@teselagen/sequence-utils 0.3.7 → 0.3.9

package/index.umd.js

@@ -6001,31 +6001,8 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   })(lodash, lodash.exports);
   var lodashExports = lodash.exports;
   const protein_letters = "ACDEFGHIKLMNPQRSTVWY";
+  const protein_letters_withUandX = "ACDEFGHIKLMNPQRSTVWYUX";
   const extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO.*-";
-  const protein_letters_1to3 = {
-    A: "Ala",
-    C: "Cys",
-    D: "Asp",
-    E: "Glu",
-    F: "Phe",
-    G: "Gly",
-    H: "His",
-    I: "Ile",
-    K: "Lys",
-    L: "Leu",
-    M: "Met",
-    N: "Asn",
-    P: "Pro",
-    Q: "Gln",
-    R: "Arg",
-    S: "Ser",
-    T: "Thr",
-    V: "Val",
-    W: "Trp",
-    Y: "Tyr",
-    O: "Pyl",
-    U: "Sec"
-  };
   const ambiguous_dna_letters = "GATCRYWSMKHBVDN";
   const unambiguous_dna_letters = "GATC";
   const ambiguous_rna_letters = "GAUCRYWSMKHBVDN";
@@ -6050,135 +6027,6 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     X: "GATC",
     N: "GATC"
   };
-  const ambiguous_rna_values = {
-    ".": ".",
-    A: "A",
-    C: "C",
-    G: "G",
-    U: "U",
-    M: "AC",
-    R: "AG",
-    W: "AU",
-    S: "CG",
-    Y: "CU",
-    K: "GU",
-    V: "ACG",
-    H: "ACU",
-    D: "AGU",
-    B: "CGU",
-    X: "GAUC",
-    N: "GAUC"
-  };
-  const ambiguous_dna_complement = {
-    ".": ".",
-    A: "T",
-    C: "G",
-    G: "C",
-    T: "A",
-    M: "K",
-    R: "Y",
-    W: "W",
-    S: "S",
-    Y: "R",
-    K: "M",
-    V: "B",
-    H: "D",
-    D: "H",
-    B: "V",
-    X: "X",
-    N: "N"
-  };
-  const ambiguous_rna_complement = {
-    ".": ".",
-    A: "U",
-    C: "G",
-    G: "C",
-    U: "A",
-    M: "K",
-    R: "Y",
-    W: "W",
-    S: "S",
-    Y: "R",
-    K: "M",
-    V: "B",
-    H: "D",
-    D: "H",
-    B: "V",
-    X: "X",
-    N: "N"
-  };
-  const unambiguous_dna_weights = {
-    A: 331.2218,
-    C: 307.1971,
-    G: 347.2212,
-    T: 322.2085
-  };
-  const monoisotopic_unambiguous_dna_weights = {
-    A: 331.06817,
-    C: 307.056936,
-    G: 347.063084,
-    T: 322.056602
-  };
-  const unambiguous_rna_weights = {
-    A: 347.2212,
-    C: 323.1965,
-    G: 363.2206,
-    U: 324.1813
-  };
-  const monoisotopic_unambiguous_rna_weights = {
-    A: 347.063084,
-    C: 323.051851,
-    G: 363.057999,
-    U: 324.035867
-  };
-  const protein_weights = {
-    A: 89.0932,
-    C: 121.1582,
-    D: 133.1027,
-    E: 147.1293,
-    F: 165.1891,
-    G: 75.0666,
-    H: 155.1546,
-    I: 131.1729,
-    K: 146.1876,
-    L: 131.1729,
-    M: 149.2113,
-    N: 132.1179,
-    O: 255.3134,
-    P: 115.1305,
-    Q: 146.1445,
-    R: 174.201,
-    S: 105.0926,
-    T: 119.1192,
-    U: 168.0532,
-    V: 117.1463,
-    W: 204.2252,
-    Y: 181.1885
-  };
-  const monoisotopic_protein_weights = {
-    A: 89.047678,
-    C: 121.019749,
-    D: 133.037508,
-    E: 147.053158,
-    F: 165.078979,
-    G: 75.032028,
-    H: 155.069477,
-    I: 131.094629,
-    K: 146.105528,
-    L: 131.094629,
-    M: 149.051049,
-    N: 132.053492,
-    O: 255.158292,
-    P: 115.063329,
-    Q: 146.069142,
-    R: 174.111676,
-    S: 105.042593,
-    T: 119.058243,
-    U: 168.964203,
-    V: 117.078979,
-    W: 204.089878,
-    Y: 181.073893
-  };
   const extended_protein_values = {
     A: "A",
     B: "ND",
@@ -6213,140 +6061,18 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     ".": "\\.\\.",
     "-": "\\-"
   };
-  const atom_weights = {
-    H: 1.00794,
-    D: 2.0141,
-    He: 4.002602,
-    Li: 6.941,
-    Be: 9.012182,
-    B: 10.811,
-    C: 12.0107,
-    N: 14.0067,
-    O: 15.9994,
-    F: 18.9984032,
-    Ne: 20.1797,
-    Na: 22.98977,
-    Mg: 24.305,
-    Al: 26.981538,
-    Si: 28.0855,
-    P: 30.973761,
-    S: 32.065,
-    Cl: 35.453,
-    Ar: 39.948,
-    K: 39.0983,
-    Ca: 40.078,
-    Sc: 44.95591,
-    Ti: 47.867,
-    V: 50.9415,
-    Cr: 51.9961,
-    Mn: 54.938049,
-    Fe: 55.845,
-    Co: 58.9332,
-    Ni: 58.6934,
-    Cu: 63.546,
-    Zn: 65.39,
-    Ga: 69.723,
-    Ge: 72.64,
-    As: 74.9216,
-    Se: 78.96,
-    Br: 79.904,
-    Kr: 83.8,
-    Rb: 85.4678,
-    Sr: 87.62,
-    Y: 88.90585,
-    Zr: 91.224,
-    Nb: 92.90638,
-    Mo: 95.94,
-    Tc: 98,
-    Ru: 101.07,
-    Rh: 102.9055,
-    Pd: 106.42,
-    Ag: 107.8682,
-    Cd: 112.411,
-    In: 114.818,
-    Sn: 118.71,
-    Sb: 121.76,
-    Te: 127.6,
-    I: 126.90447,
-    Xe: 131.293,
-    Cs: 132.90545,
-    Ba: 137.327,
-    La: 138.9055,
-    Ce: 140.116,
-    Pr: 140.90765,
-    Nd: 144.24,
-    Pm: 145,
-    Sm: 150.36,
-    Eu: 151.964,
-    Gd: 157.25,
-    Tb: 158.92534,
-    Dy: 162.5,
-    Ho: 164.93032,
-    Er: 167.259,
-    Tm: 168.93421,
-    Yb: 173.04,
-    Lu: 174.967,
