@teselagen/ove 0.8.18 → 0.8.20

package/index.cjs.js

@@ -8349,6 +8349,15 @@ function baseLt(value, other) {
   return value < other;
 }
 __name(baseLt, "baseLt");
+function mapValues$1(object3, iteratee) {
+  var result = {};
+  iteratee = baseIteratee(iteratee);
+  baseForOwn(object3, function(value, key, object4) {
+    baseAssignValue(result, key, iteratee(value, key, object4));
+  });
+  return result;
+}
+__name(mapValues$1, "mapValues$1");
 function baseExtremum(array2, iteratee, comparator) {
   var index2 = -1, length = array2.length;
   while (++index2 < length) {
@@ -13213,12 +13222,12 @@ var getComputedStyleX;
 if (typeof window !== "undefined") {
   getComputedStyleX = window.getComputedStyle ? _getComputedStyle : _getComputedStyleIE;
 }
-function each$2(arr, fn4) {
+function each(arr, fn4) {
   for (var i = 0; i < arr.length; i++) {
     fn4(arr[i]);
   }
 }
-__name(each$2, "each$2");
+__name(each, "each");
 function isBorderBoxFn(elem) {
   return getComputedStyleX(elem, "boxSizing") === "border-box";
 }
@@ -13273,7 +13282,7 @@ function isWindow(obj) {
 }
 __name(isWindow, "isWindow");
 var domUtils = {};
-each$2(["Width", "Height"], function(name2) {
+each(["Width", "Height"], function(name2) {
   domUtils["doc".concat(name2)] = function(refWin) {
     var d2 = refWin.document;
     return Math.max(
@@ -13369,7 +13378,7 @@ function css(el, name2, v2) {
   return getComputedStyleX(el, name2);
 }
 __name(css, "css");
-each$2(["width", "height"], function(name2) {
+each(["width", "height"], function(name2) {
   var first = name2.charAt(0).toUpperCase() + name2.slice(1);
   domUtils["outer".concat(first)] = function(el, includeMargin) {
     return el && getWHIgnoreDisplay(el, name2, includeMargin ? MARGIN_INDEX : BORDER_INDEX);
@@ -13420,7 +13429,7 @@ var util$2 = _objectSpread2$2({
     }
   }, "offset"),
   isWindow,
-  each: each$2,
+  each,
   css,
   clone: /* @__PURE__ */ __name(function clone(obj) {
     var ret = {};
@@ -75209,17 +75218,25 @@ function tidyUpSequenceData(pSeqData, options = {}) {
   });
   if (!noTranslationData) {
     seqData.translations = flatMap(seqData.translations, (translation) => {
+      var _a2, _b2;
       if (noCdsTranslations && translation.translationType === "CDS Feature") {
         return [];
       }
-      if (!translation.aminoAcids && !seqData.noSequence) {
-        translation.aminoAcids = getAminoAcidDataForEachBaseOfDna(
+      const codonStart = ((_b2 = (_a2 = translation == null ? void 0 : translation.notes) == null ? void 0 : _a2.codon_start) == null ? void 0 : _b2[0]) - 1 || 0;
+      const expandedRange = expandOrContractRangeByLength(
+        translation,
+        -codonStart,
+        true,
+        seqData.sequence.length
+      );
+      if (!expandedRange.aminoAcids && !seqData.noSequence) {
+        expandedRange.aminoAcids = getAminoAcidDataForEachBaseOfDna(
           seqData.sequence,
-          translation.forward,
-          translation
+          expandedRange.forward,
+          expandedRange
         );
       }
-      return translation;
+      return expandedRange;
     });
   }
   if (annotationsAsObjects) {
@@ -84332,6 +84349,160 @@ function calculateNebTm(sequence2, { monovalentCationConc = 0.05, primerConc = 5
   }
 }
 __name(calculateNebTm, "calculateNebTm");
+const PRIMER3_PARAMS = {
+  saltMonovalent: 50,
+  // mM
+  saltDivalent: 1.5,
+  // mM
+  dntpConc: 0.6,
+  // mM
+  dnaConc: 50,
+  // nM
+  R: 1.987
+  // Gas constant (cal/K·mol)
+};
+const SANTA_LUCIA_NN = {
+  AA: { dH: -7.9, dS: -22.2 },
+  TT: { dH: -7.9, dS: -22.2 },
+  AT: { dH: -7.2, dS: -20.4 },
+  TA: { dH: -7.2, dS: -21.3 },
+  CA: { dH: -8.5, dS: -22.7 },
