xy-parser - npm Package Compare versions

Comparing version 3.2.0 to 4.0.0

CHANGELOG.md

 # Changelog
 
+## [4.0.0](https://www.github.com/cheminfo/xy-parser/compare/v3.2.0...v4.0.0) (2021-11-09)
+
+
+### ⚠ BREAKING CHANGES
+
+* migrate to typescript
+
+### Features
+
+* migrate to typescript ([b067462](https://www.github.com/cheminfo/xy-parser/commit/b067462c1006045b7ec4fa9eed089ef3dcabeb1b))
+
 ## [3.2.0](https://www.github.com/cheminfo/xy-parser/compare/v3.1.1...v3.2.0) (2021-07-14)
@@ -4,0 +15,0 @@

lib/index.js

@@ -1,802 +0,114 @@
-'use strict';
-
-Object.defineProperty(exports, '__esModule', { value: true });
-
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.parseXY = void 0;
+const ensure_string_1 = require("ensure-string");
+const ml_array_max_1 = __importDefault(require("ml-array-max"));
+const ml_arrayxy_uniquex_1 = __importDefault(require("ml-arrayxy-uniquex"));
+const ml_spectra_processing_1 = require("ml-spectra-processing");
 /**
- * Ensure that the data is string. If it is an ArrayBuffer it will be converted to string using TextDecoder.
- * @param {string|ArrayBuffer} blob
- * @param {object} [options={}]
- * @param {string} [options.encoding='utf8']
- * @returns {string}
+ * Parse a text-file and convert it to an array of XY points.
+ *
+ * @param text - Csv or tsv strings.
+ * @param [options={}] -
+ * @param [options.rescale = false] - Will set the maximum value to 1.
+ * @param [options.uniqueX = false] - Make the X values unique (works only with 'xxyy' format). If the X value is repeated the sum of Y is done.
+ * @param [options.xColumn = 0] - A number that specifies the x column.
+ * @param [options.yColumn = 1] - A number that specifies the y column.
+ * @param [options.bestGuess=false] - Will try to guess which columns are the best.
+ * @param [options.numberColumns=Number.MAX_SAFE_INTEGER] - If the file has 10 columns and you specify here 2 it will reflow the file.
+ * @param [options.maxNumberColumns = (Math.max(xColumn, yColumn)+1)] - A number that specifies the maximum number of y columns.
+ * @param [options.minNumberColumns = (Math.min(xColumn, yColumn)+1)] - A number that specifies the minimum number of y columns.
+ * @param [options.keepInfo = false] - Should we keep the non numeric lines. In this case the system will return an object {data, info}.
+ * @returns -
  */
-
-function ensureString(blob, options = {}) {
-  const { encoding = 'utf8' } = options;
-  if (ArrayBuffer.isView(blob) || blob instanceof ArrayBuffer) {
-    const decoder = new TextDecoder(encoding);
-    return decoder.decode(blob);
-  }
-  return blob;
-}
-
-const toString$1 = Object.prototype.toString;
-
-function isAnyArray(object) {
-  return toString$1.call(object).endsWith('Array]');
-}
-
-function max(input) {
-  var options = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
-
-  if (!isAnyArray(input)) {
-    throw new TypeError('input must be an array');
-  }
-
-  if (input.length === 0) {
-    throw new TypeError('input must not be empty');
-  }
-
-  var _options$fromIndex = options.fromIndex,
-      fromIndex = _options$fromIndex === void 0 ? 0 : _options$fromIndex,
-      _options$toIndex = options.toIndex,
-      toIndex = _options$toIndex === void 0 ? input.length : _options$toIndex;
-
-  if (fromIndex < 0 || fromIndex >= input.length || !Number.isInteger(fromIndex)) {
-    throw new Error('fromIndex must be a positive integer smaller than length');
-  }
-
-  if (toIndex <= fromIndex || toIndex > input.length || !Number.isInteger(toIndex)) {
-    throw new Error('toIndex must be an integer greater than fromIndex and at most equal to length');
-  }
-
-  var maxValue = input[fromIndex];
-
-  for (var i = fromIndex + 1; i < toIndex; i++) {
-    if (input[i] > maxValue) maxValue = input[i];
-  }
-
-  return maxValue;
-}
-
-/**
