@sjcrh/proteinpaint-client 2.200.0 → 2.202.0

package/dist/chunk-75T7ESEO.js

@@ -0,0 +1,61 @@
+// ../shared/utils/dist/src/helpers.js
+function isNumeric(n) {
+  const v = typeof n != "string" || n === "" ? n : Number(n);
+  const f = parseFloat(n);
+  return !isNaN(f) && Number.isFinite(v) && v === f;
+}
+function isStrictNumeric(n) {
+  return typeof n === "number" && Number.isFinite(n);
+}
+function convertUnits(v, fromUnit, toUnit, scaleFactor, compact) {
+  if (scaleFactor >= 1) {
+    const toUnitV2 = Math.floor(v * scaleFactor);
+    if (compact) return `${toUnitV2}${toUnit.charAt(0)}`;
+    return `${toUnitV2} ${toUnitV2 > 1 ? toUnit + "s" : ""}`;
+  }
+  const toUnitV = Math.floor(v * scaleFactor);
+  const fromUnitV = Math.ceil(v % (1 / scaleFactor));
+  if (fromUnitV == 0) {
+    if (compact) return `${toUnitV}${toUnit.charAt(0)}`;
+    return `${toUnitV} ${toUnitV > 1 ? toUnit + "s" : ""}`;
+  }
+  if (compact) return `${toUnitV}${toUnit.charAt(0)}${fromUnitV}${fromUnit.charAt(0)}`;
+  return `${toUnitV} ${toUnitV > 1 ? toUnit + "s" : toUnit} ${fromUnitV} ${fromUnitV > 1 ? fromUnit + "s" : fromUnit}`;
+}
+function getValueConversionFactor(term) {
+  const f = Number(term?.valueConversion?.scaleFactor);
+  return Number.isFinite(f) && f > 0 ? f : 1;
+}
+function toUserUnit(v, term, digits = 2) {
+  if (!isConvertible(v, term)) return v;
+  return Number((Number(v) * getValueConversionFactor(term)).toFixed(digits));
+}
+function toStoredUnit(v, term) {
+  if (!isConvertible(v, term)) return v;
+  return Number(v) / getValueConversionFactor(term);
+}
+function isConvertible(v, term) {
+  if (getValueConversionFactor(term) == 1) return false;
+  if (v === "" || v === null || v === void 0) return false;
+  return Number.isFinite(Number(v));
+}
+var CustomError = class extends Error {
+  constructor(message, opts = {}) {
+    super(message);
+    this.level = "";
+    if (opts.name) this.name = opts.name;
+    if (opts.code) this.code = opts.code;
+    if (opts.level) this.level = opts.level;
+  }
+};
+
+export {
+  isNumeric,
+  isStrictNumeric,
+  convertUnits,
+  getValueConversionFactor,
+  toUserUnit,
+  toStoredUnit,
+  CustomError
+};
+//# sourceMappingURL=chunk-75T7ESEO.js.map

package/dist/chunk-75T7ESEO.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../shared/utils/src/helpers.ts"],
+  "sourcesContent": ["/*\nthis is a helper file with a collection of functions to be used in backend and client side code. Here is a list.\n\n1. isNumeric(n)\n2. strictNumeric(n) \n2. convertUnits\n3. TODO - move computepercentile, roundValue, etc here?\n*/\n\n// checks whether given argument n is Numeric, with option to cast from string\nexport function isNumeric(n) {\n\tconst v = typeof n != 'string' || n === '' ? n : Number(n)\n\tconst f = parseFloat(n)\n\treturn !isNaN(f) && Number.isFinite(v) && v === f\n}\n\n// like isNumeric but does not cast from string\nexport function isStrictNumeric(n) {\n\treturn typeof n === 'number' && Number.isFinite(n)\n}\n\n// converts a value from a unit to another unit\nexport function convertUnits(v, fromUnit, toUnit, scaleFactor, compact?: boolean) {\n\t// do floor() on toUnit\n\t// do ceil() on fromUnit, in case v is decimal (from violin range selection) and to keep showing integer fromUnit\n\tif (scaleFactor >= 1) {\n\t\tconst toUnitV = Math.floor(v * scaleFactor)\n\t\tif (compact) return `${toUnitV}${toUnit.charAt(0)}`\n\t\treturn `${toUnitV} ${toUnitV > 1 ? toUnit + 's' : ''}`\n\t}\n\tconst toUnitV = Math.floor(v * scaleFactor)\n\tconst fromUnitV = Math.ceil(v % (1 / scaleFactor))\n\n\tif (fromUnitV == 0) {\n\t\tif (compact) return `${toUnitV}${toUnit.charAt(0)}`\n\t\treturn `${toUnitV} ${toUnitV > 1 ? toUnit + 's' : ''}`\n\t}\n\n\tif (compact) return `${toUnitV}${toUnit.charAt(0)}${fromUnitV}${fromUnit.charAt(0)}`\n\treturn `${toUnitV} ${toUnitV > 1 ? toUnit + 's' : toUnit} ${fromUnitV} ${fromUnitV > 1 ? fromUnit + 's' : fromUnit}`\n}\n\n/*\nterm.valueConversion{} declares that a term's values are stored in .fromUnit (e.g. day), while\n.toUnit (e.g. year) is the unit that is meaningful to a user. convertUnits() above formats a value\nfor display; this instead returns the plain multiplier, for code that must compute on the converted\nvalue rather than print it (e.g. regression, so that a model estimate is per year and not per day).