@sjcrh/proteinpaint-client 2.226.0 → 2.227.1

package/dist/chunk-FA6M7PSZ.js

@@ -0,0 +1,134 @@
+import {
+  addGeneSearchbox,
+  isoformSelect,
+  pickCollectionFraction,
+  sayerror
+} from "./chunk-CXCAQOFB.js";
+import {
+  Menu
+} from "./chunk-CNFTQSNE.js";
+import {
+  dofetch3
+} from "./chunk-VVWZ4BOI.js";
+import {
+  ISOFORM_EXPRESSION,
+  getColors
+} from "./chunk-2N345NXD.js";
+
+// termdb/handlers/isoformExpression.ts
+var SearchHandler = class {
+  constructor() {
+    this.currentGene = null;
+  }
+  init(opts) {
+    this.callback = opts.callback;
+    this.app = opts.app;
+    this.termCollectionSelectionMode = opts.termCollectionSelectionMode;
+    const holder = opts.holder.append("div").style("padding", "10px 0px");
+    this.dom = {
+      errDiv: holder.append("div").style("margin", "5px 0px").style("display", "none")
+    };
+    const geneSearch = addGeneSearchbox({
+      tip: new Menu({ padding: "0px" }),
+      genome: opts.genomeObj,
+      row: holder,
+      searchOnly: "gene",
+      callback: async () => {
+        try {
+          this.dom.errDiv.style("display", "none");
+          if (!geneSearch.geneSymbol) throw new Error("No gene selected");
+          if (geneSearch.geneSymbol === this.currentGene) return;
+          this.currentGene = geneSearch.geneSymbol;
+          if (this.dom.isoformDiv) this.dom.isoformDiv.remove();
+          this.dom.isoformDiv = holder.append("div");
+          await this.showIsoforms(geneSearch.geneSymbol, opts.genomeObj);
+        } catch (e) {
+          this.dom.errDiv.style("display", "block");
+          sayerror(this.dom.errDiv, "Error: " + (e instanceof Error ? e.message : String(e)));
+        }
+      }
+    });
+  }
+  async showIsoforms(gene, genomeObj) {
+    if (!gene) throw new Error("No gene selected");
+    const data = await dofetch3("genelookup", { body: { genome: genomeObj.name, input: gene, deep: 1 } });
+    if (!data.gmlst?.length) throw new Error(`No isoforms found for ${gene}`);
+    const enstCandidates = data.gmlst.filter((gm) => gm.isoform?.startsWith("ENST"));
+    if (enstCandidates.length === 0) throw new Error(`No Ensembl transcript isoforms found for ${gene}`);
+    const { available } = await dofetch3("termdb/isoformAvailability", {
+      body: {
+        genome: genomeObj.name,
+        dslabel: this.app.vocabApi.vocab.dslabel,
+        isoforms: enstCandidates.map((gm) => gm.isoform)
+      }
+    });
+    const availableSet = new Set(available || []);
+    const enstModels = enstCandidates.filter((gm) => availableSet.has(gm.isoform));
+    if (enstModels.length === 0) throw new Error(`No isoforms with data found for ${gene}`);
+    if (gene !== this.currentGene) return;
+    const div = this.dom.isoformDiv;
+    div.append("div").style("margin-bottom", "8px").style("opacity", 0.65).text(`${gene} \u2014 select isoform(s):`);
+    isoformSelect({
+      holder: div,
+      allgm: enstModels,
+      multiSelect: true,
+      // a single checked isoform yields an individual term, 2+ yield a collection
+      getSubmitLabel: (selectedCount) => selectedCount === 1 ? "Select One Isoform" : `Create Collection (${selectedCount})`,
+      onMultiSelect: (selected) => {
+        if (selected.length === 1) {
+          this.selectIsoform(selected[0].isoform, gene);
+        } else {
+          this.selectCollection(selected, gene);
+        }
+      }
+    });
+  }
+  getUnit() {
+    return this.app.vocabApi.termdbConfig.queries.isoformExpression?.unit || "TPM";
+  }
+  selectIsoform(isoform, gene) {
+    const name = `${isoform} ${this.getUnit()}`;
+    this.callback({ isoform, gene, name, type: ISOFORM_EXPRESSION });
+  }
+  selectCollection(gms, gene) {
+    const unit = this.getUnit();
+    const termlst = gms.map((gm) => ({