- * In place modification of the 2 arrays to make X unique and sum the Y if X has the same value
- * @param {object} [points={}] : Object of points contains property x (an array) and y (an array)
- * @return points
- */
-
-function uniqueX(points = {}) {
-  const { x, y } = points;
-  if (x.length < 2) return;
-  if (x.length !== y.length) {
-    throw new Error('The X and Y arrays mush have the same length');
-  }
-
-  let current = x[0];
-  let counter = 0;
-
-  for (let i = 1; i < x.length; i++) {
-    if (current !== x[i]) {
-      counter++;
-      current = x[i];
-      x[counter] = x[i];
-      if (i !== counter) {
-        y[counter] = 0;
-      }
-    }
-    if (i !== counter) {
-      y[counter] += y[i];
-    }
-  }
-
-  x.length = counter + 1;
-  y.length = counter + 1;
-}
-
-var commonjsGlobal = typeof globalThis !== 'undefined' ? globalThis : typeof window !== 'undefined' ? window : typeof global !== 'undefined' ? global : typeof self !== 'undefined' ? self : {};
-
-function createCommonjsModule(fn, module) {
-	return module = { exports: {} }, fn(module, module.exports), module.exports;
-}
-
-createCommonjsModule(function (module) {
-(function(){function a(d){for(var e=0,f=d.length-1,g=void 0,h=void 0,i=void 0,j=c(e,f);!0;){if(f<=e)return d[j];if(f==e+1)return d[e]>d[f]&&b(d,e,f),d[j];for(g=c(e,f),d[g]>d[f]&&b(d,g,f),d[e]>d[f]&&b(d,e,f),d[g]>d[e]&&b(d,g,e),b(d,g,e+1),h=e+1,i=f;!0;){do h++;while(d[e]>d[h]);do i--;while(d[i]>d[e]);if(i<h)break;b(d,h,i);}b(d,e,i),i<=j&&(e=h),i>=j&&(f=i-1);}}var b=function b(d,e,f){var _ref;return _ref=[d[f],d[e]],d[e]=_ref[0],d[f]=_ref[1],_ref},c=function c(d,e){return ~~((d+e)/2)};module.exports?module.exports=a:window.median=a;})();
-});
-
-/**
- * Returns true if x is monotone
- * @param {Array} array
- * @return {boolean}
- */
-function xIsMonotone(array) {
-  if (array.length <= 2) {
-    return true;
-  }
-  if (array[0] === array[1]) {
-    // maybe a constant series
-    for (let i = 1; i < array.length - 1; i++) {
-      if (array[i] !== array[i + 1]) return false;
-    }
-    return true;
-  }
-
-  if (array[0] < array[array.length - 1]) {
-    for (let i = 0; i < array.length - 1; i++) {
-      if (array[i] >= array[i + 1]) return false;
-    }
-  } else {
-    for (let i = 0; i < array.length - 1; i++) {
-      if (array[i] <= array[i + 1]) return false;
-    }
-  }
-  return true;
-}
-
-createCommonjsModule(function (module, exports) {
-(function (global, factory) {
-  factory(exports) ;
-}(commonjsGlobal, function (exports) {
-  function ascending(a, b) {
-    return a < b ? -1 : a > b ? 1 : a >= b ? 0 : NaN;
-  }
-
-  function bisector(compare) {
-    if (compare.length === 1) compare = ascendingComparator(compare);
-    return {
-      left: function(a, x, lo, hi) {
-        if (lo == null) lo = 0;
-        if (hi == null) hi = a.length;
-        while (lo < hi) {
-          var mid = lo + hi >>> 1;
-          if (compare(a[mid], x) < 0) lo = mid + 1;
-          else hi = mid;
+function parseXY(text, options = {}) {
+    let { rescale = false, uniqueX = false, xColumn = 0, yColumn = 1, keepInfo = false, bestGuess = false, numberColumns = Number.MAX_SAFE_INTEGER, maxNumberColumns = Number.MAX_SAFE_INTEGER, minNumberColumns = 2, } = options;
+    text = (0, ensure_string_1.ensureString)(text);
+    maxNumberColumns = Math.max(maxNumberColumns, xColumn + 1, yColumn + 1);
+    minNumberColumns = Math.max(xColumn + 1, yColumn + 1, minNumberColumns);
+    let lines = text.split(/[\r\n]+/);
+    let matrix = [];
+    let info = [];
+    let position = 0;
+    lines.forEach((line) => {
+        line = line.trim();
+        // we will consider only lines that contains only numbers
+        if (/[0-9]+/.test(line) && /^[0-9eE,;. \t+-]+$/.test(line)) {
+            let fields = line.split(/,[; \t]+|[; \t]+/);
+            if (fields.length === 1) {
+                fields = line.split(/[,; \t]+/);
