@teselagen/sequence-utils 0.3.7 → 0.3.9

package/index.js

@@ -5999,31 +5999,8 @@ lodash.exports;
 })(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";
@@ -6048,135 +6025,6 @@ const ambiguous_dna_values = {
   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",
@@ -6211,140 +6059,18 @@ const extended_protein_values = {
   ".": "\\.\\.",
   "-": "\\-"
 };
-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 = {
   "-": "---",
@@ -6458,8 +6184,8 @@ function getOverlapsOfPotentiallyCircularRanges(rangeA, rangeB, maxRangeLength,
     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
@@ -6471,7 +6197,7 @@ function getOverlapsOfPotentiallyCircularRanges(rangeA, rangeB, maxRangeLength,
   });
   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 [];
@@ -6569,12 +6295,14 @@ function trimRangeByAnotherRange(rangeToBeTrimmed, trimmingRange, sequenceLength
     });
     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)
     ;
@@ -6673,11 +6401,19 @@ function checkIfNonCircularRangesOverlap(range, comparisonRange) {
 }
 __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) {
@@ -6686,15 +6422,19 @@ function collapseOverlapsGeneratedFromRangeComparisonIfPossible(overlaps, sequen
     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;
     }
@@ -6702,17 +6442,29 @@ function collapseOverlapsGeneratedFromRangeComparisonIfPossible(overlaps, sequen
     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;
@@ -6819,13 +6571,23 @@ function expandOrContractRangeByLength(range, shiftBy, shiftStart, sequenceLengt
 __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 {
@@ -6833,42 +6595,92 @@ function flipRelativeRange(innerRange, outerRange, sequenceLength, options) {
   }
 }
 __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");
@@ -6886,7 +6698,10 @@ function generateRandomRange(minStart, maxEnd, maxLength) {
   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);
   }
@@ -6929,18 +6744,26 @@ function getShortestDistanceBetweenTwoPositions(position1, position2, sequenceLe
 __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)
@@ -6954,7 +6777,11 @@ function getYOffsetsForPotentiallyCircularRanges(ranges, assignYOffsetToRange) {
   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;
@@ -6987,8 +6814,16 @@ function invertRange$1(rangeOrCaret, rangeMax) {
 }
 __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");
@@ -7019,9 +6854,15 @@ function reversePositionInRange(position, rangeLength, isInBetweenPositions) {
 }
 __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;
@@ -7049,12 +6890,24 @@ function modulo(n, m) {
 }
 __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;
 }
@@ -11962,7 +11815,7 @@ const proteinAlphabet = {
     hydrophobicity: 1.8,
     colorByFamily: "#00FFFF",
     color: "hsl(327.3, 100%, 69%)",
-    mass: 89.1
+    mass: 71.0779
   },
   R: {
     value: "R",
@@ -11971,7 +11824,7 @@ const proteinAlphabet = {
     hydrophobicity: -4.5,
     colorByFamily: "#FFC0CB",
     color: "hsl(258.1, 100%, 69%)",
-    mass: 174.2
+    mass: 156.18568
   },
   N: {
     value: "N",
@@ -11980,7 +11833,7 @@ const proteinAlphabet = {
     hydrophobicity: -3.5,
     colorByFamily: "#D3D3D3",
     color: "hsl(268.9, 100%, 69%)",
-    mass: 132.1
+    mass: 114.10264
   },
   D: {
     value: "D",
