@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/GB-5PYCR4SV.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/gb/model/Model.ts", "../plots/gb/trackLst.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", "export function sanitizeTrackLstConfig(config) {\n\tif (!config.trackLst?.facets) return\n\tfor (const facet of config.trackLst.facets) delete facet.tracks\n}\n", "import type { MassAppApi } from '#mass/types/mass'\nimport { getNormalRoot } from '#filter'\nimport { sanitizeTrackLstConfig } from '../trackLst.ts'\n\nexport class Interactions {\n\tapp: MassAppApi\n\tdom: any\n\tid: string\n\tfacetTrackNames = new Set<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\tsetFacetTrackNames(names: Set<string>) {\n\t\tthis.facetTrackNames = names\n\t}\n\n\tonCoordinateChange = (rglst, blockInstance?) => {\n\t\tif (!rglst?.length) return\n\t\tconst config: any = {\n\t\t\tgeneSearchResult: { chr: rglst[0].chr, start: rglst[0].start, stop: rglst[0].stop }\n\t\t}\n\t\tconst block = getBlockState(blockInstance, rglst)\n\t\tif (block) config.block = block\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\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\tblock: { rglst: [] }\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\tsanitizeTrackLstConfig(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 && this.facetTrackNames.size) {\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 && this.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\tlaunchJunctionTrack = shown => {\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig: { junction: { shown } }\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 getBlockState(blockInstance, rglst) {\n\tconst blockRglst = cloneRglst(blockInstance?.rglst || rglst)\n\tif (!blockRglst?.length) return null\n\tconst block: any = { rglst: blockRglst }\n\tfor (const key of ['startidx', 'stopidx', 'regionspace', 'gmmode']) {\n\t\tconst value = blockInstance?.[key]\n\t\tif (value !== undefined) block[key] = value\n\t}\n\tif (blockInstance?.coord?.reverse !== undefined) block.coordReverse = blockInstance.coord.reverse\n\treturn block\n}\n\nfunction cloneRglst(rglst) {\n\tif (!Array.isArray(rglst)) return null\n\treturn rglst.map(r => {\n\t\tconst r2: any = {\n\t\t\tchr: r.chr,\n\t\t\tstart: r.start,\n\t\t\tstop: r.stop\n\t\t}\n\t\tfor (const key of ['bstart', 'bstop', 'width', 'reverse', 'name']) {\n\t\t\tif (r[key] !== undefined) r2[key] = r[key]\n\t\t}\n\t\treturn r2\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\tfacetData: any[]\n\tconstructor(state, dom, opts, interactions, facetData: any[] = []) {\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\tthis.facetData = facetData\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.facetData) {\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: 'Mutation', 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 || this.state.config.junction) {\n\t\t\t\t\t// When other track types are available, show a mutation tab to toggle the mds3 track.\n\t\t\t\t\ttabs.push({ label: 'Mutation', 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.junction) {\n\t\t\ttabs.push({ label: 'Splice junction', active: this.state.config.junction.shown })\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.facetData) {\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 || this.state.config.junction) {\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 mutation 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.junction) {\n\t\t\tconst div = tabs[tabsIdx++].contentHolder.append('div')\n\t\t\tmake_one_checkbox({\n\t\t\t\tlabeltext: 'Show splice junction track',\n\t\t\t\tchecked: this.state.config.junction.shown,\n\t\t\t\tholder: div,\n\t\t\t\tcallback: this.interactions.launchJunctionTrack\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\tif (!facet.tracks?.length) {\n\t\t\tdiv.append('div').style('opacity', 0.7).style('margin', '8px 0px').text('No tracks match the current filter.')