+            }
+            if (fields &&
+                fields.length >= minNumberColumns && // we filter lines that have not enough or too many columns
+                fields.length <= maxNumberColumns) {
+                matrix.push(fields.map((value) => parseFloat(value.replace(',', '.'))));
+                position++;
+            }
         }
-        return lo;
-      },
-      right: function(a, x, lo, hi) {
-        if (lo == null) lo = 0;
-        if (hi == null) hi = a.length;
-        while (lo < hi) {
-          var mid = lo + hi >>> 1;
-          if (compare(a[mid], x) > 0) hi = mid;
-          else lo = mid + 1;
+        else if (line) {
+            info.push({ position, value: line });
         }
-        return lo;
-      }
-    };
-  }
-
-  function ascendingComparator(f) {
-    return function(d, x) {
-      return ascending(f(d), x);
-    };
-  }
-
-  var ascendingBisect = bisector(ascending);
-  var bisectRight = ascendingBisect.right;
-  var bisectLeft = ascendingBisect.left;
-
-  function descending(a, b) {
-    return b < a ? -1 : b > a ? 1 : b >= a ? 0 : NaN;
-  }
-
-  function number$1(x) {
-    return x === null ? NaN : +x;
-  }
-
-  function variance(array, f) {
-    var n = array.length,
-        m = 0,
-        a,
-        d,
-        s = 0,
-        i = -1,
-        j = 0;
-
-    if (f == null) {
-      while (++i < n) {
-        if (!isNaN(a = number$1(array[i]))) {
-          d = a - m;
-          m += d / ++j;
-          s += d * (a - m);
+    });
+    if (bestGuess) {
+        if (matrix[0] &&
+            matrix[0].length === 3 &&
+            options.xColumn === undefined &&
+            options.yColumn === undefined) {
+            // is the first column a seuqnetial number ?
+            let skipFirstColumn = true;
+            for (let i = 0; i < matrix.length - 1; i++) {
+                if (Math.abs(matrix[i][0] - matrix[i + 1][0]) !== 1) {
+                    skipFirstColumn = false;
+                }
+            }
+            if (skipFirstColumn) {
+                xColumn = 1;
+                yColumn = 2;
+            }
         }
-      }
+        if (matrix[0] && matrix[0].length > 3) {
+            const xs = [];
+            for (let row of matrix) {
+                for (let i = xColumn; i < row.length; i += 2) {
+                    xs.push(row[i]);
+                }
+            }
+            if ((0, ml_spectra_processing_1.xIsMonotone)(xs)) {
+                numberColumns = 2;
+            }
+        }
     }
-
-    else {
-      while (++i < n) {
-        if (!isNaN(a = number$1(f(array[i], i, array)))) {
-          d = a - m;
-          m += d / ++j;
-          s += d * (a - m);
+    if (numberColumns) {
+        const newMatrix = [];
+        for (const row of matrix) {
+            for (let i = 0; i < row.length; i += numberColumns) {
+                newMatrix.push(row.slice(i, i + numberColumns));
+            }
         }
-      }
+        matrix = newMatrix;
     }
-
-    if (j > 1) return s / (j - 1);
-  }
-
-  function deviation(array, f) {
-    var v = variance(array, f);
-    return v ? Math.sqrt(v) : v;
-  }
-
-  function extent(array, f) {
-    var i = -1,
-        n = array.length,
-        a,
-        b,
-        c;
-
-    if (f == null) {
-      while (++i < n) if ((b = array[i]) != null && b >= b) { a = c = b; break; }
-      while (++i < n) if ((b = array[i]) != null) {
-        if (a > b) a = b;
-        if (c < b) c = b;
-      }
-    }
-
-    else {
-      while (++i < n) if ((b = f(array[i], i, array)) != null && b >= b) { a = c = b; break; }
-      while (++i < n) if ((b = f(array[i], i, array)) != null) {
-        if (a > b) a = b;
-        if (c < b) c = b;
-      }
-    }
-
-    return [a, c];
-  }
-
-  function constant(x) {
-    return function() {
-      return x;