\nreturns 1 when the term has no valueConversion, so that callers may multiply unconditionally\n*/\nexport function getValueConversionFactor(term): number {\n\tconst f = Number(term?.valueConversion?.scaleFactor)\n\treturn Number.isFinite(f) && f > 0 ? f : 1\n}\n\n/*\nthe pair below moves a numeric value across the boundary between what is stored and what is shown.\na term's values, and everything derived from them that is persisted (bin boundaries, tvs ranges,\nspline knots), stay in .fromUnit, because that is what the server filters and bins by. only what a\nuser reads or types is in .toUnit. so a ui that shows an editable number calls toUserUnit() to fill\nthe input and toStoredUnit() to read it back\n\ntoUserUnit() rounds, since an unrounded 70.81451060916 is no more readable than the raw value it\nreplaced. that makes the round trip lossy by up to half of the last shown digit, which is immaterial\nfor a bin boundary or filter range but is why toStoredUnit() does not round again\n*/\nexport function toUserUnit(v, term, digits = 2) {\n\tif (!isConvertible(v, term)) return v\n\treturn Number((Number(v) * getValueConversionFactor(term)).toFixed(digits))\n}\n\nexport function toStoredUnit(v, term): number {\n\tif (!isConvertible(v, term)) return v\n\treturn Number(v) / getValueConversionFactor(term)\n}\n\n/* a blank or non-numeric input is handed back untouched rather than coerced, so that a caller's\nown handling of it (an empty <input>, an unbounded bin edge) is not silently turned into a 0 */\nfunction isConvertible(v, term) {\n\tif (getValueConversionFactor(term) == 1) return false\n\tif (v === '' || v === null || v === undefined) return false\n\treturn Number.isFinite(Number(v))\n}\n\nexport function deepEqual(x, y) {\n\tif (x === y) {\n\t\treturn true\n\t} else if (typeof x == 'object' && x != null && typeof y == 'object' && y != null) {\n\t\tif (Object.keys(x).length != Object.keys(y).length) {\n\t\t\treturn false\n\t\t}\n\n\t\tfor (const prop of Object.keys(x)) {\n\t\t\tif (Object.prototype.hasOwnProperty.call(y, prop)) {\n\t\t\t\tif (!deepEqual(x[prop], y[prop])) return false\n\t\t\t} else {\n\t\t\t\treturn false\n\t\t\t}\n\t\t}\n\t\treturn true\n\t} else return false\n}\n\nexport function deepFreeze(obj) {\n\tObject.freeze(obj)\n\t// not using for..in loop, in order to not descend into inherited props/methods\n\tfor (const value of Object.values(obj)) {\n\t\tif (value !== null && typeof value == 'object') deepFreeze(value)\n\t}\n\treturn obj\n}\n\nexport class CustomError extends Error {\n\tlevel = '' // '' | 'warn'\n\tcode?: string\n\n\tconstructor(message, opts: { name?: string; code?: string; level?: string } = {}) {\n\t\tsuper(message)\n\t\tif (opts.name) this.name = opts.name\n\t\tif (opts.code) this.code = opts.code\n\t\tif (opts.level) this.level = opts.level\n\t}\n}\n"],
+  "mappings": ";AAUO,SAAS,UAAU,GAAG;AAC5B,QAAM,IAAI,OAAO,KAAK,YAAY,MAAM,KAAK,IAAI,OAAO,CAAC;AACzD,QAAM,IAAI,WAAW,CAAC;AACtB,SAAO,CAAC,MAAM,CAAC,KAAK,OAAO,SAAS,CAAC,KAAK,MAAM;AACjD;AAGO,SAAS,gBAAgB,GAAG;AAClC,SAAO,OAAO,MAAM,YAAY,OAAO,SAAS,CAAC;AAClD;AAGO,SAAS,aAAa,GAAG,UAAU,QAAQ,aAAa,SAAmB;AAGjF,MAAI,eAAe,GAAG;AACrB,UAAMA,WAAU,KAAK,MAAM,IAAI,WAAW;AAC1C,QAAI,QAAS,QAAO,GAAGA,QAAO,GAAG,OAAO,OAAO,CAAC,CAAC;AACjD,WAAO,GAAGA,QAAO,IAAIA,WAAU,IAAI,SAAS,MAAM,EAAE;EACrD;AACA,QAAM,UAAU,KAAK,MAAM,IAAI,WAAW;AAC1C,QAAM,YAAY,KAAK,KAAK,KAAK,IAAI,YAAY;AAEjD,MAAI,aAAa,GAAG;AACnB,QAAI,QAAS,QAAO,GAAG,OAAO,GAAG,OAAO,OAAO,CAAC,CAAC;AACjD,WAAO,GAAG,OAAO,IAAI,UAAU,IAAI,SAAS,MAAM,EAAE;EACrD;AAEA,MAAI,QAAS,QAAO,GAAG,OAAO,GAAG,OAAO,OAAO,CAAC,CAAC,GAAG,SAAS,GAAG,SAAS,OAAO,CAAC,CAAC;AAClF,SAAO,GAAG,OAAO,IAAI,UAAU,IAAI,SAAS,MAAM,MAAM,IAAI,SAAS,IAAI,YAAY,IAAI,WAAW,MAAM,QAAQ;AACnH;AASO,SAAS,yBAAyB,MAAc;AACtD,QAAM,IAAI,OAAO,MAAM,iBAAiB,WAAW;AACnD,SAAO,OAAO,SAAS,CAAC,KAAK,IAAI,IAAI,IAAI;AAC1C;AAaO,SAAS,WAAW,GAAG,MAAM,SAAS,GAAG;AAC/C,MAAI,CAAC,cAAc,GAAG,IAAI,EAAG,QAAO;AACpC,SAAO,QAAQ,OAAO,CAAC,IAAI,yBAAyB,IAAI,GAAG,QAAQ,MAAM,CAAC;AAC3E;AAEO,SAAS,aAAa,GAAG,MAAc;AAC7C,MAAI,CAAC,cAAc,GAAG,IAAI,EAAG,QAAO;AACpC,SAAO,OAAO,CAAC,IAAI,yBAAyB,IAAI;AACjD;AAIA,SAAS,cAAc,GAAG,MAAM;AAC/B,MAAI,yBAAyB,IAAI,KAAK,EAAG,QAAO;AAChD,MAAI,MAAM,MAAM,MAAM,QAAQ,MAAM,OAAW,QAAO;AACtD,SAAO,OAAO,SAAS,OAAO,CAAC,CAAC;AACjC;AA8BO,IAAM,cAAN,cAA0B,MAAM;EAItC,YAAY,SAAS,OAAyD,CAAC,GAAG;AACjF,UAAM,OAAO;AAJd,SAAA,QAAQ;AAKP,QAAI,KAAK,KAAM,MAAK,OAAO,KAAK;AAChC,QAAI,KAAK,KAAM,MAAK,OAAO,KAAK;AAChC,QAAI,KAAK,MAAO,MAAK,QAAQ,KAAK;EACnC;AACD;",
+  "names": ["toUnitV"]
+}

package/dist/chunk-A7OWXDYA.js

@@ -0,0 +1,129 @@
+import {
+  formatRangeBounds
+} from "./chunk-FXQXCOII.js";
+import {
+  roundValueAuto
+} from "./chunk-TLT4YIG3.js";
+import {
+  brushX
+} from "./chunk-5R63Q5KH.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+
+// filter/tvs.density.js
+function addBrushes(self, new_brush_location) {
+  const brushes = self.num_obj.brushes;
+  const maxvalue = self.num_obj.density_data.max;
+  const minvalue = self.num_obj.density_data.min;
+  const rawDecile = (maxvalue - minvalue) / 10;
+  const decile = self.tvs.term.type == "integer" ? Math.floor(rawDecile) : rawDecile;
+  for (const [i, r] of self.num_obj.ranges.entries()) {
+    const _b = brushes.find((b) => b.orig === r);
+    let brush;
+    if (!_b) {
+      brush = { orig: r, range: JSON.parse(JSON.stringify(r)) };
+      brushes.push(brush);
+    } else {
+      brush = _b;
+    }
+    if (r.start === "") {
+      if (new_brush_location == "center") brush.range.start = minvalue + decile * 4;
+      else brush.range.start = minvalue + decile * 8;
+    }
+    if (r.stop === "") {
+      if (new_brush_location == "center") brush.range.stop = minvalue + decile * 6;
+      else brush.range.stop = Math.floor(maxvalue);
+    }
+  }
+  const range_brushes = self.num_obj.brush_g.selectAll(".range_brush").data(brushes, (d) => brushes.indexOf(d));
+  range_brushes.exit().remove();
+  range_brushes.each(function(d, i) {
+    select_default(this).selectAll(".overlay").style("pointer-events", "all");
+  });
+  range_brushes.enter().append("g").attr("class", "range_brush").each(function(brush, i) {
+    applyBrush(self, this, brush, i);
+  });
+}
+function applyBrush(self, elem, brush) {
+  if (!brush.elem) brush.elem = select_default(elem);
+  const range = brush.range;
+  const plot_size = self.num_obj.plot_size;
+  const xscale = self.num_obj.xscale;
+  const maxvalue = self.num_obj.density_data.max;
+  const minvalue = self.num_obj.density_data.min;
+  brush.d3brush = brushX().extent([
+    [0, 0],
+    [plot_size.width, plot_size.height]
+  ]).on("brush", function(event, d) {
+    const s = event.selection;
+    if (!s) return;
+    const inputRange = brush.rangeInput.getRange();
+    if (inputRange?.value != void 0) {
+      brush.range = inputRange;
+      return;
+    }
+    updateTempRanges(xscale, s, range, inputRange, minvalue, maxvalue, self.tvs.term.type);
+    const [start, stop] = setStartStopDisplays(range, inputRange, brush.rangeInput.scaleFactor);
+    brush.rangeInput.getInput().node().value = `${start} x ${stop}`;
+  }).on("end", function() {
+    brush.elem.selectAll(".overlay").style("pointer-events", "none");
+  });
+  const brush_start = range.startunbounded ? minvalue : range.start;
+  const brush_stop = range.stopunbounded ? maxvalue : range.stop;
+  brush.init = () => {
+    if (range.value == void 0)