+      id: gm.isoform,
+      name: gm.isoform,
+      type: ISOFORM_EXPRESSION,
+      isoform: gm.isoform
+    }));
+    const colorScale = getColors(termlst.length);
+    const term = {
+      type: "termCollection",
+      isCustom: true,
+      memberType: "numeric",
+      name: `${gene} Isoforms (${unit})`,
+      termlst,
+      propsByTermId: Object.fromEntries(termlst.map((term2) => [term2.id, { color: colorScale(term2.id) }])),
+      isleaf: true
+    };
+    if (this.termCollectionSelectionMode === "fraction") {
+      if (!this.dom?.isoformDiv) throw new Error("isoform result holder is missing");
+      this.dom.fractionDiv?.remove();
+      this.dom.fractionDiv = this.dom.isoformDiv.append("div").style("margin-top", "10px");
+      pickCollectionFraction({
+        holder: this.dom.fractionDiv,
+        term,
+        callback: (tw) => this.callback(tw)
+      });
+      return;
+    }
+    this.callback(term);
+  }
+};
+function filterIsoforms(gmlst, availableItems) {
+  const itemSet = new Set(availableItems);
+  return gmlst.filter((gm) => gm.isoform?.startsWith("ENST") && (itemSet.size === 0 || itemSet.has(gm.isoform)));
+}
+
+export {
+  SearchHandler,
+  filterIsoforms
+};
+//# sourceMappingURL=chunk-FA6M7PSZ.js.map

package/dist/chunk-FCQPQD7Z.js

@@ -0,0 +1,181 @@
+import {
+  appInit
+} from "./chunk-7E37WMAX.js";
+import {
+  showErrorsWithCounter
+} from "./chunk-CXCAQOFB.js";
+import {
+  mclass
+} from "./chunk-2N345NXD.js";
+
+// plots/disco/launch.adhoc.ts
+async function launch(arg, genomeObj, holder) {
+  const [mlst, errors] = await getMlst(arg);
+  if (errors?.length) {
+    return showErrorsWithCounter(errors, holder);
+  }
+  const opts = {
+    holder,
+    vocabApi: {
+      // api is required by plot.app.js, so create a mock one for the adhoc data
+      vocab: { terms: [] },
+      main: () => {
+        return;
+      },
+      getTermdbConfig: () => {
+        return {};
+      },
+      // PlotBase calls app.vocabApi.create() for a plot-level vocabApi, so the mock needs it too,
+      // see the create() method in termdb/Vocab.js
+      create(componentGetAbortSignal) {
+        return Object.create(this, { getAbortSignal: { value: () => componentGetAbortSignal() } });
+      }
+    },
+    state: {
+      args: {
+        data: mlst,
+        genome: genomeObj
+      },
+      plots: [
+        {
+          chartType: "Disco",
+          subfolder: "disco",
+          extension: "ts",
+          /** NOTE: Users should only override the settings in the default
+           * settings.Disco:{}, not the entire settings:{} object.*/
+          overrides: { Disco: arg?.settings || {} }
+        }
+      ]
+    }
+  };
+  const plotAppApi = await appInit(opts);
+  return plotAppApi;
+}
+async function getMlst(arg) {
+  if (Array.isArray(arg.mlst)) {
+    return [arg.mlst, null];
+  }
+  const mlst = [];
+  const errors = [];
+  if (arg.snvText) parseSnvText(arg.snvText, mlst, errors);
+  if (arg.svText) parseSvText(arg.svText, mlst, errors);
+  if (arg.cnvText) parseCnvText(arg.cnvText, mlst, errors);
+  return [mlst, errors];
+}
+function parseSnvText(text, mlst, errors) {
+  for (const line of text.trim().split("\n")) {
+    const l = line.trim().split("	");
+    if (![5, 7, 9].includes(l.length)) {
+      errors.push("snv input not equal to 5, 7, or 9 columns");
+      continue;
+    }
+    let m;
+    try {
+      m = {
+        dt: 1,
+        chr: l[0],
+        position: Number(l[1]),
+        gene: l[2],
+        mname: l[3],
+        class: validateMutation(l[4], errors)
+      };
+      const vafs = parseOptionalVafs(l, errors);
+      if (vafs.length) m.vafs = vafs;
+    } catch (e) {
+      errors.push(e);
+      continue;
+    }
+    mlst.push(m);
+  }
