@sjcrh/proteinpaint-client 2.180.0 → 2.180.1

package/dist/chunk-5OHXYXLD.js

@@ -1,46 +0,0 @@
-// ../shared/utils/src/roundValue.js
-function roundValue(value, digits) {
-  const v = Number(value);
-  if (Number.isInteger(v)) return v;
-  if (Math.abs(v) < 1) return Number(v.toPrecision(digits));
-  return Number(v.toFixed(digits));
-}
-function roundValueAuto(value, format = false, defaultDigits = 2) {
-  if (!value && value != 0) return value;
-  const dp = decimalPlacesUntilFirstNonZero(value);
-  const digits = Math.abs(value) > 1 ? defaultDigits : dp > 0 ? dp + 1 : defaultDigits;
-  if (format) return formatValue(value, digits);
-  return roundValue(value, digits);
-}
-function decimalPlacesUntilFirstNonZero(number) {
-  const numberStr = number.toString();
-  const decimalIndex = numberStr.indexOf(".");
-  if (decimalIndex === -1 || decimalIndex === numberStr.length - 1) {
-    return 0;
-  }
-  let decimalPlaces = 0;
-  for (let i = decimalIndex + 1; i < numberStr.length; i++) {
-    if (numberStr[i] === "0") {
-      decimalPlaces++;
-    } else if (numberStr[i] >= "1" && numberStr[i] <= "9") {
-      break;
-    }
-  }
-  return decimalPlaces;
-}
-function formatValue(value, digits) {
-  const v = Number(value);
-  if (Number.isInteger(v)) return v;
-  const abs = Math.abs(v);
-  if (abs < 1 || abs > 9999) {
-    return abs > 9999 ? v.toPrecision(digits) : Number(v.toPrecision(digits));
-  }
-  return Number(v.toFixed(digits));
-}
-
-export {
-  roundValue,
-  roundValueAuto,
-  decimalPlacesUntilFirstNonZero
-};
-//# sourceMappingURL=chunk-5OHXYXLD.js.map

package/dist/chunk-5OHXYXLD.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../shared/utils/src/roundValue.js"],
-  "sourcesContent": ["/*\nround a value to specified digits\n    - if value is integer, value is returned\n    - if value is a fractional float, round to precision\n    - if value is not a fractional float, round to decimal point\n    - TODO: handle scientific notation\nvalue: given value\ndigits: number of digits to round to\n*/\n\nexport function roundValue(value, digits) {\n\tconst v = Number(value)\n\tif (Number.isInteger(v)) return v\n\tif (Math.abs(v) < 1) return Number(v.toPrecision(digits))\n\treturn Number(v.toFixed(digits))\n}\n\n/** Rounds numbers to the appropriate decimal point\n * if format is true, returns either a number or string in\n * scientific notation.\n *\n * TODO: Review digit logic.\n */\n\nexport function roundValueAuto(value, format = false, defaultDigits = 2) {\n\tif (!value && value != 0) return value\n\tconst dp = decimalPlacesUntilFirstNonZero(value)\n\tconst digits = Math.abs(value) > 1 ? defaultDigits : dp > 0 ? dp + 1 : defaultDigits\n\tif (format) return formatValue(value, digits)\n\treturn roundValue(value, digits)\n}\n\nexport function decimalPlacesUntilFirstNonZero(number) {\n\t// Convert number to string\n\tconst numberStr = number.toString()\n\n\t// Find the position of the decimal point\n\tconst decimalIndex = numberStr.indexOf('.')\n\n\t// If decimal point is not found or number is an integer, return 0\n\tif (decimalIndex === -1 || decimalIndex === numberStr.length - 1) {\n\t\treturn 0\n\t}\n\n\t// Iterate through characters after the decimal point\n\tlet decimalPlaces = 0\n\tfor (let i = decimalIndex + 1; i < numberStr.length; i++) {\n\t\t// Increment the count of decimal places until a non-zero digit is found\n\t\tif (numberStr[i] === '0') {\n\t\t\tdecimalPlaces++\n\t\t} else if (numberStr[i] >= '1' && numberStr[i] <= '9') {\n\t\t\tbreak\n\t\t}\n\t}\n\n\treturn decimalPlaces\n}\n\n/* \nsimple logic to return a number close to original while rounding up decimals.