@teselagen/sequence-utils 0.3.32-beta.2 → 0.3.32

package/findOrfsInPlasmid.d.ts

@@ -7,5 +7,5 @@ export default function findOrfsInPlasmid(sequence: any, circular: any, minimumO
     forward: any;
     annotationTypePlural: string;
     isOrf: boolean;
-    id: string;
+    id: any;
 }[];

package/getOrfsFromSequence.d.ts

@@ -16,5 +16,5 @@ export default function getOrfsFromSequence(options: any): {
     forward: any;
     annotationTypePlural: string;
     isOrf: boolean;
-    id: string;
+    id: any;
 }[];

package/index.cjs

@@ -3667,15 +3667,307 @@ const getFeatureToColorMap = /* @__PURE__ */ __name(({ includeHidden } = {}) =>
 const getFeatureTypes = /* @__PURE__ */ __name(({ includeHidden } = {}) => filter(getMergedFeatureMap(), (f) => includeHidden ? true : !f.isHidden).map(
   (f) => f.name
 ), "getFeatureTypes");
-const urlAlphabet = "useandom-26T198340PX75pxJACKVERYMINDBUSHWOLF_GQZbfghjklqvwyzrict";
-let nanoid = /* @__PURE__ */ __name((size = 21) => {
-  let id = "";
-  let bytes = crypto.getRandomValues(new Uint8Array(size |= 0));
-  while (size--) {
-    id += urlAlphabet[bytes[size] & 63];
-  }
-  return id;
-}, "nanoid");
+function getDefaultExportFromCjs(x) {
+  return x && x.__esModule && Object.prototype.hasOwnProperty.call(x, "default") ? x["default"] : x;
+}
+__name(getDefaultExportFromCjs, "getDefaultExportFromCjs");
+var lib = { exports: {} };
+var randomFromSeed;
+var hasRequiredRandomFromSeed;
+function requireRandomFromSeed() {
+  if (hasRequiredRandomFromSeed) return randomFromSeed;
+  hasRequiredRandomFromSeed = 1;
+  var seed = 1;
+  function getNextValue() {
+    seed = (seed * 9301 + 49297) % 233280;
+    return seed / 233280;
+  }
+  __name(getNextValue, "getNextValue");
+  function setSeed(_seed_) {
+    seed = _seed_;
+  }
+  __name(setSeed, "setSeed");
+  randomFromSeed = {
+    nextValue: getNextValue,
+    seed: setSeed
+  };
+  return randomFromSeed;
+}
+__name(requireRandomFromSeed, "requireRandomFromSeed");
+var alphabet_1;
+var hasRequiredAlphabet;
+function requireAlphabet() {
+  if (hasRequiredAlphabet) return alphabet_1;
+  hasRequiredAlphabet = 1;
+  var randomFromSeed2 = requireRandomFromSeed();
+  var ORIGINAL = "0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ_-";
+  var alphabet;
+  var previousSeed;
+  var shuffled;
+  function reset() {
+    shuffled = false;
+  }
+  __name(reset, "reset");
+  function setCharacters(_alphabet_) {
+    if (!_alphabet_) {
+      if (alphabet !== ORIGINAL) {
+        alphabet = ORIGINAL;
+        reset();
+      }
+      return;
+    }
+    if (_alphabet_ === alphabet) {
+      return;
+    }
+    if (_alphabet_.length !== ORIGINAL.length) {
+      throw new Error("Custom alphabet for shortid must be " + ORIGINAL.length + " unique characters. You submitted " + _alphabet_.length + " characters: " + _alphabet_);
+    }
+    var unique = _alphabet_.split("").filter(function(item, ind, arr) {
+      return ind !== arr.lastIndexOf(item);
+    });
+    if (unique.length) {
+      throw new Error("Custom alphabet for shortid must be " + ORIGINAL.length + " unique characters. These characters were not unique: " + unique.join(", "));
+    }
+    alphabet = _alphabet_;
+    reset();
+  }
+  __name(setCharacters, "setCharacters");
+  function characters(_alphabet_) {
+    setCharacters(_alphabet_);
+    return alphabet;
+  }
+  __name(characters, "characters");
+  function setSeed(seed) {
+    randomFromSeed2.seed(seed);
+    if (previousSeed !== seed) {
+      reset();
+      previousSeed = seed;
+    }
+  }
+  __name(setSeed, "setSeed");
+  function shuffle() {
+    if (!alphabet) {
+      setCharacters(ORIGINAL);
+    }
+    var sourceArray = alphabet.split("");
+    var targetArray = [];
+    var r = randomFromSeed2.nextValue();
+    var characterIndex;
+    while (sourceArray.length > 0) {
+      r = randomFromSeed2.nextValue();
+      characterIndex = Math.floor(r * sourceArray.length);
+      targetArray.push(sourceArray.splice(characterIndex, 1)[0]);
+    }
+    return targetArray.join("");
+  }
+  __name(shuffle, "shuffle");
+  function getShuffled() {
+    if (shuffled) {
+      return shuffled;
+    }
+    shuffled = shuffle();
+    return shuffled;
+  }
+  __name(getShuffled, "getShuffled");
+  function lookup(index) {
