@sjcrh/proteinpaint-client 2.187.0 → 2.188.0

package/dist/GB-K3AWZQFF.js

@@ -0,0 +1,1129 @@
+import {
+  PlotBase,
+  addGeneSearchbox,
+  appInit,
+  filterInit,
+  filterJoin,
+  first_genetrack_tolist,
+  getNormalRoot,
+  make_one_checkbox,
+  renderTable,
+  sayerror
+} from "./chunk-2XPDA6NL.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-GHWHLSUX.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import {
+  Tabs
+} from "./chunk-HBW42TDT.js";
+import "./chunk-G6O3URDN.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-KWM6B3NL.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-AY4UBGLC.js";
+import "./chunk-2P6Z7JFC.js";
+import {
+  dofetch3
+} from "./chunk-MYWJQRTD.js";
+import {
+  getCompInit
+} from "./chunk-MVTCBVSX.js";
+import "./chunk-B43MTEYB.js";
+import "./chunk-2T7VYQLY.js";
+import "./chunk-FDK4UJMN.js";
+import "./chunk-X7GDCYND.js";
+import "./chunk-SJC2C77V.js";
+import "./chunk-C3SYSMNE.js";
+import "./chunk-KSGA62R2.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-NMBIT4IK.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);
+          }
+        }
+      }
+      if (config.trackLst?.activeTracks) {
+        const newLst = config.trackLst.activeTracks.filter((n) => blockInstance.tklst.find((i) => i.name == n));
+        config.trackLst.activeTracks = newLst;
+      }
+      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-EAEFNNF6.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-EHZM3FUX.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-K3AWZQFF.js.map