@sjcrh/proteinpaint-client 2.182.0 → 2.183.0

package/dist/chunk-FGMPKWT5.js

@@ -1,371 +0,0 @@
-import {
-  addBrushes,
-  addNewBrush
-} from "./chunk-UWX7W22M.js";
-import {
-  NumericRangeInput,
-  niceNumLabels,
-  violinRenderer
-} from "./chunk-F6V4AYWP.js";
-import {
-  convertUnits
-} from "./chunk-BEWDIM6H.js";
-import {
-  select_default
-} from "./chunk-NDWTN4U5.js";
-
-// filter/tvs.numeric.js
-var handler = {
-  type: "numeric",
-  term_name_gen,
-  get_pill_label,
-  getSelectRemovePos,
-  fillMenu,
-  setTvsDefaults
-};
-function term_name_gen(d) {
-  const name = d.term.name;
-  return name.length < 26 ? name : '<label title="' + name + '">' + name.substring(0, 24) + "...</label>";
-}
-function get_pill_label(tvs) {
-  if (tvs.ranges.length == 1) {
-    const v = tvs.ranges[0];
-    if ("value" in v) {
-      if (v.label) return { txt: v.label };
-      if (tvs.term.values && tvs.term.values[v.value] && tvs.term.values[v.value].label)
-        return { txt: tvs.term.values[v.value].label };
-      console.error(`key "${v.value}" not found in values{} of ${tvs.term.name}`);
-      return { txt: v.value };
-    }
-    return { txt: format_val_text(v, tvs.term) };
-  }
-  return { txt: tvs.ranges.length + " intervals" };
-}
-function format_val_text(range, term) {
-  const x = '<span style="font-family:Times;font-style:italic;font-size:1em; vertical-align:top">x</span>';
-  if (range.startunbounded && range.stopunbounded) {
-    const inf = (sign = "") => `<span style='vertical-align: middle; font-size:1.1em; line-height: 0.9em'>${sign}\u221E</span>`;
-    const lt = `<span style='vertical-align: top; font-size: 0.9em'>&lt;</span>`;
-    return `<span>${inf("\uFE63")} ${lt} ${x} ${lt} ${inf("\uFE62")}</span>`;
-  }
-  const vc = term.valueConversion;
-  if (range.startunbounded)
-    return `${x} ${range.stopinclusive ? "&le;" : "&lt;"} ${vc ? convertUnits(range.stop, vc.fromUnit, vc.toUnit, vc.scaleFactor) : range.stop}`;
-  if (range.stopunbounded)
-    return `${x} ${range.startinclusive ? "&ge;" : "&gt;"} ${vc ? convertUnits(range.start, vc.fromUnit, vc.toUnit, vc.scaleFactor) : range.start}`;
-  let startName, stopName;
-  if (vc) {
-    startName = convertUnits(range.start, vc.fromUnit, vc.toUnit, vc.scaleFactor);
-    stopName = convertUnits(range.stop, vc.fromUnit, vc.toUnit, vc.scaleFactor);
-  } else {
-    ;
-    [startName, stopName] = niceNumLabels([range.start, range.stop]);
-  }
-  return `${startName} 
-			${range.startinclusive ? "&le;" : "&lt;"}
-			${x}
-			${range.stopinclusive ? "&le;" : "&lt;"}
-			${stopName}`;
-}
-function getSelectRemovePos(j, tvs) {
-  return j - tvs.ranges.slice(0, j).filter((a) => a.start || a.stop).length;
-}
-async function fillMenu(self, div, tvs) {
-  const num_parent_div = div.append("div");
-  self.num_obj = {};
-  self.num_obj.num_div = num_parent_div.append("div").attr("class", "num_div").style("padding", "5px").style("color", "#000");
-  self.num_obj.plot_size = {
-    width: 450,
-    height: 100,
-    xpad: 10,
-    ypad: 20,
-    radius: 8
-  };
-  if (typeof self.opts.vocabApi.getViolinBox == "function") {
-    try {
-      const data = await self.opts.vocabApi.getViolinBox(
-        {
-          plotType: "violin",
-          tw: { term: tvs.term, q: { mode: "continuous" } },
-          // must supply this filter and override state filter in function, so the density plot will not be limited to range defined by current numeric tvs but will show whole range
