@sjcrh/proteinpaint-client 2.200.0 → 2.201.0

package/dist/chunk-WXPFMVU6.js

@@ -1,299 +0,0 @@
-import {
-  first_genetrack_tolist,
-  gmmode,
-  sayerror
-} from "./chunk-TKW5TW4Z.js";
-import {
-  dofetch3
-} from "./chunk-JVPWIVDT.js";
-import {
-  codon_stop,
-  nt2aa,
-  proteinDomainColorScale
-} from "./chunk-6PNPHACF.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-
-// common/snp.js
-async function string2snp(genome, str) {
-  const data = await dofetch3("snp", {
-    method: "POST",
-    body: JSON.stringify({ byName: true, genome: genome.name, lst: [str] })
-  });
-  if (data.error) throw data.error;
-  if (!data.results || data.results.length == 0) throw str + ": not a SNP";
-  for (const i of data.results) {
-    const chr = genome.chrlookup[i.chrom.toUpperCase()];
-    if (chr && chr.major) {
-      return {
-        chr: i.chrom,
-        start: i.chromStart,
-        stop: i.chromEnd
-      };
-    }
-  }
-  const r = data.results[0];
-  return {
-    chr: r.chrom,
-    start: r.chromStart,
-    stop: r.chromEnd
-  };
-}
-
-// src/block.init.js
-async function block_init_default(arg) {
-  if (!arg.holder) throw "No holder for block.init";
-  if (!arg.genome) throw "no genome";
-  if (arg.holder instanceof Element) arg.holder = select_default(arg.holder);
-  if (!arg.tklst) arg.tklst = [];
-  if (arg.query) {
-    await step1_findgm(arg);
-    return;
-  }
-  if (arg.model && arg.allmodels) {
-    await step2_getseq(arg);
-    return;
-  }
-}
-async function step1_findgm(arg) {
-  const wait = arg.holder.append("p").style("font-size", "2em").style("color", "#858585").text("Searching for " + arg.query + " ...");
-  const data = await dofetch3("genelookup", {
-    body: { deep: 1, input: arg.query, genome: arg.genome.name }
-  });
-  if (!data) throw "querying genes: server error";
-  if (data.error) throw "error querying genes: " + data.error;
-  if (!data.gmlst || data.gmlst.length == 0) {
-    if (arg.genome.hasSNP) {
-      try {
-        const r = await string2snp(arg.genome, arg.query);
-        wait.remove();
-        const par = {
-          genome: arg.genome,
-          holder: arg.holder,
-          chr: r.chr,
-          start: Math.max(0, r.start - 300),
-          stop: r.start + 300,
-          nobox: true,
-          tklst: arg.tklst,
-          debugmode: arg.debugmode
-        };
-        first_genetrack_tolist(arg.genome, par.tklst);
-        const b = await import("./block-BGSSF6XP.js");
-        const block = new b.Block(par);
-        block.addhlregion(r.chr, r.start, r.stop - 1);
-      } catch (e) {
-        wait.text("Not a gene or SNP: " + arg.query);
-      }
-    } else {
-      wait.text("No match to gene: " + arg.query);
-    }
-    return;
-  }
-  wait.remove();
-  arg.allmodels = data.gmlst;
-  for (const m of arg.allmodels) {
-    if (m.isoform.toUpperCase() == (data.found_isoform ? data.found_isoform.toUpperCase() : arg.query.toUpperCase())) {
-      arg.model = m;
-      await step2_getseq(arg);
-      return;
-    }
-  }
-  const defaultisoforms = [];
-  for (const m of arg.allmodels) {
-    if (!m.isoform) throw "isoform missing from one gene model: " + JSON.stringify(m);
-    const n = m.isoform.toUpperCase();
-    if (arg.genome.isoformcache.has(n)) {
-      let nothas = true;
-      for (const m2 of arg.genome.isoformcache.get(n)) {
-        if (m2.chr == m.chr && m2.start == m.start && m2.stop == m.stop && m2.strand == m.strand) {
-          nothas = false;
-          break;
-        }
-      }
-      if (nothas) {
-        arg.genome.isoformcache.get(n).push(m);
-      }
-    } else {
-      arg.genome.isoformcache.set(n, [m]);
-    }
-    if (m.isoform.toUpperCase() == arg.query.toUpperCase()) {
-      defaultisoforms.push(m);
-      break;
-    }
-    if (m.isdefault) {
-      defaultisoforms.push(m);
-    }
-  }
-  if (defaultisoforms.length == 1) {
-    arg.model = defaultisoforms[0];
