refactor: change variables and functions names

Change nmrPeakDetection by getRanges Change nmrPeakDetection2D by getZones Change variables names from signals to ranges or zones to make the code more comprensible. #7
cheminfo-js · Nov 17, 2016 · d0ad3a4 · d0ad3a4
1 parent ef31fd4
commit d0ad3a4
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Showing 11 changed files with 36 additions and 36 deletions.
diff --git a/dist/spectra-data.js b/dist/spectra-data.js
@@ -4700,7 +4700,7 @@ return /******/ (function(modules) { // webpackBootstrap
 
 
 	/**
-	 * @function nmrPeakDetection(parameters);
+	 * @function getRanges(parameters);
 	 * This function process the given spectraData and tries to determine the NMR signals. Returns an NMRSignal1D array containing all the detected 1D-NMR Signals
 	 * @param parameters A JSONObject containing the optional parameters:
 	 * @option fromX:   Lower limit.
@@ -4709,7 +4709,7 @@ return /******/ (function(modules) { // webpackBootstrap
 	 * @option stdev: Number of standard deviation of the noise for the threshold calculation if a threshold is not specified.
 	 * @returns {*}
 	 */
-	NMR.prototype.nmrPeakDetection=function(parameters) {
+	NMR.prototype.getRanges=function(parameters) {
 	    return peakPicking(this, parameters);
 	}
 
@@ -16379,14 +16379,14 @@ return /******/ (function(modules) { // webpackBootstrap
 	}
 
 	/**
-	 * @function nmrPeakDetection2D(options)
+	 * @function getZones(options)
 	 * This function process the given spectraData and tries to determine the NMR signals. 
 	 + Returns an NMRSignal2D array containing all the detected 2D-NMR Signals
 	 * @param	options:+Object			Object containing the options
 	 * @option	thresholdFactor:number	A factor to scale the automatically determined noise threshold.
 	 * @returns [*]	set of NMRSignal2D
 	 */
-	NMR2D.prototype.nmrPeakDetection2D=function(options){
+	NMR2D.prototype.getZones=function(options){
 	    options = options||{};
 	    if(!options.thresholdFactor)
 	        options.thresholdFactor=1;

diff --git a/examples/main1D.js b/examples/main1D.js
@@ -35,7 +35,7 @@ for (var i = 0; i < xy[0].length; i++) {
 if (true) {
     var d = new Date();
     var n = d.getTime();
-    var peakPicking = spectrum.nmrPeakDetection({nH: 10, realTop: true, thresholdFactor: 1, clean: true, compile: true,
+    var peakPicking = spectrum.getRanges({nH: 10, realTop: true, thresholdFactor: 1, clean: true, compile: true,
         gsdOptions: {minMaxRatio: 0.03, broadRatio: 0.0025, smoothY: true, nL: 4}
     });
     d = new Date();

diff --git a/src/NMR.js b/src/NMR.js
@@ -343,7 +343,7 @@ class NMR extends SD {
 
 
     /**
-     * @function nmrPeakDetection(parameters);
+     * @function getRanges(parameters);
      * This function process the given spectraData and tries to determine the NMR signals. Returns an NMRSignal1D array containing all the detected 1D-NMR Signals
      * @param parameters A JSONObject containing the optional parameters:
      * @option fromX:   Lower limit.
@@ -352,7 +352,7 @@ class NMR extends SD {
      * @option stdev: Number of standard deviation of the noise for the threshold calculation if a threshold is not specified.
      * @returns {*}
      */
-    nmrPeakDetection(parameters) {
+    getRanges(parameters) {
         return peakPicking(this, parameters);
     }
 }

diff --git a/src/NMR2D.js b/src/NMR2D.js
@@ -136,14 +136,14 @@ class NMR2D extends SD {
     }
 
     /**
-     * @function nmrPeakDetection2D(options)
+     * @function getZones(options)
      * This function process the given spectraData and tries to determine the NMR signals.
      + Returns an NMRSignal2D array containing all the detected 2D-NMR Signals
      * @param	options:+Object			Object containing the options
      * @option	thresholdFactor:number	A factor to scale the automatically determined noise threshold.
      * @returns [*]	set of NMRSignal2D
      */
-    nmrPeakDetection2D(options) {
+    getZones(options) {
         options = options || {};
         if (!options.thresholdFactor)            {
             options.thresholdFactor = 1;
@@ -164,10 +164,10 @@ class NMR2D extends SD {
         }
 
         if (options.format === 'new') {
-            var newSignals = new Array(peakList.length);
+            var zones = new Array(peakList.length);
             for (var k = peakList.length - 1; k >= 0; k--) {
                 var signal = peakList[k];
-                newSignals[k] = {
+                zones[k] = {
                     fromTo: signal.fromTo,
                     integral: signal.intensity || 1,
                     remark: '',
@@ -179,7 +179,7 @@ class NMR2D extends SD {
                     signalID: signal.signalID,
                 };
             }
-            peakList = newSignals;
+            peakList = zones;
         }
 
