@sjcrh/proteinpaint-client 2.193.0 → 2.195.0

package/dist/GB-MUPI6RL5.js

@@ -1,1151 +0,0 @@
-import {
-  PlotBase,
-  addGeneSearchbox,
-  appInit,
-  filterInit,
-  filterJoin,
-  first_genetrack_tolist,
-  getNormalRoot,
-  make_one_checkbox,
-  renderTable,
-  sayerror
-} from "./chunk-L7VDSIM7.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-UXDVUCXU.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import {
-  Tabs
-} from "./chunk-HBW42TDT.js";
-import "./chunk-LQJMCE7G.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-KM4JBR26.js";
-import "./chunk-COYULNJF.js";
-import {
-  dofetch3
-} from "./chunk-6G4YOMWW.js";
-import "./chunk-7IYJZZQI.js";
-import {
-  getCompInit
-} from "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-I73KUUYG.js";
-import "./chunk-IVXCWCKS.js";
-import "./chunk-7KRS7L4U.js";
-import "./chunk-BKPDYW5T.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-TJYRBEBK.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-SOTB4FRE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-
-// plots/gb/model/Model.ts
-var Model = class {
-  constructor(state, app) {
-    this.state = state;
-    this.app = app;
-  }
-  async preComputeData() {
-    if (!this.state.config.geneSearchResult || !this.state.config.snvindel?.shown || !this.state.config.snvindel?.details)
-      return;
-    const body = {
-      genome: this.app.opts.state.vocab.genome,
-      dslabel: this.app.opts.state.vocab.dslabel,
-      for: "mds3variantData",
-      chr: this.state.config.geneSearchResult.chr,
-      start: this.state.config.geneSearchResult.start,
-      stop: this.state.config.geneSearchResult.stop,
-      details: this.state.config.snvindel.details,
-      filter: this.state.filter,
-      filter0: this.state.filter0,
-      variantFilter: this.state.config.variantFilter?.filter
-    };
-    const data = await dofetch3("termdb", { body });
-    if (data.error) throw data.error;
-    return data;
-  }
-};
-
-// plots/gb/interactions/Interactions.ts
-var Interactions = class {
-  constructor(app, dom, id) {
-    // using arrow function to bind "this" to the Interactions class
-    // otherwise "this" can refer to the Block class
-    this.onCoordinateChange = (rglst) => {
-      this.app.dispatch({
-        type: "plot_edit",
-        id: this.id,
-        config: { geneSearchResult: { chr: rglst[0].chr, start: rglst[0].start, stop: rglst[0].stop } }
-      });
-    };
-    this.onGeneSearch = (result, blockIsProteinMode) => {
-      this.app.dispatch({
-        type: "plot_edit",
-        id: this.id,
-        config: {
-          geneSearchResult: result,
-          blockIsProteinMode
-        }
-      });
-    };
-    this.maySaveTrackUpdatesToState = (blockInstance) => {
-      if (!blockInstance) return;
-      const state = this.getState(this.app.getState());
-      const config = structuredClone(state.config);
-      config.subMds3Tks = [];
-      for (const t of blockInstance.tklst) {
-        if (t.type == "mds3" && t.filterObj) {
-          const mclassHiddenValues = t.legend?.mclass?.hiddenvalues;
-          if (!t.subtk) {
-            if (mclassHiddenValues) {
-              config.mclassHiddenValues = [...mclassHiddenValues];
-            }
-            continue;
-          } else {
-            const subtk = { filterObj: t.filterObj };
-            if (mclassHiddenValues) {
-              subtk.mclassHiddenValues = [...mclassHiddenValues];
-            }
-            config.subMds3Tks.push(subtk);
-          }
-        }
-      }
-      let facetActiveTracksChanged = false;
-      if (config.trackLst?.activeTracks && config.trackLst.facets) {
-        const facetTrackNames = /* @__PURE__ */ new Set();
-        for (const f of config.trackLst.facets) {
-          for (const t of f.tracks) facetTrackNames.add(t.name);
-        }
-        const newLst = config.trackLst.activeTracks.filter((n) => blockInstance.tklst.find((i) => i.name == n));
-        for (const t of blockInstance.tklst) {
-          if (t.name && facetTrackNames.has(t.name) && !newLst.includes(t.name)) {
-            newLst.push(t.name);
-          }
-        }
-        if (newLst.length != config.trackLst.activeTracks.length || newLst.some((n) => !config.trackLst.activeTracks.includes(n))) {
-          facetActiveTracksChanged = true;
-        }
-        config.trackLst.activeTracks = newLst;
-      }
-      if (facetActiveTracksChanged) {
-        this.app.dispatch({
-          type: "plot_edit",
-          id: this.id,
-          config
-        });
-      } else {
-        this.app.save({
-          type: "plot_edit",
-          id: this.id,
-          config
-        });
-      }
-    };
-    this.launchFacet = (config) => {
-      this.app.dispatch({
-        type: "plot_edit",
-        id: this.id,
-        config
-      });
-    };
-    this.launchVariantTrack = (toDisplay) => {
-      this.app.dispatch({
-        type: "plot_edit",
-        id: this.id,
-        config: { snvindel: { shown: toDisplay } }
-      });
-    };
-    this.launchLdTrack = (tracks) => {
-      this.app.dispatch({
-        type: "plot_edit",
-        id: this.id,
-        config: { ld: { tracks } }
-      });
-    };
-    this.launchGroupsFilter = (groups) => {
-      this.app.dispatch({
-        type: "plot_edit",
-        id: this.id,
-        config: { snvindel: { details: { groups } } }
-      });
-    };
