@sjcrh/proteinpaint-client 2.182.0 → 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": ";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAYO,IAAM,cAAN,MAAM,qBAAoB,OAAO;AAAA,EACvC,OAAO,OAAO;AAAA,EAEd,YAAY,MAAM;AACjB,UAAM,IAAI;AACV,SAAK,OAAO,aAAY;AACxB,SAAK,YAAY,aAAY;AAAA,EAC9B;AAAA,EAEA,MAAM,KAAK,UAAU;AACpB,UAAM,MAAM,KAAK,QAAQ;AAEzB,SAAK,oBAAoB,QAAQ;AAEjC,SAAK,WAAW,KAAK,eAAe;AACpC,SAAK,IAAI,aAAa,KAAK,IAAI,IAC7B,OAAO,MAAM,EACb,OAAO,UAAU,EACjB,KAAK,MAAM,KAAK,QAAQ,EAExB,KAAK,iBAAiB,gBAAgB,EACtC,OAAO,MAAM,EACb,KAAK,WAAW,OAAO;AAEzB,SAAK,IAAI,gBAAgB,KAAK,IAAI,IAChC,OAAO,KAAK,GAAG,EACf,KAAK,aAAa,QAAQ,KAAK,QAAQ,GAAG,EAC1C,OAAO,GAAG,EACV,KAAK,SAAS,wBAAwB,EACtC,KAAK,eAAe,4BAA4B,EAChD,GAAG,SAAS,WAAS;AACrB,YAAM,mBAAmB,KAAK,4BAA4B,KAAK;AAC/D,UAAI,kBAAkB;AACrB,aAAK,oBAAoB,KAAK,yBAAyB,gBAAgB;AACvE,aAAK,kBAAkB,KAAK,gBAAgB;AAE5C,cAAM,iBAAiB,KAAK,gBAAgB,WAAW,IAAI,eAAe,IAAI,gBAAgB;AAC9F,cAAM,4BAA4B,eAAe,SAAS,IAAI,OAAK,EAAE,IAAI;AACzE,aAAK,0BAA0B,2BAA2B,KAAK;AAAA,MAChE,OAAO;AAEN,eAAO,KAAK;AAAA,MACb;AAGA,UAAI,KAAK,uBAAuB;AAE/B,eAAO,KAAK;AACZ,aAAK,qBAAqB;AAAA,MAC3B,MAAO,MAAK,qBAAqB,KAAK;AAAA,IACvC,CAAC;AAEF,SAAK,IAAI,iBAAiB,KAAK,IAAI,IACjC,OAAO,KAAK,GAAG,EACf,KAAK,SAAS,wBAAwB,EACtC,KAAK,eAAe,6BAA6B,EACjD,GAAG,SAAS,WAAS;AACrB,YAAM,uBAAuB,KAAK,6BAA6B,KAAK;AACpE,UAAI,sBAAsB;AACzB,aAAK,wBAAwB,KAAK,yBAAyB,sBAAsB,IAAI;AACrF,aAAK,sBAAsB,KAAK,oBAAoB;AAEpD,cAAM,qBAAqB,KAAK,gBAAgB,WAAW,IAAI,eAAe,IAAI,oBAAoB;AAEtG,cAAM,8BAA8B,mBAAmB,SAAS,IAAI,OAAK,EAAE,IAAI;AAE/E,aAAK,uBAAuB,6BAA6B,KAAK;AAAA,MAC/D,OAAO;AAEN,eAAO,KAAK;AAAA,MACb;AAGA,UAAI,KAAK,mBAAmB;AAE3B,eAAO,KAAK;AACZ,aAAK,qBAAqB;AAAA,MAC3B,MAAO,MAAK,qBAAqB,MAAM;AAAA,IACxC,CAAC;AAAA,EAEH;AAAA,EAEA,MAAM,mBAAmB,QAAQ,CAAC,GAAG;AACpC,SAAK,iBAAiB,KAAK;AAC3B,UAAM,CAAC,GAAG,KAAK,IAAI,MAAM,KAAK,YAAY,CAAC,CAAC;AAC5C,QAAI,EAAE,MAAO,OAAM,EAAE;AACrB,SAAK,iBAAiB,gBAAgB,CAAC;AACvC,QAAI,CAAC,UAAU,KAAK,gBAAgB,KAAK,cAAc,GAAG;AAGzD,aAAO,KAAK;AACZ,aAAO,KAAK;AAAA,IACb;AACA,UAAM,IAAI,KAAK,SAAS;AAExB,QAAI,CAAC,EAAE,YAAY;AAElB,UAAI,EAAE,MAAM;AAEX,cAAM,4DAA4D,EAAE,IAAI;AAAA,MACzE;AAAA,IAED;AACA,SAAK,kBAAkB;AAEvB,UAAM,IAAI,KAAK,gBAAgB;AAC/B,SAAK,kBAAkB,CAAC;AAExB,UAAM,UAAU,CAAC;AAKjB,eAAW,CAAC,GAAG,MAAM,KAAK,EAAE,IAAI,MAAM,QAAQ,GAAG;AAChD,cAAQ,OAAO,IAAI,IAAI,EAAE,QAAQ,OAAO,KAAK;AAC7C,iBAAW,CAAC,GAAG,GAAG,KAAK,EAAE,IAAI,MAAM,QAAQ,GAAG;AAC7C,cAAM,KAAK,MAAM,KAAK,CAAAA,QAAMA