+    var alphabetShuffled = getShuffled();
+    return alphabetShuffled[index];
+  }
+  __name(lookup, "lookup");
+  function get2() {
+    return alphabet || ORIGINAL;
+  }
+  __name(get2, "get");
+  alphabet_1 = {
+    get: get2,
+    characters,
+    seed: setSeed,
+    lookup,
+    shuffled: getShuffled
+  };
+  return alphabet_1;
+}
+__name(requireAlphabet, "requireAlphabet");
+var randomByteBrowser;
+var hasRequiredRandomByteBrowser;
+function requireRandomByteBrowser() {
+  if (hasRequiredRandomByteBrowser) return randomByteBrowser;
+  hasRequiredRandomByteBrowser = 1;
+  var crypto = typeof window === "object" && (window.crypto || window.msCrypto);
+  var randomByte;
+  if (!crypto || !crypto.getRandomValues) {
+    randomByte = /* @__PURE__ */ __name(function(size) {
+      var bytes = [];
+      for (var i = 0; i < size; i++) {
+        bytes.push(Math.floor(Math.random() * 256));
+      }
+      return bytes;
+    }, "randomByte");
+  } else {
+    randomByte = /* @__PURE__ */ __name(function(size) {
+      return crypto.getRandomValues(new Uint8Array(size));
+    }, "randomByte");
+  }
+  randomByteBrowser = randomByte;
+  return randomByteBrowser;
+}
+__name(requireRandomByteBrowser, "requireRandomByteBrowser");
+var format_browser;
+var hasRequiredFormat_browser;
+function requireFormat_browser() {
+  if (hasRequiredFormat_browser) return format_browser;
+  hasRequiredFormat_browser = 1;
+  format_browser = /* @__PURE__ */ __name(function(random, alphabet, size) {
+    var mask = (2 << Math.log(alphabet.length - 1) / Math.LN2) - 1;
+    var step = -~(1.6 * mask * size / alphabet.length);
+    var id = "";
+    while (true) {
+      var bytes = random(step);
+      var i = step;
+      while (i--) {
+        id += alphabet[bytes[i] & mask] || "";
+        if (id.length === +size) return id;
+      }
+    }
+  }, "format_browser");
+  return format_browser;
+}
+__name(requireFormat_browser, "requireFormat_browser");
+var generate_1;
+var hasRequiredGenerate;
+function requireGenerate() {
+  if (hasRequiredGenerate) return generate_1;
+  hasRequiredGenerate = 1;
+  var alphabet = requireAlphabet();
+  var random = requireRandomByteBrowser();
+  var format = /* @__PURE__ */ requireFormat_browser();
+  function generate(number) {
+    var loopCounter = 0;
+    var done;
+    var str = "";
+    while (!done) {
+      str = str + format(random, alphabet.get(), 1);
+      done = number < Math.pow(16, loopCounter + 1);
+      loopCounter++;
+    }
+    return str;
+  }
+  __name(generate, "generate");
+  generate_1 = generate;
+  return generate_1;
+}
+__name(requireGenerate, "requireGenerate");
+var build_1;
+var hasRequiredBuild;
+function requireBuild() {
+  if (hasRequiredBuild) return build_1;
+  hasRequiredBuild = 1;
+  var generate = requireGenerate();
+  requireAlphabet();
+  var REDUCE_TIME = 1567752802062;
+  var version = 7;
+  var counter;
+  var previousSeconds;
+  function build(clusterWorkerId) {
+    var str = "";
+    var seconds = Math.floor((Date.now() - REDUCE_TIME) * 1e-3);
+    if (seconds === previousSeconds) {
+      counter++;
+    } else {
+      counter = 0;
+      previousSeconds = seconds;
+    }
+    str = str + generate(version);
+    str = str + generate(clusterWorkerId);
+    if (counter > 0) {
+      str = str + generate(counter);
+    }
+    str = str + generate(seconds);
+    return str;
+  }
+  __name(build, "build");
+  build_1 = build;
+  return build_1;
+}
+__name(requireBuild, "requireBuild");
+var isValid;
+var hasRequiredIsValid;
+function requireIsValid() {
+  if (hasRequiredIsValid) return isValid;
+  hasRequiredIsValid = 1;
+  var alphabet = requireAlphabet();
+  function isShortId(id) {
+    if (!id || typeof id !== "string" || id.length < 6) {
+      return false;
+    }
+    var nonAlphabetic = new RegExp("[^" + alphabet.get().replace(/[|\\{}()[\]^$+*?.-]/g, "\\$&") + "]");
+    return !nonAlphabetic.test(id);
+  }
+  __name(isShortId, "isShortId");
+  isValid = isShortId;
+  return isValid;
+}
+__name(requireIsValid, "requireIsValid");
+var clusterWorkerIdBrowser;
+var hasRequiredClusterWorkerIdBrowser;
+function requireClusterWorkerIdBrowser() {
+  if (hasRequiredClusterWorkerIdBrowser) return clusterWorkerIdBrowser;
