@sjcrh/proteinpaint-shared 2.186.0 → 2.188.0

package/dist/src/termdb.bins.js

@@ -0,0 +1,272 @@
+import { format } from "d3-format";
+import { getColors } from "./common.js";
+import { isNumeric, isStrictNumeric, convertUnits } from "./helpers.js";
+function validate_bins(binconfig) {
+  const bc = binconfig;
+  if (!bc || typeof bc !== "object") throw "bin schema must be an object";
+  if (!("type" in bc)) bc.type = "regular-bin";
+  if (bc.type == "custom-bin") {
+    if (!Array.isArray(bc.lst)) throw "binconfig.lst must be an array";
+    if (!bc.lst.length) throw "binconfig.lst must have entries";
+    const first_bin = bc.lst[0];
+    const last_bin = bc.lst[bc.lst.length - 1];
+    for (const bin of bc.lst) {
+      if (!("startinclusive" in bin) && !("stopinclusive" in bin)) {
+        throw "custom bin.startinclusive and/or bin.stopinclusive must be defined";
+      }
+      if (bin == first_bin) {
+        if ("startunbounded" in bin && !bin.startunbounded) {
+          throw `a custom first bin must not set bin.startunbounded to false`;
+        }
+        bin.startunbounded = true;
+        if ("start" in bin) {
+          throw "a custom first bin must not set a bin.start value";
+        }
+        if ("start_percentile" in bin) {
+          throw "the first bin must not set a bin.start_percentile value";
+        }
+        if (!("stop" in bin)) {
+          throw `a custom first bin must define a bin.stop value`;
+        }
+        if (!isStrictNumeric(bin.stop)) {
+          throw `a custom first bin.stop value should be numeric`;
+        }
+      } else if (bin == last_bin) {
+        if (!("start" in bin)) {
+          throw `a custom last bin must define a bin.start value`;
+        }
+        if (!isStrictNumeric(bin.start)) {
+          throw `a custom last bin.start must be numeric`;
+        }
+        if ("stopunbounded" in bin && !bin.stopunbounded) {
+          throw "a custom last bin must not set bin.stopunbounded to false";
+        }
+        bin.stopunbounded = true;
+        if ("stop" in bin) {
+          throw "a custom last bin must not set a bin.stop value";
+        }
+      } else {
+        if (bin.startunbounded || bin.stopunbounded) {
+          throw "bin.startunbounded and bin.stopunbounded must not be set for non-first/non-last bins";
+        }
+        if (!isStrictNumeric(bin.start)) throw "bin.start must be numeric for a non-first bin";
+        if (!isStrictNumeric(bin.stop)) throw "bin.stop must be numeric for a non-last bin";
+      }
+    }
+  } else if (bc.type == "regular-bin") {
+    if (!Number.isFinite(bc.bin_size)) throw "non-numeric bin_size";
+    if (bc.bin_size <= 0) throw "bin_size must be greater than 0";
+    if (!bc.startinclusive && !bc.stopinclusive) {
+      bc.startinclusive = 1;
+      bc.stopinclusive = 0;
+    }
+    if (!bc.first_bin) throw "first_bin{} missing";
+    if (typeof bc.first_bin != "object") throw "first_bin{} is not an object";
+    if (!Object.keys(bc.first_bin).length) throw "first_bin is an empty object";
+    {
+      const b = bc.first_bin;
+      b.startunbounded = true;
+      if (b.stop_percentile) {
+        if (!Number.isInteger(b.stop_percentile)) throw "first_bin.stop_percentile should be integer";
+        if (b.stop_percentile <= 0 || b.stop_percentile >= 100) throw "first_bin.stop_percentile out of bound (0-100)";
+      } else if (!Number.isFinite(b.stop)) {
+        throw "first_bin.stop not a number when stop_percentile is not set";
+      }
+    }
+    if (bc.last_bin) {
+      const b = bc.last_bin;
+      if (b.start_percentile) {
+        if (!Number.isInteger(b.start_percentile)) throw "last_bin.start_percentile should be integer";
+        if (b.start_percentile <= 0 || b.start_percentile >= 100) throw "last_bin.start_percentile out of bound (0-100)";
+      } else if (!Number.isFinite(b.start)) {
+        throw "last_bin.start not a number when start_percentile is not set";
+      }
+      b.stopunbounded = true;
+      if ("stop" in b) {
+        throw "a regular last bin must not set a bin.stop value";
+      }
+    }
+  } else {
+    throw `invalid binconfig.type="${bc.type}"`;
+  }
+}
+function compute_bins(binconfig, summaryfxn, valueConversion) {
+  const bc = binconfig;
+  validate_bins(bc);
+  if (bc.lst) {
+    const k2c2 = getColors(bc.lst.length);
+    for (const bin of bc.lst) bin.color = k2c2(bin.label);
+  }
+  if (bc.type == "custom-bin") return JSON.parse(JSON.stringify(bc.lst));