 

diff --git a/src/__tests__/NMR.js b/src/__tests__/NMR.js
@@ -68,13 +68,13 @@ describe('spectra-data examples ethylvinylether/1h.jdx', function () {
     });
 
     it('Check peak-picking in the new format', function () {
-        var peakPicking = spectrum.nmrPeakDetection({'nH': 8, realTop: true, thresholdFactor: 1, clean: true, compile: true, idPrefix: '1H', format: 'new'});
+        var peakPicking = spectrum.getRanges({'nH': 8, realTop: true, thresholdFactor: 1, clean: true, compile: true, idPrefix: '1H', format: 'new'});
         //console.log(peakPicking[0]);
         peakPicking[0].signal[0].peak.length.should.equal(4);
     });
 
     it('Check peak-picking in zone', function () {
-        var peakPicking = spectrum.nmrPeakDetection({'nH': 8, realTop: true, thresholdFactor: 1, clean: true, compile: true, idPrefix: '1H', format: 'new', from: 1, to: 2});
+        var peakPicking = spectrum.getRanges({'nH': 8, realTop: true, thresholdFactor: 1, clean: true, compile: true, idPrefix: '1H', format: 'new', from: 1, to: 2});
         //console.log(peakPicking[0]);
         peakPicking.length.should.eql(1);
         peakPicking[0].signal[0].multiplicity.should.eql('t');
@@ -86,7 +86,7 @@ describe('spectra-data examples ethylvinylether/1h.jdx', function () {
 
     it('updateIntegrals', function () {
         var nH = 8;
-        var ranges = spectrum.nmrPeakDetection({'nH': nH, realTop: true, thresholdFactor: 1, clean: true, compile: true, idPrefix: '1H', format: 'new'});
+        var ranges = spectrum.getRanges({'nH': nH, realTop: true, thresholdFactor: 1, clean: true, compile: true, idPrefix: '1H', format: 'new'});
         ranges[0].to = 6.47;
         var integral0 = ranges[0].integral;
         spectrum.updateIntegrals(ranges, {nH: nH});

diff --git a/src/__tests__/NMR2D.js b/src/__tests__/NMR2D.js
@@ -77,7 +77,7 @@ describe('spectra-data examples indometacin/hmbc.dx', function () {
     });
 
     it('Peak picking 2D', function () {
-        var signals2D = spectrum.nmrPeakDetection2D(
+        var signals2D = spectrum.getZones(
             {'thresholdFactor': 1,
                 'idPrefix': 'hmbc_',
                 'format': 'new'

diff --git a/src/peakPicking/PeakPicking.js b/src/peakPicking/PeakPicking.js
@@ -101,10 +101,10 @@ module.exports = function (spectrum, optionsEx) {
                     for (j = peaksO.length - 1; j >= 0; j--)                        {
                         peaks1.push(peaksO[j]);
                     }
-                    let newSignals = detectSignals(peaks1, spectrum, nHi, options.integralFn, options.frequencyCluster);
+                    let ranges = detectSignals(peaks1, spectrum, nHi, options.integralFn, options.frequencyCluster);
 
-                    for (j = 0; j < newSignals.length; j++)                        {
-                        signals.push(newSignals[j]);
+                    for (j = 0; j < ranges.length; j++)                        {
+                        signals.push(ranges[j]);
                     }
                 }
             }
@@ -137,10 +137,10 @@ module.exports = function (spectrum, optionsEx) {
     //removeImpurities(signals, spectrum.getSolventName(),options.nH);
 
     if (options.format === 'new') {
-        let newSignals = new Array(signals.length);
+        let ranges = new Array(signals.length);
         for (i = 0; i < signals.length; i++) {
             var signal = signals[i];
-            newSignals[i] = {
+            ranges[i] = {
                 from: signal.integralData.from,
                 to: signal.integralData.to,
                 integral: signal.integralData.value,
@@ -157,13 +157,13 @@ module.exports = function (spectrum, optionsEx) {
 
             };
             if (signal.nmrJs) {
-                newSignals[i].signal[0].j = signal.nmrJs;
+                ranges[i].signal[0].j = signal.nmrJs;
             }
             if (!signal.asymmetric || signal.multiplicity === 'm') {
-                newSignals[i].signal[0].delta = signal.delta1;
+                ranges[i].signal[0].delta = signal.delta1;
             }
         }
-        signals = newSignals;
+        signals = ranges;
     }
 
     return signals;

diff --git a/src/peakPicking/__tests__/ImpurityRemover.js b/src/peakPicking/__tests__/ImpurityRemover.js
@@ -10,11 +10,11 @@ function createSpectraData(filename, label, data) {
 }
 
