@sjcrh/proteinpaint-client 2.196.0 → 2.198.0

package/dist/chunk-OVSKJROY.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../node_modules/partjson/dist/partjson.umd.js", "../plots/barchart.data.js"],
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Date-this.times.start,Object.keys(this.focusTemplate).length?(this.parseTemplate(this.focusTemplate,{\"@\":this.reserved.notDefined}),this.template=this.focusTemplate):this.template=e,this.postLoopTerms=Object.create(null),this.done=[],this.opts.data&&this.add(this.opts.data,!1),this.errors.log(this.fillers)}setResultContext(t,e=null,s=null,r=!1,o,i=null,n=null){const l=null!==e&&e in s?s[e]:JSON.parse(t);if(this.contexts.has(l))return l;const c={branch:e,parent:s,context:this.contexts.get(s),self:l,root:this.tree?this.tree:l,joins:this.joins,errors:[],key:o};if(r&&(c.tracker=new Map),i&&n){const t=this.fillers.get(n);if(!t[\"@before\"](i,c))return;if(t[\"@join\"]&&!t[\"@join\"](i,c))return}return this.contexts.set(l,c),null!==e&&(s[e]=l),l}parseTemplate(t,e,s=[]){const r=Object.create(null);r.inputs=Object.create(null),r[\"@before\"]=this.reserved.trueFxn,r[\"@after\"]=this.reserved.trueFxn,r.postTerms={},r.errors=[];const i=this.reserved[\"@ignore\"](t,e,r);r[\"@ignore\"]=i,this.fillers.set(t,r);const n=this.steps.map(t=>[]);for(const e in t){const[l,c,p,h]=o(this,e),u=t[e],a=r.inputs[e]={term:e,subterm:l,symbols:c,keyTokens:p,templateVal:u,lineage:[...s,e],inheritedIgnore:i,errors:[]};\"@()\"==c?this.reserved.setFxn(l,a,r,u):(a.keyFxn=this.keyFiller.getFxn(a,i),a.keyFxn&&(a.valFxn=this.valFiller.getFxn(a,i),\"__:\"==p.time||this.timePost.includes(p.time)?(r.postTerms[p.time]||(r.postTerms[p.time]=[]),r.postTerms[p.time].includes(e)||r.postTerms[p.time].push(e)):n[h].push(e)))}r.steps=n.filter(t=>t.length)}add(t,e=!0){this.times.start||(this.times.start=+new Date),e&&this.errors.clear(),this.joins.clear();for(const e of t)if(this.split)for(const t of this.split(e))this.processRow(t,this.template,this.tree),this.joins.clear();else this.processRow(e,this.template,this.tree),this.joins.clear();this.processResult(this.tree);for(const t of this.timePost)if(this.postLoopTerms[t])for(const e of this.postLoopTerms[t])this.postLoop(e.self,e,t);for(const t of this.done)t.done(t.self,t);for(const[t,e]of this.temps)for(const s of e)delete t[s];this.times.total=+new Date-this.times.start,delete this.times.start,e&&this.errors.log()}processRow(t,e,s){const r=this.contexts.get(s),o=this.fillers.get(e);if(r.filler=o,o[\"@before\"](t,r)&&(!o[\"@join\"]||o[\"@join\"](t,r))){for(const e of o.steps)for(const i of e){const e=o.inputs[i];if(e.keyFxn&&e.valFxn){const o=e.keyFxn(t,r);for(const i of o)e.valFxn(t,i,s,r),\"~\"==e.keyTokens.skip&&(this.temps.has(s)||this.temps.set(s,new Set),this.temps.get(s).add(i))}}o[\"@after\"](t,r),o[\"@dist\"]&&o[\"@dist\"](r),o[\"@done\"]&&!this.done.includes(r)&&(r.done=o[\"@done\"],this.done.push(r));for(const t in o.postTerms)this.postLoopTerms[t]||(this.postLoopTerms[t]=[]),this.postLoopTerms[t].includes(r)||this.postLoopTerms[t].push(r);return!0}}postLoop(t,e,s=\"__:\"){if(e&&e.filler&&e.filler.postTerms[s])for(const r of e.filler.postTerms[s]){const s=e.filler.inputs[r];if(s.keyFxn&&s.valFxn){const r=s.keyFxn(null,e);for(const o of r)s.valFxn(null,o,t,e)}}}processResult(t){const e=this.contexts.get(t);this.postLoop(t,e,\"__:\");for(const e in t){const s=t[e];if(s)if(Array.isArray(s)||s instanceof Set||s instanceof Map)for(const t of s)\"object\"==typeof t&&this.processResult(t);else if(\"object\"==typeof s){const t=this.contexts.get(s);t&&t[\"@dist\"]&&t[\"@dist\"](s),this.processResult(s)}}e&&e.filler&&this.errors.markErrors(t,e)}copyResult(t,e={}){if(arguments.length&&void 0===t)return;const s=arguments.length?t:this.tree;for(const t in s){const r=s[t];if(r instanceof Set||r instanceof Map)e[t]=[...r];else if(Array.isArray(r)){e[t]=[];for(const s of r)if(Array.isArray(s)){const r=[];e[t].push(r),this.copyResult(s,r)}else if(s&&\"object\"==typeof s){const r=Object.create(null);e[t].push(r),this.copyResult(s,r)}else e[t]=JSON.parse(JSON.stringify(r))}else r&&\"object\"==typeof r?