\n\t\t\treturn\n\t\t}\n\t\tconst assayset = new Set<string>(),\n\t\t\tsampleset = new Set<string>()\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 facetTwLst: any[] = []\n\t\tfor (const tw of [this.state.config.facetTw1, this.state.config.facetTw2, this.state.config.facetTw3]) {\n\t\t\tif (!tw) break\n\t\t\tfacetTwLst.push(tw)\n\t\t}\n\t\tconst columns: any = [{ label: 'Sample', headerTestId: 'sjpp-gb-facettable-sample-columnheader' }] // TODO use ds sample type\n\t\tfor (const tw of facetTwLst) {\n\t\t\tcolumns.push({\n\t\t\t\tlabel: tw.term?.name || tw.term?.id || tw.id,\n\t\t\t\theaderTestId: 'sjpp-gb-facettable-tw-columnheader',\n\t\t\t\tfillCell: (td, si) => {\n\t\t\t\t\tconst sample = sampleLst[si]\n\t\t\t\t\tconst annotation = facet.samples?.[sample]?.[tw.$id]\n\t\t\t\t\tif (annotation !== undefined) td.text(annotation)\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t\tfor (const assay of assayLst) {\n\t\t\tcolumns.push({\n\t\t\t\tlabel: assay,\n\t\t\t\theaderTestId: 'sjpp-gb-facettable-assay-columnheader',\n\t\t\t\tlabelVertical: true,\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\tfor (let i = 0; i < facetTwLst.length; i++) {\n\t\t\t\trow.push({})\n\t\t\t}\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.getLatestActiveTracks() || 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\tconst currentActiveTracks = this.getLatestActiveTracks() || activeTracks\n\t\t\t\t\tlet newActiveTracks, newRemoveTracks\n\t\t\t\t\tif (currentActiveTracks.includes(tk.name)) {\n\t\t\t\t\t\ttd1.text('')\n\t\t\t\t\t\tnewActiveTracks = structuredClone(currentActiveTracks).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 = [...new Set([...currentActiveTracks, tk.name])]\n\t\t\t\t\t\tnewRemoveTracks = []\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\tgetLatestActiveTracks() {\n\t\tconst config = this.interactions.app.getState().plots.find(p => p.id === this.interactions.id)\n\t\treturn config?.trackLst?.activeTracks\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\tfacetData: any[]\n\tconstructor(state, blockInstance, data, dom, opts, interactions, facetData: any[] = []) {\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\tthis.facetData = facetData\n\t}\n\n\tasync main() {\n\t\tconst tabs = new TabsRenderer(this.state, this.dom, this.opts, this.interactions, this.facetData)\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 || this.state.config.svfusion?.shown) {\n\t\t\t// show mds3 tk driven by snvindel and/or svfusion (svfusion-only datasets rely on config.svfusion, set in GB.ts)\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.facetData) {\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.junction?.shown) {\n\t\t\tconst tk: any = {\n\t\t\t\ttype: 'j2',\n\t\t\t\t// Explicitly identifies this shared track as being hosted by the mass genome-browser plot.\n\t\t\t\tmassApp: this.opts.app,\n\t\t\t\tdslabel: this.state.vocab.dslabel,\n\t\t\t\tvocabApi: this.opts.vocabApi,\n\t\t\t\ttermdbConfig: this.opts.vocabApi?.termdbConfig,\n\t\t\t\tfilter0: this.state.filter0,\n\t\t\t\thiddentypes: this.state.config.junction.hiddentypes,\n\t\t\t\treadcountCutoff: this.state.config.junction.readcountCutoff\n\t\t\t}\n\t\t\tif (this.state.filter?.lst?.length) tk.filter = structuredClone(this.state.filter)\n\t\t\ttklst.push(tk)\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 (!this.opts.vocabApi?.termdbConfig?.gbRecreateBlock && 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// Official tracks from the same dataset can have different types (e.g. mds3 and j2).\n\t\t\t\t\ttki = this.blockInstance.tklst.findIndex(i => i.dslabel == tk.dslabel && i.type == tk.type)\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\tif (this.state.config.junction && !this.state.config.junction.shown) {\n\t\t\t\tconst i = this.blockInstance.tklst.findIndex(t => t.type == 'j2' && t.dslabel == this.state.vocab.dslabel)\n\t\t\t\tif (i != -1) this.blockInstance.tk_remove(i)\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\tconst interactions = this.interactions\n\t\targ.onCoordinateChange = function (rglst) {\n\t\t\tinteractions.onCoordinateChange(rglst, this)\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.block?.rglst?.length) {\n\t\t\targ.rglst = this.state.config.block.rglst\n\t\t} else {\n\t\t\tif (!this.state.config.geneSearchResult.chr) throw 'blockIsProteinMode=false but chr missing'\n\t\t\targ.chr = this.state.config.geneSearchResult.chr\n\t\t\targ.start = this.state.config.geneSearchResult.start\n\t\t\targ.stop = this.state.config.geneSearchResult.stop\n\t\t}\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 { getCombinedTermFilter, getNormalRoot, filterJoin } from '#filter'\nimport { fillTermWrapper } from '#termsetting'\nimport { controlsInit } from '#plots/controls.js'\nimport { Model } from './model/Model.ts'\nimport { View } from './view/View.ts'\nimport { Interactions, mayUpdateGroupTestMethodsIdx } from './interactions/Interactions.ts'\nimport { sanitizeTrackLstConfig } from './trackLst.