-          filter: self.filter,
-          svgw: self.num_obj.plot_size.width,
-          radius: self.num_obj.plot_size.radius
-        },
-        self.opts.getCategoriesArguments
-      );
-      if (data.error) throw data.error;
-      if (data.max === null && data.min === null) {
-        throw `No data available under current filter conditions.`;
-      }
-      self.num_obj.density_data = data;
-    } catch (err) {
-      throw err;
-    }
-  } else {
-    self.num_obj.density_data = {};
-  }
-  if (self.num_obj.density_data.error) throw self.num_obj.density_data.error;
-  if (!self.num_obj.density_data.charts?.[""]?.plots?.[0]?.density?.bins) {
-    addRangeTableNoDensity(self, tvs);
-    return;
-  }
-  self.vr = new violinRenderer({
-    holder: self.num_obj.num_div,
-    rd: self.num_obj.density_data,
-    width: self.num_obj.plot_size.width,
-    radius: self.num_obj.plot_size.radius,
-    height: self.num_obj.plot_size.height
-  });
-  self.vr.render();
-  self.num_obj.svg = self.vr.svg;
-  self.num_obj.range_table = self.num_obj.num_div.append("table").style("table-layout", "fixed").style("border-collapse", "collapse");
-  const ranges = [];
-  for (const [index, range] of tvs.ranges.entries()) {
-    range.index = index;
-    ranges.push(range);
-  }
-  self.num_obj.brush_g = self.vr.brushG.attr("class", "brush_g");
-  self.num_obj.xscale = self.vr.axisScale;
-  self.num_obj.ranges = ranges;
-  self.num_obj.brushes = [];
-  addBrushes(self);
-  addRangeTable(self);
-  if (!ranges.length) {
-    const callback = () => addRangeTable(self);
-    addNewBrush(self, "center", callback);
-  }
-  self.num_obj.brushes.forEach((brush) => brush.init());
-  await showCheckList_numeric(self, tvs, div);
-}
-function setTvsDefaults(tvs) {
-  if (!tvs.ranges) tvs.ranges = [];
-}
-function addRangeTableNoDensity(self, tvs) {
-  const termrange = tvs.term.range || {};
-  const range = tvs.ranges && tvs.ranges[0] ? tvs.ranges[0] : termrange;
-  range.min = "min" in tvs.term ? tvs.term.min : null;
-  range.max = "max" in tvs.term ? tvs.term.max : null;
-  const num_div = self.num_obj.num_div;
-  num_div.selectAll("*").remove();
-  const brush = {};
-  const table = num_div.append("table").style("padding-left", "5px");
-  const rangeTr = table.append("tr");
-  const rangeLabelTd = rangeTr.append("td");
-  brush.equation_td = rangeTr.append("td");
-  brush.rangeInput = new NumericRangeInput(brush.equation_td, range, () => {
-  }, { width: "125px" });
-  if (self.opts.isMafFilter) {
-    rangeLabelTd.text("MAF Range (0-1)");
-    const depthTr = table.append("tr");
-    depthTr.append("td").text("Minimum Total Depth");
-    brush.depthInput = depthTr.append("td").append("input").attr("type", "number").attr("min", 1).attr("step", 1).style("width", "125px").property("value", tvs.minAllelicDepth);
-    const applyTr = table.append("tr");
-    brush.apply_btn = applyTr.append("td").attr("class", "sja_filter_tag_btn sjpp_apply_btn").style("border-radius", "13px").style("margin-top", "10px").style("font-size", ".8em").style("text-transform", "uppercase").text("apply").on("click", clickApply);
-  } else {
-    rangeLabelTd.text("Range");
-    brush.apply_btn = rangeTr.append("td").attr("class", "sja_filter_tag_btn sjpp_apply_btn").style("border-radius", "13px").style("margin", "5px").style("margin-left", "10px").style("text-align", "center").style("font-size", ".8em").style("text-transform", "uppercase").text("apply").on("click", clickApply);