+  if (typeof summaryfxn != "function") throw "summaryfxn required for modules/termdb.bins.js compute_bins()";
+  const percentiles = target_percentiles(bc);
+  const summary = summaryfxn(percentiles);
+  if (!summary || typeof summary !== "object") throw "invalid returned value by summaryfxn";
+  bc.results = { summary };
+  if (!bc.binLabelFormatter) bc.binLabelFormatter = getNumDecimalsFormatter(bc);
+  const minFloor = Math.floor(summary.min * 100) / 100;
+  const maxCeil = Math.ceil(summary.max * 100) / 100;
+  const min = bc.first_bin.startunbounded ? minFloor : bc.first_bin.start_percentile ? summary["p" + bc.first_bin.start_percentile] : bc.first_bin.start;
+  let max = maxCeil, last_start, last_stop;
+  if (bc.last_bin) {
+    max = bc.last_bin.stopunbounded ? maxCeil : bc.last_bin.stop_percentile ? summary["p" + bc.last_bin.stop_percentile] : isNumeric(bc.last_bin.stop) && bc.last_bin.stop <= summary.max ? bc.last_bin.stop : maxCeil;
+    last_start = isStrictNumeric(bc.last_bin.start_percentile) ? summary["p" + bc.last_bin.start_percentile] : isStrictNumeric(bc.last_bin.start) ? bc.last_bin.start : void 0;
+    last_stop = bc.last_bin.stopunbounded ? null : bc.last_bin.stop_percentile ? summary["p" + bc.last_bin.stop_percentile] : isStrictNumeric(bc.last_bin.stop) ? bc.last_bin.stop : null;
+  } else if (bc.lst) {
+    const last_bin = bc.lst[bc.lst.length - 1];
+    last_start = last_bin.start;
+    last_stop = "stop" in last_bin && !last_bin.stopunbounded ? last_bin.stop : maxCeil;
+    max = last_stop;
+  } else {
+    last_start = maxCeil;
+    last_stop = maxCeil;
+  }
+  const numericMax = isStrictNumeric(max);
+  const numericLastStart = isStrictNumeric(last_start);
+  const numericLastStop = isStrictNumeric(last_stop);
+  if (!numericMax && !numericLastStart) return [];
+  const bins = [];
+  let currBin = {
+    startunbounded: bc.first_bin.startunbounded,
+    start: bc.first_bin.startunbounded ? void 0 : min,
+    stop: isStrictNumeric(bc.first_bin.stop_percentile) ? +summary["p" + bc.first_bin.stop_percentile] : isStrictNumeric(bc.first_bin.stop) ? +bc.first_bin.stop : min + bc.bin_size,
+    startinclusive: bc.startinclusive,
+    stopinclusive: bc.stopinclusive
+  };
+  if (!isStrictNumeric(currBin.stop)) throw "the computed first_bin.stop is non-numeric" + currBin.stop;
+  const maxNumBins = 100;
+  while (numericMax && currBin.stop <= max || currBin.startunbounded && !bins.length || currBin.stopunbounded) {
+    bins.push(currBin);
+    if (currBin.stop >= max) {
+      currBin.stopunbounded = true;
+      if (bins.length > 1) {
+        delete currBin.stop;
+      }
+    }
+    currBin.label = get_bin_label(currBin, bc, valueConversion);
+    if (currBin.stopunbounded) break;
+    const upper = currBin.stop + bc.bin_size;
+    const previousStop = currBin.stop;
+    currBin = {
+      startinclusive: bc.startinclusive,
+      stopinclusive: bc.stopinclusive,
+      start: previousStop,
+      stop: numericLastStop && (previousStop == last_start || upper > last_stop) ? last_stop : numericLastStart && upper > last_start && previousStop != last_start ? last_start : upper
+    };
+    if (currBin.stop >= max) {
+      currBin.stop = max;
+      if (bc.last_bin && bc.last_bin.stopunbounded) currBin.stopunbounded = 1;
+      if (bc.last_bin && bc.last_bin.stopinclusive) currBin.stopinclusive = 1;
+    }
+    if (numericLastStart && currBin.start == last_start) {
+      if (bc.last_bin && bc.last_bin.stopunbounded) currBin.stopunbounded = 1;
+    }
+    if (currBin.start > currBin.stop) {
+      if (numericLastStart && currBin.stop == last_start && bc.last_bin && bc.last_bin.stopunbounded)
+        currBin.stopunbounded = true;
+      else break;
+    }
+    if (bins.length + 1 >= maxNumBins) {
+      bc.error = "max_num_bins_reached";
+      break;
+    }
+  }
+  delete bc.binLabelFormatter;
+  if (bins.length > 1) {
+    delete bins[bins.length - 1].stop;
+  }
+  const k2c = getColors(bins.length);
+  for (const bin of bins) bin.color = k2c(bin.label);
+  return bins;
+}
+function getNumDecimalsFormatter(bc) {
+  return "rounding" in bc ? format(bc.rounding) : (d) => d;
+}
+function get_bin_label(bin, binconfig, valueConversion) {
+  if (!bin) return "missing bin.label";
+  if (bin.label) return bin.label;
+  const bc = binconfig;
+  if (!bc.binLabelFormatter) bc.binLabelFormatter = getNumDecimalsFormatter(bc);
+  if (!bin.startunbounded && !bin.stopunbounded && !("startinclusive" in bin) && !("stopinclusive" in bin)) {
+    if (bc.startinclusive) bin.startinclusive = true;
