@sjcrh/proteinpaint-client 2.226.0 → 2.227.1

package/dist/geneVariant-VI5DGDAB.js

@@ -1,289 +0,0 @@
-import {
-  excludeFilterByTag,
-  fillGroupsetGroups,
-  filterInit,
-  filterPromptInit,
-  getDtTermValues,
-  getNormalRoot,
-  getPillNameDefault,
-  make_radios,
-  renderTable,
-  vocabInit
-} from "./chunk-DPWSIN62.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KZ54E2FU.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-DOC3HBOV.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-6V7ITU5F.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-KUOXZIH4.js";
-import {
-  getDtsFromGroups,
-  getGvLabelSuffix
-} from "./chunk-T2W4JHWJ.js";
-import {
-  getColors
-} from "./chunk-2N345NXD.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-PWYMHUXY.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import {
-  rgb
-} from "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// termsetting/handlers/geneVariant.ts
-var colorScale = getColors(5);
-function getHandler(self) {
-  return {
-    getPillName(d) {
-      let name = d.name;
-      if (!name) {
-        if (d.genes) name = d.genes.map((g) => g.gene).join(", ");
-        else if (d.chr) name = `${d.chr}:${d.start}-${d.stop}`;
-        else name = d.id || "geneVariant";
-      }
-      return getPillNameDefault(self, { name });
-    },
-    getPillStatus() {
-      let text;
-      const q = self.q;
-      if (q.type == "predefined-groupset") {
-        const groupsetting = self.term.groupsetting;
-        if (!groupsetting?.lst?.length) throw "no predefined groupsets found";
-        const groupset = groupsetting.lst[q.predefined_groupset_idx];
-        text = groupset.name;
-      } else if (q.type == "custom-groupset") {
-        const n = q.customset.groups.length;
-        text = `Divided into ${n} groups`;
-      } else {
-        text = "any variant class";
-      }
-      text += getGvLabelSuffix(q, self.term);
-      return { text };
-    },
-    async showEditMenu(div) {
-      await makeEditMenu(self, div);
-    }
-  };
-}
-async function makeEditMenu(self, _div) {
-  delete self.groups;
-  const div = _div.append("div").style("margin", "10px");
-  div.append("div").style("font-size", "1.2rem").text(self.term.name);
-  const optsDiv = div.append("div").style("margin-top", "10px").style("margin-bottom", "1px");
-  const groupsDiv = div.append("div").style("display", "none").style("margin", "10px").style("vertical-align", "top");
-  optsDiv.append("div").style("font-weight", "bold").text("Group samples");
-  const q = self.q;
-  const isGroupset = q.type == "predefined-groupset" || q.type == "custom-groupset";
-  make_radios({
-    holder: optsDiv,
-    options: [
-      { label: "No sample grouping", value: "noGroup", checked: !isGroupset },
-      { label: "Assign samples to groups", value: "group", checked: isGroupset }
-    ],
-    callback: async (v) => {
-      if (v == "group") {
-        if (q.type == "values") Object.assign(q, { type: "custom-groupset", customset: { groups: [] } });
-        await makeGroupUI(self, groupsDiv);
-      } else {
-        clearGroupset(self);
-        groupsDiv.style("display", "none");
-      }
-    }
-  });
-  if (isGroupset) await makeGroupUI(self, groupsDiv);
-  if (self.usecase?.detail && ["term", "term0", "term2"].includes(self.usecase.detail) || self.opts.geneVariantEditMenuOnlyGrp) {
-    optsDiv.style("display", "none");
-    groupsDiv.style("margin", "0px");
-  }
-  div.append("div").style("margin-top", "25px").append("button").attr("data-testid", "sjpp-ts-gv-editui-applyBtn").text("Apply").on("click", () => {
-    const q2 = self.q;
-    if (q2.type == "predefined-groupset" || q2.type == "custom-groupset") {
-      if (!self.groups?.length) {
-        window.alert("Samples must be assigned to at least one group.");
-        return;
-      } else {
-        const dtLst = getDtsFromGroups(self.groups);
-        Object.assign(q2, { type: "custom-groupset", customset: { groups: self.groups }, dtLst });
-        self.vocabApi.rememberGvQ?.(self.term, q2);
-      }
-    } else {
-      if (q2.type != "values") throw `q.type must be 'values'`;
-    }
-    self.api.runCallback();
-  });
-}
-async function makeGroupUI(self, div) {
-  div.style("display", "block");
-  div.selectAll("*").remove();
-  div.append("div").style("margin", "15px 0px").text(
-    "Group samples by mutation status. Samples are assigned to first possible group. Only tested samples are considered."