\nsupplements roundValueAuto which rounds 12345 to 1.2e4 which is only suitable for human quick glance but not subsequent computing\n\nTODO:\n10000 and 10001 to 1e4\n0.00001 to 1e-5\n1.00001 to 1\n*/\nexport function roundValue2(value) {\n\tif (!Number.isFinite(value)) return value // not a number\n\tif (Number.isInteger(value)) return value // is integer, do not convert\n\tconst abs = Math.abs(value)\n\tif (abs > 100) return Math.round(value) // 12345.1234 to 12345 (compared to 1.2e4 from roundValueAuto)\n\tif (abs > 10) return Number(value.toFixed(1)) // 99.1234 to 99.1\n\tif (abs > 1) return Number(value.toFixed(2)) // 9.1234 to 9.12\n\tif (abs > 0.1) return Number(value.toFixed(3)) // 0.12345 to 0.123\n\tif (abs > 0.01) return Number(value.toFixed(4)) // 0.012345 to 0.0123\n\treturn value // as is\n}\n\n/** Use to return displayed values in scientific notation\n * Do not use for values intended for calculation later.\n */\nexport function formatValue(value, digits) {\n\tconst v = Number(value)\n\tif (Number.isInteger(v)) return v\n\tconst abs = Math.abs(v)\n\tif (abs < 1 || abs > 9999) {\n\t\t//Number() reverts positive values less than 10^21 to a whole number\n\t\t//To return the value in scientific notation, use toPrecision without Number()\n\t\treturn abs > 9999 ? v.toPrecision(digits) : Number(v.toPrecision(digits))\n\t}\n\treturn Number(v.toFixed(digits))\n}\n"],
-  "mappings": ";AAUO,SAAS,WAAW,OAAO,QAAQ;AACzC,QAAM,IAAI,OAAO,KAAK;AACtB,MAAI,OAAO,UAAU,CAAC,EAAG,QAAO;AAChC,MAAI,KAAK,IAAI,CAAC,IAAI,EAAG,QAAO,OAAO,EAAE,YAAY,MAAM,CAAC;AACxD,SAAO,OAAO,EAAE,QAAQ,MAAM,CAAC;AAChC;AASO,SAAS,eAAe,OAAO,SAAS,OAAO,gBAAgB,GAAG;AACxE,MAAI,CAAC,SAAS,SAAS,EAAG,QAAO;AACjC,QAAM,KAAK,+BAA+B,KAAK;AAC/C,QAAM,SAAS,KAAK,IAAI,KAAK,IAAI,IAAI,gBAAgB,KAAK,IAAI,KAAK,IAAI;AACvE,MAAI,OAAQ,QAAO,YAAY,OAAO,MAAM;AAC5C,SAAO,WAAW,OAAO,MAAM;AAChC;AAEO,SAAS,+BAA+B,QAAQ;AAEtD,QAAM,YAAY,OAAO,SAAS;AAGlC,QAAM,eAAe,UAAU,QAAQ,GAAG;AAG1C,MAAI,iBAAiB,MAAM,iBAAiB,UAAU,SAAS,GAAG;AACjE,WAAO;AAAA,EACR;AAGA,MAAI,gBAAgB;AACpB,WAAS,IAAI,eAAe,GAAG,IAAI,UAAU,QAAQ,KAAK;AAEzD,QAAI,UAAU,CAAC,MAAM,KAAK;AACzB;AAAA,IACD,WAAW,UAAU,CAAC,KAAK,OAAO,UAAU,CAAC,KAAK,KAAK;AACtD;AAAA,IACD;AAAA,EACD;AAEA,SAAO;AACR;AA0BO,SAAS,YAAY,OAAO,QAAQ;AAC1C,QAAM,IAAI,OAAO,KAAK;AACtB,MAAI,OAAO,UAAU,CAAC,EAAG,QAAO;AAChC,QAAM,MAAM,KAAK,IAAI,CAAC;AACtB,MAAI,MAAM,KAAK,MAAM,MAAM;AAG1B,WAAO,MAAM,OAAO,EAAE,YAAY,MAAM,IAAI,OAAO,EAAE,YAAY,MAAM,CAAC;AAAA,EACzE;AACA,SAAO,OAAO,EAAE,QAAQ,MAAM,CAAC;AAChC;",
-  "names": []
-}

package/dist/chunk-5SB27JYT.js

@@ -1,46 +0,0 @@
-import {
-  sayerror
-} from "./chunk-EPGSHRD6.js";
-import {
-  TermTypeGroups
-} from "./chunk-K535LGE2.js";
-
-// termdb/handlers/singleCellCellType.ts
-var SearchHandler = class {
-  async init(opts) {
-    this.validateOpts(opts);
-    this.callback = opts.callback;
-    this.app = opts.app;
-    const holder = opts.holder.append("div").style("padding", "10px 0px");
-    const scctTerms = opts.app.vocabApi.termdbConfig?.termType2terms?.[TermTypeGroups.SINGLECELL_CELLTYPE];
-    if (!scctTerms) {
-      sayerror(
-        holder,
-        `termType2terms[${TermTypeGroups.SINGLECELL_CELLTYPE}]:[] is required in termdbConfig for singleCellCellType handler`
-      );
-      return;
-    }
-    const filteredTerms = scctTerms.filter((t) => t.plot == opts.usecase.specialCase.config.name);
-    for (const t of filteredTerms) {
-      holder.append("div").classed("termdiv", true).style("padding", "0px 5px").append("div").classed("termlabel sja_filter_tag_btn sja_tree_click_term ts_pill", true).style("display", "inline-block").style("padding", "5px 8px").style("margin", "1px 0px").style("border-radius", "6px").text(t.name).on("click", () => {
-        this.callback(t);
-      });
-    }
-  }
-  validateOpts(opts) {
-    if (opts.callback == null) throw new Error("callback is required");
-    if (opts.app == null) throw new Error("app is required");
-    if (opts.holder == null) throw new Error("holder is required");
-    if (opts.usecase == null) throw new Error("usecase is required");
-    if (!opts.app.vocabApi.termdbConfig?.termType2terms)
-      throw new Error("termType2terms is required in termdbConfig for singleCellCellType handler");
-    if (!opts.usecase?.specialCase?.config?.name) {
-      throw new Error("usecase.specialCase.config.name defining the plot is required for singleCellCellType handler");