+    else if (bc.stopinclusive) bin.stopinclusive = true;
+  }
+  const start = bc.use_as == "bins" || bin.start;
+  const stop = bc.use_as == "bins" || bin.stop;
+  let label_offset = 0;
+  if ("label_offset" in bc) {
+    bc.label_offset_ignored = "bin_size" in bc && bc.bin_size < bc.label_offset;
+    if (!bc.label_offset_ignored) label_offset = bc.label_offset;
+  } else if (bc.bin_size === 1 && bc.termtype == "integer") {
+    label_offset = 1;
+  }
+  if (bin.startunbounded) {
+    const oper = bin.stopinclusive ? "\u2264" : "<";
+    const v1 = valueConversion ? convertUnits(stop, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true) : bc.binLabelFormatter(stop);
+    return oper + v1;
+  }
+  if (bin.stopunbounded || start === stop) {
+    const oper = bin.startinclusive ? "\u2265" : ">";
+    const v0 = valueConversion ? convertUnits(start, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true) : bc.binLabelFormatter(start);
+    return oper + v0;
+  }
+  if (label_offset && bin.startinclusive && !bin.stopinclusive) {
+    if (Number.isInteger(bc.bin_size) && Math.abs(start - stop) === label_offset) {
+      return "" + (valueConversion ? convertUnits(start, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true) : bc.binLabelFormatter(start));
+    } else {
+      const v0 = valueConversion ? convertUnits(start, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true) : bc.binLabelFormatter(start);
+      const v1 = valueConversion ? convertUnits(
+        stop - label_offset,
+        valueConversion.fromUnit,
+        valueConversion.toUnit,
+        valueConversion.scaleFactor,
+        true
+      ) : bc.binLabelFormatter(stop - label_offset);
+      return +v0 >= +v1 ? v0.toString() : v0 + " to " + v1;
+    }
+  } else {
+    const oper0 = bin.startinclusive ? "" : ">";
+    const oper1 = bin.stopinclusive ? "" : "<";
+    const v0 = valueConversion ? convertUnits(start, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true) : Number.isInteger(start) ? start : bc.binLabelFormatter(start);
+    const v1 = valueConversion ? convertUnits(stop, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true) : Number.isInteger(stop) ? stop : bc.binLabelFormatter(stop);
+    if (+v0 >= +v1) {
+      const oper = bin.startinclusive ? "\u2265" : ">";
+      return oper + v0;
+    } else {
+      return oper0 + v0 + " to " + oper1 + v1;
+    }
+  }
+}
+function get_bin_range_equation(bin, binconfig) {
+  const x = '<span style="font-family:Times;font-style:italic;">x</span>';
+  let range_eq;
+  const copy = structuredClone(bin);
+  copy.label = "";
+  const bin_label = get_bin_label(copy, binconfig);
+  if (bin.startunbounded || bin.stopunbounded) {
+    range_eq = x + " " + bin_label;
+  } else if (bin.startinclusive) {
+    range_eq = bin_label.replace("to <", "\u2264 " + x + " <");
+  } else if (bin.stopinclusive) {
+    range_eq = bin_label.replace(">", "").replace("to", "< " + x + " \u2264");
+  }
+  return range_eq;
+}
+function target_percentiles(binconfig) {
+  const percentiles = [];
+  const f = binconfig.first_bin;
+  if (f && isStrictNumeric(f.start_percentile)) percentiles.push(f.start_percentile);
+  if (f && isStrictNumeric(f.stop_percentile)) percentiles.push(f.stop_percentile);
+  const l = binconfig.last_bin;
+  if (l && isStrictNumeric(l.start_percentile)) percentiles.push(l.start_percentile);
+  if (l && isStrictNumeric(l.stop_percentile)) percentiles.push(l.stop_percentile);
+  return percentiles;
+}
+export {
+  compute_bins,
+  validate_bins as default,
+  get_bin_label,
+  get_bin_range_equation,
+  target_percentiles
+};
+//# sourceMappingURL=termdb.bins.js.map

package/dist/src/termdb.bins.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/termdb.bins.js"],
+  "sourcesContent": ["import { format } from 'd3-format'\nimport { getColors } from './common.js'\nimport { isNumeric, isStrictNumeric, convertUnits } from './helpers.js'\n\nexport default function validate_bins(binconfig) {\n\t// Number.isFinite('1') returns false, which is desired\n\n\tconst bc = binconfig\n\tif (!bc || typeof bc !== 'object') throw 'bin schema must be an object'\n\t// assign default type\n\tif (!('type' in bc)) bc.type = 'regular-bin'\n\n\tif (bc.type == 'custom-bin') {\n\t\tif (!Array.isArray(bc.lst)) throw 'binconfig.lst must be an array'\n\t\tif (!bc.lst.length) throw 'binconfig.lst must have entries'\n\t\tconst first_bin = bc.lst[0]\n\t\tconst last_bin = bc.lst[bc.lst.length - 1]\n\n\t\tfor (const bin of bc.lst) {\n\t\t\tif (!