@sjcrh/proteinpaint-client 2.185.0 → 2.186.0

package/dist/tvs.dt-CY6TOQVB.js

@@ -0,0 +1,37 @@
+import {
+  getDtTermValues,
+  handler
+} from "./chunk-2YC6ZVE4.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-RYCOJY7M.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-G6O3URDN.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-KWM6B3NL.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-I55NLUCQ.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-X4NI4JLQ.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-UWYCEYML.js";
+import "./chunk-7UHUOC6F.js";
+import "./chunk-ZYY54HBU.js";
+import "./chunk-EGWVYY7K.js";
+import "./chunk-AMYSEKPF.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-KSGA62R2.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  getDtTermValues,
+  handler
+};
+//# sourceMappingURL=tvs.dt-CY6TOQVB.js.map

package/dist/tvs.dtcnv.categorical-AYQ432TW.js

@@ -0,0 +1,38 @@
+import {
+  handler
+} from "./chunk-2YC6ZVE4.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-RYCOJY7M.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-G6O3URDN.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-KWM6B3NL.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-I55NLUCQ.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-X4NI4JLQ.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-UWYCEYML.js";
+import "./chunk-7UHUOC6F.js";
+import "./chunk-ZYY54HBU.js";
+import "./chunk-EGWVYY7K.js";
+import "./chunk-AMYSEKPF.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-KSGA62R2.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+
+// filter/tvs.dtcnv.categorical.js
+var handler2 = Object.assign({}, handler, { type: "dtcnv" });
+export {
+  handler2 as handler
+};
+//# sourceMappingURL=tvs.dtcnv.categorical-AYQ432TW.js.map

package/dist/tvs.dtcnv.continuous-XVDL6SG3.js

@@ -0,0 +1,70 @@
+import {
+  handler,
+  renderCnvConfig
+} from "./chunk-2YC6ZVE4.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-RYCOJY7M.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-G6O3URDN.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-KWM6B3NL.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-I55NLUCQ.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-X4NI4JLQ.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-UWYCEYML.js";
+import "./chunk-7UHUOC6F.js";
+import "./chunk-ZYY54HBU.js";
+import "./chunk-EGWVYY7K.js";
+import "./chunk-AMYSEKPF.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-KSGA62R2.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+
+// filter/tvs.dtcnv.continuous.js
+var handler2 = Object.assign({}, handler, { type: "dtcnv", fillMenu, get_pill_label });
+function fillMenu(self, div, tvs) {
+  const dscnv = self.opts.vocabApi.termdbConfig.queries?.cnv;
+  if (!dscnv) throw "cnv query is missing";
+  const cnvDefault = dscnv.cnvCutoffsByGene?.[tvs.term.parentTerm.name] || {
+    cnvMaxLength: dscnv.cnvMaxLength,
+    cnvGainCutoff: dscnv.cnvGainCutoff,
+    cnvLossCutoff: dscnv.cnvLossCutoff
+  };
+  const cnv = Object.assign({}, cnvDefault, tvs);
+  const arg = {
+    holder: div,
+    cnvGainCutoff: cnv.cnvGainCutoff,
+    cnvLossCutoff: cnv.cnvLossCutoff,
+    cnvMaxLength: cnv.cnvMaxLength,
+    cnvWT: cnv.cnvWT,
+    genotypeToggle: true,
+    fractionOverlap: cnv.fractionOverlap,
+    showOverlap: true,
+    callback: (config) => {
+      const new_tvs = structuredClone(tvs);
+      Object.assign(new_tvs, config);
+      new_tvs.continuousCnv = true;
+      self.dom.tip.hide();
+      self.opts.callback(new_tvs);
+    }
+  };
+  renderCnvConfig(arg);
+}
+function get_pill_label(tvs) {
+  return { txt: tvs.cnvWT ? "Wildtype" : "Altered" };
+}
+export {
+  handler2 as handler
+};
+//# sourceMappingURL=tvs.dtcnv.continuous-XVDL6SG3.js.map