(e[t]=Object.create(null),this.copyResult(r,e[t])):e[t]=JSON.parse(JSON.stringify(r))}return e}}return c.prototype.converter=l,c});\n", "import Partjson from 'partjson'\nimport { compute_bins } from '#shared/termdb.bins.js'\nimport { sample_match_termvaluesetting } from '../common/termutils'\nimport { isNumeric } from '#shared/helpers.js'\n\nexport function getBarchartData(_q, data) {\n\t/*\n\t  _q: term.q \n\t  data:  rows of data, each row is unique by sample\n\t*/\n\t// need to not overwrite original term definition data\n\tconst q = JSON.parse(JSON.stringify(_q))\n\n\t// support legacy query parameter names\n\tif (!q.term1) q.term1 = q.term ? q.term : {}\n\tif (!q.term1_q) q.term1_q = {}\n\tif (!q.term0) q.term0 = {}\n\tif (!q.term0_q) q.term0_q = {}\n\tif (!q.term2) q.term2 = {}\n\tif (!q.term2_q) q.term2_q = {}\n\tif (!q.filter) q.filter = { type: 'tvslst', join: '', lst: [] }\n\n\tconst pj = getCharts(q, data)\n\treturn pj.tree.results\n}\n\nfunction getTrackers() {\n\treturn {\n\t\tjoinFxns: { '': () => '' }, // keys are term0, term1, term2 names; ...\n\t\tnumValFxns: { '': () => {} }, // ... if key == empty string then the term is not specified\n\t\torderedLabels: [],\n\t\tbins: []\n\t}\n}\n\n// template for partjson, already stringified so that it does not\n// have to be re-stringified within partjson refresh for every request\nconst templateBar = JSON.stringify({\n\t'@before()': '=prep()',\n\t'@join()': {\n\t\tidVal: '=idVal()'\n\t},\n\tresults: {\n\t\t'_2:maxAcrossCharts': '=maxAcrossCharts()',\n\t\tcharts: [\n\t\t\t{\n\t\t\t\tchartId: '@key',\n\t\t\t\ttotal: '+1',\n\t\t\t\t'_1:maxSeriesTotal': '=maxSeriesTotal()',\n\t\t\t\t'@done()': '=filterEmptySeries()',\n\t\t\t\tserieses: [\n\t\t\t\t\t{\n\t\t\t\t\t\ttotal: '+1',\n\t\t\t\t\t\tseriesId: '@key',\n\t\t\t\t\t\tmax: '<&idVal.dataVal', // needed by client-side boxplot renderer\n\t\t\t\t\t\t'~values': ['&idVal.dataVal', 0],\n\t\t\t\t\t\t'~sum': '+&idVal.dataVal',\n\t\t\t\t\t\t'__:boxplot': '=boxplot()',\n\t\t\t\t\t\t'~samples': ['$sample', 'set'],\n\t\t\t\t\t\t//'__:AF': '=getAF()',\n\t\t\t\t\t\tdata: [\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tdataId: '@key',\n\t\t\t\t\t\t\t\ttotal: '+1'\n\t\t\t\t\t\t\t\t//samples: ['$sample']\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t'&idVal.dataId[]'\n\t\t\t\t\t\t]\n\t\t\t\t\t},\n\t\t\t\t\t'&idVal.seriesId[]'\n\t\t\t\t]\n\t\t\t},\n\t\t\t'&idVal.chartId[]'\n\t\t],\n\t\t'~sum': '+&idVal.seriesVal',\n\t\t'~values': ['&idVal.seriesVal', 0],\n\t\t'__:boxplot': '=boxplot()',\n\t\trefs: {\n\t\t\tcols: ['&idVal.seriesId[]'],\n\t\t\tcolgrps: ['-'],\n\t\t\trows: ['&idVal.dataId[]'],\n\t\t\trowgrps: ['-'],\n\t\t\tcol2name: {\n\t\t\t\t'&idVal.seriesId[]': {\n\t\t\t\t\tname: '@branch',\n\t\t\t\t\tgrp: '-'\n\t\t\t\t}\n\t\t\t},\n\t\t\trow2name: {\n\t\t\t\t'&idVal.dataId[]': {\n\t\t\t\t\tname: '@branch',\n\t\t\t\t\tgrp: '-'\n\t\t\t\t}\n\t\t\t},\n\t\t\t'__:useColOrder': '=useColOrder()',\n\t\t\t'__:useRowOrder': '=useRowOrder()',\n\t\t\t'__:bins': '=bins()',\n\t\t\t//'__:q': '=q()',\n\t\t\t'@done()': '=sortColsRows()'\n\t\t},\n\t\t'@done()': '=sortCharts()'\n\t}\n})\n\nfunction getCharts(q, data) {\n\t/*\n  q: objectified URL query string\n  inReq: request-specific closured functions and variables\n  data: rows of annotation data\n  */\n\n\t/*\n\t\tA map of functions to get a term's id and value, by its term.type\n\t\tThe function will be used in idVal() below to get the chart/series/data ID and value\n\t\tfor a given data row\n  */\n\tconst idValFxns = {\n\t\tcategorical: getCategoricalIdVal,\n\t\tinteger: getNumericIdVal,\n\t\tfloat: getNumericIdVal,\n\t\tundefined: getUndefinedIdVal\n\t\t// NOTE: condition terms are not currently supported for frontend vocab\n\t}\n\n\treturn new Partjson({\n\t\tdata,\n\t\tseed: `{\"values\": []}`, // result seed\n\t\ttemplate: templateBar,\n\t\t'=': {\n\t\t\tidVal(row, context) {\n\t\t\t\tconst [chartId, chartVal] = idValFxns[q.term0.type](row.data, q.term0, q.term0_q, data)\n\t\t\t\tconst [seriesId, seriesVal] = idValFxns[q.term1.type](row.data, q.term1, q.term1_q, data)\n\t\t\t\tconst [dataId, dataVal] = idValFxns[q.term2.type](row.data, q.term2, q.term2_q, data)\n\t\t\t\treturn {\n\t\t\t\t\tchartId,\n\t\t\t\t\tchartVal,\n\t\t\t\t\tseriesId,\n\t\t\t\t\tseriesVal,\n\t\t\t\t\tdataId,\n\t\t\t\t\tdataVal\n\t\t\t\t}\n\t\t\t},\n\t\t\tprep(row) {\n\t\t\t\treturn sample_match_termvaluesetting(row.data, q.filter)\n\t\t\t},\n\t\t\tmaxSeriesTotal(row, context) {\n\t\t\t\tlet maxSeriesTotal = 0\n\t\t\t\tfor (const grp of context.self.serieses) {\n\t\t\t\t\tif (grp && grp.total > maxSeriesTotal) {\n\t\t\t\t\t\tmaxSeriesTotal = grp.total\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\treturn maxSeriesTotal\n\t\t\t},\n\t\t\tmaxAcrossCharts(row, context) {\n\t\t\t\tlet maxAcrossCharts = 0\n\t\t\t\tfor (const chart of context.self.charts) {\n\t\t\t\t\tif (chart.maxSeriesTotal > maxAcrossCharts) {\n\t\t\t\t\t\tmaxAcrossCharts = chart.maxSeriesTotal\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\treturn maxAcrossCharts\n\t\t\t},\n\t\t\tboxplot(row, context) {\n\t\t\t\tif (!context.self.values || !context.self.values.length) return\n\t\t\t\tconst values = context.self.values.filter(d => d !