@teselagen/ove 0.7.34 → 0.7.36

package/README.md

@@ -713,6 +713,6 @@ you can either add your test to an existing cypress file or make a new test file
 
 once you're satisfied, make a pull request back to tg-oss and mention @tnrich
 
-```
+## Running unit tests
 
-```
+Run `bun test` from the root of the repo to execute all unit tests.

package/index.cjs.js

@@ -36818,6 +36818,9 @@ const defaultValidators = {
   }, "dropdownMulti"),
   number: /* @__PURE__ */ __name((newVal2, field) => {
     if (isValueEmpty(newVal2) && !field.isRequired) return;
+    if (field.allowNaN && Number.isNaN(newVal2)) {
+      return;
+    }
     if (isNaN(newVal2) || !isNumber$2(newVal2)) {
       return "Must be a number";
     }
@@ -82982,6 +82985,14 @@ const proteinAlphabet = {
     color: "hsl(264.7, 100%, 69%)",
     mass: 128.17228
   },
+  O: {
+    value: "O",
+    name: "Pyrrolysine",
+    threeLettersName: "Pyl",
+    colorByFamily: "#FFC0CB",
+    color: "hsl(264.7, 100%, 69%)",
+    mass: 255.313
+  },
   M: {
     value: "M",
     name: "Methionine",
@@ -83128,7 +83139,7 @@ const proteinAlphabet = {
     mass: 0
   }
 };
-const threeLetterSequenceStringToAminoAcidMap = {
+const initThreeLetterSequenceStringToAminoAcidMap = {
   gct: proteinAlphabet.A,
   gcc: proteinAlphabet.A,
   gca: proteinAlphabet.A,
@@ -83227,9 +83238,74 @@ const threeLetterSequenceStringToAminoAcidMap = {
   taa: proteinAlphabet["*"],
   tag: proteinAlphabet["*"],
   tga: proteinAlphabet["*"],
+  uaa: proteinAlphabet["*"],
+  uag: proteinAlphabet["*"],
+  uga: proteinAlphabet["*"],
   "...": proteinAlphabet["."],
   "---": proteinAlphabet["-"]
 };
+const IUPAC = {
+  A: ["A"],
+  C: ["C"],
+  G: ["G"],
+  T: ["T"],
+  U: ["U"],
+  R: ["A", "G"],
+  Y: ["C", "T", "U"],
+  K: ["G", "T", "U"],
+  M: ["A", "C"],
+  S: ["G", "C"],
+  W: ["A", "T", "U"],
+  B: ["C", "G", "T", "U"],
+  D: ["A", "G", "T", "U"],
+  H: ["A", "C", "T", "U"],
+  V: ["A", "C", "G"],
+  N: ["A", "C", "G", "T", "U"],
+  X: ["A", "C", "G", "T", "U"]
+};
+function expandAndResolve(threeLetterCodon) {
+  var _a2, _b2;
+  const chars = threeLetterCodon.toUpperCase().split("");
+  const picks = chars.map((c2) => IUPAC[c2] || [c2]);
+  let allPossibleThreeLetterCodons = [""];
+  for (const set6 of picks) {
+    const next = [];
+    for (const prefix2 of allPossibleThreeLetterCodons) for (const b3 of set6) next.push(prefix2 + b3);
+    allPossibleThreeLetterCodons = next;
+  }
+  let foundAminoAcid = null;
+  for (const codon of allPossibleThreeLetterCodons) {
+    const lowerCodon = codon.toLowerCase();
+    const aminoAcidObj = (_b2 = (_a2 = initThreeLetterSequenceStringToAminoAcidMap[lowerCodon]) != null ? _a2 : initThreeLetterSequenceStringToAminoAcidMap[lowerCodon.replace(/u/g, "t")]) != null ? _b2 : initThreeLetterSequenceStringToAminoAcidMap[lowerCodon.replace(/t/g, "u")];
+    if (aminoAcidObj) {
+      if (!foundAminoAcid) {
+        foundAminoAcid = aminoAcidObj;
+      } else if (foundAminoAcid.value !== aminoAcidObj.value) {
+        return null;
+      }
+    } else {
+      return null;
+    }
+  }
+  return foundAminoAcid;
+}
+__name(expandAndResolve, "expandAndResolve");
+function getCodonToAminoAcidMap() {
+  const map3 = initThreeLetterSequenceStringToAminoAcidMap;
+  const codes = Object.keys(IUPAC);
+  for (const a2 of codes)
+    for (const b3 of codes)
+      for (const c2 of codes) {
+        const codon = a2 + b3 + c2;
+        const lowerCodon = codon.toLowerCase();
+        if (map3[lowerCodon]) continue;
+        const aminoAcidObj = expandAndResolve(codon);
+        if (aminoAcidObj) map3[lowerCodon] = aminoAcidObj;
+      }
+  return map3;
+}
+__name(getCodonToAminoAcidMap, "getCodonToAminoAcidMap");
+const threeLetterSequenceStringToAminoAcidMap = getCodonToAminoAcidMap();
 const degenerateDnaToAminoAcidMap = invert(aminoAcidToDegenerateDnaMap);
 function getAminoAcidFromSequenceTriplet(sequenceString) {
   sequenceString = sequenceString.toLowerCase();
@@ -83342,7 +83418,7 @@ function getAminoAcidDataForEachBaseOfDna(originalSequenceString, forward, optio
   const aminoAcidDataForEachBaseOfDNA = [];
   for (let index2 = 0; index2 < sequenceStringLength; index2 += 3) {
