@sjcrh/proteinpaint-client 2.209.0 → 2.210.0

package/dist/chunk-IAB2PRIH.js

@@ -0,0 +1,396 @@
+import {
+  addBrushes,
+  addNewBrush
+} from "./chunk-A7OWXDYA.js";
+import {
+  niceNumLabels,
+  violinRenderer
+} from "./chunk-7X6NF7NI.js";
+import {
+  convertUnits,
+  getValueConversionFactor
+} from "./chunk-W5J3LTYS.js";
+import {
+  NumericRangeInput
+} from "./chunk-FXQXCOII.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.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,
+    // axis ticks are labeled in the term's user-facing unit, e.g. years and not days
+    scaleFactor: getValueConversionFactor(tvs.term)
+  });
+  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 holder = num_div.append("div").style("padding-left", "5px");
+  const mafFilterMode = tvs.term.mafFilterMode;
+  if (mafFilterMode == "maf" && tvs.term.child_ids?.length > 1) {
+    const ids = tvs.term.child_ids;
+    const list = ids.slice(0, -1).join(", ") + " and " + ids[ids.length - 1];
+    holder.append("div").style("margin-bottom", "8px").style("font-size", ".9em").style("opacity", 0.7).text(`MAF is computed by summing allelic depths from ${list}`);
+  }
+  const rangeRow = holder.append("div").style("display", "flex").style("align-items", "center").style("column-gap", "5px");
+  const rangeLabel = rangeRow.append("span");
+  brush.equation_div = rangeRow.append("div");
+  brush.rangeInput = new NumericRangeInput(brush.equation_div, range, () => {
+  }, {
+    width: "125px",
+    scaleFactor: getValueConversionFactor(tvs.term)
+  });
+  if (mafFilterMode == "maf") {
+    rangeLabel.text("MAF Range (0-1)");
+    const depthRow = holder.append("div").style("display", "flex").style("align-items", "center").style("column-gap", "5px").style("margin-top", "5px");
+    depthRow.append("span").text("Minimum Total Depth");
+    brush.depthInput = depthRow.append("input").attr("type", "number").attr("min", 1).attr("step", 1).style("width", "125px").property("value", tvs.minAllelicDepth);
+    brush.apply_btn = addApplyButton(holder.append("div").style("margin-top", "10px"));
+  } else if (mafFilterMode == "value") {
+    rangeLabel.text("Range");
+    brush.apply_btn = addApplyButton(rangeRow);
+  } else if (mafFilterMode == "totalDepth" || mafFilterMode == "altDepth") {
+    rangeLabel.text(mafFilterMode == "totalDepth" ? "Total Depth" : "Alt Allele Depth");
+    brush.apply_btn = addApplyButton(rangeRow);
+  } else {
+    rangeLabel.text("Range");
+    brush.apply_btn = addApplyButton(rangeRow);
+  }
+  if (mafFilterMode) brush.rangeInput.getInput().node().focus();
+  function addApplyButton(holder2) {
+    return holder2.append("button").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").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, {
+    scaleFactor: getValueConversionFactor(self.tvs.term)
+  });
+  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.toUnit}.` : ""}`
+    );
+  }
+  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("button").style("margin-left", "10px").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("button").attr("class", "sja_filter_tag_btn sjpp_delete_btn").style("display", self2.num_obj.ranges.length > 1 ? "inline-block" : "none").style("margin-left", "10px").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-IAB2PRIH.js.map