== null && !isNaN(d))\n\t\t\t\tif (!values.length) return\n\t\t\t\tvalues.sort((i, j) => i - j)\n\t\t\t\tconst stat = boxplot_getvalue(\n\t\t\t\t\tvalues.map(v => {\n\t\t\t\t\t\treturn { value: +v }\n\t\t\t\t\t})\n\t\t\t\t)\n\t\t\t\tstat.mean = context.self.sum / values.length\n\t\t\t\tlet s = 0\n\t\t\t\tfor (const v of values) {\n\t\t\t\t\ts += Math.pow(v - stat.mean, 2)\n\t\t\t\t}\n\t\t\t\tstat.sd = Math.sqrt(s / (values.length - 1))\n\t\t\t\tif (isNaN(stat.sd)) stat.sd = null\n\t\t\t\treturn stat\n\t\t\t},\n\t\t\tnumSamples(row, context) {\n\t\t\t\treturn context.self.samples.size\n\t\t\t},\n\t\t\tfilterEmptySeries(result) {\n\t\t\t\tconst nonempty = result.serieses.filter(series => series.total)\n\t\t\t\tresult.serieses.splice(0, result.serieses.length, ...nonempty)\n\t\t\t},\n\t\t\tsortColsRows(result) {\n\t\t\t\tif (q.term1_q.orderedLabels) {\n\t\t\t\t\tconst labels = q.term1_q.orderedLabels\n\t\t\t\t\tresult.cols.sort((a, b) => labels.indexOf(a) - labels.indexOf(b))\n\t\t\t\t}\n\t\t\t\tif (q.term2.orderedLabels) {\n\t\t\t\t\tconst labels = q.term2_q.orderedLabels\n\t\t\t\t\tresult.rows.sort((a, b) => labels.indexOf(a) - labels.indexOf(b))\n\t\t\t\t}\n\t\t\t},\n\t\t\tsortCharts(result) {},\n\t\t\tuseColOrder() {\n\t\t\t\treturn q.term1_q.orderedLabels && q.term1_q.orderedLabels.length > 0\n\t\t\t},\n\t\t\tuseRowOrder() {\n\t\t\t\treturn q.term2_q.orderedLabels && q.term2_q.orderedLabels.length > 0\n\t\t\t},\n\t\t\tbins() {\n\t\t\t\treturn [q.term0_q, q.term1_q, q.term2_q].map(d => d.computed_bins)\n\t\t\t},\n\t\t\tq() {}\n\t\t}\n\t})\n}\n\nfunction setDatasetAnnotations(item) {\n\tif (item.type == 'tvslst') {\n\t\tfor (const subitem of item.lst) {\n\t\t\tsetDatasetAnnotations(subitem)\n\t\t}\n\t} else {\n\t\tif (item.tvs.term.type == 'categorical') {\n\t\t\titem.tvs.valueset = new Set(item.tvs.values.map(i => i.key))\n\t\t}\n\t}\n}\n\n/* \n\tArguments: \n\td: data row, an object with sample ID and the annotation values for one or more terms,\n\t\t but this function is used specifically for annotation terms that are categorical\n\tterm\n\n\tReturns:\n\t[\t\n\t\t[id]: a list of matching chartId, seriesId, or dataId for this data row,\n\t\tvalue: the annotation value for this term\n\t]\n*/\nfunction getCategoricalIdVal(d, term) {\n\tconst id = 'id' in term ? d[term.id] : '-'\n\tconst value = 'id' in term && isNumeric(d[term.id]) ? +d[term.id] : 0\n\treturn [[id], value]\n}\n\n/* \n\tArguments: \n\td: data row, an object with sample ID and the annotation values for one or more terms,\n\t\t but this function is used specifically for annotation terms that are categorical\n\tterm\n\n\tReturns:\n\t[\n\t\t[id]: a list of matching chartId, seriesId, or dataId for this data row,\n\t\tvalue: the annotation value for this term\n\t]\n*/\nfunction getNumericIdVal(d, term, q, rows) {\n\tif (!('id' in term) || !(term.id in d)) return [[], undefined]\n\tif (!q.computed_bins) {\n\t\tconst summary = {}\n\t\trows.map(row => {\n\t\t\tif (!isNumeric(row.data[term.id])) return\n\t\t\tconst v = +row.data[term.id]\n\t\t\tif (!('min' in summary) || summary.min > v) summary.min = v\n\t\t\tif (!('max' in summary) || summary.max < v) summary.max = v\n\t\t})\n\t\tq.computed_bins = compute_bins(q, percentiles => summary)\n\t\tq.orderedLabels = q.computed_bins.map(d => d.label)\n\t}\n\tconst v = d[term.id]\n\tif (term.values && v in term.values && term.values[v].uncomputable) {\n\t\treturn [[term.values[v].label], undefined]\n\t}\n\t// ignore non-numeric values like empty string, \"\"\n\t// which may occur naturally in a csv/tab-delimited input\n\tif (isNumeric(d[term.id])) {\n\t\tconst ids = []\n\t\tfor (const b of q.computed_bins) {\n\t\t\tif (b.startunbounded) {\n\t\t\t\tif (v < b.stop) {\n\t\t\t\t\tids.push(b.label)\n\t\t\t\t} else if (b.stopinclusive && v === b.stop) {\n\t\t\t\t\tids.push(b.label)\n\t\t\t\t}\n\t\t\t} else if (b.stopunbounded) {\n\t\t\t\t// a bin should not be true for both b.startunbounded