package/dist/tvs.dtfusion-V3AV7A6Q.js

@@ -0,0 +1,38 @@
+import {
+  handler
+} from "./chunk-2YC6ZVE4.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-RYCOJY7M.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-G6O3URDN.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-KWM6B3NL.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-I55NLUCQ.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-X4NI4JLQ.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-UWYCEYML.js";
+import "./chunk-7UHUOC6F.js";
+import "./chunk-ZYY54HBU.js";
+import "./chunk-EGWVYY7K.js";
+import "./chunk-AMYSEKPF.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-KSGA62R2.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+
+// filter/tvs.dtfusion.js
+var handler2 = Object.assign({}, handler, { type: "dtfusion" });
+export {
+  handler2 as handler
+};
+//# sourceMappingURL=tvs.dtfusion-V3AV7A6Q.js.map

package/dist/tvs.dtsnvindel-XM3NXIT7.js

@@ -0,0 +1,38 @@
+import {
+  handler
+} from "./chunk-2YC6ZVE4.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-RYCOJY7M.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-G6O3URDN.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-KWM6B3NL.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-I55NLUCQ.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-X4NI4JLQ.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-UWYCEYML.js";
+import "./chunk-7UHUOC6F.js";
+import "./chunk-ZYY54HBU.js";
+import "./chunk-EGWVYY7K.js";
+import "./chunk-AMYSEKPF.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-KSGA62R2.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+
+// filter/tvs.dtsnvindel.js
+var handler2 = Object.assign({}, handler, { type: "dtsnvindel" });
+export {
+  handler2 as handler
+};
+//# sourceMappingURL=tvs.dtsnvindel-XM3NXIT7.js.map

package/dist/tvs.dtsv-Z2GYRINW.js

@@ -0,0 +1,38 @@
+import {
+  handler
+} from "./chunk-2YC6ZVE4.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-RYCOJY7M.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-G6O3URDN.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-KWM6B3NL.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-I55NLUCQ.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-X4NI4JLQ.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-UWYCEYML.js";
+import "./chunk-7UHUOC6F.js";
+import "./chunk-ZYY54HBU.js";
+import "./chunk-EGWVYY7K.js";
+import "./chunk-AMYSEKPF.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-KSGA62R2.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+
+// filter/tvs.dtsv.js
+var handler2 = Object.assign({}, handler, { type: "dtsv" });
+export {
+  handler2 as handler
+};
+//# sourceMappingURL=tvs.dtsv-Z2GYRINW.js.map

package/dist/tvs.samplelst-C4FB63G7.js

@@ -0,0 +1,102 @@
+import {
+  renderTable
+} from "./chunk-2YC6ZVE4.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-RYCOJY7M.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-G6O3URDN.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-KWM6B3NL.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-I55NLUCQ.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-X4NI4JLQ.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-UWYCEYML.js";
+import "./chunk-7UHUOC6F.js";
+import "./chunk-ZYY54HBU.js";
+import "./chunk-EGWVYY7K.js";
+import "./chunk-AMYSEKPF.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-KSGA62R2.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+
+// filter/tvs.samplelst.js
+var handler = {
+  term_name_gen,
+  get_pill_label,
+  fillMenu,
+  getSelectRemovePos,
+  getNegateText(self) {
+    return self.tvs.isnot ? "NOT IN" : "IN";
+  }
+};
+async function fillMenu(self, div, tvs) {
+  tvs = JSON.parse(JSON.stringify(tvs));
+  div.selectAll("*").remove();
+  div = div.append("div");
+  div.style("font-size", "0.8em");
+  for (const field in tvs.term.values) {
+    if (tvs.term.values[field].in === false) continue;
+    addTable(div, tvs, field);
+  }
+  div.append("div").append("div").style("display", "inline-block").style("float", "right").style("padding", "6px 20px").append("button").attr("class", "sjpp_apply_btn sja_filter_tag_btn").text("Apply").on("click", () => {
+    let firstGroup;
+    for (const field in tvs.term.values) {
+      const value = tvs.term.values[field];
+      value.list = value.list.filter((s) => !("checked" in s) || s.checked);
+    }
+    self.opts.callback(tvs);
+  });
+}
+function addTable(div, tvs, field) {
+  div.style("padding", "6px").append("div").style("margin", "10px").style("font-size", "0.8rem").html(`<b> ${field}</b>.`);
+  const value = tvs.term.values[field];
+  const rows = [];
+  for (const sample of value.list) rows.push([{ value: sample.sample }]);
+  const columns = [{ label: "Sample" }];
+  renderTable({
+    rows,
+    columns,
+    div,
+    maxWidth: "30vw",
+    maxHeight: "40vh",
+    noButtonCallback: (index, node) => {
+      value.list[index].checked = node.checked;
+    },
+    striped: false,
+    showHeader: false,
+    selectAll: true
+  });
+}
+function getSelectRemovePos(j) {
+  return j;
+}
+function term_name_gen() {
+  return "Samples";
+}
+function get_pill_label(tvs) {
+  return { txt: getGroupLabel(tvs.term) };
+}
+function getGroupLabel(term) {
+  let n = 0;
+  for (const item in term.values) {
+    if (term.values[item].in === false) continue;
+    n += term.values[item].list.length;
+  }
+  return `${term.name} n=${n}`;
+}
+export {
+  addTable,
+  handler
+};
+//# sourceMappingURL=tvs.samplelst-C4FB63G7.js.map