package/dist/chunk-IAB2PRIH.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../filter/tvs.numeric.js"],
+  "sourcesContent": ["import { select } from 'd3-selection'\nimport { scaleLinear } from 'd3'\nimport { addBrushes, addNewBrush } from './tvs.density'\nimport { NumericRangeInput } from '#dom/numericRangeInput'\nimport { convertUnits, getValueConversionFactor } from '#shared/helpers.js'\nimport { violinRenderer } from '../dom/violinRenderer'\nimport { niceNumLabels } from '../dom/niceNumLabels.ts'\n\n/*\n********************** EXPORTED\nhandler:\n\t// internal functions as part of handler\n\tterm_name_gen()\n\tget_pill_label()\n\t\tformat_val_text()\n\tgetSelectRemovePos()\n\tfillMenu()\n\tsetTvsDefaults()\n\n********************** INTERNAL\naddRangeTableNoDensity() // for terms without desnity table, show brushes but without density_plot on blank svg\naddRangeTable() // add table for existing ranges or start with empty_range with brush in center \nenterRange() // add row for each range, for existing readonly and for new or edit, show inputs\nmakeRangeButtons() // add buttons for  Apply / DELETE \nmergeOverlapRanges() // when Apply is pressed, check if ranges are overlapping, if so, merge them\nshowCheckList_numeric() // so checklist of uncomputable values\nvalidateNumericTvs() // validate tvs before sending it to callback\n\n*/\n\nexport const handler = {\n\ttype: 'numeric',\n\tterm_name_gen,\n\tget_pill_label,\n\tgetSelectRemovePos,\n\tfillMenu,\n\tsetTvsDefaults\n}\n\nfunction term_name_gen(d) {\n\tconst name = d.term.name\n\treturn name.length < 26 ? name : '<label title=\"' + name + '\">' + name.substring(0, 24) + '...' + '</label>'\n}\n\nfunction get_pill_label(tvs) {\n\tif (tvs.ranges.length == 1) {\n\t\tconst v = tvs.ranges[0]\n\t\tif ('value' in v) {\n\t\t\t// category\n\t\t\tif (v.label) return { txt: v.label }\n\t\t\tif (tvs.term.values && tvs.term.values[v.value] && tvs.term.values[v.value].label)\n\t\t\t\treturn { txt: tvs.term.values[v.value].label }\n\t\t\tconsole.error(`key \"${v.value}\" not found in values{} of ${tvs.term.name}`)\n\t\t\treturn { txt: v.value }\n\t\t}\n\t\t// numeric range\n\t\treturn { txt: format_val_text(v, tvs.term) }\n\t}\n\t// multiple\n\treturn { txt: tvs.ranges.length + ' intervals' }\n}\n\nexport function format_val_text(range, term) {\n\tconst x = '<span style=\"font-family:Times;font-style:italic;font-size:1em; vertical-align:top\">x</span>'\n\tif (range.startunbounded && range.stopunbounded) {\n\t\tconst inf = (sign = '') =>\n\t\t\t`<span style='vertical-align: middle; font-size:1.1em; line-height: 0.9em'>${sign}\u221E</span>`\n\t\tconst lt = `<span style='vertical-align: top; font-size: 0.9em'>&lt;</span>`\n\t\treturn `<span>${inf('\uFE63')} ${lt} ${x} ${lt} ${inf('\uFE62')}</span>`\n\t}\n\n\t/* logic about value converting:\n\tif term.valueConversion is present, will convert e.g. from day to years. this takes higher priority\n\telse, if range is one-sided, return as is\n\telse, apply nice method to adjust digits. this requires a