@teselagen/ove 0.5.19 → 0.5.21

package/index.cjs.js

@@ -72085,7 +72085,10 @@ const _ResizableDraggableDialog = class _ResizableDraggableDialog extends React$
 };
 __name(_ResizableDraggableDialog, "ResizableDraggableDialog");
 let ResizableDraggableDialog = _ResizableDraggableDialog;
-function MenuItemLink({ text: text2, onClick, icon, navTo, active: active3 }) {
+function MenuItemLink({ text: text2, onClick, icon, navTo, active: active3, disabled }) {
+  if (disabled) {
+    return /* @__PURE__ */ React$2.createElement("li", { className: core.Classes.POPOVER_DISMISS }, /* @__PURE__ */ React$2.createElement(core.MenuItem, { icon, disabled: true, text: text2 }));
+  }
   const handleLinkClick = /* @__PURE__ */ __name((e2) => {
     e2.target.closest(`.${core.Classes.POPOVER_DISMISS}`).click();
   }, "handleLinkClick");
@@ -72234,7 +72237,10 @@ const DynamicMenuItem = /* @__PURE__ */ __name(({
   ].reduce((v2, f2) => f2(v2, context), def);
   let out;
   if (item.divider !== void 0) {
-    out = /* @__PURE__ */ React$2.createElement(core.MenuDivider, __spreadValues({}, item.divider ? { title: item.divider } : {}));
+    out = /* @__PURE__ */ React$2.createElement(
+      core.MenuDivider,
+      __spreadValues({}, item.divider ? { title: item.divider, className: item.className } : {})
+    );
   } else {
     const ItemComponent = item.component || EnhancedMenuItem;
     out = /* @__PURE__ */ React$2.createElement(
@@ -80985,9 +80991,9 @@ const calcTmMethods = {
   // Helix initiation for deltaS
   R: 1.987,
   // Gas constant (cal/(K*mol)).
-  C: 5e-7,
+  primerConc: 5e-7,
   // Oligo concentration. 0.5uM is typical for PCR.
-  Na: 0.05,
+  monovalentCationConc: 0.05,
   // Monovalent salt concentration. 50mM is typical for PCR.
   /**
    * Calculates temperature for DNA sequence using a given algorithm.
@@ -80995,10 +81001,11 @@ const calcTmMethods = {
    * type - Either Teselagen.bio.tools.TemperatureCalculator.TABLE_BRESLAUER, TABLE_SUGIMOTO, or TABLE_UNIFIED
    * A - Helix initation for deltaS. Defaults to -10.8.
    * R - The gas constant, in cal/(K*mol). Defaults to 0.5e-6M.
-   * Na - THe monovalent salt concentration. Defaults to 50e-3M.
+   * monovalentCationConc - THe monovalent salt concentration. Defaults to 50e-3M.
    * return - Temperature for the given sequence, in Celsius.
    */
-  calculateTemperature: function(sequence2, type2, A2, R2, C, Na) {
+  calculateTemperature: function(_sequence, { type: type2, A: A2, R: R2, primerConc, monovalentCationConc } = {}) {
+    const sequence2 = _sequence.toLowerCase();
     if (typeof type2 === "undefined") {
       type2 = this.TABLE_BRESLAUER;
     } else if (type2 != this.TABLE_BRESLAUER && type2 != this.TABLE_UNIFIED && type2 != this.TABLE_SUGIMOTO) {
@@ -81010,11 +81017,11 @@ const calcTmMethods = {
     if (!R2) {
       R2 = this.R;
     }
-    if (!C) {
-      C = this.C;
+    if (!primerConc) {
+      primerConc = this.primerConc;
     }
-    if (!Na) {
-      Na = this.Na;
+    if (!monovalentCationConc) {
+      monovalentCationConc = this.monovalentCationConc;
     }
     const sequenceLength = sequence2.length;
     if (sequenceLength == 0) {
@@ -81045,11 +81052,8 @@ const calcTmMethods = {
       sumDeltaH = sumDeltaH + neighbors[i] * deltaHTable[i];
