@sjcrh/proteinpaint-client 2.220.0 → 2.221.0

package/dist/chunk-PWYMHUXY.js

@@ -0,0 +1,116 @@
+// dom/numericRangeInput.ts
+var NumericRangeInput = class {
+  constructor(holder, range, callback, opts) {
+    this.scaleFactor = opts?.scaleFactor && opts.scaleFactor > 0 ? opts.scaleFactor : 1;
+    this.min = opts?.min;
+    this.max = opts?.max;
+    this.input = holder.append("input").attr("name", "rangeInput").attr("data-testid", "sjpp-range-input").attr("aria-label", "Leave blank for the allowed minimum value").style("width", opts?.width || "180px").style("margin", "3px 5px").on("change", () => {
+      try {
+        this.parseRange();
+      } catch (ex) {
+        alert(ex);
+        this.setRange();
+      }
+    });
+    this.setRange(range);
+    this.callback = callback;
+  }
+  getInput() {
+    return this.input;
+  }
+  parseRange() {
+    const str = this.input.node().value;
+    const new_range = toStoredUnits(parseRange(str), this.scaleFactor);
+    this.validateBounds(new_range);
+    this.range = new_range;
+    this.callback(new_range);
+    return new_range;
+  }
+  /** throws on a range that selects nothing within the allowed bounds. a bound at the min or max is
+   * allowed when inclusive, e.g. x>=1 for a fraction */
+  validateBounds(r) {
+    const min = this.min, max = this.max;
+    const minLabel = toDisplayValue(min, this.scaleFactor), maxLabel = toDisplayValue(max, this.scaleFactor);
+    if (r.value != void 0) {
+      if (min != void 0 && r.value < min) throw `Invalid value < minimum allowed (${minLabel})`;
+      if (max != void 0 && r.value > max) throw `Invalid value > maximum allowed (${maxLabel})`;
+      return;
+    }
+    if (min != void 0) {
+      if (!r.startunbounded && r.start < min) throw `Invalid start value < minimum allowed (${minLabel})`;
+      if (!r.stopunbounded && (r.stop < min || r.stop == min && !r.stopinclusive))
+        throw `Invalid stop value ${r.stopinclusive ? "<" : "<="} minimum allowed (${minLabel})`;
+    }
+    if (max != void 0) {
+      if (!r.stopunbounded && r.stop > max) throw `Invalid stop value > maximum allowed (${maxLabel})`;
+      if (!r.startunbounded && (r.start > max || r.start == max && !r.startinclusive))
+        throw `Invalid start value ${r.startinclusive ? ">" : ">="} maximum allowed (${maxLabel})`;
+    }
+  }
+  getRange() {
+    return this.range;
+  }
+  setRange(range) {
+    if (!range) range = this.range;
+    else this.range = range;
+    if (!range) return;
+    const [start, stop] = formatRangeBounds(range, this.scaleFactor);
+    this.input.node().value = range.value != void 0 ? ` x=${toDisplayValue(range.value, this.scaleFactor)} ` : `${start} x ${stop}`;
+  }
+};
+function toStoredUnits(range, scaleFactor) {
+  if (scaleFactor == 1) return range;
+  for (const k of ["start", "stop", "value"]) {
+    if (Number.isFinite(range[k])) range[k] = range[k] / scaleFactor;
+  }
+  return range;
+}
+function toDisplayValue(v, scaleFactor) {
+  if (scaleFactor == 1 || !Number.isFinite(Number(v))) return v;
+  return Number((Number(v) * scaleFactor).toFixed(2));
+}
+function formatRangeBounds(range, scaleFactor = 1) {
+  const startV = toDisplayValue(range.start, scaleFactor);
+  const stopV = toDisplayValue(range.stop, scaleFactor);
+  const start = range.startunbounded || range.start == void 0 ? "" : `${startV} ${range.startinclusive ? "<=" : "<"}`;