start-stop range\n\t*/\n\n\tconst vc = term.valueConversion\n\n\tif (range.startunbounded)\n\t\treturn `${x} ${range.stopinclusive ? '&le;' : '&lt;'} ${\n\t\t\tvc ? convertUnits(range.stop, vc.fromUnit, vc.toUnit, vc.scaleFactor) : range.stop\n\t\t}`\n\n\tif (range.stopunbounded)\n\t\treturn `${x} ${range.startinclusive ? '&ge;' : '&gt;'} ${\n\t\t\tvc ? convertUnits(range.start, vc.fromUnit, vc.toUnit, vc.scaleFactor) : range.start\n\t\t}`\n\n\t// range is not unbounded and can apply nice method if there's no vc\n\n\tlet startName, stopName\n\tif (vc) {\n\t\tstartName = convertUnits(range.start, vc.fromUnit, vc.toUnit, vc.scaleFactor)\n\t\tstopName = convertUnits(range.stop, vc.fromUnit, vc.toUnit, vc.scaleFactor)\n\t} else {\n\t\t//Rms excessive number of decimals\n\t\t;[startName, stopName] = niceNumLabels([range.start, range.stop])\n\t}\n\n\treturn `${startName} \n\t\t\t${range.startinclusive ? '&le;' : '&lt;'}\n\t\t\t${x}\n\t\t\t${range.stopinclusive ? '&le;' : '&lt;'}\n\t\t\t${stopName}`\n}\n\nfunction getSelectRemovePos(j, tvs) {\n\treturn j - tvs.ranges.slice(0, j).filter(a => a.start || a.stop).length\n}\n\nasync function fillMenu(self, div, tvs) {\n\t//numerical range div\n\tconst num_parent_div = div.append('div')\n\tself.num_obj = {}\n\n\tself.num_obj.num_div = num_parent_div\n\t\t.append('div')\n\t\t.attr('class', 'num_div')\n\t\t.style('padding', '5px')\n\t\t.style('color', '#000')\n\n\tself.num_obj.plot_size = {\n\t\twidth: 450,\n\t\theight: 100,\n\t\txpad: 10,\n\t\typad: 20,\n\t\tradius: 8\n\t}\n\n\tif (typeof self.opts.vocabApi.getViolinBox == 'function') {\n\t\ttry {\n\t\t\tconst data = await self.opts.vocabApi.getViolinBox(\n\t\t\t\t{\n\t\t\t\t\tplotType: 'violin',\n\t\t\t\t\ttw: { term: tvs.term, q: { mode: 'continuous' } },\n\t\t\t\t\t// 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\n\t\t\t\t\tfilter: self.filter,\n\t\t\t\t\tsvgw: self.num_obj.plot_size.width,\n\t\t\t\t\tradius: self.num_obj.plot_size.radius\n\t\t\t\t},\n\t\t\t\tself.opts.getCategoriesArguments\n\t\t\t)\n\t\t\tif (data.error) throw data.error\n\t\t\tif (data.max === null && data.min === null) {\n\t\t\t\tthrow `No data available under current filter conditions.`\n\t\t\t}\n\t\t\tself.num_obj.density_data = data\n\t\t} catch (err) {\n\t\t\tthrow err\n\t\t}\n\t} else {\n\t\t// frontend vocab lacks this method, return no density data so ui will not show the plot\n\t\t// if the method is added to front vocab, the method must check if sample data is available for the front vocab;\n\t\t// if no sample data then return no density.\n\t\t// such is the case for INFO terms used for variant filtering\n\t\tself.num_obj.density_data = {}\n\t}\n\n\tif (self.num_obj.density_data.error) throw self.num_obj.density_data.error\n\n\tif (!self.num_obj.density_data.charts?.['']?.plots?.