+      brush.elem.call(brush.d3brush).call(brush.d3brush.move, [brush_start, brush_stop].map(xscale));
+  };
+  if (range.startunbounded) delete range.start;
+  if (range.stopunbounded) delete range.stop;
+  brush.elem.selectAll(".selection").style(
+    "fill",
+    brush.orig.start === "" && brush.orig.stop === "" || JSON.stringify(range) != JSON.stringify(brush.orig) ? "#23cba7" : "#777777"
+  );
+}
+function updateTempRanges(xscale, s, range, inputRange, minvalue, maxvalue, type) {
+  range.start = convertRangeValue(xscale, s[0]);
+  range.stop = convertRangeValue(xscale, s[1]);
+  const min = roundValueAuto(Number(minvalue));
+  const max = roundValueAuto(Number(maxvalue));
+  if (range.start < min) range.start = min;
+  if (range.stop > max) range.stop = max;
+  range.startunbounded = min == range.start && inputRange.startunbounded;
+  range.stopunbounded = max == range.stop && inputRange.stopunbounded;
+  if (type == "integer") {
+    range.start = range.startunbounded ? "" : Math.round(range.start);
+    range.stop = range.stopunbounded ? "" : Math.round(range.stop);
+  }
+}
+function setStartStopDisplays(range, inputRange, scaleFactor = 1) {
+  return formatRangeBounds(
+    {
+      ...range,
+      startinclusive: inputRange.startinclusive,
+      stopinclusive: inputRange.stopinclusive
+    },
+    scaleFactor
+  );
+}
+function convertRangeValue(xscale, sidx) {
+  const value = Number(xscale.invert(sidx));
+  return roundValueAuto(value);
+}
+function addNewBrush(self, new_brush_location = "end", callback) {
+  const new_range = { start: "", stop: "", index: self.tvs.ranges.length };
+  self.num_obj.ranges.push(new_range);
+  const brush = { orig: new_range, range: JSON.parse(JSON.stringify(new_range)) };
+  self.num_obj.brushes.push(brush);
+  addBrushes(self, new_brush_location);
+  if (callback) callback();
+  brush.init();
+}
+
+export {
+  addBrushes,
+  updateTempRanges,
+  setStartStopDisplays,
+  addNewBrush
+};
+//# sourceMappingURL=chunk-A7OWXDYA.js.map

package/dist/chunk-A7OWXDYA.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../filter/tvs.density.js"],
+  "sourcesContent": ["import { select } from 'd3-selection'\nimport { brushX } from 'd3-brush'\nimport { roundValueAuto } from '#shared/roundValue.js'\nimport { formatRangeBounds } from '#dom/numericRangeInput'\n\n/*\n********************** EXPORTED\naddBrushes()// add brushed to densityplot from self.num_obj.brushes and \n            // new brush at end or center of plot\naddNewBrush() // add new brush either at end (with existing ranges) or in center (no ranges)\n\n********************** INTERNAL\napplyBrush() // main function to define and init d3 brushes, \n             // it will handle events such as brush move, drag\n             // and will update input elements attached to brush, e.g. brush.rangeInput\n\n*/\n\nexport function addBrushes(self, new_brush_location) {\n\t// const ranges = self.num_obj.ranges\n\tconst brushes = self.num_obj.brushes\n\tconst maxvalue = self.num_obj.density_data.max\n\tconst minvalue = self.num_obj.density_data.min\n\tconst rawDecile = (maxvalue - minvalue) / 10\n\tconst decile = self.tvs.term.type == 'integer' ? Math.floor(rawDecile) : rawDecile\n\n\tfor (const [i, r] of self.num_obj.ranges.entries()) {\n\t\tconst _b = brushes.find(b => b.orig === r)\n\t\tlet brush\n\t\tif (!