     let aminoAcid;
-    const aminoAcidIndex = index2 / 3;
+    const aminoAcidIndex = Math.floor(index2 / 3);
     let codonPositionsInCDS;
     let basesRead;
     if (isProteinSequence) {
@@ -83516,7 +83592,7 @@ function getAcceptedChars({
   isRna: isRna2,
   isMixedRnaAndDna
 } = {}) {
-  return isProtein2 ? `${extended_protein_letters.toLowerCase()}}` : isOligo2 ? ambiguous_rna_letters.toLowerCase() + "t" : isRna2 ? ambiguous_rna_letters.toLowerCase() + "t" : isMixedRnaAndDna ? ambiguous_rna_letters.toLowerCase() + ambiguous_dna_letters.toLowerCase() : (
+  return isProtein2 ? `${extended_protein_letters.toLowerCase()}` : isOligo2 ? ambiguous_rna_letters.toLowerCase() + "t" : isRna2 ? 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()
   );
@@ -84530,7 +84606,7 @@ function adjustAnnotationsToDelete(annotationsToBeAdjusted, range2, maxLength) {
       return __spreadValues(__spreadProps(__spreadValues({}, newRange), {
         start: newLocations[0].start,
         end: newLocations[newLocations.length - 1].end
-      }), newLocations.length > 1 && { locations: newLocations });
+      }), newLocations.length > 0 && { locations: newLocations });
     } else {
       return newRange;
     }
@@ -117456,6 +117532,7 @@ function SelectionLayer$2(props) {
               __spreadValues({
                 key: key + "caret1"
               }, {
+                isProtein: isProtein2,
                 leftMargin,
                 onClick: _onClick || preventDefaultStopPropagation,
                 onRightClick: onSelectionContextMenu,
@@ -117475,6 +117552,7 @@ function SelectionLayer$2(props) {
               __spreadValues({
                 key: key + "caret2"
               }, {
+                isProtein: isProtein2,
                 leftMargin,
                 onClick: _onClick || preventDefaultStopPropagation,
                 onRightClick: onSelectionContextMenu,
@@ -122498,7 +122576,8 @@ function Chromatogram(props) {
         noQualityScores: !showChromQualScores
       }),
       style: {
-        position: "relative"
+        position: "relative",
+        textAlign: "left"
       },
       onContextMenu: /* @__PURE__ */ __name((e) => {
         showContextMenu([chromatogramMenu], void 0, e);
@@ -123355,7 +123434,8 @@ function RowItem(props) {
     ), caretPosition2 > -1 && /* @__PURE__ */ React.createElement(
       Caret$2,
       __spreadProps(__spreadValues({
-        caretPosition: caretPosition2
+        caretPosition: caretPosition2,
+        isProtein: isProtein2
       }, __spreadValues(__spreadValues({}, annotationCommonProps), { getGaps: void 0 })), {
         row: alignmentData ? { start: 0, end: alignmentData.sequence.length - 1 } : row
       })
@@ -124880,7 +124960,7 @@ function showFileDialog({ multiple = false, onSelect }) {
   input.click();
 }
 __name(showFileDialog, "showFileDialog");
-const version = "0.7.33";
+const version = "0.7.35";
 const packageJson = {
   version
 };
@@ -128593,7 +128673,8 @@ const _SequenceInputNoHotkeys = class _SequenceInputNoHotkeys extends React.Comp
       return;
     }
     const seqToInsert = isProtein2 ? {
-      proteinSequence: charsToInsert
+      proteinSequence: charsToInsert,
+      isProtein: true
     } : {
       sequence: charsToInsert
     };
@@ -128655,10 +128736,9 @@ const _SequenceInputNoHotkeys = class _SequenceInputNoHotkeys extends React.Comp
               });
             }, 200);
           }
-          if (maxInsertSize && sanitizedVal.lenth > maxInsertSize) {
+          if (maxInsertSize && sanitizedVal.length > maxInsertSize) {
             return window.toastr.error(
-              "Sorry, your insert is greater than ",
-              maxInsertSize
+              `Sorry, your insert is greater than ${maxInsertSize}`
             );
           }
           e.target.value = sanitizedVal;
@@ -129518,7 +129598,8 @@ function VectorInteractionHOC(Component) {
           readOnly: readOnly2,
           onPaste,
           disableBpEditing,
-          sequenceData: sequenceData2
+          sequenceData: sequenceData2,
+          maxInsertSize
         } = this.props;
         if (disableBpEditing) {
           return this.createDisableBpEditingMsg();