,IAAG,QAAQ,IAAI,QAAQA,IAAG,OAAO,IAAI,IAAI;AAKrE,cAAM,QAAQ,EAAE,OAAO,CAAC,EAAE,CAAC;AAC3B,gBAAQ,OAAO,IAAI,EAAE,GAAG,GAAG,IAAI;AAAA,UAC9B,KAAK,GAAG,KAAK;AAAA,UACb,QAAQ;AAAA,YACP;AAAA,cACC,QAAQ,OAAO;AAAA,cACf,IAAI,aAAa,KAAK,MAAM,OAAO,QAAQ;AAAA,cAC3C,OAAO,EAAE;AAAA;AAAA;AAAA;AAAA,cAIT;AAAA;AAAA;AAAA,YAGD;AAAA,UACD;AAAA,QACD;AAAA,MACD;AAAA,IACD;AAEA,SAAK,kBACJ,KAAK,SAAS,YAAY,mBAAmB,aAC1C,MAAM,IAAI,OAAK,EAAE,KAAK,IAAI,IAC1B,KAAK,SAAS,YAAY,mBAAmB,WAC7C,MAAM,IAAI,OAAK,EAAE,KAAK,IAAI,EAAE,KAAK,IACjC,EAAE,IAAI,MAAM,IAAI,SAAO,MAAM,KAAK,OAAK,EAAE,OAAO,IAAI,IAAI,GAAG,KAAK,IAAI;AAExE,QAAI,KAAK,gBAAgB,SAAS,MAAS,EAAG,OAAM;AAEpD,SAAK,eAAe,CAAC,GAAG,MAAM;AAC7B,YAAM,IAAI,KAAK,gBAAgB,QAAQ,EAAE,GAAG,KAAK,IAAI;AACrD,YAAM,IAAI,KAAK,gBAAgB,QAAQ,EAAE,GAAG,KAAK,IAAI;AACrD,UAAI,KAAK,MAAM,KAAK,GAAI,QAAO;AAC/B,UAAI,KAAK,GAAI,QAAO;AACpB,UAAI,KAAK,GAAI,QAAO;AACpB,aAAO,IAAI;AAAA,IACZ;AAEA,SAAK,oBAAoB,EAAE,IAAI,MAAM,IAAI,SAAO,IAAI,IAAI;AACxD,SAAK,iBAAiB,CAAC,GAAG,MAAM;AAC/B,YAAM,IAAI,KAAK,kBAAkB,QAAQ,EAAE,MAAM;AACjD,YAAM,IAAI,KAAK,kBAAkB,QAAQ,EAAE,MAAM;AACjD,UAAI,KAAK,MAAM,KAAK,GAAI,QAAO;AAC/B,UAAI,KAAK,GAAI,QAAO;AACpB,UAAI,KAAK,GAAI,QAAO;AACpB,aAAO,IAAI;AAAA,IACZ;AAGA,UAAM,WAAW,CAAC;AAClB,eAAW,MAAM,OAAO;AACvB,UAAI,EAAE,WAAW,GAAG,KAAK,IAAI,EAAG,UAAS,GAAG,GAAG,IAAI,EAAE,SAAS,GAAG,KAAK,IAAI;AAAA,IAC3E;AACA,SAAK,qBAAqB;AAAA,MACzB,MAAM,EAAE,UAAU,YAAY,EAAE,WAAW;AAAA,MAC3C,KAAK,EAAE,IAAI,MAAM,IAAI,CAAAC,OAAK,QAAQA,GAAE,IAAI,CAAC;AAAA,MACzC;AAAA,MACA,yBAAyB,EAAE;AAAA,IAC5B;AAAA,EACD;AAAA,EAEA,MAAM,cAAc;AAEnB,UAAM,OAAO,KAAK,iBAAiB,eAAe,KAAK,iBAAiB,KAAK,KAAK;AAClF,UAAM,QAAQ,KAAK,YAAY;AAC/B,UAAM,OAAO,MAAM,SAAS,kBAAkB,EAAE,MAAM,QAAQ,KAAK,IAAI,iBAAiB,EAAE,CAAC;AAE3F,WAAO,CAAC,MAAM,KAAK;AAAA,EACpB;AAAA,EAEA,iBAAiB,OAAO;AACvB,SAAK,cACJ,KAAK,OAAO,WAAW,KAAK,SAAO,IAAI,QAAQ,aAAa,KAC5D,KAAK,WAAW,KAAK,OAAK,EAAE,IAAI,QAAQ,aAAa,GAAG;AAEzD,UAAM,IAAI,MAAM,OAAO,SAAS;AAIhC,UAAM,yBAAyB;AAAA,MAC9B,MAAM;AAAA,MACN,IAAI;AAAA,MACJ,MAAM;AAAA,MACN,KAAK,MAAM,OAAO,kBAAkB,IAAI,OAAO,OAAK,CAAC,EAAE,IAAI,gBAAgB;AAAA,IAC5E;AACA,UAAM,QAAQ,KAAK,8BAA8B;AACjD,QAAI,CAAC,MAAM,OAAQ,OAAM;AAOzB,QAAI,CAAC,iBAAiB,KAAK,OAAK,EAAE,SAAS,EAAE,aAAa,EAAG,OAAM;AACnE,QAAI,CAAC,kBAAkB,KAAK,OAAK,EAAE,SAAS,EAAE,cAAc,EAAG,OAAM;AACrE,UAAM,OAAO;AAAA,MACZ,QAAQ,MAAM,MAAM;AAAA,MACpB,SAAS,MAAM,MAAM;AAAA,MACrB,UAAU,MAAM,OAAO;AAAA,MACvB,eAAe,EAAE;AAAA,MACjB,gBAAgB,EAAE;AAAA,MAClB