       sumDeltaS = sumDeltaS + neighbors[i] * deltaSTable[i];
     }
-    const temperature = -1e3 * sumDeltaH / (A2 + -sumDeltaS + R2 * Math.log(C / 4)) - 273.15 + 16.6 * Math.LOG10E * Math.log(Na);
-    if (temperature < 0) {
-      return 0;
-    }
-    return temperature.toFixed(2);
+    const temperature = -1e3 * sumDeltaH / (A2 + -sumDeltaS + R2 * Math.log(primerConc / 4)) - 273.15 + 16.6 * Math.LOG10E * Math.log(monovalentCationConc);
+    return temperature;
   },
   /**
    * @private
@@ -81119,6 +81123,39 @@ const calcTmMethods = {
       return null;
     }
   },
+  // "AA/TT": -7.9, 7.9
+  // "AT/TA": -7.2, 7.2
+  // "AC/TG": -8.4, 8.4
+  // "AG/TC": -7.8, 7.8
+  // "TT/AA": -7.9, 7.9
+  // "TA/AT": -7.2, 7.2
+  // "TG/AC": -8.5, 8.2
+  // "TC/AG": -8.2, 8.5
+  // "CC/GG": -8.0, 8.0
+  // "CA/GT": -8.5, 8.5
+  // "CT/GA": -7.8, 7.8
+  // "CG/GC": -10.6, 10.6
+  // "GG/CC": -8.0, 8.0
+  // "GA/CT": -8.2, 8.2,
+  // "GT/CA": -8.4, 8.4
+  // "GC/CG": -9.8, 9.8
+  // aa, at, ac, ag, tt, ta, tc, tg, cc, ca, ct, cg, gg, ga, gt, gc
+  // "AA/TT": -22.2,22.2,
+  // "AT/TA": -20.4,20.4,
+  // "AC/TG": -22.4,22.4,
+  // "AG/TC": -21.0,21.0,
+  // "TT/AA": -22.2,22.2,
+  // "TA/AT": -21.3,21.3,
+  // "TC/AG": -22.2,22.2,
+  // "TG/AC": -22.7,22.7,
+  // "CC/GG": -19.9,19.9,
+  // "CA/GT": -22.7,22.7,
+  // "CT/GA": -21.0,21.0,
+  // "CG/GC": -27.2,27.2,
+  // "GG/CC": -19.9,19.9,
+  // "GT/CA": -22.4,22.2,
+  // "GA/CT": -22.2,22.4,
+  // "GC/CG": -24.4,24.4
   /**
    * @private
    * Function to return deltaS table for given algorithm.
@@ -89720,7 +89757,7 @@ function condensePairwiseAlignmentDifferences(referenceSeq, alignedSeq) {
   return overviewMinimapTrack.join("");
 }
 __name(condensePairwiseAlignmentDifferences, "condensePairwiseAlignmentDifferences");
-function calculateNebTm(sequence2, primerConc, { monovalentCationConc } = {}) {
+function calculateNebTm(sequence2, { monovalentCationConc = 0.05, primerConc = 5e-7 } = {}) {
   try {
     const checkForDegenerateBases = /[^atgc]/i.test(sequence2);
     if (checkForDegenerateBases) {
@@ -122344,7 +122381,7 @@ function oveCommandFactory(instance, commandDefs2) {
       return args;
     },
     handleReturn: noop$6,
-    commandDefs: commandDefs2
+    commandDefs: instance.props.massageCmds ? instance.props.massageCmds(commandDefs2) : commandDefs2
   });
 }
 __name(oveCommandFactory, "oveCommandFactory");
@@ -122372,7 +122409,7 @@ function showFileDialog({ multiple = false, onSelect }) {
 }
 __name(showFileDialog, "showFileDialog");
 const name = "@teselagen/ove";
-const version = "0.5.18";
+const version = "0.5.20";
 const main = "./src/index.js";
 const type = "module";
 const exports$1 = {
@@ -138712,11 +138749,22 @@ function MeltingTemp({
   WrapperToUse = /* @__PURE__ */ __name((p2) => /* @__PURE__ */ React$2.createElement("div", null, p2.children), "WrapperToUse"),
   InnerWrapper = /* @__PURE__ */ __name((p2) => /* @__PURE__ */ React$2.createElement(core.Button, { minimal: true, small: true }, p2.children), "InnerWrapper")
 }) {
+  const [
+    primerConc
+    /* , setPrimerConcentration */
+  ] = React$2.useState(5e-7);
+  const [
+    monovalentCationConc
+    /* , setMonovalentCationConc */
+  ] = React$2.useState(0.05);
   const [tmType, setTmType] = useTmType();
