@sjcrh/proteinpaint-client 2.191.0 → 2.191.2

package/dist/chunk-VMLSRKIB.js

@@ -0,0 +1,276 @@
+import {
+  parsesample
+} from "./chunk-6VKTEMFV.js";
+import {
+  dtfusionrna,
+  dtsv,
+  mclassfusionrna,
+  mclasssv
+} from "./chunk-EBKERML3.js";
+
+// ../shared/utils/dist/src/bulk.sv.js
+function parseheader(line, flag, issv) {
+  const header = line.toLowerCase().split("	");
+  if (header.length <= 1) return "invalid file header for fusions";
+  const htry = (...lst) => {
+    for (const a of lst) {
+      const j = header.indexOf(a);
+      if (j != -1) return j;
+    }
+    return -1;
+  };
+  let i = htry("gene_a", "gene1", "genea");
+  if (i == -1) return "gene_a missing from header";
+  header[i] = "gene1";
+  i = htry("gene_b", "gene2", "geneb");
+  if (i == -1) return "gene_b missing from header";
+  header[i] = "gene2";
+  i = htry("chr_a", "chr1", "chra");
+  if (i == -1) return "chr_a missing from header";
+  header[i] = "chr1";
+  i = htry("chr_b", "chr2", "chrb");
+  if (i == -1) return "chr_b missing from header";
+  header[i] = "chr2";
+  i = htry("pos_a", "position_a", "position1", "posa");
+  if (i == -1) return "pos_a missing from header";
+  header[i] = "position1";
+  i = htry("pos_b", "position_b", "position2", "posb");
+  if (i == -1) return "pos_b missing from header";
+  header[i] = "position2";
+  i = htry("isoform_a", "refseq_a", "refseq1", "isoform1", "sv_refseqa");
+  if (i == -1) return "isoform_a missing from header";
+  header[i] = "isoform1";
+  i = htry("isoform_b", "refseq_b", "refseq2", "isoform2", "sv_refseqb");
+  if (i == -1) return "isoform_b missing from header";
+  header[i] = "isoform2";
+  i = htry("strand_a", "orta");
+  if (i == -1) return "strand_a missing from header";
+  header[i] = "strand1";
+  i = htry("strand_b", "ortb");
+  if (i == -1) return "strand_b missing from header";
+  header[i] = "strand2";
+  i = htry("sample", "sample_name", "tumor_sample_barcode");
+  if (i != -1) header[i] = "sample";
+  i = htry("patient", "donor", "target_case_id");
+  if (i != -1) header[i] = "patient";
+  i = htry("sampletype", "sample type", "sample_type");
+  if (i != -1) header[i] = "sampletype";
+  i = htry("disease");
+  if (i != -1) header[i] = "disease";
+  i = htry("origin");
+  if (i != -1) header[i] = "origin";
+  if (issv) {
+    flag.sv.loaded = true;
+    flag.sv.header = header;
+  } else {
+    flag.fusion.loaded = true;
+    flag.fusion.header = header;
+  }
+  return false;
+}
+function parseline(i, line, flag, issv) {
+  if (line == "" || line[0] == "#") return;
+  const lst = line.split("	");
+  const m = {};
+  const header = issv ? flag.sv.header : flag.fusion.header;
+  const badlines = issv ? flag.sv.badlines : flag.fusion.badlines;
+  for (let j = 0; j < header.length; j++) {
+    m[header[j]] = lst[j];
+  }
+  if (!m.chr1) {
+    badlines.push([i, "missing chr1", lst]);
+    return;
+  }
+  if (m.chr1.toLowerCase().indexOf("chr") != 0) {
+    m.chr1 = "chr" + m.chr1;
+  }
+  if (!m.chr2) {
+    badlines.push([i, "missing chr2", lst]);
+    return;
+  }
+  if (m.chr2.toLowerCase().indexOf("chr") != 0) {
+    m.chr2 = "chr" + m.chr2;
+  }
+  let v = m.position1;
+  if (!v) {
+    badlines.push([i, "missing position1", lst]);
+    return;
+  }
+  let v2 = Number.parseInt(v);
+  if (Number.isNaN(v2) || v2 <= 0) {
+    badlines.push([i, "invalid value for position1", lst]);
+    return;
+  }
+  m.position1 = v2;
+  v = m.position2;
+  if (!v) {
+    badlines.push([i, "missing position2", lst]);
+    return;
+  }
+  v2 = Number.parseInt(v);
+  if (Number.isNaN(v2) || v2 <= 0) {
+    badlines.push([i, "invalid value for position2", lst]);
+    return;
+  }
+  m.position2 = v2;
+  if (parsesample(m, flag, i, lst)) {