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\t_prevFilterSig?: string\n\tconfigTermKeys = ['facetTw1', 'facetTw2', 'facetTw3']\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\tconst body = holder.append('div').style('display', 'flex').style('align-items', 'flex-start').style('gap', '12px')\n\t\tconst controlsDiv = body.append('div').style('flex', '0 0 auto')\n\t\tconst mainDiv = body\n\t\t\t.append('div')\n\t\t\t.style('flex', '1 1 auto')\n\t\t\t.style('min-width', 0)\n\t\t\t.style('margin', '15px 0px 0px 25px')\n\t\tconst errDiv = mainDiv.append('div').style('display', 'none').style('margin', '10px')\n\t\tconst dom = {\n\t\t\ttip: new Menu(),\n\t\t\tholder,\n\t\t\terrDiv,\n\t\t\tcontrols: controlsDiv.append('div'),\n\t\t\ttabsDiv: mainDiv.append('div'),\n\t\t\tgeneSearchDiv: mainDiv.append('div').style('margin', '20px 0px'),\n\t\t\tblockHolder: mainDiv.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\tawait this.setControls()\n\t}\n\n\tasync setControls() {\n\t\tconst state = this.getState(this.app.getState())\n\t\tif (!state.config.trackLst) return\n\t\tthis.dom.holder.attr('class', 'pp-termdb-plot-viz').style('display', 'inline-block').style('min-width', '300px')\n\t\tthis.components = {\n\t\t\tcontrols: await controlsInit({\n\t\t\t\tapp: this.app,\n\t\t\t\tid: this.id,\n\t\t\t\tholder: this.dom.controls.style('display', 'inline-block'),\n\t\t\t\ttitle: 'Genome Browser',\n\t\t\t\tinputs: [\n\t\t\t\t\t{\n\t\t\t\t\t\ttype: 'term',\n\t\t\t\t\t\tconfigKey: 'facetTw1',\n\t\t\t\t\t\tchartType: 'genomeBrowser',\n\t\t\t\t\t\tusecase: { target: 'genomeBrowser', detail: 'facetTw1' },\n\t\t\t\t\t\ttitle: 'Add column',\n\t\t\t\t\t\tlabel: 'Add column',\n\t\t\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\t\t\tprocessConfig: config => {\n\t\t\t\t\t\t\tif (!config.facetTw1) {\n\t\t\t\t\t\t\t\tconfig.facetTw2 = null\n\t\t\t\t\t\t\t\tconfig.facetTw3 = null\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\ttype: 'term',\n\t\t\t\t\t\tconfigKey: 'facetTw2',\n\t\t\t\t\t\tchartType: 'genomeBrowser',\n\t\t\t\t\t\tusecase: { target: 'genomeBrowser', detail: 'facetTw2' },\n\t\t\t\t\t\ttitle: 'Add column',\n\t\t\t\t\t\tlabel: 'Add column',\n\t\t\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\t\t\tgetDisplayStyle: plot => (getGbConfig(plot).facetTw1 ? 'table-row' : 'none'),\n\t\t\t\t\t\tprocessConfig: config => {\n\t\t\t\t\t\t\tif (!config.facetTw2) config.facetTw3 = null\n\t\t\t\t\t\t}\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\ttype: 'term',\n\t\t\t\t\t\tconfigKey: 'facetTw3',\n\t\t\t\t\t\tchartType: 'genomeBrowser',\n\t\t\t\t\t\tusecase: { target: 'genomeBrowser', detail: 'facetTw3' },\n\t\t\t\t\t\ttitle: 'Add column',\n\t\t\t\t\t\tlabel: 'Add column',\n\t\t\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\t\t\tgetDisplayStyle: plot => (getGbConfig(plot).facetTw2 ? 'table-row' : 'none')\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t})\n\t\t}\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\tconst parentConfig = appState.plots.find(p => p.id === this.parentId)\n\t\tconst termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter)\n\t\treturn {\n\t\t\tconfig,\n\t\t\tfilter: getNormalRoot(termfilter.filter),\n\t\t\tfilter0: termfilter.filter0,\n\t\t\tvocab: appState.vocab\n\t\t}\n\t}\n\n\tasync main() {\n\t\tthis.dom.holder.style('opacity', 0.5).style('pointer-events', 'none')\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\n\t\t// ---- force UI/track refresh when effective filters changed ----\n\t\t// include:\n\t\t// - global/local combined filter (state.filter)\n\t\t// - filter0 mass filter\n\t\t// - snvindel local filter (used by mds3 filterObj merge in View.generateTracks)\n\t\tconst mergedTkFilter =\n\t\t\tstate.filter && state.config.snvindel?.filter\n\t\t\t\t? filterJoin([state.filter, state.config.snvindel.filter])\n\t\t\t\t: state.filter || state.config.snvindel?.filter || null\n\n\t\tconst filterSig = JSON.stringify({\n\t\t\tfilter: mergedTkFilter || null,\n\t\t\tfilter0: state.filter0 || null\n\t\t})\n\n\t\tif (this._prevFilterSig && this._prevFilterSig !