,sBAAsB,EAAE;AAAA,MACxB;AAAA,MACA,QAAQ,cAAc,WAAW,CAAC,MAAM,QAAQ,sBAAsB,CAAC,CAAC;AAAA,MACxE,SAAS,MAAM;AAAA,IAChB;AACA,QAAI,MAAM,OAAO,YAAY,qBAAqB;AACjD,WAAK,kBAAkB;AAAA,QACtB,OAAO,MAAM,OAAO,iBAAiB;AAAA,QACrC,QAAQ,MAAM,OAAO,iBAAiB;AAAA,MACvC;AAAA,IACD;AACA,WAAO;AAAA,EACR;AAAA,EAEA,cAAc;AACb,QAAI,CAAC,KAAK,mBAAoB;AAC9B,UAAM,IAAI,KAAK;AACf,UAAM,0BAA0B,KAAK,mBAAmB;AACxD,UAAM,UAAU,CAAC;AACjB,UAAM,MAAM,CAAC;AAEb,eAAW,YAAY,KAAK,mBAAmB,SAAS;AACvD,YAAM,IAAI,KAAK,mBAAmB,QAAQ,QAAQ;AAClD,cAAQ,QAAQ,IAAI;AACpB,UAAI,KAAK,CAAC;AACV,UAAI,YAAY,EAAE,QAAS,QAAO,OAAO,GAAG,EAAE,QAAQ,QAAQ,CAAC;AAC/D,YAAM,QAAQ,KAAK,mBAAmB,KAAK,WAAW,QAAQ,KAAK,CAAC;AACpE,UAAI,CAAC,EAAE,MAAO,GAAE,QAAQ;AAAA,UAEnB,QAAO,OAAO,EAAE,OAAO,KAAK;AAAA,IAClC;AAGA,UAAM,IAAI,KAAK,mBAAmB,KAAK;AACvC,eAAW,OAAO,OAAO,KAAK,CAAC,GAAG;AACjC,QAAE,KAAK,SAAS,GAAG,IAAI,OAAO,OAAO,CAAC,GAAG,EAAE,KAAK,SAAS,GAAG,KAAK,CAAC,GAAG,EAAE,GAAG,CAAC;AAAA,IAC5E;AACA,SAAK,OAAO,EAAE,SAAS,KAAK,MAAM,EAAE,MAAM,wBAAwB;AAAA,EACnE;AAAA,EAEA,kBAAkB,GAAG;AACpB,UAAM,KAAK,KAAK,SAAS;AACzB,UAAM,QAAQ,OAAY,cAAc,GAAG,UAAU,EAAE,QAAQ,cAAc,GAAG,UAAU,EAAE,KAAK,EAAE,MAAM,IAAI;AAC7G,UAAM,iBAAiB,CAAC;AACxB,eAAW,OAAO,EAAE,QAAQ;AAC3B,qBAAe,KAAK,GAAG,OAAO,GAAG,CAAC;AAAA,IACnC;AACA,UAAM,SAAS,KAAK,IAAI,GAAG,WAAW,KAAK,IAAI,GAAG,OAAO,cAAc,EAAE,IAAI,KAAK,GAAG,CAAC,CAAC;AAEvF,UAAM,CAAC,KAAK,GAAG,IAAI,GAAG,uBACnB,CAAC,CAAC,QAAQ,MAAM,IAChB,CAAC,KAAK,IAAI,GAAG,cAAc,GAAG,KAAK,IAAI,GAAG,cAAc,CAAC;AAE5D,SAAK,oBAAoB,EAAE,OAAO,KAAK,IAAI;AAAA,EAC5C;AAAA,EAEA,cAAc,OAAO;AACpB,UAAM,KAAK,KAAK,SAAS;AACzB,QAAI,GAAG,sBAAsB;AAC5B,YAAM,YAAY,KAAK,SAAS,YAAY;AAC5C,aAAO,KAAK,kBAAkB,OAAO,QAAQ,CAAC,cAAc,YAAY,EAAE;AAAA,IAC3E,OAAO;AACN,aAAO,KAAK,kBAAkB,MAAM,QAAQ,KAAK,kBAAkB,GAAG;AAAA,IACvE;AAAA,EACD;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA,EAeA,gCAAgC;AAC/B,UAAM,MAAM,KAAK,YAAY,IAAI,IAAI,KAAK,KAAK,IAAI,SAAS,YAAY;AAExE,QAAI,KAAK,CAAC,GAAG,MAAO,EAAE,KAAK,OAAO,EAAE,KAAK,OAAO,KAAK,CAAE;AACvD,WAAO;AAAA,EACR;AACD;AAEA,WAAW,WAAW,CAAC,+BAAW,iCAAa,GAAG;AACjD,aAAW,cAAc,QAAS,aAAY,UAAU,UAAU,IAAI,QAAQ,UAAU;AACzF;AAEO,IAAM,kBAAkB,YAAY,WAAW;AAC/C,IAAM,gBAAgB;",
+  "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-FVWCYGJL.js

@@ -0,0 +1,121 @@
+import {
+  roundValueAuto
+} from "./chunk-L4QG7XZE.js";
+import {
+  brushX
+} from "./chunk-SEEYV6P2.js";
+import {
+  select_default
+} from "./chunk-NDWTN4U5.js";
+