-  } else if (defaultisoforms.length > 1) {
-    for (const m of defaultisoforms) {
-      if (m.chr == "chrY") {
-        continue;
-      }
-      const chr = arg.genome.chrlookup[m.chr.toUpperCase()];
-      if (!chr) {
-        continue;
-      }
-      if (!chr.major) {
-        continue;
-      }
-      arg.model = m;
-      break;
-    }
-    if (!arg.model) {
-      arg.model = defaultisoforms[0];
-    }
-  }
-  if (!arg.model) {
-    arg.model = arg.allmodels[0];
-  }
-  await step2_getseq(arg);
-}
-async function step2_getseq(arg) {
-  if (arg.model.genomicseq) {
-    checker();
-    step2_getpdomain(arg);
-    return;
-  }
-  const par = {
-    genome: arg.genome.name,
-    coord: arg.model.chr + ":" + (arg.model.start + 1) + "-" + arg.model.stop
-  };
-  const data = await dofetch3("ntseq", { method: "POST", body: JSON.stringify(par) });
-  if (!data) throw "getting sequence: server error";
-  if (data.error) throw "getting sequence: " + data.error;
-  if (!data.seq) throw "no nt seq???";
-  arg.model.genomicseq = data.seq.toUpperCase();
-  arg.model.aaseq = nt2aa(arg.model);
-  checker();
-  await step2_getpdomain(arg);
-  function checker() {
-    if (arg.model.aaseq) {
-      const stop = arg.model.aaseq.indexOf(codon_stop);
-      const cdslen = arg.model.cdslen - (arg.model.startCodonFrame ? 3 - arg.model.startCodonFrame : 0);
-      if (stop != -1 && stop < cdslen / 3 - 1) {
-        sayerror(arg.holder, "Translating " + arg.model.isoform + " ends at " + stop + " AA, expecting " + cdslen / 3);
-      }
-    }
-  }
-}
-async function step2_getpdomain(arg) {
-  const isoform2gm = /* @__PURE__ */ new Map();
-  for (const m of arg.allmodels) {
-    if (!m.pdomains) {
-      m.pdomains = [];
-      m.domain_hidden = {};
-      if (!isoform2gm.has(m.isoform)) isoform2gm.set(m.isoform, []);
-      isoform2gm.get(m.isoform).push(m);
-    }
-  }
-  if (isoform2gm.size == 0) {
-    await step3(arg);
-    return;
-  }
-  const data = await dofetch3("pdomain", {
-    method: "POST",
-    body: JSON.stringify({ genome: arg.genome.name, isoforms: [...isoform2gm.keys()] })
-  });
-  if (data.error) throw "error getting protein domain: " + data.error;
-  if (!Array.isArray(data.lst)) throw ".lst[] not array";
-  for (const a of data.lst) {
-    for (const m of isoform2gm.get(a.name)) {
-      m.pdomains = a.pdomains;
-      if (arg.hidePdomain) {
-        for (const i of a.pdomains) {
-          m.domain_hidden[i.name + i.description] = 1;
-        }
-      }
-    }
-  }
-  if (arg.geneDomains) {
-    if (typeof arg.geneDomains != "object") throw "geneDomains not object";
-    for (const isoform in arg.geneDomains) {
-      const lst = isoform2gm.get(isoform);
-      if (!lst) throw `unknown isoform ${isoform} from geneDomains{}`;
-      for (const g of lst) {
-        if (!g.pdomains) g.pdomains = [];
-        if (!Array.isArray(arg.geneDomains[isoform])) throw `geneDomains[${isoform}] not array`;
-        for (const b of arg.geneDomains[isoform]) {
-          if (typeof b != "object") throw "element from geneDomains[] not object";
-          if (!Number.isInteger(b.start)) throw "start not integer from geneDomains[]";
-          if (!Number.isInteger(b.stop)) throw "stop not integer from geneDomains[]";
-          if (b.start > b.stop) throw "start>stop from geneDomains[]";
-          if (!b.name) b.name = "Custom domain";
-          if (!g.pdomains.find((a) => a.start == b.start && a.stop == b.stop && a.name == b.name)) g.pdomains.push(b);
-        }
-      }
-    }
-  }
-  const s = proteinDomainColorScale();
-  for (const lst of isoform2gm.values()) {
-    for (const g of lst) {
-      for (const d of g.pdomains || []) {
-        if (!d.color) d.color = s(d.name + d.description);
-      }
-    }
-  }
-  await step3(arg);
-}
-async function step3(arg) {
-  let mode = arg.gmmode;
-  if (!mode) {
-    if (arg.model.cdslen) {