-  );
-  const filterTableDiv = div.append("div");
-  const addNewGroupBtnHolder = div.append("div");
-  const q = self.q;
-  if (q.type != "predefined-groupset" && q.type != "custom-groupset") throw "unexpected q.type";
-  if (!self.groups) {
-    let groupset;
-    if (q.type == "predefined-groupset") {
-      const groupsetting = self.term.groupsetting;
-      if (!groupsetting.lst?.length) throw "no predefined groupsets found";
-      await fillGroupsetGroups(self.term, q.predefined_groupset_idx, self.vocabApi, q.origins);
-      groupset = groupsetting.lst[q.predefined_groupset_idx];
-    } else {
-      groupset = q.customset;
-    }
-    if (!groupset) throw "groupset is missing";
-    if (!Array.isArray(groupset.groups)) throw "groupset.groups is not array";
-    self.groups = structuredClone(groupset.groups);
-  }
-  const dtTerms = structuredClone(self.term.childTerms);
-  for (const dtTerm of dtTerms) {
-    await getDtTermValues(dtTerm, self.filter, self.vocabApi, { withMnames: true });
-  }
-  const vocabApi = vocabInit({ vocab: { terms: dtTerms } });
-  vocabApi.termdbConfig = {
-    queries: self.vocabApi.termdbConfig.queries,
-    assayAvailability: self.vocabApi.termdbConfig.assayAvailability
-  };
-  vocabApi.vocab.genome = self.vocabApi.vocab?.genome;
-  const filterPrompt = await filterPromptInit({
-    holder: addNewGroupBtnHolder,
-    vocabApi,
-    emptyLabel: "Add group",
-    header_mode: "hide_search",
-    callback: (f) => {
-      const filter2 = getNormalRoot(f);
-      addNewGroup(filter2, self.groups);
-      makeGroupUI(self, div);
-    },
-    debug: self.opts.debug
-  });
-  const filter = structuredClone(self.filter);
-  filterPrompt.main(excludeFilterByTag(filter, "cohortFilter"));
-  if (!self.groups.length) {
-    filterTableDiv.style("display", "none");
-    return;
-  }
-  filterTableDiv.style("display", "").selectAll("*").remove();
-  const tableArg = {
-    div: filterTableDiv,
-    columns: [
-      {},
-      // blank column to add delete buttons
-      {
-        label: "NAME",
-        editCallback: async (i, cell) => {
-          const newName = cell.value;
-          const index = self.groups.findIndex((group) => group.name == newName);
-          if (index != -1) {
-            alert(`Group named ${newName} already exists`);
-            makeGroupUI(self, div);
-          } else {
-            self.groups[i].name = newName;
-            makeGroupUI(self, div);
-          }
-        }
-      },
-      {
-        label: "COLOR",
-        editCallback: async (i, cell) => {
-          self.groups[i].color = cell.color;
-          makeGroupUI(self, div);
-        }
-      },
-      //{ label: '#SAMPLE' }, // will re-enable when filtered sample count can be supported for gdc
-      { label: "FILTER" }
-    ],
-    rows: [],
-    striped: false,
-    // no alternating row bg color so delete button appears more visible
-    showLines: false
-  };
-  for (const g of self.groups) {
-    tableArg.rows.push([
-      {},
-      // blank cell to add delete button
-      { value: g.name },
-      // to allow click to show <input>
-      { color: g.color },
-      // { value: 'n=' + (await self.vocabApi.getFilteredSampleCount(g.filter)) }, // will re-enable when filtered sample count can be supported for gdc
-      {}
-      // blank cell to show filter ui
-    ]);
-  }
-  renderTable(tableArg);
-  for (const [i, row] of tableArg.rows.entries()) {
-    row[0].__td.append("div").attr("class", "sja_menuoption").style("padding", "1px 6px").html("&times;").on("click", () => {
-      self.groups.splice(i, 1);
-      makeGroupUI(self, div);
-    });
-    const group = self.groups[i];
-    filterInit({
-      holder: row[3].__td,