== filterSig && this.blockInstance) {\n\t\t\t// clear stale block so View.main() launches a fresh block+tracks from latest filters\n\t\t\t// this guarantees mds3 main/sub tracks re-materialize with updated filterObj/filter0\n\t\t\tthis.dom.blockHolder.selectAll('*').remove()\n\t\t\tthis.blockInstance = null\n\t\t}\n\t\tthis._prevFilterSig = filterSig\n\n\t\ttry {\n\t\t\tconst model = new Model(state, this.app)\n\t\t\tconst [data, facetData] = await Promise.all([model.preComputeData(), this.getFacetData(state)])\n\t\t\tthis.interactions.setFacetTrackNames(getFacetTrackNames(facetData))\n\t\t\tconst view = new View(state, this.blockInstance, data, this.dom, opts, this.interactions, facetData)\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.holder.style('opacity', 1).style('pointer-events', 'auto')\n\t}\n\n\tasync getFacetData(state) {\n\t\tif (!state.config.trackLst?.facets?.length) return []\n\n\t\tconst headers = await this.app.vocabApi.mayGetAuthHeaders('termdb')\n\t\treturn await Promise.all(\n\t\t\tstate.config.trackLst.facets.map(async facet => {\n\t\t\t\tconst body: any = {\n\t\t\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\t\t\tfacetname: facet.name,\n\t\t\t\t\ttwLst: getFacetTwLst(state.config)\n\t\t\t\t}\n\t\t\t\tif (state.filter?.lst?.length) body.filter = state.filter\n\t\t\t\tconst data = await this.app.vocabApi.dofetch3(\n\t\t\t\t\t'termdb/facet',\n\t\t\t\t\t{ headers, body },\n\t\t\t\t\tthis.app.vocabApi.opts.fetchOpts\n\t\t\t\t)\n\t\t\t\tif (data.error) throw data.error\n\t\t\t\treturn {\n\t\t\t\t\t...facet,\n\t\t\t\t\ttracks: data.tracks || [],\n\t\t\t\t\tsamples: data.samples\n\t\t\t\t}\n\t\t\t})\n\t\t)\n\t}\n\n\t// get options for view instance\n\tgetOpts() {\n\t\tconst opts = {\n\t\t\tapp: this.app,\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\nfunction getFacetTrackNames(facets) {\n\tconst names = new Set<string>()\n\tfor (const facet of facets || []) {\n\t\tfor (const track of facet.tracks || []) {\n\t\t\tif (track.name) names.add(track.name)\n\t\t}\n\t}\n\treturn names\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\tjunction: vocabApi.termdbConfig.queries.junction,\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\tsanitizeTrackLstConfig(config)\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} else if (vocabApi.termdbConfig.queries.svfusion) {\n\t\t/* dataset has svfusion but no snvindel query;\n\t\tset up config.svfusion so generateTracks() creates the mds3 lollipop tk to show fusion/sv events.\n\t\t(without this, the GB plot only generates the mds3 tk from config.snvindel) */\n\t\tconfig.svfusion = Object.assign(structuredClone(vocabApi.termdbConfig.queries.svfusion), config.svfusion || {})\n\t\tif (typeof config.svfusion.shown != 'boolean') config.svfusion.shown = true\n\t}\n\n\tif (config.junction && typeof config.junction.shown != 'boolean') config.junction.shown = true\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\tconst facetTwLst = [config.facetTw1, config.facetTw2, config.facetTw3].some(Boolean)\n\t\t\t? [config.facetTw1, config.facetTw2, config.facetTw3]\n\t\t\t: config.trackLst.facetTwLst || []\n\t\tfor (const [i, tw] of facetTwLst.slice(0, 3).entries()) {\n\t\t\tif (!tw) continue\n\t\t\tconst key = `facetTw${i + 1}`\n\t\t\tconfig[key] = await fillTermWrapper(tw, vocabApi)\n\t\t}\n\t\tdelete config.trackLst.facetTwLst\n\t\tconfig.settings = config.settings || {}\n\t\tconfig.settings.controls = config.settings.controls || {}\n\t}\n\treturn config\n}\n\nfunction getGbConfig(plotOrState) {\n\treturn plotOrState?.config || plotOrState || {}\n}\n\nexport function getFacetTwLst(config) {\n\tconst facetTwLst: any[] = []\n\tfor (const tw of [config.facetTw1, config.facetTw2, config.facetTw3]) {\n\t\tif (!tw) break\n\t\tfacetTwLst.push(tw)\n\t}\n\treturn facetTwLst\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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