+    const result = {
+        x: matrix.map((row) => row[xColumn]),
+        y: matrix.map((row) => row[yColumn]),
     };
-  }
-
-  function identity(x) {
-    return x;
-  }
-
-  function range(start, stop, step) {
-    start = +start, stop = +stop, step = (n = arguments.length) < 2 ? (stop = start, start = 0, 1) : n < 3 ? 1 : +step;
-
-    var i = -1,
-        n = Math.max(0, Math.ceil((stop - start) / step)) | 0,
-        range = new Array(n);
-
-    while (++i < n) {
-      range[i] = start + i * step;
+    if (uniqueX) {
+        (0, ml_arrayxy_uniquex_1.default)(result);
     }
-
-    return range;
-  }
-
-  var e10 = Math.sqrt(50);
-  var e5 = Math.sqrt(10);
-  var e2 = Math.sqrt(2);
-  function ticks(start, stop, count) {
-    var step = tickStep(start, stop, count);
-    return range(
-      Math.ceil(start / step) * step,
-      Math.floor(stop / step) * step + step / 2, // inclusive
-      step
-    );
-  }
-
-  function tickStep(start, stop, count) {
-    var step0 = Math.abs(stop - start) / Math.max(0, count),
-        step1 = Math.pow(10, Math.floor(Math.log(step0) / Math.LN10)),
-        error = step0 / step1;
-    if (error >= e10) step1 *= 10;
-    else if (error >= e5) step1 *= 5;
-    else if (error >= e2) step1 *= 2;
-    return stop < start ? -step1 : step1;
-  }
-
-  function sturges(values) {
-    return Math.ceil(Math.log(values.length) / Math.LN2) + 1;
-  }
-
-  function number(x) {
-    return +x;
-  }
-
-  function histogram() {
-    var value = identity,
-        domain = extent,
-        threshold = sturges;
-
-    function histogram(data) {
-      var i,
-          n = data.length,
-          x,
-          values = new Array(n);
-
-      // Coerce values to numbers.
-      for (i = 0; i < n; ++i) {
-        values[i] = +value(data[i], i, data);
-      }
-
-      var xz = domain(values),
-          x0 = +xz[0],
-          x1 = +xz[1],
-          tz = threshold(values, x0, x1);
-
-      // Convert number of thresholds into uniform thresholds.
-      if (!Array.isArray(tz)) tz = ticks(x0, x1, +tz);
-
-      // Coerce thresholds to numbers, ignoring any outside the domain.
-      var m = tz.length;
-      for (i = 0; i < m; ++i) tz[i] = +tz[i];
-      while (tz[0] <= x0) tz.shift(), --m;
-      while (tz[m - 1] >= x1) tz.pop(), --m;
-
-      var bins = new Array(m + 1),
-          bin;
-
-      // Initialize bins.
-      for (i = 0; i <= m; ++i) {
-        bin = bins[i] = [];
-        bin.x0 = i > 0 ? tz[i - 1] : x0;
-        bin.x1 = i < m ? tz[i] : x1;
-      }
-
-      // Assign data to bins by value, ignoring any outside the domain.
-      for (i = 0; i < n; ++i) {
-        x = values[i];
-        if (x0 <= x && x <= x1) {
-          bins[bisectRight(tz, x, 0, m)].push(data[i]);
+    if (rescale) {
+        let maxY = (0, ml_array_max_1.default)(result.y);
+        for (let i = 0; i < result.y.length; i++) {
+            result.y[i] /= maxY;
         }
-      }
-
-      return bins;
     }
-
-    histogram.value = function(_) {
-      return arguments.length ? (value = typeof _ === "function" ? _ : constant(+_), histogram) : value;
+    if (!keepInfo)
+        return result;
+    return {
+        info,
+        data: result,
     };
-
-    histogram.domain = function(_) {
-      return arguments.length ? (domain = typeof _ === "function" ? _ : constant([+_[0], +_[1]]), histogram) : domain;
-    };
-
-    histogram.thresholds = function(_) {
-      if (!arguments.length) return threshold;
-      threshold = typeof _ === "function" ? _
-          : Array.isArray(_) ? constant(Array.prototype.map.call(_, number))
-          : constant(+_);
-      return histogram;
-    };
-
-    return histogram;
-  }
-
-  function quantile(array, p, f) {
-    if (f == null) f = number$1;
-    if (!(n = array.length)) return;
-    if ((p = +p) <= 0 || n < 2) return +f(array[0], 0, array);