-      mode = gmmode.protein;
-    } else {
-      mode = gmmode.exononly;
-    }
-  }
-  if (arg.dataset) {
-    if (!Array.isArray(arg.dataset)) throw "dataset is not array";
-    for (const dsname of arg.dataset) {
-      if (arg.genome.datasets[dsname] && !arg.genome.datasets[dsname].legacyDsIsUninitiated) continue;
-      const d = await dofetch3(`getDataset?genome=${arg.genome.name}&dsname=${dsname}`);
-      if (d.error) throw `invalid name from dataset[]: ${d.error}`;
-      if (!d.ds) throw ".ds missing";
-      const ds = arg.genome.datasets[d.ds.label];
-      Object.assign(ds, d.ds);
-      const _ = await import("./legacyDataset-4BXYHQTS.js");
-      _.validate_oldds(ds);
-      delete ds.legacyDsIsUninitiated;
-    }
-  }
-  const b = await import("./block-BGSSF6XP.js");
-  arg.__blockInstance = new b.Block({
-    genome: arg.genome,
-    holder: arg.holder,
-    nobox: true,
-    usegm: arg.model,
-    gmstackheight: 37,
-    allgm: arg.allmodels,
-    datasetlst: arg.dataset,
-    legacyDsFilter: arg.legacyDsFilter,
-    mset: arg.mset,
-    hlaachange: arg.hlaachange,
-    hlvariants: arg.hlvariants,
-    hlregions: arg.hlregions,
-    aarange: arg.aarange,
-    gmmode: mode,
-    hidedatasetexpression: arg.hidedatasetexpression,
-    hidegenecontrol: arg.hidegenecontrol,
-    hidegenelegend: arg.hidegenelegend,
-    variantPageCall_snv: arg.variantPageCall_snv,
-    datasetqueries: arg.datasetqueries,
-    samplecart: arg.samplecart,
-    debugmode: arg.debugmode,
-    tklst: arg.tklst,
-    mclassOverride: arg.mclassOverride,
-    hide_dsHandles: arg.hide_dsHandles,
-    onloadalltk_always: arg.onloadalltk_always,
-    onAddRemoveTk: arg.onAddRemoveTk
-  });
-}
-
-export {
-  string2snp,
-  block_init_default
-};
-//# sourceMappingURL=chunk-WXPFMVU6.js.map

package/dist/chunk-XNWUI5VL.js

@@ -1,37 +0,0 @@
-import {
-  addGeneSearchbox,
-  getGEunit
-} from "./chunk-TKW5TW4Z.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import {
-  TermTypes
-} from "./chunk-6PNPHACF.js";
-
-// termdb/handlers/geneExpression.ts
-var SearchHandler = class {
-  init(opts) {
-    this.callback = opts.callback;
-    this.app = opts.app;
-    const holder = opts.holder.append("div").style("padding", "10px 0px");
-    const geneSearch = addGeneSearchbox({
-      tip: new Menu({ padding: "0px" }),
-      genome: opts.genomeObj,
-      row: holder,
-      searchOnly: "gene",
-      callback: () => this.selectGene(geneSearch.geneSymbol)
-    });
-  }
-  async selectGene(gene) {
-    const unit = getGEunit(this.app.vocabApi);
-    const name = `${gene} ${unit}`;
-    if (!gene) throw new Error("No gene selected");
-    this.callback({ gene, name, type: TermTypes.GENE_EXPRESSION });
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-XNWUI5VL.js.map

package/dist/chunk-YBLTSYQV.js

@@ -1,216 +0,0 @@
-import {
-  make_radios
-} from "./chunk-TKW5TW4Z.js";
-import {
-  initBinConfig
-} from "./chunk-JVPWIVDT.js";
-import {
-  format
-} from "./chunk-UJELJXJG.js";
-
-// termsetting/handlers/NumRegularBinEditor.ts
-var NumRegularBinEditor = class {
-  constructor(editHandler) {
-    this.dom = {};
-    this.editHandler = editHandler;
-    this.opts = editHandler.opts;
-    this.tw = editHandler.tw;
-    this.termsetting = editHandler.termsetting;
-  }
-  render(div) {
-    this.tw = this.editHandler.tw;
-    this.q = this.getDefaultQ();
-    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
-    if (this.dom.binsTable) {
-      if (this.editHandler.dom.binsDiv?.node().contains(this.dom.binsTable.node())) return;
-      else {
-        this.dom.binsTable.remove();
-        delete this.dom.binsTable;
-      }
-    }
-    const binsTable = div.append("table");
-    this.dom.binsTable = binsTable;
-    this.renderBinSizeInput(binsTable.append("tr"));
-    this.renderFirstBinInput(binsTable.append("tr"));
-    this.renderLastBinInputs(binsTable.append("tr"));