-    Hf: 178.49,
-    Ta: 180.9479,
-    W: 183.84,
-    Re: 186.207,
-    Os: 190.23,
-    Ir: 192.217,
-    Pt: 195.078,
-    Au: 196.96655,
-    Hg: 200.59,
-    Tl: 204.3833,
-    Pb: 207.2,
-    Bi: 208.98038,
-    Po: 208.98,
-    At: 209.99,
-    Rn: 222.02,
-    Fr: 223.02,
-    Ra: 226.03,
-    Ac: 227.03,
-    Th: 232.0381,
-    Pa: 231.03588,
-    U: 238.02891,
-    Np: 237.05,
-    Pu: 244.06,
-    Am: 243.06,
-    Cm: 247.07,
-    Bk: 247.07,
-    Cf: 251.08,
-    Es: 252.08,
-    Fm: 257.1,
-    Md: 258.1,
-    No: 259.1,
-    Lr: 262.11,
-    Rf: 261.11,
-    Db: 262.11,
-    Sg: 266.12,
-    Bh: 264.12,
-    Hs: 269.13,
-    Mt: 268.14
-  };
   const bioData = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.defineProperty({
     __proto__: null,
-    ambiguous_dna_complement,
     ambiguous_dna_letters,
     ambiguous_dna_values,
-    ambiguous_rna_complement,
     ambiguous_rna_letters,
-    ambiguous_rna_values,
-    atom_weights,
     extended_dna_letters,
     extended_protein_letters,
     extended_protein_values,
-    monoisotopic_protein_weights,
-    monoisotopic_unambiguous_dna_weights,
-    monoisotopic_unambiguous_rna_weights,
     protein_letters,
-    protein_letters_1to3,
-    protein_weights,
+    protein_letters_withUandX,
     unambiguous_dna_letters,
-    unambiguous_dna_weights,
-    unambiguous_rna_letters,
-    unambiguous_rna_weights
+    unambiguous_rna_letters
   }, Symbol.toStringTag, { value: "Module" }));
   const aminoAcidToDegenerateDnaMap = {
     "-": "---",
@@ -6460,8 +6186,8 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       maxRangeLength
     );
     let overlaps = [];
-    normalizedRangeA.forEach(function(nonCircularRangeA, iA) {
-      normalizedRangeB.forEach(function(nonCircularRangeB, iB) {
+    normalizedRangeA.forEach(function(nonCircularRangeA) {
+      normalizedRangeB.forEach(function(nonCircularRangeB) {
         const overlap = getOverlapOfNonCircularRanges(
           nonCircularRangeA,
           nonCircularRangeB
@@ -6473,7 +6199,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     });
     if (joinIfPossible && normalizedRangeA.length === 2 && normalizedRangeB.length === 2 && maxRangeLength) {
       const joinedOverlap = {};
-      overlaps = lodashExports.flatMap(overlaps, (o, i) => {
+      overlaps = lodashExports.flatMap(overlaps, (o) => {
         if (o.start === 0) {
           joinedOverlap.end = o.end;
           return [];
@@ -6571,12 +6297,14 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       });
       splitRangesToBeTrimmed[index] = nonCircularRangeToBeTrimmed;
     });
-    const outputSplitRanges = splitRangesToBeTrimmed.filter(function(trimmedRange) {
-      if (trimmedRange) {
-        return true;
+    const outputSplitRanges = splitRangesToBeTrimmed.filter(
+      function(trimmedRange) {
+        if (trimmedRange) {
+          return true;
+        }
+        return false;
       }
-      return false;
-    });
+    );
     let outputTrimmedRange;
     if (outputSplitRanges.length < 0)
       ;
@@ -6675,11 +6403,19 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   }
   __name(checkIfNonCircularRangesOverlap, "checkIfNonCircularRangesOverlap");
   function checkIfPotentiallyCircularRangesOverlap(range, comparisonRange) {
-    return splitRangeIntoTwoPartsIfItIsCircular(range, Infinity).some(function(splitRange) {
-      return splitRangeIntoTwoPartsIfItIsCircular(comparisonRange, Infinity).some(function(splitComparisonRange) {
-        return checkIfNonCircularRangesOverlap(splitRange, splitComparisonRange);
-      });
-    });
+    return splitRangeIntoTwoPartsIfItIsCircular(range, Infinity).some(
+      function(splitRange) {
+        return splitRangeIntoTwoPartsIfItIsCircular(
+          comparisonRange,
+          Infinity
+        ).some(function(splitComparisonRange) {
+          return checkIfNonCircularRangesOverlap(
+            splitRange,
+            splitComparisonRange
+          );
+        });
+      }
+    );
   }
   __name(checkIfPotentiallyCircularRangesOverlap, "checkIfPotentiallyCircularRangesOverlap");
   function collapseOverlapsGeneratedFromRangeComparisonIfPossible(overlaps, sequenceLength, optionalOriginalRange) {
@@ -6688,15 +6424,19 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       return overlaps;
     } else if (overlaps.length === 2) {
       if (overlaps[0].start === 0 && overlaps[1].end + 1 === sequenceLength && !originalRangeLinear) {
-        return [{
-          start: overlaps[1].start,
-          end: overlaps[0].end
-        }];
+        return [
+          {
+            start: overlaps[1].start,
+            end: overlaps[0].end
+          }
+        ];