-  }
-  function clickApply() {
-    const r = brush.rangeInput.getRange();
-    if (!Number.isFinite(r.start) && !Number.isFinite(r.stop)) {
-      window.alert("Invalid range.");
-      return;
-    }
-    const new_tvs = { term: tvs.term, ranges: [r] };
-    if (brush.depthInput) {
-      const minAllelicDepth = Number(brush.depthInput.property("value"));
-      if (!Number.isFinite(minAllelicDepth)) {
-        window.alert("Minimum allelic depth must be a numeric value.");
-        return;
-      }
-      new_tvs.minAllelicDepth = Math.max(minAllelicDepth, 1);
-    }
-    self.dom.tip.hide();
-    self.opts.callback(new_tvs);
-  }
-}
-function addRangeTable(self) {
-  const brushes = self.num_obj.brushes;
-  const range_divs = self.num_obj.range_table.selectAll(".range_div").data(brushes);
-  range_divs.exit().each(function() {
-    select_default(this).style("opacity", 1).transition().duration(100).style("opacity", 0).remove();
-  });
-  range_divs.enter().append("tr").attr("class", "range_div").style("white-space", "nowrap").style("padding", "2px").transition().duration(200).each(function(brush, i) {
-    enterRange(self, this, brush, i);
-  });
-}
-function enterRange(self, tr, brush, i) {
-  if (!brush.range_tr) brush.range_tr = select_default(tr);
-  const range_tr = brush.range_tr;
-  const xscale = self.num_obj.xscale;
-  range_tr.append("td").append("td").style("display", "inline-block").style("margin-left", "10px").style("padding", "3px 10px").style("font-size", ".9em").text("Range " + (i + 1) + ": ");
-  brush.equation_td = range_tr.append("td").style("width", "150px");
-  brush.rangeInput = new NumericRangeInput(brush.equation_td, brush.range, apply);
-  makeRangeButtons(self, brush);
-  if (i == 0) {
-    self.num_obj.range_table.append("tr").attr("class", "note_tr").append("td").attr("colspan", "3").append("div").style("font-size", ".8em").style("margin-left", "20px").style("font-style", "italic").style("color", "#888").html("Option 1: Drag the rectangle to select a range. Overlapping ranges will be merged.");
-  }
-  if (i == 0) {
-    self.num_obj.range_table.append("tr").attr("class", "note_tr").append("td").attr("colspan", "3").append("div").style("font-size", ".8em").style("margin-left", "20px").style("font-style", "italic").style("color", "#888").html(
-      `Option 2: Type in values to select a range.${self.tvs.term.valueConversion ? ` Values are in the unit of ${self.tvs.term.valueConversion.fromUnit}.` : ""}`
-    );
-  }
-  async function apply(new_range) {
-    try {
-      brush.range = new_range;
-      const minvalue = self.num_obj.density_data.min;
-      const maxvalue = self.num_obj.density_data.max;
-      const start = new_range.value != void 0 ? new_range.value : new_range.start != void 0 ? new_range.start : minvalue;
-      const stop = new_range.value != void 0 ? new_range.value : new_range.stop != void 0 ? new_range.stop : maxvalue;
-      brush.elem.call(brush.d3brush).call(brush.d3brush.move, [start, stop].map(xscale));
-    } catch (e) {
-      window.alert(e);
-    }
-  }
-  function makeRangeButtons(self2, brush2) {
-    const buttons_td = brush2.range_tr.append("td");
-    const range = brush2.range;