@@ -11989,7 +11842,7 @@ const proteinAlphabet = {
     hydrophobicity: -3.5,
     colorByFamily: "#EE82EE",
     color: "hsl(268.9, 100%, 69%)",
-    mass: 133.1
+    mass: 115.0874
   },
   C: {
     value: "C",
@@ -11998,7 +11851,7 @@ const proteinAlphabet = {
     hydrophobicity: 2.5,
     colorByFamily: "#FFFF00",
     color: "hsl(335.1, 100%, 69%)",
-    mass: 121.2
+    mass: 103.1429
   },
   E: {
     value: "E",
@@ -12007,7 +11860,7 @@ const proteinAlphabet = {
     hydrophobicity: -3.5,
     colorByFamily: "#EE82EE",
     color: "hsl(268.9, 100%, 69%)",
-    mass: 147.1
+    mass: 129.11398
   },
   Q: {
     value: "Q",
@@ -12016,7 +11869,7 @@ const proteinAlphabet = {
     hydrophobicity: -3.5,
     colorByFamily: "#D3D3D3",
     color: "hsl(268.9, 100%, 69%)",
-    mass: 146.2
+    mass: 128.12922
   },
   G: {
     value: "G",
@@ -12025,7 +11878,7 @@ const proteinAlphabet = {
     hydrophobicity: -0.4,
     colorByFamily: "#00FFFF",
     color: "hsl(303.1, 100%, 69%)",
-    mass: 75.1
+    mass: 57.05132
   },
   H: {
     value: "H",
@@ -12034,7 +11887,7 @@ const proteinAlphabet = {
     hydrophobicity: -3.2,
     colorByFamily: "#FFC0CB",
     color: "hsl(272.2, 100%, 69%)",
-    mass: 155.2
+    mass: 137.13928
   },
   I: {
     value: "I",
@@ -12043,7 +11896,7 @@ const proteinAlphabet = {
     hydrophobicity: 4.5,
     colorByFamily: "#00FFFF",
     color: "hsl(356.9, 100%, 69%)",
-    mass: 131.2
+    mass: 113.15764
   },
   L: {
     value: "L",
@@ -12052,7 +11905,7 @@ const proteinAlphabet = {
     hydrophobicity: 3.8,
     colorByFamily: "#00FFFF",
     color: "hsl(349.4, 100%, 69%)",
-    mass: 131.2
+    mass: 113.15764
   },
   K: {
     value: "K",
@@ -12061,7 +11914,7 @@ const proteinAlphabet = {
     hydrophobicity: -3.9,
     colorByFamily: "#FFC0CB",
     color: "hsl(264.7, 100%, 69%)",
-    mass: 146.2
+    mass: 128.17228
   },
   M: {
     value: "M",
@@ -12070,7 +11923,7 @@ const proteinAlphabet = {
     hydrophobicity: 1.9,
     colorByFamily: "#FFFF00",
     color: "hsl(328.5, 100%, 69%)",
-    mass: 149.2
+    mass: 131.19606
   },
   F: {
     value: "F",
@@ -12079,7 +11932,7 @@ const proteinAlphabet = {
     hydrophobicity: 2.8,
     colorByFamily: "#FFA500",
     color: "hsl(338.4, 100%, 69%)",
-    mass: 165.2
+    mass: 147.17386
   },
   P: {
     value: "P",
@@ -12088,7 +11941,7 @@ const proteinAlphabet = {
     hydrophobicity: -1.6,
     colorByFamily: "#00FFFF",
     color: "hsl(289.9, 100%, 69%)",
-    mass: 115.1
+    mass: 97.11518
   },
   S: {
     value: "S",
@@ -12097,7 +11950,7 @@ const proteinAlphabet = {
     hydrophobicity: -0.8,
     colorByFamily: "#90EE90",
     color: "hsl(298.6, 100%, 69%)",
-    mass: 105.1
+    mass: 87.0773
   },
   T: {
     value: "T",
@@ -12106,7 +11959,7 @@ const proteinAlphabet = {
     hydrophobicity: -0.7,
     colorByFamily: "#90EE90",
     color: "hsl(299.8, 100%, 69%)",
-    mass: 119.1
+    mass: 101.10388
   },
   U: {
     value: "U",
@@ -12114,7 +11967,7 @@ const proteinAlphabet = {
     threeLettersName: "Sec",
     colorByFamily: "#FF0000",
     color: "hsl(0, 100%, 69%)",
-    mass: 168.1
+    mass: 150.3079
   },
   W: {
     value: "W",
@@ -12123,7 +11976,7 @@ const proteinAlphabet = {
     hydrophobicity: -0.9,
     colorByFamily: "#FFA500",