       } else if (overlaps[1].start === 0 && overlaps[0].end + 1 === sequenceLength && !originalRangeLinear) {
-        return [{
-          start: overlaps[0].start,
-          end: overlaps[1].end
-        }];
+        return [
+          {
+            start: overlaps[0].start,
+            end: overlaps[1].end
+          }
+        ];
       } else {
         return overlaps;
       }
@@ -6704,17 +6444,29 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       const firstOverlap = overlaps[0];
       const secondOverlap = overlaps[1];
       const thirdOverlap = overlaps[2];
-      let collapsedOverlaps = collapseOverlapsGeneratedFromRangeComparisonIfPossible([firstOverlap, secondOverlap], sequenceLength, optionalOriginalRange);
+      let collapsedOverlaps = collapseOverlapsGeneratedFromRangeComparisonIfPossible(
+        [firstOverlap, secondOverlap],
+        sequenceLength,
+        optionalOriginalRange
+      );
       if (collapsedOverlaps.length === 1) {
         collapsedOverlaps.push(thirdOverlap);
         return collapsedOverlaps;
       } else {
-        collapsedOverlaps = collapseOverlapsGeneratedFromRangeComparisonIfPossible([firstOverlap, thirdOverlap], sequenceLength, optionalOriginalRange);
+        collapsedOverlaps = collapseOverlapsGeneratedFromRangeComparisonIfPossible(
+          [firstOverlap, thirdOverlap],
+          sequenceLength,
+          optionalOriginalRange
+        );
         if (collapsedOverlaps.length === 1) {
           collapsedOverlaps.push(secondOverlap);
           return collapsedOverlaps;
         } else {
-          collapsedOverlaps = collapseOverlapsGeneratedFromRangeComparisonIfPossible([secondOverlap, thirdOverlap], sequenceLength, optionalOriginalRange);
+          collapsedOverlaps = collapseOverlapsGeneratedFromRangeComparisonIfPossible(
+            [secondOverlap, thirdOverlap],
+            sequenceLength,
+            optionalOriginalRange
+          );
           if (collapsedOverlaps.length === 1) {
             collapsedOverlaps.push(firstOverlap);
             return collapsedOverlaps;
@@ -6821,13 +6573,23 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   __name(expandOrContractRangeByLength, "expandOrContractRangeByLength");
   function translateRange(rangeToBeAdjusted, translateBy, rangeLength) {
     return lodashExports.assign({}, rangeToBeAdjusted, {
-      start: normalizePositionByRangeLength(rangeToBeAdjusted.start + translateBy, rangeLength),
-      end: normalizePositionByRangeLength(rangeToBeAdjusted.end + translateBy, rangeLength)
+      start: normalizePositionByRangeLength(
+        rangeToBeAdjusted.start + translateBy,
+        rangeLength
+      ),
+      end: normalizePositionByRangeLength(
+        rangeToBeAdjusted.end + translateBy,
+        rangeLength
+      )
     });
   }
   __name(translateRange, "translateRange");
-  function flipRelativeRange(innerRange, outerRange, sequenceLength, options) {
-    const isFullyContained = isRangeWithinRange(innerRange, outerRange, sequenceLength);
+  function flipRelativeRange(innerRange, outerRange, sequenceLength) {
+    const isFullyContained = isRangeWithinRange(
+      innerRange,
+      outerRange,
+      sequenceLength
+    );
     if (isFullyContained) {
       return flipFullyContainedRange(innerRange, outerRange, sequenceLength);
     } else {
@@ -6835,42 +6597,92 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     }
   }
   __name(flipRelativeRange, "flipRelativeRange");
-  function flipNonFullyContainedRange(innerRange, outerRange, sequenceLength, options) {
-    const outerFullyContained = isRangeWithinRange(outerRange, innerRange, sequenceLength);
+  function flipNonFullyContainedRange(innerRange, outerRange, sequenceLength) {
+    const outerFullyContained = isRangeWithinRange(
+      outerRange,
+      innerRange,
+      sequenceLength
+    );
     let flippedInnerRange;
     if (outerFullyContained) {
-      const expandBy1 = getRangeLength({
-        start: innerRange.start,
-        end: outerRange.start
-      }, sequenceLength) - 1;
-      flippedInnerRange = expandOrContractRangeByLength(outerRange, expandBy1, false, sequenceLength);
-      const expandBy2 = getRangeLength({
-        end: innerRange.end,
-        start: outerRange.end
-      }, sequenceLength) - 1;
-      flippedInnerRange = expandOrContractRangeByLength(flippedInnerRange, expandBy2, true, sequenceLength);
+      const expandBy1 = getRangeLength(
+        {
+          start: innerRange.start,
+          end: outerRange.start
+        },
+        sequenceLength
+      ) - 1;
+      flippedInnerRange = expandOrContractRangeByLength(
+        outerRange,
+        expandBy1,
+        false,
