@sjcrh/proteinpaint-client 2.191.4 → 2.192.0

package/dist/chunk-R7AV73BV.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/profile/profilePlot.ts"],
+  "sourcesContent": ["import { controlsInit } from '../controls.js'\nimport { fillTermWrapper, fillTwLst } from '#termsetting'\nimport { select } from 'd3-selection'\nimport { Menu } from '#dom/menu'\nimport { icons as icon_functions } from '#dom/control.icons'\nimport { getCategoricalTermFilter, getCombinedTermFilter } from '#filter'\nimport { DownloadMenu } from '#dom/downloadMenu'\nimport { importPlot } from '#plots/importPlot.js'\nimport { PlotBase } from '../PlotBase.ts'\nimport { type RxComponent } from '#rx'\n/*\n\nThe profilePlot is the base class for all the profile plots. It handles the common functionality such as setting controls, fetching data, and initializing the plot elements.\nAll the profile plots have the same filters:\n- Region\n- Country\n- Income group\n- Facility type\n- Teaching status\n- Referral status\n- Funding source\n- Hospital volume\n- Year of implementation\n- Sites\n\nThe profileRadarFacility2 adds at the top of these filters the facility select as here we compare a single facility with the average scores of all the facilities aggregated\n*/\n\n//order for income groups and hospital volumes\nconst orderedIncomes = ['Low income', 'Lower middle income', 'Upper middle income', 'High income']\nconst orderedVolumes = [\n\t'Small (1-25 annual newly diagnoses)',\n\t'Medium (26-80 annual newly diagnoses)',\n\t'Large (81-120 annual newly diagnoses)',\n\t'Very large (>120 annual newly diagnoses)'\n]\n\n//Cohort types\nexport const ABBREV_COHORT = 0\nexport const FULL_COHORT = 1\n\nexport abstract class profilePlot extends PlotBase implements RxComponent {\n\treadonly type: string\n\tdownloadCount: number\n\ttip: Menu\n\tscoreTerms: any[]\n\tscScoreTerms: any[]\n\tisRadarFacility: boolean\n\tcomponents: any\n\tsettings: any\n\tisComparison: any\n\tconfig: any\n\tfilter: any\n\tlegendG: any\n\tfilteredTermValues: any\n\tdata: any\n\tsites!: any[]\n\tsampleData: any\n\tfilterG: any\n\tfiltersCount: any\n\n\tconstructor(opts, type) {\n\t\tsuper(opts)\n\t\tthis.type = type\n\t\tthis.downloadCount = 0\n\t\tthis.tip = new Menu({ padding: '4px', offsetX: 10, offsetY: 15 })\n\t\tthis.scoreTerms = []\n\t\tthis.scScoreTerms = []\n\t\tthis.isRadarFacility = false\n\t\tthis.components = { plots: {} }\n\t}\n\n\t//extracts the relevant state from the appState: config, termfilter, vocab, login info\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 { logged, sites, user } = getProfileLogin(this.app, appState.activeCohort) //later on replace with real login info\n\t\tconst site = sites?.[0]\n\t\treturn {\n\t\t\tconfig,\n\t\t\ttermfilter: appState.termfilter,\n\t\t\tdslabel: appState.vocab.dslabel,\n\t\t\ttermdbConfig: appState.termdbConfig,\n\t\t\tvocab: appState.vocab,\n\t\t\tlogged, //later change to read login info\n\t\t\tsite,\n\t\t\tsites,\n\t\t\tuser,\n\t\t\tactiveCohort: appState.activeCohort,\n\t\t\t//Find plots where I am a parent. Here the child is a second plot for comparison\n\t\t\tplots: appState.plots.filter(p => p.parentId === this.id) //this property is needed to indicate that child plots need to be added to the appState plots\n\t\t}\n\t}\n\n\t//refers to the view where all the filters are shown and not the preselected site\n\tisAggregate() {\n\t\tif (!this.state.logged) return true\n\t\tif (this.settings.isAggregate) return true //marked by the user\n\t\tif (this.state.sites?.length > 1 || this.state.user == 'admin' || this.isRadarFacility) return true //multiple sites selected\n\t\treturn false\n\t}\n\n\t//initializes the plot elements\n\tasync init(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tconst state = this.getState(appState)\n\t\tif (this.opts.header) {\n\t\t\tlet chartName = config.chartType.match(/[A-Z][a-z]+/g)\n\t\t\tchartName = chartName.join(' ')\n\t\t\tchartName = config.headerTitle ? config.headerTitle + ` / ${state.user}` : chartName + ` / ${state.user}`\n\t\t\tthis.opts.header.style('text-transform', 'capitalize').text(chartName)\n\t\t}\n\t\tconst div = this.opts.holder.append('div').style('display', 'inline-block')\n\t\tconst leftDiv = div.append('div').style('display', 'inline-block').style('vertical-align', 'top')\n\n\t\tconst rightDiv = div.append('div').style('display', 'inline-block').style('vertical-align', 'top')\n\n\t\tconst controlsDiv = leftDiv.append('div').style('display', 'inline-block').style('font-size', '0.9em')\n\t\tconst iconsDiv = leftDiv.append('div').style('margin-top', '10px').style('padding-left', '12px')\n\n\t\tconst holder = rightDiv.insert('div').style('display', 'inline-block')\n\n\t\tconst plotDiv = holder.append('div')\n\t\t// loading overlay shown over the chart sandbox while the chart's data is fetched/rendered.\n\t\t// Reuses the shared .sjpp-loading-overlay box + .sjpp-spinner glyph; anchored on the\n\t\t// full-width sandbox holder (opts.holder) so the spinner stays centered even on first\n\t\t// open when the inner plot area is still empty.\n\t\tthis.opts.holder.style('position', 'relative')\n\t\tconst loadingDiv = this.opts.holder.append('div').attr('class', 'sjpp-loading-overlay').style('display', 'none')\n\t\tloadingDiv.append('div').attr('class', 'sjpp-spinner')\n\t\tthis.dom = {\n\t\t\tcontrolsDiv,\n\t\t\tholder,\n\t\t\ticonsDiv,\n\t\t\trightDiv,\n\t\t\tplotDiv,\n\t\t\tloadingDiv\n\t\t}\n\t\tselect('.sjpp-output-sandbox-content').on('scroll', event => {\n\t\t\tif (this.onMouseOut) this.onMouseOut(event)\n\t\t})\n\t\tthis.dom.rightDiv.on('mousemove', event => this.onMouseOver(event))\n\t\tthis.dom.rightDiv.on('mouseleave', event => this.onMouseOut(event))\n\t\tthis.dom.rightDiv.on('mouseout', event => this.onMouseOut(event))\n\n\t\tdocument.addEventListener('scroll', () => this?.tip?.hide())\n\n\t\tconst restartDiv = iconsDiv.append('div').style('padding-bottom', '8px')\n\t\ticon_functions['restart'](restartDiv, {\n\t\t\ttitle: 'Clear filters',\n\t\t\thandler: async () => {\n\t\t\t\tthis.clearFiltersExcept([])\n\t\t\t\tthis.