-    }
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-5SB27JYT.js.map

package/dist/chunk-5TUM3XRB.js

@@ -1,203 +0,0 @@
-import {
-  tkt
-} from "./chunk-EPGSHRD6.js";
-import {
-  stratinput
-} from "./chunk-IQIXGTQV.js";
-import {
-  stratify_default
-} from "./chunk-TOU7EVFQ.js";
-
-// src/vcf.tkconvert.js
-function vcf2dstk(arg) {
-  const ds = {
-    id2vcf: {},
-    label: arg.name || "Unnamed VCF file"
-  };
-  let vcfobj;
-  if (arg.file) {
-    const id = Math.random().toString();
-    vcfobj = {
-      file: arg.file,
-      indexURL: arg.indexURL,
-      vcfid: id
-    };
-    ds.id2vcf[id] = vcfobj;
-  } else if (arg.url) {
-    const id = Math.random().toString();
-    vcfobj = {
-      url: arg.url,
-      indexURL: arg.indexURL,
-      vcfid: id
-    };
-    ds.id2vcf[id] = vcfobj;
-  } else {
-    return ["no .file or .url"];
-  }
-  vcfobj.headernotloaded = true;
-  if (arg.samplenamemap) {
-    vcfobj.samplenamemap = arg.samplenamemap;
-  }
-  if (arg.variant2img) {
-    if (!arg.variant2img.path) return [".path missing from .variant2img{}"];
-  }
-  const tk = {
-    type: tkt.ds,
-    // to be loaded by loadvcftk() as a custom track, rather than "/dsdata" for official ds
-    isvcf: true,
-    name: ds.label,
-    ds,
-    populationfrequencyfilter: arg.populationfrequencyfilter,
-    vcfinfofilter: arg.vcfinfofilter,
-    itemlabelname: arg.itemlabelname,
-    viewrangeupperlimit: arg.viewrangeupperlimit,
-    variant2img: arg.variant2img,
-    axisheight: arg.axisheight
-  };
-  if (arg.url4variant) {
-    const err = check_url4variant(arg.url4variant);
-    if (err) return [".url4variant error: " + err];
-    tk.url4variant = arg.url4variant;
-  }
-  if (arg.button4variant) {
-    const err = check_button4variant(arg.button4variant);
-    if (err) return [".button4variant error: " + err];
-    tk.button4variant = arg.button4variant;
-  }
-  if (arg.sampleannotation) {
-    const sn = arg.sampleannotation;
-    if (!sn.annotation) return [".annotation{} missing from .sampleannotation"];
-    if (sn.levels) {
-      if (!Array.isArray(sn.levels)) return [".sampleannotation.levels should be array"];
-      const lst = [];
-      for (const sample in sn.annotation) {
-        const o = { sample_name: sample };
-        for (const k in sn.annotation[sample]) {
-          o[k] = sn.annotation[sample][k];
-        }
-        lst.push(o);
-      }
-      const nodes = stratinput(lst, sn.levels);
-      sn.root = stratify_default()(nodes);
-      sn.root.sum((i) => i.value);
-    }
-    if (sn.variantsunburst) {
-      if (!sn.levels) return [".levels missing when .variantsunburst is on from .sampleannotation"];
-    }
-    tk.ds.cohort = sn;
-  }
-  if (arg.vcfcohorttrack) {
-    if (!arg.vcfcohorttrack.file && !arg.vcfcohorttrack.url) return ["no .file or .url provided from .vcfcohorttrack"];
-    tk.ds.vcfcohorttrack = arg.vcfcohorttrack;
-  }
-  if (arg.germline2dvafplot) {
-    if (!arg.germline2dvafplot.individualkey) return [".individualkey missing from germline2dvafplot"];
-    if (!arg.germline2dvafplot.sampletypekey) return [".sampletypekey missing from germline2dvafplot"];
-    if (!arg.germline2dvafplot.xsampletype) return [".xsampletype missing from germline2dvafplot"];
-    if (!arg.germline2dvafplot.yleftsampletype) return [".yleftsampletype missing from germline2dvafplot"];
-    if (arg.germline2dvafplot.yrightsampletype) {
-      if (arg.germline2dvafplot.yrightsampletype == arg.germline2dvafplot.yleftsampletype)
-        return [".yrightsampletype should not be same as yleftsampletype"];
-    }
-    tk.ds.germline2dvafplot = arg.germline2dvafplot;
-  }
-  if (arg.vaf2coverageplot) {
-    if (arg.vaf2coverageplot.categorykey) {
-      if (!arg.vaf2coverageplot.categories)
-        return [".categories missing when .categorykey is in use for .vaf2coverageplot"];
-    }
-    tk.ds.vaf2coverageplot = arg.vaf2coverageplot;
-  }
-  if (arg.genotype2boxplot) {
-    if (arg.genotype2boxplot.boxplotvaluekey) {
