@sjcrh/proteinpaint-client 2.191.4 → 2.193.0

package/dist/GB-MUPI6RL5.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/gb/model/Model.ts", "../plots/gb/interactions/Interactions.ts", "../plots/gb/view/TabsRenderer.ts", "../plots/gb/view/GeneSearchRenderer.ts", "../plots/gb/view/View.ts", "../plots/gb/GB.ts"],
+  "sourcesContent": ["import { dofetch3 } from '#common/dofetch'\n\nexport class Model {\n\tstate: any\n\tapp: any\n\tconstructor(state, app) {\n\t\tthis.state = state\n\t\tthis.app = app\n\t}\n\n\tasync preComputeData() {\n\t\t// precompute variant data that will be displayed on track\n\n\t\tif (\n\t\t\t!this.state.config.geneSearchResult ||\n\t\t\t!this.state.config.snvindel?.shown ||\n\t\t\t!this.state.config.snvindel?.details\n\t\t)\n\t\t\treturn\n\n\t\t// state.config.snvindel.details{} contains analysis details, cohorts, and compute methods\n\t\t// send to backend to compute and get results back\n\n\t\tconst body = {\n\t\t\tgenome: this.app.opts.state.vocab.genome,\n\t\t\tdslabel: this.app.opts.state.vocab.dslabel,\n\t\t\tfor: 'mds3variantData',\n\t\t\tchr: this.state.config.geneSearchResult.chr,\n\t\t\tstart: this.state.config.geneSearchResult.start,\n\t\t\tstop: this.state.config.geneSearchResult.stop,\n\t\t\tdetails: this.state.config.snvindel.details,\n\t\t\tfilter: this.state.filter,\n\t\t\tfilter0: this.state.filter0,\n\t\t\tvariantFilter: this.state.config.variantFilter?.filter\n\t\t}\n\n\t\t// using dofetch prevents the app from working with custom dataset; may change to vocab method later\n\n\t\tconst data = await dofetch3('termdb', { body })\n\t\tif (data.error) throw data.error\n\n\t\treturn data\n\t}\n}\n", "import type { MassAppApi } from '#mass/types/mass'\nimport { getNormalRoot } from '#filter'\n\nexport class Interactions {\n\tapp: MassAppApi\n\tdom: any\n\tid: string\n\tconstructor(app: MassAppApi, dom: any, id: string) {\n\t\tthis.app = app\n\t\tthis.dom = dom\n\t\tthis.id = id\n\t}\n\n\t// using arrow function to bind \"this\" to the Interactions class\n\t// otherwise \"this\" can refer to the Block class\n\tonCoordinateChange = rglst => {\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig: { geneSearchResult: { chr: rglst[0].chr, start: rglst[0].start, stop: rglst[0].stop } }\n\t\t})\n\t}\n\n\tonGeneSearch = (result, blockIsProteinMode) => {\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig: {\n\t\t\t\tgeneSearchResult: result,\n\t\t\t\tblockIsProteinMode\n\t\t\t}\n\t\t})\n\t}\n\n\t// copied from \"GB.ts\", should try to inherit it instead\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) throw `No plot with id='${this.id}' found`\n\t\treturn {\n\t\t\tconfig,\n\t\t\tfilter: getNormalRoot(appState.termfilter.filter),\n\t\t\tvocab: appState.vocab\n\t\t}\n\t}\n\n\tmaySaveTrackUpdatesToState = blockInstance => {\n\t\t/* following changes will be saved in state:\n\t\t- when a mds3 subtk is created/updated, its tk.filterObj should be saved to state so it can be recovered from session\n\t\t- a facet track is removed by user via block ui */\n\t\tif (!blockInstance) return\n\t\t// since maySaveTrackUpdatesToState() is used as callback in block.js,\n\t\t// this.state.config will become stale; therefore need to regenerate\n\t\t// live plot state\n\t\tconst state = this.getState(this.app.getState())\n\t\tconst config = structuredClone(state.config)\n\t\tconfig.subMds3Tks = []\n\t\tfor (const t of blockInstance.tklst) {\n\t\t\tif (t.type == 'mds3' && t.filterObj) {\n\t\t\t\tconst mclassHiddenValues = t.legend?.mclass?.hiddenvalues\n\t\t\t\tif (!t.subtk) {\n\t\t\t\t\t// \"main\" track\n\t\t\t\t\tif (mclassHiddenValues) {\n\t\t\t\t\t\t// track has hidden mclass values, store in config root\n\t\t\t\t\t\tconfig.mclassHiddenValues = [...mclassHiddenValues]\n\t\t\t\t\t}\n\t\t\t\t\t// do not add this track to subMds3Tks[], as it would cause an issue of auto-creating unwanted subtk on global filter change\n\t\t\t\t\tcontinue\n\t\t\t\t} else {\n\t\t\t\t\t// sub track\n\t\t\t\t\tconst subtk: any = { filterObj: t.filterObj }\n\t\t\t\t\tif (mclassHiddenValues) {\n\t\t\t\t\t\t// track has hidden mclass values, store in subtk obj\n\t\t\t\t\t\tsubtk.mclassHiddenValues = [...mclassHiddenValues]\n\t\t\t\t\t}\n\t\t\t\t\tconfig.subMds3Tks.push(subtk)\n\t\t\t\t\t// filter0?\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tlet facetActiveTracksChanged = false\n\t\tif (config.trackLst?.activeTracks && config.trackLst.facets) {\n\t\t\t// collect names of all facet tracks (across all facet tables)\n\t\t\tconst facetTrackNames = new Set<string>()\n\t\t\tfor (const f of config.trackLst.facets) {\n\t\t\t\tfor (const t of f.tracks) facetTrackNames.add(t.name)\n\t\t\t}\n\t\t\t// active facet tracks are inuse; if user deletes such tracks from block ui, remove from activeTracks\n\t\t\tconst newLst = config.trackLst.activeTracks.filter(n => blockInstance.tklst.find(i => i.name == n))\n\t\t\t// if user re-adds a facet track from block ui (e.g. block.tk.menu), add it back to activeTracks\n\t\t\tfor (const t of blockInstance.tklst) {\n\t\t\t\tif (t.name && facetTrackNames.has(t.name) && !newLst.includes(t.name)) {\n\t\t\t\t\tnewLst.push(t.name)\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (\n\t\t\t\tnewLst.length != config.trackLst.activeTracks.length ||\n\t\t\t\tnewLst.some(n => !config.trackLst.activeTracks.includes(n))\n\t\t\t) {\n\t\t\t\tfacetActiveTracksChanged = true\n\t\t\t}\n\t\t\tconfig.trackLst.activeTracks = newLst\n\t\t}\n\t\tif (facetActiveTracksChanged) {\n\t\t\t// a facet track was added or removed via block ui (e.g. block.tk.menu);\n\t\t\t// must dispatch so the facet table ui re-renders to reflect the change\n\t\t\tthis.app.dispatch({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: this.id,\n\t\t\t\tconfig\n\t\t\t})\n\t\t} else {\n\t\t\tthis.app.save({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: this.id,\n\t\t\t\tconfig\n\t\t\t})\n\t\t}\n\t}\n\n\tlaunchFacet = config => {\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig\n\t\t})\n\t}\n\n\tlaunchVariantTrack = toDisplay => {\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig: { snvindel: { shown: toDisplay } }\n\t\t})\n\t}\n\n\tlaunchLdTrack = tracks => {\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig: { ld: { tracks } }\n\t\t})\n\t}\n\n\tlaunchGroupsFilter = groups => {\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig: { snvindel: { details: { groups } } }\n\t\t})\n\t}\n\n\tlaunchSnvIndelDetails = details => {\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig: { snvindel: { details } }\n\t\t})\n\t}\n\n\tlaunchVariantFilter = filter => {\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig: { variantFilter: { filter } }\n\t\t})\n\t}\n}\n\nexport function mayUpdateGroupTestMethodsIdx(state, d) {\n\tif (d.groups.length != 2) return // not two groups, no need to update test method\n\t// depending on types of two groups, may need to update test method\n\tconst [g1, g2] = d.groups\n\tif (g1.type == 'info' || g2.type == 'info' || (g1.type == 'population' && g2.type == 'population')) {\n\t\t// if any group is INFO, or both are population, can only allow value difference and not fisher test\n\t\tconst i = state.config.snvindel.details.groupTestMethods.findIndex(i => i.name == 'Allele frequency difference')\n\t\tif (i == -1) throw 'Allele frequency difference not found'\n\t\td.groupTestMethodsIdx = i\n\t} else {\n\t\t// otherwise, do not change existing method idx\n\t}\n}\n", "import { Tabs, make_one_checkbox, renderTable } from '#dom'\nimport { filterInit } from '#filter'\nimport { mayUpdateGroupTestMethodsIdx } from '../interactions/Interactions.ts'\nimport { appInit } from '#termdb/app'\n\nexport class TabsRenderer {\n\tstate: any\n\tdom: any\n\topts: any\n\tinteractions: any\n\ttabs: any\n\tfilterUI: any\n\tconstructor(state, dom, opts, interactions) {\n\t\tthis.state = state\n\t\tthis.dom = dom\n\t\tthis.opts = opts\n\t\tthis.interactions = interactions\n\t\tthis.filterUI = {}\n\t}\n\n\tasync main() {\n\t\t// Preserve the currently active tab label before clearing\n\t\tlet previousActiveTabLabel: string | null = null\n\t\tconst existingActiveButton = this.dom.tabsDiv.select('button.sjpp-active')\n\t\tif (!existingActiveButton.empty()) {\n\t\t\tpreviousActiveTabLabel = existingActiveButton.datum()?.label ?? null\n\t\t}\n\n\t\tthis.dom.tabsDiv.selectAll('*').remove()\n\t\tthis.getTabs()\n\n\t\t// Restore the active tab if it still exists in the new tabs array\n\t\tif (previousActiveTabLabel) {\n\t\t\tconst matchingTab = this.tabs.find(tab => tab.label === previousActiveTabLabel)\n\t\t\tif (matchingTab) {\n\t\t\t\t// Clear active state from all tabs first\n\t\t\t\tthis.tabs.forEach(tab => (tab.active = false))\n\t\t\t\t// Set the preserved tab as active\n\t\t\t\tmatchingTab.active = true\n\t\t\t}\n\t\t}\n\n\t\tawait this.mayRenderTabs()\n\t}\n\n\tgetTabs() {\n\t\tconst tabs: any[] = []\n\t\t/* based on ds configuration and data/query type availability, \n        get list of tabs corresponding to different functionalities of the genome browser\n        due to constrain of how tab works, must generate tab array first, call `new Tabs` to initiate holder for each tab\n        then render contents into each holder for each tab\n        thus has to duplicate the logic for computing tabs\n        */\n\n\t\tif (this.state.config.trackLst?.facets) {\n\t\t\t// one tab for each facet table\n\t\t\t// quick fix to hardcode showing facet table as first tab. allow customization later\n\t\t\tconst activeTracks = this.state.config.trackLst.activeTracks\n\t\t\tfor (const facet of this.state.config.trackLst.facets) {\n\t\t\t\tconst shown = facet.tracks.some(t => activeTracks.includes(t.name))\n\t\t\t\ttabs.push({ label: facet.name || 'Facet Table', active: shown })\n\t\t\t}\n\t\t}\n\n\t\tif (this.state.config.snvindel) {\n\t\t\tconst shown = this.state.config.snvindel.shown\n\t\t\t// has snvindel. some logic to decide if show tab for it\n\t\t\tif (this.state.config.snvindel.details) {\n\t\t\t\t// has details for data precomputing, must show tab in order to generate contents\n\t\t\t\ttabs.push({ label: 'Variant Values', active: shown })\n\n\t\t\t\tif (this.state.config.variantFilter) {\n\t\t\t\t\t// for now, this filter only works with snvindel.details\n\t\t\t\t\ttabs.push({ label: 'Variant Filter' })\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\t// no computing detail.