+}
+function parseOptionalVafs(line, errors) {
+  const vafs = [];
+  const addVaf = (id, totalIndex, altIndex) => {
+    if (line.length <= altIndex) return;
+    const totalCount = Number(line[totalIndex]);
+    const altCount = Number(line[altIndex]);
+    if (!Number.isInteger(totalCount) || !Number.isInteger(altCount) || totalCount <= 0 || altCount < 0 || altCount > totalCount) {
+      errors.push(`${id} total/alt counts must be integers with total > 0, alt >= 0, and alt cannot exceed total`);
+      return;
+    }
+    vafs.push({ id, totalCount, altCount });
+  };
+  addVaf("DNA", 5, 6);
+  addVaf("RNA", 7, 8);
+  return vafs;
+}
+function parseSvText(text, mlst, errors) {
+  for (const line of text.trim().split("\n")) {
+    const l = line.trim().split("	");
+    if (l.length < 4 || l.length > 6) {
+      errors.push("sv input not equal to 4 or 6 columns");
+      continue;
+    }
+    let m;
+    try {
+      const length = l.length;
+      if (length == 4) {
+        m = {
+          dt: 2,
+          chrA: l[0],
+          posA: Number(l[1]),
+          chrB: l[2],
+          posB: Number(l[3])
+        };
+      } else {
+        m = {
+          dt: 2,
+          chrA: l[0],
+          posA: Number(l[1]),
+          geneA: l[2],
+          chrB: l[3],
+          posB: Number(l[4]),
+          geneB: l[5]
+        };
+      }
+    } catch (e) {
+      errors.push(e);
+      continue;
+    }
+    mlst.push(m);
+  }
+}
+function parseCnvText(text, mlst, errors) {
+  for (const line of text.trim().split("\n")) {
+    const l = line.trim().split("	");
+    if (l.length != 4) {
+      errors.push("cnv input not equal to 4 columns");
+      continue;
+    }
+    let m;
+    try {
+      m = {
+        dt: 4,
+        chr: l[0],
+        start: Number(l[1]),
+        stop: Number(l[2]),
+        value: Number(l[3])
+      };
+    } catch (e) {
+      errors.push(e);
+      continue;
+    }
+    mlst.push(m);
+  }
+}
+function validateMutation(mutation, errors) {
+  const mut2check = mutation.toLowerCase();
+  const foundMutation = Object.values(mclass).find(
+    (m) => m.key.toLowerCase() === mut2check || m.label.toLowerCase() === mut2check
+  );
+  if (foundMutation) {
+    return foundMutation.key;
+  } else {
+    errors.push(`Invalid mutation class: ${mutation}`);
+  }
+}
+
+export {
+  launch
+};
+//# sourceMappingURL=chunk-FCQPQD7Z.js.map

package/dist/chunk-FCQPQD7Z.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/disco/launch.adhoc.ts"],
+  "sourcesContent": ["import type { Genome } from '#types'\nimport type { Selection } from 'd3-selection'\nimport { appInit } from '../plot.app'\nimport { showErrorsWithCounter } from '../../dom/sayerror'\nimport { mclass } from '#shared/common.js'\n\ntype SnvEntry = {\n\tdt: 1\n\tchr: string\n\tposition: number\n\tgene: string\n\tmname: string\n\tclass: string\n\tvafs?: Array<{ id: string; totalCount: number; altCount: number }>\n}\ntype CnvEntry = {\n\tdt: 4\n\tchr: string\n\tstart: number\n\tstop: number\n\tvalue: number\n}\ntype SvEntry4Cols = {\n\tdt: number\n\tchrA: string\n\tposA: number\n\tchrB: string\n\tposB: number\n}\n\ntype SvEntry6Cols = {\n\tdt: number\n\tchrA: string\n\tposA: number\n\tgeneA: string\n\tchrB: string\n\tposB: number\n\tgeneB: string\n}\n\ntype SvEntry = SvEntry4Cols | SvEntry6Cols\n\ntype MutationListEntry = SnvEntry | CnvEntry | SvEntry\n\n/** When disco is embedded, the arguments below are nested under arg.disco */\nexport type DiscoPlotArgs = {\n\t/**optional array of preparsed mutation events, from runpp() */\n\tmlst?: MutationListEntry[]\n\n\t/**tabular text of snv data, with follow columns.\n\t1. chr\n\t2. position\n\t3. gene\n\t4. aachange\n\t5. class\n\tOptionally, provide DNA total/alt read counts in columns 6-7 and RNA total/alt \n\tread counts in columns 8-9.