-  const tm = ({
-    default: calculateTm,
-    neb_tm: calculateNebTm
-  }[tmType] || calculateTm)((sequence2 || "").toLowerCase());
+  let tm = (tmType === "neb_tm" ? calculateNebTm : calculateTm)(sequence2, {
+    monovalentCationConc,
+    primerConc
+  });
+  if (isNumber$6(tm)) {
+    tm = tm.toFixed(1);
+  }
   const hasWarning = isString$3(tm) && tm.length > 7 && tm;
   return /* @__PURE__ */ React$2.createElement(WrapperToUse, { dataTest: "veStatusBar-selection-tm" }, /* @__PURE__ */ React$2.createElement(
     core.Popover,
@@ -138727,7 +138775,7 @@ function MeltingTemp({
         {
           rel: "noopener noreferrer",
           target: "_blank",
-          href: "https://github.com/TeselaGen/@teselagen/sequence-utils"
+          href: "https://github.com/TeselaGen/tg-oss/blob/master/packages/sequence-utils/src/calculateNebTm.js"
         },
         "algorithms"
       ), /* @__PURE__ */ React$2.createElement("br", null), /* @__PURE__ */ React$2.createElement("br", null), /* @__PURE__ */ React$2.createElement(
@@ -138735,8 +138783,8 @@ function MeltingTemp({
         {
           label: "Choose Tm Type:",
           options: [
-            { value: "default", label: "Default Tm" },
-            { value: "neb_tm", label: "NEB Tm" }
+            { value: "default", label: "Default Tm (Breslauer)" },
+            { value: "neb_tm", label: "NEB Tm (SantaLucia)" }
           ],
           onChange: (e2) => setTmType(e2.target.value),
           selectedValue: tmType
@@ -143146,6 +143194,7 @@ const userDefinedHandlersAndOpts = [
   "disableSetReadOnly",
   "allowAnnotationEditLocking",
   "disableBpEditing",
+  "massageCmds",
   "showReadOnly",
   "showCircularity",
   "onHiddenEnzymeAdd",

package/index.es.js

@@ -72067,7 +72067,10 @@ const _ResizableDraggableDialog = class _ResizableDraggableDialog extends React_
 };
 __name(_ResizableDraggableDialog, "ResizableDraggableDialog");
 let ResizableDraggableDialog = _ResizableDraggableDialog;
-function MenuItemLink({ text: text2, onClick, icon, navTo, active: active3 }) {
+function MenuItemLink({ text: text2, onClick, icon, navTo, active: active3, disabled }) {
+  if (disabled) {
+    return /* @__PURE__ */ React__default$1.createElement("li", { className: Classes.POPOVER_DISMISS }, /* @__PURE__ */ React__default$1.createElement(MenuItem, { icon, disabled: true, text: text2 }));
+  }
   const handleLinkClick = /* @__PURE__ */ __name((e2) => {
     e2.target.closest(`.${Classes.POPOVER_DISMISS}`).click();
   }, "handleLinkClick");
@@ -72216,7 +72219,10 @@ const DynamicMenuItem = /* @__PURE__ */ __name(({
   ].reduce((v2, f2) => f2(v2, context), def);
   let out;
   if (item.divider !== void 0) {
-    out = /* @__PURE__ */ React__default$1.createElement(MenuDivider, __spreadValues({}, item.divider ? { title: item.divider } : {}));
+    out = /* @__PURE__ */ React__default$1.createElement(
+      MenuDivider,
+      __spreadValues({}, item.divider ? { title: item.divider, className: item.className } : {})
+    );
   } else {
     const ItemComponent = item.component || EnhancedMenuItem;
     out = /* @__PURE__ */ React__default$1.createElement(
@@ -80967,9 +80973,9 @@ const calcTmMethods = {
   // Helix initiation for deltaS
   R: 1.987,
   // Gas constant (cal/(K*mol)).
