@teselagen/ove 0.3.28 → 0.3.30

package/index.umd.js

@@ -106643,6 +106643,7 @@ ${latestSubscriptionCallbackError.current.stack}
     ))),
     400
   );
+  const isSafari = /^((?!chrome|android).)*safari/i.test(navigator.userAgent);
   function genericCommandFactory(config) {
     const out = {};
     for (const cmdId in config.commandDefs) {
@@ -107696,30 +107697,6 @@ ${latestSubscriptionCallbackError.current.stack}
   }, Symbol.toStringTag, { value: "Module" }));
   const protein_letters = "ACDEFGHIKLMNPQRSTVWY";
   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";
@@ -107744,135 +107721,6 @@ ${latestSubscriptionCallbackError.current.stack}
     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",
@@ -107907,140 +107755,17 @@ ${latestSubscriptionCallbackError.current.stack}
     ".": "\\.\\.",
     "-": "\\-"
   };
-  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_dna_values$1,
-    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,
     unambiguous_dna_letters,
-    unambiguous_dna_weights,
-    unambiguous_rna_letters,
-    unambiguous_rna_weights
+    unambiguous_rna_letters
   }, Symbol.toStringTag, { value: "Module" }));
   const aminoAcidToDegenerateDnaMap = {
     "-": "---",
@@ -113549,7 +113274,7 @@ ${latestSubscriptionCallbackError.current.stack}
       hydrophobicity: 1.8,
       colorByFamily: "#00FFFF",
       color: "hsl(327.3, 100%, 69%)",
-      mass: 89.1
+      mass: 71.0779
     },
     R: {
       value: "R",
@@ -113558,7 +113283,7 @@ ${latestSubscriptionCallbackError.current.stack}
       hydrophobicity: -4.5,
       colorByFamily: "#FFC0CB",
       color: "hsl(258.1, 100%, 69%)",
-      mass: 174.2
+      mass: 156.18568
     },
     N: {
       value: "N",
@@ -113567,7 +113292,7 @@ ${latestSubscriptionCallbackError.current.stack}
       hydrophobicity: -3.5,
       colorByFamily: "#D3D3D3",
       color: "hsl(268.9, 100%, 69%)",
-      mass: 132.1
+      mass: 114.10264
     },
     D: {
       value: "D",
@@ -113576,7 +113301,7 @@ ${latestSubscriptionCallbackError.current.stack}
       hydrophobicity: -3.5,
       colorByFamily: "#EE82EE",
       color: "hsl(268.9, 100%, 69%)",
-      mass: 133.1
+      mass: 115.0874
     },
     C: {
       value: "C",
@@ -113585,7 +113310,7 @@ ${latestSubscriptionCallbackError.current.stack}
       hydrophobicity: 2.5,
       colorByFamily: "#FFFF00",
       color: "hsl(335.1, 100%, 69%)",
-      mass: 121.2
+      mass: 103.1429
     },
     E: {
       value: "E",
@@ -113594,7 +113319,7 @@ ${latestSubscriptionCallbackError.current.stack}
       hydrophobicity: -3.5,
       colorByFamily: "#EE82EE",
       color: "hsl(268.9, 100%, 69%)",
-      mass: 147.1
+      mass: 129.11398
     },
     Q: {
       value: "Q",
@@ -113603,7 +113328,7 @@ ${latestSubscriptionCallbackError.current.stack}
       hydrophobicity: -3.5,
       colorByFamily: "#D3D3D3",
       color: "hsl(268.9, 100%, 69%)",
-      mass: 146.2
+      mass: 128.12922
     },
     G: {
       value: "G",
@@ -113612,7 +113337,7 @@ ${latestSubscriptionCallbackError.current.stack}
       hydrophobicity: -0.4,
       colorByFamily: "#00FFFF",
       color: "hsl(303.1, 100%, 69%)",
-      mass: 75.1
+      mass: 57.05132
     },
     H: {
       value: "H",
@@ -113621,7 +113346,7 @@ ${latestSubscriptionCallbackError.current.stack}
       hydrophobicity: -3.2,
       colorByFamily: "#FFC0CB",
       color: "hsl(272.2, 100%, 69%)",
-      mass: 155.2
+      mass: 137.13928
     },
     I: {
       value: "I",
@@ -113630,7 +113355,7 @@ ${latestSubscriptionCallbackError.current.stack}
       hydrophobicity: 4.5,
       colorByFamily: "#00FFFF",
       color: "hsl(356.9, 100%, 69%)",
-      mass: 131.2
+      mass: 113.15764
     },
     L: {
       value: "L",
@@ -113639,7 +113364,7 @@ ${latestSubscriptionCallbackError.current.stack}
       hydrophobicity: 3.8,
       colorByFamily: "#00FFFF",
       color: "hsl(349.4, 100%, 69%)",
-      mass: 131.2
+      mass: 113.15764
     },
     K: {
       value: "K",
@@ -113648,7 +113373,7 @@ ${latestSubscriptionCallbackError.current.stack}
       hydrophobicity: -3.9,
       colorByFamily: "#FFC0CB",
       color: "hsl(264.7, 100%, 69%)",
-      mass: 146.2
+      mass: 128.17228
     },
     M: {
       value: "M",
@@ -113657,7 +113382,7 @@ ${latestSubscriptionCallbackError.current.stack}
       hydrophobicity: 1.9,
       colorByFamily: "#FFFF00",
       color: "hsl(328.5, 100%, 69%)",
-      mass: 149.2
+      mass: 131.19606