and b.stopunbounded,\n\t\t\t\t// since that is not a finite bin\n\t\t\t\tif (v > b.start) {\n\t\t\t\t\tids.push(b.label)\n\t\t\t\t} else if (b.stopinclusive && v === b.start) {\n\t\t\t\t\tids.push(b.label)\n\t\t\t\t}\n\t\t\t} else if (\n\t\t\t\t(v > b.start || (v === b.start && b.startinclusive)) &&\n\t\t\t\t(v < b.stop || (v === b.stop && b.stopinclusive))\n\t\t\t) {\n\t\t\t\tids.push(b.label)\n\t\t\t}\n\t\t\t// for numeric terms, may match the sample annotation to at most one chartId, seriesId, or dataId,\n\t\t\t// so break the loop as soon as a matching id is found for a data row\n\t\t\t// TODO: may allow exceptions later to have more than 1 matching id???\n\t\t\tif (ids.length) break\n\t\t}\n\t\treturn [ids, v]\n\t}\n\treturn [[], undefined]\n}\n\nfunction getUndefinedIdVal() {\n\treturn [['-'], undefined]\n}\n\nfunction boxplot_getvalue(lst) {\n\t/* ascending order\n  each element: {value}\n  */\n\tconst l = lst.length\n\tif (l < 5) {\n\t\t// less than 5 items, won't make boxplot\n\t\treturn { out: lst }\n\t}\n\tconst p50 = lst[Math.floor(l / 2)].value\n\tconst p25 = lst[Math.floor(l / 4)].value\n\tconst p75 = lst[Math.floor((l * 3) / 4)].value\n\tconst p05 = lst[Math.floor(l * 0.05)].value\n\tconst p95 = lst[Math.floor(l * 0.95)].value\n\tconst p01 = lst[Math.floor(l * 0.01)].value\n\tconst iqr = p75 - p25\n\n\tlet w1, w2\n\tif (iqr == 0) {\n\t\tw1 = 0\n\t\tw2 = 0\n\t} else {\n\t\tconst i = lst.findIndex(i => i.value > p25 - iqr * 1.5)\n\t\tw1 = lst[i == -1 ? 0 : i].value\n\t\tconst j = lst.findIndex(i => i.value > p75 + iqr * 1.5)\n\t\tw2 = lst[j == -1 ? l - 1 : Math.max(0, j - 1)].value\n\t}\n\tconst out = lst.filter(i => i.value < p25 - iqr * 1.5 || i.value > p75 + iqr * 1.5)\n\treturn { w1, w2, p05, p25, p50, p75, p95, iqr, out }\n}\n\nexport function getCategoryData(q, data) {\n\tif (!data || !data.length) {\n\t\t// support custom vocab/adhoc dictionary with no sample annotations\n\t\treturn {\n\t\t\tlst: Object.keys(q.term.values).map(k => {\n\t\t\t\treturn { key: k, label: q.term.values[k].label, value: k }\n\t\t\t})\n\t\t}\n\t}\n\t//\n\tconst pj = new Partjson({\n\t\tdata,\n\t\ttemplate: JSON.stringify({\n\t\t\t'@before()': '=prep()',\n\t\t\t'@join()': {\n\t\t\t\tidVal: '=idVal()'\n\t\t\t},\n\t\t\tresults: {\n\t\t\t\t'&idVal.id': {\n\t\t\t\t\tsamplecount: '+1',\n\t\t\t\t\t':__key': '&idVal.id',\n\t\t\t\t\t':__label': '&idVal.id',\n\t\t\t\t\t':__value': '&idVal.id'\n\t\t\t\t}\n\t\t\t}\n\t\t}),\n\t\t'=': {\n\t\t\tprep(row) {\n\t\t\t\treturn sample_match_termvaluesetting(row.data, q.filter)\n\t\t\t},\n\t\t\tidVal(row, context) {\n\t\t\t\tconst [id, value] = getCategoricalIdVal(row.data, q.term)\n\t\t\t\treturn { id: id[0], value }\n\t\t\t}\n\t\t}\n\t})\n\treturn { lst: Object.values(pj.tree.results) 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-  "names": ["t", "e", "s", "r", "o", "i", "n", "l", "c", "Partjson", "v", "d", "i", "Partjson"]
-}

package/dist/chunk-PJ3FCJBZ.js

@@ -1,480 +0,0 @@
-import {
-  renderTable
-} from "./chunk-WY2PGUVX.js";
-import {
-  clusterMethodLst,
-  distanceMethodLst
-} from "./chunk-LYVLF6HO.js";
-import {
-  termType2label
-} from "./chunk-NNFAUP2I.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import {
-  __export
-} from "./chunk-HFNDKYVF.js";
-
-// plots/matrix/hierCluster.interactivity.js
-var hierCluster_interactivity_exports = {};
-__export(hierCluster_interactivity_exports, {
-  addSelectedRowsOptions: () => addSelectedRowsOptions,
-  addSelectedSamplesOptions: () => addSelectedSamplesOptions,
-  getAllChildrenClusterIds: () => getAllChildrenClusterIds,
-  getClusterFromLeftDendrogram: () => getClusterFromLeftDendrogram,
-  getClusterFromTopDendrogram: () => getClusterFromTopDendrogram,
-  setClusteringBtn: () => setClusteringBtn,
-  showTable4selectedRows: () => showTable4selectedRows,
-  showTable4selectedSamples: () => showTable4selectedSamples,
-  triggerZoomBranch: () => triggerZoomBranch
-});
-function getAllChildrenClusterIds(clickedClusterId, left) {
-  const mergedClusters = left ? this.hierClusterData.clustering.row.mergedClusters : this.hierClusterData.clustering.col.mergedClusters;
-  const children = mergedClusters.get(clickedClusterId).childrenClusters || [];
-  let allChildren = [...children];
-  for (const child of children) {
-    allChildren = allChildren.concat(this.getAllChildrenClusterIds(child, left));
-  }
-  return allChildren;
-}
-function addSelectedSamplesOptions(clickedSampleNames, event) {