package/dist/tvs.termCollection-VHTSC2ST.js

@@ -0,0 +1,157 @@
+import {
+  renderTable
+} from "./chunk-2YC6ZVE4.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-RYCOJY7M.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-G6O3URDN.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-KWM6B3NL.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-I55NLUCQ.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-2K5DSRBJ.js";
+import {
+  format_val_text
+} from "./chunk-RTS7NVCS.js";
+import {
+  NumericRangeInput
+} from "./chunk-X4NI4JLQ.js";
+import "./chunk-2O6JF76T.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-UWYCEYML.js";
+import "./chunk-7UHUOC6F.js";
+import "./chunk-ZYY54HBU.js";
+import "./chunk-EGWVYY7K.js";
+import {
+  validateTermCollectionTvs
+} from "./chunk-AMYSEKPF.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-KSGA62R2.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+
+// filter/tvs.termCollection.ts
+var handler = {
+  type: "termCollection",
+  term_name_gen,
+  get_pill_label,
+  getSelectRemovePos,
+  fillMenu,
+  setTvsDefaults
+};
+function setTvsDefaults(tvs) {
+  if (!tvs.ranges) tvs.ranges = [];
+}
+async function fillMenu(self, div, tvs) {
+  tvs = structuredClone(tvs);
+  div.selectAll("*").remove();
+  div = div.append("div").style("font-size", "0.8em");
+  let details = self.opts.vocabApi.termdbConfig.termCollections?.find((c) => c.name === tvs.term.name);
+  if (!details) {
+    if (tvs.term.isCustom && tvs.term.termlst?.length) {
+      details = { termlst: tvs.term.termlst, type: tvs.term.memberType || "numeric" };
+    } else {
+      throw new Error(`No termCollection found for name=${tvs.term.name}`);
+    }
+  }
+  if (details.type !== "numeric") throw new Error("filter only supports numeric term collection");
+  const rangeInput = renderRangeInput(div, tvs, applyRange);
+  const getTableData = await addFilterTable({ holder: div, tvs, details, vocabApi: self.opts.vocabApi });
+  async function applyRange(tvs2) {
+    const tvsProps = getTableData();
+    if (!tvsProps) return;
+    tvs2.term.termlst = tvsProps.termlst;
+    tvs2.term.numerators = tvsProps.numerators;
+    self.dom.tip.hide();
+    self.opts.callback({ term: tvs2.term, ranges: [rangeInput.getRange()] });
+  }
+}
+function renderRangeInput(div, tvs, applyRange) {
+  const termrange = tvs.term.range || {};
+  const range = tvs.ranges && tvs.ranges[0] ? tvs.ranges[0] : termrange;
+  const num_div = div.append("div");
+  num_div.selectAll("*").remove();
+  const table = num_div.append("table");
+  const tr = table.append("tr");
+  tr.append("td").text("Percentage 0 to 100");
+  const equation_td = tr.append("td");
+  range.min = 0;
+  range.max = 100;
+  const rangeInput = new NumericRangeInput(equation_td, range, () => applyRange(tvs));
+  tr.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").text("APPLY").on("click", async () => {
+    rangeInput.parseRange();
+  });
+  return rangeInput;
+}
+async function addFilterTable(opts) {
+  if (!opts.tvs.term.numerators) opts.tvs.term.numerators = opts.tvs.term.termlst.map((t) => t.id);
+  const termlst = opts.tvs.term.termlst || [];