     },
     F: {
       value: "F",
@@ -113666,7 +113391,7 @@ ${latestSubscriptionCallbackError.current.stack}
       hydrophobicity: 2.8,
       colorByFamily: "#FFA500",
       color: "hsl(338.4, 100%, 69%)",
-      mass: 165.2
+      mass: 147.17386
     },
     P: {
       value: "P",
@@ -113675,7 +113400,7 @@ ${latestSubscriptionCallbackError.current.stack}
       hydrophobicity: -1.6,
       colorByFamily: "#00FFFF",
       color: "hsl(289.9, 100%, 69%)",
-      mass: 115.1
+      mass: 97.11518
     },
     S: {
       value: "S",
@@ -113684,7 +113409,7 @@ ${latestSubscriptionCallbackError.current.stack}
       hydrophobicity: -0.8,
       colorByFamily: "#90EE90",
       color: "hsl(298.6, 100%, 69%)",
-      mass: 105.1
+      mass: 87.0773
     },
     T: {
       value: "T",
@@ -113693,7 +113418,7 @@ ${latestSubscriptionCallbackError.current.stack}
       hydrophobicity: -0.7,
       colorByFamily: "#90EE90",
       color: "hsl(299.8, 100%, 69%)",
-      mass: 119.1
+      mass: 101.10388
     },
     U: {
       value: "U",
@@ -113701,7 +113426,7 @@ ${latestSubscriptionCallbackError.current.stack}
       threeLettersName: "Sec",
       colorByFamily: "#FF0000",
       color: "hsl(0, 100%, 69%)",
-      mass: 168.1
+      mass: 150.3079
     },
     W: {
       value: "W",
@@ -113710,7 +113435,7 @@ ${latestSubscriptionCallbackError.current.stack}
       hydrophobicity: -0.9,
       colorByFamily: "#FFA500",
       color: "hsl(297.6, 100%, 69%)",
-      mass: 204.2
+      mass: 186.2099
     },
     Y: {
       value: "Y",
@@ -113719,7 +113444,7 @@ ${latestSubscriptionCallbackError.current.stack}
       hydrophobicity: -1.3,
       colorByFamily: "#FFA500",
       color: "hsl(293.2, 100%, 69%)",
-      mass: 181.2
+      mass: 163.17326
     },
     V: {
       value: "V",
@@ -113728,7 +113453,7 @@ ${latestSubscriptionCallbackError.current.stack}
       hydrophobicity: 4.2,
       colorByFamily: "#00FFFF",
       color: "hsl(353.6, 100%, 69%)",
-      mass: 117.1
+      mass: 99.13106
     },
     "*": {
       value: "*",
@@ -123397,6 +123122,9 @@ ${latestSubscriptionCallbackError.current.stack}
     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");
@@ -150746,10 +150474,10 @@ ${seq.sequence}
       }, containerStyle);
       const width = rowSeqLen * charWidth2;
       let inner2;
-      const shared2 = {
+      const shared2 = __spreadProps(__spreadValues({}, isSafari ? { letterSpacing: "3px" } : {}), {
         y: height2 - height2 / 4,
         className: "ve-monospace-font " + (isReverse ? " ve-sequence-reverse" : "")
-      };
+      });
       if (scrollData) {
         const numChunks = Math.ceil(rowSeqLen / chunkSize);
         const chunkWidth = chunkSize * charWidth2;
@@ -155180,7 +154908,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
   }
   __name(showFileDialog, "showFileDialog");
   const name = "@teselagen/ove";
-  const version = "0.3.27";
+  const version = "0.3.29";
   const main = "./src/index.js";
   const exports$1 = {
     ".": {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.3.28",
+  "version": "0.3.30",
   "main": "./src/index.js",
   "exports": {
     ".": {
@@ -13,12 +13,12 @@
     "node": "16.20.2"
   },
   "dependencies": {
-    "@teselagen/sequence-utils": "0.3.7",
+    "@teselagen/sequence-utils": "0.3.8",
     "@teselagen/range-utils": "0.3.7",
-    "@teselagen/ui": "0.3.28",
+    "@teselagen/ui": "0.3.29",
     "@teselagen/file-utils": "0.3.9",
     "@teselagen/bounce-loader": "0.3.11",
-    "@teselagen/bio-parsers": "0.3.9",
+    "@teselagen/bio-parsers": "0.3.10",
     "@blueprintjs/core": "3.52.0",
     "@blueprintjs/datetime": "3.23.19",
     "@blueprintjs/icons": "3.33.0",

package/src/RowItem/Sequence.js

@@ -8,6 +8,7 @@ import { hoveredAnnEasyStore } from "../helperComponents/withHover";
 import { getOverlapsOfPotentiallyCircularRanges } from "@teselagen/range-utils";
 import { partOverhangs } from "./partOverhangs";
 import { isPositionWithinRange } from "@teselagen/range-utils";
+import { isSafari } from "@teselagen/ui";
 
 const getChunk = (sequence, chunkSize, chunkNumber) =>
   sequence.slice(chunkSize * chunkNumber, chunkSize * (chunkNumber + 1));
@@ -89,6 +90,7 @@ class Sequence extends React.Component {
 
     let inner;
     const shared = {
+      ...isSafari ? { letterSpacing: "3px" } : {},
       y: height - height / 4,
       className:
         "ve-monospace-font " + (isReverse ? " ve-sequence-reverse" : "")