('startinclusive' in bin) && !('stopinclusive' in bin)) {\n\t\t\t\tthrow 'custom bin.startinclusive and/or bin.stopinclusive must be defined'\n\t\t\t}\n\n\t\t\tif (bin == first_bin) {\n\t\t\t\tif ('startunbounded' in bin && !bin.startunbounded) {\n\t\t\t\t\tthrow `a custom first bin must not set bin.startunbounded to false`\n\t\t\t\t}\n\t\t\t\tbin.startunbounded = true\n\t\t\t\tif ('start' in bin) {\n\t\t\t\t\tthrow 'a custom first bin must not set a bin.start value'\n\t\t\t\t}\n\t\t\t\tif ('start_percentile' in bin) {\n\t\t\t\t\tthrow 'the first bin must not set a bin.start_percentile value'\n\t\t\t\t}\n\t\t\t\tif (!('stop' in bin)) {\n\t\t\t\t\tthrow `a custom first bin must define a bin.stop value`\n\t\t\t\t}\n\t\t\t\tif (!isStrictNumeric(bin.stop)) {\n\t\t\t\t\tthrow `a custom first bin.stop value should be numeric`\n\t\t\t\t}\n\t\t\t} else if (bin == last_bin) {\n\t\t\t\tif (!('start' in bin)) {\n\t\t\t\t\tthrow `a custom last bin must define a bin.start value`\n\t\t\t\t}\n\t\t\t\tif (!isStrictNumeric(bin.start)) {\n\t\t\t\t\tthrow `a custom last bin.start must be numeric`\n\t\t\t\t}\n\t\t\t\tif ('stopunbounded' in bin && !bin.stopunbounded) {\n\t\t\t\t\tthrow 'a custom last bin must not set bin.stopunbounded to false'\n\t\t\t\t}\n\t\t\t\tbin.stopunbounded = true\n\t\t\t\tif ('stop' in bin) {\n\t\t\t\t\tthrow 'a custom last bin must not set a bin.stop value'\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tif (bin.startunbounded || bin.stopunbounded) {\n\t\t\t\t\tthrow 'bin.startunbounded and bin.stopunbounded must not be set for non-first/non-last bins'\n\t\t\t\t}\n\t\t\t\tif (!isStrictNumeric(bin.start)) throw 'bin.start must be numeric for a non-first bin'\n\t\t\t\tif (!isStrictNumeric(bin.stop)) throw 'bin.stop must be numeric for a non-last bin'\n\t\t\t}\n\t\t}\n\t} else if (bc.type == 'regular-bin') {\n\t\t// required custom_bin parameter\n\t\tif (!Number.isFinite(bc.bin_size)) throw 'non-numeric bin_size'\n\t\tif (bc.bin_size <= 0) throw 'bin_size must be greater than 0'\n\n\t\tif (!bc.startinclusive && !bc.stopinclusive) {\n\t\t\tbc.startinclusive = 1\n\t\t\tbc.stopinclusive = 0\n\t\t}\n\n\t\tif (!bc.first_bin) throw 'first_bin{} missing'\n\t\tif (typeof bc.first_bin != 'object') throw 'first_bin{} is not an object'\n\t\tif (!Object.keys(bc.first_bin).length) throw 'first_bin is an empty object'\n\n\t\t{\n\t\t\tconst b = bc.first_bin\n\t\t\tb.startunbounded = true\n\t\t\t// requires stop_percentile, or stop\n\t\t\tif (b.stop_percentile) {\n\t\t\t\tif (!Number.isInteger(b.stop_percentile)) throw 'first_bin.stop_percentile should be integer'\n\t\t\t\tif (b.stop_percentile <= 0 || b.stop_percentile >= 100) throw 'first_bin.stop_percentile out of bound (0-100)'\n\t\t\t} else if (!Number.isFinite(b.stop)) {\n\t\t\t\tthrow 'first_bin.stop not a number when stop_percentile is not set'\n\t\t\t}\n\t\t}\n\n\t\tif (bc.last_bin) {\n\t\t\tconst b = bc.last_bin\n\t\t\t// requires start_percentile or start\n\t\t\tif (b.start_percentile) {\n\t\t\t\tif (!Number.isInteger(b.start_percentile)) throw 'last_bin.start_percentile should be integer'\n\t\t\t\tif (b.start_percentile <= 0 || b.start_percentile >= 100) throw 'last_bin.start_percentile out of bound (0-100)'\n\t\t\t} else if (!Number.isFinite(b.start)) {\n\t\t\t\tthrow 'last_bin.start not a number when start_percentile is not set'\n\t\t\t}\n\n\t\t\tb.stopunbounded = true\n\t\t\tif ('stop' in b) {\n\t\t\t\tthrow 'a regular last bin must not set a bin.stop value'\n\t\t\t}\n\t\t}\n\t} else {\n\t\tthrow `invalid binconfig.type=\"${bc.type}\"`\n\t}\n}\n\nexport function compute_bins(binconfig, summaryfxn, valueConversion) {\n\t/*\n  Bins generator\n  \nbinconfig   \n  configuration of bins per the Numerical Binning Scheme\n\nsummaryfxn (percentiles)=> return {min, max, pX, pY, ...}\n  - required function\n\n  - must accept an array of desired percentile values\n  and returns an object of computed properties\n  {\n    min: minimum value\n    max: maximum value\n    pX: percentile at X value, so p10 will be 10th percentile value\n    pY: .. corresponding to the desired percentile values \n  }\n*/\n\tconst bc = binconfig\n\n\tvalidate_bins(bc)\n\tif (bc.lst) {\n\t\tconst k2c = getColors(bc.lst.length) //to color bins\n\t\tfor (const bin of bc.lst) bin.color = k2c(bin.label)\n\t}\n\tif (bc.type == 'custom-bin') return JSON.parse(JSON.stringify(bc.lst))\n\tif (typeof summaryfxn != 'function') throw 'summaryfxn required for modules/termdb.bins.js compute_bins()'\n\tconst percentiles = target_percentiles(bc)\n\tconst summary = summaryfxn(percentiles)\n\tif (!summary || typeof summary !