-    if (p >= 1) return +f(array[n - 1], n - 1, array);
-    var n,
-        h = (n - 1) * p,
-        i = Math.floor(h),
-        a = +f(array[i], i, array),
-        b = +f(array[i + 1], i + 1, array);
-    return a + (b - a) * (h - i);
-  }
-
-  function freedmanDiaconis(values, min, max) {
-    values.sort(ascending);
-    return Math.ceil((max - min) / (2 * (quantile(values, 0.75) - quantile(values, 0.25)) * Math.pow(values.length, -1 / 3)));
-  }
-
-  function scott(values, min, max) {
-    return Math.ceil((max - min) / (3.5 * deviation(values) * Math.pow(values.length, -1 / 3)));
-  }
-
-  function max(array, f) {
-    var i = -1,
-        n = array.length,
-        a,
-        b;
-
-    if (f == null) {
-      while (++i < n) if ((b = array[i]) != null && b >= b) { a = b; break; }
-      while (++i < n) if ((b = array[i]) != null && b > a) a = b;
-    }
-
-    else {
-      while (++i < n) if ((b = f(array[i], i, array)) != null && b >= b) { a = b; break; }
-      while (++i < n) if ((b = f(array[i], i, array)) != null && b > a) a = b;
-    }
-
-    return a;
-  }
-
-  function mean(array, f) {
-    var s = 0,
-        n = array.length,
-        a,
-        i = -1,
-        j = n;
-
-    if (f == null) {
-      while (++i < n) if (!isNaN(a = number$1(array[i]))) s += a; else --j;
-    }
-
-    else {
-      while (++i < n) if (!isNaN(a = number$1(f(array[i], i, array)))) s += a; else --j;
-    }
-
-    if (j) return s / j;
-  }
-
-  function median(array, f) {
-    var numbers = [],
-        n = array.length,
-        a,
-        i = -1;
-
-    if (f == null) {
-      while (++i < n) if (!isNaN(a = number$1(array[i]))) numbers.push(a);
-    }
-
-    else {
-      while (++i < n) if (!isNaN(a = number$1(f(array[i], i, array)))) numbers.push(a);
-    }
-
-    return quantile(numbers.sort(ascending), 0.5);
-  }
-
-  function merge(arrays) {
-    var n = arrays.length,
-        m,
-        i = -1,
-        j = 0,
-        merged,
-        array;
-
-    while (++i < n) j += arrays[i].length;
-    merged = new Array(j);
-
-    while (--n >= 0) {
-      array = arrays[n];
-      m = array.length;
-      while (--m >= 0) {
-        merged[--j] = array[m];
-      }
-    }
-
-    return merged;
-  }
-
-  function min(array, f) {
-    var i = -1,
-        n = array.length,
-        a,
-        b;
-
-    if (f == null) {
-      while (++i < n) if ((b = array[i]) != null && b >= b) { a = b; break; }
-      while (++i < n) if ((b = array[i]) != null && a > b) a = b;
-    }
-
-    else {
-      while (++i < n) if ((b = f(array[i], i, array)) != null && b >= b) { a = b; break; }
-      while (++i < n) if ((b = f(array[i], i, array)) != null && a > b) a = b;
-    }
-
-    return a;
-  }
-
-  function pairs(array) {
-    var i = 0, n = array.length - 1, p = array[0], pairs = new Array(n < 0 ? 0 : n);
-    while (i < n) pairs[i] = [p, p = array[++i]];
-    return pairs;
-  }
-
-  function permute(array, indexes) {
-    var i = indexes.length, permutes = new Array(i);
-    while (i--) permutes[i] = array[indexes[i]];
-    return permutes;
-  }
-
-  function scan(array, compare) {
-    if (!(n = array.length)) return;
-    var i = 0,
-        n,
-        j = 0,
-        xi,
-        xj = array[j];
-
-    if (!compare) compare = ascending;
-
-    while (++i < n) if (compare(xi = array[i], xj) < 0 || compare(xj, xj) !== 0) xj = xi, j = i;
-
-    if (compare(xj, xj) === 0) return j;
-  }
-
-  function shuffle(array, i0, i1) {
-    var m = (i1 == null ? array.length : i1) - (i0 = i0 == null ? 0 : +i0),
-        t,
-        i;
-
-    while (m) {
-      i = Math.random() * m-- | 0;
-      t = array[m + i0];
-      array[m + i0] = array[i + i0];
-      array[i + i0] = t;
-    }
-
-    return array;
-  }
-
-  function sum(array, f) {
-    var s = 0,
-        n = array.length,
-        a,