+  TG: { dH: -8.5, dS: -22.7 },
+  GT: { dH: -8.4, dS: -22.4 },
+  AC: { dH: -8.4, dS: -22.4 },
+  CT: { dH: -7.8, dS: -21 },
+  AG: { dH: -7.8, dS: -21 },
+  GA: { dH: -8.2, dS: -22.2 },
+  TC: { dH: -8.2, dS: -22.2 },
+  CG: { dH: -10.6, dS: -27.2 },
+  GC: { dH: -9.8, dS: -24.4 },
+  GG: { dH: -8, dS: -19.9 },
+  CC: { dH: -8, dS: -19.9 }
+};
+const SANTA_LUCIA_INIT = {
+  GC: { dH: 0.1, dS: -2.8 },
+  // initiation with terminal GC
+  AT: { dH: 2.3, dS: 4.1 }
+  // initiation with terminal AT
+};
+function getEffectiveMonovalentConc() {
+  let effectiveMono = PRIMER3_PARAMS.saltMonovalent;
+  {
+    const freeMg = Math.max(
+      0,
+      PRIMER3_PARAMS.saltDivalent - PRIMER3_PARAMS.dntpConc
+    );
+    effectiveMono += 120 * Math.sqrt(freeMg);
+  }
+  return effectiveMono;
+}
+__name(getEffectiveMonovalentConc, "getEffectiveMonovalentConc");
+function applySaltCorrection(deltaS, nnPairs) {
+  const effectiveMono = getEffectiveMonovalentConc();
+  return deltaS + 0.368 * nnPairs * Math.log(effectiveMono / 1e3);
+}
+__name(applySaltCorrection, "applySaltCorrection");
+function isValidSequence(sequence2) {
+  return /^[ATGCN]+$/.test(sequence2);
+}
+__name(isValidSequence, "isValidSequence");
+function calculateSantaLuciaTm(sequence2) {
+  try {
+    sequence2 = sequence2 == null ? void 0 : sequence2.toUpperCase().trim();
+    if (!isValidSequence(sequence2)) {
+      throw new Error("Invalid sequence: contains non-DNA characters");
+    }
+    if (sequence2.length < 2) {
+      throw new Error("Sequence too short: minimum length is 2 bases");
+    }
+    let deltaH = 0;
+    let deltaS = 0;
+    for (let i = 0; i < sequence2.length - 1; i++) {
+      const dinucleotide = sequence2.substring(i, i + 2);
+      if (dinucleotide.includes("N")) {
+        continue;
+      }
+      const params = SANTA_LUCIA_NN[dinucleotide];
+      if (params) {
+        deltaH += params.dH;
+        deltaS += params.dS;
+      }
+    }
+    const firstBase = sequence2[0];
+    const lastBase = sequence2[sequence2.length - 1];
+    if (firstBase === "G" || firstBase === "C") {
+      deltaH += SANTA_LUCIA_INIT.GC.dH;
+      deltaS += SANTA_LUCIA_INIT.GC.dS;
+    } else {
+      deltaH += SANTA_LUCIA_INIT.AT.dH;
+      deltaS += SANTA_LUCIA_INIT.AT.dS;
+    }
+    if (lastBase === "G" || lastBase === "C") {
+      deltaH += SANTA_LUCIA_INIT.GC.dH;
+      deltaS += SANTA_LUCIA_INIT.GC.dS;
+    } else {
+      deltaH += SANTA_LUCIA_INIT.AT.dH;
+      deltaS += SANTA_LUCIA_INIT.AT.dS;
+    }
+    const nnPairs = sequence2.length - 1;
+    deltaS = applySaltCorrection(deltaS, nnPairs);
+    const C = PRIMER3_PARAMS.dnaConc * 1e-9;
+    const Tm = deltaH * 1e3 / (deltaS + PRIMER3_PARAMS.R * Math.log(C / 4));
+    return Tm - 273.15;
+  } catch (e) {
+    return `Error calculating Tm for sequence ${sequence2}. ${e}`;
+  }
+}
+__name(calculateSantaLuciaTm, "calculateSantaLuciaTm");
+function calculateEndStability(sequence2) {
+  try {
+    sequence2 = sequence2 == null ? void 0 : sequence2.toUpperCase().trim();
+    if (!isValidSequence(sequence2)) {
+      throw new Error("Invalid sequence: contains non-DNA characters");
+    }
+    if (sequence2.length < 5) {
+      throw new Error(
+        "Sequence too short: minimum length is 5 bases for end stability calculation"
+      );
+    }
+    const last5Bases = sequence2.substring(sequence2.length - 5);
+    let deltaH = 0;
+    let deltaS = 0;
+    for (let i = 0; i < 4; i++) {
+      const dinucleotide = last5Bases.substring(i, i + 2);
+      if (dinucleotide.includes("N")) {
+        continue;
+      }
+      const params = SANTA_LUCIA_NN[dinucleotide];
+      if (params) {