-    brush2.apply_btn = buttons_td.append("td").attr("class", "sja_filter_tag_btn sjpp_apply_btn").style("border-radius", "13px").style("margin", "5px").style("margin-left", "10px").style("text-align", "center").style("font-size", ".8em").style("text-transform", "uppercase").text("apply").on("click", async () => {
-      self2.dom.tip.hide();
-      const new_range = brush2.rangeInput.parseRange();
-      const new_tvs = JSON.parse(JSON.stringify(self2.tvs));
-      delete new_tvs.groupset_label;
-      if (self2.num_obj.ranges.length > 1) new_tvs.ranges = mergeOverlapRanges(self2, new_range);
-      else new_tvs.ranges[range.index] = new_range;
-      try {
-        validateNumericTvs(new_tvs);
-        self2.opts.callback(new_tvs);
-      } catch (ex) {
-        alert(ex);
-      }
-    });
-    buttons_td.append("td").attr("class", "sja_filter_tag_btn sjpp_delete_btn").style("border-radius", "13px").style("display", self2.num_obj.ranges.length > 1 ? "inline-block" : "none").style("margin", "5px").style("margin-left", "10px").style("text-align", "center").style("font-size", ".8em").style("text-transform", "uppercase").text("Delete").on("click", async () => {
-      const new_tvs = JSON.parse(JSON.stringify(self2.tvs));
-      new_tvs.ranges.splice(range.index, 1);
-      self2.num_obj.ranges.pop();
-      self2.num_obj.brushes.pop();
-      self2.num_obj.num_div.select(".note_tr").remove();
-      addBrushes(self2);
-      addRangeTable(self2);
-      if (new_tvs.ranges.length) self2.opts.callback(new_tvs);
-    });
-  }
-}
-function mergeOverlapRanges(self, new_range) {
-  let ranges = JSON.parse(JSON.stringify(self.tvs.ranges));
-  let merged_flag = false;
-  for (const [i, range] of ranges.entries()) {
-    if (!range.value && new_range.index != i) {
-      if (new_range.start <= range.start && new_range.stop >= range.stop) {
-        range.start = new_range.start;
-        range.stop = new_range.stop;
-        merged_flag = true;
-      } else if (new_range.start <= range.stop && new_range.stop >= range.stop) {
-        range.stop = new_range.stop;
-        merged_flag = true;
-      } else if (new_range.stop >= range.start && new_range.start <= range.start) {
-        range.start = new_range.start;
-        merged_flag = true;
-      } else if (new_range.start >= range.start && new_range.stop <= range.stop) {
-        merged_flag = true;
-      } else if (new_range.startunbounded) {
-        if (new_range.stop > range.stop) {
-          range.stop = new_range.stop;
-        }
-        delete range.start;
-        range.startunbounded = true;
-        merged_flag = true;
-      } else if (new_range.stopunbounded) {
-        if (new_range.start < range.start) {
-          range.start = new_range.start;
-        }
-        delete range.stop;
-        range.stopunbounded = true;
-        merged_flag = true;
-      }
-    }
-  }
-  if (merged_flag) {
-    if (new_range.index <= ranges.length - 1) ranges.splice(new_range.index, 1);
-  } else {
-    ranges = JSON.parse(JSON.stringify(self.tvs.ranges));
-    if (new_range.index) ranges[new_range.index] = new_range;
-    else ranges.push(new_range);
-  }
-  return ranges;
-}
-async function showCheckList_numeric(self, tvs, div) {
-  if (!tvs.term.values) {
-    return;
-  }
-  const values = await self.opts.vocabApi.getNumericUncomputableCategories(tvs.term, self.filter);
-  const unannotated_cats = [];
-  const lst = values?.lst || values;
-  for (const cat of lst) {