@@ -129545,6 +129626,11 @@ function VectorInteractionHOC(Component) {
         if (sequenceData2.isProtein && !seqDataToInsert.proteinSequence) {
           seqDataToInsert.proteinSequence = seqDataToInsert.sequence;
         }
+        if (maxInsertSize && (seqDataToInsert.proteinSequence || seqDataToInsert.sequence).length > maxInsertSize) {
+          return window.toastr.error(
+            `Sorry, the pasted sequence exceeds the maximum allowed length of ${maxInsertSize}`
+          );
+        }
         seqDataToInsert = tidyUpSequenceData(seqDataToInsert, {
           topLevelSeqData: sequenceData2,
           provideNewIdsForAnnotations: true,
@@ -129659,7 +129745,8 @@ function VectorInteractionHOC(Component) {
           selectionLayer: selectionLayer2 = { start: -1, end: -1 },
           sequenceData: sequenceData2 = { sequence: "" },
           readOnly: readOnly2,
-          disableBpEditing
+          disableBpEditing,
+          maxInsertSize
           // updateSequenceData,
           // wrappedInsertSequenceDataAtPositionOrRange
           // handleInsert
@@ -129680,6 +129767,7 @@ function VectorInteractionHOC(Component) {
             selectionLayer: selectionLayer2,
             sequenceLength,
             caretPosition: caretPosition2,
+            maxInsertSize,
             handleInsert: /* @__PURE__ */ __name((seqDataToInsert) => __async(this, null, function* () {
               yield insertAndSelectHelper({
                 props: this.props,
@@ -130038,6 +130126,8 @@ function VectorInteractionHOC(Component) {
             [this.commandEnhancer],
             e,
             () => {
+              document.body.removeEventListener("cut", this.handleCut);
+              document.body.removeEventListener("copy", this.handleCopy);
               if (lastFocusedEl) {
                 lastFocusedEl.focus();
               }
@@ -133585,6 +133675,7 @@ function SelectionLayer({
         onClick: onClick ? noop$4 : preventDefaultStopPropagation,
         selectionMessage,
         caretPosition: start2,
+        isProtein: isProtein2,
         sequenceLength,
         innerRadius,
         outerRadius: radius
@@ -133599,6 +133690,7 @@ function SelectionLayer({
         onClick: onClick ? noop$4 : preventDefaultStopPropagation,
         selectionMessage,
         caretPosition: end2 + 1,
+        isProtein: isProtein2,
         sequenceLength,
         innerRadius,
         outerRadius: radius
@@ -152958,6 +153050,7 @@ const _Editor = class _Editor extends React.Component {
       hideStatusBar,
       hoveredId,
       isFullscreen,
+      maxInsertSize,
       maxAnnotationsToDisplay,
       minHeight = 400,
       onlyShowLabelsThatDoNotFit = true,
@@ -153145,6 +153238,7 @@ const _Editor = class _Editor extends React.Component {
           doubleClickOverrides: this.props.doubleClickOverrides
         }), panelPropsToSpread), {
           editorName,
+          maxInsertSize,
           isProtein: sequenceData2.isProtein,
           onlyShowLabelsThatDoNotFit,
           tabHeight,

package/index.es.js

@@ -36800,6 +36800,9 @@ const defaultValidators = {
   }, "dropdownMulti"),
   number: /* @__PURE__ */ __name((newVal2, field) => {
     if (isValueEmpty(newVal2) && !field.isRequired) return;
+    if (field.allowNaN && Number.isNaN(newVal2)) {
+      return;
+    }
     if (isNaN(newVal2) || !isNumber$2(newVal2)) {
       return "Must be a number";
     }
@@ -82964,6 +82967,14 @@ const proteinAlphabet = {
     color: "hsl(264.7, 100%, 69%)",
     mass: 128.17228
   },
+  O: {
+    value: "O",
+    name: "Pyrrolysine",
+    threeLettersName: "Pyl",
+    colorByFamily: "#FFC0CB",
+    color: "hsl(264.7, 100%, 69%)",
+    mass: 255.313
+  },
   M: {
     value: "M",
     name: "Methionine",
@@ -83110,7 +83121,7 @@ const proteinAlphabet = {
     mass: 0
   }
 };
-const threeLetterSequenceStringToAminoAcidMap = {
+const initThreeLetterSequenceStringToAminoAcidMap = {
   gct: proteinAlphabet.A,
   gcc: proteinAlphabet.A,
   gca: proteinAlphabet.A,
@@ -83209,9 +83220,74 @@ const threeLetterSequenceStringToAminoAcidMap = {
   taa: proteinAlphabet["*"],
   tag: proteinAlphabet["*"],
   tga: proteinAlphabet["*"],
+  uaa: proteinAlphabet["*"],