[0]?.density?.bins) {\n\t\t// no density data for this term (e.g. bcf numeric info field in a custom filter)\n\t\taddRangeTableNoDensity(self, tvs)\n\t\treturn\n\t}\n\n\tself.vr = new violinRenderer({\n\t\tholder: self.num_obj.num_div,\n\t\trd: self.num_obj.density_data,\n\t\twidth: self.num_obj.plot_size.width,\n\t\tradius: self.num_obj.plot_size.radius,\n\t\theight: self.num_obj.plot_size.height,\n\t\t// axis ticks are labeled in the term's user-facing unit, e.g. years and not days\n\t\tscaleFactor: getValueConversionFactor(tvs.term)\n\t})\n\tself.vr.render()\n\tself.num_obj.svg = self.vr.svg\n\n\tself.num_obj.range_table = self.num_obj.num_div\n\t\t.append('table')\n\t\t.style('table-layout', 'fixed')\n\t\t.style('border-collapse', 'collapse')\n\n\tconst ranges = []\n\n\tfor (const [index, range] of tvs.ranges.entries()) {\n\t\trange.index = index\n\t\tranges.push(range)\n\t}\n\t// add brush_g for tvs brushes\n\tself.num_obj.brush_g = self.vr.brushG.attr('class', 'brush_g')\n\n\tself.num_obj.xscale = self.vr.axisScale\n\n\tself.num_obj.ranges = ranges\n\tself.num_obj.brushes = []\n\taddBrushes(self)\n\taddRangeTable(self)\n\t// const add_range_btn = self.num_obj.num_div\n\t// \t.append('div')\n\t// \t.style('width', '100px')\n\t// \t.attr('class', 'add_range_btn sja_menuoption')\n\t// \t.style('border-radius', '13px')\n\t// \t.style('padding', '7px 6px')\n\t// \t.style('margin', '5px')\n\t// \t.style('margin-left', '20px')\n\t// \t.style('text-align', 'center')\n\t// \t.style('font-size', '.8em')\n\t// \t.text('Add a Range')\n\t// \t.on('click', () => {\n\t// \t\tconst callback = () => addRangeTable(self)\n\t// \t\taddNewBrush(self, ranges.length ? 'end' : 'center', callback)\n\t// \t})\n\n\tif (!ranges.length) {\n\t\tconst callback = () => addRangeTable(self)\n\t\taddNewBrush(self, 'center', callback)\n\t}\n\n\tself.num_obj.brushes.forEach(brush => brush.init())\n\tawait showCheckList_numeric(self, tvs, div)\n}\n\nfunction setTvsDefaults(tvs) {\n\tif (!tvs.ranges) tvs.ranges = []\n}\n\nfunction addRangeTableNoDensity(self, tvs) {\n\tconst termrange = tvs.term.range || {}\n\tconst range = tvs.ranges && tvs.ranges[0] ? tvs.ranges[0] : termrange\n\trange.min = 'min' in tvs.term ? tvs.term.min : null\n\trange.max = 'max' in tvs.term ? tvs.term.max : null\n\tconst num_div = self.num_obj.num_div\n\tnum_div.selectAll('*').remove()\n\n\tconst brush = {}\n\tconst holder = num_div.append('div').style('padding-left', '5px')\n\n\t// a maf filter term carries its mode, which determines the metric filtered and the inputs shown.\n\t// undefined for any other numeric term\n\tconst mafFilterMode = tvs.term.mafFilterMode\n\tif (mafFilterMode == 'maf' && tvs.term.child_ids?.length > 1) {\n\t\t// the fraction sums allele counts across several FORMAT fields (e.g. WGS and WES assays); the\n\t\t// term name alone does not say so\n\t\tconst ids = tvs.term.child_ids\n\t\tconst list = ids.slice(0, -1).join(', ') + ' and ' + ids[ids.length - 1]\n\t\tholder\n\t\t\t.append('div')\n\t\t\t.style('margin-bottom', '8px')\n\t\t\t.style('font-size', '.9em')\n\t\t\t.style('opacity', 0.7)\n\t\t\t.text(`MAF is computed by summing allelic depths from ${list}`)\n\t}\n\n\tconst rangeRow = holder\n\t\t.append('div')\n\t\t.style('display', 'flex')\n\t\t.style('align-items', 'center')\n\t\t.style('column-gap', '5px')\n\tconst rangeLabel = rangeRow.append('span')\n\tbrush.equation_div = rangeRow.append('div')\n\tbrush.rangeInput = new NumericRangeInput(brush.equation_div, range, () => {}, {\n\t\twidth: '125px',\n\t\tscaleFactor: getValueConversionFactor(tvs.term)\n\t})\n\n\tif (mafFilterMode == 'maf') {\n\t\t// maf filter tvs\n\t\t// render maf range input and min allelic depth input\n\t\trangeLabel.text('MAF Range (0-1)')\n\t\tconst depthRow = holder\n\t\t\t.append('div')\n\t\t\t.style('display', 'flex')\n\t\t\t.style('align-items', 'center')\n\t\t\t.style('column-gap', '5px')\n\t\t\t.style('margin-top', '5px')\n\t\tdepthRow.append('span').text('Minimum Total Depth')\n\t\tbrush.depthInput = depthRow\n\t\t\t.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.attr('min', 1)\n\t\t\t.attr('step', 1)\n\t\t\t.style('width', '125px')\n\t\t\t.property('value', tvs.minAllelicDepth)\n\t\tbrush.apply_btn = addApplyButton(holder.append('div').style('margin-top', '10px'))\n\t} else if (mafFilterMode == 'value') {\n\t\t// any numerical FORMAT field read as-is; bounds come from the term's min/max, and no depth input\n\t\trangeLabel.text('Range')\n\t\tbrush.apply_btn = addApplyButton(rangeRow)\n\t} else if (mafFilterMode == 'totalDepth' || mafFilterMode == 'altDepth') {\n\t\t// allelic depth filter tvs; render an integer range input\n\t\trangeLabel.text(mafFilterMode == 'totalDepth' ? 'Total Depth' : 'Alt Allele Depth')\n\t\tbrush.apply_btn = addApplyButton(rangeRow)\n\t} else {\n\t\t// tvs is not part of maf filter\n\t\t// render range input\n\t\trangeLabel.text('Range')\n\t\tbrush.apply_btn = addApplyButton(rangeRow)\n\t}\n\n\t// a maf filter term opens with the range input focused, so a cutoff can be typed right away\n\tif (mafFilterMode) brush.rangeInput.getInput().node().focus()\n\n\tfunction addApplyButton(holder) {\n\t\treturn holder.append('button').text('Apply').on('click', clickApply)\n\t}\n\n\tfunction clickApply() {\n\t\tconst r = brush.rangeInput.getRange()\n\t\tif (!Number.isFinite(r.start) && !Number.isFinite(r.stop)) {\n\t\t\twindow.alert('Invalid range.')\n\t\t\treturn\n\t\t}\n\t\tconst new_tvs = { term: tvs.term, ranges: [r] }\n\t\tif (brush.depthInput) {\n\t\t\tconst minAllelicDepth = Number(brush.depthInput.property('value'))\n\t\t\tif (!Number.isFinite(minAllelicDepth)) {\n\t\t\t\twindow.alert('Minimum allelic depth must be a numeric value.')\n\t\t\t\treturn\n\t\t\t}\n\t\t\tnew_tvs.minAllelicDepth = Math.max(minAllelicDepth, 1)\n\t\t}\n\t\tself.dom.tip.hide()\n\t\tself.opts.callback(new_tvs)\n\t}\n}\n\nfunction addRangeTable(self) {\n\tconst brushes = self.num_obj.brushes\n\n\tconst range_divs = self.num_obj.range_table.selectAll('.range_div').data(brushes) //, d => brushes.indexOf(d))\n\n\trange_divs.exit().each(function () {\n\t\tselect(this).style('opacity', 1).transition().duration(100).style('opacity', 0).remove()\n\t})\n\n\trange_divs\n\t\t.enter()\n\t\t.append('tr')\n\t\t.attr('class', 'range_div')\n\t\t.style('white-space', 'nowrap')\n\t\t.style('padding', '2px')\n\t\t.transition()\n\t\t.duration(200)\n\t\t.each(function (brush, i) {\n\t\t\tenterRange(self, this, brush, i)\n\t\t})\n}\n\nfunction enterRange(self, tr, brush, i) {\n\tif (!brush.range_tr) brush.range_tr = select(tr)\n\tconst range_tr = brush.range_tr\n\tconst xscale = self.num_obj.xscale\n\n\trange_tr\n\t\t.append('td')\n\t\t.style('margin-left', '10px')\n\t\t.style('padding', '3px 