advances in the documentation

with respect to issues #19 #28 #48 #52

src/peakPicking/peaks2Ranges.js

@@ -1,4 +1,19 @@
 'use strict';
+
+const JAnalyzer = require('./jAnalyzer');
+const Ranges = require('../range/Ranges');
+//var extend = require("extend");
+//var removeImpurities = require('./ImpurityRemover');
+
+const defaultOptions = {
+    nH: 99,
+    clean: true,
+    compile: true,
+    integralFn: 0,
+    idPrefix: '',
+    format: 'old',         // TODO: remove support for old format
+    frequencyCluster: 16
+};
 /**
  * This function clustering peaks and calculate the integral value for each range from the peak list returned from extractPeaks function
  * @param {Object} spectrum - SD instance
@@ -8,22 +23,10 @@
  * @param {number} [options.integralFn] - option to chose between approx area with gaussian function or sum of the points of given range
  * @param {number} [options.frequencyCluster] - distance limit to clustering the peaks.
  * @param {boolean} [options.clean] - If true remove all the signals with integral < 0.5
+ * @param {boolean} [options.compile] - If true, the Janalyzer function is run over signals to compile the patterns.
+ * @param {string} [options.idPrefix] - prefix for signal ID
  * @returns {Array}
  */
-const JAnalyzer = require('./jAnalyzer');
-const Ranges = require('../range/Ranges');
-//var extend = require("extend");
-//var removeImpurities = require('./ImpurityRemover');
-
-const defaultOptions = {
-    nH: 99,               
-    clean: true,           
-    compile: true,         // TODO: needs documentation
-    integralFn: 0,         
-    idPrefix: '',          // TODO: needs documentation
-    format: 'old',         // TODO: remove support for old format
-    frequencyCluster: 16   
-};
 
 function createRanges(spectrum, peakList, options) {
     options = Object.assign({}, defaultOptions, options);
@@ -150,12 +153,14 @@ function createRanges(spectrum, peakList, options) {
 
 
 /**
+ * @private
  * Extract the signals from the peakList and the given spectrum.
  * @param {object} peakList - nmr signals
  * @param {object} spectrum - spectra data
  * @param {number} nH - Number of hydrogens or some number to normalize the integral data
  * @param {number} integralType - option to chose between approx area with gaussian function or sum of the points of given range
  * @param {number} frequencyCluster - distance limit to clustering the peaks.
+ * range = frequencyCluster / observeFrequency -> Peaks withing this range are considered to belongs to the same signal1D
  * @return {Array} nmr signals
  */
 function detectSignals(peakList, spectrum, nH, integralType, frequencyCluster) {
@@ -164,7 +169,7 @@ function detectSignals(peakList, spectrum, nH, integralType, frequencyCluster) {
     var signal1D = {};
     var prevPeak = {x: 100000, y: 0, width: 0};
     var peaks = null;
-    var rangeX = frequencyCluster / frequency; //Peaks withing this range are considered to belongs to the same signal1D
+    var rangeX = frequencyCluster / frequency;
     var spectrumIntegral = 0;
     var cs, sum, i, j;
     for (i = 0; i < peakList.length; i++) {

src/range/Ranges.js

@@ -84,7 +84,8 @@ class Ranges extends Array {
 
         return new Ranges(result);
     }
-
+
+
     static fromSpectrum(spectrum, opt) {
         this.options = Object.assign({}, {
             nH: 99,

src/range/peak2Vector.js

@@ -5,17 +5,17 @@
 /**
  * This function converts an array of peaks [{x, y, width}] in a vector equally x,y vector from a given window
  * TODO: This function is very general and should be placed somewhere else
- * @param {Array} peaks
- * @param {object} opt - it has some options to
- * @option {number} from - one limit of given window
- * @option {number} to - one limit of given window
- * @option {string} fnName - function name to generate the signals form
- * @option {number} nWidth - width factor of signal form
- * @option {number} nbPoints - number of points
+ * @param {Array} peaks - List of the peaks
+ * @param {object} options - it has some options to
+ * @option {number} [options.from] - one limit of given window
+ * @option {number} [options.to] - one limit of given window
+ * @option {string} [options.fnName] - function name to generate the signals form
+ * @option {number} [options.nWidth] - width factor of signal form
+ * @option {number} [options.nbPoints] - number of points that the vector will have
  * @return {{x: Array, y: Array}}
  */
-function peak2Vector(peaks, opt) {
-    var options = opt || {};
+function peak2Vector(peaks, options) {
+    var options = options || {};
     var from = options.from;
     var to = options.to;
     var nbPoints = options.nbPoints || 16 * 1024;