\n\teach line is parsed into an object:\n\t{dt:1, chr:, position:, gene:, class:} */\n\tsnvText?: string\n\t/**tp path to a text file of same content as snvText */\n\tsnvFile?: string\n\t/**url of a text file of same content as snvText */\n\tsnvUrl?: string\n\n\t/**tabular text of sv/fusion data, with follow columns\n\t1. chrA\n\t2. posA\n\t3. geneA\n\t4. chrB\n\t5. posB\n\t6. geneB\n\teach line is parsed into an object:\n\t{dt:2, chrA, posA, geneA, chrB, posB, geneB} */\n\tsvText?: string\n\tsvFile?: string\n\tsvUrl?: string\n\n\t/**tabular text of cnv data, with following columns\n\t1. chr\n\t2. start\n\t3. stop\n\t4. value\n\teach line is parsed into an object\n\t{chr, start, stop, value} */\n\tcnvText?: string\n\tcnvFile?: string\n\tcnvUrl?: string\n\tsettings?: any\n}\n\n//... more datatypes can be added later\n\n/**\n * parse input data into mlst[] and pass to disco\n * TODO display data error on ui\n * TODO later make this script a native part of disco, so that runpp() directly invokes plot.app.js...\n * @param arg\n * @param genomeObj\n * @param holder\n * @returns\n */\n\nexport async function launch(arg: DiscoPlotArgs, genomeObj: Genome, holder: Selection<HTMLDivElement, any, any, any>) {\n\tconst [mlst, errors] = await getMlst(arg)\n\n\tif (errors?.length) {\n\t\treturn showErrorsWithCounter(errors, holder)\n\t}\n\n\tconst opts = {\n\t\tholder,\n\t\tvocabApi: {\n\t\t\t// api is required by plot.app.js, so create a mock one for the adhoc data\n\t\t\tvocab: { terms: [] },\n\t\t\tmain: () => {\n\t\t\t\treturn //fix so linter doesn't yell while this is in development\n\t\t\t},\n\t\t\tgetTermdbConfig: () => {\n\t\t\t\treturn {}\n\t\t\t},\n\t\t\t// PlotBase calls app.vocabApi.create() for a plot-level vocabApi, so the mock needs it too,\n\t\t\t// see the create() method in termdb/Vocab.js\n\t\t\tcreate(componentGetAbortSignal: () => AbortSignal | undefined) {\n\t\t\t\treturn Object.create(this, { getAbortSignal: { value: () => componentGetAbortSignal() } })\n\t\t\t}\n\t\t},\n\t\tstate: {\n\t\t\targs: {\n\t\t\t\tdata: mlst,\n\t\t\t\tgenome: genomeObj\n\t\t\t},\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'Disco',\n\t\t\t\t\tsubfolder: 'disco',\n\t\t\t\t\textension: 'ts',\n\t\t\t\t\t/** NOTE: Users should only override the settings in the default\n\t\t\t\t\t * settings.Disco:{}, not the entire settings:{} object.*/\n\t\t\t\t\toverrides: { Disco: arg?.settings || {} }\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\t}\n\n\tconst plotAppApi = await appInit(opts)\n\treturn plotAppApi\n}\n\n/**\n * from multiple possible data sources, parse mutation events and put everything into one array and return, for disco rendering\n * app drawer will supply data for \"snvText, svText, cnvText\"\n * while the \"File\" and \"Url\" can come from url parameters e.g. host?disco=1&snvFile=path/to/file\n * @param arg\n * @returns\n */\nasync function getMlst(arg: DiscoPlotArgs): Promise<[MutationListEntry[], string[] | null]> {\n\tif (Array.isArray(arg.mlst)) {\n\t\t// has preformatted in runpp()\n\t\treturn [arg.mlst, null]\n\t}\n\n\t// parse data from text and files and append to one mlst[] array\n\tconst mlst = [] as MutationListEntry[]\n\tconst errors = [] as string[]\n\n\tif (arg.snvText) parseSnvText(arg.snvText, mlst, errors)\n\tif (arg.svText) parseSvText(arg.svText, mlst, errors)\n\tif (arg.cnvText) parseCnvText(arg.cnvText, mlst, errors)\n\n\t// if (arg.snvFile) {\n\t// }\n\t// if (arg.snvUrl) {\n\t// }\n\t// if (arg.svFile) {\n\t// }\n\t// if (arg.svUrl) {\n\t// }\n\t// if (arg.cnvFile) {\n\t// }\n\t// if (arg.cnvUrl) {\n\t// }\n\n\treturn [mlst, errors]\n}\n\nfunction parseSnvText(text: string, mlst: MutationListEntry[], errors: string[]) {\n\t// TODO share a parser