emdb - npm Package Compare versions

Comparing version 0.5.5 to 0.5.6

package.json

 {
   "name": "emdb",
-  "version": "0.5.5",
+  "version": "0.5.6",
   "description": "Database manager for exact mass query",
@@ -24,8 +24,8 @@ "browser": {
   "dependencies": {
-    "isotopic-distribution": "^0.5.2",
+    "isotopic-distribution": "^0.5.6",
     "jszip": "^3.1.5",
     "mf-finder": "^0.5.2",
-    "mf-from-google-sheet": "^0.5.5",
-    "mf-generator": "^0.5.5",
-    "mf-matcher": "^0.5.5",
+    "mf-from-google-sheet": "^0.5.6",
+    "mf-generator": "^0.5.6",
+    "mf-matcher": "^0.5.6",
     "mf-utilities": "^0.5.2",
@@ -32,0 +32,0 @@ "peaks-similarity": "^2.3.0",

src/__tests__/fromPeptidicSequence.js

@@ -15,3 +15,3 @@ 'use strict';
         },
-        mfFilter: {
+        filter: {
             minMSEM: 100,
@@ -18,0 +18,0 @@ maxMSEM: 300,

src/__tests__/loadCommercials.js

@@ -6,3 +6,2 @@ 'use strict';
 test('test loadCommercials', async () => {
-
     let data = await loadCommercials();
@@ -9,0 +8,0 @@ expect(data.length).toBeGreaterThan(10000);

src/__tests__/searchCommercials.js

@@ -43,5 +43,7 @@ 'use strict';
                 precision: 1e4,
-                onlyIntegerUnsaturation: true,
-                minUnsaturation: 2,
-                maxUnsaturation: 3,
+                unsaturation: {
+                    onlyInteger: true,
+                    min: 2,
+                    max: 3,
+                }
             }
@@ -48,0 +50,0 @@ });

src/fromPeptidicSequence.js

@@ -31,15 +31,16 @@ 'use strict';
  *
- * @param {object} [options.mfFilter={}] Object defining options for molecular formula filter
- * @param {number} [options.mfFilter.minMass=0] - Minimal monoisotopic mass
- * @param {number} [options.mfFilter.maxMass=+Infinity] - Maximal monoisotopic mass
- * @param {number} [options.mfFilter.minEM=0] - Minimal neutral monoisotopic mass
- * @param {number} [options.mfFilter.maxEM=+Infinity] - Maximal neutral monoisotopic mass
- * @param {number} [options.mfFilter.minMSEM=0] - Minimal observed monoisotopic mass
- * @param {number} [options.mfFilter.maxMSEM=+Infinity] - Maximal observed monoisotopic mass
- * @param {number} [options.mfFilter.minCharge=-Infinity] - Minimal charge
- * @param {number} [options.mfFilter.maxCharge=+Infinity] - Maximal charge
- * @param {number} [options.mfFilter.minUnsaturation=-Infinity] - Minimal unsaturation
- * @param {number} [options.mfFilter.maxUnsaturation=+Infinity] - Maximal unsaturation
- * @param {number} [options.mfFilter.onlyIntegerUnsaturation=false] - Integer unsaturation
- * @param {number} [options.mfFilter.onlyNonIntegerUnsaturation=false] - Non
+ * @param {object} [options.filter={}] Object defining options for molecular formula filter
+ * @param {number} [options.filter.minMass=0] - Minimal monoisotopic mass
+ * @param {number} [options.filter.maxMass=+Infinity] - Maximal monoisotopic mass
+ * @param {number} [options.filter.minEM=0] - Minimal neutral monoisotopic mass
+ * @param {number} [options.filter.maxEM=+Infinity] - Maximal neutral monoisotopic mass
+ * @param {number} [options.filter.minMSEM=0] - Minimal observed monoisotopic mass
+ * @param {number} [options.filter.maxMSEM=+Infinity] - Maximal observed monoisotopic mass
+ * @param {number} [options.filter.minCharge=-Infinity] - Minimal charge
+ * @param {number} [options.filter.maxCharge=+Infinity] - Maximal charge
+ * @param {number} [options.filter.unsaturation={}}]
+ * @param {number} [options.filter.unsaturation.min=-Infinity] - Minimal unsaturation
+ * @param {number} [options.filter.maxUnsaturation=+Infinity] - Maximal unsaturation
+ * @param {number} [options.filter.onlyIntegerUnsaturation=false] - Integer unsaturation
+ * @param {number} [options.filter.onlyNonIntegerUnsaturation=false] - Non
  */
@@ -56,3 +57,3 @@
         fragmentation = {},
-        mfFilter = {},
+        filter = {},
         ionizations = '',
@@ -92,3 +93,3 @@ } = options;
         ionizations,
-        filter: mfFilter
+        filter: filter
     });
@@ -95,0 +96,0 @@

src/index.js

@@ -6,4 +6,2 @@ 'use strict';
 const loadCommercialsPromise = require('./loadCommercials');
-const combineMFs = require('mf-generator');
-const findMFs = require('mf-finder');
 
