ms-spectrum - npm Package Compare versions

Comparing version 1.5.3 to 1.6.0

package.json

 {
   "name": "ms-spectrum",
-  "version": "1.5.3",
+  "version": "1.6.0",
   "description": "A mass spectrum",
@@ -21,9 +21,10 @@ "main": "src/index.js",
   "dependencies": {
-    "emdb": "^1.7.2",
+    "emdb": "^1.7.3",
+    "mf-parser": "^1.4.4",
     "ml-array-max": "^1.2.4",
     "ml-array-min": "^1.2.3",
     "ml-array-normed": "^1.3.7",
-    "ml-gsd": "^9.1.0",
+    "ml-gsd": "^10.0.0",
     "ml-regression-power": "^2.0.0",
-    "ml-spectra-processing": "^8.3.1",
+    "ml-spectra-processing": "^10.0.0",
     "peaks-similarity": "^2.3.1",
@@ -35,3 +36,3 @@ "xy-parser": "^4.0.1"
   },
-  "gitHead": "0cceb8fe88adb924d371419bf3738b0e2d0a438c"
+  "gitHead": "250bcb61ebf068680786fa1dd9247ebcca0c33cf"
 }

src/peakPicking.js

 'use strict';
 
 const gsd = require('ml-gsd').gsd;
-const { xFindClosestIndex } = require('ml-spectra-processing');
+const { xyEnsureGrowingX } = require('ml-spectra-processing');
 
@@ -23,3 +23,3 @@ const appendPeaksCharge = require('./appendPeaksCharge');
   const { charge: chargeOptions = {} } = options;
-  if (!spectrum.peaks) {
+  if (!spectrum.peaks || spectrum.peaks.length === 0) {
     spectrum.peaks = [];
@@ -30,7 +30,7 @@ const keys = Object.keys(spectrum.data).filter(
     if (spectrum.isContinuous()) {
-      const gsdPeaks = gsd(spectrum.data, {
-        noiseLevel: 0,
+      // some experimental data are really problematic and we need to add this line
+      const data = xyEnsureGrowingX(spectrum.data);
+      const gsdPeaks = gsd(data, {
         minMaxRatio: 0.00025, // Threshold to determine if a given peak should be considered as a noise
         realTopDetection: true,
-        maxCriteria: true, // inverted:false
         smoothY: false,
@@ -41,5 +41,4 @@ sgOptions: { windowSize: 7, polynomial: 3 },
         const peak = { x: gsdPeak.x, y: gsdPeak.y, width: gsdPeak.width };
-        const index = xFindClosestIndex(spectrum.data.x, gsdPeak.x);
         for (let key of keys) {
-          peak[key] = spectrum.data[key][index];
+          peak[key] = spectrum.data[key][gsdPeak.index];
         }
@@ -46,0 +45,0 @@ spectrum.peaks.push(peak);

src/Spectrum.js

@@ -8,2 +8,3 @@ 'use strict';
 const getBestPeaks = require('./getBestPeaks');
+const getFragmentPeaks = require('./getFragmentPeaks');
 const getMassRemainder = require('./getMassRemainder');
@@ -33,2 +34,3 @@ const getPeakChargeBySimilarity = require('./getPeakChargeBySimilarity');
   this.cache = {};
+  this.peaks = [];
 }
@@ -119,2 +121,19 @@
 
+/**
+ * Returns also peaks possible for a specific molecular formula
+ * @example
+ *  const spectrum = new Spectrum({x:[], y:[]})
+ *  await spectrum.getFragmentPeaks();
+ * @param {string} mf
+ * @param {object} options
+ * @returns
+ */
+Spectrum.prototype.getFragmentPeaks = function getFragmentPeaksFct(
+  mf,
+  options,
+) {
+  peakPicking(this);
+  return getFragmentPeaks(this.peaks, mf, options);
+};
+
 Spectrum.prototype.isContinuous = function isContinuousFct() {
@@ -121,0 +140,0 @@ return isContinuous(this);

No alert changes

Improved metrics

Total package byte prevSize

5334724

increased by0.05%

Number of package files

37

increased by5.71%

Lines of code

1446

increased by6.87%

Worsened metrics

Dependency count

10

increased by11.11%

Dependency changes

• + Addedmf-parser@^1.4.4

• + Addedcheminfo-types@0.10.1(transitive)

• + Addedml-spectra-processing@10.3.0(transitive)

• - Removedml-gsd@9.1.0(transitive)

• - Removedml-savitzky-golay-generalized@2.0.3(transitive)

• - Removedml-spectra-fitting@3.1.0(transitive)

• Updatedemdb@^1.7.3

• Updatedml-gsd@^10.0.0

• Updatedml-spectra-processing@^10.0.0