-  }
-  getDefaultQ() {
-    if (this.tw.q.type == "regular-bin") return JSON.parse(JSON.stringify(this.tw.q));
-    const t = this.tw.term;
-    const defaultQ = this.termsetting.opts.use_bins_less && t.bins?.less || t.bins?.default;
-    if (defaultQ) return JSON.parse(JSON.stringify(defaultQ));
-    const binConfig = initBinConfig(this.editHandler.handler.density_data);
-    return typeof binConfig == "string" ? JSON.parse(binConfig) : binConfig;
-  }
-  renderBinSizeInput(tr) {
-    const handler = this.editHandler.handler;
-    tr.append("td").style("margin", "5px").style("opacity", 0.5).text("Bin Size");
-    const { min, max } = handler.density_data;
-    const q = this.q;
-    const origBinSize = q.bin_size;
-    this.dom.bin_size_input = tr.append("td").append("input").attr("type", "number").attr("value", "rounding" in q ? format(q.rounding || ".0f")(q.bin_size) : q.bin_size).attr("data-testid", "sjpp-num-reg-bin-editor-size").style("margin-left", "15px").style("width", "100px").style("color", () => q.bin_size > Math.abs(max - min) ? "red" : "").on("change", (event) => {
-      const newValue = Number(event.target.value);
-      if (newValue <= 0) {
-        window.alert("Please enter non-negative bin size.");
-        event.target.value = origBinSize;
-        return;
-      }
-      if ((max - min) / newValue > 100) {
-        window.alert("Bin size too small. Try setting a bigger value.");
-        event.target.value = origBinSize;
-        return;
-      }
-      q.bin_size = newValue;
-      this.dom.bin_size_input.style("color", q.bin_size > max - min ? "red" : newValue != origBinSize ? "green" : "");
-      handler.density.setBinLines(this.getBoundaryOpts());
-    });
-  }
-  renderFirstBinInput(tr) {
-    const handler = this.editHandler.handler;
-    const q = this.q;
-    if (!q.first_bin) throw "missing q.first_bin";
-    tr.append("td").style("margin", "5px").style("opacity", 0.5).text("First Bin Stop");
-    const { min, max } = handler.density_data;
-    const origValue = q.first_bin.stop;
-    this.dom.first_stop_input = tr.append("td").append("input").attr("type", "number").property("value", origValue).style("width", "100px").style("margin-left", "15px").on("change", (event) => {
-      const newValue = Number(event.target.value);
-      if (newValue < min || newValue > max) {
-        window.alert("First bin stop value out of bound.");
-        event.target.value = origValue;
-        return;
-      }
-      this.q.first_bin.stop = newValue;
-      handler.density.setBinLines(this.getBoundaryOpts());
-    });
-    tr.append("td").append("div").style("font-size", ".6em").style("opacity", 0.5).style("display", handler.density.no_density_data ? "none" : "block").text("Indicated by left-most red line. Drag to change.");
-  }
-  renderLastBinInputs(tr) {
-    const handler = this.editHandler.handler;
-    const q = this.q;
-    const isAuto = !q.last_bin || !Number.isFinite(q.last_bin.start);
-    tr.append("td").style("padding-top", "4px").style("opacity", 0.5).style("vertical-align", "top").text("Last Bin Start");
-    const td1 = tr.append("td").style("padding-left", "15px").style("vertical-align", "top");
-    const radio_div = td1.append("div");
-    const radios = make_radios({
-      holder: radio_div,
-      options: [
-        { label: "Automatic", value: "auto", checked: isAuto },
-        { label: "Fixed", value: "fixed", checked: !isAuto }
-      ],
-      callback: (v) => {
-        if (v == "auto") {
-          delete q.last_bin;
-          edit_div.style("display", "none");
-          handler.density.setBinLines(this.getBoundaryOpts());
-          return;
-        }
-        edit_div.style("display", "inline-block");
-        if (this.dom.last_start_input.property("value") == "") {
-          this.dom.last_start_input.property("value", this.tw.q.last_bin?.start || handler.density_data.max);
-        }
