@sjcrh/proteinpaint-client 2.216.0 → 2.217.0

package/dist/chunk-RXAKFDZM.js

@@ -1,302 +0,0 @@
-import {
-  appear2 as appear,
-  axisstyle,
-  bwSetting,
-  disappear2 as disappear,
-  makeNumericAxisConfig,
-  rgb2hex
-} from "./chunk-FIFNXVTS.js";
-import {
-  dofetch3
-} from "./chunk-5MHE7AIV.js";
-import {
-  axisLeft
-} from "./chunk-EZFO5UYD.js";
-import {
-  format,
-  linear
-} from "./chunk-4OLM3KSB.js";
-
-// src/block.tk.bigwig.js
-function bigwigfromtemplate(tk, template) {
-  tk.scale = {};
-  if (template.scale) {
-    for (const k in template.scale) {
-      tk.scale[k] = template.scale[k];
-    }
-  } else {
-    tk.scale.auto = 1;
-  }
-  if (tk.normalize) {
-  } else {
-    tk.normalize = {
-      dividefactor: 1,
-      disable: 1
-    };
-  }
-  tk.barheight = template.height || 50;
-  tk.height_main = tk.toppad + tk.barheight + tk.bottompad;
-  if (!tk.ncolor) tk.ncolor = "#BD005E";
-  if (!tk.ncolor2) tk.ncolor2 = "#5E00BD";
-  if (!tk.pcolor) tk.pcolor = "#005EBD";
-  if (!tk.pcolor2) tk.pcolor2 = "#FA7D00";
-}
-function bigwigmaketk(tk, block) {
-  tk.img = tk.glider.append("image");
-  tk.tklabel.attr("y", tk.barheight / 2);
-  tk.leftaxis = tk.gleft.append("g");
-  tk.config_handle = block.maketkconfighandle(tk).on("click", () => {
-    tk.tkconfigtip.clear().showunder(tk.config_handle.node());
-    bigwigconfigpanel(tk, block, tk.tkconfigtip.d, () => bigwigload(tk, block));
-  });
-}
-async function bigwigload(tk, block) {
-  block.tkcloakon(tk);
-  const par = block.tkarg_q(tk);
-  if (tk.dotplotfactor) par.dotplotfactor = tk.dotplotfactor;
-  if (tk.bgcolor) par.bgcolor = tk.bgcolor;
-  tk.height_main = tk.toppad + tk.barheight + tk.bottompad;
-  tk.img.attr("width", block.width).attr("height", tk.barheight);
-  let errtext;
-  try {
-    let data;
-    if (tk.imgData) {
-      data = tk.imgData;
-    } else {
-      data = await dofetch3("tkbigwig", { method: "POST", body: JSON.stringify(par) });
-    }
-    if (data.error) throw data.error;
-    if (!data.src) throw "data.src missing";
-    tk.tklabel.transition().attr("y", tk.barheight / 2);
-    tk.img.attr("xlink:href", data.src);
-    if (data.minv != void 0) {
-      tk.scale.min = data.minv;
-    }
-    if (data.maxv != void 0) {
-      tk.scale.max = data.maxv;
-    }
-    tk.leftaxis.selectAll("*").remove();
-    if (data.nodata) {
-      throw "No data in view range";
-    }
-    const scale = linear().domain([tk.scale.min, tk.scale.max]).range([tk.barheight, 0]);
-    const axis = axisLeft().scale(scale).tickValues([tk.scale.min, tk.scale.max]);
-    if (tk.integer4axis) {
-      axis.tickFormat(format("d"));
-    }
-    axisstyle({
-      axis: tk.leftaxis.call(axis),
-      color: "black",
-      showline: true
-    });
-  } catch (err) {
-    tk.img.attr("width", 0).attr("height", 0);
-    if (err.stack) {
-      console.log(err.stack);
-    }
-    errtext = typeof err == "string" ? err : err.message;
-  } finally {
-    block.tkcloakoff(tk, { error: errtext });
-    block.block_setheight();
-    for (const panel of tk.subpanels) {
-      bigwigloadsubpanel(tk, block, panel);
-    }
-  }
-}
-async function bigwigloadsubpanel(tk, block, panel) {
-  block.tkcloakon_subpanel(panel);
-  const par = block.tkarg_q(tk);
-  if (tk.dotplotfactor) {
-    par.dotplotfactor = tk.dotplotfactor;
-  }
-  par.width = panel.width;
-  par.rglst = [
-    {
-      chr: panel.chr,
-      start: panel.start,
-      stop: panel.stop,
-      width: panel.width
-    }
-  ];
-  delete par.percentile;
-  delete par.autoscale;
-  panel.img.attr("width", panel.width).attr("height", tk.barheight);
-  let errtext;
-  try {
-    if (tk.imgData) throw "subpanel not supported by imgData yet";