-  C: 5e-7,
+  primerConc: 5e-7,
   // Oligo concentration. 0.5uM is typical for PCR.
-  Na: 0.05,
+  monovalentCationConc: 0.05,
   // Monovalent salt concentration. 50mM is typical for PCR.
   /**
    * Calculates temperature for DNA sequence using a given algorithm.
@@ -80977,10 +80983,11 @@ const calcTmMethods = {
    * type - Either Teselagen.bio.tools.TemperatureCalculator.TABLE_BRESLAUER, TABLE_SUGIMOTO, or TABLE_UNIFIED
    * A - Helix initation for deltaS. Defaults to -10.8.
    * R - The gas constant, in cal/(K*mol). Defaults to 0.5e-6M.
-   * Na - THe monovalent salt concentration. Defaults to 50e-3M.
+   * monovalentCationConc - THe monovalent salt concentration. Defaults to 50e-3M.
    * return - Temperature for the given sequence, in Celsius.
    */
-  calculateTemperature: function(sequence2, type2, A2, R2, C, Na) {
+  calculateTemperature: function(_sequence, { type: type2, A: A2, R: R2, primerConc, monovalentCationConc } = {}) {
+    const sequence2 = _sequence.toLowerCase();
     if (typeof type2 === "undefined") {
       type2 = this.TABLE_BRESLAUER;
     } else if (type2 != this.TABLE_BRESLAUER && type2 != this.TABLE_UNIFIED && type2 != this.TABLE_SUGIMOTO) {
@@ -80992,11 +80999,11 @@ const calcTmMethods = {
     if (!R2) {
       R2 = this.R;
     }
-    if (!C) {
-      C = this.C;
+    if (!primerConc) {
+      primerConc = this.primerConc;
     }
-    if (!Na) {
-      Na = this.Na;
+    if (!monovalentCationConc) {
+      monovalentCationConc = this.monovalentCationConc;
     }
     const sequenceLength = sequence2.length;
     if (sequenceLength == 0) {
@@ -81027,11 +81034,8 @@ const calcTmMethods = {
       sumDeltaH = sumDeltaH + neighbors[i] * deltaHTable[i];
       sumDeltaS = sumDeltaS + neighbors[i] * deltaSTable[i];
     }
-    const temperature = -1e3 * sumDeltaH / (A2 + -sumDeltaS + R2 * Math.log(C / 4)) - 273.15 + 16.6 * Math.LOG10E * Math.log(Na);
-    if (temperature < 0) {
-      return 0;
-    }
-    return temperature.toFixed(2);
+    const temperature = -1e3 * sumDeltaH / (A2 + -sumDeltaS + R2 * Math.log(primerConc / 4)) - 273.15 + 16.6 * Math.LOG10E * Math.log(monovalentCationConc);
+    return temperature;
   },
   /**
    * @private
@@ -81101,6 +81105,39 @@ const calcTmMethods = {
       return null;
     }
   },
+  // "AA/TT": -7.9, 7.9
+  // "AT/TA": -7.2, 7.2
+  // "AC/TG": -8.4, 8.4
+  // "AG/TC": -7.8, 7.8
+  // "TT/AA": -7.9, 7.9
+  // "TA/AT": -7.2, 7.2
+  // "TG/AC": -8.5, 8.2
+  // "TC/AG": -8.2, 8.5
+  // "CC/GG": -8.0, 8.0
+  // "CA/GT": -8.5, 8.5
+  // "CT/GA": -7.8, 7.8
+  // "CG/GC": -10.6, 10.6
+  // "GG/CC": -8.0, 8.0
+  // "GA/CT": -8.2, 8.2,
+  // "GT/CA": -8.4, 8.4
+  // "GC/CG": -9.8, 9.8
+  // aa, at, ac, ag, tt, ta, tc, tg, cc, ca, ct, cg, gg, ga, gt, gc
+  // "AA/TT": -22.2,22.2,
+  // "AT/TA": -20.4,20.4,
+  // "AC/TG": -22.4,22.4,
+  // "AG/TC": -21.0,21.0,
+  // "TT/AA": -22.2,22.2,
+  // "TA/AT": -21.3,21.3,
+  // "TC/AG": -22.2,22.2,
+  // "TG/AC": -22.7,22.7,
+  // "CC/GG": -19.9,19.9,
+  // "CA/GT": -22.7,22.7,
+  // "CT/GA": -21.0,21.0,
+  // "CG/GC": -27.2,27.2,
+  // "GG/CC": -19.9,19.9,
+  // "GT/CA": -22.4,22.2,
+  // "GA/CT": -22.2,22.4,
+  // "GC/CG": -24.4,24.4
   /**
    * @private
    * Function to return deltaS table for given algorithm.