-        this.setLastBinStart();
-      }
-    });
-    this.dom.fixed_radio = radios.inputs.filter((_, i) => i === 1);
-    const edit_div = tr.append("td").append("div").style("display", isAuto ? "none" : "inline-block");
-    this.dom.last_start_input = edit_div.append("input").attr("type", "number").property("value", q.last_bin?.start || "").style("width", "100px").on("change", () => this.setLastBinStart());
-    edit_div.append("div").style("font-size", ".6em").style("opacity", 0.5).style("display", handler.density.no_density_data ? "none" : "block").text("Indicated by right-most red line. Drag to change.");
-  }
-  setLastBinStart() {
-    const q = this.q;
-    const { max } = this.editHandler.handler.density_data;
-    const strInput = this.dom.last_start_input.property("value");
-    if (strInput === "") return;
-    const inputValue = Number(strInput);
-    if (q.first_bin && inputValue <= q.first_bin.stop) {
-      window.alert("Last bin start cannot be smaller than first bin stop.");
-      this.dom.last_start_input.property("value", max);
-      return;
-    }
-    if (inputValue > max) {
-      window.alert("Last bin start value out of bound.");
-      this.dom.last_start_input.property("value", max);
-      return;
-    }
-    if (q.last_bin) q.last_bin.start = inputValue;
-    else
-      q.last_bin = {
-        start: inputValue,
-        stopunbounded: true,
-        stopinclusive: false
-      };
-    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
-  }
-  getBoundaryOpts() {
-    const { min, max } = this.editHandler.handler.density_data;
-    const binLinesStop = this.q.last_bin?.start ?? max + Math.abs(this.q.first_bin.stop) - Math.min(min, 0);
-    const boundaryValues = [];
-    for (let i = this.q.first_bin.stop; i <= binLinesStop; i = i + this.q.bin_size) {
-      if (this.q.last_bin?.start === i) break;
-      if (i > binLinesStop) boundaryValues[boundaryValues.length - 1].isLastVisibleLine = true;
-      const isDraggable = i === this.q.first_bin.stop || i === this.q.bin_size - 1;
-      boundaryValues.push({ x: i, isDraggable, movesWithLineIndex: !isDraggable ? 0 : -1 });
-    }
-    if (this.q.last_bin) {
-      boundaryValues.push({
-        x: this.q.last_bin.start,
-        isDraggable: true,
-        isLastVisibleLine: true,
-        movesWithLineIndex: -1
-      });
-    }
-    return {
-      values: boundaryValues,
-      callback: (d, value) => {
-        if (d.index === 0) {
-          this.dom.first_stop_input.property("value", value);
-          this.q.first_bin.stop = value;
-        } else {
-          this.editHandler.handler.dom.last_start_input.property("value", value);
-          if (this.q.last_bin) this.q.last_bin.start = value;
-        }
-      }
-    };
-  }
-  getEditedQ(destroyDom = true) {
-    const bin_size = this.dom.bin_size_input.property("value");
-    const config = {
-      mode: "discrete",
-      type: "regular-bin",
-      startinclusive: this.editHandler.boundaryInclusion == "startinclusive",
-      stopinclusive: this.editHandler.boundaryInclusion == "stopinclusive",
-      bin_size: Number(bin_size),
-      first_bin: {
-        startunbounded: true,
-        stop: Number(this.dom.first_stop_input.property("value"))
-      },
-      rounding: bin_size.includes(".") && !bin_size.endsWith(".") ? `.${bin_size.split(".")[1].length}f` : ".0f"
-    };
-    if (this.dom.fixed_radio.property("checked")) {
-      config.last_bin = {
-        start: Number(this.dom.last_start_input.property("value")),
-        stopunbounded: true
-      };
-    }
-    if (destroyDom) {
-      for (const name of Object.keys(this.dom)) {
-        this.dom[name].remove();
-        delete this.dom[name];
-      }
-    }
-    return config;
-  }
-  undoEdits() {
-    this.q = this.getDefaultQ();
-    this.dom.binsTable.selectAll("*").remove();
-    this.renderBinSizeInput(this.dom.binsTable.append("tr"));