-  const l = this.settings.matrix.controlLabels;
-  const ss = this.opts.allow2selectSamples;
-  const optionArr = [
-    {
-      label: "Zoom in",
-      callback: () => {
-        this.triggerZoomBranch(this, clickedSampleNames);
-      }
-    },
-    {
-      label: `List ${clickedSampleNames.length} ${l.samples}`,
-      callback: () => this.showTable4selectedSamples(clickedSampleNames)
-    }
-  ];
-  if (ss) {
-    optionArr.push({
-      label: ss.buttonText || `Select ${l.samples}`,
-      callback: async () => {
-        const samples = clickedSampleNames.map((c) => this.data.samples[c]);
-        ss.callback({
-          samples: await this.app.vocabApi.convertSampleId(samples, ss.attributes),
-          source: ss.defaultSelectionLabel || `Selected ${l.samples} from gene expression`
-        });
-      }
-    });
-  } else {
-    if (this.state.nav && this.state.nav.header_mode !== "hidden") {
-      const samples = clickedSampleNames.map((c) => this.sampleOrder.find((s) => s.row.sample == c).row);
-      for (const s of samples) {
-        if (!s.sampleId) s.sampleId = s.sample;
-      }
-      optionArr.push({
-        label: "Add to a group",
-        callback: async () => {
-          const group = {
-            name: "Group",
-            items: samples
-          };
-          this.addGroup(group);
-        }
-      });
-    }
-  }
-  this.mouseout();
-  this.dom.tip.hide();
-  this.dom.dendroClickMenu.d.selectAll("*").remove();
-  this.dom.dendroClickMenu.d.selectAll("div").data(optionArr).enter().append("div").attr("class", "sja_menuoption").style("border-radius", "0px").html((d) => d.label).attr("data-testid", (d) => `hierCluster_dendro_menu_${d.label.split(" ")[0]}`).on("click", (event2) => {
-    this.dom.dendroClickMenu.d.selectAll("*").remove();
-    event2.target.__data__.callback();
-  });
-  this.dom.dendroClickMenu.show(event.clientX, event.clientY);
-}
-function addSelectedRowsOptions(clickedRowNames, event) {
-  const rowType = this.config.settings.matrix.controlLabels.terms;
-  const optionArr = [
-    {
-      label: `List ${clickedRowNames.length} ${rowType}`,
-      callback: () => this.showTable4selectedRows(clickedRowNames, rowType)
-    }
-  ];
-  if (this.config.dataType == "geneExpression" && this.app.opts.genome.termdbs) {
-    const minGeneCutoff = this.app.opts.genome.termdbs.msigdb.geneORAparam.minCutoff;
-    const maxGeneCutoff = this.app.opts.genome.termdbs.msigdb.geneORAparam.maxCutoff;
-    optionArr.push({
-      label: `Gene set overrepresentation analysis`,
-      disabled: clickedRowNames.length < minGeneCutoff || clickedRowNames.length > maxGeneCutoff,
-      callback: () => {
-        if (clickedRowNames.length < minGeneCutoff || clickedRowNames.length > maxGeneCutoff) return;
-        this.dom.dendroClickMenu.d.selectAll("*").remove();
-        const lst = [];
-        for (const x of clickedRowNames) {
-          const j = this.terms?.find?.((t) => t.tw.$id == x);
-          if (j) {
-            const n = j.tw?.term?.gene;
-            if (n) lst.push(n);
-          }
-        }
-        const config = {
-          chartType: "geneORA",
-          geneORAparams: {
-            sample_genes: lst.join(","),
-            genome: this.app.vocabApi.opts.state.vocab.genome
-          }
-        };
-        this.app.dispatch({
-          type: "plot_create",
-          config
-        });
-      }
-    });
-  }
-  this.mouseout();
-  this.dom.tip.hide();
-  this.dom.dendroClickMenu.d.selectAll("*").remove();
-  this.dom.dendroClickMenu.d.selectAll("div").data(optionArr).enter().append("div").attr("class", (d) => d.disabled ? "sja_menuoption_not_interactive" : "sja_menuoption").style("opacity", (d) => d.disabled ? 0.5 : 1).style("border-radius", "0px").html(
-    (d) => d.disabled ? `${d.label} <span style="font-size: 0.6em; display: block; margin-left: 2px; margin-top: 2px;">Only available when 15 - 500 genes selected</span>` : d.label
-  ).attr("data-testid", (d) => `hierCluster_dendro_menu_${d.label.split(" ")[0]}`).on("click", (event2) => {
-    if (event2.target.__data__?.callback) event2.target.__data__.callback();
-  });
-  this.dom.dendroClickMenu.show(event.clientX, event.clientY);
-}
-function triggerZoomBranch(self, clickedSampleNames) {
-  if (self.zoomArea) {
-    self.zoomArea.remove();
-    delete self.zoomArea;
-  }
-  const c = {