+// filter/tvs.density.js
+function addBrushes(self, new_brush_location) {
+  const brushes = self.num_obj.brushes;
+  const maxvalue = self.num_obj.density_data.max;
+  const minvalue = self.num_obj.density_data.min;
+  const rawDecile = (maxvalue - minvalue) / 10;
+  const decile = self.tvs.term.type == "integer" ? Math.floor(rawDecile) : rawDecile;
+  for (const [i, r] of self.num_obj.ranges.entries()) {
+    const _b = brushes.find((b) => b.orig === r);
+    let brush;
+    if (!_b) {
+      brush = { orig: r, range: JSON.parse(JSON.stringify(r)) };
+      brushes.push(brush);
+    } else {
+      brush = _b;
+    }
+    if (r.start === "") {
+      if (new_brush_location == "center") brush.range.start = minvalue + decile * 4;
+      else brush.range.start = minvalue + decile * 8;
+    }
+    if (r.stop === "") {
+      if (new_brush_location == "center") brush.range.stop = minvalue + decile * 6;
+      else brush.range.stop = Math.floor(maxvalue);
+    }
+  }
+  const range_brushes = self.num_obj.brush_g.selectAll(".range_brush").data(brushes, (d) => brushes.indexOf(d));
+  range_brushes.exit().remove();
+  range_brushes.each(function(d, i) {
+    select_default(this).selectAll(".overlay").style("pointer-events", "all");
+  });
+  range_brushes.enter().append("g").attr("class", "range_brush").each(function(brush, i) {
+    applyBrush(self, this, brush, i);
+  });
+}
+function applyBrush(self, elem, brush) {
+  if (!brush.elem) brush.elem = select_default(elem);
+  const range = brush.range;
+  const plot_size = self.num_obj.plot_size;
+  const xscale = self.num_obj.xscale;
+  const maxvalue = self.num_obj.density_data.max;
+  const minvalue = self.num_obj.density_data.min;
+  brush.d3brush = brushX().extent([
+    [0, 0],
+    [plot_size.width, plot_size.height]
+  ]).on("brush", function(event, d) {
+    const s = event.selection;
+    if (!s) return;
+    const inputRange = brush.rangeInput.getRange();
+    if (inputRange?.value != void 0) {
+      brush.range = inputRange;
+      return;
+    }
+    updateTempRanges(xscale, s, range, inputRange, minvalue, maxvalue, self.tvs.term.type);
+    const [start, stop] = setStartStopDisplays(range, inputRange);
+    brush.rangeInput.getInput().node().value = `${start} x ${stop}`;
+  }).on("end", function() {