 
-describe('spectra-data examples nmrPeakDetection', function () {
+describe('spectra-data examples getRanges', function () {
     it.skip('number of peaks', function () {
         var spectrum = createSpectraData('/../../../data-test/indometacin/1h.dx');
-        //console.log(spectrum.nmrPeakDetection);
-        var peakPicking = spectrum.nmrPeakDetection({
+        //console.log(spectrum.getRanges);
+        var peakPicking = spectrum.getRanges({
             'nH': 16,
             realTop: true,
             thresholdFactor: 1,

diff --git a/src/peakPicking/__tests__/ranges2ACS.js b/src/peakPicking/__tests__/ranges2ACS.js
@@ -16,8 +16,8 @@ function createSpectraData(filename, label, data) {
 
 describe('spectra-data examples peak picking in ACS format', function () {
     var spectrum = createSpectraData('/../../../data-test/ethylbenzene/h1_0.jdx');
-    var peakPicking = spectrum.nmrPeakDetection({'nH': 10, realTop: true, thresholdFactor: 0.8, clean: true, compile: true});
-    var peakPicking2 = spectrum.nmrPeakDetection({'nH': 10, realTop: true, thresholdFactor: 0.8, clean: true, compile: true, format: 'new'});
+    var peakPicking = spectrum.getRanges({'nH': 10, realTop: true, thresholdFactor: 0.8, clean: true, compile: true});
+    var peakPicking2 = spectrum.getRanges({'nH': 10, realTop: true, thresholdFactor: 0.8, clean: true, compile: true, format: 'new'});
     it('format ACS', function () {
         var acs = Data.formatter.toACS(peakPicking, {rangeForMultiplet: true});
         acs.should.equal('<sup>1</sup>H NMR (400 MHz) δ 7.26-7.32 (m, 2 H), 7.15-7.23 (m, 3 H), 2.60 (q, 2 H, <i>J</i> = 7.6 Hz), 1.19 (t, 3 H, <i>J</i> = 7.6 Hz).');

diff --git a/src/peakPicking/__tests__/rangesWithJCouplings.js b/src/peakPicking/__tests__/rangesWithJCouplings.js
@@ -17,7 +17,7 @@ function createSpectraData(filename, label, data) {
 describe('spectra-data examples peak picking', function () {
     var nH = 8;
     var spectrum = createSpectraData('/../../../data-test/ethylvinylether/1h.jdx');
-    var peakPicking = spectrum.nmrPeakDetection({'nH': nH, realTop: true, thresholdFactor: 1, clean: true, compile: true, idPrefix: '1H'});
+    var peakPicking = spectrum.getRanges({'nH': nH, realTop: true, thresholdFactor: 1, clean: true, compile: true, idPrefix: '1H'});
     //console.log(Data.ACS.formater.toACS(peakPicking,{solvent:spectrum.getSolventName()}));
     //console.log(peakPicking);
     it('Known patterns for ethylvinylether', function () {

diff --git a/src/visualizer/index.js b/src/visualizer/index.js
@@ -7,12 +7,12 @@
 var options1D = {type: 'rect', line: 0, lineLabel: 1, labelColor: 'red', strokeColor: 'red', strokeWidth: '1px', fillColor: 'green', width: 0.05, height: 10, toFixed: 1};
 var options2D = {type: 'rect', labelColor: 'red', strokeColor: 'red', strokeWidth: '1px', fillColor: 'green', width: '6px', height: '6px'};
 
-function annotations1D(signals, optionsG) {
+function annotations1D(ranges, optionsG) {
     var options = Object.assign({}, options1D, optionsG);
     var height = options.height;
     var annotations = [];
-    for (var i = 0; i < signals.length; i++) {
-        var prediction = signals[i];
+    for (var i = 0; i < ranges.length; i++) {
+        var prediction = ranges[i];
         var annotation = {};
 
         annotations.push(annotation);
@@ -59,11 +59,11 @@ function annotations1D(signals, optionsG) {
     return annotations;
 }
 
-function annotations2D(signals2D, optionsG) {
+function annotations2D(zones, optionsG) {
     var options = Object.assign({}, options2D, optionsG);
     var annotations = [];
-    for (var k = signals2D.length - 1; k >= 0; k--) {
-        var signal = signals2D[k];
+    for (var k = zones.length - 1; k >= 0; k--) {
+        var signal = zones[k];
         var annotation = {};
         annotation.type = options.type;
         annotation._highlight = signal._highlight;//["cosy"+k];