for snvindel text file with samples (with header line and non-fixed columns), but should not require sample here\n\tfor (const line of text.trim().split('\\n')) {\n\t\tconst l = line.trim().split('\\t')\n\n\t\tif (![5, 7, 9].includes(l.length)) {\n\t\t\terrors.push('snv input not equal to 5, 7, or 9 columns')\n\t\t\tcontinue\n\t\t}\n\n\t\tlet m: SnvEntry\n\t\ttry {\n\t\t\tm = {\n\t\t\t\tdt: 1,\n\t\t\t\tchr: l[0],\n\t\t\t\tposition: Number(l[1]),\n\t\t\t\tgene: l[2],\n\t\t\t\tmname: l[3],\n\t\t\t\tclass: validateMutation(l[4], errors)\n\t\t\t}\n\t\t\tconst vafs = parseOptionalVafs(l, errors)\n\t\t\tif (vafs.length) m.vafs = vafs\n\t\t} catch (e: any) {\n\t\t\terrors.push(e)\n\t\t\tcontinue\n\t\t}\n\t\tmlst.push(m)\n\t}\n}\n\nfunction parseOptionalVafs(line: string[], errors: string[]) {\n\tconst vafs: Array<{ id: string; totalCount: number; altCount: number }> = []\n\tconst addVaf = (id: string, totalIndex: number, altIndex: number) => {\n\t\tif (line.length <= altIndex) return\n\t\tconst totalCount = Number(line[totalIndex])\n\t\tconst altCount = Number(line[altIndex])\n\t\tif (\n\t\t\t!Number.isInteger(totalCount) ||\n\t\t\t!Number.isInteger(altCount) ||\n\t\t\ttotalCount <= 0 ||\n\t\t\taltCount < 0 ||\n\t\t\taltCount > totalCount\n\t\t) {\n\t\t\terrors.push(`${id} total/alt counts must be integers with total > 0, alt >= 0, and alt cannot exceed total`)\n\t\t\treturn\n\t\t}\n\n\t\tvafs.push({ id, totalCount, altCount })\n\t}\n\n\taddVaf('DNA', 5, 6)\n\taddVaf('RNA', 7, 8)\n\treturn vafs\n}\n\nfunction parseSvText(text: string, mlst: MutationListEntry[], errors: string[]) {\n\tfor (const line of text.trim().split('\\n')) {\n\t\tconst l = line.trim().split('\\t')\n\t\tif (l.length < 4 || l.length > 6) {\n\t\t\terrors.push('sv input not equal to 4 or 6 columns')\n\t\t\tcontinue\n\t\t}\n\t\tlet m: SvEntry\n\t\ttry {\n\t\t\tconst length: number = l.length\n\t\t\tif (length == 4) {\n\t\t\t\tm = {\n\t\t\t\t\tdt: 2,\n\t\t\t\t\tchrA: l[0],\n\t\t\t\t\tposA: Number(l[1]),\n\t\t\t\t\tchrB: l[2],\n\t\t\t\t\tposB: Number(l[3])\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tm = {\n\t\t\t\t\tdt: 2,\n\t\t\t\t\tchrA: l[0],\n\t\t\t\t\tposA: Number(l[1]),\n\t\t\t\t\tgeneA: l[2],\n\t\t\t\t\tchrB: l[3],\n\t\t\t\t\tposB: Number(l[4]),\n\t\t\t\t\tgeneB: l[5]\n\t\t\t\t}\n\t\t\t}\n\t\t} catch (e: any) {\n\t\t\terrors.push(e)\n\t\t\tcontinue\n\t\t}\n\t\tmlst.push(m)\n\t}\n}\n\nfunction parseCnvText(text: string, mlst: MutationListEntry[], errors: string[]) {\n\tfor (const line of text.trim().split('\\n')) {\n\t\tconst l = line.trim().split('\\t')\n\t\tif (l.length != 4) {\n\t\t\terrors.push('cnv input not equal to 4 columns')\n\t\t\tcontinue\n\t\t}\n\t\tlet m: CnvEntry\n\t\ttry {\n\t\t\tm = {\n\t\t\t\tdt: 4,\n\t\t\t\tchr: l[0],\n\t\t\t\tstart: Number(l[1]),\n\t\t\t\tstop: Number(l[2]),\n\t\t\t\tvalue: Number(l[3])\n\t\t\t}\n\t\t} catch (e: any) {\n\t\t\terrors.push(e)\n\t\t\tcontinue\n\t\t}\n\t\tmlst.push(m)\n\t}\n}\n\nfunction validateMutation(mutation: string, errors: string[]) {\n\tconst mut2check = mutation.toLowerCase()\n\tconst foundMutation = Object.values(mclass).find(\n\t\t(m: any) => m.key.toLowerCase() === mut2check || m.label.toLowerCase() === mut2check\n\t) as any\n\tif (foundMutation) {\n\t\treturn foundMutation.key\n\t} else {\n\t\terrors.push(`Invalid mutation class: ${mutation}`)\n\t}\n}\n"],
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+  "names": []
+}

package/dist/chunk-FF4J6QSF.js

@@ -0,0 +1,240 @@
+import {
+  make_radios
+} from "./chunk-CXCAQOFB.js";
+import {
+  initBinConfig
+} from "./chunk-VVWZ4BOI.js";
+import {
+  toStoredUnit,
+  toUserUnit
+} from "./chunk-W5J3LTYS.js";
+import {
+  format
+} from "./chunk-4OLM3KSB.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;
+  }