+  const stop = range.stopunbounded || range.stop == void 0 ? "" : `${range.stopinclusive ? "<=" : "<"} ${stopV}`;
+  return [start, stop];
+}
+function parseRange(str) {
+  if (!str) throw "Empty range";
+  const tokens = str.replace(/\s/g, "").split("x");
+  let start, stop, startinclusive, stopinclusive, value;
+  if (tokens[0]) parseRangeToken(tokens[0]);
+  if (tokens[1]) parseRangeToken(tokens[1]);
+  if (value != void 0) return { value, label: `x = ${value}` };
+  const startunbounded = start === void 0;
+  const stopunbounded = stop === void 0;
+  if (!startunbounded && !stopunbounded && start > stop) throw "start must be lower than stop";
+  return { start, stop, value, startinclusive, stopinclusive, startunbounded, stopunbounded };
+  function parseRangeToken(rangeToken) {
+    const floatExpr = "[+-]?\\d+(\\.\\d+)?";
+    if (new RegExp(`^${floatExpr}<$`).test(rangeToken) || new RegExp(`^>${floatExpr}$`).test(rangeToken)) {
+      start = parseFloat(rangeToken.match(floatExpr));
+      startinclusive = false;
+    } else if (new RegExp(`^${floatExpr}<=$`).test(rangeToken) || new RegExp(`^>=${floatExpr}$`).test(rangeToken)) {
+      start = parseFloat(rangeToken.match(floatExpr));
+      startinclusive = true;
+    } else if (new RegExp(`^${floatExpr}>$`).test(rangeToken) || new RegExp(`^<${floatExpr}$`).test(rangeToken)) {
+      stop = parseFloat(rangeToken.match(floatExpr));
+      stopinclusive = false;
+    } else if (new RegExp(`^${floatExpr}>=$`).test(rangeToken) || new RegExp(`^<=${floatExpr}$`).test(rangeToken)) {
+      stop = parseFloat(rangeToken.match(floatExpr));
+      stopinclusive = true;
+    } else if (new RegExp(`^${floatExpr}=$`).test(rangeToken) || new RegExp(`^=${floatExpr}$`).test(rangeToken)) {
+      value = parseFloat(rangeToken.match(floatExpr));
+      stopinclusive = true;
+      startinclusive = true;
+    } else throw `Could not parse expression '${rangeToken}'`;
+  }
+}
+
+export {
+  NumericRangeInput,
+  formatRangeBounds
+};
+//# sourceMappingURL=chunk-PWYMHUXY.js.map

package/dist/chunk-PWYMHUXY.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../dom/numericRangeInput.ts"],
+  "sourcesContent": ["import type { Elem, Input } from '../types/d3'\nimport type { FullyBoundedBin } from '#types'\n\ntype TvsRange = FullyBoundedBin & { value?: number }\ntype Opts = {\n\twidth?: string // width of input\n\t/** multiplier from the unit a term's values are stored in to the unit shown to users, from\n\t * term.valueConversion (see getValueConversionFactor()). the range handed in and given back is\n\t * always in the stored unit; only the text in the <input> is in the user-facing one */\n\tscaleFactor?: number\n\t/** the allowed bounds of a typed range, in the stored unit, e.g. 0 and 1 for a fraction. kept apart\n\t * from the range, which is replaced by every parsed entry */\n\tmin?: number | null\n\tmax?: number | null\n}\n\nexport class NumericRangeInput {\n\tcallback: (f: any) => void\n\tinput: Input\n\trange: any\n\tscaleFactor: number\n\tmin?: number | null\n\tmax?: number | null\n\n\tconstructor(holder: Elem, range: any, callback: () => void, opts?: Opts) {\n\t\tthis.scaleFactor = opts?.scaleFactor && opts.scaleFactor > 0 ? opts.scaleFactor : 1\n\t\tthis.min = opts?.min\n\t\tthis.max = opts?.max\n\t\tthis.input = holder\n\t\t\t.append('input')\n\t\t\t.attr('name', 'rangeInput')\n\t\t\t.attr('data-testid', 'sjpp-range-input')\n\t\t\t.attr('aria-label', 'Leave blank for the allowed minimum value')\n\t\t\t.style('width', opts?.width || '180px')\n\t\t\t.style('margin', '3px 5px')\n\t\t\t//.style('font-size', '20px')\n\t\t\t.on('change', () => {\n\t\t\t\ttry {\n\t\t\t\t\tthis.parseRange()\n\t\t\t\t} catch (ex) {\n\t\t\t\t\talert(ex)\n\t\t\t\t\tthis.setRange()\n\t\t\t\t}\n\t\t\t})\n\t\tthis.setRange(range)\n\t\tthis.callback = callback\n\t}\n\n\tgetInput() {\n\t\treturn this.input\n\t}\n\n\tparseRange() {\n\t\tconst str = this.input.node()!.value\n\t\tconst new_range = toStoredUnits(parseRange(str), this.scaleFactor)\n\t\tthis.validateBounds(new_range)\n\t\tthis.range = new_range\n\t\tthis.callback(new_range)\n\t\treturn new_range\n\t}\n\n\t/** throws on a range that selects nothing within the allowed bounds. a bound at the min or max is\n\t * allowed when inclusive, e.g. x>=1 for a fraction */\n\tvalidateBounds(r: any) {\n\t\tconst min = this.min,\n\t\t\tmax = this.max\n\t\tconst minLabel = toDisplayValue(min, this.scaleFactor),\n\t\t\tmaxLabel = toDisplayValue(max, this.scaleFactor)\n\t\tif (r.value != undefined) {\n\t\t\tif (min != undefined && r.value < min) throw `Invalid value < minimum allowed (${minLabel})`\n\t\t\tif (max != undefined && r.value > max) throw `Invalid value > maximum allowed (${maxLabel})`\n\t\t\treturn\n\t\t}\n\t\tif (min != undefined) {\n\t\t\tif (!r.startunbounded && r.start < min) throw `Invalid start value < minimum allowed (${minLabel})`\n\t\t\tif (!r.stopunbounded && (r.stop < min || (r.stop == min && !r.stopinclusive)))\n\t\t\t\tthrow `Invalid stop value ${r.stopinclusive ? '<' : '<='} minimum allowed (${minLabel})`\n\t\t}\n\t\tif (max != undefined) {\n\t\t\tif (!r.stopunbounded && r.stop > max) throw `Invalid stop value > maximum allowed (${maxLabel})`\n\t\t\tif (!r.startunbounded && (r.start > max || (r.start == max && !r.startinclusive)))\n\t\t\t\tthrow `Invalid start value ${r.startinclusive ? '>' : '>='} maximum allowed (${maxLabel})`\n\t\t}\n\t}\n\n\tgetRange() {\n\t\treturn this.range\n\t}\n\n\tsetRange(range?: TvsRange) {\n\t\tif (!range) range = this.range\n\t\t//When an error is thrown the previous range is restored\n\t\telse this.range = range\n\n\t\t//So ts doesn't complain\n\t\tif (!range) return\n\t\tconst [start, stop] = formatRangeBounds(range, this.scaleFactor)\n\t\tthis.input.node()!.value =\n\t\t\trange.value != undefined ? ` x=${toDisplayValue(range.value, this.scaleFactor)} ` : `${start} x ${stop}`\n\t}\n}\n\n/** convert a range parsed from the <input> text back to the unit its values are stored in */\nfunction toStoredUnits(range: any, scaleFactor: number) {\n\tif (scaleFactor == 1) return range\n\tfor (const k of ['start', 'stop', 'value']) {\n\t\tif (Number.isFinite(range[k])) range[k] = range[k] / scaleFactor\n\t}\n\treturn range\n}\n\n/** a converted value is rounded, so that an input does not read 70.81451060916.\n * this makes the round trip through parseRange() lossy by up to half of the last shown digit,\n * which is immaterial for a filter range */\nfunction toDisplayValue(v: any, scaleFactor: number) {\n\tif (scaleFactor == 1 || !Number.isFinite(Number(v))) return v\n\treturn Number((Number(v) * scaleFactor).toFixed(2))\n}\n\n/** Format the start and stop of a range as displayed to the user, e.g. ['10 <', '<= 20'].