+        sequenceLength
+      );
+      const expandBy2 = getRangeLength(
+        {
+          end: innerRange.end,
+          start: outerRange.end
+        },
+        sequenceLength
+      ) - 1;
+      flippedInnerRange = expandOrContractRangeByLength(
+        flippedInnerRange,
+        expandBy2,
+        true,
+        sequenceLength
+      );
     } else {
-      const overlaps = getOverlapsOfPotentiallyCircularRanges(innerRange, outerRange, sequenceLength);
+      const overlaps = getOverlapsOfPotentiallyCircularRanges(
+        innerRange,
+        outerRange,
+        sequenceLength
+      );
       if (overlaps.length >= 1) {
-        let overlapExtendsForward;
         const firstOverlap = overlaps[0];
-        overlapExtendsForward = firstOverlap.start !== outerRange.start;
-        const flippedTruncatedInner = flipFullyContainedRange(firstOverlap, outerRange, sequenceLength);
+        const overlapExtendsForward = firstOverlap.start !== outerRange.start;
+        const flippedTruncatedInner = flipFullyContainedRange(
+          firstOverlap,
+          outerRange,
+          sequenceLength
+        );
         const lengthToExtend = getRangeLength(innerRange, sequenceLength) - getRangeLength(flippedTruncatedInner, sequenceLength);
-        flippedInnerRange = expandOrContractRangeByLength(flippedTruncatedInner, lengthToExtend, overlapExtendsForward, sequenceLength);
+        flippedInnerRange = expandOrContractRangeByLength(
+          flippedTruncatedInner,
+          lengthToExtend,
+          overlapExtendsForward,
+          sequenceLength
+        );
       } else {
-        throw new Error("This case (relative ranges that do not overlap) is unsupported! ");
+        throw new Error(
+          "This case (relative ranges that do not overlap) is unsupported! "
+        );
       }
     }
     return flippedInnerRange;
   }
   __name(flipNonFullyContainedRange, "flipNonFullyContainedRange");
-  function flipFullyContainedRange(innerRange, outerRange, sequenceLength, options) {
+  function flipFullyContainedRange(innerRange, outerRange, sequenceLength) {
     const translateBy = -outerRange.start;
-    const translatedOuterRange = translateRange(outerRange, translateBy, sequenceLength);
-    const translatedInnerRange = translateRange(innerRange, translateBy, sequenceLength);
-    const translatedFlippedInnerRange = flipNonOriginSpanningContainedRange(translatedInnerRange, translatedOuterRange, sequenceLength);
-    const flippedInnerRange = translateRange(translatedFlippedInnerRange, -translateBy, sequenceLength);
+    const translatedOuterRange = translateRange(
+      outerRange,
+      translateBy,
+      sequenceLength
+    );
+    const translatedInnerRange = translateRange(
+      innerRange,
+      translateBy,
+      sequenceLength
+    );
+    const translatedFlippedInnerRange = flipNonOriginSpanningContainedRange(
+      translatedInnerRange,
+      translatedOuterRange,
+      sequenceLength
+    );
+    const flippedInnerRange = translateRange(
+      translatedFlippedInnerRange,
+      -translateBy,
+      sequenceLength
+    );
     return flippedInnerRange;
   }
   __name(flipFullyContainedRange, "flipFullyContainedRange");
@@ -6888,7 +6700,10 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     const start = getRandomInt$1(minStart, maxEnd);
     let end;
     if (maxLength) {
-      end = normalizePositionByRangeLength(getRandomInt$1(start, start + maxLength), maxEnd);
+      end = normalizePositionByRangeLength(
+        getRandomInt$1(start, start + maxLength),
+        maxEnd
+      );
     } else {
       end = getRandomInt$1(minStart, maxEnd);
     }
@@ -6931,18 +6746,26 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   __name(getShortestDistanceBetweenTwoPositions, "getShortestDistanceBetweenTwoPositions");
   function getYOffsetForPotentiallyCircularRange(range, YOffsetLevelsWithRanges, assignYOffsetToRange) {
     let yOffset = [];
-    const openYOffsetFound = YOffsetLevelsWithRanges.some(function(rangesAlreadyAddedToYOffset, index) {
-      const rangeBlocked = rangesAlreadyAddedToYOffset.some(function(comparisonRange) {
-        return checkIfPotentiallyCircularRangesOverlap(range, comparisonRange);
-      });
-      if (!rangeBlocked) {
-        yOffset = index;
-        if (assignYOffsetToRange)
-          range.yOffset = index;
-        rangesAlreadyAddedToYOffset.push(range);
-        return true;
+    const openYOffsetFound = YOffsetLevelsWithRanges.some(
+      function(rangesAlreadyAddedToYOffset, index) {
+        const rangeBlocked = rangesAlreadyAddedToYOffset.some(
+          function(comparisonRange) {
+            return checkIfPotentiallyCircularRangesOverlap(
