@sjcrh/proteinpaint-client 2.187.0 → 2.188.0

package/dist/chunk-NMBIT4IK.js

@@ -0,0 +1,46 @@
+// ../shared/utils/dist/src/roundValue.js
+function roundValue(value, digits) {
+  const v = Number(value);
+  if (Number.isInteger(v)) return v;
+  if (Math.abs(v) < 1) return Number(v.toPrecision(digits));
+  return Number(v.toFixed(digits));
+}
+function roundValueAuto(value, format = false, defaultDigits = 2) {
+  if (!value && value != 0) return value;
+  const dp = decimalPlacesUntilFirstNonZero(value);
+  const digits = Math.abs(value) > 1 ? defaultDigits : dp > 0 ? dp + 1 : defaultDigits;
+  if (format) return formatValue(value, digits);
+  return roundValue(value, digits);
+}
+function decimalPlacesUntilFirstNonZero(number) {
+  const numberStr = number.toString();
+  const decimalIndex = numberStr.indexOf(".");
+  if (decimalIndex === -1 || decimalIndex === numberStr.length - 1) {
+    return 0;
+  }
+  let decimalPlaces = 0;
+  for (let i = decimalIndex + 1; i < numberStr.length; i++) {
+    if (numberStr[i] === "0") {
+      decimalPlaces++;
+    } else if (numberStr[i] >= "1" && numberStr[i] <= "9") {
+      break;
+    }
+  }
+  return decimalPlaces;
+}
+function formatValue(value, digits) {
+  const v = Number(value);
+  if (Number.isInteger(v)) return v;
+  const abs = Math.abs(v);
+  if (abs < 1 || abs > 9999) {
+    return abs > 9999 ? v.toPrecision(digits) : Number(v.toPrecision(digits));
+  }
+  return Number(v.toFixed(digits));
+}
+
+export {
+  roundValue,
+  roundValueAuto,
+  decimalPlacesUntilFirstNonZero
+};
+//# sourceMappingURL=chunk-NMBIT4IK.js.map

package/dist/chunk-NMBIT4IK.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../shared/utils/src/roundValue.js"],
+  "sourcesContent": ["/*\nround a value to specified digits\n    - if value is integer, value is returned\n    - if value is a fractional float, round to precision\n    - if value is not a fractional float, round to decimal point\n    - TODO: handle scientific notation\nvalue: given value\ndigits: number of digits to round to\n*/\n\nexport function roundValue(value, digits) {\n\tconst v = Number(value)\n\tif (Number.isInteger(v)) return v\n\tif (Math.abs(v) < 1) return Number(v.toPrecision(digits))\n\treturn Number(v.toFixed(digits))\n}\n\n/** Rounds numbers to the appropriate decimal point\n * if format is true, returns either a number or string in\n * scientific notation.\n *\n * TODO: Review digit logic.\n */\n\nexport function roundValueAuto(value, format = false, defaultDigits = 2) {\n\tif (!value && value != 0) return value\n\tconst dp = decimalPlacesUntilFirstNonZero(value)\n\tconst digits = Math.abs(value) > 1 ? defaultDigits : dp > 0 ? dp + 1 : defaultDigits\n\tif (format) return formatValue(value, digits)\n\treturn roundValue(value, digits)\n}\n\nexport function decimalPlacesUntilFirstNonZero(number) {\n\t// Convert number to string\n\tconst numberStr = number.toString()\n\n\t// Find the position of the decimal point\n\tconst decimalIndex = numberStr.indexOf('.')\n\n\t// If decimal point is not found or number is an integer, return 0\n\tif (decimalIndex === -1 || decimalIndex === numberStr.length - 1) {\n\t\treturn 0\n\t}\n\n\t// Iterate through characters after the decimal point\n\tlet decimalPlaces = 0\n\tfor (let i = decimalIndex + 1; i < numberStr.length; i++) {\n\t\t// Increment the count of decimal places until a non-zero digit is found\n\t\tif (numberStr[i] === '0') {\n\t\t\tdecimalPlaces++\n\t\t} else if (numberStr[i] >= '1' && numberStr[i] <= '9') {\n\t\t\tbreak\n\t\t}\n\t}\n\n\treturn decimalPlaces\n}\n\n/* \nsimple logic to return a number close to original while rounding up decimals.