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: this.id,\n\t\t\t\t\tconfig: { filter: this.getFilter(), settings: { [this.type]: this.settings } }\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t\tif (!config.parentId) {\n\t\t\tconst iconDiv = iconsDiv.append('div').style('fill', '#aaa').style('padding', '2px')\n\n\t\t\ticon_functions['add'](iconDiv, {\n\t\t\t\ttitle: 'Open another plot for comparison',\n\t\t\t\thandler: () => {\n\t\t\t\t\tconst show = !this.isComparison\n\t\t\t\t\tconst icon = iconDiv.select('svg')\n\t\t\t\t\ticon.style('fill', show ? 'orange' : 'black')\n\t\t\t\t\tif (this.isComparison) {\n\t\t\t\t\t\tconst id = this.state.plots.find(p => p.parentId === this.id)?.id\n\t\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\t\ttype: 'plot_delete',\n\t\t\t\t\t\t\tid,\n\t\t\t\t\t\t\tparentId: this.id\n\t\t\t\t\t\t})\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\t\t\t\t\tthis.legendG.selectAll('*').remove()\n\t\t\t\t\tconst config = structuredClone(this.config)\n\t\t\t\t\tconfig.parentId = this.id\n\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\t\tconfig\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\t}\n\n\tabstract onMouseOver(event: MouseEvent): void\n\n\t//tooltip handler to hide the tooltip when mouse leaves the plot area\n\tonMouseOut(_event: MouseEvent) {\n\t\tthis.tip.hide()\n\t}\n\n\tasync main() {\n\t\tthis.config = JSON.parse(JSON.stringify(this.state.config))\n\t\tthis.settings = this.config.settings[this.type]\n\t\tthis.dom.plotDiv.selectAll('*').remove()\n\n\t\tthis.isComparison = this.config.parentId || this.state.plots.length > 0\n\t\t//Render second plot for comparison that is a duplicate of this one, that will be rendered to the right of this plot\n\t\t//Child plots need to be rendered by the father plot, a similar approach is used in the report\n\t\tfor (const config of this.state.plots) {\n\t\t\tconst plot = structuredClone(config)\n\t\t\tif (this.components.plots[plot.id]) continue\n\t\t\tconst holder = this.opts.holder.append('div').style('display', 'inline-block').style('padding', '5px')\n\t\t\tplot.holder = holder.append('div')\n\t\t\tplot.app = this.app\n\t\t\tconst { componentInit } = await importPlot(plot.chartType)\n\t\t\tthis.components.plots[plot.id] = await componentInit(plot)\n\t\t}\n\t\t//delete child plot if comparison disabled and plot deleted\n\t\tfor (const plotId in this.components.plots) {\n\t\t\tif (!this.state.plots.find(p => p.id === plotId)) {\n\t\t\t\tthis.components.plots[plotId].destroy()\n\t\t\t\tdelete this.components.plots[plotId]\n\t\t\t}\n\t\t}\n\t}\n\n\tasync setControls(additionalInputs: any[] = []) {\n\t\ttry {\n\t\t\tconst isRadarFacility = this.isRadarFacility\n\t\t\tconst filters = {}\n\t\t\tfor (const tw of this.config.filterTWs) {\n\t\t\t\tfilters[tw.term.id] = getCategoricalTermFilter(this.config.filterTWs, this.settings, tw)\n\t\t\t}\n\n\t\t\tthis.filteredTermValues = await this.app.vocabApi.filterTermValues({\n\t\t\t\tterms: this.config.filterTWs,\n\t\t\t\tfilter: this.state.termfilter.filter,\n\t\t\t\tfilters,\n\t\t\t\tfacilityTW: this.config.facilityTW,\n\t\t\t\t// safe to pass because the backend code will still compare terms[] with the the dataset's hiddenTermIds,\n\t\t\t\t// it only affects what will be included in the aggregation and does not disable user access authentication\n\t\t\t\tfilterByUserSites: this.settings.filterByUserSites,\n\t\t\t\tshowAll: true\n\t\t\t})\n\t\t\tconst regions = this.filteredTermValues[this.config.regionTW.id]\n\t\t\tconst sjgRegions = this.filteredTermValues[this.config.sjgRegionTW.id]\n\t\t\tconst countries = this.filteredTermValues[this.config.countryTW.id]\n\t\t\tconst incomes = this.filteredTermValues[this.config.incomeTW.id]\n\t\t\tconst teachingStates = this.filteredTermValues[this.config.teachingStatusTW.id]\n\t\t\tconst referralStates = this.filteredTermValues[this.config.referralStatusTW.id]\n\t\t\tconst fundingSources = this.filteredTermValues[this.config.fundingSourceTW.id]\n\t\t\tconst hospitalVolumes = this.filteredTermValues[this.config.hospitalVolumeTW.id]\n\t\t\tconst yearsOfImplementation = this.filteredTermValues[this.config.yearOfImplementationTW.id]\n\t\t\tincomes.sort((elem1, elem2) => {\n\t\t\t\tconst i1 = orderedIncomes.indexOf(elem1.value)\n\t\t\t\tconst i2 = orderedIncomes.indexOf(elem2.value)\n\t\t\t\tif (i1 < i2) return -1\n\t\t\t\treturn 1\n\t\t\t})\n\t\t\thospitalVolumes.sort((elem1, elem2) => {\n\t\t\t\tconst i1 = orderedVolumes.indexOf(elem1.value)\n\t\t\t\tconst i2 = orderedVolumes.indexOf(elem2.value)\n\t\t\t\tif (i1 < i2) return -1\n\t\t\t\treturn 1\n\t\t\t})\n\t\t\tconst types = this.filteredTermValues[this.config.typeTW.id]\n\t\t\tconst isAggregate = this.isAggregate()\n\n\t\t\tif (!this.settings[this.config.facilityTW?.term?.id] && this.state.sites?.length == 1 && !isAggregate) {\n\t\t\t\tthis.settings[this.config.facilityTW?.term?.id] = [this.state.sites[0]]\n\t\t\t}\n\n\t\t\tthis.filter = this.config.filter || this.getFilter()\n\n\t\t\tif (this.type == 'profileForms')\n\t\t\t\tthis.data = await this.app.vocabApi.getProfileFormScores({\n\t\t\t\t\tscoreTerms: this.scoreTerms,\n\t\t\t\t\tscScoreTerms: this.scScoreTerms,\n\t\t\t\t\tfilter: this.filter,\n\t\t\t\t\tfacilityTW: this.config.facilityTW,\n\t\t\t\t\tfilterByUserSites: this.settings.filterByUserSites\n\t\t\t\t})\n\t\t\telse if (this.type == 'profileRadarFacility2')\n\t\t\t\t// profileRadarFacility2 fetches aggregate + single-site in one dedicated-route call;\n\t\t\t\t// the subclass's fetchRadarFacility2Scores() also sets this.sampleData from the response\n\t\t\t\tthis.data = await (this as any).fetchRadarFacility2Scores()\n\t\t\t/*\n\t\t\tOnly profileForms and profileRadarFacility2 fetch this.data here; polar2/barchart2\n\t\t\tfetch in their own setControls() override and run their own error check afterwards.