+        deltaH += params.dH;
+        deltaS += params.dS;
+      }
+    }
+    const firstBase = last5Bases[0];
+    const lastBase = last5Bases[last5Bases.length - 1];
+    if (firstBase === "G" || firstBase === "C") {
+      deltaH += SANTA_LUCIA_INIT.GC.dH;
+      deltaS += SANTA_LUCIA_INIT.GC.dS;
+    } else {
+      deltaH += SANTA_LUCIA_INIT.AT.dH;
+      deltaS += SANTA_LUCIA_INIT.AT.dS;
+    }
+    if (lastBase === "G" || lastBase === "C") {
+      deltaH += SANTA_LUCIA_INIT.GC.dH;
+      deltaS += SANTA_LUCIA_INIT.GC.dS;
+    } else {
+      deltaH += SANTA_LUCIA_INIT.AT.dH;
+      deltaS += SANTA_LUCIA_INIT.AT.dS;
+    }
+    const T2 = 310.15;
+    const deltaG = deltaH - T2 * deltaS / 1e3;
+    return Math.round(Math.abs(deltaG) * 100) / 100;
+  } catch (e) {
+    return `Error calculating end stability for sequence ${sequence2}. ${e}`;
+  }
+}
+__name(calculateEndStability, "calculateEndStability");
 function convertAACaretPositionOrRangeToDna(rangeOrCaret) {
   if (typeof rangeOrCaret === "object" && rangeOrCaret !== null) {
     return convertAARangeToDnaRange(__spreadProps(__spreadValues({}, rangeOrCaret), {
@@ -97810,32 +97981,6 @@ const orfsSelector = createSelector(
   (state2) => state2.useAdditionalOrfStartCodons,
   findOrfsInPlasmid
 );
-var forEach_1;
-var hasRequiredForEach;
-function requireForEach() {
-  if (hasRequiredForEach) return forEach_1;
-  hasRequiredForEach = 1;
-  var arrayEach2 = require_arrayEach(), baseEach2 = require_baseEach(), castFunction2 = require_castFunction(), isArray2 = requireIsArray();
-  function forEach3(collection, iteratee) {
-    var func = isArray2(collection) ? arrayEach2 : baseEach2;
-    return func(collection, castFunction2(iteratee));
-  }
-  __name(forEach3, "forEach");
-  forEach_1 = forEach3;
-  return forEach_1;
-}
-__name(requireForEach, "requireForEach");
-var each$1;
-var hasRequiredEach;
-function requireEach() {
-  if (hasRequiredEach) return each$1;
-  hasRequiredEach = 1;
-  each$1 = requireForEach();
-  return each$1;
-}
-__name(requireEach, "requireEach");
-var eachExports = requireEach();
-const each = /* @__PURE__ */ getDefaultExportFromCjs(eachExports);
 function translationsRawSelector(sequenceData2) {
   return sequenceData2.translations;
 }
@@ -98002,14 +98147,22 @@ function translationsSelector(isCircular, translationSearchMatches, sequence2, o
     },
     {}
   ));
-  each(translationsToPass, function(translation) {
-    translation.aminoAcids = getAminoAcidDataForEachBaseOfDna(
+  return mapValues$1(translationsToPass, (translation) => {
+    var _a2, _b2;
+    const codonStart = ((_b2 = (_a2 = translation == null ? void 0 : translation.notes) == null ? void 0 : _a2.codon_start) == null ? void 0 : _b2[0]) - 1 || 0;
+    const expandedRange = expandOrContractRangeByLength(
+      translation,
+      -codonStart,
+      true,
+      sequence2.length
+    );
+    expandedRange.aminoAcids = getAminoAcidDataForEachBaseOfDna(
       sequence2,
-      translation.forward,
-      translation
+      expandedRange.forward,
+      expandedRange
     );
+    return expandedRange;
   });
-  return translationsToPass;
 }
 __name(translationsSelector, "translationsSelector");
 const translationsSelector$1 = createSelector(
@@ -109885,6 +110038,21 @@ function Orf(props) {
   );
 }
 __name(Orf, "Orf");
+var forEach_1;
+var hasRequiredForEach;
+function requireForEach() {
+  if (hasRequiredForEach) return forEach_1;
+  hasRequiredForEach = 1;
+  var arrayEach2 = require_arrayEach(), baseEach2 = require_baseEach(), castFunction2 = require_castFunction(), isArray2 = requireIsArray();
+  function forEach3(collection, iteratee) {