\nsupplements roundValueAuto which rounds 12345 to 1.2e4 which is only suitable for human quick glance but not subsequent computing\n\nTODO:\n10000 and 10001 to 1e4\n0.00001 to 1e-5\n1.00001 to 1\n*/\nexport function roundValue2(value) {\n\tif (!Number.isFinite(value)) return value // not a number\n\tif (Number.isInteger(value)) return value // is integer, do not convert\n\tconst abs = Math.abs(value)\n\tif (abs > 100) return Math.round(value) // 12345.1234 to 12345 (compared to 1.2e4 from roundValueAuto)\n\tif (abs > 10) return Number(value.toFixed(1)) // 99.1234 to 99.1\n\tif (abs > 1) return Number(value.toFixed(2)) // 9.1234 to 9.12\n\tif (abs > 0.1) return Number(value.toFixed(3)) // 0.12345 to 0.123\n\tif (abs > 0.01) return Number(value.toFixed(4)) // 0.012345 to 0.0123\n\treturn value // as is\n}\n\n/** Use to return displayed values in scientific notation\n * Do not use for values intended for calculation later.\n */\nexport function formatValue(value, digits) {\n\tconst v = Number(value)\n\tif (Number.isInteger(v)) return v\n\tconst abs = Math.abs(v)\n\tif (abs < 1 || abs > 9999) {\n\t\t//Number() reverts positive values less than 10^21 to a whole number\n\t\t//To return the value in scientific notation, use toPrecision without Number()\n\t\treturn abs > 9999 ? v.toPrecision(digits) : Number(v.toPrecision(digits))\n\t}\n\treturn Number(v.toFixed(digits))\n}\n"],
+  "mappings": ";AAUO,SAAS,WAAW,OAAO,QAAQ;AACzC,QAAM,IAAI,OAAO,KAAK;AACtB,MAAI,OAAO,UAAU,CAAC,EAAG,QAAO;AAChC,MAAI,KAAK,IAAI,CAAC,IAAI,EAAG,QAAO,OAAO,EAAE,YAAY,MAAM,CAAC;AACxD,SAAO,OAAO,EAAE,QAAQ,MAAM,CAAC;AAChC;AASO,SAAS,eAAe,OAAO,SAAS,OAAO,gBAAgB,GAAG;AACxE,MAAI,CAAC,SAAS,SAAS,EAAG,QAAO;AACjC,QAAM,KAAK,+BAA+B,KAAK;AAC/C,QAAM,SAAS,KAAK,IAAI,KAAK,IAAI,IAAI,gBAAgB,KAAK,IAAI,KAAK,IAAI;AACvE,MAAI,OAAQ,QAAO,YAAY,OAAO,MAAM;AAC5C,SAAO,WAAW,OAAO,MAAM;AAChC;AAEO,SAAS,+BAA+B,QAAQ;AAEtD,QAAM,YAAY,OAAO,SAAS;AAGlC,QAAM,eAAe,UAAU,QAAQ,GAAG;AAG1C,MAAI,iBAAiB,MAAM,iBAAiB,UAAU,SAAS,GAAG;AACjE,WAAO;EACR;AAGA,MAAI,gBAAgB;AACpB,WAAS,IAAI,eAAe,GAAG,IAAI,UAAU,QAAQ,KAAK;AAEzD,QAAI,UAAU,CAAC,MAAM,KAAK;AACzB;IACD,WAAW,UAAU,CAAC,KAAK,OAAO,UAAU,CAAC,KAAK,KAAK;AACtD;IACD;EACD;AAEA,SAAO;AACR;AA0BO,SAAS,YAAY,OAAO,QAAQ;AAC1C,QAAM,IAAI,OAAO,KAAK;AACtB,MAAI,OAAO,UAAU,CAAC,EAAG,QAAO;AAChC,QAAM,MAAM,KAAK,IAAI,CAAC;AACtB,MAAI,MAAM,KAAK,MAAM,MAAM;AAG1B,WAAO,MAAM,OAAO,EAAE,YAAY,MAAM,IAAI,OAAO,EAAE,YAAY,MAAM,CAAC;EACzE;AACA,SAAO,OAAO,EAAE,QAAQ,MAAM,CAAC;AAChC;",
+  "names": []
+}

package/dist/chunk-ONAYJVN2.js

@@ -0,0 +1,217 @@
+import {
+  dofetch,
+  dofetch2
+} from "./chunk-MYWJQRTD.js";
+import {
+  contigNameNoChr2
+} from "./chunk-X7GDCYND.js";
+
+// tracks/hic/data/parseData.ts
+async function hicParseFile(hic, debugmode, errList = []) {
+  if (debugmode) window["hic"] = hic;
+  if (hic.tklst) {
+    const lst = [];
+    for (const t of hic.tklst) {
+      if (!t.type) {
+        errList.push("type missing from one of the tracks accompanying HiC");
+      } else {
+        t.iscustom = true;
+        lst.push(t);
+      }
+    }
+    if (lst.length) {
+      hic.tklst = lst;
+    } else {
+      delete hic.tklst;
+    }
+  }
+  if (hic.enzyme) {
+    if (hic.genome.hicenzymefragment) {
+      let frag = null;
+      for (const f of hic.genome.hicenzymefragment) {
+        if (f.enzyme == hic.enzyme) {
+          frag = f;
+          break;
+        }
+      }
+      if (frag) {
+        hic.enzymefile = frag.file;
+      } else {
+        errList.push("unknown enzyme: " + hic.enzyme);
+        delete hic.enzyme;
+      }
+    } else {
+      errList.push("no enzyme fragment information available for this genome");
+      delete hic.enzyme;
+    }
+  }
+  try {
+    if (hic.sv && hic.sv.file) {
+      const re = await dofetch(hic.hostURL + "/textfile", {