+    return;
+  }
+  if (m.isoform1 && m.isoform1.indexOf(",") != -1) {
+    const lst2 = m.isoform1.split(",");
+    m.isoform1 = void 0;
+    for (const t of lst2) {
+      if (t != "") m.isoform1 = t;
+    }
+  }
+  if (m.isoform2 && m.isoform2.indexOf(",") != -1) {
+    const lst2 = m.isoform2.split(",");
+    m.isoform2 = void 0;
+    for (const t of lst2) {
+      if (t != "") m.isoform2 = t;
+    }
+  }
+  if (!m.gene1) {
+    m.isoform1 = void 0;
+  }
+  if (!m.gene2) {
+    m.isoform2 = void 0;
+  }
+  if (m.gene1) {
+    flag.good++;
+    const m2 = {
+      dt: issv ? dtsv : dtfusionrna,
+      class: issv ? mclasssv : mclassfusionrna,
+      isoform: m.isoform1,
+      mname: m.gene2 || m.chr2,
+      sample: m.sample,
+      patient: m.patient,
+      sampletype: m.sampletype,
+      origin: m.origin,
+      disease: m.disease,
+      pairlst: [
+        {
+          a: {
+            name: m.gene1,
+            isoform: m.isoform1,
+            strand: m.strand1,
+            chr: m.chr1,
+            position: m.position1
+          },
+          b: {
+            name: m.gene2,
+            isoform: m.isoform2,
+            strand: m.strand2,
+            chr: m.chr2,
+            position: m.position2
+          }
+        }
+      ]
+    };
+    const n = flag.geneToUpper ? m.gene1.toUpperCase() : m.gene1;
+    if (!flag.data[n]) {
+      flag.data[n] = [];
+    }
+    flag.data[n].push(m2);
+  }
+  if (m.gene2 && m.gene2 != m.gene1) {
+    flag.good++;
+    const m2 = {
+      dt: issv ? dtsv : dtfusionrna,
+      class: issv ? mclasssv : mclassfusionrna,
+      isoform: m.isoform2,
+      mname: m.gene1 || m.chr1,
+      sample: m.sample,
+      patient: m.patient,
+      sampletype: m.sampletype,
+      origin: m.origin,
+      disease: m.disease,
+      pairlst: [
+        {
+          a: {
+            name: m.gene1,
+            isoform: m.isoform1,
+            strand: m.strand1,
+            chr: m.chr1,
+            position: m.position1
+          },
+          b: {
+            name: m.gene2,
+            isoform: m.isoform2,
+            strand: m.strand2,
+            chr: m.chr2,
+            position: m.position2
+          }
+        }
+      ]
+    };
+    const n = flag.geneToUpper ? m.gene2.toUpperCase() : m.gene2;
+    if (!flag.data[n]) {
+      flag.data[n] = [];
+    }
+    flag.data[n].push(m2);
+  }
+}
+function duplicate(m) {
+  const n = {};
+  for (const k in m) {
+    if (k == "pairlst") continue;
+    const v = m[k];
+    const type = typeof v;
+    if (type == "object") {
+      continue;
+    }
+    n[k] = v;
+  }
+  if (m.pairlst) {
+    n.pairlst = [];
+    for (const pair of m.pairlst) {
+      const p = {};
+      for (const k in pair) {
+        if (k == "a" || k == "b" || k == "interstitial") {
+          continue;
+        }
+        p[k] = pair[k];
+      }
+      if (pair.a) {
+        p.a = {};
+        for (const k in pair.a) {
+          const v = pair.a[k];
+          if (typeof v == "object") {
+            continue;
+          }
+          p.a[k] = v;
+        }
+      }
+      if (pair.b) {
+        p.b = {};
+        for (const k in pair.b) {
+          const v = pair.b[k];
+          if (typeof v == "object") {
+            continue;
+          }
+          p.b[k] = v;
+        }
+      }
+      if (pair.interstitial) {
+        p.interstitial = {};
+        for (const k in pair.interstitial) {
+          const v = pair.interstitial[k];
+          if (typeof v == "object") {
+            continue;
+          }
+          p.interstitial[k] = v;
+        }
+      }
+      n.pairlst.push(p);
+    }
+  }
+  return n;
+}
+
+export {
+  parseheader,
+  parseline,
+  duplicate
+};
+//# sourceMappingURL=chunk-VMLSRKIB.js.map