\n\t\t\t\tif (this.state.config.trackLst) {\n\t\t\t\t\t// also there is trackLst. in order *not to show trackLst tab alone*, also show snvindel tab and allow to toggle mds3 tk on/off\n\t\t\t\t\ttabs.push({ label: 'Variants', active: shown })\n\t\t\t\t} else {\n\t\t\t\t\t// do not add tab, to avoid showing a lone snvindel tab\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tif (this.state.config.ld) {\n\t\t\tconst shown = this.state.config.ld.tracks.some(t => t.shown)\n\t\t\ttabs.push({ label: 'LD Map', active: shown })\n\t\t}\n\t\tthis.tabs = tabs\n\t}\n\n\tasync mayRenderTabs() {\n\t\tconst tabs = this.tabs\n\t\tif (!tabs?.length) return\n\t\t// has some tabs! initiate the tab ui, then at <div> of each tab, render contents\n\t\tconst toggles = new Tabs({\n\t\t\tholder: this.dom.tabsDiv.append('div').style('border-bottom', 'solid 1px #ccc').style('padding-bottom', '20px'),\n\t\t\ttabs,\n\t\t\thideOnDblClick: true\n\t\t})\n\t\ttoggles.main()\n\n\t\t////////////////////////////////////\n\t\t//\n\t\t// must repeat tab-computing logic in exact order above!! otherwise out of sync\n\t\t// after filling contents for each tab, advance index value of tabsIdx\n\t\t//\n\t\t////////////////////////////////////\n\t\tlet tabsIdx = 0\n\n\t\tif (this.state.config.trackLst?.facets) {\n\t\t\t// (above) quick fix to hardcode showing facet table as first tab. allow customization later\n\t\t\tfor (const facet of this.state.config.trackLst.facets) {\n\t\t\t\tconst div = tabs[tabsIdx++].contentHolder.append('div')\n\t\t\t\tthis.renderFacetTable(facet, div)\n\t\t\t}\n\t\t}\n\n\t\tif (this.state.config.snvindel) {\n\t\t\tif (this.state.config.snvindel.details) {\n\t\t\t\tconst div = tabs[tabsIdx++].contentHolder.append('div')\n\t\t\t\t// hardcode to 2 groups used by this.state.config.snvindel.details.groups[]\n\t\t\t\tthis.dom.group1div = div.append('div').attr('class', 'sjpp-gb-group1')\n\t\t\t\tthis.dom.group2div = div.append('div').attr('class', 'sjpp-gb-group2')\n\t\t\t\tthis.dom.testMethodDiv = div.append('div').style('margin-top', '3px')\n\t\t\t\tawait this.mayRenderGroups()\n\n\t\t\t\tif (this.state.config.variantFilter) {\n\t\t\t\t\t// the whole holder has white-space=nowrap (likely from sjpp-output-sandbox-content)\n\t\t\t\t\t// must set white-space=normal to let INFO filter wrap and not to extend beyond holder\n\t\t\t\t\tthis.dom.variantFilterHolder = tabs[tabsIdx++].contentHolder.append('div').style('white-space', 'normal')\n\t\t\t\t\tthis.mayRenderVariantFilter()\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tif (this.state.config.trackLst) {\n\t\t\t\t\t// snvindel show/hide toggling\n\t\t\t\t\tconst div = tabs[tabsIdx++].contentHolder.append('div')\n\t\t\t\t\tmake_one_checkbox({\n\t\t\t\t\t\tlabeltext: 'Show variant track',\n\t\t\t\t\t\tchecked: this.state.config.snvindel.shown,\n\t\t\t\t\t\tholder: div,\n\t\t\t\t\t\tcallback: this.interactions.launchVariantTrack\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tif (this.state.config.ld) {\n\t\t\t/* tricky: duplicate ld.tracks[] and scope it here, to pass to dispatch\n            somehow, this doesn't work for dispatch\n            config: {\n                ld: {\n                    tracks: {\n                        [i]: {shown}\n                    }\n                }\n            }\n            */\n\t\t\tconst tracks = structuredClone(this.state.config.ld.tracks)\n\n\t\t\tconst div = tabs[tabsIdx++].contentHolder.append('div')\n\t\t\tdiv.append('div').text('Show/hide linkage disequilibrium map from an ancestry:').style('opacity', 0.5)\n\t\t\tfor (const [i, t] of tracks.entries()) {\n\t\t\t\tmake_one_checkbox({\n\t\t\t\t\tlabeltext: t.name,\n\t\t\t\t\tchecked: t.shown,\n\t\t\t\t\tholder: div,\n\t\t\t\t\tcallback: checked => {\n\t\t\t\t\t\ttracks[i].shown = checked\n\t\t\t\t\t\tthis.interactions.launchLdTrack(tracks)\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t}\n\n\trenderFacetTable(facet, div) {\n\t\t/* facet.tracks[] each is {name/assay/sample}\n        layout a table with assay for columns, sample for rows, cells are tracks\n        */\n\t\tconst assayset = new Set(),\n\t\t\tsampleset = new Set()\n\t\tfor (const t of facet.tracks) {\n\t\t\tif (t.assay) assayset.add(t.assay)\n\t\t\tif (t.sample) sampleset.add(t.sample)\n\t\t}\n\n\t\tconst sampleLst = [...sampleset]\n\t\tconst assayLst = [...assayset] // TODO facet hardcodes assay order\n\n\t\t// TODO click on row/column header to batch operate\n\n\t\tconst columns: any = [{ label: 'Sample' }] // TODO use ds sample type\n\t\tfor (const assay of assayLst) {\n\t\t\tcolumns.push({\n\t\t\t\tlabel: assay,\n\t\t\t\tfillCell: (td, si) => {\n\t\t\t\t\t// \"si\" index of sample/rows[]; find tracks belonging to this assay+sample combo\n\t\t\t\t\tconst tklst = facet.tracks.filter(i => i.assay == assay && i.sample == sampleLst[si])\n\t\t\t\t\tif (tklst.length == 0) return // no tracks for this combo\n\t\t\t\t\t// has track(s) for this combo; render <div> in table cell; click to launch tracks\n\t\t\t\t\t// Count how many tracks are currently shown\n\t\t\t\t\tconst shownCount = tklst.filter(tk => this.state.config.trackLst.activeTracks.includes(tk.name)).length\n\t\t\t\t\tconst displayText = shownCount ? `${shownCount}/${tklst.length}` : `${tklst.length}`\n\t\t\t\t\ttd.append('div')\n\t\t\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t\t\t.style('text-align', 'center')\n\t\t\t\t\t\t.text(displayText)\n\t\t\t\t\t\t.on('click', event => {\n\t\t\t\t\t\t\tthis.clickFacetCell(event, tklst)\n\t\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t\tconst rows: any[] = []\n\t\tfor (const sample of sampleLst) {\n\t\t\t// 1st column is sample name\n\t\t\t// TODO may link sample to sampleview\n\t\t\tconst row: any[] = [{ value: sample }]\n\t\t\t// one blank cell for each assay\n\t\t\tfor (let i = 0; i < assayLst.length; i++) {\n\t\t\t\trow.push({})\n\t\t\t}\n\t\t\trows.push(row)\n\t\t}\n\t\trenderTable({\n\t\t\tcolumns,\n\t\t\trows,\n\t\t\tdiv\n\t\t})\n\t}\n\n\tclickFacetCell(event, tklst) {\n\t\tthis.dom.tip.clear().showunder(event.target)\n\t\tconst activeTracks = this.state.config.trackLst.activeTracks\n\t\tconst table = this.dom.tip.d.append('table').style('margin', '5px 5px 5px 2px')\n\t\tfor (const tk of tklst) {\n\t\t\tconst tr = table.append('tr')\n\t\t\tconst td1 = tr\n\t\t\t\t.append('td')\n\t\t\t\t.style('font-size', '.8em')\n\t\t\t\t.text(activeTracks.includes(tk.name) ? 'SHOWN' : '')\n\t\t\ttr.append('td')\n\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t.text(tk.name)\n\t\t\t\t.on('click', () => {\n\t\t\t\t\tthis.dom.tip.hide()\n\t\t\t\t\tlet newActiveTracks, newRemoveTracks // default undefined to not remove any track\n\t\t\t\t\tif (activeTracks.includes(tk.name)) {\n\t\t\t\t\t\ttd1.text('')\n\t\t\t\t\t\tnewActiveTracks = structuredClone(activeTracks).filter(n => n != tk.name)\n\t\t\t\t\t\tnewRemoveTracks = [tk.name]\n\t\t\t\t\t} else {\n\t\t\t\t\t\ttd1.text('SHOWN')\n\t\t\t\t\t\tnewActiveTracks = structuredClone(activeTracks)\n\t\t\t\t\t\tnewActiveTracks.push(tk.name)\n\t\t\t\t\t}\n\t\t\t\t\tconst config = {\n\t\t\t\t\t\ttrackLst: {\n\t\t\t\t\t\t\tactiveTracks: newActiveTracks,\n\t\t\t\t\t\t\tremoveTracks: newRemoveTracks\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tthis.interactions.launchFacet(config)\n\t\t\t\t})\n\t\t}\n\t}\n\n\tasync mayRenderGroups() {\n\t\tconst groups = this.state.config.snvindel.details.groups\n\t\tif (!groups) return\n\n\t\t// is equipped with comparison groups, render group ui\n\t\tawait this.render1group(0)\n\t\tawait this.render1group(1)\n\n\t\tif (this.state.config.snvindel.details.groupTestMethods) {\n\t\t\t// render the test method\n\t\t\tthis.renderTestMethod()\n\t\t}\n\t}\n\n\tmayRenderVariantFilter() {\n\t\tif (this.state.config.variantFilter) {\n\t\t\tthis.dom.variantFilterHolder.selectAll('*').remove()\n\t\t\tfilterInit({\n\t\t\t\tjoinWith: this.state.config.variantFilter.opts.joinWith,\n\t\t\t\temptyLabel: '+Add Filter',\n\t\t\t\tholder: this.dom.variantFilterHolder,\n\t\t\t\tvocab: { terms: this.state.config.variantFilter.terms },\n\t\t\t\tcallback: filter => this.interactions.launchVariantFilter(filter)\n\t\t\t}).main(this.state.config.variantFilter.filter)\n\t\t}\n\t}\n\n\t/*\n\trender ui contents of one group, both arguments are provided to be convenient for ad-hoc update\n\n\tgroupIdx: array index of self.state.config.snvindel.details.groups[]\n\t\tdetermines which <div> to render to at self.dom.group1/2div\n\tgroup{}: element of same array\n\t*/\n\tasync render1group(groupIdx) {\n\t\tconst group = this.state.config.snvindel.details.groups[groupIdx]\n\t\tconst div = groupIdx == 0 ? this.dom.group1div : this.dom.group2div\n\n\t\tlet canReuse = false\n\t\tif (group?.type == 'filter' && this.filterUI[groupIdx]) {\n\t\t\t// will reuse an existing filterUI[${groupIdx}] and div\n\t\t\tcanReuse = true\n\t\t} else {\n\t\t\tdelete this.filterUI[groupIdx] // ok to delete even if not existing\n\t\t\tdiv.selectAll('*').remove()\n\t\t}\n\n\t\tif (!group) {\n\t\t\t// group does not exist in groups[] based on array index, e.g. when there's just 1 group and groups[1] is undefined\n\t\t\t// add a prompt in place of header button\n\t\t\tthis.makePrompt2addNewGroup(groupIdx, div)\n\t\t\treturn\n\t\t}\n\n\t\t// the group exists; first show the group header button\n\t\tif (!canReuse) this.makeGroupHeaderButton(groupIdx, div)\n\n\t\tif (group.type == 'info') return this.render1group_info(groupIdx, group, div)\n\t\tif (group.type == 'population') return this.render1group_population(groupIdx, group, div)\n\t\tif (group.type == 'filter') return await this.render1group_filter(groupIdx, group, div)\n\t\tthrow 'render1group: unknown group type'\n\t}\n\n\tmakePrompt2addNewGroup(groupIdx, div) {\n\t\t// the prompt <div> is created in group2div\n\t\tdiv\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.text('Create Group 2')\n\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t.style('margin', '10px')\n\t\t\t.on('click', event => {\n\t\t\t\tthis.dom.tip.showunder(event.target).clear()\n\t\t\t\tthis.launchMenu_createGroup(groupIdx, this.dom.tip.d)\n\t\t\t})\n\t}\n\n\tmakeGroupHeaderButton(groupIdx, div) {\n\t\tdiv\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.text('Group ' + (groupIdx + 1))\n\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t.style('margin-right', '10px')\n\t\t\t.on('click', event => {\n\t\t\t\tthis.dom.tip.showunder(event.target).clear()\n\t\t\t\tif (groupIdx == 0) {\n\t\t\t\t\t// this is 1st group, directly launch menu to change group, but do not allow to delete\n\t\t\t\t\tthis.launchMenu_createGroup(0, this.dom.tip.d)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tthis.dom.tip.d\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.text('Change')\n\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t.style('border-radius', '0px')\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tthis.launchMenu_createGroup(1, this.dom.tip.clear().d)\n\t\t\t\t\t})\n\t\t\t\tthis.dom.tip.d\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.text('Delete')\n\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t.style('border-radius', '0px')\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tthis.dom.tip.hide()\n\t\t\t\t\t\t/*\n\t\t\t\t\t\t// ui is not reactive\n\t\t\t\t\t\tdiv.selectAll('*').remove()\n\t\t\t\t\t\tmakePrompt2addNewGroup(self, 1, div)\n\t\t\t\t\t\t*/\n\n\t\t\t\t\t\tconst groups = [this.state.config.snvindel.details.groups[0]] // only keep first group\n\t\t\t\t\t\tthis.interactions.launchGroupsFilter(groups)\n\t\t\t\t\t})\n\t\t\t})\n\t}\n\n\trender1group_info(groupIdx, group, div) {\n\t\t// this group is an INFO field\n\t\tlet name = group.infoKey\n\t\tif (this.state.config.variantFilter?.terms) {\n\t\t\tconst f = this.state.config.variantFilter.terms.find(i => i.id == group.infoKey)\n\t\t\tif (f && f.name) name = f.name\n\t\t}\n\t\tdiv\n\t\t\t.append('span')\n\t\t\t.text(name)\n\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t.on('click', event => {\n\t\t\t\tif (this.state.config.variantFilter.terms.length <= 1) {\n\t\t\t\t\t// only 1, no other option to switch to\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\t// multiple options, allow to replace\n\t\t\t\tthis.dom.tip\n\t\t\t\t\t.clear()\n\t\t\t\t\t.showunder(event.target)\n\t\t\t\t\t.d.append('div')\n\t\t\t\t\t.text('Replace with:')\n\t\t\t\t\t.style('margin', '10px')\n\t\t\t\t\t.style('font-size', '.8em')\n\t\t\t\tfor (const f of this.state.config.variantFilter.terms) {\n\t\t\t\t\tif (f.type != 'integer' && f.type != 'float') continue // only allow numeric fields\n\t\t\t\t\tif (f.id == group.infoKey) continue // same one\n\n\t\t\t\t\tthis.dom.tip.d\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.text(f.name)\n\t\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\t/////////////////////////////////\n\t\t\t\t\t\t\t// create a new group using this info field\n\t\t\t\t\t\t\tthis.dom.tip.hide()\n\t\t\t\t\t\t\tconst groups = structuredClone(this.state.config.snvindel.details.groups)\n\t\t\t\t\t\t\tgroups[groupIdx].infoKey = f.id\n\t\t\t\t\t\t\tgroups[groupIdx].type = 'info'\n\t\t\t\t\t\t\tthis.interactions.launchGroupsFilter(groups)\n\t\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t})\n\t\tdiv\n\t\t\t.append('span')\n\t\t\t.text('PER-VARIANT NUMERICAL VALUES')\n\t\t\t.style('font-size', '.7em')\n\t\t\t.style('opacity', 0.6)\n\t\t\t.style('margin-left', '10px')\n\t}\n\n\trender1group_population(groupIdx, group, div) {\n\t\t// this group is a predefined population\n\t\tdiv\n\t\t\t.append('span')\n\t\t\t.text(group.label)\n\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t.on('click', event => {\n\t\t\t\tif (this.state.config.snvindel.populations.length <= 1) {\n\t\t\t\t\t// only 1, no other option to switch to\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\t// multiple options, allow to replace\n\t\t\t\tthis.dom.tip\n\t\t\t\t\t.clear()\n\t\t\t\t\t.showunder(event.target)\n\t\t\t\t\t.d.append('div')\n\t\t\t\t\t.text('Replace with:')\n\t\t\t\t\t.style('margin', '10px')\n\t\t\t\t\t.style('font-size', '.8em')\n\n\t\t\t\tfor (const p of this.state.config.snvindel.populations) {\n\t\t\t\t\tif (p.key == group.key) continue\n\t\t\t\t\tthis.dom.tip.d\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.text(p.label)\n\t\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\tthis.dom.tip.hide()\n\t\t\t\t\t\t\tconst groups = structuredClone(this.state.config.snvindel.details.groups)\n\t\t\t\t\t\t\tgroups[groupIdx] = structuredClone(p)\n\t\t\t\t\t\t\tgroups[groupIdx].type = 'population'\n\t\t\t\t\t\t\tthis.interactions.launchGroupsFilter(groups)\n\t\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t})\n\t\tdiv\n\t\t\t.append('span')\n\t\t\t.text(`POPULATION${group.adjust_race ? ', RACE ADJUSTED' : ''}`)\n\t\t\t.style('font-size', '.7em')\n\t\t\t.style('margin-left', '10px')\n\t\t\t.style('opacity', 0.6)\n\n\t\tif (this.state.config.snvindel.details.groups[groupIdx == 1 ? 0 : 1]?.type == 'filter') {\n\t\t\t/*\n\t\t\t!!poor fix!!\n\t\t\tonly render the text when the other group is \"filter\",\n\t\t\tso that when the other group is no longer type=filter, the admix text will disappear from this group\n\t\t\tthis is because self._partialData is *sticky* and is never deleted, due to the way parent passing it to child\n\t\t\tand assume that pop2average must be from comparison between 2 groups of filter-vs-population\n\t\t\te.g. when info-vs-population, despite the _partialData is still there, must not render it\n\t\t\t*/\n\t\t\tdiv\n\t\t\t\t.append('span')\n\t\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t\t.attr('id', 'sjpp-gb-pop2avg')\n\t\t\t\t.style('display', 'none') // hidden for now, will display once pop2average data becomes available (see View.ts)\n\t\t\t\t.style('margin-left', '20px')\n\t\t\t\t.text(`Group ${groupIdx == 1 ? 1 : 2} average admixture:`)\n\t\t\t\t.on('click', event => {\n\t\t\t\t\tthis.dom.tip.clear().showunder(event.target).d.append('div').style('margin', '10px').style('width', '500px')\n\t\t\t\t\t\t.html(`These are average admixture coefficients based on current Group ${groupIdx == 1 ? 1 : 2} samples.\n\t\t\t\t\tThey are used to adjust variant allele counts of matching ancestries from <span class=sja_menuoption style=\"padding:2px 5px\">${\n\t\t\t\t\t\tgroup.label\n\t\t\t\t\t}</span>,\n\t\t\t\t\tso that the adjusted allele counts can be compared against Group ${groupIdx == 1 ? 1 : 2} allele counts.\n\t\t\t\t\tThis allows to account for ancestry composition difference between the two groups.\n\t\t\t\t\t`)\n\t\t\t\t})\n\t\t\t\t.append('span')\n\t\t\t\t.attr('id', 'sjpp-gb-pop2avg-values') // will fill with values once pop2average data becomes available (see View.ts)\n\t\t}\n\t}\n\n\tasync render1group_filter(groupIdx, group, div) {\n\t\t/*\n\t\tthis group is based on a termdb-filter\n\t\twhen initiating the filter ui, must join group's filter with mass global filter and submit the joined filter to main()\n\t\tthis allows tvs edit to show correct number of samples\n\t\t*/\n\t\tif (!this.filterUI[groupIdx]) {\n\t\t\tthis.filterUI[groupIdx] = await filterInit({\n\t\t\t\tholder: div,\n\t\t\t\tvocab: this.state.vocab,\n\t\t\t\temptyLabel: 'Entire cohort',\n\t\t\t\ttermdbConfig: this.opts.vocabApi.termdbConfig,\n\t\t\t\tcallback: f => {\n\t\t\t\t\tconst groups = JSON.parse(JSON.stringify(this.state.config.snvindel.details.groups))\n\t\t\t\t\tgroups[groupIdx].filter = f\n\t\t\t\t\tthis.interactions.launchGroupsFilter(groups)\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\n\t\tthis.filterUI[groupIdx].main(this.getJoinedFilter(group))\n\n\t\t// placeholder for sample count\n\t\tdiv\n\t\t\t.append('span')\n\t\t\t.attr('class', 'sjpp-gb-filter-count')\n\t\t\t.style('display', 'none')\n\t\t\t.style('margin-left', '10px')\n\t\t\t.style('opacity', 0.5)\n\t\t\t.style('font-size', '.9em')\n\t}\n\n\tgetJoinedFilter(group) {\n\t\t// clone the global filter; group filter will be joined into it\n\t\tconst joinedFilter = structuredClone(this.state.filter || { type: 'tvslst', in: true, join: '', lst: [] })\n\t\tconst gf = structuredClone(group.filter)\n\t\t// tag group filter for it to be rendered in filter ui\n\t\t// rest of state.filter will remain invisible\n\t\tgf.tag = 'filterUiRoot'\n\t\tjoinedFilter.lst.push(gf)\n\t\tjoinedFilter.join = 'and'\n\t\treturn joinedFilter\n\t}\n\n\t// show vertical toggle options: filter/population/info\n\t// when any is selected, create a new group object and set to snvindel.details.groups[groupIdx]\n\tlaunchMenu_createGroup(groupIdx, div) {\n\t\tconst opt: any = {\n\t\t\tholder: div.append('div').style('margin', '5px'),\n\t\t\ttabs: this.state.config.snvindel.details.groupTypes.map(i => {\n\t\t\t\treturn { label: i.name }\n\t\t\t}),\n\t\t\ttabsPosition: 'vertical',\n\t\t\tlinePosition: 'right'\n\t\t}\n\t\tnew Tabs(opt).main()\n\t\tfor (const [idx, groupType] of this.state.config.snvindel.details.groupTypes.entries()) {\n\t\t\t// { type:str, name:str }\n\t\t\tconst tab = opt.tabs[idx]\n\t\t\ttab.contentHolder.style('margin', '10px')\n\t\t\tif (groupType.type == 'info') {\n\t\t\t\tif (!this.state.config.variantFilter?.terms)\n\t\t\t\t\tthrow 'looking for snvindel info fields but self.state.config.variantFilter.terms[] missing'\n\t\t\t\tfor (const f of this.state.config.variantFilter.terms) {\n\t\t\t\t\tif (f.type != 'integer' && f.type != 'float') continue // only allow numeric fields\n\t\t\t\t\ttab.contentHolder\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.text(f.name)\n\t\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\t/////////////////////////////////\n\t\t\t\t\t\t\t// create a new group using this info field\n\t\t\t\t\t\t\tthis.dom.tip.hide()\n\t\t\t\t\t\t\tconst newGroup = {\n\t\t\t\t\t\t\t\ttype: 'info',\n\t\t\t\t\t\t\t\tinfoKey: f.id\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tconst details = this.makeNewDetail(newGroup, groupIdx)\n\t\t\t\t\t\t\tmayUpdateGroupTestMethodsIdx(this.state, details)\n\t\t\t\t\t\t\tthis.interactions.launchSnvIndelDetails(details)\n\t\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tif (groupType.type == 'population') {\n\t\t\t\tif (!this.state.config.snvindel.populations) throw 'state.config.snvindel.populations missing'\n\t\t\t\tfor (const p of this.state.config.snvindel.populations) {\n\t\t\t\t\t// {key,label, allowto_adjust_race, adjust_race}\n\t\t\t\t\ttab.contentHolder\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.text(p.label)\n\t\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\t\t/////////////////////////////////\n\t\t\t\t\t\t\t// create