== 'object') throw 'invalid returned value by summaryfxn'\n\tbc.results = { summary }\n\tif (!bc.binLabelFormatter) bc.binLabelFormatter = getNumDecimalsFormatter(bc)\n\n\t// round the min and max values for use as bin start and stop\n\t// in the first and last bins, respectively\n\tconst minFloor = Math.floor(summary.min * 100) / 100\n\tconst maxCeil = Math.ceil(summary.max * 100) / 100\n\tconst min = bc.first_bin.startunbounded\n\t\t? minFloor\n\t\t: bc.first_bin.start_percentile\n\t\t? summary['p' + bc.first_bin.start_percentile]\n\t\t: bc.first_bin.start\n\tlet max = maxCeil, // in order to include the max value in the last bin\n\t\tlast_start,\n\t\tlast_stop\n\n\tif (bc.last_bin) {\n\t\tmax = bc.last_bin.stopunbounded\n\t\t\t? maxCeil // in order to include the max value in the last bin\n\t\t\t: bc.last_bin.stop_percentile\n\t\t\t? summary['p' + bc.last_bin.stop_percentile]\n\t\t\t: isNumeric(bc.last_bin.stop) && bc.last_bin.stop <= summary.max // '0.0088' < 0.0088\n\t\t\t? bc.last_bin.stop\n\t\t\t: maxCeil // in order to include the max value in the last bin\n\t\tlast_start = isStrictNumeric(bc.last_bin.start_percentile)\n\t\t\t? summary['p' + bc.last_bin.start_percentile]\n\t\t\t: isStrictNumeric(bc.last_bin.start)\n\t\t\t? bc.last_bin.start\n\t\t\t: undefined\n\t\tlast_stop = bc.last_bin.stopunbounded\n\t\t\t? null\n\t\t\t: bc.last_bin.stop_percentile\n\t\t\t? summary['p' + bc.last_bin.stop_percentile]\n\t\t\t: isStrictNumeric(bc.last_bin.stop)\n\t\t\t? bc.last_bin.stop\n\t\t\t: null\n\t} else if (bc.lst) {\n\t\tconst last_bin = bc.lst[bc.lst.length - 1]\n\t\tlast_start = last_bin.start\n\t\tlast_stop = 'stop' in last_bin && !last_bin.stopunbounded ? last_bin.stop : maxCeil\n\t\tmax = last_stop\n\t} else {\n\t\tlast_start = maxCeil\n\t\tlast_stop = maxCeil\n\t}\n\n\tconst numericMax = isStrictNumeric(max)\n\tconst numericLastStart = isStrictNumeric(last_start)\n\tconst numericLastStop = isStrictNumeric(last_stop)\n\n\tif (!numericMax && !numericLastStart) return [] //throw 'unable to compute the last bin start or stop'\n\n\tconst bins = []\n\tlet currBin = {\n\t\tstartunbounded: bc.first_bin.startunbounded,\n\t\tstart: bc.first_bin.startunbounded ? undefined : min,\n\t\tstop: isStrictNumeric(bc.first_bin.stop_percentile)\n\t\t\t? +summary['p' + bc.first_bin.stop_percentile]\n\t\t\t: isStrictNumeric(bc.first_bin.stop)\n\t\t\t? +bc.first_bin.stop\n\t\t\t: min + bc.bin_size,\n\t\tstartinclusive: bc.startinclusive,\n\t\tstopinclusive: bc.stopinclusive\n\t}\n\n\tif (!isStrictNumeric(currBin.stop)) throw 'the computed first_bin.stop is non-numeric' + currBin.stop\n\tconst maxNumBins = 100 // harcoded limit for now to not stress sqlite\n\n\twhile ((numericMax && currBin.stop <= max) || (currBin.startunbounded && !bins.length) || currBin.stopunbounded) {\n\t\tbins.push(currBin)\n\t\t// force a computed last bin to have stopunbounded true\n\t\tif (currBin.stop >= max) {\n\t\t\tcurrBin.stopunbounded = true\n\t\t\tif (bins.length > 1) {\n\t\t\t\tdelete currBin.stop\n\t\t\t}\n\t\t}\n\t\tcurrBin.label = get_bin_label(currBin, bc, valueConversion)\n\t\tif (currBin.stopunbounded) break\n\n\t\tconst upper = currBin.stop + bc.bin_size\n\t\tconst previousStop = currBin.stop\n\t\tcurrBin = {\n\t\t\tstartinclusive: bc.startinclusive,\n\t\t\tstopinclusive: bc.stopinclusive,\n\t\t\tstart: previousStop,\n\t\t\tstop:\n\t\t\t\tnumericLastStop && (previousStop == last_start || upper > last_stop)\n\t\t\t\t\t? last_stop\n\t\t\t\t\t: numericLastStart && upper > last_start && previousStop != last_start\n\t\t\t\t\t? last_start\n\t\t\t\t\t: upper\n\t\t}\n\n\t\tif (currBin.stop >= max) {\n\t\t\tcurrBin.stop = max\n\t\t\tif (bc.last_bin && bc.last_bin.stopunbounded) currBin.stopunbounded = 1\n\t\t\tif (bc.last_bin && bc.last_bin.stopinclusive) currBin.stopinclusive = 1\n\t\t}\n\t\tif (numericLastStart && currBin.start == last_start) {\n\t\t\tif (bc.last_bin && bc.last_bin.stopunbounded) currBin.stopunbounded = 1\n\t\t}\n\t\tif (currBin.start > currBin.stop) {\n\t\t\tif (numericLastStart && currBin.stop == last_start && bc.last_bin && bc.last_bin.stopunbounded)\n\t\t\t\tcurrBin.stopunbounded = true\n\t\t\telse break\n\t\t}\n\t\tif (bins.length + 1 >= maxNumBins) {\n\t\t\tbc.error = 'max_num_bins_reached'\n\t\t\tbreak\n\t\t}\n\t}\n\tdelete bc.binLabelFormatter\n\tif (bins.length > 1) {\n\t\tdelete bins[bins.length - 1].stop\n\t}\n\tconst k2c = getColors(bins.length) //to color bins\n\tfor (const bin of bins) bin.color = k2c(bin.label)\n\treturn bins\n}\n\nfunction getNumDecimalsFormatter(bc) {\n\t//return format('rounding' in bc ? bc.rounding : '')\n\treturn 'rounding' in bc ? format(bc.rounding) : d => d // default to labeling using the start/stop value as-is\n}\n\nexport function get_bin_label(bin, binconfig, valueConversion) {\n\t/*\n  Generate a numeric bin label given a bin configuration and an optional term valueConversion object\n*/\n\tif (!bin) return 'missing bin.label'\n\tif (bin.label) return bin.label\n\n\tconst bc = binconfig\n\tif (!bc.binLabelFormatter) bc.binLabelFormatter = getNumDecimalsFormatter(bc)\n\tif (!bin.startunbounded && !bin.stopunbounded && !