package/dist/chunk-WET4LPLO.js

@@ -0,0 +1,117 @@
+import {
+  addGeneSearchbox,
+  isoformSelect,
+  sayerror
+} from "./chunk-L4TUTGTA.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import {
+  dofetch3
+} from "./chunk-6VKTEMFV.js";
+import {
+  ISOFORM_EXPRESSION
+} from "./chunk-TVADJLMF.js";
+
+// termdb/handlers/isoformExpression.ts
+var SearchHandler = class {
+  constructor() {
+    this.currentGene = null;
+  }
+  init(opts) {
+    this.callback = opts.callback;
+    this.app = opts.app;
+    const holder = opts.holder.append("div").style("padding", "10px 0px");
+    this.dom = {
+      errDiv: holder.append("div").style("margin", "5px 0px").style("display", "none")
+    };
+    const geneSearch = addGeneSearchbox({
+      tip: new Menu({ padding: "0px" }),
+      genome: opts.genomeObj,
+      row: holder,
+      searchOnly: "gene",
+      callback: async () => {
+        try {
+          this.dom.errDiv.style("display", "none");
+          if (!geneSearch.geneSymbol) throw new Error("No gene selected");
+          if (geneSearch.geneSymbol === this.currentGene) return;
+          this.currentGene = geneSearch.geneSymbol;
+          if (this.dom.isoformDiv) this.dom.isoformDiv.remove();
+          this.dom.isoformDiv = holder.append("div");
+          await this.showIsoforms(geneSearch.geneSymbol, opts.genomeObj);
+        } catch (e) {
+          this.dom.errDiv.style("display", "block");
+          sayerror(this.dom.errDiv, "Error: " + (e instanceof Error ? e.message : String(e)));
+        }
+      }
+    });
+  }
+  async showIsoforms(gene, genomeObj) {
+    if (!gene) throw new Error("No gene selected");
+    const data = await dofetch3("genelookup", { body: { genome: genomeObj.name, input: gene, deep: 1 } });
+    if (!data.gmlst?.length) throw new Error(`No isoforms found for ${gene}`);
+    const enstCandidates = data.gmlst.filter((gm) => gm.isoform?.startsWith("ENST"));
+    if (enstCandidates.length === 0) throw new Error(`No Ensembl transcript isoforms found for ${gene}`);
+    const { available } = await dofetch3("termdb/isoformAvailability", {
+      body: {
+        genome: genomeObj.name,
+        dslabel: this.app.vocabApi.vocab.dslabel,
+        isoforms: enstCandidates.map((gm) => gm.isoform)
+      }
+    });
+    const availableSet = new Set(available || []);
+    const enstModels = enstCandidates.filter((gm) => availableSet.has(gm.isoform));
+    if (enstModels.length === 0) throw new Error(`No isoforms with data found for ${gene}`);
+    if (gene !== this.currentGene) return;
+    const div = this.dom.isoformDiv;
+    div.append("div").style("margin-bottom", "8px").style("opacity", 0.65).text(`${gene} \u2014 select isoform(s):`);
+    isoformSelect({
+      holder: div,
+      allgm: enstModels,
+      multiSelect: true,
+      submitLabel: "Create Collection",
+      onMultiSelect: (selected) => {
+        if (selected.length === 1) {
+          this.selectIsoform(selected[0].isoform, gene);
+        } else {
+          this.selectCollection(selected, gene);
+        }
+      }
+    });
+  }
+  getUnit() {
+    return this.app.vocabApi.termdbConfig.queries.isoformExpression?.unit || "TPM";
+  }
+  selectIsoform(isoform, gene) {
+    const name = `${isoform} ${this.getUnit()}`;
+    this.callback({ isoform, gene, name, type: ISOFORM_EXPRESSION });
+  }
+  selectCollection(gms, gene) {
+    const unit = this.getUnit();
+    const termlst = gms.map((gm) => ({
+      id: gm.isoform,
+      name: gm.isoform,
+      type: ISOFORM_EXPRESSION,
+      isoform: gm.isoform
+    }));
+    this.callback({
+      type: "termCollection",
+      isCustom: true,
+      memberType: "numeric",
+      name: `${gene} Isoforms (${unit})`,
+      termlst,
+      propsByTermId: {},
+      isleaf: true
+    });
+  }
+};
+function filterIsoforms(gmlst, availableItems) {
+  const itemSet = new Set(availableItems);
+  return gmlst.filter((gm) => gm.isoform?.startsWith("ENST") && (itemSet.size === 0 || itemSet.has(gm.isoform)));
+}
+
+export {
+  SearchHandler,
+  filterIsoforms
+};
+//# sourceMappingURL=chunk-WET4LPLO.js.map

package/dist/chunk-X5X5T3AJ.js

@@ -0,0 +1,230 @@
+import {
+  keyupEnter
+} from "./chunk-L4TUTGTA.js";
+import {
+  get_bin_label,
+  get_bin_range_equation
+} from "./chunk-S4JLRRKK.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) {
+    this.tw = this.editHandler.tw;
+    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-X5X5T3AJ.js.map

package/dist/chunk-X5X5T3AJ.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\tthis.tw = this.editHandler.tw as NumCustomBins\n\t\tthis.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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+}