@sjcrh/proteinpaint-client 2.181.0 → 2.183.0

package/dist/chunk-EY2KBPHJ.js

@@ -0,0 +1,261 @@
+import {
+  hierCluster_renderers_exports
+} from "./chunk-W345H42C.js";
+import {
+  hierCluster_interactivity_exports
+} from "./chunk-AFLFPYJI.js";
+import {
+  Matrix
+} from "./chunk-APOHXHKH.js";
+import {
+  filterJoin,
+  getNormalRoot
+} from "./chunk-OXJ2TWDO.js";
+import {
+  clusterMethodLst,
+  distanceMethodLst,
+  dofetch3
+} from "./chunk-7RN3L2BX.js";
+import {
+  deepEqual,
+  getCompInit
+} from "./chunk-MVTCBVSX.js";
+import {
+  TermTypes2Dt
+} from "./chunk-6ITDJ5UR.js";
+import {
+  colorScaleMap
+} from "./chunk-XYFDBYOY.js";
+import {
+  extent,
+  linear
+} from "./chunk-OAWQ6LOO.js";
+
+// plots/matrix/hierCluster.js
+var HierCluster = class _HierCluster extends Matrix {
+  static type = "hierCluster";
+  constructor(opts) {
+    super(opts);
+    this.type = _HierCluster.type;
+    this.chartType = _HierCluster.type;
+  }
+  async init(appState) {
+    await super.init(appState);
+    this.maySetSandboxHeader(appState);
+    this.hcClipId = this.seriesClipId + "-hc";
+    this.dom.hcClipRect = this.dom.svg.select("defs").append("clipPath").attr("id", this.hcClipId).attr("clipPathUnits", "userSpaceOnUse").append("rect").attr("display", "block");
+    this.dom.topDendrogram = this.dom.svg.insert("g", "g").attr("clip-path", `url(#${this.hcClipId})`).append("g").attr("class", "sjpp-matrix-dendrogram").attr("data-testid", "hierCluster_top_dendrogram").on("click", (event) => {
+      const clickedClusterId = this.getClusterFromTopDendrogram(event);
+      if (clickedClusterId) {
+        this.clickedClusterIds = this.getAllChildrenClusterIds(clickedClusterId);
+        this.clickedClusterIds.push(clickedClusterId);
+        const clickedCluster = this.hierClusterData.clustering.col.mergedClusters.get(clickedClusterId);
+        const clickedClusterSampleNames = clickedCluster.children.map((c) => c.name);
+        this.addSelectedSamplesOptions(clickedClusterSampleNames, event);
+      } else {
+        delete this.clickedClusterIds;
+      }
+      if (this.clickedLeftClusterIds) {
+        delete this.clickedLeftClusterIds;
+        this.plotDendrogramHclust();
+      } else this.plotDendrogramHclust("top");
+    });
+    this.dom.leftDendrogram = this.dom.svg.insert("g", "g").attr("class", "sjpp-matrix-dendrogram").attr("data-testid", "hierCluster_left_dendrogram").on("click", (event) => {
+      const clickedLeftClusterId = this.getClusterFromLeftDendrogram(event);
+      if (clickedLeftClusterId) {
+        this.clickedLeftClusterIds = this.getAllChildrenClusterIds(clickedLeftClusterId, true);
+        this.clickedLeftClusterIds.push(clickedLeftClusterId);
+        const clickedLeftCluster = this.hierClusterData.clustering.row.mergedClusters.get(clickedLeftClusterId);
+        const clickedLeftClusterRowsNames = clickedLeftCluster.children.map((c) => c.name);
+        this.addSelectedRowsOptions(clickedLeftClusterRowsNames, event);
+      } else {
+        delete this.clickedLeftClusterIds;
+      }
+      if (this.clickedClusterIds) {
+        delete this.clickedClusterIds;
+        this.plotDendrogramHclust();
+      } else this.plotDendrogramHclust("left");
+    });
+  }
+  async setHierClusterData(_data = {}) {
+    this.prevServerData = this.currServerData;
+    const [d, twlst] = await this.requestData({});
+    if (d.error) throw d.error;
+    this.currServerData = structuredClone(d);
+    if (!deepEqual(this.prevServerData, this.currServerData)) {
+      delete this.clickedClusterIds;
+      delete this.clickedLeftClusterIds;
+    }
+    const s = this.settings.hierCluster;
+    if (!d.clustering) {
+      if (d.gene) {
+        throw `Cannot do clustering: data is only available for 1 gene (${d.gene}). Try again by adding more genes.`;
+      }
+    }
+    this.hierClusterData = d;
+    const c = this.hierClusterData.clustering;
+    this.setHierColorScale(c);
+    const samples = {};
+    for (const [i, column] of c.col.order.entries()) {
+      samples[column.name] = { sample: column.name };
+      for (const [j, row] of c.row.order.entries()) {
+        const tw = twlst.find((tw2) => tw2.$id === row.name || tw2.id === row.name);
+        const value = c.matrix[j][i];
+        samples[column.name][tw.$id] = {
+          key: tw.term.name,
+          values: [
+            {
+              sample: column.name,
+              dt: TermTypes2Dt[this.state.config.dataType],
+              label: s.termGroupName,
+              // gene: tw.term.name,
+              // chr: tw.term.chr,
+              // pos: `${tw.term.start}-${tw.term.stop}`,
+              value
+              // the color will be computed in matrix.cells, so that
+              // it can get updated even when there are no nonsetting state diff
+            }
+          ]
+        };
+      }
+    }
+    this.hcTermNameOrder = this.settings.hierCluster.sortClusterRows == "asListed" ? twlst.map((t) => t.term.name) : this.settings.hierCluster.sortClusterRows == "byName" ? twlst.map((t) => t.term.name).sort() : c.row.order.map((row) => twlst.find((t) => t.$id == row.name)?.term.name);
+    if (this.hcTermNameOrder.includes(void 0)) throw `unable to map row.name to term.name`;
+    this.hcTermSorter = (a, b) => {
+      const i = this.hcTermNameOrder.indexOf(a.tw.term.name);
+      const j = this.hcTermNameOrder.indexOf(b.tw.term.name);
+      if (i == -1 && j == -1) return 0;
+      if (i == -1) return 1;
+      if (j == -1) return -1;
+      return i - j;
+    };
+    this.hcSampleNameOrder = c.col.order.map((col) => col.name);
+    this.hcSampleSorter = (a, b) => {