\n *\n * A bound is exclusive unless the range marks it inclusive, matching how a range is\n * evaluated elsewhere, e.g. isInRange() on the server and the tvs pill label. The displayed\n * expression must round-trip through parseRange(), since the input text is the only source\n * of the applied range: rendering an exclusive bound as inclusive would silently widen a\n * saved range on apply.\n */\nexport function formatRangeBounds(range: any, scaleFactor = 1): [string, string] {\n\tconst startV = toDisplayValue(range.start, scaleFactor)\n\tconst stopV = toDisplayValue(range.stop, scaleFactor)\n\tconst start = range.startunbounded || range.start == undefined ? '' : `${startV} ${range.startinclusive ? '<=' : '<'}`\n\tconst stop = range.stopunbounded || range.stop == undefined ? '' : `${range.stopinclusive ? '<=' : '<'} ${stopV}`\n\treturn [start, stop]\n}\n\nexport function parseRange(str: string) {\n\tif (!str) throw 'Empty range'\n\tconst tokens = str.replace(/\\s/g, '').split('x')\n\tlet start, stop, startinclusive, stopinclusive, value\n\n\tif (tokens[0]) parseRangeToken(tokens[0])\n\tif (tokens[1]) parseRangeToken(tokens[1])\n\tif (value != undefined) return { value, label: `x = ${value}` }\n\tconst startunbounded = start === undefined\n\tconst stopunbounded = stop === undefined\n\n\tif (!startunbounded && !stopunbounded && start > stop) throw 'start must be lower than stop'\n\treturn { start, stop, value, startinclusive, stopinclusive, startunbounded, stopunbounded }\n\n\tfunction parseRangeToken(rangeToken) {\n\t\tconst floatExpr = '[+-]?\\\\d+(\\\\.\\\\d+)?'\n\n\t\tif (new RegExp(`^${floatExpr}<$`).test(rangeToken) || new RegExp(`^>${floatExpr}$`).test(rangeToken)) {\n\t\t\tstart = parseFloat(rangeToken.match(floatExpr))\n\t\t\tstartinclusive = false\n\t\t} else if (new RegExp(`^${floatExpr}<=$`).test(rangeToken) || new RegExp(`^>=${floatExpr}$`).test(rangeToken)) {\n\t\t\tstart = parseFloat(rangeToken.match(floatExpr))\n\t\t\tstartinclusive = true\n\t\t} else if (new RegExp(`^${floatExpr}>$`).test(rangeToken) || new RegExp(`^<${floatExpr}$`).test(rangeToken)) {\n\t\t\tstop = parseFloat(rangeToken.match(floatExpr))\n\t\t\tstopinclusive = false\n\t\t} else if (new RegExp(`^${floatExpr}>=$`).test(rangeToken) || new RegExp(`^<=${floatExpr}$`).test(rangeToken)) {\n\t\t\tstop = parseFloat(rangeToken.match(floatExpr))\n\t\t\tstopinclusive = true\n\t\t} else if (new RegExp(`^${floatExpr}=$`).test(rangeToken) || new RegExp(`^=${floatExpr}$`).test(rangeToken)) {\n\t\t\tvalue = parseFloat(rangeToken.match(floatExpr))\n\t\t\tstopinclusive = true\n\t\t\tstartinclusive = true\n\t\t} else throw `Could not parse expression '${rangeToken}'`\n\t}\n}\n"],
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+  "names": []
+}

package/dist/chunk-QNCE6EOK.js

@@ -0,0 +1,82 @@
+import {
+  addGeneSearchbox,
+  getGEunit,
+  getSelectedSampleTypes,
+  mayGetSampleTypeLabel,
+  renderSampleTypeSelect,
+  renderSampleTypesByTermsSelect,
+  table2col
+} from "./chunk-WD7FZ5EE.js";
+import {
+  Menu
+} from "./chunk-CNFTQSNE.js";
+import {
+  TermTypes
+} from "./chunk-WJLRU5OF.js";
+
+// termdb/handlers/geneExpression.ts
+var SearchHandler = class {
+  init(opts) {
+    this.callback = opts.callback;
+    this.app = opts.app;
+    this.dom = {};
+    const holder = opts.holder.append("div").style("padding", "10px 0px");