+  const numerators = opts.tvs.term.numerators || [];
+  const rows = [];
+  for (const term of opts.details.termlst) {
+    const numeratorChecked = numerators?.find((tid) => tid === term.id) ? "checked" : "";
+    const denominatorChecked = opts.tvs.term.termlst.find((t) => t.id === term.id) ? "checked" : "";
+    rows.push([
+      { value: term.name },
+      { html: `<input type='checkbox' ${numeratorChecked} />` },
+      { html: `<input type='checkbox' ${denominatorChecked} />` }
+    ]);
+  }
+  const selectedRows = opts.details.termlst.map((term, index) => termlst.find((t) => t.id === term.id) ? index : -1).filter((index) => index !== -1);
+  const columns = [{ label: "Variables" }, { label: "Use in numerator" }, { label: "Use in denominator" }];
+  const tableDiv = opts.holder.append("div");
+  renderTable({
+    rows,
+    columns,
+    div: tableDiv,
+    maxWidth: "30vw",
+    maxHeight: "40vh",
+    striped: false,
+    showHeader: true,
+    selectedRows,
+    columnButtons: void 0,
+    buttons: void 0
+  });
+  return () => {
+    const trs = tableDiv.select("table").select("tbody").node().querySelectorAll("tr");
+    const numerators2 = opts.details.termlst.filter((term, i) => {
+      const checked = trs[i].querySelectorAll("td")[2].querySelector("input")?.checked;
+      return checked === true;
+    }).map((t) => t.id);
+    const termlst2 = opts.details.termlst.filter((term, i) => {
+      const checked = trs[i].querySelectorAll("td")[3].querySelector("input")?.checked;
+      return checked === true;
+    });
+    try {
+      validateTermCollectionTvs(
+        numerators2,
+        termlst2.map((i) => i.id)
+      );
+      return { numerators: numerators2, termlst: termlst2 };
+    } catch (e) {
+      window.alert(e.message);
+    }
+  };
+}
+function getSelectRemovePos(j) {
+  return j;
+}
+function term_name_gen(d) {
+  return `Percentage(${d.term.numerators.join("+")})`;
+}
+function get_pill_label(tvs) {
+  return { txt: format_val_text(tvs.ranges[0], tvs.term) };
+}
+export {
+  addFilterTable,
+  handler
+};
+//# sourceMappingURL=tvs.termCollection-VHTSC2ST.js.map

package/dist/violin-KGGTUQFF.js

@@ -0,0 +1,44 @@
+import {
+  componentInit,
+  getDefaultViolinSettings,
+  getPlotConfig,
+  violinInit
+} from "./chunk-6WBIZXNI.js";
+import "./chunk-MAXFRUGM.js";
+import "./chunk-Q3J3F2NU.js";
+import "./chunk-2YC6ZVE4.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-RYCOJY7M.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-G6O3URDN.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-KWM6B3NL.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-I55NLUCQ.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-X4NI4JLQ.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-UWYCEYML.js";
+import "./chunk-7UHUOC6F.js";
+import "./chunk-ZYY54HBU.js";
+import "./chunk-EGWVYY7K.js";
+import "./chunk-AMYSEKPF.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-KSGA62R2.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  componentInit,
+  getDefaultViolinSettings,
+  getPlotConfig,
+  violinInit
+};
+//# sourceMappingURL=violin-KGGTUQFF.js.map