+    brush.elem.selectAll(".overlay").style("pointer-events", "none");
+  });
+  const brush_start = range.startunbounded ? minvalue : range.start;
+  const brush_stop = range.stopunbounded ? maxvalue : range.stop;
+  brush.init = () => {
+    if (range.value == void 0)
+      brush.elem.call(brush.d3brush).call(brush.d3brush.move, [brush_start, brush_stop].map(xscale));
+  };
+  if (range.startunbounded) delete range.start;
+  if (range.stopunbounded) delete range.stop;
+  brush.elem.selectAll(".selection").style(
+    "fill",
+    brush.orig.start === "" && brush.orig.stop === "" || JSON.stringify(range) != JSON.stringify(brush.orig) ? "#23cba7" : "#777777"
+  );
+}
+function updateTempRanges(xscale, s, range, inputRange, minvalue, maxvalue, type) {
+  range.start = convertRangeValue(xscale, s[0]);
+  range.stop = convertRangeValue(xscale, s[1]);
+  const min = roundValueAuto(Number(minvalue));
+  const max = roundValueAuto(Number(maxvalue));
+  if (range.start < min) range.start = min;
+  if (range.stop > max) range.stop = max;
+  range.startunbounded = min == range.start && inputRange.startunbounded;
+  range.stopunbounded = max == range.stop && inputRange.stopunbounded;
+  if (type == "integer") {
+    range.start = range.startunbounded ? "" : Math.round(range.start);
+    range.stop = range.stopunbounded ? "" : Math.round(range.stop);
+  }
+}
+function setStartStopDisplays(range, inputRange) {
+  const start = range.startunbounded ? "" : inputRange.startinclusive ? `${range.start} <=` : `${range.start} <`;
+  const stop = range.stopunbounded ? "" : inputRange.stopinclusive ? `<= ${range.stop}` : `< ${range.stop}`;
+  return [start, stop];
+}
+function convertRangeValue(xscale, sidx) {
+  const value = Number(xscale.invert(sidx));
+  return roundValueAuto(value);
+}
+function addNewBrush(self, new_brush_location = "end", callback) {
+  const new_range = { start: "", stop: "", index: self.tvs.ranges.length };
+  self.num_obj.ranges.push(new_range);
+  const brush = { orig: new_range, range: JSON.parse(JSON.stringify(new_range)) };
+  self.num_obj.brushes.push(brush);
+  addBrushes(self, new_brush_location);
+  if (callback) callback();
+  brush.init();
+}
+
+export {
+  addBrushes,
+  updateTempRanges,
+  setStartStopDisplays,
+  addNewBrush
+};
+//# sourceMappingURL=chunk-FVWCYGJL.js.map