+  uag: proteinAlphabet["*"],
+  uga: proteinAlphabet["*"],
   "...": proteinAlphabet["."],
   "---": proteinAlphabet["-"]
 };
+const IUPAC = {
+  A: ["A"],
+  C: ["C"],
+  G: ["G"],
+  T: ["T"],
+  U: ["U"],
+  R: ["A", "G"],
+  Y: ["C", "T", "U"],
+  K: ["G", "T", "U"],
+  M: ["A", "C"],
+  S: ["G", "C"],
+  W: ["A", "T", "U"],
+  B: ["C", "G", "T", "U"],
+  D: ["A", "G", "T", "U"],
+  H: ["A", "C", "T", "U"],
+  V: ["A", "C", "G"],
+  N: ["A", "C", "G", "T", "U"],
+  X: ["A", "C", "G", "T", "U"]
+};
+function expandAndResolve(threeLetterCodon) {
+  var _a2, _b2;
+  const chars = threeLetterCodon.toUpperCase().split("");
+  const picks = chars.map((c2) => IUPAC[c2] || [c2]);
+  let allPossibleThreeLetterCodons = [""];
+  for (const set6 of picks) {
+    const next = [];
+    for (const prefix2 of allPossibleThreeLetterCodons) for (const b3 of set6) next.push(prefix2 + b3);
+    allPossibleThreeLetterCodons = next;
+  }
+  let foundAminoAcid = null;
+  for (const codon of allPossibleThreeLetterCodons) {
+    const lowerCodon = codon.toLowerCase();
+    const aminoAcidObj = (_b2 = (_a2 = initThreeLetterSequenceStringToAminoAcidMap[lowerCodon]) != null ? _a2 : initThreeLetterSequenceStringToAminoAcidMap[lowerCodon.replace(/u/g, "t")]) != null ? _b2 : initThreeLetterSequenceStringToAminoAcidMap[lowerCodon.replace(/t/g, "u")];
+    if (aminoAcidObj) {
+      if (!foundAminoAcid) {
+        foundAminoAcid = aminoAcidObj;
+      } else if (foundAminoAcid.value !== aminoAcidObj.value) {
+        return null;
+      }
+    } else {
+      return null;
+    }
+  }
+  return foundAminoAcid;
+}
+__name(expandAndResolve, "expandAndResolve");
+function getCodonToAminoAcidMap() {
+  const map3 = initThreeLetterSequenceStringToAminoAcidMap;
+  const codes = Object.keys(IUPAC);
+  for (const a2 of codes)
+    for (const b3 of codes)
+      for (const c2 of codes) {
+        const codon = a2 + b3 + c2;
+        const lowerCodon = codon.toLowerCase();
+        if (map3[lowerCodon]) continue;
+        const aminoAcidObj = expandAndResolve(codon);
+        if (aminoAcidObj) map3[lowerCodon] = aminoAcidObj;
+      }
+  return map3;
+}
+__name(getCodonToAminoAcidMap, "getCodonToAminoAcidMap");
+const threeLetterSequenceStringToAminoAcidMap = getCodonToAminoAcidMap();
 const degenerateDnaToAminoAcidMap = invert(aminoAcidToDegenerateDnaMap);
 function getAminoAcidFromSequenceTriplet(sequenceString) {
   sequenceString = sequenceString.toLowerCase();
@@ -83324,7 +83400,7 @@ function getAminoAcidDataForEachBaseOfDna(originalSequenceString, forward, optio
   const aminoAcidDataForEachBaseOfDNA = [];
   for (let index2 = 0; index2 < sequenceStringLength; index2 += 3) {
     let aminoAcid;
-    const aminoAcidIndex = index2 / 3;
+    const aminoAcidIndex = Math.floor(index2 / 3);
     let codonPositionsInCDS;
     let basesRead;
     if (isProteinSequence) {
@@ -83498,7 +83574,7 @@ function getAcceptedChars({
   isRna: isRna2,
   isMixedRnaAndDna
 } = {}) {
-  return isProtein2 ? `${extended_protein_letters.toLowerCase()}}` : isOligo2 ? ambiguous_rna_letters.toLowerCase() + "t" : isRna2 ? ambiguous_rna_letters.toLowerCase() + "t" : isMixedRnaAndDna ? ambiguous_rna_letters.toLowerCase() + ambiguous_dna_letters.toLowerCase() : (
+  return isProtein2 ? `${extended_protein_letters.toLowerCase()}` : isOligo2 ? ambiguous_rna_letters.toLowerCase() + "t" : isRna2 ? 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()
   );
@@ -84512,7 +84588,7 @@ function adjustAnnotationsToDelete(annotationsToBeAdjusted, range2, maxLength) {
       return __spreadValues(__spreadProps(__spreadValues({}, newRange), {
         start: newLocations[0].start,
         end: newLocations[newLocations.length - 1].end
-      }), newLocations.length > 1 && { locations: newLocations });
+      }), newLocations.length > 0 && { locations: newLocations });
     } else {
       return newRange;
     }
@@ -117438,6 +117514,7 @@ function SelectionLayer$2(props) {
               __spreadValues({
                 key: key + "caret1"
               }, {
+                isProtein: isProtein2,
                 leftMargin,
                 onClick: _onClick || preventDefaultStopPropagation,