-    } else if (arg.genotype2boxplot.sampleannotationkey) {
-      if (!tk.ds.cohort) return ["sampleannotation missing when using genotype2boxplot.sampleannotationkey"];
-      if (!tk.ds.cohort.annotation)
-        return ["sampleannotation.annotation missing when using genotype2boxplot.sampleannotationkey"];
-      let found = false;
-      for (const k in tk.ds.cohort.annotation) {
-        if (arg.genotype2boxplot.sampleannotationkey in tk.ds.cohort.annotation[k]) {
-          found = true;
-          break;
-        }
-      }
-      if (!found) return [arg.genotype2boxplot.sampleannotationkey + " not found in any sample annotation"];
-    } else {
-      return ["incomplete instruction for genotype2boxplot"];
-    }
-    tk.ds.genotype2boxplot = arg.genotype2boxplot;
-  }
-  if (arg.discardsymbolicallele) {
-    tk.ds.discardsymbolicallele = true;
-  }
-  if (arg.samplebynumericvalue) {
-    if (!arg.samplebynumericvalue.attrkey) return ["attrkey missing from samplebynumericvalue"];
-    if (!tk.ds.cohort) return ["sampleannotation missing when using samplebynumericvalue"];
-    if (!tk.ds.cohort.annotation) return ["sampleannotation.annotation missing when using samplebynumericvalue"];
-    let found = false;
-    for (const k in tk.ds.cohort.annotation) {
-      if (Number.isFinite(tk.ds.cohort.annotation[k][arg.samplebynumericvalue.attrkey])) {
-        found = true;
-        break;
-      }
-    }
-    if (!found) return ["samplebynumericvalue.attrkey not found in any sample annotation"];
-    tk.ds.samplebynumericvalue = arg.samplebynumericvalue;
-  }
-  {
-    const g = arg.genotypebynumericvalue;
-    if (g) {
-      if (!g.refref) return [tk.name + ": refref missing from genotypebynumericvalue"];
-      if (!g.refalt) return [tk.name + ": refalt missing from genotypebynumericvalue"];
-      if (!g.altalt) return [tk.name + ": altalt missing from genotypebynumericvalue"];
-      if (!g.refref.infokey) return [tk.name + ": refref.infokey missing from genotypebynumericvalue"];
-      if (!g.refalt.infokey) return [tk.name + ": refalt.infokey missing from genotypebynumericvalue"];
-      if (!g.altalt.infokey) return [tk.name + ": altalt.infokey missing from genotypebynumericvalue"];
-      if (g.refref.genotypeCountInfokey || g.refalt.genotypeCountInfokey || g.altalt.genotypeCountInfokey) {
-        if (!g.refref.genotypeCountInfokey)
-          return [tk.name + ": genotypeCountInfokey missing from genotypebynumericvalue.refref{}"];
-        if (!g.refalt.genotypeCountInfokey)
-          return [tk.name + ": genotypeCountInfokey missing from genotypebynumericvalue.refalt{}"];
-        if (!g.altalt.genotypeCountInfokey)
-          return [tk.name + ": genotypeCountInfokey missing from genotypebynumericvalue.altalt{}"];
-      }
-      tk.ds.genotypebynumericvalue = g;
-    }
-  }
-  if (arg.pointdown) {
-    tk.aboveprotein = false;
-  }
-  if (arg.dstk_novcferror) {
-    tk.dstk_novcferror = true;
-  }
-  return [null, tk];
-}
-function check_url4variant(lst) {
-  if (!Array.isArray(lst)) return "value is not an array";
-  for (const item of lst) {
-    if (!item.makeurl) {
-      return ".makeurl missing";
-    }
-    if (typeof item.makeurl != "function") {
-      return ".makeurl must be a function";
-    }
-  }
-  return false;
-}
-function check_button4variant(lst) {
-  if (!Array.isArray(lst)) return "value is not an array";
-  for (const item of lst) {
-    if (!item.makebutton) {
-      return ".makebutton missing";
-    }
-    if (typeof item.makebutton != "function") {
-      return ".makebutton must be a function";
-    }
-  }
-  return false;
-}
-
-export {
-  vcf2dstk
-};
-//# sourceMappingURL=chunk-5TUM3XRB.js.map

package/dist/chunk-5UDKSRQK.js

@@ -1,370 +0,0 @@
-import {
-  addBrushes,
-  addNewBrush
-} from "./chunk-UWX7W22M.js";
-import {
-  NumericRangeInput,
-  niceNumLabels,
-  violinRenderer
-} from "./chunk-EAHT56LQ.js";
-import {
-  convertUnits
-} from "./chunk-BEWDIM6H.js";
-import {