+      const i = this.hcSampleNameOrder.indexOf(a.sample);
+      const j = this.hcSampleNameOrder.indexOf(b.sample);
+      if (i == -1 && j == -1) return 0;
+      if (i == -1) return 1;
+      if (j == -1) return -1;
+      return i - j;
+    };
+    const byTermId = {};
+    for (const tw of twlst) {
+      if (d.byTermId?.[tw.term.name]) byTermId[tw.$id] = d.byTermId[tw.term.name];
+    }
+    this.hierClusterSamples = {
+      refs: { byTermId, bySampleId: d.bySampleId },
+      lst: c.col.order.map((c2) => samples[c2.name]),
+      samples,
+      removedHierClusterTerms: d.removedHierClusterTerms
+    };
+  }
+  async requestData() {
+    const body = this.currRequestOpts?.hierCluster || this.getHCRequestBody(this.state);
+    const twlst = this.hcTermGroup.lst;
+    const data = await dofetch3("termdb/cluster", { body, signal: this.api.getAbortSignal?.() });
+    return [data, twlst];
+  }
+  getHCRequestBody(state) {
+    this.hcTermGroup = this.config.termgroups.find((grp) => grp.type == "hierCluster") || this.termOrder?.find((t) => t.grp.type == "hierCluster")?.grp;
+    const s = state.config.settings.hierCluster;
+    const dictionaryLegendFilter = {
+      type: "tvslst",
+      in: true,
+      join: "and",
+      lst: state.config.legendValueFilter.lst.filter((f) => !f.tvs.legendFilterType)
+    };
+    const terms = this.getClusterRowTermsAsParameter();
+    if (!terms.length) throw "no data";
+    if (!clusterMethodLst.find((i) => i.value == s.clusterMethod)) throw "Invalid cluster method";
+    if (!distanceMethodLst.find((i) => i.value == s.distanceMethod)) throw "Invalid distance method";
+    const body = {
+      genome: state.vocab.genome,
+      dslabel: state.vocab.dslabel,
+      dataType: state.config.dataType,
+      clusterMethod: s.clusterMethod,
+      distanceMethod: s.distanceMethod,
+      zScoreTransformation: s.zScoreTransformation,
+      terms,
+      filter: getNormalRoot(filterJoin([state.filter, dictionaryLegendFilter])),
+      filter0: state.filter0
+    };
+    if (state.config.dataType == "proteomeAbundance") {
+      body.proteomeDetails = {
+        assay: state.config.proteomeDetails?.assay,
+        cohort: state.config.proteomeDetails?.cohort
+      };
+    }
+    return body;
+  }
+  combineData() {
+    if (!this.hierClusterSamples) return;
+    const d = this.data;
+    const removedHierClusterTerms = this.hierClusterSamples.removedHierClusterTerms;
+    const samples = {};
+    const lst = [];
+    for (const sampleId in this.hierClusterSamples.samples) {
+      const s = this.hierClusterSamples.samples[sampleId];
+      samples[sampleId] = s;
+      lst.push(s);
+      if (sampleId in d.samples) Object.assign(s, d.samples[sampleId]);
+      const _ref_ = this.hierClusterSamples.refs.bySampleId[sampleId] || {};
+      if (!s._ref_) s._ref_ = _ref_;
+      else Object.assign(s._ref_, _ref_);
+    }
+    const t = this.hierClusterSamples.refs.byTermId;
+    for (const $id of Object.keys(t)) {
+      d.refs.byTermId[$id] = Object.assign({}, d.refs.byTermId[$id] || {}, t[$id]);
+    }
+    this.data = { samples, lst, refs: d.refs, removedHierClusterTerms };
+  }
+  setHierColorScale(c) {
+    const hc = this.settings.hierCluster;
+    const scale = linear(colorScaleMap[hc.colorScale].domain, colorScaleMap[hc.colorScale].range).clamp(true);
+    const globalMinMaxes = [];
+    for (const row of c.matrix) {
+      globalMinMaxes.push(...extent(row));
+    }
+    const absMax = Math.min(hc.zScoreCap, Math.max(...extent(globalMinMaxes).map(Math.abs)));
+    const [min, max] = hc.zScoreTransformation ? [-absMax, absMax] : [Math.min(...globalMinMaxes), Math.max(...globalMinMaxes)];
+    this.hierClusterValues = { scale, min, max };
+  }
+  getValueColor(value) {
+    const hc = this.settings.hierCluster;
+    if (hc.zScoreTransformation) {
+      const zScoreCap = this.settings.hierCluster.zScoreCap;
+      return this.hierClusterValues.scale((value - -zScoreCap) / (zScoreCap * 2));
+    } else {
+      return this.hierClusterValues.scale(value / this.hierClusterValues.max);
+    }
+  }
+  /* returns list of gene terms as request parameter, e.g. {gene,chr,start,stop}
+  	request parameter only need term but not tw, as it will simply fetch continuous sample values on terms without transform
+  
+  	use of this function is unfortunate because:
+  		the incomplete migration of {name} to {gene} for gene-based term
+  		geneset edit ui is hardcoded to return {name}
+  		existing plot states contain {name}
+  
+  	!!! migration instruction !!!
+  	- term.name is for display only, if a term is gene-based, it has term.gene=str
+  	- a geneVariant term can be based on a genomic range (and not a gene), in that case it won't have term.gene and cannot be used where gene is expected, e.g. gene-based clustering analysis
+  
+  	*/
+  getClusterRowTermsAsParameter() {
+    const lst = this.hcTermGroup.lst.map(this.opts.app.vocabApi.getTwMinCopy);
+    lst.sort((a, b) => a.term.name < b.term.name ? -1 : 1);
+    return lst;
+  }
+};
+for (const methods of [hierCluster_renderers_exports, hierCluster_interactivity_exports]) {
+  for (const methodName in methods) HierCluster.prototype[methodName] = methods[methodName];
+}
+var hierClusterInit = getCompInit(HierCluster);
+var componentInit = hierClusterInit;
+
+export {
+  HierCluster,
+  hierClusterInit,
+  componentInit
+};
+//# sourceMappingURL=chunk-EY2KBPHJ.js.map

package/dist/chunk-EY2KBPHJ.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/matrix/hierCluster.js"],