+              range,
+              comparisonRange
+            );
+          }
+        );
+        if (!rangeBlocked) {
+          yOffset = index;
+          if (assignYOffsetToRange)
+            range.yOffset = index;
+          rangesAlreadyAddedToYOffset.push(range);
+          return true;
+        }
+        return false;
       }
-    });
+    );
     if (!openYOffsetFound) {
       yOffset = YOffsetLevelsWithRanges.length;
       if (assignYOffsetToRange)
@@ -6956,7 +6779,11 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     let maxYOffset = 0;
     const yOffsetLevels = [];
     ranges.forEach(function(range) {
-      const yOffset = getYOffsetForPotentiallyCircularRange(range, yOffsetLevels, assignYOffsetToRange);
+      const yOffset = getYOffsetForPotentiallyCircularRange(
+        range,
+        yOffsetLevels,
+        assignYOffsetToRange
+      );
       yOffsets.push(yOffset);
       if (yOffset > maxYOffset) {
         maxYOffset = yOffset;
@@ -6989,8 +6816,16 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   }
   __name(invertRange$1, "invertRange$1");
   function isPositionCloserToRangeStartThanRangeEnd(position, range, maxLength) {
-    const distanceFromStart = getShortestDistanceBetweenTwoPositions(range.start, position, maxLength);
-    const distanceFromEnd = getShortestDistanceBetweenTwoPositions(range.end, position, maxLength);
+    const distanceFromStart = getShortestDistanceBetweenTwoPositions(
+      range.start,
+      position,
+      maxLength
+    );
+    const distanceFromEnd = getShortestDistanceBetweenTwoPositions(
+      range.end,
+      position,
+      maxLength
+    );
     return distanceFromStart <= distanceFromEnd;
   }
   __name(isPositionCloserToRangeStartThanRangeEnd, "isPositionCloserToRangeStartThanRangeEnd");
@@ -7021,9 +6856,15 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   }
   __name(reversePositionInRange, "reversePositionInRange");
   function zeroSubrangeByContainerRange(subRange, containerRange, sequenceLength) {
-    const trimmedSubRange = trimRangeByAnotherRange(subRange, containerRange, sequenceLength);
+    const trimmedSubRange = trimRangeByAnotherRange(
+      subRange,
+      containerRange,
+      sequenceLength
+    );
     if (trimmedSubRange) {
-      throw new Error("subRange must be fully contained by containerRange! Otherwise this function does not make sense");
+      throw new Error(
+        "subRange must be fully contained by containerRange! Otherwise this function does not make sense"
+      );
     }
     const newSubrange = {};
     newSubrange.start = subRange.start - containerRange.start;
@@ -7051,12 +6892,24 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   }
   __name(modulo, "modulo");
   function getZeroedRangeOverlaps(annotation, selection, sequenceLength) {
-    const overlaps = collapseOverlapsGeneratedFromRangeComparisonIfPossible(getOverlapsOfPotentiallyCircularRanges(annotation, selection, sequenceLength), sequenceLength, annotation);
+    const overlaps = collapseOverlapsGeneratedFromRangeComparisonIfPossible(
+      getOverlapsOfPotentiallyCircularRanges(
+        annotation,
+        selection,
+        sequenceLength
+      ),
+      sequenceLength,
+      annotation
+    );
     const zeroedOverlaps = overlaps.map((overlap) => {
-      return zeroSubrangeByContainerRange(overlap, {
-        start: selection.start,
-        end: normalizePositionByRangeLength(selection.start - 1, sequenceLength)
-      }, sequenceLength);
+      return zeroSubrangeByContainerRange(
+        overlap,
+        {
+          start: selection.start,
+          end: normalizePositionByRangeLength(selection.start - 1, sequenceLength)
+        },
+        sequenceLength
+      );
     });
     return zeroedOverlaps;
   }
@@ -11964,7 +11817,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       hydrophobicity: 1.8,
       colorByFamily: "#00FFFF",
       color: "hsl(327.3, 100%, 69%)",
-      mass: 89.1
+      mass: 71.0779
     },
     R: {
       value: "R",
@@ -11973,7 +11826,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       hydrophobicity: -4.5,
       colorByFamily: "#FFC0CB",
       color: "hsl(258.1, 100%, 69%)",
-      mass: 174.2
+      mass: 156.18568
     },
     N: {
       value: "N",
@@ -11982,7 +11835,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       hydrophobicity: -3.5,
       colorByFamily: "#D3D3D3",
       color: "hsl(268.9, 100%, 69%)",
-      mass: 132.1
+      mass: 114.10264
     },
     D: {
       value: "D",
@@ -11991,7 +11844,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       hydrophobicity: -3.5,
       colorByFamily: "#EE82EE",
       color: "hsl(268.9, 100%, 69%)",