a new group using this population\n\t\t\t\t\t\t\tthis.dom.tip.hide()\n\t\t\t\t\t\t\tconst newGroup = {\n\t\t\t\t\t\t\t\ttype: 'population',\n\t\t\t\t\t\t\t\tkey: p.key,\n\t\t\t\t\t\t\t\tlabel: p.label,\n\t\t\t\t\t\t\t\tallowto_adjust_race: p.allowto_adjust_race,\n\t\t\t\t\t\t\t\tadjust_race: p.adjust_race\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tconst details = this.makeNewDetail(newGroup, groupIdx)\n\t\t\t\t\t\t\tmayUpdateGroupTestMethodsIdx(this.state, details)\n\t\t\t\t\t\t\tthis.interactions.launchSnvIndelDetails(details)\n\t\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tif (groupType.type == 'filter') {\n\t\t\t\tconst arg = {\n\t\t\t\t\tholder: tab.contentHolder,\n\t\t\t\t\tvocabApi: this.opts.vocabApi,\n\t\t\t\t\tstate: {\n\t\t\t\t\t\tactiveCohort: this.state.activeCohort,\n\t\t\t\t\t\ttermfilter: { filter: this.state.filter }\n\t\t\t\t\t},\n\t\t\t\t\ttree: {\n\t\t\t\t\t\tclick_term2select_tvs: tvs => {\n\t\t\t\t\t\t\t/////////////////////////////////\n\t\t\t\t\t\t\t// create a new group using this tvs\n\t\t\t\t\t\t\tthis.dom.tip.hide()\n\t\t\t\t\t\t\tconst newGroup = {\n\t\t\t\t\t\t\t\ttype: 'filter',\n\t\t\t\t\t\t\t\tfilter: {\n\t\t\t\t\t\t\t\t\tin: true,\n\t\t\t\t\t\t\t\t\tjoin: '',\n\t\t\t\t\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\t\t\t\t\tlst: [{ type: 'tvs', tvs }]\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tconst details = this.makeNewDetail(newGroup, groupIdx)\n\t\t\t\t\t\t\tmayUpdateGroupTestMethodsIdx(this.state, details)\n\t\t\t\t\t\t\tthis.interactions.launchSnvIndelDetails(details)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tappInit(arg)\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tthrow 'unknown group type'\n\t\t}\n\t}\n\n\tmakeNewDetail(newGroup, groupIdx) {\n\t\tconst newDetail = {\n\t\t\tgroups: JSON.parse(JSON.stringify(this.state.config.snvindel.details.groups))\n\t\t}\n\t\tnewDetail.groups[groupIdx] = newGroup\n\t\treturn newDetail\n\t}\n\n\trenderTestMethod() {\n\t\tconst div = this.dom.testMethodDiv\n\t\tdiv.selectAll('*').remove()\n\n\t\tconst [g1, g2] = this.state.config.snvindel.details.groups\n\t\tif (!g2) {\n\t\t\t// only 1 group, do not show ui as test method is not configurable\n\t\t\treturn\n\t\t}\n\n\t\tdiv.append('span').text('TEST METHOD').style('font-size', '.8em').style('opacity', 0.6)\n\n\t\tif (g1.type != 'filter' && g2.type != 'filter') {\n\t\t\t// neither group is filter, test method can only be value diff and also not configurable\n\t\t\tdiv.append('span').style('padding-left', '10px').text('Value difference').style('opacity', 0.6)\n\t\t\treturn\n\t\t}\n\n\t\tconst select = div\n\t\t\t.append('select')\n\t\t\t.style('margin-left', '10px')\n\t\t\t.on('change', () => {\n\t\t\t\tconst details = { groupTestMethodsIdx: select.property('selectedIndex') }\n\t\t\t\tthis.interactions.launchSnvIndelDetails(details)\n\t\t\t})\n\t\tfor (const m of this.state.config.snvindel.details.groupTestMethods) {\n\t\t\tselect.append('option').text(m.name)\n\t\t}\n\t\tselect.property('selectedIndex', this.state.config.snvindel.details.groupTestMethodsIdx)\n\t}\n}\n", "import { addGeneSearchbox, Menu } from '#dom'\n\nexport class GeneSearchRenderer {\n\tstate: any\n\tholder: any\n\topts: any\n\tinteractions: any\n\tconstructor(state, holder, opts, interactions) {\n\t\tthis.state = state\n\t\tthis.holder = holder\n\t\tthis.opts = opts\n\t\tthis.interactions = interactions\n\t}\n\n\tmain() {\n\t\tthis.renderGeneSearch()\n\t}\n\n\trenderGeneSearch() {\n\t\tconst gbRestrictMode = this.opts.vocabApi.termdbConfig.queries.gbRestrictMode\n\t\tthis.holder.selectAll('*').remove()\n\t\tconst row = this.holder.append('div')\n\t\trow.append('span').html('Search')\n\t\tconst arg: any = {\n\t\t\ttip: new Menu({ padding: '0px' }),\n\t\t\tgenome: this.opts.genome,\n\t\t\trow,\n\t\t\tcallback: async () => {\n\t\t\t\t// found a hit {chr,start,stop,geneSymbol}\n\t\t\t\tif (result.geneSymbol && !gbRestrictMode) {\n\t\t\t\t\t// user found a gene and no restricted mode from ds, ask user if to use either protein/genomic mode\n\n\t\t\t\t\t// on repeated gene search, detect if btndiv is present, and remove, avoiding showing duplicate buttons\n\t\t\t\t\tthis.holder.select('.sjpp_gbmodebtndiv').remove()\n\t\t\t\t\t// create new div and buttons\n\t\t\t\t\tconst btndiv = this.holder.append('div').attr('class', 'sjpp_gbmodebtndiv').style('margin-top', '10px')\n\t\t\t\t\tbtndiv\n\t\t\t\t\t\t.append('button')\n\t\t\t\t\t\t.style('margin-right', '10px')\n\t\t\t\t\t\t.text('Protein view of ' + result.geneSymbol)\n\t\t\t\t\t\t.on('click', async () => {\n\t\t\t\t\t\t\tawait this.interactions.onGeneSearch(result, true)\n\t\t\t\t\t\t})\n\t\t\t\t\tbtndiv\n\t\t\t\t\t\t.append('button')\n\t\t\t\t\t\t.text('Genomic view of ' + result.geneSymbol)\n\t\t\t\t\t\t.on('click', async () => {\n\t\t\t\t\t\t\tawait this.interactions.onGeneSearch(result, false)\n\t\t\t\t\t\t})\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\t// only one possibility of gb mode and it can be auto determined\n\t\t\t\tawait this.interactions.onGeneSearch(result, gbRestrictMode == 'protein')\n\t\t\t}\n\t\t}\n\n\t\tswitch (gbRestrictMode) {\n\t\t\tcase undefined:\n\t\t\t\t// not set. allowed\n\t\t\t\tbreak\n\t\t\tcase 'genomic':\n\t\t\t\t// gb can only be block mode, add default coord to arg\n\t\t\t\targ.defaultCoord = this.opts.vocabApi.termdbConfig.queries.defaultCoord\n\t\t\t\tbreak\n\t\t\tcase 'protein':\n\t\t\t\t// gb can only be protein mode, only allow searching gene\n\t\t\t\targ.searchOnly = 'gene'\n\t\t\t\tbreak\n\t\t\tdefault:\n\t\t\t\tthrow 'unknown gbRestrictMode'\n\t\t}\n\n\t\tconst result = addGeneSearchbox(arg)\n\t}\n}\n", "import { first_genetrack_tolist } from '#common/1stGenetk'\nimport { filterJoin } from '#filter'\nimport { TabsRenderer } from './TabsRenderer.ts'\nimport { GeneSearchRenderer } from './GeneSearchRenderer.ts'\n\nexport class View {\n\tstate: any\n\tblockInstance: any\n\tdata: any\n\tdom: any\n\topts: any\n\tinteractions: any\n\tconstructor(state, blockInstance, data, dom, opts, interactions) {\n\t\tthis.state = state\n\t\tthis.blockInstance = blockInstance\n\t\tthis.data = data\n\t\tthis.dom = dom\n\t\tthis.opts = opts\n\t\tthis.interactions = interactions\n\t}\n\n\tasync main() {\n\t\tconst tabs = new TabsRenderer(this.state, this.dom, this.opts, this.interactions)\n\t\tawait tabs.main()\n\t\tconst geneSearch = new GeneSearchRenderer(this.state, this.dom.geneSearchDiv, this.opts, this.interactions)\n\t\tgeneSearch.main()\n\t\tif (this.state.config.geneSearchResult) {\n\t\t\t// valid gene search result\n\t\t\t// launch block\n\t\t\tthis.dom.geneSearchDiv.style('display', 'none')\n\t\t\tconst tklst = await this.generateTracks()\n\t\t\tawait this.launchBlockWithTracks(tklst)\n\t\t}\n\t}\n\n\tasync generateTracks() {\n\t\t// handle multiple possibilities of generating genome browser tracks\n\n\t\tconst tklst: any = [] // list of tracks to be shown in block\n\n\t\tif (this.state.config.snvindel?.shown) {\n\t\t\t// show snvindel-based mds3 tk\n\t\t\tif (this.data) {\n\t\t\t\t// variant data has been precomputed\n\t\t\t\t// TODO move computing logic to official mds3 tk and avoid tricky workaround using custom tk\n\t\t\t\tif (this.blockInstance) {\n\t\t\t\t\t// block already launched, update variant data on tk and rerender\n\t\t\t\t\tthis.updateCustomMds3tk()\n\t\t\t\t} else {\n\t\t\t\t\t// block not present, launch custom mds3 tk to display variant data\n\t\t\t\t\tconst tk = await this.launchCustomMds3tk()\n\t\t\t\t\tif (tk) {\n\t\t\t\t\t\t// tricky! will not return obj when block is already shown, since it updates data for existing tk obj\n\t\t\t\t\t\ttklst.push(tk)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\t// official mds3 tk without precomputed tk data\n\t\t\t\tconst tk: any = {\n\t\t\t\t\ttype: 'mds3',\n\t\t\t\t\tdslabel: this.state.vocab.dslabel,\n\t\t\t\t\tallow2selectSamples: this.opts.allow2selectSamples,\n\t\t\t\t\tonClose: () => {\n\t\t\t\t\t\t// on closing subtk, the filterObj corresponding to the subtk will be \"removed\" from subMds3Tks[], by regenerating the array\n\t\t\t\t\t\tthis.interactions.maySaveTrackUpdatesToState(this.blockInstance)\n\t\t\t\t\t},\n\t\t\t\t\tcallbackOnRender: () => {\n\t\t\t\t\t\t// will allow legend filtering changes to be saved to state\n\t\t\t\t\t\tthis.interactions.maySaveTrackUpdatesToState(this.blockInstance)\n\t\t\t\t\t},\n\t\t\t\t\t// for showing disco etc as ad-hoc sandbox, persistently in the mass plotDiv, rather than a menu\n\t\t\t\t\tnewChartHolder: this.opts.plotDiv\n\t\t\t\t}\n\t\t\t\t// any cohort filter for this tk\n\t\t\t\t{\n\t\t\t\t\tconst lst: any = []\n\t\t\t\t\t// register both global filter and local filter to pass to mds3 data queries\n\t\t\t\t\tif (this.state.filter?.lst?.length) lst.push(this.state.filter)\n\t\t\t\t\tif (this.state.config.snvindel.filter) lst.push(this.state.config.snvindel.filter)\n\t\t\t\t\tif (lst.length == 1) {\n\t\t\t\t\t\ttk.filterObj = structuredClone(lst[0])\n\t\t\t\t\t} else if (lst.length > 1) {\n\t\t\t\t\t\ttk.filterObj = filterJoin(lst)\n\t\t\t\t\t}\n\t\t\t\t\t// TODO this will cause mds3 tk to show a leftlabel to indicate the filtering, which should be hidden\n\t\t\t\t}\n\t\t\t\tif (this.state.filter0) tk.filter0 = this.state.filter0\n\t\t\t\tif (this.state.config.mclassHiddenValues) {\n\t\t\t\t\ttk.legend = { mclass: { hiddenvalues: new Set(this.state.config.mclassHiddenValues) } }\n\t\t\t\t}\n\t\t\t\ttklst.push(tk)\n\n\t\t\t\tif (this.state.config?.subMds3Tks) {\n\t\t\t\t\tfor (const subtk of this.state.config.subMds3Tks) {\n\t\t\t\t\t\t// for every element, create a new subtk\n\t\t\t\t\t\tconst t2: any = {\n\t\t\t\t\t\t\ttype: 'mds3',\n\t\t\t\t\t\t\tsubtk: true,\n\t\t\t\t\t\t\tdslabel: this.state.vocab.dslabel,\n\t\t\t\t\t\t\tonClose: () => {\n\t\t\t\t\t\t\t\t// on closing subtk, the filterObj corresponding to the subtk will be \"removed\" from subMds3Tks[], by regenerating the array\n\t\t\t\t\t\t\t\tthis.interactions.maySaveTrackUpdatesToState(this.blockInstance)\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\tcallbackOnRender: () => {\n\t\t\t\t\t\t\t\t// will allow legend filtering changes to be saved to