@@ -25,4 +23,6 @@ function DBManager() {
     const {
-        databaseName = 'knapSack'
+        databaseName = 'knapSack',
+        forceReload = false
     } = options;
+    if (this.databases[databaseName] && !forceReload) return;
     this.databases[databaseName] = await loadKnapSackPromise();
@@ -37,4 +37,6 @@ };
     const {
-        databaseName = 'commercials'
+        databaseName = 'commercials',
+        forceReload = false
     } = options;
+    if (this.databases[databaseName] && !forceReload) return;
     this.databases[databaseName] = await loadCommercialsPromise();
@@ -54,4 +56,6 @@ };
     const {
-        databaseName = 'contaminants'
+        databaseName = 'contaminants',
+        forceReload = false,
     } = options;
+    if (this.databases[databaseName] && !forceReload) return;
     this.databases[databaseName] = await loadGoogleSheetPromise();
@@ -68,37 +72,9 @@ };
     const {
-        databaseName = 'sheet'
+        databaseName = 'sheet',
+        forceReload = false,
     } = options;
+    if (this.databases[databaseName] && !forceReload) return;
     this.databases[databaseName] = await loadGoogleSheetPromise();
 };
 
-/**
- * Generates a database 'generated' from an array of molecular formula
- * @param {*} options
- * @param {string} ['generated'] databaseName
- * @param {number} [options.limit=10000000] - Maximum number of results
- * @param {boolean} [canonizeMF=true] - Canonize molecular formula
- * @param {boolean} [uniqueMFs=true] - Force canonization and make MF unique
- * @param {number} [options.filter.minMass=0] - Minimal monoisotopic mass
- * @param {number} [options.filter.maxMass=+Infinity] - Maximal monoisotopic mass
- * @param {number} [options.filter.minEM=0] - Minimal neutral monoisotopic mass
- * @param {number} [options.filter.maxEM=+Infinity] - Maximal neutral monoisotopic mass
- * @param {number} [options.filter.minMSEM=0] - Minimal observed monoisotopic mass
- * @param {number} [options.filter.maxMSEM=+Infinity] - Maximal observed monoisotopic mass
- * @param {number} [options.filter.minCharge=-Infinity] - Minimal charge
- * @param {number} [options.filter.maxCharge=+Infinity] - Maximal charge
- * @param {number} [options.filter.minUnsaturation=-Infinity] - Minimal unsaturation
- * @param {number} [options.filter.maxUnsaturation=+Infinity] - Maximal unsaturation
- * @param {number} [options.filter.onlyIntegerUnsaturation=false] - Integer unsaturation
- * @param {number} [options.filter.onlyNonIntegerUnsaturation=false] - Non integer unsaturation
- * @param {object} [options.filter.atoms] - object of atom:{min, max}
- */
-
-DBManager.prototype.fromArray = function fromArray(mfsArray, options = {}) {
-    const {
-        databaseName = 'generated'
-    } = options;
-    this.databases[databaseName] = combineMFs(mfsArray, options);
-
-};
-
 DBManager.prototype.loadTest = function loadTest() {
@@ -109,20 +85,2 @@ this.fromArray(['C1-100'], { databaseName: 'test', ionizations: '+' });
 
-/**
- * Generates a database 'monoisotopic' from an array of molecular formula
- * @param {*} options
- * @param {number} [mass=0] - Target mass
- * @param {string} [options.databaseName='monoisotopic']
- * @param {number} [options.precision=1000] - Minimal charge
- * @param {number} [options.minCharge=-Infinity] - Minimal charge
- * @param {number} [options.maxCharge=+Infinity] - Maximal charge
- * @param {number} [options.minUnsaturation=-Infinity] - Minimal unsaturation
- * @param {number} [options.maxUnsaturation=+Infinity] - Maximal unsaturation
- * @param {number} [options.onlyIntegerUnsaturation=false] - Integer unsaturation
- * @param {number} [options.onlyNonIntegerUnsaturation=false] - Non integer unsaturation
- * @param {number} [options.maxIterations=1e8] - Max number of iterations
- * @param {boolean} [options.allowNeutral=false] - Allow neutral molecules
- * @param {string} [options.ionizations=''] - Comma separated list of ionizations
- * @param {string} [options.ranges=''] - Range to search the molecular formula like 'C0-10 H0-10'
- */
-
 DBManager.prototype.fromMonoisotopicMass = function fromMonoisotopicMass(mass, options = {}) {
@@ -132,5 +90,12 @@ const {
     } = options;
-    this.databases[databaseName] = findMFs(mass, options).mfs;
+    this.databases[databaseName] = require('./fromMonoisotopicMass')(mass, options);
 };
 