-  select_default
-} from "./chunk-NDWTN4U5.js";
-
-// filter/tvs.numeric.js
-var handler = {
-  type: "numeric",
-  term_name_gen,
-  get_pill_label,
-  getSelectRemovePos,
-  fillMenu,
-  setTvsDefaults
-};
-function term_name_gen(d) {
-  const name = d.term.name;
-  return name.length < 26 ? name : '<label title="' + name + '">' + name.substring(0, 24) + "...</label>";
-}
-function get_pill_label(tvs) {
-  if (tvs.ranges.length == 1) {
-    const v = tvs.ranges[0];
-    if ("value" in v) {
-      if (v.label) return { txt: v.label };
-      if (tvs.term.values && tvs.term.values[v.value] && tvs.term.values[v.value].label)
-        return { txt: tvs.term.values[v.value].label };
-      console.error(`key "${v.value}" not found in values{} of ${tvs.term.name}`);
-      return { txt: v.value };
-    }
-    return { txt: format_val_text(v, tvs.term) };
-  }
-  return { txt: tvs.ranges.length + " intervals" };
-}
-function format_val_text(range, term) {
-  const x = '<span style="font-family:Times;font-style:italic;font-size:1em; vertical-align:top">x</span>';
-  if (range.startunbounded && range.stopunbounded) {
-    const inf = (sign = "") => `<span style='vertical-align: middle; font-size:1.1em; line-height: 0.9em'>${sign}\u221E</span>`;
-    const lt = `<span style='vertical-align: top; font-size: 0.9em'>&lt;</span>`;
-    return `<span>${inf("\uFE63")} ${lt} ${x} ${lt} ${inf("\uFE62")}</span>`;
-  }
-  const vc = term.valueConversion;
-  if (range.startunbounded)
-    return `${x} ${range.stopinclusive ? "&le;" : "&lt;"} ${vc ? convertUnits(range.stop, vc.fromUnit, vc.toUnit, vc.scaleFactor) : range.stop}`;
-  if (range.stopunbounded)
-    return `${x} ${range.startinclusive ? "&ge;" : "&gt;"} ${vc ? convertUnits(range.start, vc.fromUnit, vc.toUnit, vc.scaleFactor) : range.start}`;
-  let startName, stopName;
-  if (vc) {
-    startName = convertUnits(range.start, vc.fromUnit, vc.toUnit, vc.scaleFactor);
-    stopName = convertUnits(range.stop, vc.fromUnit, vc.toUnit, vc.scaleFactor);
-  } else {
-    ;
-    [startName, stopName] = niceNumLabels([range.start, range.stop]);
-  }
-  return `${startName} 
-			${range.startinclusive ? "&le;" : "&lt;"}
-			${x}
-			${range.stopinclusive ? "&le;" : "&lt;"}
-			${stopName}`;
-}
-function getSelectRemovePos(j, tvs) {
-  return j - tvs.ranges.slice(0, j).filter((a) => a.start || a.stop).length;
-}
-async function fillMenu(self, div, tvs) {
-  const num_parent_div = div.append("div");
-  self.num_obj = {};
-  self.num_obj.num_div = num_parent_div.append("div").attr("class", "num_div").style("padding", "5px").style("color", "#000");
-  self.num_obj.plot_size = {
-    width: 450,
-    height: 100,
-    xpad: 10,
-    ypad: 20,
-    radius: 8
-  };
-  if (typeof self.opts.vocabApi.getViolinPlotData == "function") {
-    try {
-      const data = await self.opts.vocabApi.getViolinPlotData(
-        {
-          tw: { term: tvs.term, q: { mode: "continuous" } },
-          // must supply this filter and override state filter in function, so the density plot will not be limited to range defined by current numeric tvs but will show whole range
-          filter: self.filter,
-          svgw: self.num_obj.plot_size.width,
-          radius: self.num_obj.plot_size.radius
-        },
-        self.opts.getCategoriesArguments
-      );
-      if (data.error) throw data.error;
-      if (data.max === null && data.min === null) {
-        throw `No data available under current filter conditions.`;
-      }
-      self.num_obj.density_data = data;
-    } catch (err) {
-      throw err;
-    }
-  } else {
-    self.num_obj.density_data = {};
-  }
-  if (self.num_obj.density_data.error) throw self.num_obj.density_data.error;
-  if (!self.num_obj.density_data.charts?.[""]?.plots?.[0]?.density?.bins) {
-    addRangeTableNoDensity(self, tvs);
-    return;
-  }
-  self.vr = new violinRenderer({
-    holder: self.num_obj.num_div,
-    rd: self.num_obj.density_data,
-    width: self.num_obj.plot_size.width,
