options = {}) {
     .join(' ');
   peaks = getPeaks(peaks, options);
   for (let peak of peaks) {
-    const { mfs } = await emdb.fromMonoisotopicMass(peak.x, {
+    const { mfs } = await fromMonoisotopicMass(peak.x, {
       precision,
       ranges,
       ionizations,

diff --git a/packages/ms-spectrum/src/index.js b/packages/ms-spectrum/src/index.js
@@ -3,3 +3,4 @@ export * from './getPeaks.js';
 export * from './getBestPeaks.js';
 export * from './MSComparator.js';
 export * from './jsgraph/index.js';
+export * from './from/fromMonoisotopicMass.js';
diff --git a/packages/ms-spectrum/src/jsgraph/__tests__/__snapshots__/getPeaksAnnotation.test.js.snap b/packages/ms-spectrum/src/jsgraph/__tests__/__snapshots__/getPeaksAnnotation.test.js.snap
@@ -1,5 +1,132 @@
 // Vitest Snapshot v1, https://vitest.dev/guide/snapshot.html
 
+exports[`test getPeaksAnnotation > cap numberMFs to 2 1`] = `
+[
+  {
+    "_highlight": undefined,
+    "labels": [
+      {
+        "color": "red",
+        "position": {
+          "dx": "2px",
+          "dy": "-17px",
+          "x": 12,
+          "y": 1,
+        },
+        "text": "12.00000",
+      },
+    ],
+    "position": [
+      {
+        "dy": "-5px",
+        "x": 12,
+        "y": 1,
+      },
+      {
+        "dy": "-25px",
+        "x": 12,
+        "y": 1,
+      },
+    ],
+    "type": "line",
+  },
+  {
+    "_highlight": undefined,
+    "labels": [
+      {
+        "color": "red",
+        "position": {
+          "dx": "2px",
+          "dy": "-17px",
+          "x": 24,
+          "y": 2,
+        },
+        "text": "24.00000",
+      },
+    ],
+    "position": [
+      {
+        "dy": "-5px",
+        "x": 24,
+        "y": 2,
+      },
+      {
+        "dy": "-25px",
+        "x": 24,
+        "y": 2,
+      },
+    ],
+    "type": "line",
+  },
+  {
+    "_highlight": undefined,
+    "labels": [
+      {
+        "color": "red",
+        "position": {
+          "dx": "2px",
+          "dy": "-17px",
+          "x": 36,
+          "y": 3,
+        },
+        "text": "36.00000",
+      },
+    ],
+    "position": [
+      {
+        "dy": "-5px",
+        "x": 36,
+        "y": 3,
+      },
+      {
+        "dy": "-25px",
+        "x": 36,
+        "y": 3,
+      },
+    ],
+    "type": "line",
+  },
+  {
+    "_highlight": undefined,
+    "labels": [
+      {
+        "color": "red",
+        "position": {
+          "dx": "2px",
+          "dy": "-17px",
+          "x": 42,
+          "y": 4,
+        },
+        "text": "42.00000",
+      },
+      {
+        "color": "grey",
+        "position": {
+          "dx": "2px",
+          "dy": "-4px",
+          "x": 42,
+          "y": 4,
+        },
+        "text": "Z:1",
+      },
+    ],
+    "position": [
+      {
+        "dy": "-5px",
+        "x": 42,
+        "y": 4,
+      },
+      {
+        "dy": "-25px",
+        "x": 42,
+        "y": 4,
+      },
+    ],
+    "type": "line",
+  },
+]
+`;
+
 exports[`test getPeaksAnnotation > default options 1`] = `
 [
   {

diff --git a/packages/ms-spectrum/src/jsgraph/__tests__/getPeaksAnnotation.test.js b/packages/ms-spectrum/src/jsgraph/__tests__/getPeaksAnnotation.test.js
@@ -22,4 +22,11 @@ describe('test getPeaksAnnotation', () => {
     });
     expect(result).toMatchSnapshot();
   });
+
+  it('cap numberMFs to 2', async () => {
+    let result = await getPeaksAnnotation(peaks, {
+      numberMFs: 2,
+    });
+    expect(result).toMatchSnapshot();
+  });
 });
diff --git a/packages/ms-spectrum/src/jsgraph/getPeaksAnnotation.js b/packages/ms-spectrum/src/jsgraph/getPeaksAnnotation.js
@@ -1,4 +1,4 @@
-import { EMDB } from 'emdb';
+import { fromMonoisotopicMass } from '../from/fromMonoisotopicMass';
 
 /**
  *
@@ -16,8 +16,6 @@ import { EMDB } from 'emdb';
  * @returns {Promise}
  */
 export async function getPeaksAnnotation(bestPeaks, options = {}) {
-  const emdb = new EMDB();
-
   let {
     numberDigits = 5,
     shift = 0,
@@ -119,6 +117,8 @@ export async function getPeaksAnnotation(bestPeaks, options = {}) {
         });
       }
 
+      let mfs = [];
+
       if (numberMFs) {
         // we have 2 cases. Either there is a shift and we deal with differences
         // otherwise it is absolute
@@ -135,16 +135,17 @@ export async function getPeaksAnnotation(bestPeaks, options = {}) {
           currentMfPrefs.precision =
             (currentMfPrefs.precision / Math.max(Math.abs(peak.x + shift), 1)) *
             peak.x;
-          await emdb.fromMonoisotopicMass(
+          ({ mfs } = await fromMonoisotopicMass(
             Math.abs((peak.x + shift) * charge),
             currentMfPrefs,
-          );
+          ));
         } else {
-          await emdb.fromMonoisotopicMass(Math.abs(peak.x * charge), mfPrefs);
+          ({ mfs } = await fromMonoisotopicMass(
+            Math.abs(peak.x * charge),
+            mfPrefs,
+          ));
         }
 
-        let mfs = emdb.get('monoisotopic');
-
         let numberOfMFS = Math.min(mfs.length, numberMFs);
 
         for (let i = 0; i < numberOfMFS; i++) {