                 onRightClick: onSelectionContextMenu,
@@ -117457,6 +117534,7 @@ function SelectionLayer$2(props) {
               __spreadValues({
                 key: key + "caret2"
               }, {
+                isProtein: isProtein2,
                 leftMargin,
                 onClick: _onClick || preventDefaultStopPropagation,
                 onRightClick: onSelectionContextMenu,
@@ -122480,7 +122558,8 @@ function Chromatogram(props) {
         noQualityScores: !showChromQualScores
       }),
       style: {
-        position: "relative"
+        position: "relative",
+        textAlign: "left"
       },
       onContextMenu: /* @__PURE__ */ __name((e) => {
         showContextMenu([chromatogramMenu], void 0, e);
@@ -123337,7 +123416,8 @@ function RowItem(props) {
     ), caretPosition2 > -1 && /* @__PURE__ */ React__default.createElement(
       Caret$2,
       __spreadProps(__spreadValues({
-        caretPosition: caretPosition2
+        caretPosition: caretPosition2,
+        isProtein: isProtein2
       }, __spreadValues(__spreadValues({}, annotationCommonProps), { getGaps: void 0 })), {
         row: alignmentData ? { start: 0, end: alignmentData.sequence.length - 1 } : row
       })
@@ -124862,7 +124942,7 @@ function showFileDialog({ multiple = false, onSelect }) {
   input.click();
 }
 __name(showFileDialog, "showFileDialog");
-const version = "0.7.33";
+const version = "0.7.35";
 const packageJson = {
   version
 };
@@ -128575,7 +128655,8 @@ const _SequenceInputNoHotkeys = class _SequenceInputNoHotkeys extends React__def
       return;
     }
     const seqToInsert = isProtein2 ? {
-      proteinSequence: charsToInsert
+      proteinSequence: charsToInsert,
+      isProtein: true
     } : {
       sequence: charsToInsert
     };
@@ -128637,10 +128718,9 @@ const _SequenceInputNoHotkeys = class _SequenceInputNoHotkeys extends React__def
               });
             }, 200);
           }
-          if (maxInsertSize && sanitizedVal.lenth > maxInsertSize) {
+          if (maxInsertSize && sanitizedVal.length > maxInsertSize) {
             return window.toastr.error(
-              "Sorry, your insert is greater than ",
-              maxInsertSize
+              `Sorry, your insert is greater than ${maxInsertSize}`
             );
           }
           e.target.value = sanitizedVal;
@@ -129500,7 +129580,8 @@ function VectorInteractionHOC(Component2) {
           readOnly: readOnly2,
           onPaste,
           disableBpEditing,
-          sequenceData: sequenceData2
+          sequenceData: sequenceData2,
+          maxInsertSize
         } = this.props;
         if (disableBpEditing) {
           return this.createDisableBpEditingMsg();
@@ -129527,6 +129608,11 @@ function VectorInteractionHOC(Component2) {
         if (sequenceData2.isProtein && !seqDataToInsert.proteinSequence) {
           seqDataToInsert.proteinSequence = seqDataToInsert.sequence;
         }
+        if (maxInsertSize && (seqDataToInsert.proteinSequence || seqDataToInsert.sequence).length > maxInsertSize) {
+          return window.toastr.error(
+            `Sorry, the pasted sequence exceeds the maximum allowed length of ${maxInsertSize}`
+          );
+        }
         seqDataToInsert = tidyUpSequenceData(seqDataToInsert, {
           topLevelSeqData: sequenceData2,
           provideNewIdsForAnnotations: true,
@@ -129641,7 +129727,8 @@ function VectorInteractionHOC(Component2) {
           selectionLayer: selectionLayer2 = { start: -1, end: -1 },
           sequenceData: sequenceData2 = { sequence: "" },
           readOnly: readOnly2,
-          disableBpEditing
+          disableBpEditing,
+          maxInsertSize
           // updateSequenceData,
           // wrappedInsertSequenceDataAtPositionOrRange
           // handleInsert
@@ -129662,6 +129749,7 @@ function VectorInteractionHOC(Component2) {
             selectionLayer: selectionLayer2,
             sequenceLength,
             caretPosition: caretPosition2,
+            maxInsertSize,
             handleInsert: /* @__PURE__ */ __name((seqDataToInsert) => __async(this, null, function* () {
               yield insertAndSelectHelper({
                 props: this.props,
