peptide - npm Package Compare versions

Comparing version 1.5.0 to 1.5.1

bower.json

 {
   "name": "peptide",
-  "version": "1.5.0",
+  "version": "1.5.1",
   "description": "Peptide",
@@ -5,0 +5,0 @@ "keywords": [

package.json

 {
   "name": "peptide",
-  "version": "1.5.0",
+  "version": "1.5.1",
   "description": "Peptide",
@@ -5,0 +5,0 @@ "keywords": [

src/chargePeptide.js

@@ -8,2 +8,4 @@ 'use strict';
 function chargePeptide(mf, options) {
+    var options=options || {};
+    if (options.pH === undefined) options.pH=0;
     if (Array.isArray(mf)) {
@@ -20,4 +22,2 @@ for (var i=0; i<mf.length; i++) {
 function chargeOnePeptide(mf, options) {
-    var options=options || {};
-    if (options.pH === undefined) options.pH=0;
     var pH=options.pH;
@@ -24,0 +24,0 @@ // we will allow to charge the peptide at a specific pH

src/getAA.js

@@ -22,4 +22,2 @@ 'use strict';
 
-
-module.exports = getAA;
-
+module.exports = getAA;

src/index.js

@@ -9,2 +9,3 @@ 'use strict';
 var digestPeptide = require('./digestPeptide');
+var generatePeptideFragments = require('./generatePeptideFragments');
 
@@ -42,54 +43,4 @@ exports.getInfo = function () {
 
-exports.generatePeptideFragments = function generatePeptideFragments(mf, options) {
-    if (options === undefined) {
-        options = {
-            a: false,
-            b: true,
-            c: false,
-            x: false,
-            y: true,
-            z: false,
-            i: false,
-            yb: false,
-            ya: false
-        };
-    }
-    options.maxInternal = options.maxInternal || Number.MAX_VALUE;
-    options.minInternal = options.minInternal || 0;
+exports.generatePeptideFragments = generatePeptideFragments;
 
-    var mfs = [];
-    var mfparts=mf.replace(/([a-z\)])([A-Z][a-z](?=[a-z]))/g,"$1 $2").split(/ /);
-
-    var nTerm="";
-    var cTerm="";
-
-    for (var i=1; i<mfparts.length; i++) {
-        nTerm+=mfparts[i-1];
-        cTerm=mfparts[mfparts.length-i]+cTerm;
-        addNTerm(mfs, nTerm, i, options);
-        addCTerm(mfs, cTerm, i, options);
-        if (options.i) mfs.push(mfparts[i]+"HC-1O-1(+1)$i:"+mfparts[i]);
-
-        if (options.ya || options.yb) { // we have double fragmentations
-            for (var j=i+1; j<Math.min(mfparts.length,options.maxInternal+i+1);j++) {
-                var iTerm='';
-                if ((j-i)>=options.minInternal){
-                    for (var k = i; k < j; k++) {
-                        iTerm += mfparts[k];
-                    }
-                    addITerm(mfs, iTerm, mfparts.length - i, j, options);
-                }
-            }
-        }
-    }
-
-
-    if (mfs.length === 0) {
-        mfs = mfs.concat([mf]);
-    }
-
-    return mfs;
-
-};
-
 exports.chargePeptide = chargePeptide;
@@ -159,18 +110,1 @@ exports.allowNeutralLoss = allowNeutralLoss;
 };
-
-function addNTerm(mfs, nTerm, i, options) {
-    if (options.a) mfs.push(nTerm+"C-1O-1(+1)$a"+i);
-    if (options.b) mfs.push(nTerm+"(+1)$b"+i);
-    if (options.c) mfs.push(nTerm+"NH3(+1)$c"+i);
-}
-
-function addITerm(mfs, iTerm, i, j, options) {
-    if (options.ya) mfs.push("H"+iTerm+"C-1O-1(+1)$a"+j+"y"+i);
-    if (options.yb) mfs.push("H"+iTerm+"(+1)$b"+j+"y"+i);
-}
-
-function addCTerm(mfs, cTerm, i, options) {
-    if (options.x) mfs.push("CO(+1)"+cTerm+"$x"+i);
-    if (options.y) mfs.push("H2(+1)"+cTerm+"$y"+i);
-    if (options.z) mfs.push("N-1H-1(+1)"+cTerm+"$z"+i);
-}

No alert changes

Improved metrics

Total package byte prevSize

26008

increased by1.29%

Number of package files

19

increased by11.76%

Lines of code

717

increased by1.13%

No dependency changes