-      mass: 133.1
+      mass: 115.0874
     },
     C: {
       value: "C",
@@ -12000,7 +11853,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       hydrophobicity: 2.5,
       colorByFamily: "#FFFF00",
       color: "hsl(335.1, 100%, 69%)",
-      mass: 121.2
+      mass: 103.1429
     },
     E: {
       value: "E",
@@ -12009,7 +11862,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       hydrophobicity: -3.5,
       colorByFamily: "#EE82EE",
       color: "hsl(268.9, 100%, 69%)",
-      mass: 147.1
+      mass: 129.11398
     },
     Q: {
       value: "Q",
@@ -12018,7 +11871,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       hydrophobicity: -3.5,
       colorByFamily: "#D3D3D3",
       color: "hsl(268.9, 100%, 69%)",
-      mass: 146.2
+      mass: 128.12922
     },
     G: {
       value: "G",
@@ -12027,7 +11880,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       hydrophobicity: -0.4,
       colorByFamily: "#00FFFF",
       color: "hsl(303.1, 100%, 69%)",
-      mass: 75.1
+      mass: 57.05132
     },
     H: {
       value: "H",
@@ -12036,7 +11889,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       hydrophobicity: -3.2,
       colorByFamily: "#FFC0CB",
       color: "hsl(272.2, 100%, 69%)",
-      mass: 155.2
+      mass: 137.13928
     },
     I: {
       value: "I",
@@ -12045,7 +11898,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       hydrophobicity: 4.5,
       colorByFamily: "#00FFFF",
       color: "hsl(356.9, 100%, 69%)",
-      mass: 131.2
+      mass: 113.15764
     },
     L: {
       value: "L",
@@ -12054,7 +11907,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       hydrophobicity: 3.8,
       colorByFamily: "#00FFFF",
       color: "hsl(349.4, 100%, 69%)",
-      mass: 131.2
+      mass: 113.15764
     },
     K: {
       value: "K",
@@ -12063,7 +11916,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       hydrophobicity: -3.9,
       colorByFamily: "#FFC0CB",
       color: "hsl(264.7, 100%, 69%)",
-      mass: 146.2
+      mass: 128.17228
     },
     M: {
       value: "M",
@@ -12072,7 +11925,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       hydrophobicity: 1.9,
       colorByFamily: "#FFFF00",
       color: "hsl(328.5, 100%, 69%)",
-      mass: 149.2
+      mass: 131.19606
     },
     F: {
       value: "F",
@@ -12081,7 +11934,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       hydrophobicity: 2.8,
       colorByFamily: "#FFA500",
       color: "hsl(338.4, 100%, 69%)",
-      mass: 165.2
+      mass: 147.17386
     },
     P: {
       value: "P",
@@ -12090,7 +11943,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       hydrophobicity: -1.6,
       colorByFamily: "#00FFFF",
       color: "hsl(289.9, 100%, 69%)",
-      mass: 115.1
+      mass: 97.11518
     },
     S: {
       value: "S",
@@ -12099,7 +11952,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       hydrophobicity: -0.8,
       colorByFamily: "#90EE90",
       color: "hsl(298.6, 100%, 69%)",
-      mass: 105.1
+      mass: 87.0773
     },
     T: {
       value: "T",
@@ -12108,7 +11961,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       hydrophobicity: -0.7,
       colorByFamily: "#90EE90",
       color: "hsl(299.8, 100%, 69%)",
-      mass: 119.1
+      mass: 101.10388
     },
     U: {
       value: "U",
@@ -12116,7 +11969,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       threeLettersName: "Sec",
       colorByFamily: "#FF0000",
       color: "hsl(0, 100%, 69%)",
-      mass: 168.1
+      mass: 150.3079
     },
     W: {
       value: "W",
@@ -12125,7 +11978,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       hydrophobicity: -0.9,
       colorByFamily: "#FFA500",
       color: "hsl(297.6, 100%, 69%)",
-      mass: 204.2
+      mass: 186.2099
     },
     Y: {
       value: "Y",
@@ -12134,7 +11987,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       hydrophobicity: -1.3,
       colorByFamily: "#FFA500",
       color: "hsl(293.2, 100%, 69%)",
-      mass: 181.2
+      mass: 163.17326
     },
     V: {
       value: "V",
@@ -12143,7 +11996,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       hydrophobicity: 4.2,
       colorByFamily: "#00FFFF",
       color: "hsl(353.6, 100%, 69%)",
-      mass: 117.1
+      mass: 99.13106
     },
     "*": {
       value: "*",
@@ -12472,20 +12325,91 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     "primers",
     "guides"
   ];
-  function filterSequenceString(sequenceString, additionalValidChars = "", charOverrides) {
-    if (sequenceString) {
-      return sequenceString.replace(
-        new RegExp(
-          `[^${charOverrides || `atgcyrswkmbvdhnu${additionalValidChars.split("").join("\\")}`}]`,