+  "sourcesContent": ["import { Matrix } from './matrix'\nimport { getCompInit, deepEqual } from '#rx'\nimport * as renderers from './hierCluster.renderers'\nimport * as interactivity from './hierCluster.interactivity'\nimport { dofetch3 } from '#common/dofetch'\nimport { extent } from 'd3-array'\nimport { scaleLinear } from 'd3-scale'\nimport { filterJoin, getNormalRoot } from '#filter'\nimport { clusterMethodLst, distanceMethodLst } from '#shared/clustering.js'\nimport { TermTypes2Dt } from '#shared/terms.js'\nimport { colorScaleMap } from '#shared/common.js'\n\nexport class HierCluster extends Matrix {\n\tstatic type = 'hierCluster'\n\n\tconstructor(opts) {\n\t\tsuper(opts)\n\t\tthis.type = HierCluster.type\n\t\tthis.chartType = HierCluster.type\n\t}\n\n\tasync init(appState) {\n\t\tawait super.init(appState)\n\n\t\tthis.maySetSandboxHeader(appState)\n\n\t\tthis.hcClipId = this.seriesClipId + '-hc'\n\t\tthis.dom.hcClipRect = this.dom.svg\n\t\t\t.select('defs')\n\t\t\t.append('clipPath')\n\t\t\t.attr('id', this.hcClipId)\n\t\t\t//.attr('clipPathUnits', 'objectBoundingBox')\n\t\t\t.attr('clipPathUnits', 'userSpaceOnUse')\n\t\t\t.append('rect')\n\t\t\t.attr('display', 'block')\n\n\t\tthis.dom.topDendrogram = this.dom.svg\n\t\t\t.insert('g', 'g')\n\t\t\t.attr('clip-path', `url(#${this.hcClipId})`)\n\t\t\t.append('g')\n\t\t\t.attr('class', 'sjpp-matrix-dendrogram')\n\t\t\t.attr('data-testid', 'hierCluster_top_dendrogram')\n\t\t\t.on('click', event => {\n\t\t\t\tconst clickedClusterId = this.getClusterFromTopDendrogram(event)\n\t\t\t\tif (clickedClusterId) {\n\t\t\t\t\tthis.clickedClusterIds = this.getAllChildrenClusterIds(clickedClusterId)\n\t\t\t\t\tthis.clickedClusterIds.push(clickedClusterId)\n\n\t\t\t\t\tconst clickedCluster = this.hierClusterData.clustering.col.mergedClusters.get(clickedClusterId)\n\t\t\t\t\tconst clickedClusterSampleNames = clickedCluster.children.map(c => c.name)\n\t\t\t\t\tthis.addSelectedSamplesOptions(clickedClusterSampleNames, event)\n\t\t\t\t} else {\n\t\t\t\t\t// if not clicking on a cluster, change highlighted cluster color from red back to black\n\t\t\t\t\tdelete this.clickedClusterIds\n\t\t\t\t}\n\n\t\t\t\t// rerender the row Dendrogram\n\t\t\t\tif (this.clickedLeftClusterIds) {\n\t\t\t\t\t// when left dendrogram has highlight, clicking top dendro should cancel it\n\t\t\t\t\tdelete this.clickedLeftClusterIds\n\t\t\t\t\tthis.plotDendrogramHclust()\n\t\t\t\t} else this.plotDendrogramHclust('top')\n\t\t\t})\n\n\t\tthis.dom.leftDendrogram = this.dom.svg\n\t\t\t.insert('g', 'g')\n\t\t\t.attr('class', 'sjpp-matrix-dendrogram')\n\t\t\t.attr('data-testid', 'hierCluster_left_dendrogram')\n\t\t\t.on('click', event => {\n\t\t\t\tconst clickedLeftClusterId = this.getClusterFromLeftDendrogram(event)\n\t\t\t\tif (clickedLeftClusterId) {\n\t\t\t\t\tthis.clickedLeftClusterIds = this.getAllChildrenClusterIds(clickedLeftClusterId, true)\n\t\t\t\t\tthis.clickedLeftClusterIds.push(clickedLeftClusterId)\n\n\t\t\t\t\tconst clickedLeftCluster = this.hierClusterData.clustering.row.mergedClusters.get(clickedLeftClusterId)\n\n\t\t\t\t\tconst clickedLeftClusterRowsNames = clickedLeftCluster.children.map(c => c.name)\n\n\t\t\t\t\tthis.addSelectedRowsOptions(clickedLeftClusterRowsNames, event)\n\t\t\t\t} else {\n\t\t\t\t\t// if not clicking on a cluster, change highlighted cluster color from red back to black\n\t\t\t\t\tdelete this.clickedLeftClusterIds\n\t\t\t\t}\n\n\t\t\t\t// rerender the row Dendrogram\n\t\t\t\tif (this.clickedClusterIds) {\n\t\t\t\t\t// when top dendrogram has highlight, clicking left dendro should cancel it\n\t\t\t\t\tdelete this.clickedClusterIds\n\t\t\t\t\tthis.plotDendrogramHclust()\n\t\t\t\t} else this.plotDendrogramHclust('left')\n\t\t\t})\n\t\t//.attr('clip-path', `url(#${this.seriesClipId})`)\n\t}\n\n\tasync setHierClusterData(_data = {}) {\n\t\tthis.prevServerData = this.currServerData\n\t\tconst [d, twlst] = await this.requestData({})\n\t\tif (d.error) throw d.error\n\t\tthis.currServerData = structuredClone(d)\n\t\tif (!deepEqual(this.prevServerData, this.currServerData)) {\n\t\t\t// do not persist highlighted top/left dendrogram branch selection\n\t\t\t// when the cohort, clustering method, or other config changes the server data\n\t\t\tdelete this.clickedClusterIds\n\t\t\tdelete this.clickedLeftClusterIds\n\t\t}\n\t\tconst s = this.settings.hierCluster\n\n\t\tif (!d.clustering) {\n\t\t\t// stop-gap data validation, lacks essential data part\n\t\t\tif (d.gene) {\n\t\t\t\t// for now backend returns {gene:str, data:{}} if there's only 1 eligible gene\n\t\t\t\tthrow `Cannot do clustering: data is only available for 1 gene (${d.gene}). Try again by adding more genes.`\n\t\t\t}\n\t\t\t//throw 'Cannot do clustering: invalid server response (lacks .clustering{})'\n\t\t}\n\t\tthis.hierClusterData = d\n\n\t\tconst c = this.hierClusterData.clustering\n\t\tthis.setHierColorScale(c)\n\n\t\tconst samples = {}\n\n\t\t/* see comments inside plotDendrogramHclust() on structure of d.clustering.row{} and col{}\n\t\tassumes c.col is samples and c.row is non-sample things (genes for now); later may flip to c.row be samples instead!!\n\t\t*/\n\t\tfor (const [i, column] of c.col.order.entries()) {\n\t\t\tsamples[column.name] = { sample: column.name }\n\t\t\tfor (const [j, row] of c.row.order.entries()) {\n\t\t\t\tconst tw = twlst.find(tw => tw.$id === row.name || tw.id === row.name)\n\t\t\t\t// if (!tw) {\n\t\t\t\t// \tconsole.warn(`no matching tw for row.name='${row.name}'`)\n\t\t\t\t// \tcontinue\n\t\t\t\t// }\n\t\t\t\tconst value = c.matrix[j][i]\n\t\t\t\tsamples[column.name][tw.