+        method: "POST",
+        body: JSON.stringify({ file: hic.sv.file, jwt: hic.jwt })
+      });
+      const data2 = re.json();
+      const [err2, header, items] = parseSV(data2.text);
+      if (err2) throw { message: "Error parsing SV: " + err2 };
+      hic.sv.header = header;
+      hic.sv.items = items;
+    }
+    const data = await dofetch2("hicstat?" + (hic.file ? "file=" + hic.file : "url=" + hic.url));
+    if (data.error) {
+      errList.push(data.error);
+      return;
+    }
+    const err = hicparsestat(hic, data.out);
+    if (err) throw { message: err };
+  } catch (err) {
+    errList.push(err.message || err);
+    if (err.stack) {
+      console.log(err.stack);
+    }
+  }
+  return hic;
+}
+function parseSV(txt) {
+  const lines = txt.trim().split(/\r?\n/);
+  const [err, header] = parseSVheader(lines[0]);
+  if (err) return ["header error: " + err];
+  const items = [];
+  for (let i = 1; i < lines.length; i++) {
+    const line = lines[i];
+    if (line[0] == "#") continue;
+    const [e, m] = parseSVline(line, header);
+    if (e) return ["line " + (i + 1) + " error: " + e];
+    items.push(m);
+  }
+  return [null, header, items];
+}
+function parseSVheader(line) {
+  const header = line.toLowerCase().split("	");
+  if (header.length <= 1) return "invalid file header for fusions";
+  const htry = (...lst) => {
+    for (const a of lst) {
+      const j = header.indexOf(a);
+      if (j != -1) return j;
+    }
+    return -1;
+  };
+  let i = htry("chr_a", "chr1", "chra");
+  if (i == -1) return "chr_A missing from header";
+  header[i] = "chr1";
+  i = htry("chr_b", "chr2", "chrb");
+  if (i == -1) return "chr_B missing from header";
+  header[i] = "chr2";
+  i = htry("pos_a", "position_a", "position1", "posa");
+  if (i == -1) return "pos_a missing from header";
+  header[i] = "position1";
+  i = htry("pos_b", "position_b", "position2", "posb");
+  if (i == -1) return "pos_b missing from header";
+  header[i] = "position2";
+  i = htry("strand_a", "orta", "orienta");
+  if (i == -1) return "strand_a missing from header";
+  header[i] = "strand1";
+  i = htry("strand_b", "ortb", "orientb");
+  if (i == -1) return "strand_b missing from header";
+  header[i] = "strand2";
+  i = htry("numreadsa");
+  if (i != -1) header[i] = "reads1";
+  i = htry("numreadsb");
+  if (i != -1) header[i] = "reads2";
+  return [null, header];
+}
+function parseSVline(line, header) {
+  const lst = line.split("	");
+  const m = {};
+  for (let j = 0; j < header.length; j++) {
+    m[header[j]] = lst[j];
+  }
+  if (!m.chr1) return ["missing chr1"];
+  if (m.chr1.toLowerCase().indexOf("chr") != 0) {
+    m.chr1 = "chr" + m.chr1;
+  }
+  if (!m.chr2) return ["missing chr2"];
+  if (m.chr2.toLowerCase().indexOf("chr") != 0) {
+    m.chr2 = "chr" + m.chr2;
+  }
+  if (!m.position1) return ["missing position1"];
+  let v = Number.parseInt(m.position1);
+  if (Number.isNaN(v) || v <= 0) return ["position1 invalid value"];
+  m.position1 = v;
+  if (!m.position2) return ["missing position2"];
+  v = Number.parseInt(m.position2);
+  if (Number.isNaN(v) || v <= 0) return ["position2 invalid value"];
+  m.position2 = v;
+  if (m.reads1) {
+    v = Number.parseInt(m.reads1);
+    if (Number.isNaN(v)) return ["reads1 invalid value"];
+    m.reads1 = v;
+  }
+  if (m.reads2) {
+    v = Number.parseInt(m.reads2);
+    if (Number.isNaN(v)) return ["reads2 invalid value"];
+    m.reads2 = v;
+  }
+  return [null, m];
+}
+function hicparsestat(hic, j) {
+  if (!j) return "cannot stat hic file";
+  hic.normalization = j.normalization;
+  hic.version = j.version;
+  if (!j.Chromosomes) return "Chromosomes not found in file stat";