+  hasRequiredClusterWorkerIdBrowser = 1;
+  clusterWorkerIdBrowser = 0;
+  return clusterWorkerIdBrowser;
+}
+__name(requireClusterWorkerIdBrowser, "requireClusterWorkerIdBrowser");
+var hasRequiredLib;
+function requireLib() {
+  if (hasRequiredLib) return lib.exports;
+  hasRequiredLib = 1;
+  (function(module2) {
+    var alphabet = requireAlphabet();
+    var build = requireBuild();
+    var isValid2 = requireIsValid();
+    var clusterWorkerId = requireClusterWorkerIdBrowser() || 0;
+    function seed(seedValue) {
+      alphabet.seed(seedValue);
+      return module2.exports;
+    }
+    __name(seed, "seed");
+    function worker(workerId) {
+      clusterWorkerId = workerId;
+      return module2.exports;
+    }
+    __name(worker, "worker");
+    function characters(newCharacters) {
+      if (newCharacters !== void 0) {
+        alphabet.characters(newCharacters);
+      }
+      return alphabet.shuffled();
+    }
+    __name(characters, "characters");
+    function generate() {
+      return build(clusterWorkerId);
+    }
+    __name(generate, "generate");
+    module2.exports = generate;
+    module2.exports.generate = generate;
+    module2.exports.seed = seed;
+    module2.exports.worker = worker;
+    module2.exports.characters = characters;
+    module2.exports.isValid = isValid2;
+  })(lib);
+  return lib.exports;
+}
+__name(requireLib, "requireLib");
+var shortid$1;
+var hasRequiredShortid;
+function requireShortid() {
+  if (hasRequiredShortid) return shortid$1;
+  hasRequiredShortid = 1;
+  shortid$1 = requireLib();
+  return shortid$1;
+}
+__name(requireShortid, "requireShortid");
+var shortidExports = requireShortid();
+const shortid = /* @__PURE__ */ getDefaultExportFromCjs(shortidExports);
 function cutSequenceByRestrictionEnzyme(pSequence, circular, restrictionEnzyme) {
   if (restrictionEnzyme.forwardRegex.length === 0 || restrictionEnzyme.reverseRegex.length === 0) {
     const returnArray = [];
@@ -3883,7 +4175,7 @@ function cutSequence(forwardRegExpPattern, restrictionEnzyme, sequence, circular
       }
       const overhangBps = getSequenceWithinRange(cutRange, originalSequence);
       restrictionCutSite = {
-        id: nanoid(),
+        id: shortid(),
         start,
         end,
         topSnipPosition,
@@ -3941,7 +4233,7 @@ function computeDigestFragments({
   });
   if (!circular && cutsites.length) {
     sortedCutsites.push({
-      id: "seqTerm_" + nanoid(),
+      id: "seqTerm_" + shortid(),
       start: 0,
       end: 0,
       overhangBps: "",
@@ -4075,10 +4367,6 @@ function getDigestFragsForSeqAndEnzymes({
   });
 }
 __name(getDigestFragsForSeqAndEnzymes, "getDigestFragsForSeqAndEnzymes");
-function getDefaultExportFromCjs(x) {
-  return x && x.__esModule && Object.prototype.hasOwnProperty.call(x, "default") ? x["default"] : x;
-}
-__name(getDefaultExportFromCjs, "getDefaultExportFromCjs");
 var jsondiffpatch_umd$1 = { exports: {} };
 var empty = {};
 var hasRequiredEmpty;
@@ -8677,10 +8965,10 @@ function tidyUpAnnotation(_annotation, {
     annotation.name = "Untitled annotation";
   }
   if (provideNewIdsForAnnotations) {
-    annotation.id = nanoid();
+    annotation.id = shortid();
   }
   if (!annotation.id && annotation.id !== 0 && !doNotProvideIdsForAnnotations) {
-    annotation.id = nanoid();
+    annotation.id = shortid();
     messages.push(
       "Unable to detect valid ID for annotation, setting ID to " + annotation.id
     );
@@ -8924,7 +9212,7 @@ function tidyUpSequenceData(pSeqData, options = {}) {
         if (item.id || item.id === 0) {
           itemId = item.id;
         } else {
-          itemId = nanoid();
+          itemId = shortid();
           if (!doNotProvideIdsForAnnotations) {
             item.id = itemId;
           }
@@ -17494,7 +17782,7 @@ function generateAnnotation(start, end, maxLength) {
   return __spreadProps(__spreadValues({}, range), {
     name: getRandomInt(0, 1e5).toString(),
     type: "misc_feature",
-    id: nanoid(),
+    id: shortid(),
     forward: Math.random() > 0.5,
     notes: {}
   });
@@ -17617,7 +17905,7 @@ function getOrfsFromSequence(options) {
           forward,
           annotationTypePlural: "orfs",
           isOrf: true,
-          id: nanoid()
+          id: shortid()
         });
       }
     }