-    this.launchSnvIndelDetails = (details) => {
-      this.app.dispatch({
-        type: "plot_edit",
-        id: this.id,
-        config: { snvindel: { details } }
-      });
-    };
-    this.launchVariantFilter = (filter) => {
-      this.app.dispatch({
-        type: "plot_edit",
-        id: this.id,
-        config: { variantFilter: { filter } }
-      });
-    };
-    this.app = app;
-    this.dom = dom;
-    this.id = id;
-  }
-  // copied from "GB.ts", should try to inherit it instead
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) throw `No plot with id='${this.id}' found`;
-    return {
-      config,
-      filter: getNormalRoot(appState.termfilter.filter),
-      vocab: appState.vocab
-    };
-  }
-};
-function mayUpdateGroupTestMethodsIdx(state, d) {
-  if (d.groups.length != 2) return;
-  const [g1, g2] = d.groups;
-  if (g1.type == "info" || g2.type == "info" || g1.type == "population" && g2.type == "population") {
-    const i = state.config.snvindel.details.groupTestMethods.findIndex((i2) => i2.name == "Allele frequency difference");
-    if (i == -1) throw "Allele frequency difference not found";
-    d.groupTestMethodsIdx = i;
-  } else {
-  }
-}
-
-// plots/gb/view/TabsRenderer.ts
-var TabsRenderer = class {
-  constructor(state, dom, opts, interactions) {
-    this.state = state;
-    this.dom = dom;
-    this.opts = opts;
-    this.interactions = interactions;
-    this.filterUI = {};
-  }
-  async main() {
-    let previousActiveTabLabel = null;
-    const existingActiveButton = this.dom.tabsDiv.select("button.sjpp-active");
-    if (!existingActiveButton.empty()) {
-      previousActiveTabLabel = existingActiveButton.datum()?.label ?? null;
-    }
-    this.dom.tabsDiv.selectAll("*").remove();
-    this.getTabs();
-    if (previousActiveTabLabel) {
-      const matchingTab = this.tabs.find((tab) => tab.label === previousActiveTabLabel);
-      if (matchingTab) {
-        this.tabs.forEach((tab) => tab.active = false);
-        matchingTab.active = true;
-      }
-    }
-    await this.mayRenderTabs();
-  }
-  getTabs() {
-    const tabs = [];
-    if (this.state.config.trackLst?.facets) {
-      const activeTracks = this.state.config.trackLst.activeTracks;
-      for (const facet of this.state.config.trackLst.facets) {
-        const shown = facet.tracks.some((t) => activeTracks.includes(t.name));
-        tabs.push({ label: facet.name || "Facet Table", active: shown });
-      }
-    }
-    if (this.state.config.snvindel) {
-      const shown = this.state.config.snvindel.shown;
-      if (this.state.config.snvindel.details) {
-        tabs.push({ label: "Variant Values", active: shown });
-        if (this.state.config.variantFilter) {
-          tabs.push({ label: "Variant Filter" });
-        }
-      } else {
-        if (this.state.config.trackLst) {
-          tabs.push({ label: "Variants", active: shown });
-        } else {
-        }
-      }
-    }
-    if (this.state.config.ld) {
-      const shown = this.state.config.ld.tracks.some((t) => t.shown);
-      tabs.push({ label: "LD Map", active: shown });
-    }
-    this.tabs = tabs;
-  }
-  async mayRenderTabs() {
-    const tabs = this.tabs;
-    if (!tabs?.length) return;
-    const toggles = new Tabs({
-      holder: this.dom.tabsDiv.append("div").style("border-bottom", "solid 1px #ccc").style("padding-bottom", "20px"),
-      tabs,
-      hideOnDblClick: true
-    });
-    toggles.main();
-    let tabsIdx = 0;
-    if (this.state.config.trackLst?.facets) {
-      for (const facet of this.state.config.trackLst.facets) {
-        const div = tabs[tabsIdx++].contentHolder.append("div");
-        this.renderFacetTable(facet, div);
-      }
-    }
-    if (this.state.config.snvindel) {
-      if (this.state.config.snvindel.details) {
-        const div = tabs[tabsIdx++].contentHolder.append("div");
-        this.dom.group1div = div.append("div").attr("class", "sjpp-gb-group1");
-        this.dom.group2div = div.append("div").attr("class", "sjpp-gb-group2");
-        this.dom.testMethodDiv = div.append("div").style("margin-top", "3px");
-        await this.mayRenderGroups();
-        if (this.state.config.variantFilter) {
-          this.dom.variantFilterHolder = tabs[tabsIdx++].contentHolder.append("div").style("white-space", "normal");
-          this.mayRenderVariantFilter();
-        }
-      } else {
-        if (this.state.config.trackLst) {
-          const div = tabs[tabsIdx++].contentHolder.append("div");
-          make_one_checkbox({
-            labeltext: "Show variant track",
-            checked: this.state.config.snvindel.shown,
-            holder: div,
-            callback: this.interactions.launchVariantTrack
-          });
-        }
-      }
-    }
-    if (this.state.config.ld) {
-      const tracks = structuredClone(this.state.config.ld.tracks);
-      const div = tabs[tabsIdx++].contentHolder.append("div");
-      div.append("div").text("Show/hide linkage disequilibrium map from an ancestry:").style("opacity", 0.5);
-      for (const [i, t] of tracks.entries()) {
-        make_one_checkbox({
-          labeltext: t.name,
-          checked: t.shown,
-          holder: div,
-          callback: (checked) => {
-            tracks[i].shown = checked;
-            this.interactions.launchLdTrack(tracks);
-          }
-        });
-      }
-    }
-  }
-  renderFacetTable(facet, div) {