+  if (!Array.isArray(j.chrorder)) return ".chrorder[] missing";
+  if (j.chrorder.length == 0) return ".chrorder[] empty array";
+  hic.chrorder = j.chrorder;
+  if (!j["Base pair-delimited resolutions"]) return "Base pair-delimited resolutions not found in file stat";
+  if (!Array.isArray(j["Base pair-delimited resolutions"])) return "Base pair-delimited resolutions should be array";
+  hic.bpresolution = j["Base pair-delimited resolutions"];
+  if (!j["Fragment-delimited resolutions"]) return "Fragment-delimited resolutions not found in file stat";
+  if (!Array.isArray(j["Fragment-delimited resolutions"])) return "Fragment-delimited resolutions is not array";
+  hic.fragresolution = j["Fragment-delimited resolutions"];
+  const chrlst = [];
+  for (const chr in j.Chromosomes) {
+    chrlst.push(chr);
+  }
+  const [nochrcount, haschrcount] = contigNameNoChr2(hic.genome, chrlst);
+  if (nochrcount + haschrcount == 0) return "chromosome names do not match with genome build";
+  if (nochrcount > 0) {
+    hic.nochr = true;
+    for (let i = 0; i < hic.chrorder.length; i++) hic.chrorder[i] = "chr" + hic.chrorder[i];
+  }
+  hic.chrlst = [];
+  for (const chr of hic.genome.majorchrorder) {
+    const c2 = hic.nochr ? chr.replace("chr", "") : chr;
+    if (chrlst.indexOf(c2) != -1) {
+      hic.chrlst.push(chr);
+    }
+  }
+}
+function hicparsefragdata(items) {
+  const id2coord = /* @__PURE__ */ new Map();
+  let min = null, max;
+  for (const i of items) {
+    if (!i.rest || !i.rest[0]) {
+      return ["items[].rest data problem"];
+    }
+    const id = Number.parseInt(i.rest[0]);
+    if (Number.isNaN(id)) {
+      return [i.start + "." + i.stop + " invalid fragment id: " + i.rest[0]];
+    }
+    id2coord.set(id, [i.start, i.stop]);
+    if (min == null) {
+      min = id;
+      max = id;
+    } else {
+      min = Math.min(min, id);
+      max = Math.max(max, id);
+    }
+  }
+  return [null, id2coord, min, max];
+}
+
+export {
+  hicParseFile,
+  hicparsestat,
+  hicparsefragdata
+};
+//# sourceMappingURL=chunk-ONAYJVN2.js.map

package/dist/chunk-PP7K4R2E.js

@@ -0,0 +1,141 @@
+// plots/proteomeAbundance.ts
+function renderAssayAndCohortRadios({
+  holder,
+  organisms,
+  selectedProteomeDetails,
+  onChange,
+  organismTitle = "Organism",
+  assayTitle = "Assay Type",
+  cohortTitle = "Sample Set"
+}) {
+  const organismEntries = Object.entries(organisms || {});
+  if (!organismEntries.length) {
+    holder.append("div").attr("class", "sja_sharp_border").style("padding", "8px").text("No proteome organisms available.");
+    return {
+      getSelected: () => ({ organism: void 0, assay: void 0, cohort: void 0 })
+    };
+  }
+  const initialProteomeDetails = selectedProteomeDetails || {};
+  const organismRadioName = `sjpp-proteome-organism-${Math.random().toString().slice(-6)}`;
+  const assayRadioName = `sjpp-proteome-assay-${Math.random().toString().slice(-6)}`;
+  const cohortRadioName = `sjpp-proteome-cohort-${Math.random().toString().slice(-6)}`;
+  let selectedOrganism = organisms[initialProteomeDetails.organism || ""] ? initialProteomeDetails.organism : organismEntries[0][0];
+  let selectedAssay = initialProteomeDetails.assay;
+  let selectedCohort = initialProteomeDetails.cohort;
+  holder.append("div").style("margin", "3px 5px").style("padding", "3px 5px").style("font-weight", 600).text(organismTitle);
+  const organismListDiv = holder.append("div").style("margin-bottom", "10px");
+  holder.append("div").style("margin", "3px 5px").style("padding", "3px 5px").style("font-weight", 600).text(assayTitle);
+  const assayListDiv = holder.append("div").style("margin-bottom", "10px");