\n\t\t\tRestrict this throw to those two types so we don't re-throw a stale this.data error\n\t\t\tleft over from a previous render, which would otherwise block recovery (e.g. clearing\n\t\t\tfilters after an error) before the subclass re-fetches.\n\t\t\t*/\n\t\t\tif ((this.type == 'profileForms' || this.type == 'profileRadarFacility2') && this.data && 'error' in this.data)\n\t\t\t\tthrow this.data.error\n\t\t\tthis.sites = this.filteredTermValues[this.config.facilityTW.id]?.filter(s => !s.disabled && s.value)\n\n\t\t\tif (this.settings[this.config.facilityTW?.term?.id])\n\t\t\t\tfor (const site of this.settings[this.config.facilityTW?.term?.id]) {\n\t\t\t\t\tconst siteOption = this.sites.find(s => s.value == site)\n\t\t\t\t\tif (siteOption) siteOption.selected = true //mark selected sites\n\t\t\t\t}\n\t\t\tconst chartType = this.type\n\t\t\tthis.dom.controlsDiv.selectAll('*').remove()\n\t\t\tconst inputs: any[] = []\n\t\t\tconst userSitesFilterInput = {\n\t\t\t\tlabel: 'Use accessible sites only',\n\t\t\t\tboxLabel: '',\n\t\t\t\ttype: 'checkbox',\n\t\t\t\tchartType,\n\t\t\t\tsettingsKey: 'filterByUserSites'\n\t\t\t}\n\t\t\tif (this.state.sites?.length == 1 && !isRadarFacility) {\n\t\t\t\tconst dataInput = {\n\t\t\t\t\tlabel: 'Data',\n\t\t\t\t\ttype: 'radio',\n\t\t\t\t\tchartType,\n\t\t\t\t\tsettingsKey: 'isAggregate',\n\t\t\t\t\tstyles: { display: 'inline-block' },\n\t\t\t\t\toptions: [\n\t\t\t\t\t\t{ label: this.state.site, value: false },\n\t\t\t\t\t\t{ label: 'Aggregate', value: true }\n\t\t\t\t\t],\n\t\t\t\t\tcallback: isAggregate => {\n\t\t\t\t\t\tthis.settings.isAggregate = isAggregate\n\t\t\t\t\t\tconst id = this.sites.find(s => s.value == this.state.site)?.value\n\t\t\t\t\t\tconst value = isAggregate ? [] : [id]\n\t\t\t\t\t\tthis.setFilterValue(this.config.facilityTW.term.id, value)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tinputs.push(dataInput)\n\t\t\t}\n\t\t\tif (isAggregate || isRadarFacility) {\n\t\t\t\tinputs.push(\n\t\t\t\t\t...[\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'WHO Region',\n\t\t\t\t\t\t\ttype: 'dropdown',\n\t\t\t\t\t\t\tchartType,\n\t\t\t\t\t\t\tsettingsKey: this.config.regionTW.term.id,\n\t\t\t\t\t\t\toptions: regions,\n\t\t\t\t\t\t\tcallback: value => this.setFilterValue(this.config.regionTW.term.id, value)\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'SJG Region',\n\t\t\t\t\t\t\ttype: 'dropdown',\n\t\t\t\t\t\t\tchartType,\n\t\t\t\t\t\t\tsettingsKey: this.config.sjgRegionTW.term.id,\n\t\t\t\t\t\t\toptions: sjgRegions,\n\t\t\t\t\t\t\tcallback: value => this.setFilterValue(this.config.sjgRegionTW.term.id, value)\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Country',\n\t\t\t\t\t\t\ttype: 'dropdown',\n\t\t\t\t\t\t\tchartType,\n\t\t\t\t\t\t\tsettingsKey: this.config.countryTW.term.id,\n\t\t\t\t\t\t\toptions: countries,\n\t\t\t\t\t\t\tcallback: value => this.setFilterValue(this.config.countryTW.term.id, value)\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Income group',\n\t\t\t\t\t\t\ttype: 'dropdown',\n\t\t\t\t\t\t\tchartType,\n\t\t\t\t\t\t\tsettingsKey: this.config.incomeTW.term.id,\n\t\t\t\t\t\t\toptions: incomes,\n\t\t\t\t\t\t\tcallback: value => this.setFilterValue(this.config.incomeTW.term.id, value)\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: 'Facility type',\n\t\t\t\t\t\t\ttype: 'dropdown',\n\t\t\t\t\t\t\tchartType,\n\t\t\t\t\t\t\tsettingsKey: this.config.typeTW.term.id,\n\t\t\t\t\t\t\toptions: types,\n\t\t\t\t\t\t\tcallback: value => this.setFilterValue(this.config.typeTW.term.id, value)\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: this.config.teachingStatusTW.term.name,\n\t\t\t\t\t\t\ttype: 'dropdown',\n\t\t\t\t\t\t\tchartType,\n\t\t\t\t\t\t\tsettingsKey: this.config.teachingStatusTW.term.id,\n\t\t\t\t\t\t\toptions: teachingStates,\n\t\t\t\t\t\t\tcallback: value => this.setFilterValue(this.config.teachingStatusTW.term.id, value)\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: this.config.referralStatusTW.term.name,\n\t\t\t\t\t\t\ttype: 'dropdown',\n\t\t\t\t\t\t\tchartType,\n\t\t\t\t\t\t\tsettingsKey: this.config.referralStatusTW.term.id,\n\t\t\t\t\t\t\toptions: referralStates,\n\t\t\t\t\t\t\tcallback: value => this.setFilterValue(this.config.referralStatusTW.term.id, value)\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: this.config.fundingSourceTW.term.name,\n\t\t\t\t\t\t\ttype: 'dropdown',\n\t\t\t\t\t\t\tchartType,\n\t\t\t\t\t\t\tsettingsKey: this.config.fundingSourceTW.term.id,\n\t\t\t\t\t\t\toptions: fundingSources,\n\t\t\t\t\t\t\tcallback: value => this.setFilterValue(this.config.fundingSourceTW.term.id, value)\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: this.config.hospitalVolumeTW.term.name,\n\t\t\t\t\t\t\ttype: 'dropdown',\n\t\t\t\t\t\t\tchartType,\n\t\t\t\t\t\t\tsettingsKey: this.config.hospitalVolumeTW.term.id,\n\t\t\t\t\t\t\toptions: hospitalVolumes,\n\t\t\t\t\t\t\tcallback: value => this.setFilterValue(this.config.hospitalVolumeTW.term.id, value)\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tlabel: this.config.yearOfImplementationTW.term.name,\n\t\t\t\t\t\t\ttype: 'dropdown',\n\t\t\t\t\t\t\tchartType,\n\t\t\t\t\t\t\tsettingsKey: this.config.yearOfImplementationTW.term.id,\n\t\t\t\t\t\t\toptions: yearsOfImplementation,\n\t\t\t\t\t\t\tcallback: value => this.setFilterValue(this.config.yearOfImplementationTW.term.id, value)\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\tif (this.state.logged) {\n\t\t\t\tif (isAggregate && this.sites.length > 1) {\n\t\t\t\t\tconst sitesInput = {\n\t\t\t\t\t\tlabel: 'Sites',\n\t\t\t\t\t\ttype: 'dropdown',\n\t\t\t\t\t\tchartType,\n\t\t\t\t\t\toptions: this.sites,\n\t\t\t\t\t\tmultiple: true,\n\t\t\t\t\t\tcallback: values => this.setFilterValue(this.config.facilityTW.term.id, values)\n\t\t\t\t\t}\n\t\t\t\t\tinputs.push(sitesInput)\n\t\t\t\t\tif (this.state.user != 'admin') inputs.unshift(userSitesFilterInput) //add filter by user sites only for non-admin users\n\t\t\t\t}\n\t\t\t\tif (isRadarFacility) {\n\t\t\t\t\t// profileRadarFacility2's fetchRadarFacility2Scores() above populated this.sampleData\n\t\t\t\t\t// from the dedicated-route response. Skip the facility-site dropdown when sampleData\n\t\t\t\t\t// is unavailable (e.g. public role, or when the filter excludes all sites) \u2014 turns\n\t\t\t\t\t// a would-be TypeError into a graceful no-op.