feat(spectraComparison): finds similar peaks

src/spectraComparison.js

@@ -0,0 +1,106 @@
+'use strict';
+
+const peakPicking = require('./peakPicking');
+const massInPeaks = require('./massInPeaks');
+const vectorify = require('./vectorify');
+const cosine = require('./cosine');
+
+function preprocessing(chromatography, options) {
+    // peak picking
+    let peaks = peakPicking(chromatography, options);
+    peaks = peaks.sort((a, b) => a.index - b.index);
+
+    // integrate mass in the peaks
+    let ms = chromatography.findSerieByName('ms').data;
+    let integratedMs = massInPeaks(peaks, ms, options);
+    let vector = vectorify(integratedMs, options);
+
+    return {
+        peaks,
+        ms,
+        integratedMs,
+        vector
+    };
+}
+
+const defaultOption = {
+    thresholdFactor: 0,
+    maxNumberPeaks: Number.MAX_VALUE,
+    groupWidth: 0,
+    heightFilter: 2,
+    massPower: 3,
+    intPower: 0.6,
+    similarityThreshold: 0.7
+};
+
+function spectraComparison(chrom1, chrom2, options) {
+    options = Object.extends({}, defaultOption, options);
+
+    // peak picking
+    let reference = preprocessing(chrom1, options);
+    let sample = preprocessing(chrom2, options);
+
+    // similarity between MS
+    const len = Math.max(sample.peaks.length, reference.peaks.length);
+    let similarityPeaks = {
+        chrom1: new Array(len),
+        chrom2: new Array(len),
+        similarity: new Array(len)
+    };
+    let similarLen = 0;
+
+    // Similarity matrix
+    for (let i = 0; i < sample.peaks.length; ++i) {
+        let max = {similarity: -3};
+        let biggerCounter = 0;
+        for (let j = 0; j < reference.peaks.length; ++j) {
+            let sim = cosine(sample.vector[i].x, sample.vector[i].y, reference.vector[j].x, reference.vector[j].y);
+
+            if (sim > options.similarityThreshold && sim > max.similarity) {
+                max = {
+                    similarity: sim,
+                    chrom1: reference.peaks[j],
+                    chrom2: sample.peaks[i]
+                };
+            }
+            if (sim > options.similarityThreshold) {
+                ++biggerCounter;
+            }
+        }
+        if (biggerCounter === 1) {
+            similarityPeaks.chrom1[similarLen] = max.chrom1;
+            similarityPeaks.chrom2[similarLen] = max.chrom2;
+            similarityPeaks.similarity[similarLen++] = max.similarity;
+        }
+    }
+    similarityPeaks.chrom1.length = similarLen;
+    similarityPeaks.chrom2.length = similarLen;
+
+    let duplicates = {};
+    for (let i = 0; i < similarLen; ++i) {
+        if (duplicates.hasOwnProperty(similarityPeaks.chrom1.peaks[i].x)) {
+            duplicates[similarityPeaks.chrom1.peaks[i].x].push(i);
+        } else {
+            duplicates[similarityPeaks.chrom1.peaks[i].x] = [i];
+        }
+    }
+
+    let peaksChrom1 = [];
+    let peaksChrom2 = [];
+    let peaksSimilarity = [];
+    for (let val in duplicates) {
+        if (duplicates[val].length === 1) {
+            peaksChrom1.push(similarityPeaks.chrom1[duplicates[val][0]]);
+            peaksChrom2.push(similarityPeaks.chrom2[duplicates[val][0]]);
+            peaksSimilarity.push(similarityPeaks.similarity[duplicates[val][0]]);
+        }
+    }
+
+    return {
+        peaksFirst: peaksChrom1,
+        peaksSecond: peaksChrom2,
+        peaksSimilarity: peaksSimilarity,
+    };
+}
+
+module.exports = spectraComparison;