+    this.dom.sampleTypeDiv = holder.append("div");
+    this.mayRenderSampleTypeSelect();
+    const geneSearch = addGeneSearchbox({
+      tip: new Menu({ padding: "0px" }),
+      genome: opts.genomeObj,
+      row: holder,
+      searchOnly: "gene",
+      callback: () => this.selectGene(geneSearch)
+    });
+    holder.select(".sja_genesearchinput").style("margin", "0px");
+  }
+  mayRenderSampleTypeSelect() {
+    this.dom.sampleTypeDiv.selectAll("*").remove();
+    this.querySampleTypes = this.app.vocabApi.termdbConfig?.queries.geneExpression.sampleTypes;
+    this.querySampleTypesByTerms = this.app.vocabApi.termdbConfig?.queries.geneExpression.sampleTypesByTerms;
+    if (Array.isArray(this.querySampleTypes) && this.querySampleTypes.length >= 2 || this.querySampleTypesByTerms) {
+      const table = table2col({ holder: this.dom.sampleTypeDiv, margin: "0px 0px 15px 0px" });
+      const [td1, td2] = table.addRow();
+      td1.text("Sample Type");
+      td2.style("padding-left", "10px");
+      if (this.querySampleTypesByTerms) {
+        this.sampleTypeSelect = renderSampleTypesByTermsSelect(
+          td2,
+          this.querySampleTypesByTerms,
+          this.app.vocabApi.termdbConfig
+        );
+      } else {
+        this.sampleTypeSelect = renderSampleTypeSelect(td2, this.querySampleTypes, this.app.vocabApi.termdbConfig);
+      }
+    }
+  }
+  async selectGene(geneSearch) {
+    const gene = geneSearch?.geneSymbol;
+    if (!gene) throw new Error("No gene selected");
+    const sampleTypes = getSelectedSampleTypes({
+      sampleTypeSelect: this.sampleTypeSelect,
+      querySampleTypes: this.querySampleTypes,
+      querySampleTypesByTerms: this.querySampleTypesByTerms
+    });
+    if (this.sampleTypeSelect && !sampleTypes?.length) {
+      return;
+    }
+    const unit = getGEunit(this.app.vocabApi);
+    const name = `${gene} ${unit}`;
+    const term = { gene, name, type: TermTypes.GENE_EXPRESSION, sampleTypes };
+    term.sampleTypeLabel = mayGetSampleTypeLabel({
+      sampleTypeSelect: this.sampleTypeSelect,
+      querySampleTypes: this.querySampleTypes,
+      querySampleTypesByTerms: this.querySampleTypesByTerms,
+      termdbConfig: this.app.vocabApi.termdbConfig
+    });
+    this.callback(term);
+  }
+};
+
+export {
+  SearchHandler
+};
+//# sourceMappingURL=chunk-QNCE6EOK.js.map

package/dist/chunk-RV335DF2.js

@@ -0,0 +1,266 @@
+import {
+  DATermTypes,
+  DMRCATE_DEFAULTS,
+  getOthersGroup
+} from "./chunk-WD7FZ5EE.js";
+import {
+  dofetch3
+} from "./chunk-4TJO2DGU.js";
+import {
+  DMR_SCAN_ELEMENT_TYPE
+} from "./chunk-WJLRU5OF.js";
+import {
+  rgb
+} from "./chunk-Q5RDQNIT.js";
+
+// plots/volcano/colors.ts
+function getGroupColors(config) {
+  const groups = config?.samplelst?.groups;
+  const termValues = config?.tw?.term?.values;
+  const rawDown = termValues?.[groups?.[0]?.name]?.color || "red";
+  const rawUp = termValues?.[groups?.[1]?.name]?.color || "blue";
+  return {
+    controlColor: toHex(rawDown, "red"),
+    caseColor: toHex(rawUp, "blue")
+  };
+}
+function toHex(color, fallback) {
+  const c = rgb(color || fallback);
+  return c.displayable() ? c.formatHex() : rgb(fallback).formatHex();
+}
+
+// plots/volcano/model/VolcanoModel.ts
+var VolcanoModel = class {
+  /** TODO: This model is used in both the volcano and gsea.