-    radius: self.num_obj.plot_size.radius,
-    height: self.num_obj.plot_size.height
-  });
-  self.vr.render();
-  self.num_obj.svg = self.vr.svg;
-  self.num_obj.range_table = self.num_obj.num_div.append("table").style("table-layout", "fixed").style("border-collapse", "collapse");
-  const ranges = [];
-  for (const [index, range] of tvs.ranges.entries()) {
-    range.index = index;
-    ranges.push(range);
-  }
-  self.num_obj.brush_g = self.vr.brushG.attr("class", "brush_g");
-  self.num_obj.xscale = self.vr.axisScale;
-  self.num_obj.ranges = ranges;
-  self.num_obj.brushes = [];
-  addBrushes(self);
-  addRangeTable(self);
-  if (!ranges.length) {
-    const callback = () => addRangeTable(self);
-    addNewBrush(self, "center", callback);
-  }
-  self.num_obj.brushes.forEach((brush) => brush.init());
-  await showCheckList_numeric(self, tvs, div);
-}
-function setTvsDefaults(tvs) {
-  if (!tvs.ranges) tvs.ranges = [];
-}
-function addRangeTableNoDensity(self, tvs) {
-  const termrange = tvs.term.range || {};
-  const range = tvs.ranges && tvs.ranges[0] ? tvs.ranges[0] : termrange;
-  range.min = "min" in tvs.term ? tvs.term.min : null;
-  range.max = "max" in tvs.term ? tvs.term.max : null;
-  const num_div = self.num_obj.num_div;
-  num_div.selectAll("*").remove();
-  const brush = {};
-  const table = num_div.append("table").style("padding-left", "5px");
-  const rangeTr = table.append("tr");
-  const rangeLabelTd = rangeTr.append("td");
-  brush.equation_td = rangeTr.append("td");
-  brush.rangeInput = new NumericRangeInput(brush.equation_td, range, () => {
-  }, { width: "125px" });
-  if (self.opts.isMafFilter) {
-    rangeLabelTd.text("MAF Range (0-1)");
-    const depthTr = table.append("tr");
-    depthTr.append("td").text("Minimum Total Depth");
-    brush.depthInput = depthTr.append("td").append("input").attr("type", "number").attr("min", 1).attr("step", 1).style("width", "125px").property("value", tvs.minAllelicDepth);
-    const applyTr = table.append("tr");
-    brush.apply_btn = applyTr.append("td").attr("class", "sja_filter_tag_btn sjpp_apply_btn").style("border-radius", "13px").style("margin-top", "10px").style("font-size", ".8em").style("text-transform", "uppercase").text("apply").on("click", clickApply);
-  } else {
-    rangeLabelTd.text("Range");
-    brush.apply_btn = rangeTr.append("td").attr("class", "sja_filter_tag_btn sjpp_apply_btn").style("border-radius", "13px").style("margin", "5px").style("margin-left", "10px").style("text-align", "center").style("font-size", ".8em").style("text-transform", "uppercase").text("apply").on("click", clickApply);
-  }
-  function clickApply() {
-    const r = brush.rangeInput.getRange();
-    if (!Number.isFinite(r.start) && !Number.isFinite(r.stop)) {
-      window.alert("Invalid range.");
-      return;
-    }
-    const new_tvs = { term: tvs.term, ranges: [r] };
-    if (brush.depthInput) {
-      const minAllelicDepth = Number(brush.depthInput.property("value"));
-      if (!Number.isFinite(minAllelicDepth)) {
-        window.alert("Minimum allelic depth must be a numeric value.");
-        return;
-      }
-      new_tvs.minAllelicDepth = Math.max(minAllelicDepth, 1);
-    }
-    self.dom.tip.hide();
-    self.opts.callback(new_tvs);
-  }
-}
-function addRangeTable(self) {
-  const brushes = self.num_obj.brushes;
-  const range_divs = self.num_obj.range_table.selectAll(".range_div").data(brushes);
-  range_divs.exit().each(function() {
-    select_default(this).style("opacity", 1).transition().duration(100).style("opacity", 0).remove();
-  });
-  range_divs.enter().append("tr").attr("class", "range_div").style("white-space", "nowrap").style("padding", "2px").transition().duration(200).each(function(brush, i) {
-    enterRange(self, this, brush, i);
-  });
-}
-function enterRange(self, tr, brush, i) {
-  if (!brush.range_tr) brush.range_tr = select_default(tr);
-  const range_tr = brush.range_tr;
-  const xscale = self.num_obj.xscale;