\n\t\t\t\t\tif (this.sampleData?.sites?.length) {\n\t\t\t\t\t\tconst facilitySites = this.sampleData.sites\n\t\t\t\t\t\tconst facilitySite = this.settings.facilitySite\n\t\t\t\t\t\t\t? facilitySites.find(s => s.value == this.settings.facilitySite)\n\t\t\t\t\t\t\t: facilitySites[0]\n\t\t\t\t\t\tif (!facilitySite)\n\t\t\t\t\t\t\t//probably a session recovery\n\t\t\t\t\t\t\tthrow new Error(`Access to ${this.settings.facilitySite} facility not allowed`)\n\t\t\t\t\t\tfacilitySite.selected = true //mark selected facility site\n\n\t\t\t\t\t\tinputs.unshift({\n\t\t\t\t\t\t\tlabel: 'Facility site',\n\t\t\t\t\t\t\ttype: 'dropdown',\n\t\t\t\t\t\t\tchartType,\n\t\t\t\t\t\t\toptions: facilitySites,\n\t\t\t\t\t\t\tcallback: value => {\n\t\t\t\t\t\t\t\tthis.setFacilitySite(value)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tinputs.unshift(...additionalInputs)\n\t\t\tthis.components.controls = await controlsInit({\n\t\t\t\tapp: this.app,\n\t\t\t\tid: this.id,\n\t\t\t\tholder: this.dom.controlsDiv,\n\t\t\t\tinputs,\n\t\t\t\ttitle: 'Filters'\n\t\t\t})\n\t\t\tthis.components.controls.on(`downloadClick.${chartType}`, event => this.download(event))\n\t\t\tthis.components.controls.on(`helpClick.${chartType}`, () => {\n\t\t\t\tconst activeCohort = this.state.activeCohort\n\t\t\t\tlet link\n\t\t\t\tif (activeCohort == ABBREV_COHORT) {\n\t\t\t\t\tif (chartType == 'profileBarchart2')\n\t\t\t\t\t\tlink =\n\t\t\t\t\t\t\t'https://global.stjude.org/content/dam/global/en-us/documents/no-index/bar-graph-abbr-profiledash.pdf'\n\t\t\t\t\telse if (chartType == 'profilePolar2')\n\t\t\t\t\t\tlink =\n\t\t\t\t\t\t\t'https://global.stjude.org/content/dam/global/en-us/documents/no-index/polar-graph-abbr-profiledash.pdf'\n\t\t\t\t\telse if (chartType.startsWith('profileRadar'))\n\t\t\t\t\t\tlink = 'https://global.stjude.org/content/dam/global/en-us/documents/no-index/radar-abbr-profiledash.pdf'\n\t\t\t\t} else if (activeCohort == FULL_COHORT) {\n\t\t\t\t\tif (chartType == 'profileBarchart2')\n\t\t\t\t\t\tlink =\n\t\t\t\t\t\t\t'https://global.stjude.org/content/dam/global/en-us/documents/no-index/bar-graph-full-profiledash.pdf'\n\t\t\t\t\telse if (chartType == 'profilePolar2')\n\t\t\t\t\t\tlink =\n\t\t\t\t\t\t\t'https://global.stjude.org/content/dam/global/en-us/documents/no-index/polar-graph-full-profiledash.pdf'\n\t\t\t\t\telse if (chartType.startsWith('profileRadar'))\n\t\t\t\t\t\tlink = 'https://global.stjude.org/content/dam/global/en-us/documents/no-index/radar-full-profiledash.pdf'\n\t\t\t\t}\n\t\t\t\tif (link) window.open(link)\n\t\t\t})\n\t\t\tthis.filtersCount = 0\n\t\t} catch (e) {\n\t\t\tconsole.log(e)\n\t\t\tthrow e\n\t\t}\n\t}\n\n\tsetFilterValue(key, value) {\n\t\tconst config = this.config\n\t\tthis.settings[key] = value\n\t\tconfig.filter = this.getFilter()\n\t\tthis.app.dispatch({ type: 'plot_edit', id: this.id, config: this.config })\n\t}\n\n\tgetFilterWithSettings(settings) {\n\t\tlet filter = getCategoricalTermFilter(this.config.filterTWs, settings, null)\n\t\tfilter = getCombinedTermFilter(this.state, filter)\n\t\treturn filter.filter\n\t}\n\n\tgetFilter() {\n\t\tlet filter = getCategoricalTermFilter(this.config.filterTWs, this.settings, null)\n\t\tfilter = getCombinedTermFilter(this.state, filter)\n\t\treturn filter.filter\n\t}\n\n\tclearFiltersExcept(ids) {\n\t\tfor (const tw of this.config.filterTWs) if (!ids.includes(tw.term.id)) this.settings[tw.term.id] = ''\n\t}\n\n\tsetFacilitySite(site) {\n\t\tthis.settings.facilitySite = site\n\t\tthis.app.dispatch({ type: 'plot_edit', id: this.id, config: this.config })\n\t}\n\n\taddFilterLegend() {\n\t\tconst hasFilters = this.config.filterTWs.some(tw => this.settings[tw.term.id])\n\t\tconst title = hasFilters ? 'Filters' : 'No filter applied'\n\t\tthis.filterG\n\t\t\t.attr('font-size', '0.9em')\n\t\t\t.append('text')\n\t\t\t.attr('text-anchor', 'left')\n\t\t\t.style('font-weight', 'bold')\n\t\t\t.text(`${title} (n=${this.data.n})`)\n\t\t\t.attr('transform', `translate(0, -5)`)\n\t\tfor (const tw of this.config.filterTWs) this.addFilterLegendItem(tw.term.name, this.settings[tw.term.id])\n\t}\n\n\taddFilterLegendItem(filter, value) {\n\t\tif (!value || value?.length === 0) return\n\t\tthis.filtersCount++\n\t\tconst isArray = Array.isArray(value)\n\t\tlet text = isArray ? value.join(', ') : value\n\t\tif (text.length > 40) {\n\t\t\ttext = text.slice(0, 40) + '...'\n\t\t}\n\t\tconst itemG = this.filterG.append('g').attr('font-size', '0.95em')\n\t\tconst textElem = itemG\n\t\t\t.append('text')\n\t\t\t.attr('transform', `translate(0, ${this.filtersCount * 22})`)\n\t\t\t.attr('text-anchor', 'left')\n\t\ttextElem.append('tspan').attr('font-weight', 'bold').text(`${filter}: `)\n\t\ttextElem.append('tspan').text(text)\n\t}\n\n\taddEndUserImpressionNote(uiG) {\n\t\tuiG.attr('font-size', '0.9em')\n\t\tconst textElem = uiG.append('text').attr('transform', `translate(0, 115)`)\n\t\ttextElem.append('tspan').attr('font-weight', 'bold').text('End-user Impression: ')\n\t\ttextElem.append('tspan').text('It is provided by the local liaison who completed the assessment ')\n\t\tuiG\n\t\t\t.append('text')\n\t\t\t.attr('transform', `translate(0, 140)`)\n\t\t\t.text('in consultation with the PHO medical director or directly by the PHO medical director.')\n\t\tuiG\n\t\t\t.append('text')\n\t\t\t.attr('transform', `translate(0, 165)`)\n\t\t\t.text('The end-user was asked to rate the current status of the domains and subdomains included.')