_b) {\n\t\t\tbrush = { orig: r, range: JSON.parse(JSON.stringify(r)) }\n\t\t\tbrushes.push(brush)\n\t\t} else {\n\t\t\tbrush = _b\n\t\t}\n\t\t// strict equality to not have false positive with start=0\n\t\tif (r.start === '') {\n\t\t\tif (new_brush_location == 'center') brush.range.start = minvalue + decile * 4\n\t\t\telse brush.range.start = minvalue + decile * 8\n\t\t}\n\t\tif (r.stop === '') {\n\t\t\tif (new_brush_location == 'center') brush.range.stop = minvalue + decile * 6\n\t\t\telse brush.range.stop = Math.floor(maxvalue)\n\t\t}\n\t}\n\n\tconst range_brushes = self.num_obj.brush_g.selectAll('.range_brush').data(brushes, d => brushes.indexOf(d))\n\n\trange_brushes.exit().remove()\n\n\t// add update to brush if required\n\trange_brushes.each(function (d, i) {\n\t\tselect(this).selectAll('.overlay').style('pointer-events', 'all')\n\t})\n\n\trange_brushes\n\t\t.enter()\n\t\t.append('g')\n\t\t.attr('class', 'range_brush')\n\t\t.each(function (brush, i) {\n\t\t\tapplyBrush(self, this, brush, i)\n\t\t})\n}\n\nfunction applyBrush(self, elem, brush) {\n\tif (!brush.elem) brush.elem = select(elem)\n\tconst range = brush.range\n\tconst plot_size = self.num_obj.plot_size\n\tconst xscale = self.num_obj.xscale\n\tconst maxvalue = self.num_obj.density_data.max\n\tconst minvalue = self.num_obj.density_data.min\n\n\tbrush.d3brush = brushX()\n\t\t.extent([\n\t\t\t[0, 0],\n\t\t\t[plot_size.width, plot_size.height]\n\t\t])\n\t\t.on('brush', function (event, d) {\n\t\t\tconst s = event.selection\n\t\t\tif (!s) return // not an event triggered by brush dragging\n\t\t\t// brush.rangeInput is created from NumericRangeInput() as called in tvs.numeric.js\n\t\t\t// when filling a menu with or without density plot, should always be present\n\t\t\tconst inputRange = brush.rangeInput.getRange()\n\t\t\tif (inputRange?.value != undefined) {\n\t\t\t\tbrush.range = inputRange\n\t\t\t\treturn\n\t\t\t}\n\t\t\t//update temp_ranges\n\t\t\tupdateTempRanges(xscale, s, range, inputRange, minvalue, maxvalue, self.tvs.term.type)\n\n\t\t\t// the brush works in the unit the term's values are stored in, the <input> in the user-facing one\n\t\t\tconst [start, stop] = setStartStopDisplays(range, inputRange, brush.rangeInput.scaleFactor)\n\t\t\t// update inputs from brush move\n\t\t\tbrush.rangeInput.getInput().node().value = `${start} x ${stop}`\n\t\t})\n\t\t.on('end', function () {\n\t\t\t//diable pointer-event for multiple brushes\n\t\t\tbrush.elem.selectAll('.overlay').style('pointer-events', 'none')\n\t\t})\n\n\tconst brush_start = range.startunbounded ? minvalue : range.start\n\tconst brush_stop = range.stopunbounded ? maxvalue : range.stop\n\tbrush.init = () => {\n\t\tif (range.value == undefined)\n\t\t\tbrush.elem.call(brush.d3brush).call(brush.d3brush.move, [brush_start, brush_stop].map(xscale))\n\t}\n\n\tif (range.startunbounded) delete range.start\n\tif (range.stopunbounded) delete range.stop\n\tbrush.elem\n\t\t.selectAll('.selection')\n\t\t.style(\n\t\t\t'fill',\n\t\t\t(brush.orig.start === '' && brush.orig.stop === '') || JSON.stringify(range) != JSON.stringify(brush.orig)\n\t\t\t\t? '#23cba7'\n\t\t\t\t: '#777777'\n\t\t)\n}\n\n/** Updates the number range returned from the brushing into\n * rounded values or integers.  Encapsulated and exported to verify\n * usage via testing and CI.\n *\n * xscale: d3 scale for x-axis\n * s: selection from brush, [start, stop]\n * range: range object to update\n * inputRange: input range object\n * minValue: min value of the density plot\n * maxValue: max value of the density plot\n * termType: term type\n */\nexport function updateTempRanges(xscale, s, range, inputRange, minvalue, maxvalue, type) {\n\trange.start = convertRangeValue(xscale, s[0])\n\trange.stop = convertRangeValue(xscale, s[1])\n\tconst min = roundValueAuto(Number(minvalue))\n\tconst max = roundValueAuto(Number(maxvalue))\n\t//If the user inputs a value outside the brush, limit it to the brush\n\t//Otherwise the input displays a calculated position closest to the value.\n\tif (range.start < min) range.start = min\n\tif (range.stop > max) range.stop = max\n\t//Limit by the brush, not by the user\n\trange.startunbounded = min == range.start && inputRange.startunbounded\n\trange.stopunbounded = max == range.stop && inputRange.stopunbounded\n\t//Do not show decimals for integer types\n\tif (type == 'integer') {\n\t\trange.start = range.startunbounded ? '' : Math.round(range.start)\n\t\trange.stop = range.stopunbounded ? '' : Math.round(range.stop)\n\t}\n}\n\n/** Set the start and stop displayed to the user\n * Encapsulated and exported to verify usage via testing and CI.\n *\n * range: range object to update. 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+  "names": []