package/index.js

@@ -3665,15 +3665,307 @@ const getFeatureToColorMap = /* @__PURE__ */ __name(({ includeHidden } = {}) =>
 const getFeatureTypes = /* @__PURE__ */ __name(({ includeHidden } = {}) => filter(getMergedFeatureMap(), (f) => includeHidden ? true : !f.isHidden).map(
   (f) => f.name
 ), "getFeatureTypes");
-const urlAlphabet = "useandom-26T198340PX75pxJACKVERYMINDBUSHWOLF_GQZbfghjklqvwyzrict";
-let nanoid = /* @__PURE__ */ __name((size = 21) => {
-  let id = "";
-  let bytes = crypto.getRandomValues(new Uint8Array(size |= 0));
-  while (size--) {
-    id += urlAlphabet[bytes[size] & 63];
-  }
-  return id;
-}, "nanoid");
+function getDefaultExportFromCjs(x) {
+  return x && x.__esModule && Object.prototype.hasOwnProperty.call(x, "default") ? x["default"] : x;
+}
+__name(getDefaultExportFromCjs, "getDefaultExportFromCjs");
+var lib = { exports: {} };
+var randomFromSeed;
+var hasRequiredRandomFromSeed;
+function requireRandomFromSeed() {
+  if (hasRequiredRandomFromSeed) return randomFromSeed;
+  hasRequiredRandomFromSeed = 1;
+  var seed = 1;
+  function getNextValue() {
+    seed = (seed * 9301 + 49297) % 233280;
+    return seed / 233280;
+  }
+  __name(getNextValue, "getNextValue");
+  function setSeed(_seed_) {
+    seed = _seed_;
+  }
+  __name(setSeed, "setSeed");
+  randomFromSeed = {
+    nextValue: getNextValue,
+    seed: setSeed
+  };
+  return randomFromSeed;
+}
+__name(requireRandomFromSeed, "requireRandomFromSeed");
+var alphabet_1;
+var hasRequiredAlphabet;
+function requireAlphabet() {
+  if (hasRequiredAlphabet) return alphabet_1;
+  hasRequiredAlphabet = 1;
+  var randomFromSeed2 = requireRandomFromSeed();
+  var ORIGINAL = "0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ_-";
+  var alphabet;
+  var previousSeed;
+  var shuffled;
+  function reset() {
+    shuffled = false;
+  }
+  __name(reset, "reset");
+  function setCharacters(_alphabet_) {
+    if (!_alphabet_) {
+      if (alphabet !== ORIGINAL) {
+        alphabet = ORIGINAL;
+        reset();
+      }
+      return;
+    }
+    if (_alphabet_ === alphabet) {
+      return;
+    }
+    if (_alphabet_.length !== ORIGINAL.length) {
+      throw new Error("Custom alphabet for shortid must be " + ORIGINAL.length + " unique characters. You submitted " + _alphabet_.length + " characters: " + _alphabet_);
+    }
+    var unique = _alphabet_.split("").filter(function(item, ind, arr) {
+      return ind !== arr.lastIndexOf(item);
+    });
+    if (unique.length) {
+      throw new Error("Custom alphabet for shortid must be " + ORIGINAL.length + " unique characters. These characters were not unique: " + unique.join(", "));
+    }
+    alphabet = _alphabet_;
+    reset();
+  }
+  __name(setCharacters, "setCharacters");
+  function characters(_alphabet_) {
+    setCharacters(_alphabet_);
+    return alphabet;
+  }
+  __name(characters, "characters");
+  function setSeed(seed) {
+    randomFromSeed2.seed(seed);
+    if (previousSeed !== seed) {
+      reset();
+      previousSeed = seed;
+    }
+  }
+  __name(setSeed, "setSeed");
+  function shuffle() {
+    if (!alphabet) {
+      setCharacters(ORIGINAL);
+    }
+    var sourceArray = alphabet.split("");
+    var targetArray = [];
+    var r = randomFromSeed2.nextValue();
+    var characterIndex;
+    while (sourceArray.length > 0) {
+      r = randomFromSeed2.nextValue();
+      characterIndex = Math.floor(r * sourceArray.length);
+      targetArray.push(sourceArray.splice(characterIndex, 1)[0]);
+    }
+    return targetArray.join("");
+  }
+  __name(shuffle, "shuffle");
+  function getShuffled() {
+    if (shuffled) {
+      return shuffled;
+    }
+    shuffled = shuffle();
+    return shuffled;
+  }
+  __name(getShuffled, "getShuffled");
+  function lookup(index) {
+    var alphabetShuffled = getShuffled();
+    return alphabetShuffled[index];
+  }
+  __name(lookup, "lookup");
+  function get2() {
+    return alphabet || ORIGINAL;
+  }
+  __name(get2, "get");
+  alphabet_1 = {
+    get: get2,
+    characters,
+    seed: setSeed,
+    lookup,
+    shuffled: getShuffled
+  };
+  return alphabet_1;
+}
+__name(requireAlphabet, "requireAlphabet");
+var randomByteBrowser;
+var hasRequiredRandomByteBrowser;
+function requireRandomByteBrowser() {
+  if (hasRequiredRandomByteBrowser) return randomByteBrowser;
+  hasRequiredRandomByteBrowser = 1;
+  var crypto = typeof window === "object" && (window.crypto || window.msCrypto);
+  var randomByte;
+  if (!crypto || !crypto.getRandomValues) {
+    randomByte = /* @__PURE__ */ __name(function(size) {
+      var bytes = [];
+      for (var i = 0; i < size; i++) {
+        bytes.push(Math.floor(Math.random() * 256));
+      }
+      return bytes;
+    }, "randomByte");
+  } else {
+    randomByte = /* @__PURE__ */ __name(function(size) {
+      return crypto.getRandomValues(new Uint8Array(size));
+    }, "randomByte");
+  }
+  randomByteBrowser = randomByte;
+  return randomByteBrowser;
+}
+__name(requireRandomByteBrowser, "requireRandomByteBrowser");
+var format_browser;
+var hasRequiredFormat_browser;
+function requireFormat_browser() {
+  if (hasRequiredFormat_browser) return format_browser;
+  hasRequiredFormat_browser = 1;
+  format_browser = /* @__PURE__ */ __name(function(random, alphabet, size) {
+    var mask = (2 << Math.log(alphabet.length - 1) / Math.LN2) - 1;
+    var step = -~(1.6 * mask * size / alphabet.length);
+    var id = "";
+    while (true) {
+      var bytes = random(step);
+      var i = step;
+      while (i--) {
+        id += alphabet[bytes[i] & mask] || "";
+        if (id.length === +size) return id;
+      }
+    }
+  }, "format_browser");
+  return format_browser;
+}
+__name(requireFormat_browser, "requireFormat_browser");
+var generate_1;
+var hasRequiredGenerate;
+function requireGenerate() {
+  if (hasRequiredGenerate) return generate_1;
+  hasRequiredGenerate = 1;
+  var alphabet = requireAlphabet();
+  var random = requireRandomByteBrowser();
+  var format = /* @__PURE__ */ requireFormat_browser();
+  function generate(number) {
+    var loopCounter = 0;
+    var done;
+    var str = "";
+    while (!done) {
+      str = str + format(random, alphabet.get(), 1);