+DBManager.prototype.fromArray = function fromArray(sequence, options = {}) {
+    const {
+        databaseName = 'generated'
+    } = options;
+    this.databases[databaseName] = require('./fromArray')(sequence, options);
+};
+
 DBManager.prototype.fromPeptidicSequence = function fromPeptidicSequence(sequence, options = {}) {
@@ -137,0 +102,0 @@ const {

src/loadCommercials.js

@@ -6,2 +6,4 @@ 'use strict';
 
+const loadingPromises = {};
+
 module.exports = async function loadCommercials(options = {}) {
@@ -12,3 +14,6 @@ const {
 
-    const buffer = await fetch(url);
+    if (!loadingPromises[url]) {
+        loadingPromises[url] = fetch(url);
+    }
+    const buffer = await loadingPromises[url];
 
@@ -15,0 +20,0 @@ const jsZip = new JSZip();

src/loadKnapSack.js

@@ -6,2 +6,4 @@ 'use strict';
 
+const loadingPromises = {};
+
 module.exports = async function loadKnapSack(options = {}) {
@@ -12,3 +14,6 @@ const {
 
-    const buffer = await fetch(url);
+    if (!loadingPromises[url]) {
+        loadingPromises[url] = fetch(url);
+    }
+    const buffer = await loadingPromises[url];
 
@@ -15,0 +20,0 @@ const jsZip = new JSZip();

src/search.js

@@ -15,6 +15,7 @@ 'use strict';
 * @param {number}   [filter.maxCharge=+Infinity] - Maximal charge
-* @param {number}   [filter.minUnsaturation=-Infinity] - Minimal unsaturation
-* @param {number}   [filter.maxUnsaturation=+Infinity] - Maximal unsaturation
-* @param {number}   [filter.onlyIntegerUnsaturation=false] - Integer unsaturation
-* @param {number}   [filter.onlyNonIntegerUnsaturation=false] - Non integer unsaturation
+* @param {object}   [filter.unsaturation={}}]
+* @param {number}   [filter.unsaturation.min=-Infinity] - Minimal unsaturation
+* @param {number}   [filter.unsaturation.max=+Infinity] - Maximal unsaturation
+* @param {number}   [filter.unsaturation.onlyIntege=false] - Integer unsaturation
+* @param {number}   [filter.unsaturation.onlyNonInteger=false] - Non integer unsaturation
 * @param {object}   [filter.atoms] - object of atom:{min, max}
@@ -21,0 +22,0 @@

src/searchMSEM.js

@@ -18,6 +18,7 @@ 'use strict';
 * @param {number}   [options.filter.maxCharge=+Infinity] - Maximal charge
-* @param {number}   [options.filter.minUnsaturation=-Infinity] - Minimal unsaturation
-* @param {number}   [options.filter.maxUnsaturation=+Infinity] - Maximal unsaturation
-* @param {number}   [options.filter.onlyIntegerUnsaturation=false] - Integer unsaturation
-* @param {number}   [options.filter.onlyNonIntegerUnsaturation=false] - Non integer unsaturation
+* @param {object}   [options.filter.unsaturation={}}]
+* @param {number}   [options.filter.unsaturation.min=-Infinity] - Minimal unsaturation
+* @param {number}   [options.filter.unsaturation.max=+Infinity] - Maximal unsaturation
+* @param {number}   [options.filter.unsaturation.onlyIntege=false] - Integer unsaturation
+* @param {number}   [options.filter.unsaturation.onlyNonInteger=false] - Non integer unsaturation
 * @param {object}   [options.filter.atoms] - object of atom:{min, max}
@@ -24,0 +25,0 @@

src/searchSimilarity.js

@@ -18,6 +18,7 @@ 'use strict';
 * @param {number}   [options.filter.maxCharge=+Infinity] - Maximal charge
-* @param {number}   [options.filter.minUnsaturation=-Infinity] - Minimal unsaturation
-* @param {number}   [options.filter.maxUnsaturation=+Infinity] - Maximal unsaturation
-* @param {number}   [options.filter.onlyIntegerUnsaturation=false] - Integer unsaturation
-* @param {number}   [options.filter.onlyNonIntegerUnsaturation=false] - Non integer unsaturation
+* @param {object}   [options.filter.unsaturation={}}]
+* @param {number}   [options.filter.unsaturation.min=-Infinity] - Minimal unsaturation
+* @param {number}   [options.filter.unsaturation.max=+Infinity] - Maximal unsaturation
+* @param {number}   [options.filter.unsaturation.onlyIntege=false] - Integer unsaturation
+* @param {number}   [options.filter.unsaturation.onlyNonInteger=false] - Non integer unsaturation
 * @param {object}   [options.filter.atoms] - object of atom:{min, max}
@@ -24,0 +25,0 @@

No alert changes

Improved metrics

Total package byte prevSize

80411

increased by2.32%

Number of package files

32

increased by6.67%

Lines of code

838

increased by5.67%

Dependency changes

• Updatedisotopic-distribution@^0.5.6

• Updatedmf-from-google-sheet@^0.5.6

• Updatedmf-generator@^0.5.6

• Updatedmf-matcher@^0.5.6