-        i = -1;
-
-    if (f == null) {
-      while (++i < n) if (a = +array[i]) s += a; // Note: zero and null are equivalent.
-    }
-
-    else {
-      while (++i < n) if (a = +f(array[i], i, array)) s += a;
-    }
-
-    return s;
-  }
-
-  function transpose(matrix) {
-    if (!(n = matrix.length)) return [];
-    for (var i = -1, m = min(matrix, length), transpose = new Array(m); ++i < m;) {
-      for (var j = -1, n, row = transpose[i] = new Array(n); ++j < n;) {
-        row[j] = matrix[j][i];
-      }
-    }
-    return transpose;
-  }
-
-  function length(d) {
-    return d.length;
-  }
-
-  function zip() {
-    return transpose(arguments);
-  }
-
-  var version = "0.7.1";
-
-  exports.version = version;
-  exports.bisect = bisectRight;
-  exports.bisectRight = bisectRight;
-  exports.bisectLeft = bisectLeft;
-  exports.ascending = ascending;
-  exports.bisector = bisector;
-  exports.descending = descending;
-  exports.deviation = deviation;
-  exports.extent = extent;
-  exports.histogram = histogram;
-  exports.thresholdFreedmanDiaconis = freedmanDiaconis;
-  exports.thresholdScott = scott;
-  exports.thresholdSturges = sturges;
-  exports.max = max;
-  exports.mean = mean;
-  exports.median = median;
-  exports.merge = merge;
-  exports.min = min;
-  exports.pairs = pairs;
-  exports.permute = permute;
-  exports.quantile = quantile;
-  exports.range = range;
-  exports.scan = scan;
-  exports.shuffle = shuffle;
-  exports.sum = sum;
-  exports.ticks = ticks;
-  exports.tickStep = tickStep;
-  exports.transpose = transpose;
-  exports.variance = variance;
-  exports.zip = zip;
-
-}));
-});
-
-/*!
- * assign-symbols <https://github.com/jonschlinkert/assign-symbols>
- *
- * Copyright (c) 2015-present, Jon Schlinkert.
- * Licensed under the MIT License.
- */
-
-const toString = Object.prototype.toString;
-const isEnumerable = Object.prototype.propertyIsEnumerable;
-const getSymbols = Object.getOwnPropertySymbols;
-
-var assignSymbols = (target, ...args) => {
-  if (!isObject(target)) {
-    throw new TypeError('expected the first argument to be an object');
-  }
-
-  if (args.length === 0 || typeof Symbol !== 'function' || typeof getSymbols !== 'function') {
-    return target;
-  }
-
-  for (let arg of args) {
-    let names = getSymbols(arg);
-
-    for (let key of names) {
-      if (isEnumerable.call(arg, key)) {
-        target[key] = arg[key];
-      }
-    }
-  }
-  return target;
-};
-
-function isObject(val) {
-  return typeof val === 'function' || toString.call(val) === '[object Object]' || Array.isArray(val);
 }
-
-createCommonjsModule(function (module) {
-
-const toString = Object.prototype.toString;
-
-
-const isValidKey = key => {
-  return key !== '__proto__' && key !== 'constructor' && key !== 'prototype';
-};
-
-const assign = module.exports = (target, ...args) => {
-  let i = 0;
-  if (isPrimitive(target)) target = args[i++];
-  if (!target) target = {};
-  for (; i < args.length; i++) {
-    if (isObject(args[i])) {
-      for (const key of Object.keys(args[i])) {
-        if (isValidKey(key)) {
-          if (isObject(target[key]) && isObject(args[i][key])) {
-            assign(target[key], args[i][key]);
-          } else {
-            target[key] = args[i][key];
-          }
-        }
-      }
-      assignSymbols(target, args[i]);
-    }
-  }
-  return target;
-};
-
-function isObject(val) {
-  return typeof val === 'function' || toString.call(val) === '[object Object]';
-}
-
-function isPrimitive(val) {
-  return typeof val === 'object' ? val === null : typeof val !== 'function';
-}
-});
-
-/**
- * Parse a text-file and convert it to an array of XY points
- * @param {string} text - csv or tsv strings
- * @param {object} [options={}]
- * @param {boolean} [options.rescale = false] - will set the maximum value to 1