-    const data = await dofetch3("tkbigwig", { method: "POST", body: JSON.stringify(par) });
-    if (data.error) throw data.error;
-    panel.img.attr("xlink:href", data.src);
-  } catch (err) {
-    panel.img.attr("width", 0).attr("height", 0);
-    if (err.stack) {
-      console.log(err.stack);
-    }
-    errtext = typeof err == "string" ? err : err.message;
-  } finally {
-    block.tkcloakoff_subpanel(panel, { error: errtext });
-  }
-}
-function bigwigconfigpanel(tk, block, holder, loader) {
-  const config = {
-    pcolor: {},
-    ncolor: {},
-    pcolor2: {},
-    ncolor2: {},
-    // .row
-    // .lab
-    dotplot: {},
-    // .row
-    dividefactor: {}
-  };
-  {
-    const row = holder.append("div").style("margin-bottom", "15px");
-    row.append("span").html("Height  ");
-    row.append("input").attr("size", 5).property("value", tk.barheight).on("keyup", (event) => {
-      if (event.code != "Enter") return;
-      const s = event.target.value;
-      if (s == "") return;
-      const v = Number.parseInt(s);
-      if (Number.isNaN(v) || v <= 1) {
-        alert("track height must be positive integer");
-        return;
-      }
-      tk.barheight = v;
-      loader(bwSetting.height);
-    });
-  }
-  config.pcolor.row = holder.append("div").style("margin-bottom", "15px");
-  config.pcolor.lab = config.pcolor.row.append("span").text("Positive value color").style("padding-right", "10px");
-  config.pcolor.row.append("input").attr("type", "color").property("value", rgb2hex(tk.pcolor)).on("change", (event) => {
-    tk.pcolor = event.target.value;
-    loader(bwSetting.pcolor);
-  });
-  config.ncolor.row = holder.append("div").style("margin-bottom", "15px");
-  config.ncolor.lab = config.ncolor.row.append("span").text("Negative value color").style("padding-right", "10px");
-  config.ncolor.row.append("input").attr("type", "color").property("value", rgb2hex(tk.ncolor)).on("change", (event) => {
-    tk.ncolor = event.target.value;
-    loader(bwSetting.ncolor);
-  });
-  if (!tk.scale.auto) {
-    config.pcolor2.row = holder.append("div").style("margin-bottom", "15px");
-    config.pcolor2.lab = config.pcolor2.row.append("span").html("&ge;Max color").style("padding-right", "10px");
-    config.pcolor2.row.append("input").attr("type", "color").property("value", rgb2hex(tk.pcolor2)).on("change", (event) => {
-      tk.pcolor2 = event.target.value;
-      loader(bwSetting.pcolor2);
-    });
-    config.ncolor2.row = holder.append("div").style("margin-bottom", "15px");
-    config.ncolor2.lab = config.ncolor2.row.append("span").html("&le;Min color").style("padding-right", "10px");
-    config.ncolor2.row.append("input").attr("type", "color").property("value", rgb2hex(tk.ncolor2)).on("change", (event) => {
-      tk.ncolor2 = event.target.value;
-      loader(bwSetting.ncolor2);
-    });
-  }
-  {
-    const setting = {};
-    if (tk.scale.auto) {
-      setting.auto = 1;
-    } else if (tk.scale.percentile) {
-      setting.percentile = tk.scale.percentile;
-    } else {
-      setting.fixed = { min: tk.scale.min, max: tk.scale.max };
-    }
-    makeNumericAxisConfig({
-      holder: holder.append("div").style("margin-bottom", "15px"),
-      setting,
-      callback: (s) => {
-        if (s.auto) {
-          tk.scale.auto = 1;
-          loader(bwSetting.autoscale);
-          return;
-        }
-        if (s.fixed) {
-          delete tk.scale.auto;
-          delete tk.scale.percentile;
-          tk.scale.max = s.fixed.max;
-          tk.scale.min = s.fixed.min;
-          loader(bwSetting.fixedscale);
-          return;
-        }
-        delete tk.scale.auto;
-        tk.scale.percentile = s.percentile;
-        loader(bwSetting.percentilescale);
-      }
-    });
-  }
-  {