-    const assayset = /* @__PURE__ */ new Set(), sampleset = /* @__PURE__ */ new Set();
-    for (const t of facet.tracks) {
-      if (t.assay) assayset.add(t.assay);
-      if (t.sample) sampleset.add(t.sample);
-    }
-    const sampleLst = [...sampleset];
-    const assayLst = [...assayset];
-    const columns = [{ label: "Sample" }];
-    for (const assay of assayLst) {
-      columns.push({
-        label: assay,
-        fillCell: (td, si) => {
-          const tklst = facet.tracks.filter((i) => i.assay == assay && i.sample == sampleLst[si]);
-          if (tklst.length == 0) return;
-          const shownCount = tklst.filter((tk) => this.state.config.trackLst.activeTracks.includes(tk.name)).length;
-          const displayText = shownCount ? `${shownCount}/${tklst.length}` : `${tklst.length}`;
-          td.append("div").attr("class", "sja_clbtext").style("text-align", "center").text(displayText).on("click", (event) => {
-            this.clickFacetCell(event, tklst);
-          });
-        }
-      });
-    }
-    const rows = [];
-    for (const sample of sampleLst) {
-      const row = [{ value: sample }];
-      for (let i = 0; i < assayLst.length; i++) {
-        row.push({});
-      }
-      rows.push(row);
-    }
-    renderTable({
-      columns,
-      rows,
-      div
-    });
-  }
-  clickFacetCell(event, tklst) {
-    this.dom.tip.clear().showunder(event.target);
-    const activeTracks = this.state.config.trackLst.activeTracks;
-    const table = this.dom.tip.d.append("table").style("margin", "5px 5px 5px 2px");
-    for (const tk of tklst) {
-      const tr = table.append("tr");
-      const td1 = tr.append("td").style("font-size", ".8em").text(activeTracks.includes(tk.name) ? "SHOWN" : "");
-      tr.append("td").attr("class", "sja_menuoption").text(tk.name).on("click", () => {
-        this.dom.tip.hide();
-        let newActiveTracks, newRemoveTracks;
-        if (activeTracks.includes(tk.name)) {
-          td1.text("");
-          newActiveTracks = structuredClone(activeTracks).filter((n) => n != tk.name);
-          newRemoveTracks = [tk.name];
-        } else {
-          td1.text("SHOWN");
-          newActiveTracks = structuredClone(activeTracks);
-          newActiveTracks.push(tk.name);
-        }
-        const config = {
-          trackLst: {
-            activeTracks: newActiveTracks,
-            removeTracks: newRemoveTracks
-          }
-        };
-        this.interactions.launchFacet(config);
-      });
-    }
-  }
-  async mayRenderGroups() {
-    const groups = this.state.config.snvindel.details.groups;
-    if (!groups) return;
-    await this.render1group(0);
-    await this.render1group(1);
-    if (this.state.config.snvindel.details.groupTestMethods) {
-      this.renderTestMethod();
-    }
-  }
-  mayRenderVariantFilter() {
-    if (this.state.config.variantFilter) {
-      this.dom.variantFilterHolder.selectAll("*").remove();
-      filterInit({
-        joinWith: this.state.config.variantFilter.opts.joinWith,
-        emptyLabel: "+Add Filter",
-        holder: this.dom.variantFilterHolder,
-        vocab: { terms: this.state.config.variantFilter.terms },
-        callback: (filter) => this.interactions.launchVariantFilter(filter)
-      }).main(this.state.config.variantFilter.filter);
-    }
-  }
-  /*
-  	render ui contents of one group, both arguments are provided to be convenient for ad-hoc update
-  
-  	groupIdx: array index of self.state.config.snvindel.details.groups[]
-  		determines which <div> to render to at self.dom.group1/2div
-  	group{}: element of same array
-  	*/
-  async render1group(groupIdx) {
-    const group = this.state.config.snvindel.details.groups[groupIdx];
-    const div = groupIdx == 0 ? this.dom.group1div : this.dom.group2div;
-    let canReuse = false;
-    if (group?.type == "filter" && this.filterUI[groupIdx]) {
-      canReuse = true;
-    } else {
-      delete this.filterUI[groupIdx];
-      div.selectAll("*").remove();
-    }
-    if (!group) {
-      this.makePrompt2addNewGroup(groupIdx, div);
-      return;
-    }
-    if (!canReuse) this.makeGroupHeaderButton(groupIdx, div);
-    if (group.type == "info") return this.render1group_info(groupIdx, group, div);
-    if (group.type == "population") return this.render1group_population(groupIdx, group, div);
-    if (group.type == "filter") return await this.render1group_filter(groupIdx, group, div);
-    throw "render1group: unknown group type";
-  }
-  makePrompt2addNewGroup(groupIdx, div) {
-    div.append("div").style("display", "inline-block").text("Create Group 2").attr("class", "sja_clbtext").style("margin", "10px").on("click", (event) => {
-      this.dom.tip.showunder(event.target).clear();
-      this.launchMenu_createGroup(groupIdx, this.dom.tip.d);
-    });
-  }
-  makeGroupHeaderButton(groupIdx, div) {
-    div.append("div").style("display", "inline-block").text("Group " + (groupIdx + 1)).attr("class", "sja_menuoption").style("margin-right", "10px").on("click", (event) => {
-      this.dom.tip.showunder(event.target).clear();
-      if (groupIdx == 0) {
-        this.launchMenu_createGroup(0, this.dom.tip.d);
-        return;
-      }
-      this.dom.tip.d.append("div").text("Change").attr("class", "sja_menuoption").style("border-radius", "0px").on("click", () => {
-        this.launchMenu_createGroup(1, this.dom.tip.clear().d);
-      });