-    this.renderFirstBinInput(this.dom.binsTable.append("tr"));
-    this.renderLastBinInputs(this.dom.binsTable.append("tr"));
-    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
-  }
-};
-
-export {
-  NumRegularBinEditor
-};
-//# sourceMappingURL=chunk-YBLTSYQV.js.map

package/dist/chunk-YBLTSYQV.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../termsetting/handlers/NumRegularBinEditor.ts"],
-  "sourcesContent": ["import { format } from 'd3-format'\n//import { setDensityPlot } from './density'\nimport { make_radios } from '#dom'\nimport initBinConfig from '#shared/termdb.initbinconfig.js'\nimport type { NumRegularBin } from '#tw'\nimport type { NumDiscreteEditor } from './NumDiscreteEditor.ts'\nimport type { BoundaryOpts, BoundaryValue, DraggedLineData } from './NumericDensity.ts'\nimport type { TermSetting } from '../TermSetting.ts'\nimport type { RegularNumericBinConfig } from '#types'\n\n// This is a bin editor for NumDiscreteEditor\n// NumericHandler (handler) -> NumDiscreteEditor (editor) -> NumRegularBinEditor (bin editor)\nexport class NumRegularBinEditor {\n\ttw: NumRegularBin\n\tq!: RegularNumericBinConfig\n\teditHandler: NumDiscreteEditor\n\ttermsetting: TermSetting\n\topts: any\n\tdom: {\n\t\t[elemName: string]: any\n\t} = {}\n\n\tconstructor(editHandler) {\n\t\tthis.editHandler = editHandler\n\t\tthis.opts = editHandler.opts\n\t\tthis.tw = editHandler.tw\n\t\tthis.termsetting = editHandler.termsetting\n\t}\n\n\trender(div) {\n\t\tthis.tw = this.editHandler.tw as NumRegularBin\n\t\tthis.q = this.getDefaultQ()\n\t\tthis.editHandler.handler.density.setBinLines(this.getBoundaryOpts())\n\t\tif (this.dom.binsTable) {\n\t\t\tif (this.editHandler.dom.binsDiv?.node().contains(this.dom.binsTable.node())) return\n\t\t\telse {\n\t\t\t\tthis.dom.binsTable.remove()\n\t\t\t\tdelete this.dom.binsTable\n\t\t\t}\n\t\t}\n\t\tconst binsTable = div.append('table')\n\t\tthis.dom.binsTable = binsTable\n\t\tthis.renderBinSizeInput(binsTable.append('tr'))\n\t\tthis.renderFirstBinInput(binsTable.append('tr'))\n\t\tthis.renderLastBinInputs(binsTable.append('tr'))\n\t}\n\n\tgetDefaultQ(): RegularNumericBinConfig {\n\t\tif (this.tw.q.type == 'regular-bin') return JSON.parse(JSON.stringify(this.tw.q))\n\t\tconst t = this.tw.term\n\t\tconst defaultQ = (this.termsetting.opts.use_bins_less && t.bins?.less) || t.bins?.default\n\t\tif (defaultQ) return JSON.parse(JSON.stringify(defaultQ))\n\t\tconst binConfig = initBinConfig(this.editHandler.handler.density_data)\n\t\treturn typeof binConfig == 'string' ? JSON.parse(binConfig) : binConfig\n\t}\n\n\trenderBinSizeInput(tr: any) {\n\t\tconst handler = this.editHandler.handler\n\t\ttr.append('td').style('margin', '5px').style('opacity', 0.5).text('Bin Size')\n\n\t\tconst { min, max } = handler.density_data\n\t\tconst q = this.q\n\t\tconst origBinSize = q.bin_size\n\n\t\tthis.dom.bin_size_input = tr\n\t\t\t.append('td')\n\t\t\t.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.attr('value', 'rounding' in q ? format(q.rounding || '.0f')(q.bin_size) : q.bin_size)\n\t\t\t.attr('data-testid', 'sjpp-num-reg-bin-editor-size')\n\t\t\t.style('margin-left', '15px')\n\t\t\t.style('width', '100px')\n\t\t\t.style('color', () => (q.bin_size > Math.abs(max - min) ? 'red' : ''))\n\t\t\t.on('change', event => {\n\t\t\t\tconst newValue = Number(event.target.value)\n\t\t\t\t// must validate input value\n\t\t\t\tif (newValue <= 0) {\n\t\t\t\t\twindow.alert('Please enter non-negative bin size.')\n\t\t\t\t\t// must reset value in <input>, otherwise the wrong value will be recorded in self.q upon clicking Submit\n\t\t\t\t\tevent.target.value = origBinSize\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tif ((max - min) / newValue > 100) {\n\t\t\t\t\t// avoid rendering too many svg lines and lock up browser\n\t\t\t\t\twindow.alert('Bin size too small. Try setting a bigger value.')