\n\t}\n\n\taddPOCNote(uiG) {\n\t\tuiG.attr('font-size', '0.9em')\n\t\tconst textElem = uiG.append('text').attr('transform', `translate(0, 115)`)\n\t\ttextElem.append('tspan').attr('font-weight', 'bold').text('Point of Care (POC) Staff: ')\n\t\ttextElem.append('tspan').text('All members of the assessment team, ')\n\t\tuiG\n\t\t\t.append('text')\n\t\t\t.attr('transform', `translate(0, 140)`)\n\t\t\t.text('excluding the Site Coordinator. POC staff provide subjective information based ')\n\t\tuiG\n\t\t\t.append('text')\n\t\t\t.attr('transform', `translate(0, 165)`)\n\t\t\t.text('on their experience and perception about service delivery at the PHO facility.')\n\t}\n\n\taddLegendItem(category, description, index) {\n\t\tconst text = this.legendG\n\t\t\t.append('text')\n\t\t\t.attr('font-size', '0.9em')\n\t\t\t.attr('transform', `translate(0, ${index * 20})`)\n\t\t\t.attr('text-anchor', 'left')\n\t\ttext.append('tspan').attr('font-weight', 'bold').text(category)\n\t\ttext.append('tspan').text(`: ${description}`)\n\t}\n\n\tgetDownloadFilename() {\n\t\tthis.downloadCount++\n\t\tlet filename = `${this.type}${this.downloadCount}`\n\t\tfilename = filename.split(' ').join('_')\n\t\treturn filename\n\t}\n\n\tgetPercentage(d) {\n\t\tif (!d) return 0\n\t\tconst score = this.data.term2Score[d.score.term.id]\n\t\treturn score\n\t}\n\n\tasync download(event) {\n\t\tconst chartImages = this.getChartImages()\n\t\tconst menu = new DownloadMenu(chartImages, this.getDownloadFilename())\n\t\tmenu.show(event.clientX, event.clientY, event.target)\n\t}\n\n\tpreApiFreeze(api) {\n\t\tapi.download = this.download\n\t\tapi.getChartImages = () => this.getChartImages()\n\t}\n\n\tgetChartImages() {\n\t\tconst plots: any[] = Object.values(this.components.plots)\n\t\tconst note = '\u00A9 2025 St. Jude Children\u2019s Research Hospital'\n\t\tlet name = plots.length > 0 ? 'Original' : ''\n\t\tname += ` ${note}`\n\t\tconst charts = [{ name, svg: this.dom.svg }]\n\t\tlet i = 1\n\t\tfor (const plot of plots) {\n\t\t\t//Adding comparison plots\n\t\t\tconst chartImages = plot.getChartImages()\n\n\t\t\tfor (const chartImage of chartImages) {\n\t\t\t\tconst svg = chartImage.svg\n\t\t\t\tconst name =\n\t\t\t\t\tchartImages.length > 1\n\t\t\t\t\t\t? `Comparison ${i}. ${chartImage.name} ${note}`\n\t\t\t\t\t\t: `Comparison ${chartImage.name} ${note}`\n\t\t\t\tcharts.push({ name, svg })\n\t\t\t}\n\t\t\ti++\n\t\t}\n\t\treturn charts\n\t}\n}\n\nexport function makeChartBtnMenu(holder, chartsInstance, chartType) {\n\t/*\n\tholder: the holder in the tooltip\n\tchartsInstance: MassCharts instance\n\t\ttermdbConfig is accessible at chartsInstance.state.termdbConfig{}\n\t\tmass option is accessible at chartsInstance.app.opts{}\n\t*/\n\tconst state = chartsInstance.state\n\tconst key = state.activeCohort == FULL_COHORT ? 'full' : 'abbrev'\n\tconst typeConfig = state.termdbConfig?.plotConfigByCohort[key][chartType]\n\tif (typeConfig.options.length == 1) {\n\t\tcreatePlot(typeConfig.options[0], chartType, chartsInstance)\n\t\treturn\n\t}\n\tconst menuDiv = holder.append('div')\n\tfor (const plotConfig of typeConfig.options) {\n\t\tmenuDiv\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t.text(plotConfig.title)\n\t\t\t.on('click', () => {\n\t\t\t\tcreatePlot(plotConfig, chartType, chartsInstance)\n\t\t\t\tchartsInstance.dom.tip.hide()\n\t\t\t})\n\t}\n\n\tfunction createPlot(plotConfig, chartType, chartsInstance) {\n\t\tconst config = structuredClone(plotConfig)\n\t\tconfig.chartType = chartType\n\t\tchartsInstance.app.dispatch({\n\t\t\ttype: 'plot_create',\n\t\t\tchartType,\n\t\t\tconfig\n\t\t})\n\t}\n}\n\nexport async function getProfilePlotConfig(activeCohort, app, opts) {\n\tconst key = activeCohort == FULL_COHORT ? 'full' : 'abbrev'\n\tconst config = structuredClone(app.vocabApi.termdbConfig?.plotConfigByCohort[key]?.[opts.chartType])\n\tif (!config) throw `No data available for the plot ${opts.chartType} in this dataset`\n\tconst cohortPreffix = activeCohort == FULL_COHORT ? 'F' : 'A'\n\tconfig.facilityTW = { id: cohortPreffix + 'UNIT' } //All the plots want the facility term to show the hospital name if a site is selected\n\tconfig.hidePlotFilter = true\n\tawait fillTermWrapper(config.facilityTW, app.vocabApi)\n\tawait loadFilterTerms(config, activeCohort, app)\n\treturn config\n}\n\nexport async function loadFilterTerms(config, activeCohort, app) {\n\t//These are the profile filters for each plot. Hardcoded here\n\tconst cohortPreffix = activeCohort == FULL_COHORT ? 'F' : 'A'\n\tconfig.countryTW = { id: cohortPreffix + 'country' }\n\tconfig.regionTW = { id: cohortPreffix + 'WHO_region' }\n\tconfig.sjgRegionTW = { id: cohortPreffix + 'SJG_region' }\n\tconfig.incomeTW = { id: cohortPreffix + 'Income_group' }\n\tconfig.typeTW = { id: cohortPreffix + 'FC_TypeofFacility' }\n\tconfig.teachingStatusTW = { id: cohortPreffix + 'FC_TeachingFacility' }\n\tconfig.referralStatusTW = { id: cohortPreffix + 'FC_ReferralFacility' }\n\tconfig.fundingSourceTW = { id: cohortPreffix + 'FC_FundingSrc' }\n\t//config.annualDiagnosisNumber = {id: 'PO_TotalDxAll'}\n\tconfig.hospitalVolumeTW = { id: cohortPreffix + 'PO_HospitalVolume' }\n\tconfig.yearOfImplementationTW = { id: cohortPreffix + 'Year_implementation' }\n\n\tconst filterTWs = [\n\t\tconfig.facilityTW,\n\t\tconfig.countryTW,\n\t\tconfig.regionTW,\n\t\tconfig.sjgRegionTW,\n\t\tconfig.incomeTW,\n\t\tconfig.typeTW,\n\t\tconfig.teachingStatusTW,\n\t\tconfig.referralStatusTW,\n\t\tconfig.fundingSourceTW,\n\t\tconfig.hospitalVolumeTW,\n\t\tconfig.yearOfImplementationTW\n\t]\n\tawait fillTwLst(filterTWs, app.vocabApi)\n\tconfig.filterTWs = filterTWs\n}\n\nexport function clearLocalFilters(plot) {\n\tplot.settings = getDefaultProfilePlotSettings()\n}\n\nexport function getDefaultProfilePlotSettings() {\n\treturn {\n\t\tisAggregate: false,\n\t\tfilterByUserSites: false //if true, the aggregation will be limited to the user sites only\n\t}\n}\n\nexport function getProfileLogin(app, cohort = FULL_COHORT) {\n\tconst auth = app.vocabApi.getClientAuthResult()\n\tif (!auth) return { logged: false, sites: [], user: 'public' }\n\tconst auth_info = cohort == FULL_COHORT ? auth.full : auth.abbrev\n\tconst logged = auth_info?.role != 'public'\n\tif (!auth_info) return { logged: false, sites: [], user: 'public' } //no login info for the cohort, treat it as not logged in, public view for that cohort\n\tconst user = auth_info?.role || 'public'\n\tconst sites = user == 'admin' ? null : auth_info.sites //site only matters if you are not admin\n\treturn { logged, sites, user }\n}\n"],