+      done = number < Math.pow(16, loopCounter + 1);
+      loopCounter++;
+    }
+    return str;
+  }
+  __name(generate, "generate");
+  generate_1 = generate;
+  return generate_1;
+}
+__name(requireGenerate, "requireGenerate");
+var build_1;
+var hasRequiredBuild;
+function requireBuild() {
+  if (hasRequiredBuild) return build_1;
+  hasRequiredBuild = 1;
+  var generate = requireGenerate();
+  requireAlphabet();
+  var REDUCE_TIME = 1567752802062;
+  var version = 7;
+  var counter;
+  var previousSeconds;
+  function build(clusterWorkerId) {
+    var str = "";
+    var seconds = Math.floor((Date.now() - REDUCE_TIME) * 1e-3);
+    if (seconds === previousSeconds) {
+      counter++;
+    } else {
+      counter = 0;
+      previousSeconds = seconds;
+    }
+    str = str + generate(version);
+    str = str + generate(clusterWorkerId);
+    if (counter > 0) {
+      str = str + generate(counter);
+    }
+    str = str + generate(seconds);
+    return str;
+  }
+  __name(build, "build");
+  build_1 = build;
+  return build_1;
+}
+__name(requireBuild, "requireBuild");
+var isValid;
+var hasRequiredIsValid;
+function requireIsValid() {
+  if (hasRequiredIsValid) return isValid;
+  hasRequiredIsValid = 1;
+  var alphabet = requireAlphabet();
+  function isShortId(id) {
+    if (!id || typeof id !== "string" || id.length < 6) {
+      return false;
+    }
+    var nonAlphabetic = new RegExp("[^" + alphabet.get().replace(/[|\\{}()[\]^$+*?.-]/g, "\\$&") + "]");
+    return !nonAlphabetic.test(id);
+  }
+  __name(isShortId, "isShortId");
+  isValid = isShortId;
+  return isValid;
+}
+__name(requireIsValid, "requireIsValid");
+var clusterWorkerIdBrowser;
+var hasRequiredClusterWorkerIdBrowser;
+function requireClusterWorkerIdBrowser() {
+  if (hasRequiredClusterWorkerIdBrowser) return clusterWorkerIdBrowser;
+  hasRequiredClusterWorkerIdBrowser = 1;
+  clusterWorkerIdBrowser = 0;
+  return clusterWorkerIdBrowser;
+}
+__name(requireClusterWorkerIdBrowser, "requireClusterWorkerIdBrowser");
+var hasRequiredLib;
+function requireLib() {
+  if (hasRequiredLib) return lib.exports;
+  hasRequiredLib = 1;
+  (function(module2) {
+    var alphabet = requireAlphabet();
+    var build = requireBuild();
+    var isValid2 = requireIsValid();
+    var clusterWorkerId = requireClusterWorkerIdBrowser() || 0;
+    function seed(seedValue) {
+      alphabet.seed(seedValue);
+      return module2.exports;
+    }
+    __name(seed, "seed");
+    function worker(workerId) {
+      clusterWorkerId = workerId;
+      return module2.exports;
+    }
+    __name(worker, "worker");
+    function characters(newCharacters) {
+      if (newCharacters !== void 0) {
+        alphabet.characters(newCharacters);
+      }
+      return alphabet.shuffled();
+    }
+    __name(characters, "characters");
+    function generate() {
+      return build(clusterWorkerId);
+    }
+    __name(generate, "generate");
+    module2.exports = generate;
+    module2.exports.generate = generate;
+    module2.exports.seed = seed;
+    module2.exports.worker = worker;
+    module2.exports.characters = characters;
+    module2.exports.isValid = isValid2;
+  })(lib);
+  return lib.exports;
+}
+__name(requireLib, "requireLib");
+var shortid$1;
+var hasRequiredShortid;
+function requireShortid() {
+  if (hasRequiredShortid) return shortid$1;
+  hasRequiredShortid = 1;
+  shortid$1 = requireLib();
+  return shortid$1;
+}
+__name(requireShortid, "requireShortid");
+var shortidExports = requireShortid();
+const shortid = /* @__PURE__ */ getDefaultExportFromCjs(shortidExports);
 function cutSequenceByRestrictionEnzyme(pSequence, circular, restrictionEnzyme) {
   if (restrictionEnzyme.forwardRegex.length === 0 || restrictionEnzyme.reverseRegex.length === 0) {
     const returnArray = [];
@@ -3881,7 +4173,7 @@ function cutSequence(forwardRegExpPattern, restrictionEnzyme, sequence, circular
       }
       const overhangBps = getSequenceWithinRange(cutRange, originalSequence);
       restrictionCutSite = {
-        id: nanoid(),
+        id: shortid(),
         start,
         end,
         topSnipPosition,
@@ -3939,7 +4231,7 @@ function computeDigestFragments({
   });
   if (!circular && cutsites.length) {
     sortedCutsites.push({
-      id: "seqTerm_" + nanoid(),
+      id: "seqTerm_" + shortid(),
       start: 0,
       end: 0,
       overhangBps: "",
@@ -4073,10 +4365,6 @@ function getDigestFragsForSeqAndEnzymes({
   });
 }
 __name(getDigestFragsForSeqAndEnzymes, "getDigestFragsForSeqAndEnzymes");
-function getDefaultExportFromCjs(x) {
-  return x && x.__esModule && Object.prototype.hasOwnProperty.call(x, "default") ? x["default"] : x;
-}
-__name(getDefaultExportFromCjs, "getDefaultExportFromCjs");
 var jsondiffpatch_umd$1 = { exports: {} };
 var empty = {};
 var hasRequiredEmpty;
@@ -8675,10 +8963,10 @@ function tidyUpAnnotation(_annotation, {
     annotation.name = "Untitled annotation";
   }
   if (provideNewIdsForAnnotations) {
-    annotation.id = nanoid();
+    annotation.id = shortid();
   }
   if (!annotation.id && annotation.id !== 0 && !doNotProvideIdsForAnnotations) {
-    annotation.id = nanoid();
+    annotation.id = shortid();
     messages.push(
       "Unable to detect valid ID for annotation, setting ID to " + annotation.id
     );
@@ -8922,7 +9210,7 @@ function tidyUpSequenceData(pSeqData, options = {}) {
         if (item.id || item.id === 0) {
           itemId = item.id;
         } else {
-          itemId = nanoid();
+          itemId = shortid();
           if (!doNotProvideIdsForAnnotations) {
             item.id = itemId;
           }
@@ -17492,7 +17780,7 @@ function generateAnnotation(start, end, maxLength) {
   return __spreadProps(__spreadValues({}, range), {
     name: getRandomInt(0, 1e5).toString(),
     type: "misc_feature",
-    id: nanoid(),
+    id: shortid(),
     forward: Math.random() > 0.5,
     notes: {}
   });
@@ -17615,7 +17903,7 @@ function getOrfsFromSequence(options) {
           forward,
           annotationTypePlural: "orfs",
           isOrf: true,
-          id: nanoid()
+          id: shortid()
         });
       }
     }