+   * In the future, create base model in DA and use specific
+   * classes for the volcano and gsea. */
+  constructor(plot, termType) {
+    this.plot = plot;
+    this.app = plot.app;
+    this.termType = termType;
+  }
+  /** May use mapper instead as more termTypes are added */
+  async getData(config, settings) {
+    this.config = config;
+    this.settings = settings;
+    if (this.termType === DATermTypes.GENE_EXPRESSION) {
+      const body = await this.getGERequestBody();
+      const response = await dofetch3("termdb/DE", { body, signal: this.plot.api?.getAbortSignal() });
+      if (response && !response.error) {
+        response.daRequest = body;
+        this.setGroupSizes(response);
+      }
+      return response;
+    }
+    if (this.termType === DATermTypes.DNA_METHYLATION) {
+      const body = await this.getDMRequestBody();
+      const response = await dofetch3("termdb/diffMeth", { body, signal: this.plot.api?.getAbortSignal() });
+      if (response && !response.error) {
+        response.daRequest = body;
+        this.setGroupSizes(response);
+      }
+      return response;
+    }
+    if (this.termType === DATermTypes.JUNCTION) {
+      const body = await this.getDSRequestBody();
+      const response = await dofetch3("termdb/diffSplice", { body, signal: this.plot.api?.getAbortSignal() });
+      if (response && !response.error) {
+        response.daRequest = body;
+        this.setGroupSizes(response);
+      }
+      return response;
+    }
+    if (this.termType === DATermTypes.SINGLECELL_CELLTYPE) {
+      const body = await this.getSCCTRequestBody();
+      return await dofetch3("termdb/singlecellDEgenes", { body, signal: this.plot.api?.getAbortSignal() });
+    }
+    if (this.termType === DATermTypes.PROTEOME_DAP) {
+      const body = this.getDapRequestBody();
+      return await dofetch3("termdb/dapVolcano", { body, signal: this.plot.api?.getAbortSignal() });
+    }
+    if (this.termType === DATermTypes.SINGLECELL_GENE_EXPRESSION) {
+    }
+    throw new Error(`Volcano plot does not support route for termType='${this.termType}'`);
+  }
+  //Gene expression
+  async getGERequestBody() {
+    this.setOthersGroup(this.config.samplelst);
+    const state = this.app.getState();
+    const body = {
+      kind: "DE",
+      genome: this.app.vocabApi.vocab.genome,
+      dslabel: this.app.vocabApi.vocab.dslabel,
+      method: this.settings.method,
+      min_count: this.settings.minCount,
+      min_total_count: this.settings.minTotalCount,
+      samplelst: this.config.samplelst,
+      filter: state.termfilter.filter,
+      filter0: state.termfilter.filter0,
+      cpm_cutoff: this.settings.cpmCutoff,
+      volcanoRender: this.getVolcanoRender()
+    };
+    const pseudobulk = this.config.tw?.pseudobulk;
+    if (pseudobulk) body.pseudobulk = pseudobulk;
+    this.addConfounderTw(body);
+    return body;
+  }
+  //DNA methylation
+  async getDMRequestBody() {
+    this.setOthersGroup(this.config.samplelst);
+    const state = this.app.getState();
+    const body = {
+      kind: "DM",
+      genome: this.app.vocabApi.vocab.genome,
+      dslabel: this.app.vocabApi.vocab.dslabel,
+      samplelst: this.config.samplelst,
+      filter: state.termfilter.filter,
+      filter0: state.termfilter.filter0,
+      min_samples_per_group: this.settings.minSamplesPerGroup,
+      exclude_sex_chr: this.settings.excludeSexChr,
+      /* Omitted rather than sent as 'promoter' when it is the default, so a request