-      vocabApi,
-      header_mode: "hide_search",
-      callback: (f) => {
-        if (!f || f.lst.length == 0) {
-          const i2 = self.groups.findIndex((g) => g.name == group.name);
-          self.groups.splice(i2, 1);
-        } else {
-          excludeGeneNameFromFilter(f);
-          group.filter = f;
-        }
-        makeGroupUI(self, div);
-      }
-    }).main(group.filter);
-  }
-}
-function addNewGroup(filter, groups, name) {
-  if (!groups) throw "groups is missing";
-  if (!name) {
-    const base = "New group";
-    name = base;
-    for (let i = 0; ; i++) {
-      name = base + (i === 0 ? "" : " " + i);
-      if (!groups.find((g) => g.name === name)) break;
-    }
-  }
-  excludeGeneNameFromFilter(filter);
-  const newGroup = {
-    name,
-    type: "filter",
-    filter,
-    color: rgb(colorScale(groups.length)).formatHex()
-  };
-  groups.push(newGroup);
-}
-function excludeGeneNameFromFilter(filter) {
-  for (const item of filter.lst) {
-    if (item.type == "tvslst") {
-      excludeGeneNameFromFilter(item);
-    } else if (item.type == "tvs") {
-      item.tvs.excludeGeneName = true;
-    } else {
-      throw "unexpected item.type";
-    }
-  }
-}
-function clearGroupset(self) {
-  self.q.type = "values";
-  delete self.q.predefined_groupset_idx;
-  delete self.q.customset;
-  delete self.q.dtLst;
-  delete self.q.origins;
-  delete self.q.originLabel;
-  self.q.hiddenValues = {};
-}
-export {
-  getHandler
-};
-//# sourceMappingURL=geneVariant-VI5DGDAB.js.map

package/dist/geneVariant-VI5DGDAB.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../termsetting/handlers/geneVariant.ts"],
-  "sourcesContent": ["import { getPillNameDefault } from '../utils.ts'\nimport { make_radios, renderTable } from '#dom'\nimport { filterInit, filterPromptInit, getNormalRoot, excludeFilterByTag } from '#filter/filter'\nimport type { TermSetting } from '../TermSetting.ts'\nimport { vocabInit } from '#termdb/vocabulary'\nimport { getDtTermValues } from '#filter/tvs.dt'\nimport { getColors } from '#shared/common.js'\nimport { getDtsFromGroups, getGvLabelSuffix } from '#shared/terms.js'\nimport { fillGroupsetGroups } from '../../tw/geneVariant'\nimport { rgb } from 'd3-color'\n\nconst colorScale = getColors(5)\n\n// self is the termsetting instance\nexport function getHandler(self: TermSetting) {\n\treturn {\n\t\tgetPillName(d: any) {\n\t\t\tlet name = d.name\n\t\t\tif (!name) {\n\t\t\t\tif (d.genes) name = d.genes.map(g => g.gene).join(', ')\n\t\t\t\telse if (d.chr) name = `${d.chr}:${d.start}-${d.stop}`\n\t\t\t\telse name = d.id || 'geneVariant'\n\t\t\t}\n\t\t\treturn getPillNameDefault(self, { name })\n\t\t},\n\n\t\tgetPillStatus() {\n\t\t\tlet text\n\t\t\tconst q = self.q as any // TODO: migrate this handler to use client/tw code\n\t\t\tif (q.type == 'predefined-groupset') {\n\t\t\t\tconst groupsetting = self.term.groupsetting\n\t\t\t\tif (!groupsetting?.lst?.length) throw 'no predefined groupsets found'\n\t\t\t\tconst groupset = groupsetting.lst[q.predefined_groupset_idx]\n\t\t\t\ttext = groupset.name\n\t\t\t} else if (q.type == 'custom-groupset') {\n\t\t\t\tconst n = q.customset.groups.length\n\t\t\t\ttext = `Divided into ${n} groups`\n\t\t\t} else {\n\t\t\t\ttext = 'any variant class'\n\t\t\t}\n\t\t\ttext += getGvLabelSuffix(q, self.term)\n\t\t\treturn { text }\n\t\t},\n\n\t\tasync showEditMenu(div: Element) {\n\t\t\tawait makeEditMenu(self, div)\n\t\t}\n\t}\n}\n\nasync function makeEditMenu(self: TermSetting, _div: any) {\n\t/* TODO: instead of directly modifying self.q here, should create a separate property on the handler to store pending user\n\tconfigurations (similar to numeric continuous/discrete switching)\n\tconst handler = self.handlerByType.geneVariant */\n\t/* groups[] is scratch state of this menu, held only so that edits survive the re-render\n\tthat each change to it triggers, see makeGroupUI(). it must not outlive the menu: the\n\ttermsetting instance is reused across tws (see main() in TermSettingApi.ts, and the pill\n\tshared by every matrix row in matrix.interactivity.js), and nothing on a cached groups[]\n\tsays which tw it was built for. this runs once per opening of the menu, while every\n\tmakeGroupUI() call descends from it */\n\tdelete self.groups\n\tconst div = _div.append('div').style('margin', '10px')\n\tdiv.append('div').style('font-size', '1.2rem').text(self.term.name)\n\tconst optsDiv = div.append('div').style('margin-top', '10px').style('margin-bottom', '1px')\n\tconst groupsDiv = div.append('div').style('display', 'none').style('margin', '10px').style('vertical-align', 'top')\n\t// radio buttons for whether or not to group samples\n\toptsDiv.append('div').style('font-weight', 'bold').text('Group samples')\n\tconst q = self.q as any // TODO: migrate this handler to use client/tw code\n\tconst isGroupset = q.type == 'predefined-groupset' || q.type == 'custom-groupset'\n\tmake_radios({\n\t\tholder: optsDiv,\n\t\toptions: [\n\t\t\t{ label: 'No sample grouping', value: 'noGroup', checked: !isGroupset },\n\t\t\t{ label: 'Assign samples to groups', value: 'group', checked: isGroupset }\n\t\t],\n\t\tcallback: async v => {\n\t\t\tif (v == 'group') {\n\t\t\t\tif (q.type == 'values') Object.assign(q, { type: 'custom-groupset', customset: { groups: [] } })\n\t\t\t\tawait makeGroupUI(self, groupsDiv)\n\t\t\t} else {\n\t\t\t\tclearGroupset(self)\n\t\t\t\tgroupsDiv.style('display', 'none')\n\t\t\t}\n\t\t}\n\t})\n\tif (isGroupset) await makeGroupUI(self, groupsDiv)\n\n\tif (\n\t\t(self.usecase?.detail && ['term', 'term0', 'term2'].includes(self.usecase.detail)) ||\n\t\tself.opts.geneVariantEditMenuOnlyGrp\n\t) {\n\t\t// only groupsetting is allowed\n\t\t// hide option for turning off groupsetting\n\t\toptsDiv.style('display', 'none')\n\t\tgroupsDiv.style('margin', '0px')\n\t}\n\n\t// apply button\n\tdiv\n\t\t.append('div')\n\t\t.style('margin-top', '25px')\n\t\t.append('button')\n\t\t.attr('data-testid', 'sjpp-ts-gv-editui-applyBtn')\n\t\t.text('Apply')\n\t\t.on('click', () => {\n\t\t\tconst q = self.q as any // TODO: migrate this handler to use client/tw code\n\t\t\tif (q.type == 'predefined-groupset' || q.type == 'custom-groupset') {\n\t\t\t\t// groupsetting\n\t\t\t\tif (!self.groups?.length) {\n\t\t\t\t\t// no groups created\n\t\t\t\t\twindow.alert('Samples must be assigned to at least one group.')\n\t\t\t\t\treturn\n\t\t\t\t} else {\n\t\t\t\t\t// groups created, assign to custom groupset\n\t\t\t\t\tconst dtLst = getDtsFromGroups(self.groups)\n\t\t\t\t\tObject.assign(q, { type: 'custom-groupset', customset: { groups: self.groups }, dtLst })\n\t\t\t\t\t/* remember this grouping, so that a term built later for the same gene can offer\n\t\t\t\t\tit back, e.g. the BCR-ABL1 fusion grouping of a barchart overlay when the same\n\t\t\t\t\tgene is picked as the overlay of a survival plot. Only the mass store tracks\n\t\t\t\t\tthese, see rememberGvQ() in client/termdb/Vocab.js */\n\t\t\t\t\tself.vocabApi.rememberGvQ?.(self.term, q)\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\t// no groupsetting\n\t\t\t\tif (q.type != 'values') throw `q.type must be 'values'`\n\t\t\t}\n\t\t\tself.api.runCallback()\n\t\t})\n}\n\n// make UI for grouping variants\nasync function makeGroupUI(self: TermSetting, div) {\n\tdiv.style('display', 'block')\n\tdiv.selectAll('*').remove()\n\n\t// message\n\tdiv\n\t\t.append('div')\n\t\t.style('margin', '15px 0px')\n\t\t.text(\n\t\t\t'Group samples by mutation status. Samples are assigned to first possible group. Only tested samples are considered.'