package/index.umd.cjs

@@ -3669,15 +3669,307 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   const getFeatureTypes = /* @__PURE__ */ __name(({ includeHidden } = {}) => filter(getMergedFeatureMap(), (f) => includeHidden ? true : !f.isHidden).map(
     (f) => f.name
   ), "getFeatureTypes");
-  const urlAlphabet = "useandom-26T198340PX75pxJACKVERYMINDBUSHWOLF_GQZbfghjklqvwyzrict";
-  let nanoid = /* @__PURE__ */ __name((size = 21) => {
-    let id = "";
-    let bytes = crypto.getRandomValues(new Uint8Array(size |= 0));
-    while (size--) {
-      id += urlAlphabet[bytes[size] & 63];
-    }
-    return id;
-  }, "nanoid");
+  function getDefaultExportFromCjs(x) {
+    return x && x.__esModule && Object.prototype.hasOwnProperty.call(x, "default") ? x["default"] : x;
+  }
+  __name(getDefaultExportFromCjs, "getDefaultExportFromCjs");
+  var lib = { exports: {} };
+  var randomFromSeed;
+  var hasRequiredRandomFromSeed;
+  function requireRandomFromSeed() {
+    if (hasRequiredRandomFromSeed) return randomFromSeed;
+    hasRequiredRandomFromSeed = 1;
+    var seed = 1;
+    function getNextValue() {
+      seed = (seed * 9301 + 49297) % 233280;
+      return seed / 233280;
+    }
+    __name(getNextValue, "getNextValue");
+    function setSeed(_seed_) {
+      seed = _seed_;
+    }
+    __name(setSeed, "setSeed");
+    randomFromSeed = {
+      nextValue: getNextValue,
+      seed: setSeed
+    };
+    return randomFromSeed;
+  }
+  __name(requireRandomFromSeed, "requireRandomFromSeed");
+  var alphabet_1;
+  var hasRequiredAlphabet;
+  function requireAlphabet() {
+    if (hasRequiredAlphabet) return alphabet_1;
+    hasRequiredAlphabet = 1;
+    var randomFromSeed2 = requireRandomFromSeed();
+    var ORIGINAL = "0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ_-";
+    var alphabet;
+    var previousSeed;
+    var shuffled;
+    function reset() {
+      shuffled = false;
+    }
+    __name(reset, "reset");
+    function setCharacters(_alphabet_) {
+      if (!_alphabet_) {
+        if (alphabet !== ORIGINAL) {
+          alphabet = ORIGINAL;
+          reset();
+        }
+        return;
+      }
+      if (_alphabet_ === alphabet) {
+        return;
+      }
+      if (_alphabet_.length !== ORIGINAL.length) {
+        throw new Error("Custom alphabet for shortid must be " + ORIGINAL.length + " unique characters. You submitted " + _alphabet_.length + " characters: " + _alphabet_);
+      }
+      var unique = _alphabet_.split("").filter(function(item, ind, arr) {
+        return ind !== arr.lastIndexOf(item);
+      });
+      if (unique.length) {
+        throw new Error("Custom alphabet for shortid must be " + ORIGINAL.length + " unique characters. These characters were not unique: " + unique.join(", "));
+      }
+      alphabet = _alphabet_;
+      reset();
+    }
+    __name(setCharacters, "setCharacters");
+    function characters(_alphabet_) {
+      setCharacters(_alphabet_);
+      return alphabet;
+    }
+    __name(characters, "characters");
+    function setSeed(seed) {
+      randomFromSeed2.seed(seed);
+      if (previousSeed !== seed) {
+        reset();
+        previousSeed = seed;
+      }
+    }
+    __name(setSeed, "setSeed");
+    function shuffle() {
+      if (!alphabet) {
+        setCharacters(ORIGINAL);
+      }
+      var sourceArray = alphabet.split("");
+      var targetArray = [];
+      var r = randomFromSeed2.nextValue();
+      var characterIndex;
+      while (sourceArray.length > 0) {
+        r = randomFromSeed2.nextValue();
+        characterIndex = Math.floor(r * sourceArray.length);
+        targetArray.push(sourceArray.splice(characterIndex, 1)[0]);
+      }
+      return targetArray.join("");
+    }
+    __name(shuffle, "shuffle");
+    function getShuffled() {
+      if (shuffled) {
+        return shuffled;
+      }
+      shuffled = shuffle();
+      return shuffled;
+    }
+    __name(getShuffled, "getShuffled");
+    function lookup(index) {
+      var alphabetShuffled = getShuffled();
+      return alphabetShuffled[index];
+    }
+    __name(lookup, "lookup");
+    function get2() {
+      return alphabet || ORIGINAL;
+    }
+    __name(get2, "get");
+    alphabet_1 = {
+      get: get2,
+      characters,
+      seed: setSeed,
+      lookup,
+      shuffled: getShuffled
+    };
+    return alphabet_1;
+  }
+  __name(requireAlphabet, "requireAlphabet");
+  var randomByteBrowser;
+  var hasRequiredRandomByteBrowser;
+  function requireRandomByteBrowser() {
+    if (hasRequiredRandomByteBrowser) return randomByteBrowser;
+    hasRequiredRandomByteBrowser = 1;
+    var crypto = typeof window === "object" && (window.crypto || window.msCrypto);
+    var randomByte;
+    if (!crypto || !crypto.getRandomValues) {
+      randomByte = /* @__PURE__ */ __name(function(size) {
+        var bytes = [];
+        for (var i = 0; i < size; i++) {
+          bytes.push(Math.floor(Math.random() * 256));
+        }
+        return bytes;
+      }, "randomByte");
+    } else {
+      randomByte = /* @__PURE__ */ __name(function(size) {
+        return crypto.getRandomValues(new Uint8Array(size));
+      }, "randomByte");
+    }
+    randomByteBrowser = randomByte;
+    return randomByteBrowser;
+  }
+  __name(requireRandomByteBrowser, "requireRandomByteBrowser");
+  var format_browser;
+  var hasRequiredFormat_browser;
+  function requireFormat_browser() {
+    if (hasRequiredFormat_browser) return format_browser;
+    hasRequiredFormat_browser = 1;
+    format_browser = /* @__PURE__ */ __name(function(random, alphabet, size) {
+      var mask = (2 << Math.log(alphabet.length - 1) / Math.LN2) - 1;
+      var step = -~(1.6 * mask * size / alphabet.length);
+      var id = "";
+      while (true) {
+        var bytes = random(step);
+        var i = step;
+        while (i--) {
+          id += alphabet[bytes[i] & mask] || "";
+          if (id.length === +size) return id;
+        }
+      }
+    }, "format_browser");
+    return format_browser;
+  }
+  __name(requireFormat_browser, "requireFormat_browser");
+  var generate_1;
+  var hasRequiredGenerate;
+  function requireGenerate() {
+    if (hasRequiredGenerate) return generate_1;
+    hasRequiredGenerate = 1;
+    var alphabet = requireAlphabet();
+    var random = requireRandomByteBrowser();
+    var format = /* @__PURE__ */ requireFormat_browser();
+    function generate(number) {
+      var loopCounter = 0;
+      var done;
+      var str = "";
+      while (!done) {
+        str = str + format(random, alphabet.get(), 1);