-      this.dom.tip.d.append("div").text("Delete").attr("class", "sja_menuoption").style("border-radius", "0px").on("click", () => {
-        this.dom.tip.hide();
-        const groups = [this.state.config.snvindel.details.groups[0]];
-        this.interactions.launchGroupsFilter(groups);
-      });
-    });
-  }
-  render1group_info(groupIdx, group, div) {
-    let name = group.infoKey;
-    if (this.state.config.variantFilter?.terms) {
-      const f = this.state.config.variantFilter.terms.find((i) => i.id == group.infoKey);
-      if (f && f.name) name = f.name;
-    }
-    div.append("span").text(name).attr("class", "sja_menuoption").on("click", (event) => {
-      if (this.state.config.variantFilter.terms.length <= 1) {
-        return;
-      }
-      this.dom.tip.clear().showunder(event.target).d.append("div").text("Replace with:").style("margin", "10px").style("font-size", ".8em");
-      for (const f of this.state.config.variantFilter.terms) {
-        if (f.type != "integer" && f.type != "float") continue;
-        if (f.id == group.infoKey) continue;
-        this.dom.tip.d.append("div").text(f.name).attr("class", "sja_menuoption").on("click", () => {
-          this.dom.tip.hide();
-          const groups = structuredClone(this.state.config.snvindel.details.groups);
-          groups[groupIdx].infoKey = f.id;
-          groups[groupIdx].type = "info";
-          this.interactions.launchGroupsFilter(groups);
-        });
-      }
-    });
-    div.append("span").text("PER-VARIANT NUMERICAL VALUES").style("font-size", ".7em").style("opacity", 0.6).style("margin-left", "10px");
-  }
-  render1group_population(groupIdx, group, div) {
-    div.append("span").text(group.label).attr("class", "sja_menuoption").on("click", (event) => {
-      if (this.state.config.snvindel.populations.length <= 1) {
-        return;
-      }
-      this.dom.tip.clear().showunder(event.target).d.append("div").text("Replace with:").style("margin", "10px").style("font-size", ".8em");
-      for (const p of this.state.config.snvindel.populations) {
-        if (p.key == group.key) continue;
-        this.dom.tip.d.append("div").text(p.label).attr("class", "sja_menuoption").on("click", () => {
-          this.dom.tip.hide();
-          const groups = structuredClone(this.state.config.snvindel.details.groups);
-          groups[groupIdx] = structuredClone(p);
-          groups[groupIdx].type = "population";
-          this.interactions.launchGroupsFilter(groups);
-        });
-      }
-    });
-    div.append("span").text(`POPULATION${group.adjust_race ? ", RACE ADJUSTED" : ""}`).style("font-size", ".7em").style("margin-left", "10px").style("opacity", 0.6);
-    if (this.state.config.snvindel.details.groups[groupIdx == 1 ? 0 : 1]?.type == "filter") {
-      div.append("span").attr("class", "sja_clbtext").attr("id", "sjpp-gb-pop2avg").style("display", "none").style("margin-left", "20px").text(`Group ${groupIdx == 1 ? 1 : 2} average admixture:`).on("click", (event) => {
-        this.dom.tip.clear().showunder(event.target).d.append("div").style("margin", "10px").style("width", "500px").html(`These are average admixture coefficients based on current Group ${groupIdx == 1 ? 1 : 2} samples.
-					They are used to adjust variant allele counts of matching ancestries from <span class=sja_menuoption style="padding:2px 5px">${group.label}</span>,
-					so that the adjusted allele counts can be compared against Group ${groupIdx == 1 ? 1 : 2} allele counts.
-					This allows to account for ancestry composition difference between the two groups.
-					`);
-      }).append("span").attr("id", "sjpp-gb-pop2avg-values");
-    }
-  }
-  async render1group_filter(groupIdx, group, div) {
-    if (!this.filterUI[groupIdx]) {
-      this.filterUI[groupIdx] = await filterInit({
-        holder: div,
-        vocab: this.state.vocab,
-        emptyLabel: "Entire cohort",
-        termdbConfig: this.opts.vocabApi.termdbConfig,
-        callback: (f) => {
-          const groups = JSON.parse(JSON.stringify(this.state.config.snvindel.details.groups));
-          groups[groupIdx].filter = f;
-          this.interactions.launchGroupsFilter(groups);
-        }
-      });
-    }
-    this.filterUI[groupIdx].main(this.getJoinedFilter(group));
-    div.append("span").attr("class", "sjpp-gb-filter-count").style("display", "none").style("margin-left", "10px").style("opacity", 0.5).style("font-size", ".9em");
-  }
-  getJoinedFilter(group) {
-    const joinedFilter = structuredClone(this.state.filter || { type: "tvslst", in: true, join: "", lst: [] });
-    const gf = structuredClone(group.filter);
-    gf.tag = "filterUiRoot";
-    joinedFilter.lst.push(gf);
-    joinedFilter.join = "and";
-    return joinedFilter;
-  }
-  // show vertical toggle options: filter/population/info
-  // when any is selected, create a new group object and set to snvindel.details.groups[groupIdx]
-  launchMenu_createGroup(groupIdx, div) {
-    const opt = {
-      holder: div.append("div").style("margin", "5px"),
-      tabs: this.state.config.snvindel.details.groupTypes.map((i) => {
-        return { label: i.name };
-      }),
-      tabsPosition: "vertical",
-      linePosition: "right"
-    };
-    new Tabs(opt).main();
-    for (const [idx, groupType] of this.state.config.snvindel.details.groupTypes.entries()) {
-      const tab = opt.tabs[idx];
-      tab.contentHolder.style("margin", "10px");