-  range_tr.append("td").append("td").style("display", "inline-block").style("margin-left", "10px").style("padding", "3px 10px").style("font-size", ".9em").text("Range " + (i + 1) + ": ");
-  brush.equation_td = range_tr.append("td").style("width", "150px");
-  brush.rangeInput = new NumericRangeInput(brush.equation_td, brush.range, apply);
-  makeRangeButtons(self, brush);
-  if (i == 0) {
-    self.num_obj.range_table.append("tr").attr("class", "note_tr").append("td").attr("colspan", "3").append("div").style("font-size", ".8em").style("margin-left", "20px").style("font-style", "italic").style("color", "#888").html("Option 1: Drag the rectangle to select a range. Overlapping ranges will be merged.");
-  }
-  if (i == 0) {
-    self.num_obj.range_table.append("tr").attr("class", "note_tr").append("td").attr("colspan", "3").append("div").style("font-size", ".8em").style("margin-left", "20px").style("font-style", "italic").style("color", "#888").html(
-      `Option 2: Type in values to select a range.${self.tvs.term.valueConversion ? ` Values are in the unit of ${self.tvs.term.valueConversion.fromUnit}.` : ""}`
-    );
-  }
-  async function apply(new_range) {
-    try {
-      brush.range = new_range;
-      const minvalue = self.num_obj.density_data.min;
-      const maxvalue = self.num_obj.density_data.max;
-      const start = new_range.value != void 0 ? new_range.value : new_range.start != void 0 ? new_range.start : minvalue;
-      const stop = new_range.value != void 0 ? new_range.value : new_range.stop != void 0 ? new_range.stop : maxvalue;
-      brush.elem.call(brush.d3brush).call(brush.d3brush.move, [start, stop].map(xscale));
-    } catch (e) {
-      window.alert(e);
-    }
-  }
-  function makeRangeButtons(self2, brush2) {
-    const buttons_td = brush2.range_tr.append("td");
-    const range = brush2.range;
-    brush2.apply_btn = buttons_td.append("td").attr("class", "sja_filter_tag_btn sjpp_apply_btn").style("border-radius", "13px").style("margin", "5px").style("margin-left", "10px").style("text-align", "center").style("font-size", ".8em").style("text-transform", "uppercase").text("apply").on("click", async () => {
-      self2.dom.tip.hide();
-      const new_range = brush2.rangeInput.parseRange();
-      const new_tvs = JSON.parse(JSON.stringify(self2.tvs));
-      delete new_tvs.groupset_label;
-      if (self2.num_obj.ranges.length > 1) new_tvs.ranges = mergeOverlapRanges(self2, new_range);
-      else new_tvs.ranges[range.index] = new_range;
-      try {
-        validateNumericTvs(new_tvs);
-        self2.opts.callback(new_tvs);
-      } catch (ex) {
-        alert(ex);
-      }
-    });
-    buttons_td.append("td").attr("class", "sja_filter_tag_btn sjpp_delete_btn").style("border-radius", "13px").style("display", self2.num_obj.ranges.length > 1 ? "inline-block" : "none").style("margin", "5px").style("margin-left", "10px").style("text-align", "center").style("font-size", ".8em").style("text-transform", "uppercase").text("Delete").on("click", async () => {
-      const new_tvs = JSON.parse(JSON.stringify(self2.tvs));
-      new_tvs.ranges.splice(range.index, 1);
-      self2.num_obj.ranges.pop();
-      self2.num_obj.brushes.pop();
-      self2.num_obj.num_div.select(".note_tr").remove();
-      addBrushes(self2);
-      addRangeTable(self2);
-      if (new_tvs.ranges.length) self2.opts.callback(new_tvs);
-    });
-  }
-}
-function mergeOverlapRanges(self, new_range) {
-  let ranges = JSON.parse(JSON.stringify(self.tvs.ranges));
-  let merged_flag = false;
-  for (const [i, range] of ranges.entries()) {
-    if (!range.value && new_range.index != i) {
-      if (new_range.start <= range.start && new_range.stop >= range.stop) {
-        range.start = new_range.start;
-        range.stop = new_range.stop;
-        merged_flag = true;
-      } else if (new_range.start <= range.stop && new_range.stop >= range.stop) {
-        range.stop = new_range.stop;
-        merged_flag = true;
-      } else if (new_range.stop >= range.start && new_range.start <= range.start) {