- * @param {boolean} [options.uniqueX = false] - Make the X values unique (works only with 'xxyy' format). If the X value is repeated the sum of Y is done.
- * @param {number} [options.xColumn = 0] - A number that specifies the x column
- * @param {number} [options.yColumn = 1] - A number that specifies the y column
- * @param {boolean} [options.bestGuess=false] Will try to guess which columns are the best
- * @param {number} [options.numberColumns=Number.MAX_SAFE_INTEGER] If the file has 10 columns and you specify here 2 it will reflow the file
- * @param {number} [options.maxNumberColumns = (Math.max(xColumn, yColumn)+1)] - A number that specifies the maximum number of y columns
- * @param {number} [options.minNumberColumns = (Math.min(xColumn, yColumn)+1)] - A number that specifies the minimum number of y columns
- * @param {boolean} [options.keepInfo = false] - shoud we keep the non numeric lines. In this case the system will return an object {data, info}
- * @return {object{x:<Array<number>>,y:<Array<number>>}
- */
-function parseXY(text, options = {}) {
-  let {
-    rescale = false,
-    uniqueX: uniqueX$1 = false,
-    xColumn = 0,
-    yColumn = 1,
-    keepInfo = false,
-    bestGuess = false,
-    numberColumns = Number.MAX_SAFE_INTEGER,
-    maxNumberColumns = Number.MAX_SAFE_INTEGER,
-    minNumberColumns = 2,
-  } = options;
-
-  text = ensureString(text);
-
-  maxNumberColumns = Math.max(maxNumberColumns, xColumn + 1, yColumn + 1);
-  minNumberColumns = Math.max(xColumn + 1, yColumn + 1, minNumberColumns);
-
-  let lines = text.split(/[\r\n]+/);
-
-  let matrix = [];
-  let info = [];
-  let position = 0;
-  for (let l = 0; l < lines.length; l++) {
-    let line = lines[l].trim();
-    // we will consider only lines that contains only numbers
-    if (line.match(/[0-9]+/) && line.match(/^[0-9eE,;. \t+-]+$/)) {
-      let fields = line.split(/,[; \t]+|[; \t]+/);
-      if (fields.length === 1) {
-        fields = line.split(/[,; \t]+/);
-      }
-      if (
-        fields &&
-        fields.length >= minNumberColumns && // we filter lines that have not enough or too many columns
-        fields.length <= maxNumberColumns
-      ) {
-        matrix.push(fields.map((value) => parseFloat(value.replace(",", "."))));
-        position++;
-      }
-    } else if (line) {
-      info.push({ position, value: line });
-    }
-  }
-
-  if (bestGuess) {
-    if (
-      matrix[0] &&
-      matrix[0].length === 3 &&
-      options.xColumn === undefined &&
-      options.yColumn === undefined
-    ) {
-      // is the first column a seuqnetial number ?
-      let skipFirstColumn = true;
-      for (let i = 0; i < matrix.length - 1; i++) {
-        if (Math.abs(matrix[i][0] - matrix[i + 1][0]) !== 1) {
-          skipFirstColumn = false;
-        }
-      }
-      if (skipFirstColumn) {
-        xColumn = 1;
-        yColumn = 2;
-      }
-    }
-    if (matrix[0] && matrix[0].length > 3) {
-      let xs = [];
-      for (let row of matrix) {
-        for (let i = xColumn; i < row.length; i += 2) {
-          xs.push(row[i]);
-        }
-      }
-      if (xIsMonotone(xs)) {
-        numberColumns = 2;
-      }
-    }
-  }
-
-  if (numberColumns) {
-    const newMatrix = [];
-    for (const row of matrix) {
-      for (let i = 0; i < row.length; i += numberColumns) {
-        newMatrix.push(row.slice(i, i + numberColumns));
-      }
-    }
-    matrix = newMatrix;
-  }
-  const result = {
-    x: matrix.map((row) => row[xColumn]),
-    y: matrix.map((row) => row[yColumn]),
-  };
-
-  if (uniqueX$1) {
-    uniqueX(result);
-  }
-
-  if (rescale) {
-    let maxY = max(result.y);
-    for (let i = 0; i < result.y.length; i++) {
-      result.y[i] /= maxY;
-    }
-  }
-
-  if (!keepInfo) return result;
-
-  return {
-    info,
-    data: result,
-  };
-}
-
 exports.parseXY = parseXY;
+//# sourceMappingURL=index.js.map