10px')\n\t\t.style('font-size', '.9em')\n\t\t.text('Range ' + (i + 1) + ': ')\n\n\tbrush.equation_td = range_tr.append('td').style('width', '150px')\n\t// brush.range stays in the unit the term's values are stored in; only the <input> text is converted\n\tbrush.rangeInput = new NumericRangeInput(brush.equation_td, brush.range, apply, {\n\t\tscaleFactor: getValueConversionFactor(self.tvs.term)\n\t})\n\n\tmakeRangeButtons(self, brush)\n\t// note for empty range\n\tif (i == 0) {\n\t\tself.num_obj.range_table\n\t\t\t.append('tr')\n\t\t\t.attr('class', 'note_tr')\n\t\t\t.append('td')\n\t\t\t.attr('colspan', '3')\n\t\t\t.append('div')\n\t\t\t.style('font-size', '.8em')\n\t\t\t.style('margin-left', '20px')\n\t\t\t.style('font-style', 'italic')\n\t\t\t.style('color', '#888')\n\t\t\t.html('Option 1: Drag the rectangle to select a range. Overlapping ranges will be merged.')\n\t}\n\n\t// A note showing there is also the option to type values to select range\n\tif (i == 0) {\n\t\tself.num_obj.range_table\n\t\t\t.append('tr')\n\t\t\t.attr('class', 'note_tr')\n\t\t\t.append('td')\n\t\t\t.attr('colspan', '3')\n\t\t\t.append('div')\n\t\t\t.style('font-size', '.8em')\n\t\t\t.style('margin-left', '20px')\n\t\t\t.style('font-style', 'italic')\n\t\t\t.style('color', '#888')\n\t\t\t.html(\n\t\t\t\t`Option 2: Type in values to select a range.${\n\t\t\t\t\tself.tvs.term.valueConversion ? ` Values are in the unit of ${self.tvs.term.valueConversion.toUnit}.` : ''\n\t\t\t\t}`\n\t\t\t)\n\t}\n\n\tasync function apply(new_range) {\n\t\ttry {\n\t\t\tbrush.range = new_range\n\t\t\tconst minvalue = self.num_obj.density_data.min\n\t\t\tconst maxvalue = self.num_obj.density_data.max\n\n\t\t\tconst start =\n\t\t\t\tnew_range.value != undefined ? new_range.value : new_range.start != undefined ? new_range.start : minvalue\n\t\t\tconst stop =\n\t\t\t\tnew_range.value != undefined ? new_range.value : new_range.stop != undefined ? new_range.stop : maxvalue\n\t\t\tbrush.elem.call(brush.d3brush).call(brush.d3brush.move, [start, stop].map(xscale))\n\t\t} catch (e) {\n\t\t\twindow.alert(e)\n\t\t}\n\t}\n\n\tfunction makeRangeButtons(self, brush) {\n\t\tconst buttons_td = brush.range_tr.append('td')\n\t\tconst range = brush.range\n\n\t\t//'Apply' button\n\t\tbrush.apply_btn = buttons_td\n\t\t\t.append('button')\n\t\t\t.style('margin-left', '10px')\n\t\t\t.text('Apply')\n\t\t\t.on('click', async () => {\n\t\t\t\tself.dom.tip.hide()\n\t\t\t\tconst new_range = brush.rangeInput.parseRange()\n\t\t\t\tconst new_tvs = JSON.parse(JSON.stringify(self.tvs))\n\t\t\t\tdelete new_tvs.groupset_label\n\t\t\t\t// merge overlapping ranges\n\t\t\t\tif (self.num_obj.ranges.length > 1) new_tvs.ranges = mergeOverlapRanges(self, new_range)\n\t\t\t\telse new_tvs.ranges[range.index] = new_range\n\t\t\t\ttry {\n\t\t\t\t\tvalidateNumericTvs(new_tvs)\n\t\t\t\t\tself.opts.callback(new_tvs)\n\t\t\t\t} catch (ex) {\n\t\t\t\t\talert(ex)\n\t\t\t\t}\n\t\t\t})\n\n\t\t//'Delete' button\n\t\tbuttons_td\n\t\t\t.append('button')\n\t\t\t.attr('class', 'sja_filter_tag_btn sjpp_delete_btn')\n\t\t\t.style('display', self.num_obj.ranges.length > 1 ? 