-    startCell: self.serieses[0].cells.find((d2) => d2.sample == clickedSampleNames[0]),
-    endCell: self.serieses[0].cells.find((d2) => d2.sample == clickedSampleNames[clickedSampleNames.length - 1])
-  };
-  const s = self.settings.matrix;
-  const d = self.dimensions;
-  const start = c.startCell.totalIndex < c.endCell.totalIndex ? c.startCell : c.endCell;
-  const zoomIndex = Math.floor(start.totalIndex + Math.abs(c.endCell.totalIndex - c.startCell.totalIndex) / 2);
-  const centerCell = self.sampleOrder[zoomIndex];
-  const colw = self.computedSettings.colw || self.settings.matrix.colw;
-  const maxZoomLevel = s.colwMax / colw;
-  const minZoomLevel = s.colwMin / colw;
-  const tentativeZoomLevel = Math.max(
-    1,
-    s.zoomLevel * d.mainw / Math.max(c.endCell.x - c.startCell.x, 2 * d.colw) * 0.7
-  );
-  const zoomLevel = Math.max(minZoomLevel, Math.min(tentativeZoomLevel, maxZoomLevel));
-  self.app.dispatch({
-    type: "plot_edit",
-    id: self.id,
-    config: {
-      settings: {
-        matrix: {
-          zoomLevel,
-          zoomCenterPct: 0.5,
-          //zoomLevel < 1 && d.mainw >= d.zoomedMainW ? 0.5 : zoomCenter / d.mainw,
-          zoomIndex,
-          zoomGrpIndex: centerCell.grpIndex
-        }
-      }
-    }
-  });
-  self.resetInteractions();
-}
-function showTable4selectedSamples(clickedSampleNames) {
-  const templates = this.state.termdbConfig.urlTemplates;
-  const rows = templates?.sample ? clickedSampleNames.map((c) => [
-    { value: this.hierClusterData.bySampleId[c].label, url: `${templates.sample.base}${c}` }
-  ]) : clickedSampleNames.map((c) => [{ value: this.hierClusterData.bySampleId[c].label }]);
-  const columns = [{ label: this.settings.matrix.controlLabels.Sample }];
-  renderTable({
-    rows,
-    columns,
-    div: this.dom.dendroClickMenu.clear().d.append("div").style("margin", "10px"),
-    showLines: true,
-    maxHeight: "35vh",
-    resize: true
-  });
-}
-function showTable4selectedRows(clickedRowNames, rowType) {
-  const templates = this.state.termdbConfig.urlTemplates;
-  const rows = [];
-  if (templates?.gene && this.config.dataType == "geneExpression" && this.hierClusterData.byTermId) {
-    for (const i of clickedRowNames) {
-      const genesymbol = this.terms.find((t) => t.tw?.$id == i)?.tw?.term?.gene;
-      if (!genesymbol) continue;
-      const gencode = this.hierClusterData.byTermId[i]?.gencodeId;
-      if (gencode) {
-        rows.push([{ value: genesymbol, url: `${templates.gene.base}${gencode}` }]);
-      } else {
-        rows.push([{ value: genesymbol }]);
-      }
-    }
-  } else {
-    for (const i of clickedRowNames) {
-      const tw = this.terms.find((t) => t.tw?.$id == i)?.tw;
-      if (!tw) continue;
-      const n = tw.term?.gene || tw.term?.name;
-      if (!n) continue;
-      rows.push([{ value: n }]);
-    }
-  }
-  const div = this.dom.dendroClickMenu.clear().d.append("div").style("margin", "10px");
-  const buttonDiv = div.append("div").style("padding", "5px");
-  const copyButton = buttonDiv.append("button").html(`Copy ${rowType}`).attr("class", ".sja_menu_div button").style("margin-top", "2px").style("padding", "5px").on("click", () => {
-    const geneNames = rows.map((row) => row[0].value).join("\n");
-    navigator.clipboard.writeText(geneNames).then(() => {
-    }, console.warn);
-    copyButton.html(`Copy ${rowType}&nbsp;&check;`);
-  });
-  renderTable({
-    rows,
-    columns: [{ label: rowType }],
-    div: div.append("div"),
-    showLines: true,
-    maxHeight: "35vh",
-    resize: true
-  });
-}
-function getClusterFromTopDendrogram(event) {
-  if (event.target.tagName == "image") this.imgBox = event.target.getBoundingClientRect();
-  else return;
-  const y = event.clientY - this.imgBox.y - event.target.clientTop;
-  const xMin = this.dimensions.xMin;
-  const x = event.clientX - this.imgBox.x - event.target.clientLeft + xMin;
-  for (const [clusterId, cluster] of this.hierClusterData.clustering.col.mergedClusters) {
-    const { x1, y1, x2, y2, clusterY } = cluster.clusterPosition;
-    if (x1 <= x && x <= x2 && clusterY - 5 < y && y < clusterY + 5 || clusterY <= y && y <= y1 && x1 - 5 < x && x < x1 + 5 || clusterY <= y && y <= y2 && x2 - 5 < x && x < x2 + 5) {
-      return clusterId;
-    }
-  }
-}
-function getClusterFromLeftDendrogram(event) {
-  if (event.target.tagName == "image") this.imgBox = event.target.getBoundingClientRect();
-  else return;