     color: "hsl(297.6, 100%, 69%)",
-    mass: 204.2
+    mass: 186.2099
   },
   Y: {
     value: "Y",
@@ -12132,7 +11985,7 @@ const proteinAlphabet = {
     hydrophobicity: -1.3,
     colorByFamily: "#FFA500",
     color: "hsl(293.2, 100%, 69%)",
-    mass: 181.2
+    mass: 163.17326
   },
   V: {
     value: "V",
@@ -12141,7 +11994,7 @@ const proteinAlphabet = {
     hydrophobicity: 4.2,
     colorByFamily: "#00FFFF",
     color: "hsl(353.6, 100%, 69%)",
-    mass: 117.1
+    mass: 99.13106
   },
   "*": {
     value: "*",
@@ -12470,20 +12323,91 @@ const modifiableTypes = [
   "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,
@@ -12596,13 +12520,13 @@ function coerceLocation({
     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(
@@ -12612,14 +12536,6 @@ function coerceLocation({
   }
 }
 __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("");
 }
@@ -12631,11 +12547,10 @@ function tidyUpSequenceData(pSeqData, options = {}) {
     removeUnwantedChars,
     additionalValidChars,
     noTranslationData,
-    charOverrides,
     doNotProvideIdsForAnnotations,
-    proteinFilterOptions,
     noCdsTranslations,
-    convertAnnotationsFromAAIndices
+    convertAnnotationsFromAAIndices,
+    topLevelSeqData
   } = options;
   let seqData = lodashExports.cloneDeep(pSeqData);
   const response = {
@@ -12665,16 +12580,15 @@ function tidyUpSequenceData(pSeqData, options = {}) {
   }
   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) {
@@ -13108,7 +13022,7 @@ const calcTmMethods = {
   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) {
@@ -21470,12 +21384,7 @@ function findSequenceMatches(sequence, searchString, options = {}) {
 }
 __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) {
@@ -21608,7 +21517,10 @@ function getComplementAminoAcidStringFromSequenceString(sequenceString) {
 __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) {
@@ -21912,7 +21824,9 @@ function getReverseAminoAcidStringFromSequenceString(sequenceString) {
 }
 __name(getReverseAminoAcidStringFromSequenceString, "getReverseAminoAcidStringFromSequenceString");
 function getReverseComplementAminoAcidStringFromSequenceString(sequenceString) {
-  return getAminoAcidStringFromSequenceString(getReverseComplementSequenceString(sequenceString));
+  return getAminoAcidStringFromSequenceString(
+    getReverseComplementSequenceString(sequenceString)
+  );
 }
 __name(getReverseComplementAminoAcidStringFromSequenceString, "getReverseComplementAminoAcidStringFromSequenceString");
 function getReverseComplementAnnotation(annotation, sequenceLength) {
@@ -22762,6 +22676,9 @@ function getMassOfAaString(aaString, numsAfterDecimal = 2, divideByThree = false
   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");
@@ -22811,7 +22728,6 @@ exports.degenerateRnaToAminoAcidMap = degenerateRnaToAminoAcidMap;
 exports.deleteSequenceDataAtRange = deleteSequenceDataAtRange;
 exports.doesEnzymeChopOutsideOfRecognitionSite = doesEnzymeChopOutsideOfRecognitionSite;
 exports.featureColors = featureColors;
-exports.filterAminoAcidSequenceString = filterAminoAcidSequenceString;
 exports.filterSequenceString = filterSequenceString;
 exports.findNearestRangeOfSequenceOverlapToPosition = findNearestRangeOfSequenceOverlapToPosition;
 exports.findOrfsInPlasmid = findOrfsInPlasmid;