$id] = {\n\t\t\t\t\tkey: tw.term.name,\n\t\t\t\t\tvalues: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tsample: column.name,\n\t\t\t\t\t\t\tdt: TermTypes2Dt[this.state.config.dataType],\n\t\t\t\t\t\t\tlabel: s.termGroupName,\n\t\t\t\t\t\t\t// gene: tw.term.name,\n\t\t\t\t\t\t\t// chr: tw.term.chr,\n\t\t\t\t\t\t\t// pos: `${tw.term.start}-${tw.term.stop}`,\n\t\t\t\t\t\t\tvalue\n\t\t\t\t\t\t\t// the color will be computed in matrix.cells, so that\n\t\t\t\t\t\t\t// it can get updated even when there are no nonsetting state diff\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}\n\n\t\tthis.hcTermNameOrder =\n\t\t\tthis.settings.hierCluster.sortClusterRows == 'asListed'\n\t\t\t\t? twlst.map(t => t.term.name)\n\t\t\t\t: this.settings.hierCluster.sortClusterRows == 'byName'\n\t\t\t\t? twlst.map(t => t.term.name).sort()\n\t\t\t\t: c.row.order.map(row => twlst.find(t => t.$id == row.name)?.term.name)\n\n\t\tif (this.hcTermNameOrder.includes(undefined)) throw `unable to map row.name to term.name`\n\n\t\tthis.hcTermSorter = (a, b) => {\n\t\t\tconst i = this.hcTermNameOrder.indexOf(a.tw.term.name)\n\t\t\tconst j = this.hcTermNameOrder.indexOf(b.tw.term.name)\n\t\t\tif (i == -1 && j == -1) return 0\n\t\t\tif (i == -1) return 1\n\t\t\tif (j == -1) return -1\n\t\t\treturn i - j\n\t\t}\n\n\t\tthis.hcSampleNameOrder = c.col.order.map(col => col.name)\n\t\tthis.hcSampleSorter = (a, b) => {\n\t\t\tconst i = this.hcSampleNameOrder.indexOf(a.sample)\n\t\t\tconst j = this.hcSampleNameOrder.indexOf(b.sample)\n\t\t\tif (i == -1 && j == -1) return 0\n\t\t\tif (i == -1) return 1\n\t\t\tif (j == -1) return -1\n\t\t\treturn i - j\n\t\t}\n\n\t\t// from d.byTermId to byTermId: change byTermId keys from gene names to $ids\n\t\tconst byTermId = {}\n\t\tfor (const tw of twlst) {\n\t\t\tif (d.byTermId?.[tw.term.name]) byTermId[tw.$id] = d.byTermId[tw.term.name]\n\t\t}\n\t\tthis.hierClusterSamples = {\n\t\t\trefs: { byTermId, bySampleId: d.bySampleId },\n\t\t\tlst: c.col.order.map(c => samples[c.name]),\n\t\t\tsamples,\n\t\t\tremovedHierClusterTerms: d.removedHierClusterTerms\n\t\t}\n\t}\n\n\tasync requestData() {\n\t\t// may revert to using {signal} argument if detectStale() is used to wrap this function\n\t\tconst body = this.currRequestOpts?.hierCluster || this.getHCRequestBody(this.state)\n\t\tconst twlst = this.hcTermGroup.lst\n\t\tconst data = await dofetch3('termdb/cluster', { body, signal: this.api.getAbortSignal?.() })\n\t\t// return the twlst that was submitted in the data request, this data-to-twlst reference will not be affected by race condition\n\t\treturn [data, twlst]\n\t}\n\n\tgetHCRequestBody(state) {\n\t\tthis.hcTermGroup =\n\t\t\tthis.config.termgroups.find(grp => grp.type == 'hierCluster') ||\n\t\t\tthis.termOrder?.find(t => t.grp.type == 'hierCluster')?.grp\n\n\t\tconst s = state.config.settings.hierCluster\n\t\t// temporary fix to get rid of hard/soft filter and only keep dictionary legend filter,\n\t\t// soft filter shouldn't be used to filter out any samples for hierCluster\n\t\t// TODO: add hard filter back to filter out samples\n\t\tconst dictionaryLegendFilter = {\n\t\t\ttype: 'tvslst',\n\t\t\tin: true,\n\t\t\tjoin: 'and',\n\t\t\tlst: state.config.legendValueFilter.lst.filter(f => !f.tvs.legendFilterType)\n\t\t}\n\t\tconst terms = this.getClusterRowTermsAsParameter()\n\t\tif (!terms.length) throw 'no data'\n\t\t// !!! NOTE !!!\n\t\t// all parameters here must remove payload properties that are\n\t\t// not relevant to the data request, so that the dofetch and/or\n\t\t// browser caching would work\n\n\t\t// Checking if cluster and distance method for hierarchial clustering is valid\n\t\tif (!clusterMethodLst.find(i => i.value == s.clusterMethod)) throw 'Invalid cluster method'\n\t\tif (!distanceMethodLst.find(i => i.value == s.distanceMethod)) throw 'Invalid distance method'\n\t\tconst body = {\n\t\t\tgenome: state.vocab.genome,\n\t\t\tdslabel: state.vocab.dslabel,\n\t\t\tdataType: state.config.dataType,\n\t\t\tclusterMethod: s.clusterMethod,\n\t\t\tdistanceMethod: s.distanceMethod,\n\t\t\tzScoreTransformation: s.zScoreTransformation,\n\t\t\tterms,\n\t\t\tfilter: getNormalRoot(filterJoin([state.filter, dictionaryLegendFilter])),\n\t\t\tfilter0: state.filter0\n\t\t}\n\t\tif (state.config.dataType == 'proteomeAbundance') {\n\t\t\tbody.proteomeDetails = {\n\t\t\t\tassay: state.config.proteomeDetails?.assay,\n\t\t\t\tcohort: state.config.proteomeDetails?.cohort\n\t\t\t}\n\t\t}\n\t\treturn body\n\t}\n\n\tcombineData() {\n\t\tif (!this.hierClusterSamples) return\n\t\tconst d = this.data // matrix data\n\t\tconst removedHierClusterTerms = this.hierClusterSamples.removedHierClusterTerms\n\t\tconst samples = {}\n\t\tconst lst = []\n\t\t// the gene expression samples will be used as a filter for the matrix samples\n\t\tfor (const sampleId in this.hierClusterSamples.samples) {\n\t\t\tconst s = this.hierClusterSamples.samples[sampleId]\n\t\t\tsamples[sampleId] = s\n\t\t\tlst.push(s)\n\t\t\tif (sampleId in d.samples) Object.assign(s, d.samples[sampleId])\n\t\t\tconst _ref_ = this.hierClusterSamples.refs.bySampleId[sampleId] || {}\n\t\t\tif (!s._ref_) s._ref_ = _ref_\n\t\t\t// hierCluster refs.bySampleId will overwrite matrix reference properties with the same name\n\t\t\telse Object.assign(s._ref_, _ref_)\n\t\t}\n\n\t\t// combine this.hierClusterSamples.refs.byTermId into this.data.refs.byTermId\n\t\tconst t = this.hierClusterSamples.refs.byTermId\n\t\tfor (const $id of Object.keys(t)) {\n\t\t\td.refs.byTermId[$id] = Object.assign({}, d.refs.byTermId[$id] || {}, t[$id])\n\t\t}\n\t\tthis.data = { samples, lst, refs: d.refs, removedHierClusterTerms }\n\t}\n\n\tsetHierColorScale(c) {\n\t\tconst hc = this.settings.hierCluster\n\t\tconst scale = scaleLinear(colorScaleMap[hc.colorScale].domain, colorScaleMap[hc.colorScale].range).clamp(true)\n\t\tconst globalMinMaxes = []\n\t\tfor (const row of c.matrix) {\n\t\t\tglobalMinMaxes.push(...extent(row))\n\t\t}\n\t\tconst absMax = Math.min(hc.zScoreCap, Math.max(...extent(globalMinMaxes).map(Math.abs)))\n\t\t// if zScore transformation is not performed, should use min/max value from data\n\t\tconst [min, max] = hc.zScoreTransformation\n\t\t\t? [-absMax, absMax]\n\t\t\t: [Math.min(...globalMinMaxes), Math.max(...globalMinMaxes)]\n\t\t// what's purpose of assigning this.hierClusterValues{}, to signal something to matrix code?