\n\t\t\t\t\tevent.target.value = origBinSize\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tq.bin_size = newValue\n\t\t\t\tthis.dom.bin_size_input.style('color', q.bin_size > max - min ? 'red' : newValue != origBinSize ? 'green' : '')\n\t\t\t\thandler.density.setBinLines(this.getBoundaryOpts())\n\t\t\t})\n\t}\n\n\trenderFirstBinInput(tr: any) {\n\t\tconst handler = this.editHandler.handler\n\t\tconst q = this.q\n\t\tif (!q.first_bin) throw 'missing q.first_bin'\n\n\t\ttr.append('td').style('margin', '5px').style('opacity', 0.5).text('First Bin Stop')\n\n\t\tconst { min, max } = handler.density_data\n\t\tconst origValue = q.first_bin.stop\n\n\t\tthis.dom.first_stop_input = tr\n\t\t\t.append('td')\n\t\t\t.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.property('value', origValue)\n\t\t\t.style('width', '100px')\n\t\t\t.style('margin-left', '15px')\n\t\t\t.on('change', event => {\n\t\t\t\tconst newValue = Number(event.target.value)\n\t\t\t\tif (newValue < min || newValue > max) {\n\t\t\t\t\twindow.alert('First bin stop value out of bound.')\n\t\t\t\t\tevent.target.value = origValue\n\t\t\t\t\treturn\n\t\t\t\t}\n\n\t\t\t\t// first_bin should have already been set; adding the check just to skip the tsc error...\n\t\t\t\tthis.q.first_bin.stop = newValue\n\t\t\t\thandler.density.setBinLines(this.getBoundaryOpts())\n\t\t\t})\n\n\t\ttr.append('td')\n\t\t\t.append('div')\n\t\t\t.style('font-size', '.6em')\n\t\t\t.style('opacity', 0.5)\n\t\t\t.style('display', handler.density.no_density_data ? 'none' : 'block')\n\t\t\t.text('Indicated by left-most red line. Drag to change.')\n\t}\n\n\trenderLastBinInputs(tr) {\n\t\tconst handler = this.editHandler.handler\n\t\tconst q = this.q\n\t\t// tell if last bin is automatic (not fixed)\n\t\tconst isAuto = !q.last_bin || !Number.isFinite(q.last_bin.start)\n\n\t\ttr.append('td')\n\t\t\t.style('padding-top', '4px')\n\t\t\t.style('opacity', 0.5)\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.text('Last Bin Start')\n\n\t\tconst td1 = tr.append('td').style('padding-left', '15px').style('vertical-align', 'top')\n\t\tconst radio_div = td1.append('div')\n\n\t\tconst radios = make_radios({\n\t\t\tholder: radio_div,\n\t\t\toptions: [\n\t\t\t\t{ label: 'Automatic', value: 'auto', checked: isAuto },\n\t\t\t\t{ label: 'Fixed', value: 'fixed', checked: !isAuto }\n\t\t\t],\n\t\t\tcallback: v => {\n\t\t\t\tif (v == 'auto') {\n\t\t\t\t\tdelete q.last_bin\n\t\t\t\t\t// if just deleting last_bin.start and keeps q.last_bin{}, density plot may set last_bin.bin='last' and will break bin validation\n\t\t\t\t\tedit_div.style('display', 'none')\n\t\t\t\t\thandler.density.setBinLines(this.getBoundaryOpts())\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\t// v is \"fixed\", to assign a number to self.q.last_bin.start\n\t\t\t\tedit_div.style('display', 'inline-block')\n\t\t\t\tif (this.dom.last_start_input.property('value') == '') {\n\t\t\t\t\t// blank input, fill max\n\t\t\t\t\tthis.dom.last_start_input.property('value', this.tw.q.last_bin?.start || handler.density_data.max)\n\t\t\t\t}\n\t\t\t\tthis.setLastBinStart()\n\t\t\t}\n\t\t})\n\n\t\tthis.dom.fixed_radio = radios.inputs.filter((_, i) => i === 1)\n\n\t\tconst edit_div = tr\n\t\t\t.append('td')\n\t\t\t.append('div')\n\t\t\t.style('display', isAuto ? 'none' : 'inline-block')\n\n\t\tthis.dom.last_start_input = edit_div\n\t\t\t.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.property('value', q.last_bin?.start || '')\n\t\t\t.style('width', '100px')\n\t\t\t.on('change', () => this.setLastBinStart())\n\n\t\tedit_div\n\t\t\t.append('div')\n\t\t\t.style('font-size', '.6em')\n\t\t\t.style('opacity', 0.5)\n\t\t\t.style('display', handler.density.no_density_data ? 'none' : 'block')\n\t\t\t.text('Indicated by right-most red line. Drag to change.')