+  /* q holds bin boundaries in the unit the term's values are stored in, while the <input>s and the
+  density plot show them in the term's user-facing unit. toDisplay()/toStored() cross that boundary;
+  both are identity functions unless the term declares valueConversion{} */
+  toDisplay(v) {
+    return toUserUnit(v, this.tw.term);
+  }
+  toStored(v) {
+    return toStoredUnit(v, this.tw.term);
+  }
+  render(div) {
+    this.tw = this.editHandler.tw;
+    const isRemounting = !!this.dom.binsTable && this.editHandler.dom.binsDiv?.node().contains(this.dom.binsTable.node());
+    if (!isRemounting) this.q = this.getDefaultQ();
+    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
+    if (isRemounting) return;
+    if (this.dom.binsTable) {
+      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 = this.toDisplay(q.bin_size);
+    this.dom.bin_size_input = tr.append("td").append("input").attr("type", "number").attr(
+      "value",
+      handler.density.scaleFactor == 1 && "rounding" in q ? format(q.rounding || ".0f")(q.bin_size) : origBinSize
+    ).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 = this.toStored(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" : this.toDisplay(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 = this.toDisplay(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 = this.toStored(Number(event.target.value));
+      if (Number(event.target.value) < this.toDisplay(min) || Number(event.target.value) > this.toDisplay(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.toDisplay(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", Number.isFinite(q.last_bin?.start) ? this.toDisplay(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 = this.toStored(Number(strInput));
+    if (q.first_bin && Number(strInput) <= this.toDisplay(q.first_bin.stop)) {
+      window.alert("Last bin start cannot be smaller than first bin stop.");
+      this.dom.last_start_input.property("value", this.toDisplay(max));
+      return;
+    }
+    if (Number(strInput) > this.toDisplay(max)) {
+      window.alert("Last bin start value out of bound.");
+      this.dom.last_start_input.property("value", this.toDisplay(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: this.toDisplay(i), isDraggable, movesWithLineIndex: !isDraggable ? 0 : -1 });
+    }
+    if (this.q.last_bin) {
+      boundaryValues.push({
+        x: this.toDisplay(this.q.last_bin.start),
+        isDraggable: true,
+        isLastVisibleLine: true,
+        movesWithLineIndex: -1
+      });
+    }
+    return {
+      values: boundaryValues,
+      // the dragged value arrives in display units, matching what the <input>s show
+      callback: (d, value) => {
+        if (d.index === 0) {
+          this.dom.first_stop_input.property("value", value);
+          this.q.first_bin.stop = this.toStored(value);
+        } else {
+          this.dom.last_start_input.property("value", value);
+          if (this.q.last_bin) this.q.last_bin.start = this.toStored(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: this.toStored(Number(bin_size)),
+      first_bin: {
+        startunbounded: true,
+        stop: this.toStored(Number(this.dom.first_stop_input.property("value")))
+      },
+      /* rounding formats the stored bin size, so it cannot be derived from the decimals of a
+      converted input. a converted term labels its bins through valueConversion instead */
+      rounding: this.editHandler.handler.density.scaleFactor != 1 ? ".0f" : bin_size.includes(".") && !bin_size.endsWith(".") ? `.${bin_size.split(".")[1].length}f` : ".0f"
+    };
+    if (this.dom.fixed_radio.property("checked")) {
+      config.last_bin = {
+        start: this.toStored(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-FF4J6QSF.js.map