+}

package/dist/chunk-AOVDTRFY.js

@@ -0,0 +1,272 @@
+import {
+  fillbar,
+  make_table_2col
+} from "./chunk-73PFJ2VF.js";
+
+// src/block.mds.expressionstat.js
+var color_noinfo = "#858585";
+function init_config(cfg) {
+  if (!cfg.datatype) cfg.datatype = "FPKM";
+  if (!cfg.itemcolor) cfg.itemcolor = "green";
+  if (!cfg.ase) cfg.ase = {};
+  if (cfg.ase.qvalue == void 0) cfg.ase.qvalue = 0.05;
+  if (cfg.ase.meandelta_monoallelic == void 0) cfg.ase.meandelta_monoallelic = 0.3;
+  if (cfg.ase.asemarkernumber_biallelic == void 0) cfg.ase.asemarkernumber_biallelic = 0;
+  if (!cfg.ase.color_noinfo) cfg.ase.color_noinfo = color_noinfo;
+  if (!cfg.ase.color_uncertain) cfg.ase.color_uncertain = "#A8E0B5";
+  if (!cfg.ase.color_biallelic) cfg.ase.color_biallelic = "#40859C";
+  if (!cfg.ase.color_monoallelic) cfg.ase.color_monoallelic = "#d95f02";
+  if (!cfg.outlier) cfg.outlier = {};
+  if (cfg.outlier.pvalue_cutoff == void 0) cfg.outlier.pvalue_cutoff = 0.05;
+  if (cfg.outlier.rank_asehigh_cutoff == void 0) cfg.outlier.rank_asehigh_cutoff = 0.1;
+  if (!cfg.outlier.color_outlier) cfg.outlier.color_outlier = "#FF8875";
+  if (!cfg.outlier.color_outlier_asehigh) cfg.outlier.color_outlier_asehigh = "blue";
+}
+function measure(v, cfg) {
+  if (!cfg) return;
+  v.estat = {};
+  if (v.ase && cfg.ase) {
+    const qvalue = v.ase.qvalue || v.ase.geometricmean;
+    if (qvalue == void 0) {
+      v.estat.ase_noinfo = true;
+    } else if (qvalue <= cfg.ase.qvalue) {
+      if (v.ase.mean_delta >= cfg.ase.meandelta_monoallelic) {
+        v.estat.ase_monoallelic = true;
+      } else {
+        v.estat.ase_uncertain = true;
+      }
+    } else {
+      if (v.ase.ase_markers == cfg.ase.asemarkernumber_biallelic) {
+        v.estat.ase_biallelic = true;
+      } else {
+        v.estat.ase_uncertain = true;
+      }
+    }
+  } else {
+    v.estat.ase_noinfo = true;
+  }
+  if (v.outlier && cfg.outlier) {
+    if (v.outlier.test_whitelist) {
+      if (v.outlier.test_whitelist.pvalue <= cfg.outlier.pvalue_cutoff) {
+        v.estat.outlier = true;
+      } else {
+        if (v.estat.ase_monoallelic) {
+          if (Number.isInteger(v.outlier.test_whitelist.rank) && Number.isInteger(v.outlier.test_whitelist.size) && v.outlier.test_whitelist.rank / v.outlier.test_whitelist.size <= cfg.outlier.rank_asehigh_cutoff) {
+            v.estat.outlier_asehigh = true;
+            v.outlier.test_whitelist.asehigh = true;
+          }
+        }
+      }
+    } else if (v.outlier.test_biallelic) {
+      if (v.outlier.test_biallelic.pvalue <= cfg.outlier.pvalue_cutoff) {
+        v.estat.outlier = true;
+      } else {
+        if (v.estat.ase_monoallelic) {
+          if (Number.isInteger(v.outlier.test_biallelic.rank) && Number.isInteger(v.outlier.test_biallelic.size) && v.outlier.test_biallelic.rank / v.outlier.test_biallelic.size <= cfg.outlier.rank_asehigh_cutoff) {
+            v.estat.outlier_asehigh = true;
+            v.outlier.test_biallelic.asehigh = true;
+          }
+        }
+      }
+    } else if (v.outlier.test_entirecohort) {
+      if (v.outlier.test_entirecohort.pvalue <= cfg.outlier.pvalue_cutoff) {
+        v.estat.outlier = true;
+      } else {
+        if (v.estat.ase_monoallelic) {
+          if (Number.isInteger(v.outlier.test_entirecohort.rank) && Number.isInteger(v.outlier.test_entirecohort.size) && v.outlier.test_entirecohort.rank / v.outlier.test_entirecohort.size <= cfg.outlier.rank_asehigh_cutoff) {
+            v.estat.outlier_asehigh = true;
+            v.outlier.test_entirecohort.asehigh = true;
+          }