@@ -89702,7 +89739,7 @@ function condensePairwiseAlignmentDifferences(referenceSeq, alignedSeq) {
   return overviewMinimapTrack.join("");
 }
 __name(condensePairwiseAlignmentDifferences, "condensePairwiseAlignmentDifferences");
-function calculateNebTm(sequence2, primerConc, { monovalentCationConc } = {}) {
+function calculateNebTm(sequence2, { monovalentCationConc = 0.05, primerConc = 5e-7 } = {}) {
   try {
     const checkForDegenerateBases = /[^atgc]/i.test(sequence2);
     if (checkForDegenerateBases) {
@@ -122326,7 +122363,7 @@ function oveCommandFactory(instance, commandDefs2) {
       return args;
     },
     handleReturn: noop$6,
-    commandDefs: commandDefs2
+    commandDefs: instance.props.massageCmds ? instance.props.massageCmds(commandDefs2) : commandDefs2
   });
 }
 __name(oveCommandFactory, "oveCommandFactory");
@@ -122354,7 +122391,7 @@ function showFileDialog({ multiple = false, onSelect }) {
 }
 __name(showFileDialog, "showFileDialog");
 const name = "@teselagen/ove";
-const version = "0.5.18";
+const version = "0.5.20";
 const main = "./src/index.js";
 const type = "module";
 const exports$1 = {
@@ -138694,11 +138731,22 @@ function MeltingTemp({
   WrapperToUse = /* @__PURE__ */ __name((p2) => /* @__PURE__ */ React__default$1.createElement("div", null, p2.children), "WrapperToUse"),
   InnerWrapper = /* @__PURE__ */ __name((p2) => /* @__PURE__ */ React__default$1.createElement(Button, { minimal: true, small: true }, p2.children), "InnerWrapper")
 }) {
+  const [
+    primerConc
+    /* , setPrimerConcentration */
+  ] = React__default$1.useState(5e-7);
+  const [
+    monovalentCationConc
+    /* , setMonovalentCationConc */
+  ] = React__default$1.useState(0.05);
   const [tmType, setTmType] = useTmType();
-  const tm = ({
-    default: calculateTm,
-    neb_tm: calculateNebTm
-  }[tmType] || calculateTm)((sequence2 || "").toLowerCase());
+  let tm = (tmType === "neb_tm" ? calculateNebTm : calculateTm)(sequence2, {
+    monovalentCationConc,
+    primerConc
+  });
+  if (isNumber$6(tm)) {
+    tm = tm.toFixed(1);
+  }
   const hasWarning = isString$3(tm) && tm.length > 7 && tm;
   return /* @__PURE__ */ React__default$1.createElement(WrapperToUse, { dataTest: "veStatusBar-selection-tm" }, /* @__PURE__ */ React__default$1.createElement(
     Popover,
@@ -138709,7 +138757,7 @@ function MeltingTemp({
         {
           rel: "noopener noreferrer",
           target: "_blank",
-          href: "https://github.com/TeselaGen/@teselagen/sequence-utils"
+          href: "https://github.com/TeselaGen/tg-oss/blob/master/packages/sequence-utils/src/calculateNebTm.js"
         },
         "algorithms"
       ), /* @__PURE__ */ React__default$1.createElement("br", null), /* @__PURE__ */ React__default$1.createElement("br", null), /* @__PURE__ */ React__default$1.createElement(
@@ -138717,8 +138765,8 @@ function MeltingTemp({
         {
           label: "Choose Tm Type:",