\n\t}\n\n\tsetLastBinStart() {\n\t\tconst q = this.q\n\t\tconst { max } = this.editHandler.handler.density_data\n\t\t// only get value from <input>\n\t\tconst strInput = this.dom.last_start_input.property('value')\n\t\tif (strInput === '') return\n\t\tconst inputValue = Number(strInput)\n\n\t\t// TODO first_bin should be required\n\t\tif (q.first_bin && inputValue <= q.first_bin.stop) {\n\t\t\twindow.alert('Last bin start cannot be smaller than first bin stop.')\n\t\t\tthis.dom.last_start_input.property('value', max)\n\t\t\treturn\n\t\t}\n\t\tif (inputValue > max) {\n\t\t\twindow.alert('Last bin start value out of bound.')\n\t\t\tthis.dom.last_start_input.property('value', max)\n\t\t\treturn\n\t\t}\n\t\tif (q.last_bin) q.last_bin.start = inputValue\n\t\telse\n\t\t\tq.last_bin = {\n\t\t\t\tstart: inputValue,\n\t\t\t\tstopunbounded: true,\n\t\t\t\tstopinclusive: false\n\t\t\t}\n\n\t\tthis.editHandler.handler.density.setBinLines(this.getBoundaryOpts())\n\t}\n\n\tgetBoundaryOpts(): BoundaryOpts {\n\t\tconst { min, max } = this.editHandler.handler.density_data\n\t\tconst binLinesStop = this.q.last_bin?.start ?? max + Math.abs(this.q.first_bin.stop) - Math.min(min, 0)\n\t\tconst boundaryValues: BoundaryValue[] = []\n\t\tfor (let i = this.q.first_bin.stop; i <= binLinesStop; i = i + this.q.bin_size) {\n\t\t\tif (this.q.last_bin?.start === i) break\n\t\t\tif (i > binLinesStop) boundaryValues[boundaryValues.length - 1].isLastVisibleLine = true\n\t\t\tconst isDraggable = i === this.q.first_bin.stop || i === this.q.bin_size - 1\n\t\t\t// non-draggable lines should move with the first bin boundary line\n\t\t\tboundaryValues.push({ x: i, isDraggable, movesWithLineIndex: !isDraggable ? 0 : -1 })\n\t\t}\n\t\tif (this.q.last_bin) {\n\t\t\tboundaryValues.push({\n\t\t\t\tx: this.q.last_bin.start,\n\t\t\t\tisDraggable: true,\n\t\t\t\tisLastVisibleLine: true,\n\t\t\t\tmovesWithLineIndex: -1\n\t\t\t})\n\t\t}\n\n\t\treturn {\n\t\t\tvalues: boundaryValues,\n\t\t\tcallback: (d: DraggedLineData, value) => {\n\t\t\t\t//d.scaledX = Math.round(xscale(value))\n\t\t\t\tif (d.index === 0) {\n\t\t\t\t\tthis.dom.first_stop_input.property('value', value)\n\t\t\t\t\tthis.q.first_bin.stop = value as number\n\t\t\t\t} else {\n\t\t\t\t\tthis.editHandler.handler.dom.last_start_input.property('value', value)\n\t\t\t\t\t//if (!this.q.last_bin) this.q.last_bin = {}\n\t\t\t\t\tif (this.q.last_bin) this.q.last_bin.start = value\n\t\t\t\t\t//middleLines.style('display', (c: any) => (d.draggedX && c.scaledX >= d.draggedX ? 'none' : ''))\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\tgetEditedQ(destroyDom = true): RegularNumericBinConfig {\n\t\tconst bin_size = this.dom.bin_size_input.property('value')\n\t\tconst config: RegularNumericBinConfig = {\n\t\t\tmode: 'discrete',\n\t\t\ttype: 'regular-bin',\n\t\t\tstartinclusive: this.editHandler.boundaryInclusion == 'startinclusive',\n\t\t\tstopinclusive: this.editHandler.boundaryInclusion == 'stopinclusive',\n\t\t\tbin_size: Number(bin_size),\n\t\t\tfirst_bin: {\n\t\t\t\tstartunbounded: true,\n\t\t\t\tstop: Number(this.dom.first_stop_input.property('value'))\n\t\t\t},\n\t\t\trounding: bin_size.includes('.') && !bin_size.endsWith('.') ? `.${bin_size.split('.')[1].length}f` : '.0f'\n\t\t}\n\n\t\tif (this.dom.fixed_radio.property('checked')) {\n\t\t\tconfig.last_bin = {\n\t\t\t\tstart: Number(this.dom.last_start_input.property('value')),\n\t\t\t\tstopunbounded: true\n\t\t\t}\n\t\t}\n\n\t\tif (destroyDom) {\n\t\t\tfor (const name of Object.keys(this.dom)) {\n\t\t\t\tthis.dom[name].remove()\n\t\t\t\tdelete this.dom[name]\n\t\t\t}\n\t\t}\n\n\t\treturn config\n\t}\n\n\tundoEdits() {\n\t\tthis.q = this.getDefaultQ()\n\t\tthis.dom.binsTable.selectAll('*').remove()\n\t\tthis.renderBinSizeInput(this.dom.binsTable.append('tr'))\n\t\tthis.renderFirstBinInput(this.dom.binsTable.append('tr'))\n\t\tthis.renderLastBinInputs(this.dom.binsTable.append('tr'))\n\t\tthis.editHandler.handler.density.setBinLines(this.getBoundaryOpts())\n\t}\n}\n"],
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