+      from a promoter-only dataset is byte-identical to what this client sent before
+      the element picker existed. The server resolves an absent element_type to
+      'promoter'. This does NOT preserve cache keys -- the key object gained the
+      field server-side, so every pre-existing dm/ entry is orphaned on deploy
+      regardless of what the client sends. */
+      ...this.settings.elementType && this.settings.elementType != "promoter" ? { element_type: this.settings.elementType } : {},
+      // the scan's own knobs; the server ignores them for any other element type
+      ...this.settings.elementType == DMR_SCAN_ELEMENT_TYPE ? {
+        scan: {
+          ...this.settings.scanChromosome ? { chromosome: this.settings.scanChromosome } : {},
+          backgroundCorrection: !!this.settings.backgroundCorrection,
+          minCpgs: this.settings.minCpgs,
+          profileBinBp: this.settings.profileBinBp,
+          // only when changed: an explicit default would orphan every cached scan
+          ...this.settings.lambda != DMRCATE_DEFAULTS.lambda ? { lambda: this.settings.lambda } : {},
+          ...this.settings.C != DMRCATE_DEFAULTS.C ? { C: this.settings.C } : {},
+          ...this.settings.fdrCutoff != DMRCATE_DEFAULTS.fdrCutoff ? { fdrCutoff: this.settings.fdrCutoff } : {}
+        }
+      } : {},
+      volcanoRender: this.getVolcanoRender()
+    };
+    if (this.settings.elementType != DMR_SCAN_ELEMENT_TYPE) this.addConfounderTw(body);
+    return body;
+  }
+  //Splicing
+  async getDSRequestBody() {
+    this.setOthersGroup(this.config.samplelst);
+    const state = this.app.getState();
+    const body = {
+      kind: "DS",
+      genome: this.app.vocabApi.vocab.genome,
+      dslabel: this.app.vocabApi.vocab.dslabel,
+      samplelst: this.config.samplelst,
+      filter: state.termfilter.filter,
+      filter0: state.termfilter.filter0,
+      method: this.settings.method,
+      /* leafcutter's own cluster filters, applied by the edgeR screen too so both engines
+      rank the same cluster set. Sent already scaled to cohort size by validateDSSettings --
+      as absolute counts they silently loosen as N grows. */
+      minSamplesPerIntron: this.settings.minSamplesPerIntron,
+      minSamplesPerGroup: this.settings.minSamplesPerGroup,
+      minCountsPerCluster: this.settings.minCountsPerCluster,
+      volcanoRender: this.getVolcanoRender()
+    };
+    this.addConfounderTw(body);
+    return body;
+  }
+  /** Parameters telling the server to run the `volcano` Rust renderer and return a
+   * volcano PNG + top-significant rows instead of the full dot list. */
+  getVolcanoRender() {
+    const dotRadius = Math.max(this.settings.width, this.settings.height) / 80;
+    const { caseColor, controlColor } = getGroupColors(this.config);
+    const useDeltaBeta = this.termType === DATermTypes.DNA_METHYLATION && this.settings.xAxis == "delta_beta";
+    const render = {
+      significanceThresholds: {
+        pValueCutoff: this.settings.pValue,
+        pValueType: this.settings.pValueType,
+        foldChangeCutoff: useDeltaBeta ? this.settings.deltaBetaCutoff : this.settings.foldChangeCutoff
+      },
+      ...useDeltaBeta ? { xField: "delta_beta" } : {},
+      // Tied to the delta-beta axis: the control that sets it is only offered for
+      // methylation, and centering a log2 fold-change axis is a different conversation.