state\n\t\t\t\t\t\t\t\tthis.interactions.maySaveTrackUpdatesToState(this.blockInstance)\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t// for showing disco etc as ad-hoc sandbox, persistently in the mass plotDiv, rather than a menu\n\t\t\t\t\t\t\tnewChartHolder: this.opts.plotDiv\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (this.state.filter?.lst?.length) {\n\t\t\t\t\t\t\t// join sub filter with global\n\t\t\t\t\t\t\tt2.filterObj = filterJoin([this.state.filter, subtk.filterObj])\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t// no global. only sub\n\t\t\t\t\t\t\tt2.filterObj = structuredClone(subtk.filterObj)\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (this.state.filter0) t2.filter0 = this.state.filter0\n\t\t\t\t\t\tif (subtk.mclassHiddenValues) {\n\t\t\t\t\t\t\tt2.legend = { mclass: { hiddenvalues: new Set(subtk.mclassHiddenValues) } }\n\t\t\t\t\t\t}\n\t\t\t\t\t\ttklst.push(t2)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tif (this.state.config?.trackLst?.activeTracks?.length) {\n\t\t\t// include active facet tracks\n\t\t\tfor (const n of this.state.config.trackLst.activeTracks) {\n\t\t\t\tfor (const f of this.state.config.trackLst.facets) {\n\t\t\t\t\tfor (const t of f.tracks) {\n\t\t\t\t\t\tif (t.name == n) tklst.push(t)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tif (this.state.config.ld?.tracks) {\n\t\t\tfor (const t of this.state.config.ld.tracks) {\n\t\t\t\tif (t.shown) tklst.push(t)\n\t\t\t}\n\t\t}\n\t\treturn tklst\n\t}\n\n\tasync launchCustomMds3tk() {\n\t\tthis.mayGetSampleCounts()\n\n\t\tconst nm = {\n\t\t\t// numeric mode object; to fill in based on snvindel.details{}\n\t\t\ttype: 'numeric',\n\t\t\tinuse: true,\n\t\t\tbyAttribute: 'nm_axis_value'\n\t\t}\n\t\tfurbishViewModeWithSnvindelComputeDetails(this, nm)\n\t\tconst tk = {\n\t\t\ttype: 'mds3',\n\t\t\t// despite having custom data, still provide dslabel for the mds3 tk to function as an official dataset\n\t\t\tdslabel: this.state.vocab.dslabel,\n\t\t\tname: 'Variants',\n\t\t\tcustom_variants: this.data.mlst,\n\t\t\tskewerModes: [nm],\n\t\t\tfilter0: this.state.filter0\n\t\t}\n\t\treturn tk\n\t}\n\n\tupdateCustomMds3tk() {\n\t\tif (!this.blockInstance) throw 'blockInstance is missing'\n\t\tthis.mayGetSampleCounts()\n\n\t\tconst t2 = this.blockInstance.tklst.find(i => i.type == 'mds3')\n\t\tt2.custom_variants = this.data.mlst\n\n\t\t// details.groups[] may have changed. update label and tooltip callback etc, of tk numeric axis view mode object\n\t\tfurbishViewModeWithSnvindelComputeDetails(\n\t\t\tthis,\n\t\t\tt2.skewer.viewModes.find(i => i.type == 'numeric')\n\t\t)\n\n\t\tt2.load()\n\t}\n\n\tmayGetSampleCounts() {\n\t\tconst data = this.data\n\t\tthis.mayRenderSampleCount('group1', data.totalSampleCount_group1)\n\t\tthis.mayRenderSampleCount('group2', data.totalSampleCount_group2)\n\t\tthis.mayRenderPop2Avg(data.pop2average)\n\t}\n\n\tmayRenderSampleCount(group, count) {\n\t\tif (!Number.isInteger(count)) return\n\t\tthis.dom.tabsDiv\n\t\t\t.select(`.sjpp-gb-${group}`)\n\t\t\t.select('.sjpp-gb-filter-count')\n\t\t\t.style('display', 'inline')\n\t\t\t.text('n=' + count)\n\t}\n\n\tmayRenderPop2Avg(pop2average) {\n\t\tif (!pop2average) return\n\t\tconst span = this.dom.tabsDiv.select('#sjpp-gb-pop2avg')\n\t\tconst lst: any = []\n\t\tfor (const k in pop2average) {\n\t\t\tconst value = pop2average[k]\n\t\t\tif (!Number.isFinite(value)) continue // if there are no samples involved in current view, admix value is null\n\t\t\tlst.push(`${k}=${value.toFixed(2)}`)\n\t\t}\n\t\tif (lst.length) {\n\t\t\t// has valid admix values to display\n\t\t\tspan.style('display', 'inline')\n\t\t\tspan.select('#sjpp-gb-pop2avg-values').text(` ${lst.join(', ')}`)\n\t\t} else {\n\t\t\tspan.style('display', 'none')\n\t\t}\n\t}\n\n\t/* tricky logic */\n\tasync launchBlockWithTracks(tklst) {\n\t\tif (!['GDC', 'MMRF'].includes(this.state?.vocab?.dslabel) && this.blockInstance) {\n\t\t\t/* block instance is present\n            this should be updating tracks in this block, by adding new ones listed in tklst[],\n            and deleting old ones via a tricky method\n            */\n\t\t\tfor (const tk of tklst) {\n\t\t\t\tlet tki // index of this tk in block\n\t\t\t\tif (tk.dslabel) {\n\t\t\t\t\t// tk has dslabel and must be identified by it\n\t\t\t\t\ttki = this.blockInstance.tklst.findIndex(i => i.dslabel == tk.dslabel)\n\t\t\t\t} else if (tk.name) {\n\t\t\t\t\t// identify tk by name\n\t\t\t\t\ttki = this.blockInstance.tklst.findIndex(i => i.name == tk.name)\n\t\t\t\t} else {\n\t\t\t\t\tthrow 'tk missing dslabel & name'\n\t\t\t\t}\n\t\t\t\tif (tki == -1) {\n\t\t\t\t\t// this tk is not in block, add to block\n\t\t\t\t\tconst t = this.blockInstance.block_addtk_template(tk)\n\t\t\t\t\tthis.blockInstance.tk_load(t)\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (this.state.config.trackLst?.removeTracks) {\n\t\t\t\t// facet table marks these tracks for removal. they are all identified by tk.name\n\t\t\t\tfor (const n of this.state.config.trackLst.removeTracks) {\n\t\t\t\t\tconst i = this.blockInstance.tklst.findIndex(i => i.name == n)\n\t\t\t\t\tif (i != -1) this.blockInstance.tk_remove(i)\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (this.state.config.ld?.tracks) {\n\t\t\t\tfor (const t of this.state.config.ld.tracks) {\n\t\t\t\t\tconst i = this.blockInstance.tklst.findIndex(i => i.name == t.name)\n\t\t\t\t\tif (!t.shown && i != -1) this.blockInstance.tk_remove(i)\n\t\t\t\t}\n\t\t\t}\n\t\t\t// tricky! if snvindel.shown is false, means user has toggled it off. thus find all mds3 tk and remove them\n\t\t\tif (this.state.config.snvindel && !this.state.config.snvindel.shown) {\n\t\t\t\tlet found = true\n\t\t\t\twhile (found) {\n\t\t\t\t\tfound = false\n\t\t\t\t\tfor (const [i, tk] of this.blockInstance.tklst.entries()) {\n\t\t\t\t\t\tif (tk.type == 'mds3') {\n\t\t\t\t\t\t\tthis.blockInstance.tk_remove(i)\n\t\t\t\t\t\t\tfound = true\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\treturn\n\t\t}\n\n\t\t// is GDC, MMRF, and/or no block instance, create new block\n\n\t\tthis.dom.blockHolder.selectAll('*').remove()\n\t\tconst arg: any = {\n\t\t\tholder: this.dom.blockHolder,\n\t\t\tgenome: this.opts.genome, // genome obj\n\t\t\tnobox: true,\n\t\t\ttklst,\n\t\t\tdebugmode: this.opts.debug,\n\t\t\tonAddRemoveTk: () => {\n\t\t\t\tthis.interactions.maySaveTrackUpdatesToState(this.blockInstance)\n\t\t\t},\n\t\t\tfilter0: this.state.filter0\n\t\t}\n\n\t\tif (this.data) {\n\t\t\t// variant data has been precomputed\n\t\t\t// need to recompute upon coordinate change\n\t\t\targ.onCoordinateChange = this.interactions.onCoordinateChange\n\t\t}\n\n\t\tif (this.state.config.blockIsProteinMode) {\n\t\t\t// must be in protein mode and requires gene symbol\n\t\t\tif (!this.state.config.geneSearchResult.geneSymbol) throw 'blockIsProteinMode=true but geneSymbol missing'\n\t\t\t// dataset config wants to default to gene view, and gene symbol is available\n\t\t\t// call block.init to launch gene view\n\t\t\targ.query = this.state.config.geneSearchResult.geneSymbol\n\t\t\tconst _ = await import('#src/block.init')\n\t\t\tawait _.default(arg)\n\t\t\tthis.blockInstance = arg.__blockInstance\n\n\t\t\t// update sandbox header with gene name\n\t\t\tif (this.opts.header) this.opts.header.text(arg.query)\n\t\t\treturn\n\t\t}\n\t\t// must be in genomic mode and requires coord\n\t\tif (!this.state.config.geneSearchResult.chr) throw 'blockIsProteinMode=false but chr missing'\n\t\targ.chr = this.state.config.geneSearchResult.chr\n\t\targ.start = this.state.config.geneSearchResult.start\n\t\targ.stop = this.state.config.geneSearchResult.stop\n\t\tfirst_genetrack_tolist(this.opts.genome, arg.tklst)\n\n\t\tconst _ = await import('#src/block')\n\t\tthis.blockInstance = new _.Block(arg)\n\t}\n}\n\n/* given group configuration, determine: numeric track axis label\n- viewmode.label as axis label of numeric mode\n- viewmode.tooltipPrintValue()\n*/\nfunction furbishViewModeWithSnvindelComputeDetails(self, viewmode) {\n\tdelete viewmode.tooltipPrintValue\n\n\tconst [g1, g2] = self.state.config.snvindel.details.groups\n\tif (g1 && g2) {\n\t\tif (g1.type == 'info' || g2.type == 'info') {\n\t\t\t// either group is info field. value type can only be value difference\n\t\t\tviewmode.label = 'Value difference'\n\t\t\treturn\n\t\t}\n\t\t// none of the group is info field. each group should derive AF and there can be different ways of comparing it from two groups\n\t\tconst testMethod =\n\t\t\tself.state.config.snvindel.details.groupTestMethods[self.state.config.snvindel.details.groupTestMethodsIdx]\n\t\tviewmode.label = testMethod.axisLabel || testMethod.name\n\t\tif (testMethod.name == 'Allele frequency difference') {\n\t\t\t// callback returns value separated by ' = ', which allows this to be also displayed in itemtable.js\n\t\t\tviewmode.tooltipPrintValue = m => [{ k: 'AF diff', v: m.nm_axis_value }]\n\t\t} else if (testMethod.name == \"Fisher's exact test\") {\n\t\t\tviewmode.tooltipPrintValue = m => [{ k: 'p-value', v: m.p_value }]\n\t\t}\n\t\treturn\n\t}\n\n\t// only 1 group\n\tif (g1.type == 'info') {\n\t\tconst f = self.state.config.variantFilter?.terms?.find(i => i.id == g1.infoKey)\n\t\tviewmode.label = f?.name || g1.infoKey\n\t\tviewmode.tooltipPrintValue = m => [{ k: viewmode.label, v: m.info[g1.infoKey] }]\n\t\treturn\n\t}\n\tif (g1.type == 'filter') {\n\t\tviewmode.label = 'Allele frequency'\n\t\tviewmode.tooltipPrintValue = m => [{ k: 'Allele frequency', v: m.nm_axis_value }]\n\t\treturn\n\t}\n\tif (g1.type == 'population') {\n\t\tviewmode.label = 'Allele frequency'\n\t\tviewmode.tooltipPrintValue = m => [{ k: 'Allele frequency', v: m.nm_axis_value }]\n\t\treturn\n\t}\n\tthrow 'unknown type of the only group'\n}\n", "import { PlotBase } from '../PlotBase.ts'\nimport { getCompInit, type ComponentApi, type RxComponent } from '#rx'\nimport { Menu, sayerror } from '#dom'\nimport { getNormalRoot } from '#filter'\nimport { Model } from './model/Model.ts'\nimport { View } from './view/View.ts'\nimport { Interactions, mayUpdateGroupTestMethodsIdx } from './interactions/Interactions.ts'\n\nclass TdbGenomeBrowser extends PlotBase implements RxComponent {\n\tstatic type = 'genomeBrowser'\n\n\t// expected RxComponentInner props, some are already declared/set in PlotBase\n\ttype: string\n\tparentId?: string\n\tdom!: {\n\t\t[index: string]: any\n\t}\n\tcomponents: {\n\t\t[name: string]: ComponentApi | { [name: string]: ComponentApi }\n\t} = {}\n\tinteractions: any\n\tblockInstance: any\n\n\tconstructor(opts, api) {\n\t\tsuper(opts, api)\n\t\tthis.type = TdbGenomeBrowser.type\n\t\tthis.dom = this.getDom()\n\t}\n\n\tgetDom() {\n\t\tconst holder = this.opts.holder.append('div')\n\t\tif (this.opts.header) {\n\t\t\t/** Plot may not launch in a sandbox (such as in GDC), hence no header. */\n\t\t\tthis.opts.header\n\t\t\t\t.append('div')\n\t\t\t\t.style('opacity', 0.6)\n\t\t\t\t.style('padding-left', '10px')\n\t\t\t\t.style('font-size', '0.75em')\n\t\t\t\t.text('GENOME BROWSER')\n\t\t}\n\t\t// layout rows from top to bottom\n\t\tconst loadingDiv = holder.append('div').style('display', 'none').style('margin-left', '25px').text('Loading...')