-      if (groupType.type == "info") {
-        if (!this.state.config.variantFilter?.terms)
-          throw "looking for snvindel info fields but self.state.config.variantFilter.terms[] missing";
-        for (const f of this.state.config.variantFilter.terms) {
-          if (f.type != "integer" && f.type != "float") continue;
-          tab.contentHolder.append("div").text(f.name).attr("class", "sja_menuoption").on("click", () => {
-            this.dom.tip.hide();
-            const newGroup = {
-              type: "info",
-              infoKey: f.id
-            };
-            const details = this.makeNewDetail(newGroup, groupIdx);
-            mayUpdateGroupTestMethodsIdx(this.state, details);
-            this.interactions.launchSnvIndelDetails(details);
-          });
-        }
-        continue;
-      }
-      if (groupType.type == "population") {
-        if (!this.state.config.snvindel.populations) throw "state.config.snvindel.populations missing";
-        for (const p of this.state.config.snvindel.populations) {
-          tab.contentHolder.append("div").text(p.label).attr("class", "sja_menuoption").on("click", () => {
-            this.dom.tip.hide();
-            const newGroup = {
-              type: "population",
-              key: p.key,
-              label: p.label,
-              allowto_adjust_race: p.allowto_adjust_race,
-              adjust_race: p.adjust_race
-            };
-            const details = this.makeNewDetail(newGroup, groupIdx);
-            mayUpdateGroupTestMethodsIdx(this.state, details);
-            this.interactions.launchSnvIndelDetails(details);
-          });
-        }
-        continue;
-      }
-      if (groupType.type == "filter") {
-        const arg = {
-          holder: tab.contentHolder,
-          vocabApi: this.opts.vocabApi,
-          state: {
-            activeCohort: this.state.activeCohort,
-            termfilter: { filter: this.state.filter }
-          },
-          tree: {
-            click_term2select_tvs: (tvs) => {
-              this.dom.tip.hide();
-              const newGroup = {
-                type: "filter",
-                filter: {
-                  in: true,
-                  join: "",
-                  type: "tvslst",
-                  lst: [{ type: "tvs", tvs }]
-                }
-              };
-              const details = this.makeNewDetail(newGroup, groupIdx);
-              mayUpdateGroupTestMethodsIdx(this.state, details);
-              this.interactions.launchSnvIndelDetails(details);
-            }
-          }
-        };
-        appInit(arg);
-        continue;
-      }
-      throw "unknown group type";
-    }
-  }
-  makeNewDetail(newGroup, groupIdx) {
-    const newDetail = {
-      groups: JSON.parse(JSON.stringify(this.state.config.snvindel.details.groups))
-    };
-    newDetail.groups[groupIdx] = newGroup;
-    return newDetail;
-  }
-  renderTestMethod() {
-    const div = this.dom.testMethodDiv;
-    div.selectAll("*").remove();
-    const [g1, g2] = this.state.config.snvindel.details.groups;
-    if (!g2) {
-      return;
-    }
-    div.append("span").text("TEST METHOD").style("font-size", ".8em").style("opacity", 0.6);
-    if (g1.type != "filter" && g2.type != "filter") {
-      div.append("span").style("padding-left", "10px").text("Value difference").style("opacity", 0.6);
-      return;
-    }
-    const select = div.append("select").style("margin-left", "10px").on("change", () => {
-      const details = { groupTestMethodsIdx: select.property("selectedIndex") };
-      this.interactions.launchSnvIndelDetails(details);
-    });
-    for (const m of this.state.config.snvindel.details.groupTestMethods) {
-      select.append("option").text(m.name);
-    }
-    select.property("selectedIndex", this.state.config.snvindel.details.groupTestMethodsIdx);
-  }
-};
-
-// plots/gb/view/GeneSearchRenderer.ts
-var GeneSearchRenderer = class {
-  constructor(state, holder, opts, interactions) {
-    this.state = state;
-    this.holder = holder;
-    this.opts = opts;
-    this.interactions = interactions;
-  }
-  main() {
-    this.renderGeneSearch();
-  }
-  renderGeneSearch() {
-    const gbRestrictMode = this.opts.vocabApi.termdbConfig.queries.gbRestrictMode;
-    this.holder.selectAll("*").remove();
-    const row = this.holder.append("div");
-    row.append("span").html("Search");
-    const arg = {
-      tip: new Menu({ padding: "0px" }),
-      genome: this.opts.genome,
-      row,
-      callback: async () => {
-        if (result.geneSymbol && !gbRestrictMode) {
-          this.holder.select(".sjpp_gbmodebtndiv").remove();
-          const btndiv = this.holder.append("div").attr("class", "sjpp_gbmodebtndiv").style("margin-top", "10px");
-          btndiv.append("button").style("margin-right", "10px").text("Protein view of " + result.geneSymbol).on("click", async () => {
-            await this.interactions.onGeneSearch(result, true);
-          });
-          btndiv.append("button").text("Genomic view of " + result.geneSymbol).on("click", async () => {
-            await this.interactions.onGeneSearch(result, false);
-          });
-          return;
-        }
-        await this.interactions.onGeneSearch(result, gbRestrictMode == "protein");
-      }
-    };
-    switch (gbRestrictMode) {
-      case void 0:
-        break;
-      case "genomic":