-    const key = "key" in cat ? cat.key : cat.value;
-    if (!("key" in cat)) cat.key = key;
-    if (!("value" in cat)) cat.value = key;
-    if (key in tvs.term.values) {
-      cat.label = tvs.term.values[key].label;
-      unannotated_cats.push(cat);
-    }
-  }
-  const sortedVals = unannotated_cats.sort((a, b) => {
-    return b.samplecount - a.samplecount;
-  });
-  const unanno_div = div.append("div").style("padding", "5px").style("color", "#000");
-  const callback = (indexes) => {
-    try {
-      const new_tvs = JSON.parse(JSON.stringify(tvs));
-      delete new_tvs.groupset_label;
-      new_tvs.ranges = [
-        ...new_tvs.ranges.filter((r) => !("value" in r)),
-        ...indexes.map((i) => ({ value: sortedVals[i].value, label: sortedVals[i].label }))
-      ];
-      self.dom.tip.hide();
-      if (new_tvs.ranges.length == 0) throw "select at least one range or category";
-      if (JSON.parse(JSON.stringify(tvs) != new_tvs)) {
-        try {
-          validateNumericTvs(new_tvs);
-        } catch (e) {
-          window.alert(e);
-          return;
-        }
-        self.opts.callback(new_tvs);
-      }
-    } catch (e) {
-      window.alert(e);
-    }
-  };
-  const values_table = self.makeValueTable(unanno_div, tvs, sortedVals, callback).node();
-}
-function validateNumericTvs(tvs) {
-  if (!tvs.term) throw "tvs.term is not defined";
-  if (!tvs.ranges) throw `.values[] missing for a term ${tvs.term.name}`;
-  if (!Array.isArray(tvs.ranges)) throw `.values[] is not an array for a term ${tvs.term.name}`;
-  if (!tvs.ranges.length) throw `no categories selected for ${tvs.term.name}`;
-  for (const range of tvs.ranges) {
-    if (range.value != void 0) {
-      if (!range.label) throw `.label missing for special category for a term ${tvs.term.name}`;
-    } else {
-      if (range.startunbounded) {
-        if (range.stopunbounded) throw `both start & stop are unbounded for a term ${tvs.term.name}`;
-        if (!Number.isFinite(range.stop)) throw `.stop undefined when start is unbounded for a term ${tvs.term.name}`;
-      } else if (range.stopunbounded) {
-        if (!Number.isFinite(range.start)) throw `.start undefined when stop is unbounded for a term ${tvs.term.name}`;
-      } else {
-        if (!Number.isFinite(range.start))
-          throw `.start undefined when start is not unbounded for a term ${tvs.term.name}`;
-        if (!Number.isFinite(range.stop)) throw `.stop undefined when stop is not unbounded for a term ${tvs.term.name}`;
-        if (range.start >= range.stop) throw `.start is not lower than stop for a term ${tvs.term.name}`;
-      }
-    }
-  }
-}
-
-export {
-  handler,
-  format_val_text
-};
-//# sourceMappingURL=chunk-FGMPKWT5.js.map

package/dist/chunk-FK4MYVW2.js

@@ -1,261 +0,0 @@
-import {
-  hierCluster_renderers_exports
-} from "./chunk-TIQPSXFJ.js";
-import {
-  hierCluster_interactivity_exports
-} from "./chunk-E6DRQJJT.js";
-import {
-  Matrix
-} from "./chunk-IBTPGSYI.js";
-import {
-  filterJoin,
-  getNormalRoot
-} from "./chunk-7FEHI46K.js";
-import {
-  clusterMethodLst,
-  distanceMethodLst,
-  dofetch3
-} from "./chunk-TCPU43TU.js";
-import {
-  deepEqual,
-  getCompInit
-} from "./chunk-MVTCBVSX.js";
-import {
-  TermTypes2Dt
-} from "./chunk-MDL2HG3N.js";
-import {
-  colorScaleMap
-} from "./chunk-IGEQI6MR.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-FK4MYVW2.js.map