@@ -130020,6 +130108,8 @@ function VectorInteractionHOC(Component2) {
             [this.commandEnhancer],
             e,
             () => {
+              document.body.removeEventListener("cut", this.handleCut);
+              document.body.removeEventListener("copy", this.handleCopy);
               if (lastFocusedEl) {
                 lastFocusedEl.focus();
               }
@@ -133567,6 +133657,7 @@ function SelectionLayer({
         onClick: onClick ? noop$4 : preventDefaultStopPropagation,
         selectionMessage,
         caretPosition: start2,
+        isProtein: isProtein2,
         sequenceLength,
         innerRadius,
         outerRadius: radius
@@ -133581,6 +133672,7 @@ function SelectionLayer({
         onClick: onClick ? noop$4 : preventDefaultStopPropagation,
         selectionMessage,
         caretPosition: end2 + 1,
+        isProtein: isProtein2,
         sequenceLength,
         innerRadius,
         outerRadius: radius
@@ -152940,6 +153032,7 @@ const _Editor = class _Editor extends React__default.Component {
       hideStatusBar,
       hoveredId,
       isFullscreen,
+      maxInsertSize,
       maxAnnotationsToDisplay,
       minHeight = 400,
       onlyShowLabelsThatDoNotFit = true,
@@ -153127,6 +153220,7 @@ const _Editor = class _Editor extends React__default.Component {
           doubleClickOverrides: this.props.doubleClickOverrides
         }), panelPropsToSpread), {
           editorName,
+          maxInsertSize,
           isProtein: sequenceData2.isProtein,
           onlyShowLabelsThatDoNotFit,
           tabHeight,

package/index.umd.js

@@ -65806,6 +65806,9 @@ ${latestSubscriptionCallbackError.current.stack}
     }, "dropdownMulti"),
     number: /* @__PURE__ */ __name((newVal2, field) => {
       if (isValueEmpty(newVal2) && !field.isRequired) return;
+      if (field.allowNaN && Number.isNaN(newVal2)) {
+        return;
+      }
       if (isNaN(newVal2) || !isNumber$2(newVal2)) {
         return "Must be a number";
       }
@@ -111885,6 +111888,14 @@ ${latestSubscriptionCallbackError.current.stack}
       color: "hsl(264.7, 100%, 69%)",
       mass: 128.17228
     },
+    O: {
+      value: "O",
+      name: "Pyrrolysine",
+      threeLettersName: "Pyl",
+      colorByFamily: "#FFC0CB",
+      color: "hsl(264.7, 100%, 69%)",
+      mass: 255.313
+    },
     M: {
       value: "M",
       name: "Methionine",
@@ -112031,7 +112042,7 @@ ${latestSubscriptionCallbackError.current.stack}
       mass: 0
     }
   };
-  const threeLetterSequenceStringToAminoAcidMap = {
+  const initThreeLetterSequenceStringToAminoAcidMap = {
     gct: proteinAlphabet.A,
     gcc: proteinAlphabet.A,
     gca: proteinAlphabet.A,
@@ -112130,9 +112141,74 @@ ${latestSubscriptionCallbackError.current.stack}
     taa: proteinAlphabet["*"],
     tag: proteinAlphabet["*"],
     tga: proteinAlphabet["*"],
+    uaa: proteinAlphabet["*"],
+    uag: proteinAlphabet["*"],
+    uga: proteinAlphabet["*"],
     "...": proteinAlphabet["."],
     "---": proteinAlphabet["-"]
   };
+  const IUPAC = {
+    A: ["A"],
+    C: ["C"],
+    G: ["G"],
+    T: ["T"],
+    U: ["U"],
+    R: ["A", "G"],
+    Y: ["C", "T", "U"],
+    K: ["G", "T", "U"],
+    M: ["A", "C"],
+    S: ["G", "C"],
+    W: ["A", "T", "U"],
+    B: ["C", "G", "T", "U"],
+    D: ["A", "G", "T", "U"],
+    H: ["A", "C", "T", "U"],
+    V: ["A", "C", "G"],
+    N: ["A", "C", "G", "T", "U"],
+    X: ["A", "C", "G", "T", "U"]
+  };
+  function expandAndResolve(threeLetterCodon) {
+    var _a2, _b2;
+    const chars2 = threeLetterCodon.toUpperCase().split("");
+    const picks = chars2.map((c2) => IUPAC[c2] || [c2]);
+    let allPossibleThreeLetterCodons = [""];
+    for (const set2 of picks) {
+      const next = [];
+      for (const prefix2 of allPossibleThreeLetterCodons) for (const b3 of set2) next.push(prefix2 + b3);
+      allPossibleThreeLetterCodons = next;
+    }
+    let foundAminoAcid = null;
+    for (const codon of allPossibleThreeLetterCodons) {
+      const lowerCodon = codon.toLowerCase();
+      const aminoAcidObj = (_b2 = (_a2 = initThreeLetterSequenceStringToAminoAcidMap[lowerCodon]) != null ? _a2 : initThreeLetterSequenceStringToAminoAcidMap[lowerCodon.replace(/u/g, "t")]) != null ? _b2 : initThreeLetterSequenceStringToAminoAcidMap[lowerCodon.replace(/t/g, "u")];