+        }
+      }
+    }
+  }
+}
+function showsingleitem_table(v, cfg, table) {
+  if (!v.estat) return;
+  if (cfg.no_ase) return;
+  if (v.ase) {
+    const tr = table.append("tr");
+    tr.append("td").attr("colspan", 2).style("background", ase_color(v, cfg)).style("color", "white").html(
+      (v.estat.ase_monoallelic ? "Mono-allelic" : v.estat.ase_biallelic ? "Bi-allelic" : "ASE uncertain") + "<br>(allele-specific expression)"
+    );
+    const lst = [
+      {
+        k: "#SNPs heterozygous in DNA",
+        v: v.ase.markers
+      },
+      {
+        k: "#SNPs showing ASE in RNA",
+        v: v.ase.ase_markers
+      },
+      {
+        k: "Mean delta of ASE SNPs",
+        v: v.ase.mean_delta
+      }
+    ];
+    if (v.ase.qvalue) {
+      lst.push({
+        k: "Q-value",
+        v: v.ase.qvalue
+      });
+    } else if (v.ase.geometricmean) {
+      lst.push({
+        k: "Geometric mean of binomial P-values of ASE SNPs",
+        v: v.ase.geometricmean
+      });
+    }
+    const td = tr.append("td");
+    make_table_2col(td, lst);
+  } else {
+    const tr = table.append("tr");
+    tr.append("td").attr("colspan", 3).style("background", cfg.ase.color_noinfo).style("color", "white").text("No info on allele-specific expression");
+  }
+  if (v.snps && v.snps.length > 0) {
+    const hetsnp = v.snps.filter((i) => i.dnacount && i.dnacount.ishet);
+    if (hetsnp.length > 0) {
+      const lst = [];
+      for (const m of hetsnp) {
+        lst.push(
+          "<tr><td>" + m.chr + ":" + (m.pos + 1) + " " + m.ref + ">" + m.alt + "</td><td>" + fillbar(null, { f: m.dnacount.f }) + " " + m.dnacount.ref + "/" + m.dnacount.alt + "</td><td>" + (m.rnacount.nocoverage ? '<span style="font-size:.8em;opacity:.5">No coverage</span>' : fillbar(null, { f: m.rnacount.f }) + " " + m.rnacount.ref + "/" + m.rnacount.alt) + "</td><td>" + (m.rnacount.pvalue || "-") + "</td></tr>"
+        );
+      }
+      table.append("tr").append("td").attr("colspan", 3).html(
+        '<table style="margin-top:10px;border:solid 1px #ededed;border-spacing:5px;"><tr style="opacity:.5"><td>SNP</td><td>DNA</td><td>RNA</td><td>Binomial test P-value</td></tr>' + lst.join("") + "</table>"
+      );
+    }
+  }
+  if (v.outlier) {
+    if (v.outlier.test_whitelist) {
+      const tr = table.append("tr");
+      tr.append("td").attr("colspan", 2).text("Outlier (white list)");
+      const lst = [];
+      for (const k in v.outlier.test_whitelist) {
+        lst.push({ k, v: v.outlier.test_whitelist[k] });
+      }
+      const td = tr.append("td");
+      make_table_2col(td, lst);
+      if (v.outlier.test_whitelist.asehigh) {
+        td.append("div").style("background", cfg.outlier.color_outlier_asehigh).style("padding", "2px 10px").style("color", "white").text("ASE high");
+      }
+    }
+    if (v.outlier.test_biallelic) {
+      const tr = table.append("tr");
+      tr.append("td").attr("colspan", 2).text("Outlier (biallelic)");
+      const lst = [];
+      for (const k in v.outlier.test_biallelic) {
+        lst.push({ k, v: v.outlier.test_biallelic[k] });
+      }
+      const td = tr.append("td");
+      make_table_2col(td, lst);
+      if (v.outlier.test_biallelic.asehigh) {
+        td.append("div").style("background", cfg.outlier.color_outlier_asehigh).style("padding", "2px 10px").style("color", "white").text("ASE high");
+      }
+    }
+    if (v.outlier.test_entirecohort) {
+      const tr = table.append("tr");
+      tr.append("td").attr("colspan", 2).text("Outlier (all samples)");
+      const lst = [];
+      for (const k in v.outlier.test_entirecohort) {
+        lst.push({ k, v: v.outlier.test_entirecohort[k] });
+      }
+      const td = tr.append("td");
+      make_table_2col(td, lst);
+      if (v.outlier.test_entirecohort.asehigh) {
+        td.append("div").style("background", cfg.outlier.color_outlier_asehigh).style("padding", "2px 10px").style("color", "white").text("ASE high");