+      ...useDeltaBeta && this.settings.centerDeltaBeta ? { centerX: true } : {},
+      pixelWidth: this.settings.width,
+      pixelHeight: this.settings.height,
+      colorSignificant: toHex(this.settings.defaultSignColor, "red"),
+      colorSignificantUp: caseColor,
+      colorSignificantDown: controlColor,
+      colorNonsignificant: toHex(this.settings.defaultNonSignColor, "black"),
+      dotRadius,
+      maxInteractiveDots: this.settings.maxInteractiveDots,
+      // Render the PNG at device-pixel resolution so it stays sharp on
+      // retina screens. The server reports the plot extent in CSS-space,
+      // so SVG overlay coords are unaffected.
+      //
+      // Oversample by 2× so the PNG also stays sharp when the user
+      // *zooms in after* the initial render (the captured DPR is frozen
+      // at fetch time — bigger headroom = more tolerable post-render
+      // zoom before pixelation appears). The server clamp keeps the
+      // bitmap memory bounded.
+      devicePixelRatio: (typeof window !== "undefined" ? window.devicePixelRatio : 1) * 2
+    };
+    if (this.termType === DATermTypes.JUNCTION) {
+      render.xField = "delta_psi";
+      render.significanceThresholds.foldChangeCutoff = this.settings.deltaPsiCutoff;
+    }
+    return render;
+  }
+  //This is a workaround until the server can accept an arr of confounder tws
+  addConfounderTw(body) {
+    const confounders = this.config?.confounderTws;
+    if (confounders?.length) {
+      body.tw = this.config.confounderTws[0];
+      if (confounders.length > 1) body.tw2 = this.config.confounderTws[1];
+    }
+  }
+  //Single cell cell type
+  getSCCTRequestBody() {
+    const body = {
+      genome: this.app.vocabApi.vocab.genome,
+      dslabel: this.app.vocabApi.vocab.dslabel,
+      sample: this.config.sample,
+      termId: this.config.termId,
+      categoryName: this.config.categoryName,
+      volcanoRender: this.getVolcanoRender()
+    };
+    return body;
+  }
+  getDapRequestBody() {
+    const { organism, assay, cohort } = this.config.proteomeDetails;
+    return {
+      genome: this.app.vocabApi.vocab.genome,
+      dslabel: this.app.vocabApi.vocab.dslabel,
+      organism,
+      assay,
+      cohort,
+      volcanoRender: this.getVolcanoRender()
+    };
+  }
+  /** The "others" group arrives as a placeholder with {in: false}. Replace it with the group that
+   * it stands for: the filter of the app without the samples of the other group, which the server
+   * resolves. */
+  setOthersGroup(samplelst) {
+    const i = samplelst.groups.findIndex((g) => !g.in);
+    if (i == -1) return;
+    const samplesGroup = samplelst.groups.find((g) => g.in);
+    samplelst.groups[i] = getOthersGroup(
+      { name: samplelst.groups[i].name, values: samplesGroup.values },
+      this.app.getState().termfilter
+    );
+  }
+  /** A group that the server resolved from a filter lists no sample here. Keep the number of its
+   * samples that the analysis ran on, where the group does not carry one, for getSampleNum(). */
+  setGroupSizes(response) {
+    for (const [i, g] of this.config.samplelst.groups.entries()) {
+      const n = response[`sample_size${i + 1}`];
+      if (!Array.isArray(g.values) && g.sampleCount === void 0 && Number.isFinite(n)) g.sampleCount = n;
+    }
+  }
+};
+
+export {
+  getGroupColors,
+  VolcanoModel
+};
+//# sourceMappingURL=chunk-RV335DF2.js.map