+      if (aminoAcidObj) {
+        if (!foundAminoAcid) {
+          foundAminoAcid = aminoAcidObj;
+        } else if (foundAminoAcid.value !== aminoAcidObj.value) {
+          return null;
+        }
+      } else {
+        return null;
+      }
+    }
+    return foundAminoAcid;
+  }
+  __name(expandAndResolve, "expandAndResolve");
+  function getCodonToAminoAcidMap() {
+    const map2 = initThreeLetterSequenceStringToAminoAcidMap;
+    const codes = Object.keys(IUPAC);
+    for (const a2 of codes)
+      for (const b3 of codes)
+        for (const c2 of codes) {
+          const codon = a2 + b3 + c2;
+          const lowerCodon = codon.toLowerCase();
+          if (map2[lowerCodon]) continue;
+          const aminoAcidObj = expandAndResolve(codon);
+          if (aminoAcidObj) map2[lowerCodon] = aminoAcidObj;
+        }
+    return map2;
+  }
+  __name(getCodonToAminoAcidMap, "getCodonToAminoAcidMap");
+  const threeLetterSequenceStringToAminoAcidMap = getCodonToAminoAcidMap();
   const degenerateDnaToAminoAcidMap = invert(aminoAcidToDegenerateDnaMap);
   function getAminoAcidFromSequenceTriplet(sequenceString) {
     sequenceString = sequenceString.toLowerCase();
@@ -112245,7 +112321,7 @@ ${latestSubscriptionCallbackError.current.stack}
     const aminoAcidDataForEachBaseOfDNA = [];
     for (let index2 = 0; index2 < sequenceStringLength; index2 += 3) {
       let aminoAcid;
-      const aminoAcidIndex = index2 / 3;
+      const aminoAcidIndex = Math.floor(index2 / 3);
       let codonPositionsInCDS;
       let basesRead;
       if (isProteinSequence) {
@@ -112419,7 +112495,7 @@ ${latestSubscriptionCallbackError.current.stack}
     isRna: isRna2,
     isMixedRnaAndDna
   } = {}) {
-    return isProtein2 ? `${extended_protein_letters.toLowerCase()}}` : isOligo2 ? ambiguous_rna_letters.toLowerCase() + "t" : isRna2 ? ambiguous_rna_letters.toLowerCase() + "t" : isMixedRnaAndDna ? ambiguous_rna_letters.toLowerCase() + ambiguous_dna_letters.toLowerCase() : (
+    return isProtein2 ? `${extended_protein_letters.toLowerCase()}` : isOligo2 ? ambiguous_rna_letters.toLowerCase() + "t" : isRna2 ? 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()
     );
@@ -113433,7 +113509,7 @@ ${latestSubscriptionCallbackError.current.stack}
         return __spreadValues(__spreadProps(__spreadValues({}, newRange), {
           start: newLocations[0].start,
           end: newLocations[newLocations.length - 1].end
-        }), newLocations.length > 1 && { locations: newLocations });
+        }), newLocations.length > 0 && { locations: newLocations });
       } else {
         return newRange;
       }
@@ -145604,6 +145680,7 @@ ${seq.sequence}
                 __spreadValues({
                   key: key + "caret1"
                 }, {
+                  isProtein: isProtein2,
                   leftMargin,
                   onClick: _onClick || preventDefaultStopPropagation,
                   onRightClick: onSelectionContextMenu,
@@ -145623,6 +145700,7 @@ ${seq.sequence}
                 __spreadValues({
                   key: key + "caret2"
                 }, {
+                  isProtein: isProtein2,
                   leftMargin,
                   onClick: _onClick || preventDefaultStopPropagation,
                   onRightClick: onSelectionContextMenu,
@@ -150596,7 +150674,8 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
           noQualityScores: !showChromQualScores
         }),
         style: {
-          position: "relative"
+          position: "relative",
+          textAlign: "left"
         },
         onContextMenu: /* @__PURE__ */ __name((e2) => {
           showContextMenu([chromatogramMenu], void 0, e2);
@@ -151453,7 +151532,8 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
       ), caretPosition2 > -1 && /* @__PURE__ */ React.createElement(
         Caret$2,
         __spreadProps(__spreadValues({
-          caretPosition: caretPosition2
+          caretPosition: caretPosition2,
+          isProtein: isProtein2
         }, __spreadValues(__spreadValues({}, annotationCommonProps), { getGaps: void 0 })), {