('startinclusive' in bin) && !('stopinclusive' in bin)) {\n\t\tif (bc.startinclusive) bin.startinclusive = true\n\t\telse if (bc.stopinclusive) bin.stopinclusive = true\n\t}\n\n\tconst start = bc.use_as == 'bins' || bin.start\n\tconst stop = bc.use_as == 'bins' || bin.stop\n\n\tlet label_offset = 0\n\tif ('label_offset' in bc) {\n\t\tbc.label_offset_ignored = 'bin_size' in bc && bc.bin_size < bc.label_offset\n\t\tif (!bc.label_offset_ignored) label_offset = bc.label_offset\n\t} else if (bc.bin_size === 1 && bc.termtype == 'integer') {\n\t\tlabel_offset = 1\n\t}\n\n\t// one side-unbounded bins\n\t// label will be \">v\" or \"<v\"\n\tif (bin.startunbounded) {\n\t\tconst oper = bin.stopinclusive ? '\u2264' : '<' // \\u2264\n\t\tconst v1 = valueConversion\n\t\t\t? convertUnits(stop, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true)\n\t\t\t: bc.binLabelFormatter(stop) //bin.startinclusive && label_offset ? stop - label_offset : stop)\n\t\treturn oper + v1\n\t}\n\t// a data value may coincide with the last bin's start\n\tif (bin.stopunbounded || start === stop) {\n\t\tconst oper = bin.startinclusive /*|| label_offset*/ ? '\u2265' : '>' // \\u2265\n\t\tconst v0 = valueConversion\n\t\t\t? convertUnits(start, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true)\n\t\t\t: bc.binLabelFormatter(start) //bin.startinclusive || start == min ? start : start + label_offset)\n\t\treturn oper + v0\n\t}\n\n\t// two-sided bins\n\tif (label_offset && bin.startinclusive && !bin.stopinclusive) {\n\t\tif (Number.isInteger(bc.bin_size) && Math.abs(start - stop) === label_offset) {\n\t\t\t// make a simpler label when the range simply spans the bin_size\n\t\t\treturn (\n\t\t\t\t'' +\n\t\t\t\t(valueConversion\n\t\t\t\t\t? convertUnits(start, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true)\n\t\t\t\t\t: bc.binLabelFormatter(start))\n\t\t\t)\n\t\t} else {\n\t\t\tconst v0 = valueConversion\n\t\t\t\t? convertUnits(start, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true)\n\t\t\t\t: bc.binLabelFormatter(start)\n\t\t\tconst v1 = valueConversion\n\t\t\t\t? convertUnits(\n\t\t\t\t\t\tstop - label_offset,\n\t\t\t\t\t\tvalueConversion.fromUnit,\n\t\t\t\t\t\tvalueConversion.toUnit,\n\t\t\t\t\t\tvalueConversion.scaleFactor,\n\t\t\t\t\t\ttrue\n\t\t\t\t  )\n\t\t\t\t: bc.binLabelFormatter(stop - label_offset)\n\t\t\t// ensure that last two bin labels make sense (the last is stopunbounded)\n\t\t\treturn +v0 >= +v1 ? v0.toString() : v0 + ' to ' + v1\n\t\t}\n\t} else {\n\t\t// stop_inclusive || label_offset == 0\n\t\tconst oper0 = bin.startinclusive ? '' : '>'\n\t\tconst oper1 = bin.stopinclusive ? '' : '<'\n\t\tconst v0 = valueConversion\n\t\t\t? convertUnits(start, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true)\n\t\t\t: Number.isInteger(start)\n\t\t\t? start\n\t\t\t: bc.binLabelFormatter(start)\n\t\tconst v1 = valueConversion\n\t\t\t? convertUnits(stop, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true)\n\t\t\t: Number.isInteger(stop)\n\t\t\t? stop\n\t\t\t: bc.binLabelFormatter(stop)\n\t\t// after rounding the bin labels, the bin start may equal the last bin stop as derived from actual data\n\t\tif (+v0 >= +v1) {\n\t\t\tconst oper = bin.startinclusive ? '\u2265' : '>' // \\u2265\n\t\t\treturn oper + v0\n\t\t} else {\n\t\t\treturn oper0 + v0 + ' to ' + oper1 + v1\n\t\t}\n\t}\n}\n\n// get bin range equation from bin label and bin properties\nexport function get_bin_range_equation(bin, binconfig) {\n\tconst x = '<span style=\"font-family:Times;font-style:italic;\">x</span>'\n\tlet range_eq\n\t// should always use computed (not user-customized) bin label to determine bin range text\n\tconst copy = structuredClone(bin)\n\tcopy.label = '' // mutate only the copy, and not the original bin argument\n\tconst bin_label = get_bin_label(copy, binconfig)\n\tif (bin.startunbounded || bin.stopunbounded) {\n\t\t// first