+  holder.append("div").style("margin", "3px 5px").style("padding", "3px 5px").style("font-weight", 600).text(cohortTitle);
+  const cohortListDiv = holder.append("div").style("max-height", "300px").style("overflow-y", "auto").style("border", "1px solid #ddd").style("border-radius", "4px").style("padding", "5px");
+  for (const [organismKey] of organismEntries) {
+    const organismLabel = organismListDiv.append("label").attr("class", "sja_sharp_border").style("display", "block").style("cursor", "pointer").style("padding", "6px 8px").style("border-radius", "4px");
+    organismLabel.append("input").attr("type", "radio").attr("name", organismRadioName).attr("value", organismKey).property("checked", organismKey === selectedOrganism).style("margin-right", "6px").on("change", () => {
+      selectedOrganism = organismKey;
+      selectedAssay = void 0;
+      selectedCohort = void 0;
+      renderAssayOptions();
+      renderCohortOptions();
+      onChange?.({ organism: selectedOrganism, assay: selectedAssay, cohort: selectedCohort });
+    });
+    organismLabel.append("span").text(organismKey);
+  }
+  renderAssayOptions();
+  renderCohortOptions();
+  onChange?.({ organism: selectedOrganism, assay: selectedAssay, cohort: selectedCohort });
+  return {
+    getSelected: () => ({ organism: selectedOrganism, assay: selectedAssay, cohort: selectedCohort })
+  };
+  function renderAssayOptions() {
+    assayListDiv.selectAll("*").remove();
+    const assays = organisms[selectedOrganism || ""]?.assays || {};
+    const assayEntries = Object.entries(assays);
+    if (!assayEntries.length) {
+      selectedAssay = void 0;
+      selectedCohort = void 0;
+      assayListDiv.append("div").attr("class", "sja_sharp_border").style("padding", "8px").text("No assays available.");
+      return;
+    }
+    if (!selectedAssay || !assays[selectedAssay]) {
+      selectedAssay = assayEntries.some(([k]) => k === initialProteomeDetails.assay) ? initialProteomeDetails.assay : assayEntries[0][0];
+    }
+    for (const [assayKey] of assayEntries) {
+      const assayLabel = assayListDiv.append("label").attr("class", "sja_sharp_border").style("display", "block").style("cursor", "pointer").style("padding", "6px 8px").style("border-radius", "4px");
+      assayLabel.append("input").attr("type", "radio").attr("name", assayRadioName).attr("value", assayKey).property("checked", assayKey === selectedAssay).style("margin-right", "6px").on("change", () => {
+        selectedAssay = assayKey;
+        selectedCohort = void 0;
+        renderCohortOptions();
+        onChange?.({ organism: selectedOrganism, assay: selectedAssay, cohort: selectedCohort });
+      });
+      assayLabel.append("span").text(assayKey);
+    }
+  }
+  function renderCohortOptions() {
+    cohortListDiv.selectAll("*").remove();
+    const cohorts = Object.keys(organisms[selectedOrganism || ""]?.assays?.[selectedAssay || ""]?.cohorts || {});
+    if (!cohorts.length) {
+      selectedCohort = void 0;
+      cohortListDiv.append("div").attr("class", "sja_sharp_border").style("padding", "8px").text("No cohorts available.");
+      return;
+    }
+    if (!selectedCohort || !organisms[selectedOrganism || ""]?.assays?.[selectedAssay || ""]?.cohorts?.[selectedCohort]) {
+      selectedCohort = cohorts.includes(initialProteomeDetails.cohort || "") ? initialProteomeDetails.cohort : cohorts[0];
+    }
+    for (const cohortKey of cohorts) {
+      const cohortLabel = cohortListDiv.append("label").attr("class", "sja_sharp_border").style("display", "block").style("cursor", "pointer").style("padding", "6px 8px").style("border-radius", "4px");