-    config.dotplot.row = holder.append("div").style("margin-bottom", "15px");
-    config.dotplot.row.append("span").html("Dot plot&nbsp;&nbsp;");
-    const s = config.dotplot.row.append("select").on("change", (event) => {
-      const i = event.target.selectedIndex;
-      if (i == 0) {
-        delete tk.dotplotfactor;
-      } else {
-        tk.dotplotfactor = Number.parseInt(event.target.options[i].innerHTML);
-      }
-      loader(i == 0 ? bwSetting.nodotplot : bwSetting.usedotplot);
-    });
-    let o = s.append("option").text("no");
-    if (!tk.dotplotfactor) {
-      o.property("selected", 1);
-    }
-    o = s.append("option").text("5");
-    if (tk.dotplotfactor == 5) {
-      o.property("selected", 1);
-    }
-    o = s.append("option").text("10");
-    if (tk.dotplotfactor == 10) {
-      o.property("selected", 1);
-    }
-    o = s.append("option").text("15");
-    if (tk.dotplotfactor == 15) {
-      o.property("selected", 1);
-    }
-    o = s.append("option").text("20");
-    if (tk.dotplotfactor == 20) {
-      o.property("selected", 1);
-    }
-  }
-  config.dividefactor.row = holder.append("div");
-  {
-    const id = Math.random().toString();
-    const input = config.dividefactor.row.append("input").attr("type", "checkbox").attr("id", id);
-    if (!tk.normalize.disable) {
-      input.property("checked", 1);
-    }
-    config.dividefactor.row.append("label").html("&nbsp;Apply normalization").attr("for", id);
-    const folder = config.dividefactor.row.append("div").style("margin", "5px 10px 0px 20px").style("display", tk.normalize.disable ? "none" : "block");
-    folder.append("span").html("Divide raw value by&nbsp;");
-    const factorinput = folder.append("input").attr("type", "number").style("width", "60px").property("value", tk.normalize.dividefactor).on("keyup", (event) => {
-      if (event.code != "Enter" && event.code != "NumpadEnter") return;
-      const v = event.target.value;
-      if (v <= 0) {
-        return;
-      }
-      tk.normalize.dividefactor = v;
-      loader(bwSetting.usedividefactor);
-    });
-    folder.append("div").text("Enter a value above zero").style("font-size", ".7em").style("color", "#858585");
-    input.on("change", (event) => {
-      if (event.target.checked) {
-        appear(folder);
-        delete tk.normalize.disable;
-        factorinput.property("value", tk.normalize.dividefactor);
-        loader(bwSetting.usedividefactor);
-        return;
-      }
-      disappear(folder);
-      tk.normalize.disable = 1;
-      loader(bwSetting.nodividefactor);
-    });
-  }
-  return config;
-}
-
-export {
-  bigwigfromtemplate,
-  bigwigmaketk,
-  bigwigload,
-  bigwigloadsubpanel,
-  bigwigconfigpanel
-};
-//# sourceMappingURL=chunk-RXAKFDZM.js.map

package/dist/chunk-STDPI4K3.js

@@ -1,281 +0,0 @@
-import {
-  getMclassSorter,
-  getSampleGroupSorter,
-  getSampleSorter,
-  getTermSorter
-} from "./chunk-D4UCM6R7.js";
-import {
-  setRelatedSamples
-} from "./chunk-C2MCQZWH.js";
-import {
-  filterVariantValues,
-  sample_match_termvaluesetting
-} from "./chunk-6WYKPBZI.js";
-import {
-  dtcnv,
-  dtfusionrna,
-  dtgeneexpression,
-  dtsnvindel
-} from "./chunk-EZFO5UYD.js";
-import {
-  __export
-} from "./chunk-HS5PO5ZQ.js";
-
-// plots/matrix/matrix.groups.js
-var matrix_groups_exports = {};
-__export(matrix_groups_exports, {
-  classifyValues: () => classifyValues,
-  getSampleGroups: () => getSampleGroups,
-  getSampleOrder: () => getSampleOrder,
-  getTermOrder: () => getTermOrder,
-  stackSiblingCellsByClass: () => stackSiblingCellsByClass
-});
-function getTermOrder(data) {
-  const s = this.settings.matrix;
-  this.termSorter = getTermSorter(this, s);
-  const termOrder = [];
-  let totalIndex = 0, visibleGrpIndex = 0, numClusterTerms = 0;