           options: [
-            { value: "default", label: "Default Tm" },
-            { value: "neb_tm", label: "NEB Tm" }
+            { value: "default", label: "Default Tm (Breslauer)" },
+            { value: "neb_tm", label: "NEB Tm (SantaLucia)" }
           ],
           onChange: (e2) => setTmType(e2.target.value),
           selectedValue: tmType
@@ -143128,6 +143176,7 @@ const userDefinedHandlersAndOpts = [
   "disableSetReadOnly",
   "allowAnnotationEditLocking",
   "disableBpEditing",
+  "massageCmds",
   "showReadOnly",
   "showCircularity",
   "onHiddenEnzymeAdd",

package/index.umd.js

@@ -101255,7 +101255,10 @@ ${latestSubscriptionCallbackError.current.stack}
   };
   __name(_ResizableDraggableDialog, "ResizableDraggableDialog");
   let ResizableDraggableDialog = _ResizableDraggableDialog;
-  function MenuItemLink({ text: text2, onClick, icon, navTo, active: active2 }) {
+  function MenuItemLink({ text: text2, onClick, icon, navTo, active: active2, disabled }) {
+    if (disabled) {
+      return /* @__PURE__ */ React$2.createElement("li", { className: POPOVER_DISMISS }, /* @__PURE__ */ React$2.createElement(MenuItem, { icon, disabled: true, text: text2 }));
+    }
     const handleLinkClick = /* @__PURE__ */ __name((e2) => {
       e2.target.closest(`.${POPOVER_DISMISS}`).click();
     }, "handleLinkClick");
@@ -101404,7 +101407,10 @@ ${latestSubscriptionCallbackError.current.stack}
     ].reduce((v2, f2) => f2(v2, context), def);
     let out;
     if (item.divider !== void 0) {
-      out = /* @__PURE__ */ React$2.createElement(MenuDivider, __spreadValues({}, item.divider ? { title: item.divider } : {}));
+      out = /* @__PURE__ */ React$2.createElement(
+        MenuDivider,
+        __spreadValues({}, item.divider ? { title: item.divider, className: item.className } : {})
+      );
     } else {
       const ItemComponent = item.component || EnhancedMenuItem;
       out = /* @__PURE__ */ React$2.createElement(
@@ -110081,9 +110087,9 @@ ${latestSubscriptionCallbackError.current.stack}
     // Helix initiation for deltaS
     R: 1.987,
     // Gas constant (cal/(K*mol)).
-    C: 5e-7,
+    primerConc: 5e-7,
     // Oligo concentration. 0.5uM is typical for PCR.
-    Na: 0.05,
+    monovalentCationConc: 0.05,
     // Monovalent salt concentration. 50mM is typical for PCR.
     /**
      * Calculates temperature for DNA sequence using a given algorithm.
@@ -110091,10 +110097,11 @@ ${latestSubscriptionCallbackError.current.stack}
      * type - Either Teselagen.bio.tools.TemperatureCalculator.TABLE_BRESLAUER, TABLE_SUGIMOTO, or TABLE_UNIFIED
      * A - Helix initation for deltaS. Defaults to -10.8.
      * R - The gas constant, in cal/(K*mol). Defaults to 0.5e-6M.
-     * Na - THe monovalent salt concentration. Defaults to 50e-3M.
+     * monovalentCationConc - THe monovalent salt concentration. Defaults to 50e-3M.
      * return - Temperature for the given sequence, in Celsius.