or last bins, e.g. x \u2264 14 and x > 16\n\t\trange_eq = x + ' ' + bin_label\n\t} else if (bin.startinclusive) {\n\t\t// bins with startinclusive, e.g. 14 \u2264 x < 16\n\t\trange_eq = bin_label.replace('to <', '\u2264 ' + x + ' <')\n\t} else if (bin.stopinclusive) {\n\t\t// bins with stopinclusive, e.g. 14 < x \u2264 16\n\t\trange_eq = bin_label.replace('>', '').replace('to', '< ' + x + ' \u2264')\n\t}\n\treturn range_eq\n}\n\nexport function target_percentiles(binconfig) {\n\tconst percentiles = []\n\tconst f = binconfig.first_bin\n\tif (f && isStrictNumeric(f.start_percentile)) percentiles.push(f.start_percentile)\n\tif (f && isStrictNumeric(f.stop_percentile)) percentiles.push(f.stop_percentile)\n\tconst l = binconfig.last_bin\n\tif (l && isStrictNumeric(l.start_percentile)) percentiles.push(l.start_percentile)\n\tif (l && isStrictNumeric(l.stop_percentile)) percentiles.push(l.stop_percentile)\n\treturn percentiles\n}\n"],
+  "mappings": 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+  "names": ["k2c"]
+}

package/dist/src/termdb.initbinconfig.js

@@ -0,0 +1,79 @@
+function initBinConfig(data, opts = {}) {
+  if (!data.length)
+    return { mode: "discrete", type: "regular-bin", startinclusive: true, bin_size: null, first_bin: { stop: null } };
+  if (data.find((d) => !Number.isFinite(d))) throw new Error("non-numeric values found");
+  let binConfig;
+  const s = new Set(data);
+  if (s.size === 1) {
+    const value = [...s][0];
+    binConfig = {
+      type: "custom-bin",
+      lst: [
+        { stop: value, stopinclusive: false, startunbounded: true, label: "<" + value },
+        { start: value, stop: value, startinclusive: true, stopinclusive: true, label: "=" + value },
+        { start: value, startinclusive: false, stopunbounded: true, label: ">" + value }
+      ]
+    };
+  } else {
+    data.sort((a, b) => a - b);
+    const l = data.length;
+    const min = data[0];
+    const max = data[l - 1];
+    const p5idx = Math.ceil(l * 0.05) - 1;
+    const p98idx = Math.ceil(l * 0.98) - 1;
+    const p5 = data[p5idx];
+    const p98 = data[p98idx];
+    const binSize = p98 != p5 ? (p98 - p5) / 8 : (max - min) / 8;
+    const firstBinStop = Math.max(min + binSize, p5);
+    let [binSize_rnd, firstBinStop_rnd, lastBinStart_rnd, rounding] = roundBinVals(binSize, firstBinStop, max, min);
+    binConfig = {
+      type: "regular-bin",
+      startinclusive: true,
+      bin_size: binSize_rnd,
+      first_bin: { stop: firstBinStop_rnd }
+    };
+    if (lastBinStart_rnd) binConfig.last_bin = { start: lastBinStart_rnd };
+    if (rounding) binConfig.rounding = rounding;
+  }
+  if ("format" in opts) {
+    if (opts.format === "string") {
+      return JSON.stringify(binConfig);
+    } else {
+      throw "options are not in the correct format";
+    }
+  } else {
+    return binConfig;
+  }
+}
+function roundBinVals(binSize, firstBinStop, max, min) {
+  let binSize_rnd, firstBinStop_rnd, lastBinStart_rnd, rounding;
+  const log = Math.floor(Math.log10(binSize));
+  if (binSize >= 0.1 && binSize <= 2) {
+    binSize_rnd = Math.round(binSize / (1 * 10 ** log)) * (1 * 10 ** log);
+    firstBinStop_rnd = Math.round(firstBinStop / (1 * 10 ** log)) * (1 * 10 ** log);
+  } else {
+    binSize_rnd = Math.round(binSize / (5 * 10 ** log)) * (5 * 10 ** log);
+    firstBinStop_rnd = Math.round(firstBinStop / (5 * 10 ** log)) * (5 * 10 ** log);
+    if (binSize_rnd === 0) binSize_rnd = 1 * 10 ** log;
+    if (firstBinStop_rnd === 0) firstBinStop_rnd = 1 * 10 ** log;
+    if (binSize_rnd === 5 * 10 ** log && firstBinStop_rnd === 1 * 10 ** log) firstBinStop_rnd = 5 * 10 ** log;
+  }
+  if (firstBinStop_rnd < min) firstBinStop_rnd = firstBinStop_rnd * 2;
+  const eighthBinStop_rnd = firstBinStop_rnd + binSize_rnd * 7;
+  if (max > eighthBinStop_rnd) {
+    lastBinStart_rnd = firstBinStop_rnd + binSize_rnd * 6;
+  }
+  if (binSize < 1) {
+    const digits = Math.abs(log);
+    binSize_rnd = Number(binSize_rnd.toFixed(digits));
+    firstBinStop_rnd = Number(firstBinStop_rnd.toFixed(digits));
+    if (lastBinStart_rnd) lastBinStart_rnd = Number(lastBinStart_rnd.toFixed(digits));
+    rounding = "." + digits + "f";
+  }
+  if (Object.is(firstBinStop_rnd, -0)) firstBinStop_rnd = 0;
+  return [binSize_rnd, firstBinStop_rnd, lastBinStart_rnd, rounding];
+}
+export {
+  initBinConfig as default
+};
+//# sourceMappingURL=termdb.initbinconfig.js.map

package/dist/src/termdb.initbinconfig.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/termdb.initbinconfig.js"],