-  this.mclassSorter = getMclassSorter(this);
-  this.samplesByAncestorId = /* @__PURE__ */ new Map();
-  const seenAncestorSamples = /* @__PURE__ */ new Set();
-  for (const sd of data.lst) {
-    if (seenAncestorSamples.has(sd.sample)) continue;
-    seenAncestorSamples.add(sd.sample);
-    if (!sd._ref_?.ancestors) continue;
-    for (const a of sd._ref_.ancestors) {
-      const id = a.ancestor_id;
-      if (id === void 0) continue;
-      if (!this.samplesByAncestorId.has(id)) this.samplesByAncestorId.set(id, /* @__PURE__ */ new Set());
-      this.samplesByAncestorId.get(id).add(sd);
-    }
-  }
-  for (const [grpIndex, grp] of this.termGroups.entries()) {
-    const lst = [];
-    for (const [index, tw] of grp.lst.entries()) {
-      const counts = { samples: 0, hits: 0 };
-      const countedSamples = /* @__PURE__ */ new Set();
-      for (const sd of data.lst) {
-        if (countedSamples.has(sd.sample)) continue;
-        countedSamples.add(sd.sample);
-        const anno = sd[tw.$id];
-        if (anno) {
-          const { filteredValues, countedValues, renderedValues } = this.classifyValues(anno, tw, grp, s, sd);
-          anno.filteredValues = filteredValues;
-          anno.countedValues = countedValues;
-          anno.renderedValues = renderedValues;
-          if (anno.countedValues?.length) {
-            const v = tw.term.values?.[anno.value];
-            if (v?.uncountable) continue;
-            counts.samples += 1;
-            counts.hits += anno.countedValues.length;
-            if (tw.q?.mode == "continuous") {
-              const v2 = anno.value;
-              if (!("minval" in counts) || counts.minval > v2) counts.minval = v2;
-              if (!("maxval" in counts) || counts.maxval < v2) counts.maxval = v2;
-            }
-          }
-        }
-      }
-      if (grp.type != "hierCluster" || counts.samples) lst.push({ tw, counts, index });
-      if (grp.type == "hierCluster") numClusterTerms++;
-    }
-    const termSorter = grp.sortTermsBy || grp.type == "hierCluster" ? getTermSorter(this, s, grp) : this.termSorter;
-    const processedLst = lst.filter((t) => {
-      if ("minNumSamples" in t.tw) return t.tw.minNumSamples <= t.counts.samples;
-      if (!grp.settings) return true;
-      return !("minNumSamples" in grp.settings) || t.counts.samples >= grp.settings.minNumSamples;
-    }).sort(termSorter);
-    if (!processedLst.length) continue;
-    for (const [index, t] of processedLst.entries()) {
-      const { tw, counts } = t;
-      const ref = data.refs.byTermId[t.tw.$id] || {};
-      termOrder.push({
-        grp,
-        grpIndex,
-        visibleGrpIndex,
-        tw,
-        index,
-        // rendered index
-        lstIndex: t.index,
-        // as-listed index, before applying term filters
-        processedLst,
-        prevGrpTotalIndex: totalIndex,
-        totalIndex: totalIndex + index,
-        ref,
-        allCounts: counts
-        // note: term label will be assigned after sample counts are known
-        // label: t.tw.label || t.tw.term.name,
-      });
-    }
-    totalIndex += processedLst.length;
-    visibleGrpIndex += 1;
-  }
-  for (const [ancestor_id, samples] of this.samplesByAncestorId.entries()) {
-    if (samples.size < 2) this.samplesByAncestorId.delete(ancestor_id);
-  }
-  this.numTerms = termOrder.length;
-  this.numClusterTerms = numClusterTerms;
-  return termOrder;
-}
-function getSampleGroups(data) {
-  const s = this.settings.matrix;
-  const defaultSampleGrp = {
-    id: this.config.divideBy?.$id,
-    name: this.config.divideBy ? "Not annotated" : "",
-    lst: []
-  };
-  const sampleGroups = /* @__PURE__ */ new Map();
-  const term = this.config.divideBy?.term || {};