\n\t\tconst errDiv = holder.append('div').style('display', 'none').style('margin', '10px')\n\t\tconst controlsDiv = holder.append('div').style('margin', '15px 0px 0px 25px')\n\t\tconst dom = {\n\t\t\ttip: new Menu(),\n\t\t\tholder,\n\t\t\tloadingDiv,\n\t\t\terrDiv,\n\t\t\ttabsDiv: controlsDiv.append('div'),\n\t\t\tgeneSearchDiv: controlsDiv.append('div').style('margin', '20px 0px'),\n\t\t\tblockHolder: holder.append('div')\n\t\t}\n\t\treturn dom\n\t}\n\n\tasync init() {\n\t\tthis.interactions = new Interactions(this.app, this.dom, this.id)\n\t}\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) throw `No plot with id='${this.id}' found`\n\t\treturn {\n\t\t\tconfig,\n\t\t\tfilter: getNormalRoot(appState.termfilter.filter),\n\t\t\tfilter0: appState.termfilter.filter0,\n\t\t\tvocab: appState.vocab\n\t\t}\n\t}\n\n\tasync main() {\n\t\tthis.dom.loadingDiv.style('display', 'block')\n\t\tthis.dom.errDiv.style('display', 'none')\n\t\tconst state = this.getState(this.app.getState())\n\t\tif (state.config.chartType != this.type) return\n\t\tconst opts = this.getOpts()\n\t\ttry {\n\t\t\tconst model = new Model(state, this.app)\n\t\t\tconst data = await model.preComputeData()\n\t\t\tconst view = new View(state, this.blockInstance, data, this.dom, opts, this.interactions)\n\t\t\tawait view.main()\n\t\t\tthis.blockInstance = view.blockInstance\n\t\t} catch (e: any) {\n\t\t\tthis.dom.errDiv.style('display', 'block')\n\t\t\tsayerror(this.dom.errDiv, 'Error: ' + (e.message || e))\n\t\t\tif (e.stack) console.log(e.stack)\n\t\t}\n\t\tthis.dom.loadingDiv.style('display', 'none')\n\t}\n\n\t// get options for view instance\n\tgetOpts() {\n\t\tconst opts = {\n\t\t\tgenome: this.app.opts.genome,\n\t\t\tvocabApi: this.app.vocabApi,\n\t\t\tdebug: this.app.opts.debug,\n\t\t\tplotDiv: this.opts.plotDiv,\n\t\t\theader: this.opts.header,\n\t\t\tallow2selectSamples: this.opts.allow2selectSamples\n\t\t}\n\t\treturn opts\n\t}\n}\n\nexport const genomeBrowserInit = getCompInit(TdbGenomeBrowser)\n// this alias will allow abstracted dynamic imports\nexport const componentInit = genomeBrowserInit\n\nexport async function getPlotConfig(opts, app, activeCohort) {\n\ttry {\n\t\t// request default queries config from dataset, and allows opts to override\n\t\tconst c = await getDefaultConfig(app.vocabApi, opts, activeCohort)\n\t\treturn c\n\t} catch (e) {\n\t\tthrow `${e} [genomeBrowser getPlotConfig()]`\n\t}\n}\n\n/* compute default config\nvocabApi\noverride? {}\n    optional custom state to override default\nactiveCohort\n\tindex of active cohort (-1/0/1)\n*/\nasync function getDefaultConfig(vocabApi, override, activeCohort) {\n\tconst config = Object.assign(\n\t\t// clone for modifying\n\t\tstructuredClone({\n\t\t\tsnvindel: vocabApi.termdbConfig.queries.snvindel,\n\t\t\ttrackLst: vocabApi.termdbConfig.queries.trackLst,\n\t\t\tld: vocabApi.termdbConfig.queries.ld\n\t\t}),\n\t\toverride || {}\n\t)\n\tcomputeBlockModeFlag(config, vocabApi)\n\n\tif (config.snvindel) {\n\t\t// presence of snvindel will generate the \"mds3\" tk, here setup associated config\n\t\t// request default variant filter (vcf INFO), required for snvindel\n\t\tif (!config.variantFilter) {\n\t\t\tconst vf = await vocabApi.get_variantFilter()\n\t\t\tif (vf?.filter) {\n\t\t\t\tconfig.variantFilter = vf\n\t\t\t}\n\t\t}\n\t\tif (config.snvindel.details) {\n\t\t\t// test method may be inconsistent with group configuration (e.g. no fisher for INFO fields), update test method here\n\t\t\t// 1st arg is a fake \"self\"\n\t\t\tmayUpdateGroupTestMethodsIdx({ config }, config.snvindel.details)\n\t\t\t// a type=filter group may use filterByCohort. in such case, modify default state to assign proper filter based on current cohort\n\t\t\tconst gf = config.snvindel.details.groups.find(i => i.type == 'filter')\n\t\t\tif (gf?.filterByCohort) {\n\t\t\t\tif (!Number.isInteger(activeCohort)) throw 'filterByCohort but activeCohort not integer'\n\t\t\t\t// modify and assign\n\t\t\t\tgf.filter = gf.filterByCohort[vocabApi.termdbConfig.selectCohort.values[activeCohort].keys.join(',')]\n\t\t\t\tif (!gf.filter) throw 'unknown filter by current cohort name'\n\t\t\t\tdelete gf.filterByCohort\n\t\t\t}\n\t\t}\n\n\t\tif (typeof config.snvindel.shown != 'boolean') {\n\t\t\t// create missing tracker property with default value to determine if to show/hide snvindel mds3 tk\n\t\t\tif (config.trackLst) {\n\t\t\t\t// also has track lst/facet\n\t\t\t\t// hardcoded! hide snvindel by default! definitely change it later!\n\t\t\t\tconfig.snvindel.shown = false\n\t\t\t} else {\n\t\t\t\t// no tklst/facet\n\t\t\t\tconfig.snvindel.shown = true\n\t\t\t}\n\t\t}\n\t}\n\n\tif (config.trackLst) {\n\t\tif (!config.trackLst.facets) throw 'trackLst.facets[] missing'\n\t\tif (!config.trackLst.activeTracks) config.trackLst.activeTracks = []\n\t}\n\treturn config\n}\n\nexport function computeBlockModeFlag(config, vocabApi?) {\n\t// steps follow the order of priority\n\tif (typeof config.blockIsProteinMode == 'boolean') {\n\t\t// state has predefined mode, do not modify\n\t\treturn\n\t}\n\t// lack of mode e.g. from urlparam shorthand state. compute default value\n\tswitch (vocabApi.termdbConfig.queries.gbRestrictMode) {\n\t\tcase undefined:\n\t\t\t// ds doesn't restrict mode; when user searched gene, assume it should be in genomic mode\n\t\t\tif (config.geneSearchResult?.geneSymbol) {\n\t\t\t\tconfig.blockIsProteinMode = true\n\t\t\t} else {\n\t\t\t\tconfig.blockIsProteinMode = false\n\t\t\t}\n\t\t\tbreak\n\t\tcase 'protein':\n\t\t\t// ds only allow protein mode\n\t\t\tconfig.blockIsProteinMode = true\n\t\t\tbreak\n\t\tcase 'genomic':\n\t\t\t// ds only allow genomic mode\n\t\t\tconfig.blockIsProteinMode = false\n\t\t\tbreak\n\t\tdefault:\n\t\t\tthrow 'unknown gbRestrictMode'\n\t}\n}\n\n/*\ncalled in mass/charts.js, to render the menu upon clicking the chart button in the charts tray\n\tholder: the holder in the tooltip\n\tchartsInstance: MassCharts instance\n*/\nexport function makeChartBtnMenu(_holder, chartsInstance) {\n\tconst chart = { config: { chartType: 'genomeBrowser' } }\n\tchartsInstance.prepPlot(chart)\n}\n"],
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+  "names": ["i", "i", "_"]
+}

package/dist/GeneExpInput-3AQEPTFZ.js

@@ -0,0 +1,367 @@
+import {
+  GeneSetEditUI,
+  PlotBase,
+  addGeneSearchbox,
+  getCurrentCohortChartTypes,
+  getGEunit,
+  getSCGEunit,
+  sayerror
+} from "./chunk-L7VDSIM7.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import {
+  importPlot
+} from "./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 "./chunk-6G4YOMWW.js";
+import "./chunk-7IYJZZQI.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-I73KUUYG.js";
+import {
+  GENE_EXPRESSION,
+  SINGLECELL_GENE_EXPRESSION,
+  SSGSEA,
+  typeGroup
+} from "./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/GeneExpInput.ts
+var GeneExpInput = class _GeneExpInput extends PlotBase {
+  static {
+    this.type = "GeneExpInput";
+  }
+  constructor(opts, api) {
+    super(opts, api);
+    this.type = _GeneExpInput.type;
+    this.opts = opts;
+    this.components = {
+      plots: {}
+    };
+  }
+  makeTerm(_term) {
+    const termProperties = this.state.config?.termProperties || {};
+    const term = { ..._term, ...termProperties, type: this.termType, unit: this.unit };
+    return term;
+  }
+  makeConfig(_config) {
+    const spawnConfig = this.state.config?.spawnConfig || {};
+    const tmp = { ..._config, ...spawnConfig };
+    return tmp;
+  }
+  getState(appState) {
+    const config = appState.plots.find((p) => p.id === this.id);
+    if (!config) {
+      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
+    }
+    const subplots = appState.plots.filter((p) => p.parentId === this.id);
+    return {
+      config,
+      termdbConfig: appState.termdbConfig,
+      subplots
+    };
+  }
+  async init(appState) {
+    const state = this.getState(appState);
+    this.genome = this.app.opts.genome;
+    this.termType = state.config.termType;
+    this.unit = this.getUnit();
+    this.dom = this.initDom();
+    const chartTypes = new Set(getCurrentCohortChartTypes(appState));
+    this.tabs = [
+      {
+        label: "One gene",
+        isVisible: () => true,
+        callback: (event, tab) => {
+          this.renderGeneSelect(tab);
+          delete tab.callback;
+        }
+      },
+      {
+        label: "Two genes",
+        isVisible: () => true,
+        callback: (event, tab) => {
+          this.renderTwoGeneSelect(tab);
+          delete tab.callback;
+        }
+      },
+      {
+        label: "Hierarchical clustering",
+        isVisible: () => chartTypes.has("matrix"),
+        callback: (event, tab) => {
+          this.renderGeneMultiSelect(tab);
+          delete tab.callback;
+        }
+      },
+      {
+        label: `Differential ${typeGroup[this.termType].toLowerCase()} analysis`,
+        //Only enabling for gene expression for now
+        chartType: "DEinput",
+        isVisible: () => chartTypes.has("DA") && this.termType === GENE_EXPRESSION,
+        callback: async (event, tab) => {
+          await this.app.dispatch({
+            type: "plot_create",
+            parentId: this.id,
+            config: {
+              chartType: "DEinput",
+              parentId: this.id,
+              /** ' ' overrides the default 'hide_search' mode in DEInput.