-          "gi"
-        ),
-        ""
+  function filterSequenceString(sequenceString, {
+    additionalValidChars = "",
+    isOligo,
+    name,
+    isProtein,
+    isRna,
+    isMixedRnaAndDna,
+    includeStopCodon
+  } = {}) {
+    const acceptedChars = getAcceptedChars({
+      isOligo,
+      isProtein,
+      isRna,
+      isMixedRnaAndDna,
+      includeStopCodon
+    });
+    const replaceChars = getReplaceChars({
+      isOligo,
+      isProtein,
+      isRna,
+      isMixedRnaAndDna
+    });
+    let sanitizedVal = "";
+    const invalidChars = [];
+    const chars = `${acceptedChars}${additionalValidChars.split("").join("\\")}`;
+    const warnings = [];
+    const replaceCount = {};
+    sequenceString.split("").forEach((letter) => {
+      const lowerLetter = letter.toLowerCase();
+      if (replaceChars && replaceChars[lowerLetter]) {
+        if (!replaceCount[lowerLetter]) {
+          replaceCount[lowerLetter] = 0;
+        }
+        replaceCount[lowerLetter]++;
+        const isUpper = lowerLetter !== letter;
+        sanitizedVal += isUpper ? replaceChars[lowerLetter].toUpperCase() : replaceChars[lowerLetter];
+      } else if (chars.includes(lowerLetter)) {
+        sanitizedVal += letter;
+      } else {
+        invalidChars.push(letter);
+      }
+    });
+    Object.keys(replaceCount).forEach((letter) => {
+      warnings.push(
+        `Replaced "${letter}" with "${replaceChars[letter]}"${replaceCount[letter] > 1 ? ` ${replaceCount[letter]} times` : ""}`
       );
-    } else {
-      return sequenceString;
+    });
+    if (sequenceString.length !== sanitizedVal.length) {
+      warnings.push(
+        `${name ? `Sequence ${name}: ` : ""}Invalid character(s) detected and removed: ${invalidChars.slice(0, 100).join(", ")} `
+      );
+    }
+    if (typeof window !== "undefined" && window.toastr && warnings.length) {
+      warnings.forEach((warning) => {
+        window.toastr.warning(warning);
+      });
     }
+    return [sanitizedVal, warnings];
   }
   __name(filterSequenceString, "filterSequenceString");
+  function getAcceptedChars({
+    isOligo,
+    isProtein,
+    isRna,
+    isMixedRnaAndDna,
+    includeStopCodon
+  } = {}) {
+    return isProtein ? `${protein_letters_withUandX.toLowerCase()}${includeStopCodon ? "*." : ""}}` : isOligo ? ambiguous_rna_letters.toLowerCase() + "t" : isRna ? ambiguous_rna_letters.toLowerCase() + "t" : isMixedRnaAndDna ? ambiguous_rna_letters.toLowerCase() + ambiguous_dna_letters.toLowerCase() : (
+      //just plain old dna
+      ambiguous_rna_letters.toLowerCase() + ambiguous_dna_letters.toLowerCase()
+    );
+  }
+  __name(getAcceptedChars, "getAcceptedChars");
+  function getReplaceChars({
+    isOligo,
+    isProtein,
+    isRna,
+    isMixedRnaAndDna
+  } = {}) {
+    return isProtein ? {} : isOligo ? {} : isRna ? { t: "u" } : isMixedRnaAndDna ? {} : (
+      //just plain old dna
+      {}
+    );
+  }
+  __name(getReplaceChars, "getReplaceChars");
   function tidyUpAnnotation(_annotation, {
     sequenceData = {},
     convertAnnotationsFromAAIndices,
@@ -12598,13 +12522,13 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       messages.push(
         "Invalid annotation start: " + location.start + " detected for " + location.name + " and set to size: " + size
       );
-      location.start = size - (isProtein ? 3 : 1);
+      location.start = Math.max(0, size - (isProtein ? 3 : 1));
     }
     if (location.end < 0 || !(location.end <= size - 1) || location.end > size - 1) {
       messages.push(
         "Invalid annotation end:  " + location.end + " detected for " + location.name + " and set to seq size: " + size
       );
-      location.end = size - 1;
+      location.end = Math.max(0, size - 1);
     }
     if (location.start > location.end && circular === false) {
       messages.push(
@@ -12614,14 +12538,6 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     }
   }
   __name(coerceLocation, "coerceLocation");
-  function filterAminoAcidSequenceString(sequenceString, options) {
-    options = options || {};
-    if (options.includeStopCodon) {
-      return sequenceString.replace(/[^xtgalmfwkqespvicyhrndu.*]/gi, "");
-    }
-    return sequenceString.replace(/[^xtgalmfwkqespvicyhrndu]/gi, "");
-  }
-  __name(filterAminoAcidSequenceString, "filterAminoAcidSequenceString");
   function getDegenerateDnaStringFromAAString(aaString) {
     return aaString.split("").map((char) => aminoAcidToDegenerateDnaMap[char.toLowerCase()] || "nnn").join("");
   }
@@ -12633,11 +12549,10 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
       removeUnwantedChars,
       additionalValidChars,