-  const $id = this.config.divideBy?.$id || "-";
-  const exclude = this.config.divideBy?.exclude || [];
-  const values = term.values || {};
-  const ref = data.refs.byTermId[$id] || {};
-  for (const row of data.lst) {
-    if ($id in row) {
-      const cell = row[$id];
-      const keys = term.type == "multivalue" && Array.isArray(cell.values) ? cell.values.map((v) => v.key) : [cell.key];
-      for (const key of keys) {
-        const name = key in values && values[key].label ? values[key].label : key;
-        if (!sampleGroups.has(key)) {
-          const grp = {
-            name: `${name}`,
-            // convert to a string
-            id: key,
-            lst: [],
-            tw: this.config.divideBy,
-            legendGroups: {},
-            isExcluded: exclude.includes(key)
-          };
-          if (ref.bins && s.sortSampleGrpsBy == "name") grp.order = ref.bins.findIndex((bin) => bin.name == key);
-          else delete grp.order;
-          sampleGroups.set(key, grp);
-        }
-        sampleGroups.get(key).lst.push(row);
-      }
-    } else {
-      defaultSampleGrp.lst.push(row);
-    }
-  }
-  const sampleGrpsArr = [...sampleGroups.values()];
-  const n = sampleGroups.size;
-  if (n > 100 && sampleGrpsArr.filter((sg) => sg.lst.length < 3).length > 0.8 * n) {
-    const l = s.controlLabels;
-    throw `Did not group ${l.samples} by "${term.name}": too many ${l.sample} groups (${n}), with the majority of groups having <= 2 ${l.samples} per group.`;
-  }
-  if (defaultSampleGrp.lst.length && !sampleGroups.size) {
-    sampleGroups.set(void 0, defaultSampleGrp);
-    sampleGrpsArr.push(...sampleGroups.values());
-  }
-  this.asListedSampleOrder = [];
-  for (const grp of sampleGrpsArr) {
-    this.asListedSampleOrder.push(...grp.lst.map((s2) => s2.sample));
-  }
-  const selectedDictTerms = this.termOrder.filter((t) => t.tw.sortSamples && t.tw.term.type != "geneVariant");
-  const noGrpSampleSorter = getSampleSorter(this, s, data.lst, {
-    skipSorter: (p, tw) => !p.types?.includes("geneVariant") && selectedDictTerms.find((t) => t.tw.$id === tw.$id)
-  });
-  const noGrpSampleOrder = data.lst.sort(noGrpSampleSorter);
-  const allowedSamples = noGrpSampleOrder.slice(0, s.maxSample);
-  const dataFilter = (d) => allowedSamples.includes(d);
-  const hitsPerSample = (t, c) => t + (typeof c == "object" && c.countedValues?.length ? 1 : 0);
-  const countHits = (total, d) => total + (Object.values(d).reduce(hitsPerSample, 0) ? 1 : 0);
-  const grpLstSampleSorter = getSampleSorter(this, s, data.lst);
-  for (const grp of sampleGrpsArr) {
-    grp.lst = grp.lst.filter(dataFilter);
-    grp.totalCountedValues = grp.lst.reduce(countHits, 0);
-    grp.lst.sort(grpLstSampleSorter);
-    if (this.config.chartType == "matrix" && s.sortBySampleAncestry) setRelatedSamples(grp);
-  }
-  const sampleGrpSorter = getSampleGroupSorter(this);
-  return sampleGrpsArr.sort(sampleGrpSorter);
-}
-function getSampleOrder(data) {
-  const s = this.settings.matrix;
-  this.visibleSampleGrps = /* @__PURE__ */ new Set();
-  const sampleOrder = [];
-  let total = 0, numHiddenGrps = 0;
-  for (const [grpIndex, grp] of this.sampleGroups.entries()) {
-    if (!grp.lst.length) continue;
-    if (grp.isExcluded) numHiddenGrps++;
-    let processedLst = grp.lst;
-    for (const [index, row] of processedLst.entries()) {
-      sampleOrder.push({
-        grp,
-        grpIndex: grpIndex - numHiddenGrps,
-        // : this.sampleGroups.length,
-        row,
-        index,
-        prevGrpTotalIndex: total,
-        totalIndex: total + index,
-        totalHtAdjustments: 0,
-        // may be required when transposed???
-        grpTotals: { htAdjustment: 0 },
-        // may be required when transposed???