+      }
+    }
+  }
+}
+function ase_color(v, cfg) {
+  if (cfg.no_ase) return color_noinfo;
+  if (!cfg.ase) return color_noinfo;
+  if (!v.estat) return cfg.ase.color_noinfo;
+  if (v.estat.ase_monoallelic) return cfg.ase.color_monoallelic;
+  if (v.estat.ase_biallelic) return cfg.ase.color_biallelic;
+  if (v.estat.ase_uncertain) return cfg.ase.color_uncertain;
+  return cfg.ase.color_noinfo;
+}
+function ui_config(holder, cfg, tk, call) {
+  const indent = 30;
+  {
+    const row = holder.append("div").style("margin-bottom", "5px");
+    row.append("span").html("If " + (tk.checkrnabam ? "p-value geometric mean" : "Q-VALUE") + " &le;&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", cfg.ase.qvalue).on("keyup", (event) => {
+      if (event.code != "Enter" && event.code != "NumpadEnter") return;
+      let v = Number.parseFloat(event.target.value);
+      if (!v || v <= 0) {
+        return;
+      }
+      if (cfg.ase.qvalue == v) {
+        return;
+      }
+      cfg.ase.qvalue = v;
+      call();
+    });
+    row.append("span").html("&nbsp;:");
+  }
+  {
+    const row = holder.append("div").style("margin", "0px 5px 5px " + indent + "px");
+    row.append("span").html("If MEAN_DELTA &ge;&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", cfg.ase.meandelta_monoallelic).on("keyup", (event) => {
+      if (event.code != "Enter" && event.code != "NumpadEnter") return;
+      let v = Number.parseFloat(event.target.value);
+      if (!v || v <= 0) {
+        return;
+      }
+      if (cfg.ase.meandelta_monoallelic == v) {
+        return;
+      }
+      cfg.ase.meandelta_monoallelic = v;
+      call();
+    });
+    row.append("span").html("&nbsp;:&nbsp;");
+  }
+  holder.append("div").style("margin", "0px 5px 5px " + indent * 2 + "px").html(
+    'Is <span style="background:' + cfg.ase.color_monoallelic + ';padding:1px 5px;color:white;">mono-allelic expression</span>'
+  );
+  holder.append("div").style("margin", "0px 5px 5px " + indent + "px").html("Else:");
+  holder.append("div").style("margin", "0px 5px 5px " + indent * 2 + "px").html(
+    'Is <span style="background:' + cfg.ase.color_uncertain + ';padding:1px 5px;color:white;">ASE uncertain</span>'
+  );
+  holder.append("div").style("margin", "0px 5px 5px 0px").html("Else:");
+  {
+    const row = holder.append("div").style("margin", "0px 5px 5px " + indent + "px");
+    row.append("span").html("If number of ASE markers &le;&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", cfg.ase.asemarkernumber_biallelic).on("keyup", (event) => {
+      if (event.code != "Enter" && event.code != "NumpadEnter") return;
+      let v = Number.parseInt(event.target.value);
+      if (v < 0) {
+        return;
+      }
+      if (cfg.ase.asemarkernumber_biallelic == v) {
+        return;
+      }
+      cfg.ase.asemarkernumber_biallelic = v;
+      call();
+    });
+    row.append("span").html("&nbsp;:&nbsp;");
+  }
+  holder.append("div").style("margin", "0px 5px 5px " + indent * 2 + "px").html(
+    'Is <span style="background:' + cfg.ase.color_biallelic + ';padding:1px 5px;color:white;">bi-allelic expression</span>'
+  );
+  holder.append("div").style("margin", "0px 5px 5px " + indent + "px").html("Else:");
+  holder.append("div").style("margin", "0px 5px 5px " + indent * 2 + "px").html(
+    'Is <span style="background:' + cfg.ase.color_uncertain + ';padding:1px 5px;color:white;">ASE uncertain</span>'
+  );
+  holder.append("div").style("margin", "10px").append("button").text("Default ASE parameters").on("click", () => {
+    cfg.ase.qvalue = 0.05;
+    cfg.ase.meandelta_monoallelic = 0.3;
+    cfg.ase.asemarkernumber_biallelic = 0;
+    call();
+  });
+}
+
+export {
+  init_config,
+  measure,
+  showsingleitem_table,
+  ase_color,
+  ui_config
+};
+//# sourceMappingURL=chunk-AOVDTRFY.js.map