+               * 'hide_search' by default expands all terms. */
+              header_mode: " "
+            }
+          });
+          delete tab.callback;
+        }
+      },
+      {
+        label: typeGroup[SSGSEA],
+        isVisible: () => {
+          return this.termType === GENE_EXPRESSION && state.termdbConfig?.allowedTermTypes?.includes(SSGSEA);
+        },
+        callback: async (event, tab) => {
+          await this.renderSSGSEA(tab);
+          delete tab.callback;
+        }
+      }
+    ];
+    const chartTabs = new Tabs({
+      holder: this.dom.tabs,
+      tabs: this.tabs,
+      tabsPosition: "vertical"
+    });
+    await chartTabs.main();
+  }
+  getUnit() {
+    return this.termType === GENE_EXPRESSION ? getGEunit(this.app.vocabApi) : getSCGEunit(this.app.vocabApi);
+  }
+  initDom() {
+    const headerText = this.opts.headerText ? `${this.opts.headerText} ` : "";
+    const dom = {
+      header: {
+        title: this.opts.header.append("span").style("padding-right", "5px").text(headerText).attr("data-testid", "sjpp-gene-exp-input-headerText"),
+        plot: this.opts.header.append("span").text(typeGroup[this.termType].toUpperCase()).style("font-size", "0.7em").style("opacity", "0.6").attr("data-testid", "sjpp-gene-exp-input-termType")
+      },
+      tabs: this.opts.holder.append("div").style("margin", "10px").attr("data-testid", "sjpp-gene-exp-input-tabs-wrapper")
+    };
+    return dom;
+  }
+  async main() {
+    const state = this.getState(this.app.getState());
+    for (const subplot of state.subplots || []) {
+      if (!this.components.plots[subplot.id]) await this.initSubplotInTab(subplot);
+    }
+  }
+  renderGeneSelect(tab) {
+    const row = tab.contentHolder.style("padding", "15px");
+    row.append("span").style("padding", "5px").text("Select a gene:");
+    const geneSearch = addGeneSearchbox({
+      row,
+      genome: this.genome,
+      tip: new Menu({ padding: "0px" }),
+      searchOnly: "gene",
+      callback: async () => {
+        const tw = {
+          term: this.makeTerm({
+            gene: geneSearch.geneSymbol,
+            name: `${geneSearch.geneSymbol} ${this.unit}`
+          })
+        };
+        const config = this.makeConfig({
+          chartType: "summary",
+          term: tw
+        });
+        await this.dispatchEdits(config);
+      }
+    });
+  }
+  /** Guide the user to select the first gene then
+   * a second to launch the summary plot on submit.*/
+  renderTwoGeneSelect(tab) {
+    const term = {};
+    const term2 = {};
+    const holder = tab.contentHolder.style("padding", "10px");
+    const gene1row = holder.append("div").style("padding", "5px");
+    const gene2row = holder.append("div").style("padding", "5px").style("display", "none");
+    const submitButton = holder.append("button").attr("type", "button").attr("disabled", true);
+    gene1row.append("span").text("Select the first gene:");
+    const geneSearch1 = addGeneSearchbox({
+      row: gene1row,
+      genome: this.genome,
+      tip: new Menu({ padding: "0px" }),
+      searchOnly: "gene",
+      callback: async () => {
+        gene2row.style("display", "block");
+        if (!geneSearch1.geneSymbol) throw new Error("First gene result is required");
+        term.gene = geneSearch1.geneSymbol;
+        term.name = `${geneSearch1.geneSymbol} ${this.unit}`;
+      }
+    });
+    gene2row.append("span").text("Select the second gene:");
+    const geneSearch2 = addGeneSearchbox({
+      row: gene2row,
+      genome: this.genome,
+      tip: new Menu({ padding: "0px" }),
+      searchOnly: "gene",
+      callback: async () => {
+        if (!geneSearch2.geneSymbol) throw new Error("Second gene result is required");
+        term2.gene = geneSearch2.geneSymbol;
+        term2.name = `${geneSearch2.geneSymbol} ${this.unit}`;
+        submitButton.attr("disabled", null);
+      }
+    });
+    submitButton.text("Submit").style("border", "none").style("border-radius", "20px").style("padding", "10px 15px").on("click", async () => {
+      if (!term.name || !term.gene) {
+        sayerror(holder, "Missing first gene. Please provide a valid gene.");
+        return;
+      }
+      if (!term2.name || !term2.gene) {
+        sayerror(holder, "Missing second gene. Please provide a valid gene.");
+        return;
+      }
+      const config = this.makeConfig({
+        chartType: "summary",
+        term: { term: this.makeTerm(term) },
+        term2: { term: this.makeTerm(term2) }
+      });
+      await this.dispatchEdits(config);
+    });
+  }
+  // /** Render the GeneSetEdit UI for selection and then
+  //  * launch the hierarchical clustering on submit.*/
+  renderGeneMultiSelect(tab) {
+    const holder = tab.contentHolder.style("padding", "10px");
+    const grpWrapper = holder.append("div").style("padding", "10px");
+    grpWrapper.append("span").style("font-weight", "bold").text("Group name:");
+    let customName = "New custom group";
+    const input = grpWrapper.append("input").style("margin", "2px 5px").style("width", "210px").attr("placeholder", "Group Name").on("input", () => {
+      customName = input.property("value");
+    });
+    new GeneSetEditUI({
+      holder: holder.append("div"),
+      /** running hier clustering and the editing group
+       * is the group used for clustering pass this mode
+       * value to inform ui to support the optional button
+       * "top variably exp gene" this is hardcoded for
+       * the purpose of gene expression and should be improved. */
+      genome: this.genome,
+      mode: "geneExpression",
+      vocabApi: this.app.vocabApi,
+      callback: async ({ geneList, name }) => {
+        if (geneList.length <= 2) {
+          return alert("At least three genes are required for hierarchical clustering. Please select more genes.");
+        }
+        const group = {
+          name: name || customName,
+          lst: [],
+          type: "hierCluster"
+        };
+        const tws = await Promise.all(
+          geneList.map((d) => {
+            const gene = d.symbol || d.gene;
+            const name2 = `${gene} ${this.unit}`;
+            const term = this.makeTerm({ gene, name: name2 });
+            return { term, q: {} };
+          })
+        );
+        group.lst = [...tws];
+        const config = this.makeConfig({
+          chartType: "hierCluster",
+          termgroups: [group],
+          //TODO: Need to allow singleCellGeneExpression as well
+          dataType: GENE_EXPRESSION
+        });
+        await this.dispatchEdits(config);
+      }
+    });
+  }
+  async renderSSGSEA(tab) {
+    const holder = tab.contentHolder.style("padding", "10px");
+    const _ = await import("./ssGSEA-BFTCECV3.js");
+    const searchHandler = new _.SearchHandler();
+    await searchHandler.init({
+      holder,
+      app: this.app,
+      genomeObj: this.genome,
+      callback: async (term) => {
+        const config = this.makeConfig({
+          chartType: "summary",
+          term: { term }
+        });
+        await this.dispatchEdits(config);
+      }
+    });
+  }
+  async initSubplotInTab(subplot) {
+    const holder = this.tabs.find((tab) => tab.chartType === subplot.chartType)?.contentHolder;
+    if (!holder) throw new Error(`No tab found for chart type ${subplot.chartType}`);
+    const opts = Object.assign({}, subplot, {
+      holder,
+      app: this.app,
+      parentId: this.id,
+      id: subplot.id
+    });
+    const { componentInit: componentInit2 } = await importPlot(opts.chartType);
+    this.components.plots[subplot.id] = await componentInit2(opts);
+  }
+  async dispatchEdits(config) {
+    await this.app.dispatch({
+      type: "app_refresh",
+      subactions: [
+        {
+          type: "plot_create",
+          config
+        },
+        {
+          type: "plot_delete",
+          id: this.id
+        }
+      ]
+    });
+  }
+};
+var geneExpInputInit = getCompInit(GeneExpInput);
+var componentInit = geneExpInputInit;
+var enabledTermTypes = /* @__PURE__ */ new Set([GENE_EXPRESSION, SINGLECELL_GENE_EXPRESSION]);
+function getPlotConfig(opts) {
+  if (!opts?.termType) throw new Error("termType is required in opts");
+  if (!enabledTermTypes.has(opts.termType)) throw new Error(`Invalid termType: ${opts.termType}`);
+  const config = {
+    chartType: "GeneExpInput",
+    termType: opts.termType,
+    hidePlotFilter: true
+  };
+  return copyMerge(config, opts);
+}
+export {
+  GeneExpInput,
+  componentInit,
+  geneExpInputInit,
+  getPlotConfig
+};
+//# sourceMappingURL=GeneExpInput-3AQEPTFZ.js.map

package/dist/GeneExpInput-3AQEPTFZ.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/GeneExpInput.ts"],