+      cohortLabel.append("input").attr("type", "radio").attr("name", cohortRadioName).attr("value", cohortKey).property("checked", cohortKey === selectedCohort).style("margin-right", "6px").on("change", () => {
+        selectedCohort = cohortKey;
+        onChange?.({ organism: selectedOrganism, assay: selectedAssay, cohort: selectedCohort });
+      });
+      cohortLabel.append("span").text(cohortKey);
+    }
+  }
+}
+function makeChartBtnMenu(holder, chartsInstance) {
+  chartsInstance.dom.tip.clear();
+  const organisms = chartsInstance.state.termdbConfig?.queries?.proteome?.organisms || {};
+  const menuDiv = holder.append("div");
+  let selectedProteomeDetails;
+  const toolsBtnHolder = menuDiv.append("div").style("text-align", "center");
+  const toolsBtn = toolsBtnHolder.append("button").attr("class", "sjpp_apply_btn sja_filter_tag_btn sja_sharp_border").style("display", "block").style("margin", "10px auto 10px").text("Analytics Tools").on("click", () => {
+    const current = selectedProteomeDetails;
+    if (!current?.organism || !current.assay || !current.cohort) return;
+    chartsInstance.dom.tip.hide();
+    chartsInstance.prepPlot({
+      config: {
+        chartType: "ProteomeInput",
+        proteomeDetails: { organism: current.organism, assay: current.assay, cohort: current.cohort },
+        hidePlotFilter: true
+      }
+    });
+  });
+  const syncButtonState = () => {
+    if (selectedProteomeDetails?.cohort) toolsBtn.style("opacity", 1).style("pointer-events", "auto");
+    else toolsBtn.style("opacity", 0.5).style("pointer-events", "none");
+  };
+  renderAssayAndCohortRadios({
+    holder: menuDiv,
+    organisms,
+    onChange: (details) => {
+      selectedProteomeDetails = details;
+      syncButtonState();
+    }
+  });
+  syncButtonState();
+}
+function toTvslstFilter(filterConfig) {
+  if (filterConfig && Array.isArray(filterConfig) && filterConfig.length)
+    return {
+      type: "tvslst",
+      in: true,
+      join: filterConfig.length > 1 ? "and" : "",
+      lst: filterConfig.map((tvs) => ({ type: "tvs", tvs }))
+    };
+}
+
+export {
+  renderAssayAndCohortRadios,
+  makeChartBtnMenu,
+  toTvslstFilter
+};
+//# sourceMappingURL=chunk-PP7K4R2E.js.map

package/dist/chunk-PP7K4R2E.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/proteomeAbundance.ts"],
+  "sourcesContent": ["import type { ProteomeDetails } from '#types'\n\ntype RenderAssayAndCohortRadiosOpts = {\n\tholder: any\n\torganisms: any\n\tselectedProteomeDetails?: Partial<ProteomeDetails>\n\tonChange?: (details: Partial<ProteomeDetails>) => void\n\torganismTitle?: string\n\tassayTitle?: string\n\tcohortTitle?: string\n}\n\nexport function renderAssayAndCohortRadios({\n\tholder,\n\torganisms,\n\tselectedProteomeDetails,\n\tonChange,\n\torganismTitle = 'Organism',\n\tassayTitle = 'Assay Type',\n\tcohortTitle = 'Sample Set'\n}: RenderAssayAndCohortRadiosOpts) {\n\tconst organismEntries = Object.entries(organisms || {})\n\tif (!organismEntries.length) {\n\t\tholder\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_sharp_border')\n\t\t\t.style('padding', '8px')\n\t\t\t.text('No proteome organisms available.')\n\t\treturn {\n\t\t\tgetSelected: () => ({ organism: undefined, assay: undefined, cohort: undefined })\n\t\t}\n\t}\n\n\tconst initialProteomeDetails = selectedProteomeDetails || {}\n\n\tconst organismRadioName = `sjpp-proteome-organism-${Math.random().toString().slice(-6)}`\n\tconst assayRadioName = `sjpp-proteome-assay-${Math.random().toString().slice(-6)}`\n\tconst cohortRadioName = `sjpp-proteome-cohort-${Math.random().toString().slice(-6)}`\n\n\tlet selectedOrganism = organisms[initialProteomeDetails.organism || '']\n\t\t? initialProteomeDetails.organism\n\t\t: organismEntries[0][0]\n\tlet