-  const y = event.clientY - this.imgBox.y - event.target.clientTop;
-  const xMin = this.dimensions.xMin;
-  const x = event.clientX - this.imgBox.x - event.target.clientLeft + xMin;
-  for (const [clusterId, cluster] of this.hierClusterData.clustering.row.mergedClusters) {
-    const { x1, y1, x2, y2, clusterX } = cluster.clusterPosition;
-    if (y1 <= y && y <= y2 && clusterX - 5 < x && x < clusterX + 5 || clusterX <= x && x <= x1 && y1 - 5 < y && y < y1 + 5 || clusterX <= x && x <= x2 && y2 - 5 < y && y < y2 + 5) {
-      return clusterId;
-    }
-  }
-}
-function setClusteringBtn(holder, callback) {
-  const cl = this.config.settings.matrix.controlLabels;
-  const dataType = this.config.dataType;
-  const clusterRowLabel = cl.Terms;
-  const cluteringButtonLabel = `${termType2label(dataType)} Clustering`;
-  holder.append("button").datum({
-    label: cluteringButtonLabel,
-    getCount: () => this.hcTermGroup?.lst.length || 0,
-    showCount: "hide",
-    rows: [
-      {
-        label: `Cluster ${cl.Samples}`,
-        title: `Option to enable ${cl.samples} clustering, instead of enabling ${cl.samples} sorting.`,
-        type: "checkbox",
-        chartType: "hierCluster",
-        settingsKey: "clusterSamples",
-        boxLabel: `Cluster ${cl.Samples} (Disable ${cl.Samples} Sorting)`,
-        callback: (checked) => {
-          if (!checked) {
-            this.config.settings.hierCluster.yDendrogramHeight = 0;
-            this.config.settings.hierCluster.clusterSamples = false;
-          } else {
-            this.config.divideBy = null;
-            this.config.settings.hierCluster.yDendrogramHeight = 200;
-            this.config.settings.hierCluster.clusterSamples = true;
-          }
-          this.app.dispatch({
-            type: "plot_edit",
-            id: this.id,
-            config: this.config
-          });
-        }
-      },
-      {
-        label: `Cluster ${clusterRowLabel}`,
-        title: `Option to enable ${clusterRowLabel} clustering, instead of enabling ${clusterRowLabel} sorting.`,
-        type: "checkbox",
-        chartType: "hierCluster",
-        settingsKey: "clusterRows",
-        boxLabel: `Cluster ${clusterRowLabel} (Disable ${clusterRowLabel} Sorting)`,
-        callback: (checked) => {
-          if (!checked) {
-            this.config.settings.hierCluster.clusterRows = false;
-            this.config.settings.hierCluster.sortClusterRows = "asListed";
-          } else {
-            this.config.settings.hierCluster.clusterRows = true;
-            this.config.settings.hierCluster.sortClusterRows = void 0;
-          }
-          this.app.dispatch({
-            type: "plot_edit",
-            id: this.id,
-            config: this.config
-          });
-        }
-      },
-      {
-        label: `Sort ${clusterRowLabel}`,
-        title: `Set how to order the ${clusterRowLabel} as rows`,
-        type: "radio",
-        chartType: "hierCluster",
-        settingsKey: "sortClusterRows",
-        options: [
-          { label: `By input ${clusterRowLabel} order`, value: "asListed" },
-          { label: `By ${clusterRowLabel} name`, value: "byName" }
-        ],
-        styles: { padding: 0, "padding-right": "10px", margin: 0, display: "inline-block" },
-        getDisplayStyle(plot) {
-          return plot.settings.hierCluster.clusterRows ? "none" : "table-row";
-        }
-      },
-      {
-        label: "Z-score Transformation",
-        title: `Option to do Z-score transformation`,
-        type: "checkbox",
-        chartType: "hierCluster",
-        settingsKey: "zScoreTransformation",
-        boxLabel: `Perform Z-score Transformation`,
-        callback: (checked) => {
-          if (!checked) {
-            this.config.settings.hierCluster.zScoreTransformation = false;
-            this.config.settings.hierCluster.colorScale = "whiteRed";
-          } else {
-            this.config.settings.hierCluster.zScoreTransformation = true;
-            this.config.settings.hierCluster.colorScale = "blueWhiteRed";
-          }
-          this.app.dispatch({
-            type: "plot_edit",
-            id: this.id,
-            config: this.config
-          });
-        }
-      },
-      {
-        label: `Clustering Method`,
-        title: `Sets which clustering method to use`,
-        type: "radio",
-        chartType: "hierCluster",
-        settingsKey: "clusterMethod",
-        options: clusterMethodLst