      */
-    calculateTemperature: function(sequence2, type2, A2, R2, C2, Na2) {
+    calculateTemperature: function(_sequence, { type: type2, A: A2, R: R2, primerConc, monovalentCationConc } = {}) {
+      const sequence2 = _sequence.toLowerCase();
       if (typeof type2 === "undefined") {
         type2 = this.TABLE_BRESLAUER;
       } else if (type2 != this.TABLE_BRESLAUER && type2 != this.TABLE_UNIFIED && type2 != this.TABLE_SUGIMOTO) {
@@ -110106,11 +110113,11 @@ ${latestSubscriptionCallbackError.current.stack}
       if (!R2) {
         R2 = this.R;
       }
-      if (!C2) {
-        C2 = this.C;
+      if (!primerConc) {
+        primerConc = this.primerConc;
       }
-      if (!Na2) {
-        Na2 = this.Na;
+      if (!monovalentCationConc) {
+        monovalentCationConc = this.monovalentCationConc;
       }
       const sequenceLength = sequence2.length;
       if (sequenceLength == 0) {
@@ -110141,11 +110148,8 @@ ${latestSubscriptionCallbackError.current.stack}
         sumDeltaH = sumDeltaH + neighbors[i2] * deltaHTable[i2];
         sumDeltaS = sumDeltaS + neighbors[i2] * deltaSTable[i2];
       }
-      const temperature = -1e3 * sumDeltaH / (A2 + -sumDeltaS + R2 * Math.log(C2 / 4)) - 273.15 + 16.6 * Math.LOG10E * Math.log(Na2);
-      if (temperature < 0) {
-        return 0;
-      }
-      return temperature.toFixed(2);
+      const temperature = -1e3 * sumDeltaH / (A2 + -sumDeltaS + R2 * Math.log(primerConc / 4)) - 273.15 + 16.6 * Math.LOG10E * Math.log(monovalentCationConc);
+      return temperature;
     },
     /**
      * @private
@@ -110215,6 +110219,39 @@ ${latestSubscriptionCallbackError.current.stack}
         return null;
       }
     },
+    // "AA/TT": -7.9, 7.9
+    // "AT/TA": -7.2, 7.2
+    // "AC/TG": -8.4, 8.4
+    // "AG/TC": -7.8, 7.8
+    // "TT/AA": -7.9, 7.9
+    // "TA/AT": -7.2, 7.2
+    // "TG/AC": -8.5, 8.2
+    // "TC/AG": -8.2, 8.5
+    // "CC/GG": -8.0, 8.0
+    // "CA/GT": -8.5, 8.5
+    // "CT/GA": -7.8, 7.8
+    // "CG/GC": -10.6, 10.6
+    // "GG/CC": -8.0, 8.0
+    // "GA/CT": -8.2, 8.2,
+    // "GT/CA": -8.4, 8.4
+    // "GC/CG": -9.8, 9.8
+    // aa, at, ac, ag, tt, ta, tc, tg, cc, ca, ct, cg, gg, ga, gt, gc
+    // "AA/TT": -22.2,22.2,
+    // "AT/TA": -20.4,20.4,
+    // "AC/TG": -22.4,22.4,
+    // "AG/TC": -21.0,21.0,
+    // "TT/AA": -22.2,22.2,
+    // "TA/AT": -21.3,21.3,
+    // "TC/AG": -22.2,22.2,
+    // "TG/AC": -22.7,22.7,
+    // "CC/GG": -19.9,19.9,
+    // "CA/GT": -22.7,22.7,
+    // "CT/GA": -21.0,21.0,
+    // "CG/GC": -27.2,27.2,
+    // "GG/CC": -19.9,19.9,
+    // "GT/CA": -22.4,22.2,
+    // "GA/CT": -22.2,22.4,
+    // "GC/CG": -24.4,24.4
     /**
      * @private
      * Function to return deltaS table for given algorithm.