+  "mappings": 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+  "names": ["config", "isAggregate", "name", "chartType", "chartsInstance"]
+}

package/dist/chunk-RITTG5WN.js

@@ -0,0 +1,158 @@
+import {
+  NumericDensity
+} from "./chunk-MNIBZTQE.js";
+import {
+  HandlerBase
+} from "./chunk-LSEFWW72.js";
+import {
+  Tabs
+} from "./chunk-HBW42TDT.js";
+
+// termsetting/handlers/NumericHandler.ts
+var NumericHandler = class extends HandlerBase {
+  constructor(opts) {
+    super(opts);
+    this.tabs = [];
+    this.handlerByMode = {};
+    this.dom = {};
+    this.opts = opts;
+    this.termsetting = opts.termsetting;
+    this.tw = opts.termsetting.tw;
+    this.tabs = this.setTabData();
+    this.density = new NumericDensity(opts);
+  }
+  getPillStatus() {
+    this.tw = this.termsetting.tw;
+    return this.tw.getStatus(this.termsetting.usecase, this.termsetting.data);
+  }
+  setTabData() {
+    const self = this.termsetting;
+    const tabs = [];
+    const callback = async (event, tabData) => {
+      if (event) event.stopPropagation();
+      try {
+        await this.setEditHandler(tabData);
+        await this.editHandler.showEditMenu(tabData.contentHolder);
+      } catch (e) {
+        this.dom.errdiv.style("display", "").text(e);
+      }
+    };
+    const numTabs = self.opts.numericEditMenuVersion.length;
+    if (self.opts.numericEditMenuVersion.includes("continuous")) {
+      tabs.push({
+        mode: "continuous",
+        label: self.term.type == "survival" ? "Time to Event" : "Continuous",
+        callback,
+        active: this.tw.q.mode === "continuous" || numTabs === 1
+      });
+    }
+    if (self.opts.numericEditMenuVersion.includes("discrete")) {
+      tabs.push({
+        mode: "discrete",
+        label: self.term.type == "survival" ? "Exit code" : "Discrete",
+        callback,
+        active: this.tw.q.mode === "discrete" || numTabs === 1
+      });
+    }
+    if (self.opts.numericEditMenuVersion.includes("spline")) {
+      tabs.push({
+        mode: "spline",
+        label: "Cubic spline",
+        callback,
+        active: this.tw.q.mode === "spline" || numTabs === 1
+      });
+    }
+    if (self.opts.numericEditMenuVersion.includes("binary")) {
+      tabs.push({
+        mode: "binary",
+        label: "Binary",
+        callback,
+        active: this.tw.q.mode === "binary" || numTabs === 1
+      });
+    }
+    return tabs;
+  }
+  async setEditHandler(tabData) {
+    if (!this.handlerByMode[tabData.mode]) {
+      switch (tabData.mode) {
+        case "continuous": {
+          const { NumContEditor } = await import("./NumContEditor-7KK6CIB3.js");
+          this.handlerByMode.continuous = new NumContEditor(this.opts, this);
+          break;
+        }
+        case "discrete": {
+          const { NumDiscreteEditor } = await import("./NumDiscreteEditor-YTKUHG6Z.js");
+          this.handlerByMode.discrete = new NumDiscreteEditor(this.opts, this);
+          break;
+        }
+        case "binary": {
+          const { NumBinaryEditor } = await import("./NumBinaryEditor-EUOYSGPM.js");
+          this.handlerByMode.binary = new NumBinaryEditor(this.opts, this);
+          break;
+        }
+        case "spline": {
+          const { NumSplineEditor } = await import("./NumSplineEditor-56RJ2HT2.js");
+          this.handlerByMode.spline = new NumSplineEditor(this.opts, this);
+          break;
+        }
+        default:
+          throw `unexpected numeric tabData.mode='${tabData.mode}'`;
+          break;
+      }
+    }
+    this.editHandler = this.handlerByMode[tabData.mode];
+  }
+  async showEditMenu(div) {
+    try {
+      this.showLoading(div);
+      this.dom.errdiv = div.append("div").attr("class", "sja_errorbar").style("display", "none");
+      this.tw = this.termsetting.tw;
+      const self = this.tw;
+      for (const t of this.tabs) {
+        t.active = this.tabs.length === 1 || self.q.mode == t.mode || t.mode == "continuous" && !self.q.mode;
+      }
+      this.density_data = await this.density.setData();
+      await this.setEditHandler(this.tabs.find((t) => t.active));
+      this.dom.editDiv = div.append("div").attr("data-testid", "sjpp-num-ts-edit-div");
+      this.dom.btnDiv = div.append("div");
+      this.renderButtons(this.dom.btnDiv);
+      if (this.tabs.length > 1) {
+        this.dom.topBar = this.dom.editDiv.append("div").style("padding", "10px");
+        this.dom.topBar.append("span").html("Use as ");
+        new Tabs({
+          holder: this.dom.topBar.append("div").style("display", "inline-block"),
+          contentHolder: this.dom.editDiv.append("div"),
+          noTopContentStyle: true,
+          tabs: this.tabs
+        }).main();
+      } else {
+        await this.editHandler.showEditMenu(this.dom.editDiv);
+      }
+      this.dom.loadingDiv.style("display", "none");
+    } catch (e) {
+      this.hideLoading();
+      this.dom.errdiv.style("display", "").text(typeof e == "object" ? e.message || e.error || e : e);
+    }
+  }
+  renderButtons(btnDiv) {
+    btnDiv.append("button").style("margin", "5px").attr("data-testId", "sjpp_numeric_edit_apply").html("Apply").on("click", () => {
+      this.termsetting.q = this.editHandler.getEditedQ();
+      this.termsetting.dom.tip.hide();