-        arg.defaultCoord = this.opts.vocabApi.termdbConfig.queries.defaultCoord;
-        break;
-      case "protein":
-        arg.searchOnly = "gene";
-        break;
-      default:
-        throw "unknown gbRestrictMode";
-    }
-    const result = addGeneSearchbox(arg);
-  }
-};
-
-// plots/gb/view/View.ts
-var View = class {
-  constructor(state, blockInstance, data, dom, opts, interactions) {
-    this.state = state;
-    this.blockInstance = blockInstance;
-    this.data = data;
-    this.dom = dom;
-    this.opts = opts;
-    this.interactions = interactions;
-  }
-  async main() {
-    const tabs = new TabsRenderer(this.state, this.dom, this.opts, this.interactions);
-    await tabs.main();
-    const geneSearch = new GeneSearchRenderer(this.state, this.dom.geneSearchDiv, this.opts, this.interactions);
-    geneSearch.main();
-    if (this.state.config.geneSearchResult) {
-      this.dom.geneSearchDiv.style("display", "none");
-      const tklst = await this.generateTracks();
-      await this.launchBlockWithTracks(tklst);
-    }
-  }
-  async generateTracks() {
-    const tklst = [];
-    if (this.state.config.snvindel?.shown) {
-      if (this.data) {
-        if (this.blockInstance) {
-          this.updateCustomMds3tk();
-        } else {
-          const tk = await this.launchCustomMds3tk();
-          if (tk) {
-            tklst.push(tk);
-          }
-        }
-      } else {
-        const tk = {
-          type: "mds3",
-          dslabel: this.state.vocab.dslabel,
-          allow2selectSamples: this.opts.allow2selectSamples,
-          onClose: () => {
-            this.interactions.maySaveTrackUpdatesToState(this.blockInstance);
-          },
-          callbackOnRender: () => {
-            this.interactions.maySaveTrackUpdatesToState(this.blockInstance);
-          },
-          // for showing disco etc as ad-hoc sandbox, persistently in the mass plotDiv, rather than a menu
-          newChartHolder: this.opts.plotDiv
-        };
-        {
-          const lst = [];
-          if (this.state.filter?.lst?.length) lst.push(this.state.filter);
-          if (this.state.config.snvindel.filter) lst.push(this.state.config.snvindel.filter);
-          if (lst.length == 1) {
-            tk.filterObj = structuredClone(lst[0]);
-          } else if (lst.length > 1) {
-            tk.filterObj = filterJoin(lst);
-          }
-        }
-        if (this.state.filter0) tk.filter0 = this.state.filter0;
-        if (this.state.config.mclassHiddenValues) {
-          tk.legend = { mclass: { hiddenvalues: new Set(this.state.config.mclassHiddenValues) } };
-        }
-        tklst.push(tk);
-        if (this.state.config?.subMds3Tks) {
-          for (const subtk of this.state.config.subMds3Tks) {
-            const t2 = {
-              type: "mds3",
-              subtk: true,
-              dslabel: this.state.vocab.dslabel,
-              onClose: () => {
-                this.interactions.maySaveTrackUpdatesToState(this.blockInstance);
-              },
-              callbackOnRender: () => {
-                this.interactions.maySaveTrackUpdatesToState(this.blockInstance);
-              },
-              // for showing disco etc as ad-hoc sandbox, persistently in the mass plotDiv, rather than a menu
-              newChartHolder: this.opts.plotDiv
-            };
-            if (this.state.filter?.lst?.length) {
-              t2.filterObj = filterJoin([this.state.filter, subtk.filterObj]);
-            } else {
-              t2.filterObj = structuredClone(subtk.filterObj);
-            }
-            if (this.state.filter0) t2.filter0 = this.state.filter0;
-            if (subtk.mclassHiddenValues) {
-              t2.legend = { mclass: { hiddenvalues: new Set(subtk.mclassHiddenValues) } };
-            }
-            tklst.push(t2);
-          }
-        }
-      }
-    }
-    if (this.state.config?.trackLst?.activeTracks?.length) {
-      for (const n of this.state.config.trackLst.activeTracks) {
-        for (const f of this.state.config.trackLst.facets) {
-          for (const t of f.tracks) {
-            if (t.name == n) tklst.push(t);
-          }
-        }
-      }
-    }
-    if (this.state.config.ld?.tracks) {
-      for (const t of this.state.config.ld.tracks) {
-        if (t.shown) tklst.push(t);
-      }
-    }
-    return tklst;
-  }
-  async launchCustomMds3tk() {
-    this.mayGetSampleCounts();
-    const nm = {
-      // numeric mode object; to fill in based on snvindel.details{}
-      type: "numeric",
-      inuse: true,
-      byAttribute: "nm_axis_value"
-    };
-    furbishViewModeWithSnvindelComputeDetails(this, nm);
-    const tk = {
-      type: "mds3",
-      // despite having custom data, still provide dslabel for the mds3 tk to function as an official dataset
-      dslabel: this.state.vocab.dslabel,
-      name: "Variants",
-      custom_variants: this.data.mlst,
-      skewerModes: [nm],
-      filter0: this.state.filter0
-    };
-    return tk;
-  }
-  updateCustomMds3tk() {
-    if (!this.blockInstance) throw "blockInstance is missing";
-    this.mayGetSampleCounts();
-    const t2 = this.blockInstance.tklst.find((i) => i.type == "mds3");
-    t2.custom_variants = this.data.mlst;
-    furbishViewModeWithSnvindelComputeDetails(
-      this,
-      t2.skewer.viewModes.find((i) => i.type == "numeric")
-    );
-    t2.load();
-  }
-  mayGetSampleCounts() {
-    const data = this.data;