\n\t\tthis.hierClusterValues = { scale, min, max }\n\t}\n\n\tgetValueColor(value) {\n\t\tconst hc = this.settings.hierCluster\n\t\tif (hc.zScoreTransformation) {\n\t\t\tconst zScoreCap = this.settings.hierCluster.zScoreCap\n\t\t\treturn this.hierClusterValues.scale((value - -zScoreCap) / (zScoreCap * 2))\n\t\t} else {\n\t\t\treturn this.hierClusterValues.scale(value / this.hierClusterValues.max)\n\t\t}\n\t}\n\n\t/* returns list of gene terms as request parameter, e.g. {gene,chr,start,stop}\n\trequest parameter only need term but not tw, as it will simply fetch continuous sample values on terms without transform\n\n\tuse of this function is unfortunate because:\n\t\tthe incomplete migration of {name} to {gene} for gene-based term\n\t\tgeneset edit ui is hardcoded to return {name}\n\t\texisting plot states contain {name}\n\n\t!!! migration instruction !!!\n\t- term.name is for display only, if a term is gene-based, it has term.gene=str\n\t- a geneVariant term can be based on a genomic range (and not a gene), in that case it won't have term.gene and cannot be used where gene is expected, e.g. gene-based clustering analysis\n\n\t*/\n\tgetClusterRowTermsAsParameter() {\n\t\tconst lst = this.hcTermGroup.lst.map(this.opts.app.vocabApi.getTwMinCopy)\n\t\t// this helps caching by having a more consistent URL string\n\t\tlst.sort((a, b) => (a.term.name < b.term.name ? -1 : 1))\n\t\treturn lst\n\t}\n}\n\nfor (const methods of [renderers, interactivity]) {\n\tfor (const methodName in methods) HierCluster.prototype[methodName] = methods[methodName]\n}\n\nexport const hierClusterInit = getCompInit(HierCluster)\nexport const componentInit = hierClusterInit\n"],
+  "mappings": 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+  "names": ["tw", "c"]
+}

package/dist/chunk-FRBYOOWT.js

@@ -0,0 +1,229 @@
+import {
+  keyupEnter
+} from "./chunk-OXJ2TWDO.js";
+import {
+  get_bin_label,
+  get_bin_range_equation
+} from "./chunk-WGL6FIUE.js";
+
+// termsetting/handlers/NumCustomBinEditor.ts
+var NumCustomBinEditor = class {
+  constructor(editHandler) {
+    this.dom = {};
+    this.editHandler = editHandler;
+    this.opts = editHandler.opts;
+    this.tw = editHandler.tw;
+    this.termsetting = editHandler.termsetting;
+  }
+  async render(div) {
+    if (this.q?.type != "custom-bin") this.q = this.getDefaultQ();
+    await this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
+    if (this.dom.inputsDiv) {
+      if (this.editHandler.dom.binsDiv?.node().contains(this.dom.inputsDiv.node())) return;
+      else {
+        this.dom.inputsDiv.remove();
+        delete this.dom.inputsDiv;
+      }
+    }
+    this.dom.inputsDiv = div.append("div").style("display", "flex").style("width", "100%");
+    this.renderCustomBinInputs();
+  }
+  getBoundaryOpts() {
+    return {
+      values: this.q.lst.slice(1).map((bin) => ({ x: bin.startunbounded ? bin.stop : bin.start, isDraggable: true })),
+      callback: (d, value) => {
+        const boundaryValues = this.q.lst.slice(1).map((d2) => "start" in d2 ? d2.start : "");
+        boundaryValues[d.index] = value;
+        this.dom.customBinBoundaryInput.text(boundaryValues.join(",\n"));
+        this.handleInputChange("drag");
+        return 0;
+      }
+    };
+  }
+  getDefaultQ() {
+    if (this.tw.q.mode == "discrete" && this.tw.q.type == "custom-bin") {
+      const copy = JSON.parse(JSON.stringify(this.tw.q));
+      copy.lst.forEach((bin) => {
+        if (!bin.label) bin.label = get_bin_label(bin, this.tw.q, this.tw.term.valueConversion);
+        bin.range = get_bin_range_equation(bin, this.tw.q);
+      });
+      return copy;
+    }
+    const { min, max } = this.editHandler.handler.density_data;
+    const defaultCustomBoundary = (
+      /* when no sample is annotated by this term,
+      minvalue and maxvalue are both null
+      setting defaultCustomBoundary to arbitrary "0" will allow existing UI to work
+      but remains to be evaluated if is really okay to use 0
+      */
+      !Number.isFinite(min) || !Number.isFinite(max) ? 0 : (
+        // minvalue and maxvalue is valid number
+        max != min ? min + (max - min) / 2 : max
+      )
+    );
+    const firstBin = {
+      startunbounded: true,
+      startinclusive: false,
+      stopinclusive: false,
+      stop: +defaultCustomBoundary.toFixed(this.tw.term.type == "integer" ? 0 : 2)
+    };
+    const lastBin = {
+      stopunbounded: true,
+      startinclusive: true,
+      stopinclusive: false,
+      start: +defaultCustomBoundary.toFixed(this.tw.term.type == "integer" ? 0 : 2)
+    };
+    return {
+      mode: "discrete",
+      type: "custom-bin",
+      lst: [
+        // Type '{ label: any; range: any; startunbounded: boolean; startinclusive: boolean; stopinclusive: boolean; stop: number; }' is not assignable to type 'StartUnboundedBin | FullyBoundedBin'.
+        // Property 'start' is missing in type '{ label: any; range: any; startunbounded: boolean; startinclusive: boolean; stopinclusive: boolean; stop: number; }' but required in type 'FullyBoundedBin'.