@@ -118816,7 +118853,7 @@ ${latestSubscriptionCallbackError.current.stack}
     return overviewMinimapTrack.join("");
   }
   __name(condensePairwiseAlignmentDifferences, "condensePairwiseAlignmentDifferences");
-  function calculateNebTm(sequence2, primerConc, { monovalentCationConc } = {}) {
+  function calculateNebTm(sequence2, { monovalentCationConc = 0.05, primerConc = 5e-7 } = {}) {
     try {
       const checkForDegenerateBases = /[^atgc]/i.test(sequence2);
       if (checkForDegenerateBases) {
@@ -150811,7 +150848,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
         return args;
       },
       handleReturn: noop$6,
-      commandDefs: commandDefs2
+      commandDefs: instance.props.massageCmds ? instance.props.massageCmds(commandDefs2) : commandDefs2
     });
   }
   __name(oveCommandFactory, "oveCommandFactory");
@@ -150839,7 +150876,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
   }
   __name(showFileDialog, "showFileDialog");
   const name = "@teselagen/ove";
-  const version = "0.5.18";
+  const version = "0.5.20";
   const main = "./src/index.js";
   const type = "module";
   const exports$1 = {
@@ -165574,11 +165611,22 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
     WrapperToUse = /* @__PURE__ */ __name((p2) => /* @__PURE__ */ React$2.createElement("div", null, p2.children), "WrapperToUse"),
     InnerWrapper = /* @__PURE__ */ __name((p2) => /* @__PURE__ */ React$2.createElement(Button, { minimal: true, small: true }, p2.children), "InnerWrapper")
   }) {
+    const [
+      primerConc
+      /* , setPrimerConcentration */
+    ] = React$2.useState(5e-7);
+    const [
+      monovalentCationConc
+      /* , setMonovalentCationConc */
+    ] = React$2.useState(0.05);
     const [tmType, setTmType] = useTmType();
-    const tm = ({
-      default: calculateTm,
-      neb_tm: calculateNebTm
-    }[tmType] || calculateTm)((sequence2 || "").toLowerCase());
+    let tm = (tmType === "neb_tm" ? calculateNebTm : calculateTm)(sequence2, {
+      monovalentCationConc,
+      primerConc
+    });
+    if (isNumber$6(tm)) {
+      tm = tm.toFixed(1);
+    }
     const hasWarning = isString$3(tm) && tm.length > 7 && tm;
     return /* @__PURE__ */ React$2.createElement(WrapperToUse, { dataTest: "veStatusBar-selection-tm" }, /* @__PURE__ */ React$2.createElement(
       Popover,
@@ -165589,7 +165637,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
           {
             rel: "noopener noreferrer",
             target: "_blank",
-            href: "https://github.com/TeselaGen/@teselagen/sequence-utils"
+            href: "https://github.com/TeselaGen/tg-oss/blob/master/packages/sequence-utils/src/calculateNebTm.js"
           },
           "algorithms"
         ), /* @__PURE__ */ React$2.createElement("br", null), /* @__PURE__ */ React$2.createElement("br", null), /* @__PURE__ */ React$2.createElement(
@@ -165597,8 +165645,8 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
           {
             label: "Choose Tm Type:",
             options: [
-              { value: "default", label: "Default Tm" },
-              { value: "neb_tm", label: "NEB Tm" }
+              { value: "default", label: "Default Tm (Breslauer)" },
+              { value: "neb_tm", label: "NEB Tm (SantaLucia)" }
             ],
             onChange: (e2) => setTmType(e2.target.value),
             selectedValue: tmType
@@ -169496,6 +169544,7 @@ ${seqDataToCopy}\r
     "disableSetReadOnly",
     "allowAnnotationEditLocking",
     "disableBpEditing",
+    "massageCmds",
     "showReadOnly",
     "showCircularity",
     "onHiddenEnzymeAdd",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.5.19",
+  "version": "0.5.21",
   "main": "./src/index.js",
   "exports": {
     ".": {
@@ -10,12 +10,12 @@
     "./style.css": "./style.css"
   },
   "dependencies": {
-    "@teselagen/sequence-utils": "0.3.24",
+    "@teselagen/sequence-utils": "0.3.25",
     "@teselagen/range-utils": "0.3.7",
-    "@teselagen/ui": "0.4.16",
+    "@teselagen/ui": "0.4.18",
     "@teselagen/file-utils": "0.3.16",
     "@teselagen/bounce-loader": "0.3.11",
-    "@teselagen/bio-parsers": "0.4.18",
+    "@teselagen/bio-parsers": "0.4.19",
     "@blueprintjs/core": "3.52.0",
     "@blueprintjs/datetime": "3.23.19",
     "@blueprintjs/icons": "3.33.0",

package/src/Editor/userDefinedHandlersAndOpts.js

@@ -22,6 +22,7 @@ export const userDefinedHandlersAndOpts = [
   "disableSetReadOnly",
   "allowAnnotationEditLocking",
   "disableBpEditing",
+  "massageCmds",
   "showReadOnly",
   "showCircularity",
   "onHiddenEnzymeAdd",