+    var func = isArray2(collection) ? arrayEach2 : baseEach2;
+    return func(collection, castFunction2(iteratee));
+  }
+  __name(forEach3, "forEach");
+  forEach_1 = forEach3;
+  return forEach_1;
+}
+__name(requireForEach, "requireForEach");
 var forEachExports = requireForEach();
 const forEach2 = /* @__PURE__ */ getDefaultExportFromCjs(forEachExports);
 var lib = {};
@@ -116640,7 +116808,7 @@ function showFileDialog({ multiple = false, onSelect }) {
   input.click();
 }
 __name(showFileDialog, "showFileDialog");
-const version = "0.8.17";
+const version = "0.8.19";
 const packageJson = {
   version
 };
@@ -124292,6 +124460,7 @@ const __LinearView = class __LinearView extends React.Component {
           RowItem$1,
           __spreadProps(__spreadValues({}, __spreadValues(__spreadProps(__spreadValues({}, rest), {
             editorName,
+            showAminoAcidUnitAsCodon,
             onScroll: /* @__PURE__ */ __name(() => {
               this.easyStore.viewportWidth = width;
               const row = this.linearView.querySelector(".veRowItemWrapper");
@@ -137339,7 +137508,7 @@ function MeltingTemp({
     /* , setMonovalentCationConc */
   ] = React.useState(0.05);
   const [tmType, setTmType] = useTmType();
-  let tm = (tmType === "neb_tm" ? calculateNebTm : calculateTm)(sequence2, {
+  let tm = (tmType === "neb_tm" ? calculateNebTm : tmType === "default" ? calculateSantaLuciaTm : calculateTm)(sequence2, {
     monovalentCationConc,
     primerConc
   });
@@ -137364,8 +137533,9 @@ function MeltingTemp({
         {
           label: "Choose Tm Type:",
           options: [
-            { value: "default", label: "Default Tm (Breslauer)" },
-            { value: "neb_tm", label: "NEB Tm (SantaLucia)" }
+            { value: "default", label: "Santa Lucia (Default)" },
+            { value: "breslauer", label: "Breslauer" },
+            { value: "neb_tm", label: "NEB Tm" }
           ],
           onChange: /* @__PURE__ */ __name((e) => setTmType(e.target.value), "onChange"),
           selectedValue: tmType
@@ -137379,7 +137549,7 @@ function MeltingTemp({
         }
       ), hasWarning, /* @__PURE__ */ React.createElement("br", null), /* @__PURE__ */ React.createElement("br", null), "Try using the Default Tm"))
     },
-    /* @__PURE__ */ React.createElement(React.Fragment, null, /* @__PURE__ */ React.createElement(InnerWrapper, null, "Melting Temp: ", Number(tm) || 0, " "), hasWarning && /* @__PURE__ */ React.createElement(
+    /* @__PURE__ */ React.createElement(React.Fragment, null, /* @__PURE__ */ React.createElement(InnerWrapper, null, "Melting Temp: ", Number(tm) || 0, "°C"), hasWarning && /* @__PURE__ */ React.createElement(
       core.Icon,
       {
         style: { marginLeft: 5, marginRight: 5 },
@@ -137643,12 +137813,24 @@ const RenderBases = /* @__PURE__ */ __name((props) => {
     )), /* @__PURE__ */ React.createElement(
       MeltingTemp,
       {
-        InnerWrapper: InnerWrapperMeltingTemp,
+        InnerWrapper: TextInnerWrapper,
         sequence: bases
       }
-    ))
+    ), /* @__PURE__ */ React.createElement(TextInnerWrapper, null, "GC content: ", bases && calculatePercentGC(bases).toFixed(1), "%"), /* @__PURE__ */ React.createElement(TextInnerWrapper, null, "3' Stability: ", bases && calculateEndStability(bases), " kcal/mol"))
   );
 }, "RenderBases");
+const TextInnerWrapper = /* @__PURE__ */ __name((p2) => /* @__PURE__ */ React.createElement(
+  "div",
+  {
+    className: "bp3-text-muted bp3-text-small",
+    style: {
+      marginBottom: 15,
+      marginTop: -5,
+      fontStyle: "italic"
+    }
+  },
+  p2.children
+), "TextInnerWrapper");
 const AddOrEditPrimerDialog = AddOrEditAnnotationDialog$1({