+        {
+          ...firstBin,
+          label: get_bin_label(firstBin, this.tw.q, this.tw.term.valueConversion),
+          range: get_bin_range_equation(firstBin, this.tw.q)
+        },
+        {
+          ...lastBin,
+          label: get_bin_label(lastBin, this.tw.q, this.tw.term.valueConversion),
+          range: get_bin_range_equation(lastBin, this.tw.q)
+        }
+        //satisfies StopUnboundedBin
+      ]
+    };
+  }
+  /******************* Functions for Numerical Custom size bins *******************/
+  renderCustomBinInputs() {
+    const q = this.q;
+    const boundaryDiv = this.dom.inputsDiv.append("div").style("margin-right", "20px");
+    this.dom.rangeAndLabelDiv = this.dom.inputsDiv.append("div");
+    boundaryDiv.append("div").style("margin-bottom", "5px").style("color", "rgb(136, 136, 136)").text("Bin boundaries");
+    this.dom.customBinBoundaryInput = boundaryDiv.append("textarea").style("width", "100px").style("height", "70px").text(
+      q.lst.slice(1).map((d) => "start" in d ? d.start : "").join("\n")
+    ).on("change", () => this.handleInputChange()).on("keyup", async (event) => {
+      if (!keyupEnter(event) && event.key != 8 && event.key != "Enter") return;
+      if (!this.dom.inputsDiv.selectAll("input").node().value) return;
+      this.handleInputChange();
+    });
+    boundaryDiv.append("div").style("font-size", ".6em").style("margin-left", "1px").style("color", "#858585").html("Enter numeric values </br>seperated by ENTER");
+    this.renderBoundaryInputDivs();
+  }
+  renderBoundaryInputDivs() {
+    const data = this.q.lst;
+    const holder = this.dom.rangeAndLabelDiv;
+    holder.selectAll("*").remove();
+    const grid = holder.append("div").style("display", "grid").style("grid-template-columns", "auto auto").style("column-gap", "20px").style("align-items", "center");
+    grid.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Range");
+    grid.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Bin label");
+    for (const d of data) {
+      grid.append("div").attr("name", "range").html(d.range);
+      grid.append("div").append("input").attr("type", "text").style("margin", "2px 0px").property("value", d.label).on("change", function() {
+        d.label = this.value;
+      });
+    }
+    this.dom.customBinRanges = this.dom.inputsDiv.selectAll('div[name="range"]').data(data);
+    this.dom.customBinLabelInput = this.dom.inputsDiv.selectAll("input").data(data);
+  }
+  handleInputChange(eventType = "") {
+    const self = this.tw;
+    const inputs = this.dom.inputsDiv.selectAll("input");
+    inputs.property("value", "");
+    const data = this.processCustomBinInputs();
+    if (data == void 0) {
+      return;
+    }
+    if (self.q.hiddenValues) this.tw.q.hiddenValues = self.q.hiddenValues;
+    if (this.binsChanged(data, this.q.lst)) {
+      this.q.lst = data;
+    }
+    this.renderBoundaryInputDivs();
+    if (eventType != "drag") this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
+  }
+  binsChanged(data, qlst) {
+    if (data.length != qlst.length) return true;
+    if (Object.keys(data[0]).length !== Object.keys(qlst[0]).length) return true;
+    for (const [i, bin] of qlst.entries()) {
+      for (const k of Object.keys(bin)) {
+        if (bin[k] && bin[k] !== data[i][k]) {
+          return true;
+        }
+      }
+    }
+    return false;
+  }
+  processCustomBinInputs() {
+    const self = this.termsetting;
+    const startinclusive = this.editHandler.boundaryInclusion == "startinclusive";
+    const stopinclusive = this.editHandler.boundaryInclusion == "stopinclusive";
+    const inputs = this.dom.inputsDiv.node().querySelectorAll("input");
+    const inputData = this.dom.customBinBoundaryInput.property("value").split("\n").filter((d) => d != "" && !isNaN(d));
+    const trackBins = new Set(inputData);
+    if (!trackBins.size) return this.tw.q.lst;
+    const sortedBins = Array.from(trackBins).map(Number).sort((a, b) => a - b);
+    const data = [
+      // first bin: StartUnbounded type
+      {
+        startunbounded: true,
+        stop: sortedBins[0],
+        startinclusive: false,
+        stopinclusive,
+        label: inputs[0].value
+      }
+    ];
+    if (!data[0].label) data[0].label = get_bin_label(data[0], self.q, self.term.valueConversion);
+    if (!data[0].range) data[0].range = get_bin_range_equation(data[0], self.q);
+    for (const [i, d] of sortedBins.entries()) {
+      let bin;
+      const label = inputs[i + 1]?.value || "";
+      if (i !== trackBins.size - 1) {
+        bin = {
+          start: +d,
+          startinclusive,
+          stopinclusive,
+          stop: sortedBins[i + 1],
+          label
+          //range: ''
+        };
+      } else {
+        bin = {
+          start: +d,
+          startinclusive,
+          stopinclusive: false,
+          stopunbounded: true,
+          label
+          //range: ''
+        };
+      }
+      if (bin.label === "" || bin.label === void 0) bin.label = get_bin_label(bin, self.q, self.term.valueConversion);
+      if (bin.range === "" || bin.range === void 0) bin.range = get_bin_range_equation(bin, self.q);
+      data.push(bin);
+    }
+    return data;
+  }
+  getEditedQ(destroyDom = true) {
+    const lst = this.processCustomBinInputs();
+    if (destroyDom) {
+      for (const name of Object.keys(this.dom)) {
+        this.dom[name].remove();
+        delete this.dom[name];
+      }
+    }
+    return {
+      mode: "discrete",
+      type: "custom-bin",
+      lst
+    };
+  }
+  undoEdits() {
+    this.q = this.getDefaultQ();
+    this.dom.inputsDiv.selectAll("*").remove();
+    this.renderCustomBinInputs();