-        range.start = new_range.start;
-        merged_flag = true;
-      } else if (new_range.start >= range.start && new_range.stop <= range.stop) {
-        merged_flag = true;
-      } else if (new_range.startunbounded) {
-        if (new_range.stop > range.stop) {
-          range.stop = new_range.stop;
-        }
-        delete range.start;
-        range.startunbounded = true;
-        merged_flag = true;
-      } else if (new_range.stopunbounded) {
-        if (new_range.start < range.start) {
-          range.start = new_range.start;
-        }
-        delete range.stop;
-        range.stopunbounded = true;
-        merged_flag = true;
-      }
-    }
-  }
-  if (merged_flag) {
-    if (new_range.index <= ranges.length - 1) ranges.splice(new_range.index, 1);
-  } else {
-    ranges = JSON.parse(JSON.stringify(self.tvs.ranges));
-    if (new_range.index) ranges[new_range.index] = new_range;
-    else ranges.push(new_range);
-  }
-  return ranges;
-}
-async function showCheckList_numeric(self, tvs, div) {
-  if (!tvs.term.values) {
-    return;
-  }
-  const values = await self.opts.vocabApi.getNumericUncomputableCategories(tvs.term, self.filter);
-  const unannotated_cats = [];
-  const lst = values?.lst || values;
-  for (const cat of lst) {
-    const key = "key" in cat ? cat.key : cat.value;
-    if (!("key" in cat)) cat.key = key;
-    if (!("value" in cat)) cat.value = key;
-    if (key in tvs.term.values) {
-      cat.label = tvs.term.values[key].label;
-      unannotated_cats.push(cat);
-    }
-  }
-  const sortedVals = unannotated_cats.sort((a, b) => {
-    return b.samplecount - a.samplecount;
-  });
-  const unanno_div = div.append("div").style("padding", "5px").style("color", "#000");
-  const callback = (indexes) => {
-    try {
-      const new_tvs = JSON.parse(JSON.stringify(tvs));
-      delete new_tvs.groupset_label;
-      new_tvs.ranges = [
-        ...new_tvs.ranges.filter((r) => !("value" in r)),
-        ...indexes.map((i) => ({ value: sortedVals[i].value, label: sortedVals[i].label }))
-      ];
-      self.dom.tip.hide();
-      if (new_tvs.ranges.length == 0) throw "select at least one range or category";
-      if (JSON.parse(JSON.stringify(tvs) != new_tvs)) {
-        try {
-          validateNumericTvs(new_tvs);
-        } catch (e) {
-          window.alert(e);
-          return;
-        }
-        self.opts.callback(new_tvs);
-      }
-    } catch (e) {
-      window.alert(e);
-    }
-  };
-  const values_table = self.makeValueTable(unanno_div, tvs, sortedVals, callback).node();
-}
-function validateNumericTvs(tvs) {
-  if (!tvs.term) throw "tvs.term is not defined";
-  if (!tvs.ranges) throw `.values[] missing for a term ${tvs.term.name}`;
-  if (!Array.isArray(tvs.ranges)) throw `.values[] is not an array for a term ${tvs.term.name}`;
-  if (!tvs.ranges.length) throw `no categories selected for ${tvs.term.name}`;
-  for (const range of tvs.ranges) {
-    if (range.value != void 0) {
-      if (!range.label) throw `.label missing for special category for a term ${tvs.term.name}`;
-    } else {
-      if (range.startunbounded) {
-        if (range.stopunbounded) throw `both start & stop are unbounded for a term ${tvs.term.name}`;
-        if (!Number.isFinite(range.stop)) throw `.stop undefined when start is unbounded for a term ${tvs.term.name}`;
-      } else if (range.stopunbounded) {
-        if (!Number.isFinite(range.start)) throw `.start undefined when stop is unbounded for a term ${tvs.term.name}`;
-      } else {
-        if (!Number.isFinite(range.start))
-          throw `.start undefined when start is not unbounded for a term ${tvs.term.name}`;
-        if (!Number.isFinite(range.stop)) throw `.stop undefined when stop is not unbounded for a term ${tvs.term.name}`;
-        if (range.start >= range.stop) throw `.start is not lower than stop for a term ${tvs.term.name}`;
-      }
-    }
-  }
-}
-
-export {
-  handler,
-  format_val_text
-};
-//# sourceMappingURL=chunk-5UDKSRQK.js.map