\n\t\t)\n\n\t// filter table\n\tconst filterTableDiv = div.append('div')\n\t// add new group button\n\tconst addNewGroupBtnHolder = div.append('div')\n\n\tconst q = self.q as any // TODO: migrate this handler to use client/tw code\n\t// get groups\n\tif (q.type != 'predefined-groupset' && q.type != 'custom-groupset') throw 'unexpected q.type'\n\t// groups[] is built once per opening of the edit menu, which cleared it, and is\n\t// then reused across the re-renders that the edits below trigger\n\tif (!self.groups) {\n\t\tlet groupset\n\t\tif (q.type == 'predefined-groupset') {\n\t\t\tconst groupsetting = self.term.groupsetting\n\t\t\tif (!groupsetting.lst?.length) throw 'no predefined groupsets found'\n\t\t\t/* a groupset only carries groups[] once it has been selected, and this UI can be\n\t\t\topened on a q whose index was not the one the term was last filled for, so build\n\t\t\ton demand rather than assume (see listPredefinedGroupsets() in tw/geneVariant.ts) */\n\t\t\tawait fillGroupsetGroups(self.term, q.predefined_groupset_idx, self.vocabApi as any, q.origins)\n\t\t\tgroupset = groupsetting.lst[q.predefined_groupset_idx]\n\t\t} else {\n\t\t\tgroupset = q.customset\n\t\t}\n\t\tif (!groupset) throw 'groupset is missing'\n\t\tif (!Array.isArray(groupset.groups)) throw 'groupset.groups is not array'\n\t\tself.groups = structuredClone(groupset.groups)\n\t}\n\n\t// fill values of child dt terms with mutation classes of gene in dataset.\n\t// filled into copies rather than self.term.childTerms[], because each of those\n\t// is shared by reference with the tvs of every groupset, and the mname tally\n\t// requested here would then be serialized once per tvs into the saved term\n\tconst dtTerms = structuredClone(self.term.childTerms)\n\tfor (const dtTerm of dtTerms) {\n\t\tawait getDtTermValues(dtTerm, self.filter, self.vocabApi, { withMnames: true })\n\t}\n\n\t// build frontend vocab using child dt terms. it is the only source of values and\n\t// mnames for the tvs of this UI, since a frontend vocab cannot query the db\n\t// (see getDtTermValues() in filter/tvs.dt.js)\n\tconst vocabApi: any = vocabInit({ vocab: { terms: dtTerms } })\n\t// need termdbConfig.queries for cnv tvs (see getDtCnvType() in filter/tvs.js and\n\t// fillMenu() in filter/tvs.dtcnv.continuous.js), and .assayAvailability so that a tvs\n\t// over an origin-split dt offers its origin selector here (see getTvsByOrigin() in\n\t// filter/tvs.dt.js) -- this menu is where mutation types of differing origins are\n\t// combined, so it is the one place that selector matters most\n\t// not passing complete termdbConfig as presence of .allowedTermTypes will\n\t// trigger term type toggles (see init() in termdb/TermTypeSearch.ts)\n\tvocabApi.termdbConfig = {\n\t\tqueries: self.vocabApi.termdbConfig.queries,\n\t\tassayAvailability: self.vocabApi.termdbConfig.assayAvailability\n\t}\n\t// genome is needed to look up the isoform models of a gene, to chart the breakpoints\n\t// of a sv/fusion over (see fillMenu() in filter/tvs.dt.js)\n\tvocabApi.vocab.genome = self.vocabApi.vocab?.genome\n\n\t// filter prompt\n\tconst filterPrompt = await filterPromptInit({\n\t\tholder: addNewGroupBtnHolder,\n\t\tvocabApi,\n\t\temptyLabel: 'Add group',\n\t\theader_mode: 'hide_search',\n\t\tcallback: f => {\n\t\t\tconst filter = getNormalRoot(f)\n\t\t\taddNewGroup(filter, self.groups)\n\t\t\tmakeGroupUI(self, div)\n\t\t},\n\t\tdebug: self.opts.debug\n\t})\n\n\t// filterPrompt.main() always empties the filterUiRoot data\n\tconst filter = structuredClone(self.filter)\n\tfilterPrompt.main(excludeFilterByTag(filter, 'cohortFilter')) // provide