+    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
+  }
+};
+
+export {
+  NumCustomBinEditor
+};
+//# sourceMappingURL=chunk-FRBYOOWT.js.map

package/dist/chunk-FRBYOOWT.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../termsetting/handlers/NumCustomBinEditor.ts"],
+  "sourcesContent": ["import { keyupEnter } from '#src/client'\nimport type { NumCustomBins } from '#tw'\nimport type { NumDiscreteEditor } from './NumDiscreteEditor.ts'\nimport type { BoundaryOpts, LineData } from './NumericDensity.ts'\nimport type { TermSetting } from '../TermSetting.ts'\nimport type { CustomNumericBinConfig, CustomNumericBinConfigLst, StartUnboundedBin, StopUnboundedBin } from '#types'\nimport { get_bin_label, get_bin_range_equation } from '#shared/termdb.bins.js'\n\n// This is a bin editor for NumDiscreteEditor\n// NumericHandler (handler) -> NumDiscreteEditor (editor) -> NumCustomBinEditor (bin editor)\nexport class NumCustomBinEditor {\n\ttw: NumCustomBins\n\tq!: CustomNumericBinConfig\n\teditHandler: NumDiscreteEditor\n\ttermsetting: TermSetting\n\topts: any\n\tdom: {\n\t\t[elemName: string]: any\n\t} = {}\n\n\tconstructor(editHandler) {\n\t\tthis.editHandler = editHandler\n\t\tthis.opts = editHandler.opts\n\t\tthis.tw = editHandler.tw\n\t\tthis.termsetting = editHandler.termsetting\n\t}\n\n\tasync render(div) {\n\t\tif (this.q?.type != 'custom-bin') this.q = this.getDefaultQ()\n\t\tawait this.editHandler.handler.density.setBinLines(this.getBoundaryOpts())\n\t\tif (this.dom.inputsDiv) {\n\t\t\tif (this.editHandler.dom.binsDiv?.node().contains(this.dom.inputsDiv.node())) return\n\t\t\telse {\n\t\t\t\tthis.dom.inputsDiv.remove()\n\t\t\t\tdelete this.dom.inputsDiv\n\t\t\t}\n\t\t}\n\t\tthis.dom.inputsDiv = div.append('div').style('display', 'flex').style('width', '100%')\n\t\tthis.renderCustomBinInputs()\n\t}\n\n\tgetBoundaryOpts(): BoundaryOpts {\n\t\treturn {\n\t\t\tvalues: this.q.lst.slice(1).map(bin => ({ x: bin.startunbounded ? bin.stop : bin.start, isDraggable: true })),\n\t\t\tcallback: (d: LineData, value) => {\n\t\t\t\tconst boundaryValues = this.q.lst.slice(1).map(d => ('start' in d ? d.start : ''))\n\t\t\t\tboundaryValues[d.index] = value\n\t\t\t\tthis.dom.customBinBoundaryInput.text(boundaryValues.join(',\\n'))\n\t\t\t\tthis.handleInputChange('drag')\n\t\t\t\treturn 0\n\t\t\t}\n\t\t}\n\t}\n\n\tgetDefaultQ(): CustomNumericBinConfig {\n\t\tif (this.tw.q.mode == 'discrete' && this.tw.q.type == 'custom-bin') {\n\t\t\tconst copy = JSON.parse(JSON.stringify(this.tw.q))\n\t\t\tcopy.lst.forEach(bin => {\n\t\t\t\tif (!bin.label) bin.label = get_bin_label(bin, this.tw.q, this.tw.term.valueConversion)\n\t\t\t\tbin.range = get_bin_range_equation(bin, this.tw.q)\n\t\t\t})\n\t\t\treturn copy\n\t\t}\n\t\tconst { min, max } = this.editHandler.handler.density_data\n\t\tconst defaultCustomBoundary =\n\t\t\t/* when no sample is annotated by this term,\n\t\t\tminvalue and maxvalue are both null\n\t\t\tsetting defaultCustomBoundary to arbitrary \"0\" will allow existing UI to work\n\t\t\tbut remains to be evaluated if is really okay to use 0\n\t\t\t*/\n\t\t\t!Number.isFinite(min) || !Number.isFinite(max)\n\t\t\t\t? 0\n\t\t\t\t: // minvalue and maxvalue is valid number\n\t\t\t\tmax != min\n\t\t\t\t? min + (max - min) / 2\n\t\t\t\t: max\n\n\t\tconst firstBin = {\n\t\t\tstartunbounded: true,\n\t\t\tstartinclusive: false,\n\t\t\tstopinclusive: false,\n\t\t\tstop: +defaultCustomBoundary.toFixed(this.tw.term.type == 'integer' ? 0 : 2)\n\t\t} satisfies StartUnboundedBin\n\n\t\tconst lastBin = {\n\t\t\tstopunbounded: true,\n\t\t\tstartinclusive: true,\n\t\t\tstopinclusive: false,\n\t\t\tstart: +defaultCustomBoundary.toFixed(this.tw.term.type == 'integer' ? 0 : 2)\n\t\t} satisfies StopUnboundedBin\n\n\t\treturn {\n\t\t\tmode: 'discrete',\n\t\t\ttype: 'custom-bin',\n\t\t\tlst: [\n\t\t\t\t// Type '{ label: any; range: any; startunbounded: boolean; startinclusive: boolean; stopinclusive: boolean; stop: number; }' is not assignable to type 'StartUnboundedBin | FullyBoundedBin'.\n\t\t\t\t// Property 'start' is missing in type '{ label: any; range: any; startunbounded: boolean; startinclusive: boolean; stopinclusive: boolean; stop: number; }' but required in type 'FullyBoundedBin'.\n\t\t\t\t{\n\t\t\t\t\t...firstBin,\n\t\t\t\t\tlabel: get_bin_label(firstBin, this.tw.q, this.tw.term.valueConversion),\n\t\t\t\t\trange: get_bin_range_equation(firstBin, this.tw.q)\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\t...lastBin,\n\t\t\t\t\tlabel: get_bin_label(lastBin, this.tw.q, this.tw.term.valueConversion),\n\t\t\t\t\trange: get_bin_range_equation(lastBin, this.tw.q)\n\t\t\t\t} //satisfies StopUnboundedBin\n\t\t\t]\n\t\t}\n\t}\n\n\t/******************* Functions for Numerical Custom size bins *******************/\n\trenderCustomBinInputs() {\n\t\tconst q = this.q\n\t\t// boundaryDiv for entering bin boundaries\n\t\t// rangeAndLabelDiv for rendering ranges and labels\n\t\tconst boundaryDiv = this.dom.inputsDiv.append('div').style('margin-right', '20px')\n\t\tthis.dom.rangeAndLabelDiv = this.dom.inputsDiv.append('div')\n\n\t\tboundaryDiv.append('div').style('margin-bottom', '5px').style('color', 'rgb(136, 136, 136)').text('Bin boundaries')\n\n\t\tthis.dom.customBinBoundaryInput = boundaryDiv\n\t\t\t.append('textarea')\n\t\t\t.style('width', '100px')\n\t\t\t.style('height', '70px')\n\t\t\t.text(\n\t\t\t\tq.lst\n\t\t\t\t\t.slice(1)\n\t\t\t\t\t.map(d => ('start' in d ? d.start : ''))\n\t\t\t\t\t.join('\\n')\n\t\t\t)\n\t\t\t.on('change', () => this.handleInputChange())\n\t\t\t.on('keyup', async (event: any) => {\n\t\t\t\t// enter or backspace/delete\n\t\t\t\t// i don't think backspace works\n\t\t\t\tif (!keyupEnter(event) && event.key != 8 && event.key != 'Enter') return\n\t\t\t\tif (!this.dom.inputsDiv.selectAll('input').node().value) return\n\t\t\t\t// Fix for if user hits enter with no values. Reverts to default cutoff.