-      },
-      {
-        label: `Distance Method`,
-        title: `Sets which distance method to use for clustering`,
-        type: "radio",
-        chartType: "hierCluster",
-        settingsKey: "distanceMethod",
-        options: distanceMethodLst
-      },
-      {
-        label: `Column Dendrogram Height`,
-        title: `The maximum height to render the column dendrogram`,
-        type: "number",
-        chartType: "hierCluster",
-        settingsKey: "yDendrogramHeight",
-        getDisplayStyle(plot) {
-          return plot.settings.hierCluster.clusterSamples ? "table-row" : "none";
-        }
-      },
-      {
-        label: `Row Dendrogram Width`,
-        title: `The maximum width to render the row dendrogram`,
-        type: "number",
-        chartType: "hierCluster",
-        settingsKey: "xDendrogramHeight",
-        getDisplayStyle(plot) {
-          return plot.settings.hierCluster.clusterRows ? "table-row" : "none";
-        }
-      },
-      {
-        label: `Z-score Cap`,
-        title: `Cap the Z-score scale to not exceed this absolute value`,
-        type: "number",
-        chartType: "hierCluster",
-        settingsKey: "zScoreCap"
-      },
-      {
-        label: `Color Scheme`,
-        title: `Sets which color scheme to use`,
-        type: "radio",
-        chartType: "hierCluster",
-        settingsKey: "colorScale",
-        options: [
-          {
-            label: "Blue-White-Red",
-            value: "blueWhiteRed",
-            title: `color scheme Blue-White-Red`
-          },
-          {
-            label: "Green-Black-Red",
-            value: "greenBlackRed",
-            title: `color scheme Green-Black-Red`
-          },
-          {
-            label: "Blue-Yellow-Red",
-            value: "blueYellowRed",
-            title: `color scheme Blue-Yellow-Red`
-          },
-          {
-            label: "Green-White-Red",
-            value: "greenWhiteRed",
-            title: `color scheme Green-White-Red`
-          },
-          {
-            label: "Blue-Black-Yellow",
-            value: "blueBlackYellow",
-            title: `color scheme Blue-Black-Yellow`
-          }
-        ]
-      }
-    ],
-    customInputs: updateClusteringControls
-  }).html((d) => d.label).style("margin", "2px 0").on("click", callback);
-}
-function updateClusteringControls(self, app, parent, table) {
-  if (parent.chartType == "hierCluster" && !parent.config.settings.hierCluster.zScoreTransformation) {
-    const zScoreCapControl = select_default(
-      table.selectAll("td").filter(function() {
-        return select_default(this).text() == "Z-score Cap";
-      }).node().closest("tr")
-    );
-    zScoreCapControl.style("display", "none");
-    const colorSchemeControl = select_default(
-      table.selectAll("td").filter(function() {
-        return select_default(this).text() == "Color Scheme";
-      }).node().closest("tr")
-    );
-    colorSchemeControl.style("display", "none");
-  }
-  if (parent.chartType == "hierCluster" && parent.config.dataType !== "geneExpression") {
-    const geneInputTr = table.insert("tr", () => table.select("tr").node());
-    geneInputTr.append("td").attr("class", "sja-termdb-config-row-label").html("Hierarchical Clustering Term Set");
-    const td1 = geneInputTr.append("td").style("display", "block").style("padding", "5px 0px");
-    const editGrpDiv = td1.append("div").append("label");
-    const clusteringBtn = self.btns.node();
-    editGrpDiv.append("button").html("Edit Set").on("click", () => {
-      app.tip.clear();
-      const backDiv = app.tip.d.append("div").style("padding", "5px");
-      backDiv.attr("tabindex", 0).style("padding", "5px").style("text-decoration", "underline").style("cursor", "pointer").style("margin-bottom", "12px").html(`&#171; Back`).on("click", () => clusteringBtn.click()).on("keyup", (event) => {
-        if (event.key == "Enter") event.target.click();
-      });
-      const setEdiUiHolder = app.tip.d.append("div");
-      parent.showDictTermSelection(setEdiUiHolder);
-    });
-  }
-}
-
-export {
-  getAllChildrenClusterIds,
-  addSelectedSamplesOptions,
-  addSelectedRowsOptions,
-  triggerZoomBranch,
-  showTable4selectedSamples,
-  showTable4selectedRows,
-  getClusterFromTopDendrogram,
-  getClusterFromLeftDendrogram,
-  setClusteringBtn,
-  hierCluster_interactivity_exports
-};
-//# sourceMappingURL=chunk-PJ3FCJBZ.js.map