selectedAssay = initialProteomeDetails.assay\n\tlet selectedCohort = initialProteomeDetails.cohort\n\n\tholder\n\t\t.append('div')\n\t\t.style('margin', '3px 5px')\n\t\t.style('padding', '3px 5px')\n\t\t.style('font-weight', 600)\n\t\t.text(organismTitle)\n\tconst organismListDiv = holder.append('div').style('margin-bottom', '10px')\n\n\tholder.append('div').style('margin', '3px 5px').style('padding', '3px 5px').style('font-weight', 600).text(assayTitle)\n\tconst assayListDiv = holder.append('div').style('margin-bottom', '10px')\n\n\tholder\n\t\t.append('div')\n\t\t.style('margin', '3px 5px')\n\t\t.style('padding', '3px 5px')\n\t\t.style('font-weight', 600)\n\t\t.text(cohortTitle)\n\tconst cohortListDiv = holder\n\t\t.append('div')\n\t\t.style('max-height', '300px')\n\t\t.style('overflow-y', 'auto')\n\t\t.style('border', '1px solid #ddd')\n\t\t.style('border-radius', '4px')\n\t\t.style('padding', '5px')\n\n\tfor (const [organismKey] of organismEntries) {\n\t\tconst organismLabel = organismListDiv\n\t\t\t.append('label')\n\t\t\t.attr('class', 'sja_sharp_border')\n\t\t\t.style('display', 'block')\n\t\t\t.style('cursor', 'pointer')\n\t\t\t.style('padding', '6px 8px')\n\t\t\t.style('border-radius', '4px')\n\n\t\torganismLabel\n\t\t\t.append('input')\n\t\t\t.attr('type', 'radio')\n\t\t\t.attr('name', organismRadioName)\n\t\t\t.attr('value', organismKey)\n\t\t\t.property('checked', organismKey === selectedOrganism)\n\t\t\t.style('margin-right', '6px')\n\t\t\t.on('change', () => {\n\t\t\t\tselectedOrganism = organismKey\n\t\t\t\tselectedAssay = undefined\n\t\t\t\tselectedCohort = undefined\n\t\t\t\trenderAssayOptions()\n\t\t\t\trenderCohortOptions()\n\t\t\t\tonChange?.({ organism: selectedOrganism, assay: selectedAssay, cohort: selectedCohort })\n\t\t\t})\n\t\torganismLabel.append('span').text(organismKey)\n\t}\n\n\trenderAssayOptions()\n\trenderCohortOptions()\n\tonChange?.({ organism: selectedOrganism, assay: selectedAssay, cohort: selectedCohort })\n\n\treturn {\n\t\tgetSelected: () => ({ organism: selectedOrganism, assay: selectedAssay, cohort: selectedCohort })\n\t}\n\n\tfunction renderAssayOptions() {\n\t\tassayListDiv.selectAll('*').remove()\n\t\tconst assays = organisms[selectedOrganism || '']?.assays || {}\n\t\tconst assayEntries = Object.entries(assays)\n\t\tif (!assayEntries.length) {\n\t\t\tselectedAssay = undefined\n\t\t\tselectedCohort = undefined\n\t\t\tassayListDiv.append('div').attr('class', 'sja_sharp_border').style('padding', '8px').text('No assays available.')\n\t\t\treturn\n\t\t}\n\n\t\tif (!selectedAssay || !assays[selectedAssay]) {\n\t\t\tselectedAssay = assayEntries.some(([k]) => k === initialProteomeDetails.assay)\n\t\t\t\t? initialProteomeDetails.assay\n\t\t\t\t: assayEntries[0][0]\n\t\t}\n\n\t\tfor (const [assayKey] of assayEntries) {\n\t\t\tconst assayLabel = assayListDiv\n\t\t\t\t.append('label')\n\t\t\t\t.attr('class', 'sja_sharp_border')\n\t\t\t\t.style('display', 'block')\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.style('padding', '6px 8px')\n\t\t\t\t.style('border-radius', '4px')\n\n\t\t\tassayLabel\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'radio')\n\t\t\t\t.attr('name', assayRadioName)\n\t\t\t\t.attr('value', assayKey)\n\t\t\t\t.property('checked', assayKey === selectedAssay)\n\t\t\t\t.style('margin-right', '6px')\n\t\t\t\t.on('change', () => {\n\t\t\t\t\tselectedAssay = assayKey\n\t\t\t\t\tselectedCohort = undefined\n\t\t\t\t\trenderCohortOptions()\n\t\t\t\t\tonChange?.({ organism: selectedOrganism, assay: selectedAssay, cohort: selectedCohort })\n\t\t\t\t})\n\t\t\tassayLabel.append('span').text(assayKey)\n\t\t}\n\t}\n\n\tfunction renderCohortOptions() {\n\t\tcohortListDiv.selectAll('*').remove()\n\t\tconst cohorts = Object.keys(organisms[selectedOrganism || '']?.assays?.