\n\t\t\t\tthis.handleInputChange()\n\t\t\t})\n\n\t\t// help note\n\t\tboundaryDiv\n\t\t\t.append('div')\n\t\t\t.style('font-size', '.6em')\n\t\t\t.style('margin-left', '1px')\n\t\t\t.style('color', '#858585')\n\t\t\t.html('Enter numeric values </br>seperated by ENTER')\n\n\t\tthis.renderBoundaryInputDivs()\n\n\t\t// add help message for custom bin labels\n\t}\n\n\trenderBoundaryInputDivs() {\n\t\tconst data = this.q.lst\n\t\tconst holder = this.dom.rangeAndLabelDiv\n\t\tholder.selectAll('*').remove()\n\n\t\tconst grid = holder\n\t\t\t.append('div')\n\t\t\t.style('display', 'grid')\n\t\t\t.style('grid-template-columns', 'auto auto')\n\t\t\t.style('column-gap', '20px')\n\t\t\t.style('align-items', 'center')\n\n\t\tgrid.append('div').style('margin-bottom', '3px').style('color', 'rgb(136, 136, 136)').text('Range')\n\n\t\tgrid.append('div').style('margin-bottom', '3px').style('color', 'rgb(136, 136, 136)').text('Bin label')\n\n\t\tfor (const d of data) {\n\t\t\tgrid.append('div').attr('name', 'range').html(d.range)\n\n\t\t\tgrid\n\t\t\t\t.append('div')\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'text')\n\t\t\t\t.style('margin', '2px 0px')\n\t\t\t\t.property('value', d.label)\n\t\t\t\t.on('change', function (this: any) {\n\t\t\t\t\td.label = this.value\n\t\t\t\t})\n\t\t}\n\n\t\tthis.dom.customBinRanges = this.dom.inputsDiv.selectAll('div[name=\"range\"]').data(data)\n\t\tthis.dom.customBinLabelInput = this.dom.inputsDiv.selectAll('input').data(data)\n\t}\n\n\thandleInputChange(eventType = '') {\n\t\tconst self = this.tw\n\t\tconst inputs = this.dom.inputsDiv.selectAll('input')\n\t\tinputs.property('value', '')\n\t\tconst data = this.processCustomBinInputs()\n\t\tif (data == undefined) {\n\t\t\t// alert('Enter custom bin value(s)')\n\t\t\treturn\n\t\t}\n\t\t// update self.q.lst and render bin lines only if bin boundry changed\n\t\t//const q = self.numqByTermIdModeType[self.term.id].discrete[self.q.type!]\n\t\tif (self.q.hiddenValues) this.tw.q.hiddenValues = self.q.hiddenValues\n\t\tif (this.binsChanged(data, this.q.lst)) {\n\t\t\tthis.q.lst = data\n\t\t}\n\t\tthis.renderBoundaryInputDivs()\n\t\tif (eventType != 'drag') this.editHandler.handler.density.setBinLines(this.getBoundaryOpts())\n\t\t//self.q.lst = q.lst //store the new ranges in self.q, the mode is initialized when selecting the tab\n\t}\n\n\tbinsChanged(data, qlst) {\n\t\tif (data.length != qlst.length) return true\n\t\tif (Object.keys(data[0]).length !== Object.keys(qlst[0]).length) return true\n\t\tfor (const [i, bin] of qlst.entries()) {\n\t\t\tfor (const k of Object.keys(bin)) {\n\t\t\t\tif (bin[k] && bin[k] !== data[i][k]) {\n\t\t\t\t\treturn true\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\treturn false\n\t}\n\n\tprocessCustomBinInputs() {\n\t\tconst self = this.termsetting\n\t\tconst startinclusive = this.editHandler.boundaryInclusion == 'startinclusive'\n\t\tconst stopinclusive = this.editHandler.boundaryInclusion == 'stopinclusive'\n\t\tconst inputs = this.dom.inputsDiv.node().querySelectorAll('input')\n\n\t\tconst inputData = this.dom.customBinBoundaryInput\n\t\t\t.property('value')\n\t\t\t.split('\\n')\n\t\t\t.filter((d: any) => d != '' && !isNaN(d))\n\n\t\t// Fix for when user enters in the same number more than once.\n\t\t// UI will ignore duplicate entries completely.\n\t\tconst trackBins = new Set(inputData)\n\t\tif (!trackBins.size) return this.tw.q.lst\n\n\t\tconst sortedBins = Array.from(trackBins)\n\t\t\t.map(Number)\n\t\t\t.sort((a, b) => a - b)\n\n\t\tconst data: CustomNumericBinConfigLst = [\n\t\t\t// first bin: StartUnbounded type\n\t\t\t{\n\t\t\t\tstartunbounded: true,\n\t\t\t\tstop: sortedBins[0],\n\t\t\t\tstartinclusive: false,\n\t\t\t\tstopinclusive,\n\t\t\t\tlabel: inputs[0].value\n\t\t\t}\n\t\t]\n\t\t// first bin\n\t\tif (!data[0].label) data[0].label = get_bin_label(data[0], self.q, self.term.valueConversion)\n\t\tif (!data[0].range) data[0].range = get_bin_range_equation(data[0], self.q)\n\t\tfor (const [i, d] of sortedBins.entries()) {\n\t\t\tlet bin\n\t\t\tconst label = inputs[i + 1]?.value || ''\n\t\t\tif (i !== trackBins.size - 1) {\n\t\t\t\t// intermediate bin: FullyBounded type\n\t\t\t\tbin = {\n\t\t\t\t\tstart: +d,\n\t\t\t\t\tstartinclusive,\n\t\t\t\t\tstopinclusive,\n\t\t\t\t\tstop: sortedBins[i + 1],\n\t\t\t\t\tlabel\n\t\t\t\t\t//range: ''\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\t// last bin: StopUnbounded type\n\t\t\t\tbin = {\n\t\t\t\t\tstart: +d,\n\t\t\t\t\tstartinclusive,\n\t\t\t\t\tstopinclusive: false,\n\t\t\t\t\tstopunbounded: true,\n\t\t\t\t\tlabel\n\t\t\t\t\t//range: ''\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tif (bin.label === '' || bin.label === undefined) bin.label = get_bin_label(bin, self.q, self.term.valueConversion)\n\t\t\tif (bin.range === '' || bin.range === undefined) bin.range = get_bin_range_equation(bin, self.q)\n\t\t\tdata.push(bin)\n\t\t}\n\t\treturn data\n\t}\n\n\tgetEditedQ(destroyDom = true): CustomNumericBinConfig {\n\t\tconst lst = this.processCustomBinInputs()\n\t\tif (destroyDom) {\n\t\t\tfor (const name of Object.keys(this.dom)) {\n\t\t\t\tthis.dom[name].remove()\n\t\t\t\tdelete this.dom[name]\n\t\t\t}\n\t\t}\n\t\treturn {\n\t\t\tmode: 'discrete',\n\t\t\ttype: 'custom-bin',\n\t\t\tlst\n\t\t}\n\t}\n\n\tundoEdits() {\n\t\tthis.q = this.getDefaultQ()\n\t\tthis.dom.inputsDiv.selectAll('*').remove()\n\t\tthis.renderCustomBinInputs()\n\t\tthis.editHandler.handler.density.setBinLines(this.getBoundaryOpts())\n\t}\n}\n"],
+  "mappings": 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+}