'inline-block' : 'none')\n\t\t\t.style('margin-left', '10px')\n\t\t\t.style('text-transform', 'uppercase')\n\t\t\t.text('Delete')\n\t\t\t.on('click', async () => {\n\t\t\t\tconst new_tvs = JSON.parse(JSON.stringify(self.tvs))\n\t\t\t\tnew_tvs.ranges.splice(range.index, 1)\n\t\t\t\tself.num_obj.ranges.pop()\n\t\t\t\tself.num_obj.brushes.pop()\n\t\t\t\tself.num_obj.num_div.select('.note_tr').remove()\n\t\t\t\taddBrushes(self)\n\t\t\t\taddRangeTable(self)\n\t\t\t\tif (new_tvs.ranges.length) self.opts.callback(new_tvs) //Remove the filter if no ranges\n\t\t\t})\n\t}\n}\n\nfunction mergeOverlapRanges(self, new_range) {\n\tlet ranges = JSON.parse(JSON.stringify(self.tvs.ranges))\n\tlet merged_flag = false\n\tfor (const [i, range] of ranges.entries()) {\n\t\t// skip unannotated categories and same range edits\n\t\tif (!range.value && new_range.index != i) {\n\t\t\tif (new_range.start <= range.start && new_range.stop >= range.stop) {\n\t\t\t\t// if new range is covering any existing range\n\t\t\t\trange.start = new_range.start\n\t\t\t\trange.stop = new_range.stop\n\t\t\t\tmerged_flag = true\n\t\t\t} else if (new_range.start <= range.stop && new_range.stop >= range.stop) {\n\t\t\t\t// if overlapping only at start of new range\n\t\t\t\trange.stop = new_range.stop\n\t\t\t\tmerged_flag = true\n\t\t\t} else if (new_range.stop >= range.start && new_range.start <= range.start) {\n\t\t\t\t// if overlapping only at end of new range\n\t\t\t\trange.start = new_range.start\n\t\t\t\tmerged_flag = true\n\t\t\t} else if (new_range.start >= range.start && new_range.stop <= range.stop) {\n\t\t\t\t//new_range is covered by existing range\n\t\t\t\tmerged_flag = true\n\t\t\t} else if (new_range.startunbounded) {\n\t\t\t\tif (new_range.stop > range.stop) {\n\t\t\t\t\t// if new_range is startunbounded and covering existing range\n\t\t\t\t\trange.stop = new_range.stop\n\t\t\t\t}\n\t\t\t\tdelete range.start\n\t\t\t\trange.startunbounded = true\n\t\t\t\tmerged_flag = true\n\t\t\t} else if (new_range.stopunbounded) {\n\t\t\t\tif (new_range.start < range.start) {\n\t\t\t\t\t// if new_range is stopunbounded and covering existing range\n\t\t\t\t\trange.start = new_range.start\n\t\t\t\t}\n\t\t\t\tdelete range.stop\n\t\t\t\trange.stopunbounded = true\n\t\t\t\tmerged_flag = true\n\t\t\t}\n\t\t}\n\t}\n\n\tif (merged_flag) {\n\t\t// if overlapped and existing range merged then remove existing merged range\n\t\tif (new_range.index <= ranges.length - 1) ranges.splice(new_range.index, 1)\n\t} else {\n\t\t//if not overlapped then add to ranges[]\n\t\tranges = JSON.parse(JSON.stringify(self.tvs.ranges))\n\t\tif (new_range.index) ranges[new_range.index] = new_range\n\t\telse ranges.push(new_range)\n\t}\n\treturn ranges\n}\n\nasync function showCheckList_numeric(self, tvs, div) {\n\tif (!tvs.term.values) {\n\t\t// no special categories available for this term\n\t\treturn\n\t}\n\t// numerical checkbox for unannotated cats\n\tconst values = await self.opts.vocabApi.getNumericUncomputableCategories(tvs.term, self.filter)\n\tconst unannotated_cats = []\n\tconst lst = values?.lst || values\n\tfor (const cat of lst) {\n\t\tconst key = 'key' in cat ? 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+  "names": ["holder", "self", "brush"]
+}