+      this.termsetting.api.runCallback();
+    });
+    btnDiv.append("button").style("margin", "5px").attr("data-testId", "sjpp_numeric_edit_reset").html("Reset").on("click", () => {
+      this.editHandler.undoEdits();
+    });
+  }
+  destroy() {
+    for (const s of Object.values(this.dom)) {
+      if (typeof s.remove == "function") s.remove();
+    }
+    this.density.destroy();
+  }
+};
+
+export {
+  NumericHandler
+};
+//# sourceMappingURL=chunk-RITTG5WN.js.map

package/dist/chunk-SMSFTTEO.js

@@ -0,0 +1,272 @@
+import {
+  fillbar,
+  make_table_2col
+} from "./chunk-KUZPTJJO.js";
+
+// src/block.mds.expressionstat.js
+var color_noinfo = "#858585";
+function init_config(cfg) {
+  if (!cfg.datatype) cfg.datatype = "FPKM";
+  if (!cfg.itemcolor) cfg.itemcolor = "green";
+  if (!cfg.ase) cfg.ase = {};
+  if (cfg.ase.qvalue == void 0) cfg.ase.qvalue = 0.05;
+  if (cfg.ase.meandelta_monoallelic == void 0) cfg.ase.meandelta_monoallelic = 0.3;
+  if (cfg.ase.asemarkernumber_biallelic == void 0) cfg.ase.asemarkernumber_biallelic = 0;
+  if (!cfg.ase.color_noinfo) cfg.ase.color_noinfo = color_noinfo;
+  if (!cfg.ase.color_uncertain) cfg.ase.color_uncertain = "#A8E0B5";
+  if (!cfg.ase.color_biallelic) cfg.ase.color_biallelic = "#40859C";
+  if (!cfg.ase.color_monoallelic) cfg.ase.color_monoallelic = "#d95f02";
+  if (!cfg.outlier) cfg.outlier = {};
+  if (cfg.outlier.pvalue_cutoff == void 0) cfg.outlier.pvalue_cutoff = 0.05;
+  if (cfg.outlier.rank_asehigh_cutoff == void 0) cfg.outlier.rank_asehigh_cutoff = 0.1;
+  if (!cfg.outlier.color_outlier) cfg.outlier.color_outlier = "#FF8875";
+  if (!cfg.outlier.color_outlier_asehigh) cfg.outlier.color_outlier_asehigh = "blue";
+}
+function measure(v, cfg) {
+  if (!cfg) return;
+  v.estat = {};
+  if (v.ase && cfg.ase) {
+    const qvalue = v.ase.qvalue || v.ase.geometricmean;
+    if (qvalue == void 0) {
+      v.estat.ase_noinfo = true;
+    } else if (qvalue <= cfg.ase.qvalue) {
+      if (v.ase.mean_delta >= cfg.ase.meandelta_monoallelic) {
+        v.estat.ase_monoallelic = true;
+      } else {
+        v.estat.ase_uncertain = true;
+      }
+    } else {
+      if (v.ase.ase_markers == cfg.ase.asemarkernumber_biallelic) {
+        v.estat.ase_biallelic = true;
+      } else {
+        v.estat.ase_uncertain = true;
+      }
+    }
+  } else {
+    v.estat.ase_noinfo = true;
+  }
+  if (v.outlier && cfg.outlier) {
+    if (v.outlier.test_whitelist) {
+      if (v.outlier.test_whitelist.pvalue <= cfg.outlier.pvalue_cutoff) {
+        v.estat.outlier = true;
+      } else {
+        if (v.estat.ase_monoallelic) {
+          if (Number.isInteger(v.outlier.test_whitelist.rank) && Number.isInteger(v.outlier.test_whitelist.size) && v.outlier.test_whitelist.rank / v.outlier.test_whitelist.size <= cfg.outlier.rank_asehigh_cutoff) {
+            v.estat.outlier_asehigh = true;
+            v.outlier.test_whitelist.asehigh = true;
+          }
+        }
+      }
+    } else if (v.outlier.test_biallelic) {
+      if (v.outlier.test_biallelic.pvalue <= cfg.outlier.pvalue_cutoff) {
+        v.estat.outlier = true;
+      } else {
+        if (v.estat.ase_monoallelic) {
+          if (Number.isInteger(v.outlier.test_biallelic.rank) && Number.isInteger(v.outlier.test_biallelic.size) && v.outlier.test_biallelic.rank / v.outlier.test_biallelic.size <= cfg.outlier.rank_asehigh_cutoff) {
+            v.estat.outlier_asehigh = true;
+            v.outlier.test_biallelic.asehigh = true;
+          }
+        }
+      }
+    } else if (v.outlier.test_entirecohort) {
+      if (v.outlier.test_entirecohort.pvalue <= cfg.outlier.pvalue_cutoff) {
+        v.estat.outlier = true;
+      } else {
+        if (v.estat.ase_monoallelic) {
+          if (Number.isInteger(v.outlier.test_entirecohort.rank) && Number.isInteger(v.outlier.test_entirecohort.size) && v.outlier.test_entirecohort.rank / v.outlier.test_entirecohort.size <= cfg.outlier.rank_asehigh_cutoff) {
+            v.estat.outlier_asehigh = true;
+            v.outlier.test_entirecohort.asehigh = true;
+          }
+        }
+      }
+    }
+  }
+}
+function showsingleitem_table(v, cfg, table) {
+  if (!v.estat) return;
+  if (cfg.no_ase) return;
+  if (v.ase) {
+    const tr = table.append("tr");
+    tr.append("td").attr("colspan", 2).style("background", ase_color(v, cfg)).style("color", "white").html(
+      (v.estat.ase_monoallelic ? "Mono-allelic" : v.estat.ase_biallelic ? "Bi-allelic" : "ASE uncertain") + "<br>(allele-specific expression)"
+    );
+    const lst = [
+      {
+        k: "#SNPs heterozygous in DNA",
+        v: v.ase.markers
+      },
+      {
+        k: "#SNPs showing ASE in RNA",
+        v: v.ase.ase_markers
+      },
+      {
+        k: "Mean delta of ASE SNPs",
+        v: v.ase.mean_delta
+      }
+    ];
+    if (v.ase.qvalue) {
+      lst.push({
+        k: "Q-value",
+        v: v.ase.qvalue
+      });
+    } else if (v.ase.geometricmean) {
+      lst.push({
+        k: "Geometric mean of binomial P-values of ASE SNPs",
+        v: v.ase.geometricmean
+      });
+    }
+    const td = tr.append("td");
+    make_table_2col(td, lst);
+  } else {
+    const tr = table.append("tr");
+    tr.append("td").attr("colspan", 3).style("background", cfg.ase.color_noinfo).style("color", "white").text("No info on allele-specific expression");
+  }
+  if (v.snps && v.snps.length > 0) {
+    const hetsnp = v.snps.filter((i) => i.dnacount && i.dnacount.ishet);
+    if (hetsnp.length > 0) {
+      const lst = [];
+      for (const m of hetsnp) {
+        lst.push(
+          "<tr><td>" + m.chr + ":" + (m.pos + 1) + " " + m.ref + ">" + m.alt + "</td><td>" + fillbar(null, { f: m.dnacount.f }) + " " + m.dnacount.ref + "/" + m.dnacount.alt + "</td><td>" + (m.rnacount.nocoverage ? '<span style="font-size:.8em;opacity:.5">No coverage</span>' : fillbar(null, { f: m.rnacount.f }) + " " + m.rnacount.ref + "/" + m.rnacount.alt) + "</td><td>" + (m.rnacount.pvalue || "-") + "</td></tr>"