+  "sourcesContent": ["import { PlotBase } from './PlotBase.ts'\nimport { getCompInit, copyMerge, type ComponentApi, type RxComponent } from '#rx'\nimport { GENE_EXPRESSION, SINGLECELL_GENE_EXPRESSION, SSGSEA, typeGroup } from '#shared/terms.js'\nimport { getGEunit } from '../tw/geneExpression'\nimport { getSCGEunit } from '../tw/singleCellGeneExpression'\nimport { addGeneSearchbox, GeneSetEditUI, Menu, sayerror, Tabs } from '#dom'\nimport type { ClientGenome } from '../types/clientGenome'\nimport { getCurrentCohortChartTypes } from '../mass/charts.js'\nimport { importPlot } from '#plots/importPlot.js'\n\ntype GeneExpInputOpts = {\n\t/** sandbox header\n\t * Normally this is optional but there's no reason to launch this plot\n\t * sans sandbox. */\n\theader: any\n\t/** Optional text to display in the header before the term type */\n\theaderText?: string\n\ttermProperties?: { [key: string]: any }\n\tspawnConfig?: { [key: string]: any }\n}\n\n/** Transient plot for users to pick gene(s) of interest and launch\n * the appropriate plot. */\nexport class GeneExpInput extends PlotBase implements RxComponent {\n\tstatic type = 'GeneExpInput'\n\n\ttype: string\n\tcomponents: { plots: { [key: string]: any } }\n\tgenome!: ClientGenome\n\ttermType!: string\n\t/** termType dependent */\n\tunit!: string\n\tdom!: { [index: string]: any }\n\ttabs!: any\n\n\tconstructor(opts: GeneExpInputOpts, api: ComponentApi) {\n\t\tsuper(opts, api)\n\t\tthis.type = GeneExpInput.type\n\t\tthis.opts = opts\n\t\tthis.components = {\n\t\t\tplots: {}\n\t\t}\n\t}\n\n\tmakeTerm(_term) {\n\t\tconst termProperties = this.state.config?.termProperties || {}\n\t\tconst term = { ..._term, ...termProperties, type: this.termType, unit: this.unit }\n\t\treturn term\n\t}\n\n\tmakeConfig(_config) {\n\t\tconst spawnConfig = this.state.config?.spawnConfig || {}\n\t\tconst tmp = { ..._config, ...spawnConfig }\n\t\treturn tmp\n\t}\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) {\n\t\t\tthrow `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`\n\t\t}\n\t\tconst subplots = appState.plots.filter(p => p.parentId === this.id)\n\t\treturn {\n\t\t\tconfig,\n\t\t\ttermdbConfig: appState.termdbConfig,\n\t\t\tsubplots\n\t\t}\n\t}\n\n\tasync init(appState) {\n\t\tconst state = this.getState(appState)\n\t\tthis.genome = this.app.opts.genome\n\t\tthis.termType = state.config.termType\n\t\tthis.unit = this.getUnit()\n\t\tthis.dom = this.initDom()\n\n\t\tconst chartTypes = new Set(getCurrentCohortChartTypes(appState))\n\n\t\tthis.tabs = [\n\t\t\t{\n\t\t\t\tlabel: 'One gene',\n\t\t\t\tisVisible: () => true,\n\t\t\t\tcallback: (event, tab) => {\n\t\t\t\t\tthis.renderGeneSelect(tab)\n\t\t\t\t\tdelete tab.callback\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Two genes',\n\t\t\t\tisVisible: () => true,\n\t\t\t\tcallback: (event, tab) => {\n\t\t\t\t\tthis.renderTwoGeneSelect(tab)\n\t\t\t\t\tdelete tab.callback\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Hierarchical clustering',\n\t\t\t\tisVisible: () => chartTypes.has('matrix'),\n\t\t\t\tcallback: (event, tab) => {\n\t\t\t\t\tthis.renderGeneMultiSelect(tab)\n\t\t\t\t\tdelete tab.callback\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: `Differential ${typeGroup[this.termType].toLowerCase()} analysis`,\n\t\t\t\t//Only enabling for gene expression for now\n\t\t\t\tchartType: 'DEinput',\n\t\t\t\tisVisible: () => chartTypes.has('DA') && this.termType === GENE_EXPRESSION,\n\t\t\t\tcallback: async (event, tab) => {\n\t\t\t\t\tawait this.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\t\tparentId: this.id,\n\t\t\t\t\t\tconfig: {\n\t\t\t\t\t\t\tchartType: 'DEinput',\n\t\t\t\t\t\t\tparentId: this.id,\n\t\t\t\t\t\t\t/** ' ' overrides the default 'hide_search' mode in DEInput.\n\t\t\t\t\t\t\t * 'hide_search' by default expands all terms. */\n\t\t\t\t\t\t\theader_mode: ' '\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\t\tdelete tab.callback\n\t\t\t\t}\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: typeGroup[SSGSEA],\n\t\t\t\tisVisible: () => {\n\t\t\t\t\treturn this.termType === GENE_EXPRESSION && state.termdbConfig?.allowedTermTypes?.includes(SSGSEA)\n\t\t\t\t},\n\t\t\t\tcallback: async (event, tab) => {\n\t\t\t\t\tawait this.renderSSGSEA(tab)\n\t\t\t\t\tdelete tab.callback\n\t\t\t\t}\n\t\t\t}\n\t\t]\n\n\t\tconst chartTabs = new Tabs({\n\t\t\tholder: this.dom.tabs,\n\t\t\ttabs: this.tabs,\n\t\t\ttabsPosition: 'vertical'\n\t\t})\n\t\tawait chartTabs.main()\n\t}\n\n\tgetUnit() {\n\t\treturn this.termType === GENE_EXPRESSION ? getGEunit(this.app.vocabApi) : getSCGEunit(this.app.vocabApi)\n\t}\n\n\tinitDom() {\n\t\tconst headerText = this.opts.headerText ? `${this.opts.headerText} ` : ''\n\t\tconst dom: { [index: string]: any } = {\n\t\t\theader: {\n\t\t\t\ttitle: this.opts.header\n\t\t\t\t\t.append('span')\n\t\t\t\t\t.style('padding-right', '5px')\n\t\t\t\t\t.text(headerText)\n\t\t\t\t\t.attr('data-testid', 'sjpp-gene-exp-input-headerText'),\n\t\t\t\tplot: this.opts.header\n\t\t\t\t\t.append('span')\n\t\t\t\t\t.text(typeGroup[this.termType].toUpperCase())\n\t\t\t\t\t.style('font-size', '0.7em')\n\t\t\t\t\t.style('opacity', '0.6')\n\t\t\t\t\t.attr('data-testid', 'sjpp-gene-exp-input-termType')\n\t\t\t},\n\t\t\ttabs: this.opts.holder\n\t\t\t\t.append('div')\n\t\t\t\t.style('margin', '10px')\n\t\t\t\t.attr('data-testid', 'sjpp-gene-exp-input-tabs-wrapper')\n\t\t}\n\n\t\treturn dom\n\t}\n\n\tasync main() {\n\t\tconst state = this.getState(this.app.getState())\n\n\t\tfor (const subplot of state.subplots || []) {\n\t\t\tif (!this.components.plots[subplot.id]) await this.initSubplotInTab(subplot)\n\t\t}\n\t}\n\n\trenderGeneSelect(tab) {\n\t\tconst row = tab.contentHolder.style('padding', '15px')\n\t\trow.append('span').style('padding', '5px').text('Select a gene:')\n\t\tconst geneSearch = addGeneSearchbox({\n\t\t\trow,\n\t\t\tgenome: this.genome,\n\t\t\ttip: new Menu({ padding: '0px' }),\n\t\t\tsearchOnly: 'gene',\n\t\t\tcallback: async () => {\n\t\t\t\tconst tw = {\n\t\t\t\t\tterm: this.makeTerm({\n\t\t\t\t\t\tgene: geneSearch.geneSymbol,\n\t\t\t\t\t\tname: `${geneSearch.geneSymbol} ${this.unit}`\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t\tconst config = this.makeConfig({\n\t\t\t\t\tchartType: 'summary',\n\t\t\t\t\tterm: tw\n\t\t\t\t})\n\t\t\t\tawait this.dispatchEdits(config)\n\t\t\t}\n\t\t})\n\t}\n\n\t/** Guide the user to select the first gene then\n\t * a second to launch the summary plot on submit.*/\n\trenderTwoGeneSelect(tab) {\n\t\tconst term: any = {}\n\t\tconst term2: any = {}\n\n\t\tconst holder = tab.contentHolder.style('padding', '10px')\n\n\t\tconst gene1row = holder.append('div').style('padding', '5px')\n\t\tconst gene2row = holder.append('div').style('padding', '5px').style('display', 'none')\n\t\tconst submitButton = holder.append('button').attr('type', 'button').attr('disabled', true)\n\n\t\tgene1row.append('span').text('Select the first gene:')\n\t\tconst geneSearch1 = addGeneSearchbox({\n\t\t\trow: gene1row,\n\t\t\tgenome: this.genome,\n\t\t\ttip: new Menu({ padding: '0px' }),\n\t\t\tsearchOnly: 'gene',\n\t\t\tcallback: async () => {\n\t\t\t\tgene2row.style('display', 'block')\n\t\t\t\tif (!geneSearch1.geneSymbol) throw new Error('First gene result is required')\n\t\t\t\tterm.gene = geneSearch1.geneSymbol\n\t\t\t\tterm.name = `${geneSearch1.geneSymbol} ${this.unit}`\n\t\t\t}\n\t\t})\n\n\t\tgene2row.append('span').text('Select the second gene:')\n\t\tconst geneSearch2 = addGeneSearchbox({\n\t\t\trow: gene2row,\n\t\t\tgenome: this.genome,\n\t\t\ttip: new Menu({ padding: '0px' }),\n\t\t\tsearchOnly: 'gene',\n\t\t\tcallback: async () => {\n\t\t\t\tif (!geneSearch2.geneSymbol) throw new Error('Second gene result is required')\n\t\t\t\tterm2.gene = geneSearch2.geneSymbol\n\t\t\t\tterm2.name = `${geneSearch2.geneSymbol} ${this.unit}`\n\t\t\t\tsubmitButton.attr('disabled', null)\n\t\t\t}\n\t\t})\n\n\t\tsubmitButton\n\t\t\t.text('Submit')\n\t\t\t.style('border', 'none')\n\t\t\t.style('border-radius', '20px')\n\t\t\t.style('padding', '10px 15px')\n\t\t\t.on('click', async () => {\n\t\t\t\tif (!term.name || !term.gene) {\n\t\t\t\t\tsayerror(holder, 'Missing first gene. Please provide a valid gene.')\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tif (!term2.name || !term2.gene) {\n\t\t\t\t\tsayerror(holder, 'Missing second gene. Please provide a valid gene.')\n\t\t\t\t\treturn\n\t\t\t\t}\n\n\t\t\t\tconst config = this.makeConfig({\n\t\t\t\t\tchartType: 'summary',\n\t\t\t\t\tterm: { term: this.makeTerm(term) },\n\t\t\t\t\tterm2: { term: this.makeTerm(term2) }\n\t\t\t\t})\n\t\t\t\tawait this.dispatchEdits(config)\n\t\t\t})\n\t}\n\t// /** Render the GeneSetEdit UI for selection and then\n\t//  * launch the hierarchical clustering on submit.*/\n\trenderGeneMultiSelect(tab) {\n\t\tconst holder = tab.contentHolder.style('padding', '10px')\n\t\tconst grpWrapper = holder.append('div').style('padding', '10px')\n\t\tgrpWrapper.append('span').style('font-weight', 'bold').text('Group name:')\n\n\t\tlet customName: string = 'New custom group'\n\t\tconst input = grpWrapper\n\t\t\t.append('input')\n\t\t\t.style('margin', '2px 5px')\n\t\t\t.style('width', '210px')\n\t\t\t.attr('placeholder', 'Group Name')\n\t\t\t.on('input', () => {\n\t\t\t\tcustomName = input.property('value')\n\t\t\t})\n\n\t\tnew GeneSetEditUI({\n\t\t\tholder: holder.append('div'),\n\t\t\t/** running hier clustering and the editing group\n\t\t\t * is the group used for clustering pass this mode\n\t\t\t * value to inform ui to support the optional button\n\t\t\t * \"top variably exp gene\" this is hardcoded for\n\t\t\t * the purpose of gene expression and should be improved. */\n\t\t\tgenome: this.genome,\n\t\t\tmode: 'geneExpression',\n\t\t\tvocabApi: this.app.vocabApi,\n\t\t\tcallback: async ({ geneList, name }) => {\n\t\t\t\tif (geneList.length <= 2) {\n\t\t\t\t\treturn alert('At least three genes are required for hierarchical clustering. 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+}