package.json

 {
   "name": "xy-parser",
-  "version": "3.2.0",
+  "version": "4.0.0",
   "description": "Parse a text-file and convert it to an array of XY points",
-  "main": "lib/index.js",
-  "module": "src/index.js",
+  "main": "./lib/index.js",
+  "module": "./lib-esm/index.js",
+  "types": "./lib/index.d.ts",
   "files": [
     "lib",
-    "src"
+    "src",
+    "lib-esm"
   ],
   "scripts": {
-    "build": "rollup -c && cheminfo-build --root XYParser",
     "build-doc": "cheminfo doc",
+    "check-types": "tsc --noEmit",
+    "clean": "rimraf lib lib-esm",
     "eslint": "eslint src",
     "eslint-fix": "npm run eslint -- --fix",
-    "prepublishOnly": "rollup -c",
-    "test": "npm run testonly && npm run eslint",
+    "prepack": "npm run tsc",
+    "prettier": "prettier --check src",
+    "prettier-write": "prettier --write src",
+    "test": "npm run test-only && npm run eslint && npm run check-types",
     "test-coverage": "jest --coverage",
-    "testonly": "jest"
+    "test-only": "jest",
+    "tsc": "npm run clean && npm run tsc-cjs && npm run tsc-esm",
+    "tsc-cjs": "tsc --project tsconfig.cjs.json",
+    "tsc-esm": "tsc --project tsconfig.esm.json"
   },
@@ -35,29 +43,21 @@ "repository": {
   "homepage": "https://github.com/cheminfo/xy-parser#readme",
-  "jest": {
-    "testEnvironment": "node"
-  },
   "devDependencies": {
-    "@types/jest": "^26.0.24",
+    "@types/jest": "^27.0.2",
     "babel-plugin-transform-es2015-modules-commonjs": "^6.26.2",
-    "cheminfo-build": "^1.1.11",
     "cheminfo-tools": "^1.23.3",
-    "codecov": "^3.8.2",
-    "eslint": "^7.30.0",
-    "eslint-config-cheminfo": "^5.2.4",
-    "eslint-plugin-import": "^2.23.4",
-    "eslint-plugin-jest": "^24.3.6",
-    "eslint-plugin-no-only-tests": "^2.6.0",
-    "eslint-plugin-prettier": "^3.4.0",
-    "jest": "^27.0.6",
-    "prettier": "^2.3.2",
-    "rollup": "^2.53.1",
-    "rollup-plugin-commonjs": "^10.1.0",
-    "rollup-plugin-node-resolve": "^5.2.0"
+    "codecov": "^3.8.3",
+    "eslint": "^8.2.0",
+    "eslint-config-cheminfo-typescript": "^10.2.2",
+    "jest": "^27.3.1",
+    "prettier": "^2.4.1",
+    "rimraf": "^3.0.2",
+    "ts-jest": "^27.0.7",
+    "typescript": "^4.4.4"
   },
   "dependencies": {
-    "ensure-string": "^0.1.1",
+    "ensure-string": "^1.1.0",
     "ml-array-max": "^1.2.3",
     "ml-arrayxy-uniquex": "1.0.2",
-    "ml-spectra-processing": "^6.7.1"
+    "ml-spectra-processing": "^6.8.0"
   }
 }

README.md

@@ -15,5 +15,6 @@ # xy-parser
 
-  [![NPM version][npm-image]][npm-url]
-  [![Test coverage][codecov-image]][codecov-url]
-  [![npm download][download-image]][download-url]
+[![NPM version][npm-image]][npm-url]
+[![Test coverage][codecov-image]][codecov-url]
+[![npm download][download-image]][download-url]
+[![DOI](https://www.zenodo.org/badge/35540080.svg)](https://www.zenodo.org/badge/latestdoi/35540080)
 
@@ -59,3 +60,3 @@ </h3>
 
-If there are 3 columns and the first column is a sequential number starting at '1' it looks 
+If there are 3 columns and the first column is a sequential number starting at '1' it looks
 like this is a line number, we will ignore it.
@@ -62,0 +63,0 @@

New alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Major refactor

Supply chain risk

Package has recently undergone a major refactor. It may be unstable or indicate significant internal changes. Use caution when updating to versions that include significant changes.

Found 1 instance in 1 package

Fixed alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Filesystem access

Supply chain risk

Accesses the file system, and could potentially read sensitive data.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

38744

increased by2.95%

Dev dependency count

11

decreased by-31.25%

Number of package files

18

increased by80%

Number of lines in readme file

77

increased by1.32%

Number of low supply chain risk alerts

0

decreased by-100%

Worsened metrics

Lines of code

642

decreased by-34.76%

Number of medium supply chain risk alerts

1

increased byInfinity%

Dependency changes

• + Addedcheminfo-types@1.8.1(transitive)

• + Addedensure-string@1.2.0(transitive)

• + Addedisutf8@4.0.1(transitive)

• - Removedensure-string@0.1.1(transitive)

• Updatedensure-string@^1.1.0

• Updatedml-spectra-processing@^6.8.0