+        );
+      }
+      table.append("tr").append("td").attr("colspan", 3).html(
+        '<table style="margin-top:10px;border:solid 1px #ededed;border-spacing:5px;"><tr style="opacity:.5"><td>SNP</td><td>DNA</td><td>RNA</td><td>Binomial test P-value</td></tr>' + lst.join("") + "</table>"
+      );
+    }
+  }
+  if (v.outlier) {
+    if (v.outlier.test_whitelist) {
+      const tr = table.append("tr");
+      tr.append("td").attr("colspan", 2).text("Outlier (white list)");
+      const lst = [];
+      for (const k in v.outlier.test_whitelist) {
+        lst.push({ k, v: v.outlier.test_whitelist[k] });
+      }
+      const td = tr.append("td");
+      make_table_2col(td, lst);
+      if (v.outlier.test_whitelist.asehigh) {
+        td.append("div").style("background", cfg.outlier.color_outlier_asehigh).style("padding", "2px 10px").style("color", "white").text("ASE high");
+      }
+    }
+    if (v.outlier.test_biallelic) {
+      const tr = table.append("tr");
+      tr.append("td").attr("colspan", 2).text("Outlier (biallelic)");
+      const lst = [];
+      for (const k in v.outlier.test_biallelic) {
+        lst.push({ k, v: v.outlier.test_biallelic[k] });
+      }
+      const td = tr.append("td");
+      make_table_2col(td, lst);
+      if (v.outlier.test_biallelic.asehigh) {
+        td.append("div").style("background", cfg.outlier.color_outlier_asehigh).style("padding", "2px 10px").style("color", "white").text("ASE high");
+      }
+    }
+    if (v.outlier.test_entirecohort) {
+      const tr = table.append("tr");
+      tr.append("td").attr("colspan", 2).text("Outlier (all samples)");
+      const lst = [];
+      for (const k in v.outlier.test_entirecohort) {
+        lst.push({ k, v: v.outlier.test_entirecohort[k] });
+      }
+      const td = tr.append("td");
+      make_table_2col(td, lst);
+      if (v.outlier.test_entirecohort.asehigh) {
+        td.append("div").style("background", cfg.outlier.color_outlier_asehigh).style("padding", "2px 10px").style("color", "white").text("ASE high");
+      }
+    }
+  }
+}
+function ase_color(v, cfg) {
+  if (cfg.no_ase) return color_noinfo;
+  if (!cfg.ase) return color_noinfo;
+  if (!v.estat) return cfg.ase.color_noinfo;
+  if (v.estat.ase_monoallelic) return cfg.ase.color_monoallelic;
+  if (v.estat.ase_biallelic) return cfg.ase.color_biallelic;
+  if (v.estat.ase_uncertain) return cfg.ase.color_uncertain;
+  return cfg.ase.color_noinfo;
+}
+function ui_config(holder, cfg, tk, call) {
+  const indent = 30;
+  {
+    const row = holder.append("div").style("margin-bottom", "5px");
+    row.append("span").html("If " + (tk.checkrnabam ? "p-value geometric mean" : "Q-VALUE") + " &le;&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", cfg.ase.qvalue).on("keyup", (event) => {
+      if (event.code != "Enter" && event.code != "NumpadEnter") return;
+      let v = Number.parseFloat(event.target.value);
+      if (!v || v <= 0) {
+        return;
+      }
+      if (cfg.ase.qvalue == v) {
+        return;
+      }
+      cfg.ase.qvalue = v;
+      call();
+    });
+    row.append("span").html("&nbsp;:");
+  }
+  {
+    const row = holder.append("div").style("margin", "0px 5px 5px " + indent + "px");
+    row.append("span").html("If MEAN_DELTA &ge;&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", cfg.ase.meandelta_monoallelic).on("keyup", (event) => {
+      if (event.code != "Enter" && event.code != "NumpadEnter") return;
+      let v = Number.parseFloat(event.target.value);
+      if (!v || v <= 0) {
+        return;
+      }
+      if (cfg.ase.meandelta_monoallelic == v) {
+        return;
+      }
+      cfg.ase.meandelta_monoallelic = v;
+      call();
+    });
+    row.append("span").html("&nbsp;:&nbsp;");
+  }
+  holder.append("div").style("margin", "0px 5px 5px " + indent * 2 + "px").html(
+    'Is <span style="background:' + cfg.ase.color_monoallelic + ';padding:1px 5px;color:white;">mono-allelic expression</span>'
+  );
+  holder.append("div").style("margin", "0px 5px 5px " + indent + "px").html("Else:");
+  holder.append("div").style("margin", "0px 5px 5px " + indent * 2 + "px").html(
+    'Is <span style="background:' + cfg.ase.color_uncertain + ';padding:1px 5px;color:white;">ASE uncertain</span>'
+  );
+  holder.append("div").style("margin", "0px 5px 5px 0px").html("Else:");
+  {
+    const row = holder.append("div").style("margin", "0px 5px 5px " + indent + "px");
+    row.append("span").html("If number of ASE markers &le;&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", cfg.ase.asemarkernumber_biallelic).on("keyup", (event) => {
+      if (event.code != "Enter" && event.code != "NumpadEnter") return;
+      let v = Number.parseInt(event.target.value);
+      if (v < 0) {
+        return;
+      }
+      if (cfg.ase.asemarkernumber_biallelic == v) {
+        return;
+      }
+      cfg.ase.asemarkernumber_biallelic = v;
+      call();
+    });
+    row.append("span").html("&nbsp;:&nbsp;");
+  }
+  holder.append("div").style("margin", "0px 5px 5px " + indent * 2 + "px").html(
+    'Is <span style="background:' + cfg.ase.color_biallelic + ';padding:1px 5px;color:white;">bi-allelic expression</span>'
+  );
+  holder.append("div").style("margin", "0px 5px 5px " + indent + "px").html("Else:");
+  holder.append("div").style("margin", "0px 5px 5px " + indent * 2 + "px").html(
+    'Is <span style="background:' + cfg.ase.color_uncertain + ';padding:1px 5px;color:white;">ASE uncertain</span>'
+  );
+  holder.append("div").style("margin", "10px").append("button").text("Default ASE parameters").on("click", () => {
+    cfg.ase.qvalue = 0.05;
+    cfg.ase.meandelta_monoallelic = 0.3;
+    cfg.ase.asemarkernumber_biallelic = 0;
+    call();
+  });
+}
+
+export {
+  init_config,
+  measure,
+  showsingleitem_table,
+  ase_color,
+  ui_config
+};
+//# sourceMappingURL=chunk-SMSFTTEO.js.map