filter resulting combineMF based on various criteria of mass and charge

Author: lpatiny

Diff for: src/combineMFs.js

@@ -7,9 +7,27 @@ var removeMFLastPart = require('./util/removeMFLastPart.js');
 // TODO replace from the value coming from chemcalc
 var ELECTRON_MASS=5.4857990946e-4;
 
+/**
+ *
+ * @param keys
+ * @param options
+ * @param {number} [options.limit=1000000] - Maximum number of results
+ * @param {number} [options.minMass=0] - Minimal monoisotopic mass
+ * @param {number} [options.maxMass=+Infinity] - Maximal monoisotopic mass
+ * @param {number} [options.minMSMass=0] - Minimal observed monoisotopic mass
+ * @param {number} [options.maxMSMass=+Infinity] - Maximal observed monoisotopic mass
+ * @param {number} [options.minCharge=-Infinity] - Minimal charge
+ * @param {number} [options.maxCharge=+Infinity] - Maximal charge
+ * @returns {Array}
+ */
+
 function combineMFs (keys, options) {
-    var options=options || {};
-    options.limit=options.limit || 1000000;
+
+    options=Object.assign({}, {
+        limit:1000000,
+        minCharge:Number.NEGATIVE_INFINITY,
+        maxCharge:Number.POSITIVE_INFINITY
+    }, options);
     if (!Array.isArray(keys)) return [];
 
 
@@ -52,7 +70,7 @@ function combineMFs (keys, options) {
     while (position < currents.length) {
         if (currents[position] < sizes[position]) {
             evolution++;
-            appendResult(results, currents, keys);
+            appendResult(results, currents, keys, options);
             currents[position]++;
             for (var i = 0; i < position; i++) {
                 currents[i] = 0;
@@ -65,7 +83,7 @@ function combineMFs (keys, options) {
             throw new Error('You have reached the limit of '+options.limit+'. You could still change this value using options.limit but it is likely to crash.');
         }
     }
-    appendResult(results, currents, keys);
+    appendResult(results, currents, keys, options);
     return results;
 }
 
@@ -115,13 +133,30 @@ function getEMFromParts(parts, currents) {
     }
 }
 
-function appendResult(results, currents, keys) {
+function appendResult(results, currents, keys, options) {
     // this script is designed to combine molecular formula
     // that may contain comments after a "$" sign
     // therefore we should put all the comments at the ned
+
+    var info=getEMFromParts(keys, currents);
+
+    var em=info.em;
+    var msem=info.msem;
+    var charge=info.charge;
+
+    if ( (typeof options.minMass!=='undefined' && em<options.minMass)
+        || (typeof options.maxMass!=='undefined' && em>options.maxMass)) return;
+    if ( (typeof options.minMSMass!=='undefined' && msem<options.minMSMass)
+        || (typeof options.maxMSMass!=='undefined' && msem>options.maxMSMass)) return;
+    if (charge<options.minCharge || charge>options.maxCharge) return;
+
     var result = {mf: ''};
     var comments = [];
 
+    result.em=em;
+    result.msem=msem;
+    result.charge=charge;
+
     for (var i = 0; i < keys.length; i++) {
         var key = keys[i][currents[i]];
         if (key) {
@@ -132,12 +167,12 @@ function appendResult(results, currents, keys) {
             }
             result.mf += key;
         }
-        var info=getEMFromParts(keys, currents);
-        result.em=info.em;
-        result.msem=info.msem;
-        result.charge=info.charge;
     }
 
+
+
+
+
     if (comments.length > 0) result.mf += '$' + comments.join(' ');
 
     results.push(result);

Diff for: test/combineMF.js

@@ -89,6 +89,16 @@ describe('combine MFs test', function () {
         result.length.should.equal(101*101);
     });
 
+    it('From array of string to large array and filter', function () {
+        var mfsArray=["C0-100","O0-100"];
+        var result=CE.combineMFs(mfsArray,
+            {
+                minMass: 0.1,
+                maxMass:13
+            });
+        result.length.should.equal(1);
+    });
+
     it('Strange comments', function () {
         var mfsArray=["C$1>10","O$D2>20"];
         var result=CE.combineMFs(mfsArray);