-        processedLst
-      });
-    }
-    if (!grp.isExcluded) total += processedLst.length;
-    this.visibleSampleGrps.add(grp);
-  }
-  this.unfilteredSampleOrder = sampleOrder;
-  return sampleOrder.filter((so) => !so.grp.isExcluded);
-}
-function classifyValues(anno, tw, grp, s, sample) {
-  let values = "value" in anno ? [anno.value] : anno.values;
-  if (!values) return { filteredValues: null, countedValues: null, renderedValues: null };
-  if (tw.term.type == "geneVariant" && tw.q?.type == "values" && tw.q.variantFilter) {
-    values = filterVariantValues(values, tw.q.variantFilter);
-  }
-  const isSpecific = [tw.valueFilter || grp.valueFilter].filter((v) => v && true);
-  if (isSpecific.length && isSpecific[0].type !== "tvs" && isSpecific[0].type !== "tvslst")
-    throw `unknown matrix value filter type='${isSpecific.type}'`;
-  let filteredValues = !isSpecific.length ? values : values.filter((v) => sample_match_termvaluesetting(v, isSpecific[0], tw.term, sample));
-  const renderedValues = [];
-  if (tw.term.type == "geneVariant" && tw.q?.type == "values") {
-    filteredValues.sort(this.mclassSorter);
-    if (s.cellEncoding == "") renderedValues.push(...filteredValues);
-    else {
-      const sortedFilteredValues = [];
-      for (const dt of [dtcnv, dtsnvindel, dtfusionrna, dtgeneexpression]) {
-        const v = dt == dtgeneexpression ? filteredValues.find((v2) => v2.dt === dt) : filteredValues.find((v2) => v2.dt === dt && v2.class !== "WT" && v2.class !== "Blank");
-        if (v) renderedValues.push(v);
-        const oneDtV = filteredValues.filter((v2) => v2.dt === dt);
-        sortedFilteredValues.push(...oneDtV);
-      }
-      filteredValues = sortedFilteredValues;
-    }
-  } else {
-    renderedValues.push(...filteredValues);
-  }
-  return {
-    filteredValues,
-    countedValues: filteredValues.filter((v) => {
-      if (tw.term.type == "geneVariant") {
-        if (tw.q?.type == "predefined-groupset" || tw.q?.type == "custom-groupset") {
-          const groupset = tw.q.type == "predefined-groupset" ? tw.term.groupsetting.lst[tw.q.predefined_groupset_idx] : tw.q.customset;
-          if (!groupset) throw "groupset not found";
-          const group = groupset.groups[0];
-          if (v != group.name) return false;
-        } else {
-          if (v.class == "WT" || v.class == "Blank" || s.geneVariantCountSamplesSkipMclass.includes(v.class))
-            return false;
-        }
-      }
-      return true;
-    }),
-    renderedValues
-  };
-}
-function stackSiblingCellsByClass(a, b) {
-  return a.class === b.class ? 0 : a.class === "Blank" ? 1 : b.class == "Blank" ? -1 : a.class < b.class ? -1 : 1;
-}
-
-export {
-  getTermOrder,
-  getSampleGroups,
-  getSampleOrder,
-  classifyValues,
-  stackSiblingCellsByClass,
-  matrix_groups_exports
-};
-//# sourceMappingURL=chunk-STDPI4K3.js.map

package/dist/chunk-SYDK5RV5.js

@@ -1,54 +0,0 @@
-import {
-  addGeneSearchbox
-} from "./chunk-FIFNXVTS.js";
-import {
-  Menu
-} from "./chunk-CNFTQSNE.js";
-
-// termdb/handlers/snp.ts
-var SearchHandler = class {
-  init(opts) {
-    this.callback = opts.callback;
-    const geneSearch = addGeneSearchbox({
-      tip: new Menu({ padding: "0px" }),
-      genome: opts.genomeObj,
-      row: opts.holder,
-      searchOnly: "snp",
-      allowVariant: true,
-      callback: () => this.selectSnp(geneSearch)
-    });
-  }
-  async selectSnp(geneSearch) {
-    const { chr, ref, alt, fromWhat } = geneSearch;
-    if (!chr || !ref || !alt || !fromWhat) throw "missing chr, ref, alt, or fromWhat of snp";
-    let start, stop;
-    if (!geneSearch.start && !geneSearch.stop) {
-      if (geneSearch.pos) {
-        start = geneSearch.pos - 1;
-        stop = geneSearch.pos;
-      } else {
-        throw "missing coordinate of snp";
-      }
-    } else {
-      start = geneSearch.start;
-      stop = geneSearch.stop;
-    }
-    const term = {
-      id: fromWhat,
-      chr,
-      start,
-      stop,
-      name: fromWhat,
-      ref,
-      alt: typeof alt == "string" ? [alt] : alt,
-      // is string if input to geneSearch was in variant or hgvs format // TODO: update genesearch.ts to parse alternative alleles from any input format into arrays
-      type: "snp"
-    };
-    this.callback(term);
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-SYDK5RV5.js.map