[selectedAssay || '']?.cohorts || {})\n\t\tif (!cohorts.length) {\n\t\t\tselectedCohort = undefined\n\t\t\tcohortListDiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_sharp_border')\n\t\t\t\t.style('padding', '8px')\n\t\t\t\t.text('No cohorts available.')\n\t\t\treturn\n\t\t}\n\n\t\tif (\n\t\t\t!selectedCohort ||\n\t\t\t!organisms[selectedOrganism || '']?.assays?.[selectedAssay || '']?.cohorts?.[selectedCohort]\n\t\t) {\n\t\t\tselectedCohort = cohorts.includes(initialProteomeDetails.cohort || '')\n\t\t\t\t? initialProteomeDetails.cohort\n\t\t\t\t: cohorts[0]\n\t\t}\n\n\t\tfor (const cohortKey of cohorts) {\n\t\t\tconst cohortLabel = cohortListDiv\n\t\t\t\t.append('label')\n\t\t\t\t.attr('class', 'sja_sharp_border')\n\t\t\t\t.style('display', 'block')\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.style('padding', '6px 8px')\n\t\t\t\t.style('border-radius', '4px')\n\t\t\tcohortLabel\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'radio')\n\t\t\t\t.attr('name', cohortRadioName)\n\t\t\t\t.attr('value', cohortKey)\n\t\t\t\t.property('checked', cohortKey === selectedCohort)\n\t\t\t\t.style('margin-right', '6px')\n\t\t\t\t.on('change', () => {\n\t\t\t\t\tselectedCohort = cohortKey\n\t\t\t\t\tonChange?.({ organism: selectedOrganism, assay: selectedAssay, cohort: selectedCohort })\n\t\t\t\t})\n\n\t\t\tcohortLabel.append('span').text(cohortKey)\n\t\t}\n\t}\n}\n\nexport function makeChartBtnMenu(holder: any, chartsInstance: any): void {\n\tchartsInstance.dom.tip.clear()\n\tconst organisms = chartsInstance.state.termdbConfig?.queries?.proteome?.organisms || {}\n\tconst menuDiv = holder.append('div')\n\n\tlet selectedProteomeDetails: Partial<ProteomeDetails> | undefined\n\n\tconst toolsBtnHolder = menuDiv.append('div').style('text-align', 'center')\n\tconst toolsBtn = toolsBtnHolder\n\t\t.append('button')\n\t\t.attr('class', 'sjpp_apply_btn sja_filter_tag_btn sja_sharp_border')\n\t\t.style('display', 'block')\n\t\t.style('margin', '10px auto 10px')\n\t\t.text('Analytics Tools')\n\t\t.on('click', () => {\n\t\t\tconst current = selectedProteomeDetails\n\t\t\tif (!current?.organism || !current.assay || !current.cohort) return\n\t\t\tchartsInstance.dom.tip.hide()\n\t\t\tchartsInstance.prepPlot({\n\t\t\t\tconfig: {\n\t\t\t\t\tchartType: 'ProteomeInput',\n\t\t\t\t\tproteomeDetails: { organism: current.organism, assay: current.assay, cohort: current.cohort },\n\t\t\t\t\thidePlotFilter: true\n\t\t\t\t}\n\t\t\t})\n\t\t})\n\n\tconst syncButtonState = () => {\n\t\tif (selectedProteomeDetails?.cohort) toolsBtn.style('opacity', 1).style('pointer-events', 'auto')\n\t\telse toolsBtn.style('opacity', 0.5).style('pointer-events', 'none')\n\t}\n\n\trenderAssayAndCohortRadios({\n\t\tholder: menuDiv,\n\t\torganisms,\n\t\tonChange: details => {\n\t\t\tselectedProteomeDetails = details\n\t\t\tsyncButtonState()\n\t\t}\n\t})\n\n\tsyncButtonState()\n}\n\nexport function toTvslstFilter(filterConfig: any): any {\n\tif (filterConfig && Array.isArray(filterConfig) && filterConfig.length)\n\t\treturn {\n\t\t\ttype: 'tvslst',\n\t\t\tin: true,\n\t\t\tjoin: filterConfig.length > 1 ? 'and' : '',\n\t\t\tlst: filterConfig.map((tvs: any) => ({ type: 'tvs', tvs }))\n\t\t}\n}\n"],
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+  "names": []
+}

package/dist/chunk-PSMFOARZ.js

@@ -0,0 +1,14 @@
+// src/block.lazyload.js
+var Block;
+async function blocklazyload(arg) {
+  if (!Block) {
+    const b = await import("./block-EHZM3FUX.js");
+    Block = b.Block;
+  }
+  return new Block(arg);
+}
+
+export {
+  blocklazyload
+};
+//# sourceMappingURL=chunk-PSMFOARZ.js.map