-    this.mayRenderSampleCount("group1", data.totalSampleCount_group1);
-    this.mayRenderSampleCount("group2", data.totalSampleCount_group2);
-    this.mayRenderPop2Avg(data.pop2average);
-  }
-  mayRenderSampleCount(group, count) {
-    if (!Number.isInteger(count)) return;
-    this.dom.tabsDiv.select(`.sjpp-gb-${group}`).select(".sjpp-gb-filter-count").style("display", "inline").text("n=" + count);
-  }
-  mayRenderPop2Avg(pop2average) {
-    if (!pop2average) return;
-    const span = this.dom.tabsDiv.select("#sjpp-gb-pop2avg");
-    const lst = [];
-    for (const k in pop2average) {
-      const value = pop2average[k];
-      if (!Number.isFinite(value)) continue;
-      lst.push(`${k}=${value.toFixed(2)}`);
-    }
-    if (lst.length) {
-      span.style("display", "inline");
-      span.select("#sjpp-gb-pop2avg-values").text(` ${lst.join(", ")}`);
-    } else {
-      span.style("display", "none");
-    }
-  }
-  /* tricky logic */
-  async launchBlockWithTracks(tklst) {
-    if (!["GDC", "MMRF"].includes(this.state?.vocab?.dslabel) && this.blockInstance) {
-      for (const tk of tklst) {
-        let tki;
-        if (tk.dslabel) {
-          tki = this.blockInstance.tklst.findIndex((i) => i.dslabel == tk.dslabel);
-        } else if (tk.name) {
-          tki = this.blockInstance.tklst.findIndex((i) => i.name == tk.name);
-        } else {
-          throw "tk missing dslabel & name";
-        }
-        if (tki == -1) {
-          const t = this.blockInstance.block_addtk_template(tk);
-          this.blockInstance.tk_load(t);
-        }
-      }
-      if (this.state.config.trackLst?.removeTracks) {
-        for (const n of this.state.config.trackLst.removeTracks) {
-          const i = this.blockInstance.tklst.findIndex((i2) => i2.name == n);
-          if (i != -1) this.blockInstance.tk_remove(i);
-        }
-      }
-      if (this.state.config.ld?.tracks) {
-        for (const t of this.state.config.ld.tracks) {
-          const i = this.blockInstance.tklst.findIndex((i2) => i2.name == t.name);
-          if (!t.shown && i != -1) this.blockInstance.tk_remove(i);
-        }
-      }
-      if (this.state.config.snvindel && !this.state.config.snvindel.shown) {
-        let found = true;
-        while (found) {
-          found = false;
-          for (const [i, tk] of this.blockInstance.tklst.entries()) {
-            if (tk.type == "mds3") {
-              this.blockInstance.tk_remove(i);
-              found = true;
-              break;
-            }
-          }
-        }
-      }
-      return;
-    }
-    this.dom.blockHolder.selectAll("*").remove();
-    const arg = {
-      holder: this.dom.blockHolder,
-      genome: this.opts.genome,
-      // genome obj
-      nobox: true,
-      tklst,
-      debugmode: this.opts.debug,
-      onAddRemoveTk: () => {
-        this.interactions.maySaveTrackUpdatesToState(this.blockInstance);
-      },
-      filter0: this.state.filter0
-    };
-    if (this.data) {
-      arg.onCoordinateChange = this.interactions.onCoordinateChange;
-    }
-    if (this.state.config.blockIsProteinMode) {
-      if (!this.state.config.geneSearchResult.geneSymbol) throw "blockIsProteinMode=true but geneSymbol missing";
-      arg.query = this.state.config.geneSearchResult.geneSymbol;
-      const _2 = await import("./block.init-7FHXQJNE.js");
-      await _2.default(arg);
-      this.blockInstance = arg.__blockInstance;
-      if (this.opts.header) this.opts.header.text(arg.query);
-      return;
-    }
-    if (!this.state.config.geneSearchResult.chr) throw "blockIsProteinMode=false but chr missing";
-    arg.chr = this.state.config.geneSearchResult.chr;
-    arg.start = this.state.config.geneSearchResult.start;
-    arg.stop = this.state.config.geneSearchResult.stop;
-    first_genetrack_tolist(this.opts.genome, arg.tklst);
-    const _ = await import("./block-TCWYUB4R.js");
-    this.blockInstance = new _.Block(arg);
-  }
-};
-function furbishViewModeWithSnvindelComputeDetails(self, viewmode) {
-  delete viewmode.tooltipPrintValue;
-  const [g1, g2] = self.state.config.snvindel.details.groups;
-  if (g1 && g2) {
-    if (g1.type == "info" || g2.type == "info") {
-      viewmode.label = "Value difference";
-      return;
-    }
-    const testMethod = self.state.config.snvindel.details.groupTestMethods[self.state.config.snvindel.details.groupTestMethodsIdx];
-    viewmode.label = testMethod.axisLabel || testMethod.name;
-    if (testMethod.name == "Allele frequency difference") {
-      viewmode.tooltipPrintValue = (m) => [{ k: "AF diff", v: m.nm_axis_value }];
-    } else if (testMethod.name == "Fisher's exact test") {
-      viewmode.tooltipPrintValue = (m) => [{ k: "p-value", v: m.p_value }];
-    }
-    return;
-  }
-  if (g1.type == "info") {
-    const f = self.state.config.variantFilter?.terms?.find((i) => i.id == g1.infoKey);
-    viewmode.label = f?.name || g1.infoKey;
-    viewmode.tooltipPrintValue = (m) => [{ k: viewmode.label, v: m.info[g1.infoKey] }];
-    return;
-  }
-  if (g1.type == "filter") {
-    viewmode.label = "Allele frequency";
-    viewmode.tooltipPrintValue = (m) => [{ k: "Allele frequency", v: m.nm_axis_value }];
-    return;
-  }
-  if (g1.type == "population") {
-    viewmode.label = "Allele frequency";
-    viewmode.tooltipPrintValue = (m) => [{ k: "Allele frequency", v: m.nm_axis_value }];
-    return;
-  }