mass filter to limit the term tree\n\n\tif (!self.groups.length) {\n\t\t// no groups, hide table\n\t\tfilterTableDiv.style('display', 'none')\n\t\treturn\n\t}\n\n\t// clear table and populate rows\n\tfilterTableDiv.style('display', '').selectAll('*').remove()\n\tconst tableArg: any = {\n\t\tdiv: filterTableDiv,\n\t\tcolumns: [\n\t\t\t{}, // blank column to add delete buttons\n\t\t\t{\n\t\t\t\tlabel: 'NAME',\n\t\t\t\teditCallback: async (i, cell) => {\n\t\t\t\t\tconst newName = cell.value\n\t\t\t\t\tconst index = self.groups.findIndex(group => group.name == newName)\n\t\t\t\t\tif (index != -1) {\n\t\t\t\t\t\talert(`Group named ${newName} already exists`)\n\t\t\t\t\t\tmakeGroupUI(self, div)\n\t\t\t\t\t} else {\n\t\t\t\t\t\tself.groups[i].name = newName\n\t\t\t\t\t\tmakeGroupUI(self, div)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'COLOR',\n\t\t\t\teditCallback: async (i, cell) => {\n\t\t\t\t\tself.groups[i].color = cell.color\n\t\t\t\t\tmakeGroupUI(self, div)\n\t\t\t\t}\n\t\t\t},\n\t\t\t//{ label: '#SAMPLE' }, // will re-enable when filtered sample count can be supported for gdc\n\t\t\t{ label: 'FILTER' }\n\t\t],\n\t\trows: [],\n\t\tstriped: false, // no alternating row bg color so delete button appears more visible\n\t\tshowLines: false\n\t}\n\n\tfor (const g of 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'hide_search',\n\t\t\tcallback: f => {\n\t\t\t\tif (!f || f.lst.length == 0) {\n\t\t\t\t\t// blank filter (user removed last tvs from this filter), delete this element from groups[]\n\t\t\t\t\tconst i = self.groups.findIndex(g => g.name == group.name)\n\t\t\t\t\tself.groups.splice(i, 1)\n\t\t\t\t} else {\n\t\t\t\t\t// update filter\n\t\t\t\t\texcludeGeneNameFromFilter(f) // no need to show gene name in filter pill\n\t\t\t\t\tgroup.filter = f\n\t\t\t\t}\n\t\t\t\tmakeGroupUI(self, div)\n\t\t\t}\n\t\t}).main(group.filter)\n\t}\n}\n\nfunction addNewGroup(filter, groups, name?: string) {\n\tif (!groups) throw 'groups is missing'\n\tif (!name) {\n\t\tconst base = 'New group'\n\t\tname = base\n\t\tfor (let i = 0; ; i++) {\n\t\t\tname = base + (i === 0 ? '' : ' ' + i)\n\t\t\tif (!groups.find(g => g.name === name)) break\n\t\t}\n\t}\n\texcludeGeneNameFromFilter(filter) // no need to show gene name in filter pill\n\tconst newGroup = {\n\t\tname,\n\t\ttype: 'filter',\n\t\tfilter,\n\t\tcolor: rgb(colorScale(groups.length)).formatHex()\n\t}\n\tgroups.push(newGroup)\n}\n\nfunction excludeGeneNameFromFilter(filter) {\n\tfor (const item of filter.lst) {\n\t\tif (item.type == 'tvslst') {\n\t\t\texcludeGeneNameFromFilter(item)\n\t\t} else if (item.type == 'tvs') {\n\t\t\titem.tvs.excludeGeneName = true\n\t\t} else {\n\t\t\tthrow 'unexpected item.type'\n\t\t}\n\t}\n}\n\nfunction clearGroupset(self) {\n\tself.q.type = 'values'\n\tdelete self.q.predefined_groupset_idx\n\tdelete self.q.customset\n\t// dtLst limits the dts queried for the term and is only meaningful for a\n\t// groupset; leaving it behind would silently restrict an ungrouped term to\n\t// the dts of the groupset that was just cleared (see getDtsToQuery() in\n\t// server/src/mds3.init.js)\n\tdelete self.q.dtLst\n\t// the seed a predefined groupset stamps onto its tvs (see OriginSeedQ in #types). an\n\t// ungrouped term has no tvs and queries every origin, so a seed left behind is dead\n\t// state that would come back into effect when a groupset is selected again\n\tdelete self.q.origins\n\tdelete self.q.originLabel\n\t// hiddenValues of a groupset are keyed by group name, which is meaningless\n\t// once the term is back to mutation classes. reset rather than delete, as\n\t// consumers may read it without a guard\n\tself.q.hiddenValues = {}\n}\n"],
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