+  "sourcesContent": ["/*\nInitialize a bin configuration for a numeric dataset\n<data>: array of numeric data values\n<opts> (optional): object of options\n    {}: output bin config as JavaScript object (default)\n    {format: 'string'}: output bin config as JSON string\n*/\nexport default function initBinConfig(data, opts = {}) {\n\tif (!data.length)\n\t\treturn { mode: 'discrete', type: 'regular-bin', startinclusive: true, bin_size: null, first_bin: { stop: null } }\n\tif (data.find(d => !Number.isFinite(d))) throw new Error('non-numeric values found')\n\n\tlet binConfig\n\tconst s = new Set(data)\n\tif (s.size === 1) {\n\t\t// single unique value in data array\n\t\t// prepare custom bin config for 3 bins: first bin\n\t\t// for values less than the value, second bin for values\n\t\t// equal to the value, and third bin one for values\n\t\t// greater than the value\n\t\t// all data values will fall into the second bin\n\t\tconst value = [...s][0]\n\t\tbinConfig = {\n\t\t\ttype: 'custom-bin',\n\t\t\tlst: [\n\t\t\t\t{ stop: value, stopinclusive: false, startunbounded: true, label: '<' + value },\n\t\t\t\t{ start: value, stop: value, startinclusive: true, stopinclusive: true, label: '=' + value },\n\t\t\t\t{ start: value, startinclusive: false, stopunbounded: true, label: '>' + value }\n\t\t\t]\n\t\t}\n\t} else {\n\t\t// multiple unique values in data array\n\t\t// prepare regular bin config\n\n\t\t// compute the bin size for a maximum bin number of 8\n\t\tdata.sort((a, b) => a - b)\n\t\tconst l = data.length\n\t\tconst min = data[0]\n\t\tconst max = data[l - 1]\n\t\tconst p5idx = Math.ceil(l * 0.05) - 1\n\t\tconst p98idx = Math.ceil(l * 0.98) - 1\n\t\tconst p5 = data[p5idx]\n\t\tconst p98 = data[p98idx]\n\t\t// use 98th and 5th percentiles to compute bin size to reduce outlier influence\n\t\t// if 98th = 5th, use max and min instead\n\t\tconst binSize = p98 != p5 ? (p98 - p5) / 8 : (max - min) / 8\n\t\t// first bin stop will equal either (minimum + bin size) or (5th percentile), whichever is larger.\n\t\tconst firstBinStop = Math.max(min + binSize, p5)\n\t\t// round the bin values\n\t\tlet [binSize_rnd, firstBinStop_rnd, lastBinStart_rnd, rounding] = roundBinVals(binSize, firstBinStop, max, min)\n\t\t// generate the bin configuration\n\t\tbinConfig = {\n\t\t\ttype: 'regular-bin',\n\t\t\tstartinclusive: true,\n\t\t\tbin_size: binSize_rnd,\n\t\t\tfirst_bin: { stop: firstBinStop_rnd }\n\t\t}\n\t\tif (lastBinStart_rnd) binConfig.last_bin = { start: lastBinStart_rnd }\n\t\tif (rounding) binConfig.rounding = rounding\n\t}\n\tif ('format' in opts) {\n\t\tif (opts.format === 'string') {\n\t\t\treturn JSON.stringify(binConfig)\n\t\t} else {\n\t\t\tthrow 'options are not in the correct format'\n\t\t}\n\t} else {\n\t\treturn binConfig\n\t}\n}\n\nfunction roundBinVals(binSize, firstBinStop, max, min) {\n\tlet binSize_rnd, firstBinStop_rnd, lastBinStart_rnd, rounding\n\tconst log = Math.floor(Math.log10(binSize))\n\tif (binSize >= 0.1 && binSize <= 2) {\n\t\t// Round to the nearest one for small bin sizes\n\t\tbinSize_rnd = Math.round(binSize / (1 * 10 ** log)) * (1 * 10 ** log)\n\t\tfirstBinStop_rnd = Math.round(firstBinStop / (1 * 10 ** log)) * (1 * 10 ** log)\n\t} else {\n\t\t// Round to the nearest five for large bin sizes\n\t\tbinSize_rnd = Math.round(binSize / (5 * 10 ** log)) * (5 * 10 ** log)\n\t\tfirstBinStop_rnd = Math.round(firstBinStop / (5 * 10 ** log)) * (5 * 10 ** log)\n\t\tif (binSize_rnd === 0) binSize_rnd = 1 * 10 ** log\n\t\tif (firstBinStop_rnd === 0) firstBinStop_rnd = 1 * 10 ** log\n\t\tif (binSize_rnd === 5 * 10 ** log && firstBinStop_rnd === 1 * 10 ** log) firstBinStop_rnd = 5 * 10 ** log\n\t}\n\tif (firstBinStop_rnd < min) firstBinStop_rnd = firstBinStop_rnd * 2\n\t// if the number of bins is above 8 after rounding, then set the last bin start to restrict the number of bins to 8\n\tconst eighthBinStop_rnd = firstBinStop_rnd + binSize_rnd * 7\n\tif (max > eighthBinStop_rnd) {\n\t\tlastBinStart_rnd = firstBinStop_rnd + binSize_rnd * 6\n\t}\n\tif (binSize < 1) {\n\t\tconst digits = Math.abs(log)\n\t\tbinSize_rnd = Number(binSize_rnd.toFixed(digits))\n\t\tfirstBinStop_rnd = Number(firstBinStop_rnd.toFixed(digits))\n\t\tif (lastBinStart_rnd) lastBinStart_rnd = Number(lastBinStart_rnd.toFixed(digits))\n\t\trounding = '.' + digits + 'f'\n\t}\n\tif (Object.is(firstBinStop_rnd, -0)) firstBinStop_rnd = 0\n\treturn [binSize_rnd, firstBinStop_rnd, lastBinStart_rnd, rounding]\n}\n"],
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