-  throw "unknown type of the only group";
-}
-
-// plots/gb/GB.ts
-var TdbGenomeBrowser = class _TdbGenomeBrowser extends PlotBase {
-  constructor(opts, api) {
-    super(opts, api);
-    this.components = {};
-    this.type = _TdbGenomeBrowser.type;
-    this.dom = this.getDom();
-  }
-  static {
-    this.type = "genomeBrowser";
-  }
-  getDom() {
-    const holder = this.opts.holder.append("div");
-    if (this.opts.header) {
-      this.opts.header.append("div").style("opacity", 0.6).style("padding-left", "10px").style("font-size", "0.75em").text("GENOME BROWSER");
-    }
-    const loadingDiv = holder.append("div").style("display", "none").style("margin-left", "25px").text("Loading...");
-    const errDiv = holder.append("div").style("display", "none").style("margin", "10px");
-    const controlsDiv = holder.append("div").style("margin", "15px 0px 0px 25px");
-    const dom = {
-      tip: new Menu(),
-      holder,
-      loadingDiv,
-      errDiv,
-      tabsDiv: controlsDiv.append("div"),
-      geneSearchDiv: controlsDiv.append("div").style("margin", "20px 0px"),
-      blockHolder: holder.append("div")
-    };
-    return dom;
-  }
-  async init() {
-    this.interactions = new Interactions(this.app, this.dom, this.id);
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) throw `No plot with id='${this.id}' found`;
-    return {
-      config,
-      filter: getNormalRoot(appState.termfilter.filter),
-      filter0: appState.termfilter.filter0,
-      vocab: appState.vocab
-    };
-  }
-  async main() {
-    this.dom.loadingDiv.style("display", "block");
-    this.dom.errDiv.style("display", "none");
-    const state = this.getState(this.app.getState());
-    if (state.config.chartType != this.type) return;
-    const opts = this.getOpts();
-    try {
-      const model = new Model(state, this.app);
-      const data = await model.preComputeData();
-      const view = new View(state, this.blockInstance, data, this.dom, opts, this.interactions);
-      await view.main();
-      this.blockInstance = view.blockInstance;
-    } catch (e) {
-      this.dom.errDiv.style("display", "block");
-      sayerror(this.dom.errDiv, "Error: " + (e.message || e));
-      if (e.stack) console.log(e.stack);
-    }
-    this.dom.loadingDiv.style("display", "none");
-  }
-  // get options for view instance
-  getOpts() {
-    const opts = {
-      genome: this.app.opts.genome,
-      vocabApi: this.app.vocabApi,
-      debug: this.app.opts.debug,
-      plotDiv: this.opts.plotDiv,
-      header: this.opts.header,
-      allow2selectSamples: this.opts.allow2selectSamples
-    };
-    return opts;
-  }
-};
-var genomeBrowserInit = getCompInit(TdbGenomeBrowser);
-var componentInit = genomeBrowserInit;
-async function getPlotConfig(opts, app, activeCohort) {
-  try {
-    const c = await getDefaultConfig(app.vocabApi, opts, activeCohort);
-    return c;
-  } catch (e) {
-    throw `${e} [genomeBrowser getPlotConfig()]`;
-  }
-}
-async function getDefaultConfig(vocabApi, override, activeCohort) {
-  const config = Object.assign(
-    // clone for modifying
-    structuredClone({
-      snvindel: vocabApi.termdbConfig.queries.snvindel,
-      trackLst: vocabApi.termdbConfig.queries.trackLst,
-      ld: vocabApi.termdbConfig.queries.ld
-    }),
-    override || {}
-  );
-  computeBlockModeFlag(config, vocabApi);
-  if (config.snvindel) {
-    if (!config.variantFilter) {
-      const vf = await vocabApi.get_variantFilter();
-      if (vf?.filter) {
-        config.variantFilter = vf;
-      }
-    }
-    if (config.snvindel.details) {
-      mayUpdateGroupTestMethodsIdx({ config }, config.snvindel.details);
-      const gf = config.snvindel.details.groups.find((i) => i.type == "filter");
-      if (gf?.filterByCohort) {
-        if (!Number.isInteger(activeCohort)) throw "filterByCohort but activeCohort not integer";
-        gf.filter = gf.filterByCohort[vocabApi.termdbConfig.selectCohort.values[activeCohort].keys.join(",")];
-        if (!gf.filter) throw "unknown filter by current cohort name";
-        delete gf.filterByCohort;
-      }
-    }
-    if (typeof config.snvindel.shown != "boolean") {
-      if (config.trackLst) {
-        config.snvindel.shown = false;
-      } else {
-        config.snvindel.shown = true;
-      }
-    }
-  }
-  if (config.trackLst) {
-    if (!config.trackLst.facets) throw "trackLst.facets[] missing";
-    if (!config.trackLst.activeTracks) config.trackLst.activeTracks = [];
-  }
-  return config;
-}
-function computeBlockModeFlag(config, vocabApi) {
-  if (typeof config.blockIsProteinMode == "boolean") {
-    return;
-  }
-  switch (vocabApi.termdbConfig.queries.gbRestrictMode) {
-    case void 0:
-      if (config.geneSearchResult?.geneSymbol) {
-        config.blockIsProteinMode = true;
-      } else {
-        config.blockIsProteinMode = false;
-      }
-      break;
-    case "protein":
-      config.blockIsProteinMode = true;
-      break;
-    case "genomic":
-      config.blockIsProteinMode = false;
-      break;
-    default:
-      throw "unknown gbRestrictMode";
-  }
-}
-function makeChartBtnMenu(_holder, chartsInstance) {
-  const chart = { config: { chartType: "genomeBrowser" } };
-  chartsInstance.prepPlot(chart);
-}
-export {
-  componentInit,
-  computeBlockModeFlag,
-  genomeBrowserInit,
-  getPlotConfig,
-  makeChartBtnMenu
-};
-//# sourceMappingURL=GB-MUPI6RL5.js.map