+        done = number < Math.pow(16, loopCounter + 1);
+        loopCounter++;
+      }
+      return str;
+    }
+    __name(generate, "generate");
+    generate_1 = generate;
+    return generate_1;
+  }
+  __name(requireGenerate, "requireGenerate");
+  var build_1;
+  var hasRequiredBuild;
+  function requireBuild() {
+    if (hasRequiredBuild) return build_1;
+    hasRequiredBuild = 1;
+    var generate = requireGenerate();
+    requireAlphabet();
+    var REDUCE_TIME = 1567752802062;
+    var version = 7;
+    var counter;
+    var previousSeconds;
+    function build(clusterWorkerId) {
+      var str = "";
+      var seconds = Math.floor((Date.now() - REDUCE_TIME) * 1e-3);
+      if (seconds === previousSeconds) {
+        counter++;
+      } else {
+        counter = 0;
+        previousSeconds = seconds;
+      }
+      str = str + generate(version);
+      str = str + generate(clusterWorkerId);
+      if (counter > 0) {
+        str = str + generate(counter);
+      }
+      str = str + generate(seconds);
+      return str;
+    }
+    __name(build, "build");
+    build_1 = build;
+    return build_1;
+  }
+  __name(requireBuild, "requireBuild");
+  var isValid;
+  var hasRequiredIsValid;
+  function requireIsValid() {
+    if (hasRequiredIsValid) return isValid;
+    hasRequiredIsValid = 1;
+    var alphabet = requireAlphabet();
+    function isShortId(id) {
+      if (!id || typeof id !== "string" || id.length < 6) {
+        return false;
+      }
+      var nonAlphabetic = new RegExp("[^" + alphabet.get().replace(/[|\\{}()[\]^$+*?.-]/g, "\\$&") + "]");
+      return !nonAlphabetic.test(id);
+    }
+    __name(isShortId, "isShortId");
+    isValid = isShortId;
+    return isValid;
+  }
+  __name(requireIsValid, "requireIsValid");
+  var clusterWorkerIdBrowser;
+  var hasRequiredClusterWorkerIdBrowser;
+  function requireClusterWorkerIdBrowser() {
+    if (hasRequiredClusterWorkerIdBrowser) return clusterWorkerIdBrowser;
+    hasRequiredClusterWorkerIdBrowser = 1;
+    clusterWorkerIdBrowser = 0;
+    return clusterWorkerIdBrowser;
+  }
+  __name(requireClusterWorkerIdBrowser, "requireClusterWorkerIdBrowser");
+  var hasRequiredLib;
+  function requireLib() {
+    if (hasRequiredLib) return lib.exports;
+    hasRequiredLib = 1;
+    (function(module2) {
+      var alphabet = requireAlphabet();
+      var build = requireBuild();
+      var isValid2 = requireIsValid();
+      var clusterWorkerId = requireClusterWorkerIdBrowser() || 0;
+      function seed(seedValue) {
+        alphabet.seed(seedValue);
+        return module2.exports;
+      }
+      __name(seed, "seed");
+      function worker(workerId) {
+        clusterWorkerId = workerId;
+        return module2.exports;
+      }
+      __name(worker, "worker");
+      function characters(newCharacters) {
+        if (newCharacters !== void 0) {
+          alphabet.characters(newCharacters);
+        }
+        return alphabet.shuffled();
+      }
+      __name(characters, "characters");
+      function generate() {
+        return build(clusterWorkerId);
+      }
+      __name(generate, "generate");
+      module2.exports = generate;
+      module2.exports.generate = generate;
+      module2.exports.seed = seed;
+      module2.exports.worker = worker;
+      module2.exports.characters = characters;
+      module2.exports.isValid = isValid2;
+    })(lib);
+    return lib.exports;
+  }
+  __name(requireLib, "requireLib");
+  var shortid$1;
+  var hasRequiredShortid;
+  function requireShortid() {
+    if (hasRequiredShortid) return shortid$1;
+    hasRequiredShortid = 1;
+    shortid$1 = requireLib();
+    return shortid$1;
+  }
+  __name(requireShortid, "requireShortid");
+  var shortidExports = requireShortid();
+  const shortid = /* @__PURE__ */ getDefaultExportFromCjs(shortidExports);
   function cutSequenceByRestrictionEnzyme(pSequence, circular, restrictionEnzyme) {
     if (restrictionEnzyme.forwardRegex.length === 0 || restrictionEnzyme.reverseRegex.length === 0) {
       const returnArray = [];
@@ -3885,7 +4177,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
         }
         const overhangBps = getSequenceWithinRange(cutRange, originalSequence);
         restrictionCutSite = {
-          id: nanoid(),
+          id: shortid(),
           start,
           end,
           topSnipPosition,
@@ -3943,7 +4235,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     });
     if (!circular && cutsites.length) {
       sortedCutsites.push({
-        id: "seqTerm_" + nanoid(),
+        id: "seqTerm_" + shortid(),
         start: 0,
         end: 0,
         overhangBps: "",
@@ -4077,10 +4369,6 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     });
   }
   __name(getDigestFragsForSeqAndEnzymes, "getDigestFragsForSeqAndEnzymes");
-  function getDefaultExportFromCjs(x) {
-    return x && x.__esModule && Object.prototype.hasOwnProperty.call(x, "default") ? x["default"] : x;
-  }
-  __name(getDefaultExportFromCjs, "getDefaultExportFromCjs");
   var jsondiffpatch_umd$1 = { exports: {} };
   var empty = {};
   var hasRequiredEmpty;
@@ -8679,10 +8967,10 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       annotation.name = "Untitled annotation";
     }
     if (provideNewIdsForAnnotations) {
-      annotation.id = nanoid();
+      annotation.id = shortid();
     }
     if (!annotation.id && annotation.id !== 0 && !doNotProvideIdsForAnnotations) {
-      annotation.id = nanoid();
+      annotation.id = shortid();
       messages.push(
         "Unable to detect valid ID for annotation, setting ID to " + annotation.id
       );
@@ -8926,7 +9214,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
           if (item.id || item.id === 0) {
             itemId = item.id;
           } else {
-            itemId = nanoid();
+            itemId = shortid();
             if (!doNotProvideIdsForAnnotations) {
               item.id = itemId;
             }
@@ -17496,7 +17784,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     return __spreadProps(__spreadValues({}, range), {
       name: getRandomInt(0, 1e5).toString(),
       type: "misc_feature",
-      id: nanoid(),
+      id: shortid(),
       forward: Math.random() > 0.5,
       notes: {}
     });
@@ -17619,7 +17907,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
             forward,
             annotationTypePlural: "orfs",
             isOrf: true,
-            id: nanoid()
+            id: shortid()
           });
         }
       }

