@sjcrh/proteinpaint-client 2.184.0 → 2.185.0

package/dist/chunk-ST644IDH.js

@@ -0,0 +1,217 @@
+import {
+  dofetch,
+  dofetch2
+} from "./chunk-6ZCHECOT.js";
+import {
+  contigNameNoChr2
+} from "./chunk-AMYSEKPF.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-ST644IDH.js.map

package/dist/chunk-TV74I3Y5.js

@@ -0,0 +1,43 @@
+// ../shared/utils/src/helpers.js
+function isNumeric(n) {
+  const v = typeof n != "string" || n === "" ? n : Number(n);
+  const f = parseFloat(n);
+  return !isNaN(f) && Number.isFinite(v) && v === f;
+}
+function isStrictNumeric(n) {
+  return typeof n === "number" && Number.isFinite(n);
+}
+function convertUnits(v, fromUnit, toUnit, scaleFactor, compact) {
+  if (scaleFactor >= 1) {
+    const toUnitV2 = Math.floor(v * scaleFactor);
+    if (compact) return `${toUnitV2}${toUnit.charAt(0)}`;
+    return `${toUnitV2} ${toUnitV2 > 1 ? toUnit + "s" : ""}`;
+  }
+  const toUnitV = Math.floor(v * scaleFactor);
+  const fromUnitV = Math.ceil(v % (1 / scaleFactor));
+  if (fromUnitV == 0) {
+    if (compact) return `${toUnitV}${toUnit.charAt(0)}`;
+    return `${toUnitV} ${toUnitV > 1 ? toUnit + "s" : ""}`;
+  }
+  if (compact)
+    return `${toUnitV}${toUnit.charAt(0)}${fromUnitV}${fromUnit.charAt(0)}`;
+  return `${toUnitV} ${toUnitV > 1 ? toUnit + "s" : toUnit} ${fromUnitV} ${fromUnitV > 1 ? fromUnit + "s" : fromUnit}`;
+}
+var CustomError = class extends Error {
+  level = "";
+  // '' | 'warn'
+  constructor(message, opts = {}) {
+    super(message);
+    if (opts.name) this.name = opts.name;
+    if (opts.code) this.code = opts.code;
+    if (opts.level) this.level = opts.level;
+  }
+};
+
+export {
+  isNumeric,
+  isStrictNumeric,
+  convertUnits,
+  CustomError
+};
+//# sourceMappingURL=chunk-TV74I3Y5.js.map

package/dist/chunk-TV74I3Y5.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../shared/utils/src/helpers.js"],
+  "sourcesContent": ["/*\nthis is a helper file with a collection of functions to be used in backend and client side code. Here is a list.\n\n1. isNumeric(n)\n2. strictNumeric(n) \n2. convertUnits\n3. TODO - move computepercentile, roundValue, etc here?\n*/\n\n// checks whether given argument n is Numeric, with option to cast from string\nexport function isNumeric(n) {\n\tconst v = typeof n != \"string\" || n === \"\" ? n : Number(n)\n\tconst f = parseFloat(n)\n\treturn !isNaN(f) && Number.isFinite(v) && v === f\n}\n\n// like isNumeric but does not cast from string\nexport function isStrictNumeric(n) {\n\treturn typeof n === \"number\" && Number.isFinite(n)\n}\n\n// converts a value from a unit to another unit\nexport function convertUnits(v, fromUnit, toUnit, scaleFactor, compact) {\n\t// do floor() on toUnit\n\t// do ceil() on fromUnit, in case v is decimal (from violin range selection) and to keep showing integer fromUnit\n\tif (scaleFactor >= 1) {\n\t\tconst toUnitV = Math.floor(v * scaleFactor)\n\t\tif (compact) return `${toUnitV}${toUnit.charAt(0)}`\n\t\treturn `${toUnitV} ${toUnitV > 1 ? toUnit + \"s\" : \"\"}`\n\t}\n\tconst toUnitV = Math.floor(v * scaleFactor)\n\tconst fromUnitV = Math.ceil(v % (1 / scaleFactor))\n\n\tif (fromUnitV == 0) {\n\t\tif (compact) return `${toUnitV}${toUnit.charAt(0)}`\n\t\treturn `${toUnitV} ${toUnitV > 1 ? toUnit + \"s\" : \"\"}`\n\t}\n\n\tif (compact)\n\t\treturn `${toUnitV}${toUnit.charAt(0)}${fromUnitV}${fromUnit.charAt(0)}`\n\treturn `${toUnitV} ${toUnitV > 1 ? toUnit + \"s\" : toUnit} ${fromUnitV} ${\n\t\tfromUnitV > 1 ? fromUnit + \"s\" : fromUnit\n\t}`\n}\n\nexport function deepEqual(x, y) {\n\tif (x === y) {\n\t\treturn true\n\t} else if (\n\t\ttypeof x == \"object\" &&\n\t\tx != null &&\n\t\ttypeof y == \"object\" &&\n\t\ty != null\n\t) {\n\t\tif (Object.keys(x).length != Object.keys(y).length) {\n\t\t\treturn false\n\t\t}\n\n\t\tfor (var prop in x) {\n\t\t\tif (y.hasOwnProperty(prop)) {\n\t\t\t\tif (!deepEqual(x[prop], y[prop])) return false\n\t\t\t} else {\n\t\t\t\treturn false\n\t\t\t}\n\t\t}\n\t\treturn true\n\t} else return false\n}\n\nexport function deepFreeze(obj) {\n\tObject.freeze(obj)\n\t// not using for..in loop, in order to not descend into inherited props/methods\n\tfor (const value of Object.values(obj)) {\n\t\tif (value !== null && typeof value == \"object\") deepFreeze(value)\n\t}\n\treturn obj\n}\n\nexport class CustomError extends Error {\n\tlevel = \"\" // '' | 'warn'\n\n\tconstructor(message, opts = {}) {\n\t\tsuper(message)\n\t\tif (opts.name) this.name = opts.name\n\t\tif (opts.code) this.code = opts.code\n\t\tif (opts.level) this.level = opts.level\n\t}\n}\n"],
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+  "names": ["toUnitV"]
+}