       noTranslationData,
-      charOverrides,
       doNotProvideIdsForAnnotations,
-      proteinFilterOptions,
       noCdsTranslations,
-      convertAnnotationsFromAAIndices
+      convertAnnotationsFromAAIndices,
+      topLevelSeqData
     } = options;
     let seqData = lodashExports.cloneDeep(pSeqData);
     const response = {
@@ -12667,16 +12582,15 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     }
     if (removeUnwantedChars) {
       if (seqData.isProtein) {
-        seqData.proteinSequence = filterAminoAcidSequenceString(
-          seqData.proteinSequence,
-          __spreadValues({ includeStopCodon: true }, proteinFilterOptions)
-        );
+        const [newSeq] = filterSequenceString(seqData.proteinSequence, __spreadValues({
+          includeStopCodon: true
+        }, topLevelSeqData || seqData));
+        seqData.proteinSequence = newSeq;
       } else {
-        seqData.sequence = filterSequenceString(
-          seqData.sequence,
-          `${additionalValidChars || ""}${seqData.isRna || seqData.isMixedRnaAndDna ? "u" : ""}`,
-          charOverrides
-        );
+        const [newSeq] = filterSequenceString(seqData.sequence, __spreadValues({
+          additionalValidChars
+        }, topLevelSeqData || seqData));
+        seqData.sequence = newSeq;
       }
     }
     if (seqData.isProtein) {
@@ -13110,7 +13024,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     calculateTemperature: function(sequence, type, A, R, C, Na) {
       if (typeof type === "undefined") {
         type = this.TABLE_BRESLAUER;
-      } else if (type != this.TABLE_BRESLAUER && (type != this.TABLE_UNIFIED && type != this.TABLE_SUGIMOTO)) {
+      } else if (type != this.TABLE_BRESLAUER && type != this.TABLE_UNIFIED && type != this.TABLE_SUGIMOTO) {
         throw new Error("Invalid table type!");
       }
       if (!A) {
@@ -21472,12 +21386,7 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   }
   __name(findSequenceMatches, "findSequenceMatches");
   function findSequenceMatchesTopStrand(sequence, searchString, options = {}) {
-    const {
-      isCircular,
-      isAmbiguous,
-      isProteinSequence,
-      isProteinSearch
-    } = options;
+    const { isCircular, isAmbiguous, isProteinSequence, isProteinSearch } = options;
     let searchStringToUse = escapeStringRegexp(searchString);
     if (isAmbiguous) {
       if (isProteinSearch || isProteinSequence) {
@@ -21610,7 +21519,10 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   __name(getComplementAminoAcidStringFromSequenceString, "getComplementAminoAcidStringFromSequenceString");
   function getComplementSequenceString(sequence, isRna) {
     let complementSeqString = "";
-    const complementMap = lodashExports.merge(DNAComplementMap, isRna ? { a: "u", A: "U" } : { a: "t", A: "T" });
+    const complementMap = lodashExports.merge(
+      DNAComplementMap,
+      isRna ? { a: "u", A: "U" } : { a: "t", A: "T" }
+    );
     for (let i = 0; i < sequence.length; i++) {
       let complementChar = complementMap[sequence[i]];
       if (!complementChar) {
@@ -21914,7 +21826,9 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   }
   __name(getReverseAminoAcidStringFromSequenceString, "getReverseAminoAcidStringFromSequenceString");
   function getReverseComplementAminoAcidStringFromSequenceString(sequenceString) {
-    return getAminoAcidStringFromSequenceString(getReverseComplementSequenceString(sequenceString));
+    return getAminoAcidStringFromSequenceString(
+      getReverseComplementSequenceString(sequenceString)
+    );
   }
   __name(getReverseComplementAminoAcidStringFromSequenceString, "getReverseComplementAminoAcidStringFromSequenceString");
   function getReverseComplementAnnotation(annotation, sequenceLength) {
@@ -22764,6 +22678,9 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
     if (divideByThree) {
       sumMass /= 3;
     }
+    if (aaString.length > 0) {
+      sumMass = sumMass + 18.0153;
+    }
     return Math.round(sumMass * __pow(10, numsAfterDecimal)) / __pow(10, numsAfterDecimal);
   }
   __name(getMassOfAaString, "getMassOfAaString");
@@ -22813,7 +22730,6 @@ var __name = (target, value) => __defProp(target, "name", { value, configurable:
   exports2.deleteSequenceDataAtRange = deleteSequenceDataAtRange;
   exports2.doesEnzymeChopOutsideOfRecognitionSite = doesEnzymeChopOutsideOfRecognitionSite;
   exports2.featureColors = featureColors;
-  exports2.filterAminoAcidSequenceString = filterAminoAcidSequenceString;
   exports2.filterSequenceString = filterSequenceString;
   exports2.findNearestRangeOfSequenceOverlapToPosition = findNearestRangeOfSequenceOverlapToPosition;
   exports2.findOrfsInPlasmid = findOrfsInPlasmid;