package/package.json

@@ -1,14 +1,14 @@
 {
   "name": "@teselagen/sequence-utils",
-  "version": "0.3.32-beta.2",
+  "version": "0.3.32",
   "type": "module",
   "dependencies": {
-    "@teselagen/range-utils": "0.3.14-beta.1",
     "escape-string-regexp": "5.0.0",
     "jsondiffpatch": "0.4.1",
+    "string-splice": "^1.3.0",
     "lodash-es": "^4.17.21",
-    "nanoid": "^5.1.5",
-    "string-splice": "^1.3.0"
+    "shortid": "2.2.16",
+    "@teselagen/range-utils": "0.3.13"
   },
   "exports": {
     ".": {
@@ -16,9 +16,5 @@
       "require": "./index.cjs"
     }
   },
-  "volta": {
-    "node": "18.18.0",
-    "yarn": "1.22.22"
-  },
   "license": "MIT"
 }

package/src/computeDigestFragments.js

@@ -1,4 +1,4 @@
-import { nanoid } from "nanoid";
+import shortid from "shortid";
 import { flatMap, cloneDeep } from "lodash-es";
 import {
   normalizePositionByRangeLength,
@@ -27,7 +27,7 @@ function computeDigestFragments({
   });
   if (!circular && cutsites.length) {
     sortedCutsites.push({
-      id: "seqTerm_" + nanoid(),
+      id: "seqTerm_" + shortid(),
       start: 0,
       end: 0,
       overhangBps: "",

package/src/cutSequenceByRestrictionEnzyme.js

@@ -1,5 +1,5 @@
 import { assign } from "lodash-es";
-import { nanoid } from "nanoid";
+import shortid from "shortid";
 import getReverseComplementSequenceString from "./getReverseComplementSequenceString";
 
 import {
@@ -268,7 +268,7 @@ function cutSequence(
       const overhangBps = getSequenceWithinRange(cutRange, originalSequence);
 
       restrictionCutSite = {
-        id: nanoid(),
+        id: shortid(),
         start,
         end,
         topSnipPosition,

package/src/generateAnnotations.js

@@ -1,5 +1,5 @@
 import { generateRandomRange } from "@teselagen/range-utils";
-import { nanoid } from "nanoid";
+import shortid from "shortid";
 
 function generateAnnotations(
   numberOfAnnotationsToGenerate,
@@ -21,7 +21,7 @@ function generateAnnotation(start, end, maxLength) {
     ...range,
     name: getRandomInt(0, 100000).toString(),
     type: "misc_feature",
-    id: nanoid(),
+    id: shortid(),
     forward: Math.random() > 0.5,
     notes: {}
   };

package/src/getOrfsFromSequence.js

@@ -1,4 +1,4 @@
-import { nanoid } from "nanoid";
+import shortid from "shortid";
 import getReverseComplementSequenceString from "./getReverseComplementSequenceString";
 
 /**
@@ -61,7 +61,7 @@ export default function getOrfsFromSequence(options) {
           forward: forward,
           annotationTypePlural: "orfs",
           isOrf: true,
-          id: nanoid()
+          id: shortid()
         });
       }
     }

package/src/tidyUpAnnotation.js

@@ -1,6 +1,6 @@
 import { cloneDeep, get, some } from "lodash-es";
 import { getFeatureToColorMap, getFeatureTypes } from "./featureTypesAndColors";
-import { nanoid } from "nanoid";
+import shortid from "shortid";
 
 export default function tidyUpAnnotation(
   _annotation,
@@ -34,10 +34,10 @@ export default function tidyUpAnnotation(
     annotation.name = "Untitled annotation";
   }
   if (provideNewIdsForAnnotations) {
-    annotation.id = nanoid();
+    annotation.id = shortid();
   }
   if (!annotation.id && annotation.id !== 0 && !doNotProvideIdsForAnnotations) {
-    annotation.id = nanoid();
+    annotation.id = shortid();
     messages.push(
       "Unable to detect valid ID for annotation, setting ID to " + annotation.id
     );

package/src/tidyUpSequenceData.js

@@ -1,5 +1,5 @@
 // tnrtodo: figure out where to insert this validation exactly..
-import { nanoid } from "nanoid";
+import shortid from "shortid";
 
 import getAminoAcidDataForEachBaseOfDna from "./getAminoAcidDataForEachBaseOfDna";
 import { cloneDeep, flatMap } from "lodash-es";
@@ -155,7 +155,7 @@ export default function tidyUpSequenceData(pSeqData, options = {}) {
         if (item.id || item.id === 0) {
           itemId = item.id;
         } else {
-          itemId = nanoid();
+          itemId = shortid();
           if (!doNotProvideIdsForAnnotations) {
             item.id = itemId; //assign the newly created id to the item
           }