   formName: "AddOrEditPrimerDialog",
   getProps: /* @__PURE__ */ __name((props) => ({
@@ -137657,14 +137839,6 @@ const AddOrEditPrimerDialog = AddOrEditAnnotationDialog$1({
     RenderBases
   }), "getProps")
 });
-const InnerWrapperMeltingTemp = /* @__PURE__ */ __name((p2) => /* @__PURE__ */ React.createElement(
-  "div",
-  {
-    className: "bp3-text-muted bp3-text-small",
-    style: { marginBottom: 15, marginTop: -5, fontStyle: "italic" }
-  },
-  p2.children
-), "InnerWrapperMeltingTemp");
 const Dialogs = {
   RenameSequenceDialog,
   PrintDialog: PrintDialog$1,
@@ -138096,7 +138270,7 @@ const PropertySidePanel = /* @__PURE__ */ __name(({ properties: properties2, set
         item: selection && selection.start > -1 ? /* @__PURE__ */ React.createElement("span", null, selection.start + 1, " - ", selection.end + 1) : /* @__PURE__ */ React.createElement("span", null, "1 - ", isProtein2 ? proteinSize : size),
         title: "Region"
       }
-    )), /* @__PURE__ */ React.createElement("h5", null, isProtein2 ? "Amino Acid" : "Base Pair", " Frequencies"), /* @__PURE__ */ React.createElement("div", { className: "sidebar-table" }, /* @__PURE__ */ React.createElement("div", { className: "sidebar-row" }, /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, "Amino Acid"), /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, "Count"), /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, "Percentage")), frequencyEntries.map(([aa, data], idx) => {
+    )), /* @__PURE__ */ React.createElement("h5", null, isProtein2 ? "Amino Acid" : "Base Pair", " Frequencies"), /* @__PURE__ */ React.createElement("div", { className: "sidebar-table" }, /* @__PURE__ */ React.createElement("div", { className: "sidebar-row" }, /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, isProtein2 ? "Amino Acid" : "Base"), /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, "Count"), /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, "Percentage")), frequencyEntries.map(([aa, data], idx) => {
       return /* @__PURE__ */ React.createElement("div", { className: `sidebar-row property-amino-acid-${idx}` }, /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, aa, " ", isProtein2 ? `(${aminoAcidShortNames[aa]})` : ""), /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, data.count), /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, data.percentage.toFixed(1), "%"));
     })));
   } else {
@@ -138596,7 +138770,11 @@ ${seqDataToCopy}\r
   }, [alignmentTracks, id2, store2]);
   React.useEffect(() => {
     const handleAlignmentCopy = /* @__PURE__ */ __name((event) => {
+      var _a3, _b2, _c;
       if (event.key === "c" && !event.shiftKey && (event.metaKey === true || event.ctrlKey === true)) {
+        if (!((_a3 = document.activeElement) == null ? void 0 : _a3.classList.contains("alignmentView"))) {
+          return;
+        }
         const input = document.createElement("textarea");
         document.body.appendChild(input);
         const seqDataToCopy = getAllAlignmentsFastaText();
@@ -138610,6 +138788,8 @@ ${seqDataToCopy}\r
         }
         document.body.removeChild(input);
         event.preventDefault();
+        (_b2 = document.activeElement) == null ? void 0 : _b2.blur();
+        (_c = document.querySelector(".alignmentView")) == null ? void 0 : _c.focus();
       }
     }, "handleAlignmentCopy");
     document.addEventListener("keydown", handleAlignmentCopy);
@@ -139768,6 +139948,7 @@ ${seqDataToCopy}\r
           position: "relative",
           overflowY: "auto"
         }, style2),
+        tabIndex: 0,
         className: "alignmentView"
       },
       /* @__PURE__ */ React.createElement(