           row: alignmentData ? { start: 0, end: alignmentData.sequence.length - 1 } : row
         })
@@ -152978,7 +153058,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
     input.click();
   }
   __name(showFileDialog, "showFileDialog");
-  const version = "0.7.33";
+  const version = "0.7.35";
   const packageJson = {
     version
   };
@@ -155089,7 +155169,8 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
         return;
       }
       const seqToInsert = isProtein2 ? {
-        proteinSequence: charsToInsert
+        proteinSequence: charsToInsert,
+        isProtein: true
       } : {
         sequence: charsToInsert
       };
@@ -155151,10 +155232,9 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
                 });
               }, 200);
             }
-            if (maxInsertSize && sanitizedVal.lenth > maxInsertSize) {
+            if (maxInsertSize && sanitizedVal.length > maxInsertSize) {
               return window.toastr.error(
-                "Sorry, your insert is greater than ",
-                maxInsertSize
+                `Sorry, your insert is greater than ${maxInsertSize}`
               );
             }
             e2.target.value = sanitizedVal;
@@ -156014,7 +156094,8 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
             readOnly: readOnly2,
             onPaste,
             disableBpEditing,
-            sequenceData: sequenceData2
+            sequenceData: sequenceData2,
+            maxInsertSize
           } = this.props;
           if (disableBpEditing) {
             return this.createDisableBpEditingMsg();
@@ -156041,6 +156122,11 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
           if (sequenceData2.isProtein && !seqDataToInsert.proteinSequence) {
             seqDataToInsert.proteinSequence = seqDataToInsert.sequence;
           }
+          if (maxInsertSize && (seqDataToInsert.proteinSequence || seqDataToInsert.sequence).length > maxInsertSize) {
+            return window.toastr.error(
+              `Sorry, the pasted sequence exceeds the maximum allowed length of ${maxInsertSize}`
+            );
+          }
           seqDataToInsert = tidyUpSequenceData(seqDataToInsert, {
             topLevelSeqData: sequenceData2,
             provideNewIdsForAnnotations: true,
@@ -156155,7 +156241,8 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
             selectionLayer: selectionLayer2 = { start: -1, end: -1 },
             sequenceData: sequenceData2 = { sequence: "" },
             readOnly: readOnly2,
-            disableBpEditing
+            disableBpEditing,
+            maxInsertSize
             // updateSequenceData,
             // wrappedInsertSequenceDataAtPositionOrRange
             // handleInsert
@@ -156176,6 +156263,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
               selectionLayer: selectionLayer2,
               sequenceLength,
               caretPosition: caretPosition2,
+              maxInsertSize,
               handleInsert: /* @__PURE__ */ __name((seqDataToInsert) => __async(this, null, function* () {
                 yield insertAndSelectHelper({
                   props: this.props,
@@ -156534,6 +156622,8 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
               [this.commandEnhancer],
               e2,
               () => {
+                document.body.removeEventListener("cut", this.handleCut);
+                document.body.removeEventListener("copy", this.handleCopy);
                 if (lastFocusedEl) {
                   lastFocusedEl.focus();
                 }
@@ -160081,6 +160171,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
           onClick: onClick ? noop$4 : preventDefaultStopPropagation,
           selectionMessage,
           caretPosition: start2,
+          isProtein: isProtein2,
           sequenceLength,
           innerRadius,
           outerRadius: radius
@@ -160095,6 +160186,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
           onClick: onClick ? noop$4 : preventDefaultStopPropagation,
           selectionMessage,
           caretPosition: end2 + 1,
+          isProtein: isProtein2,
           sequenceLength,
           innerRadius,
           outerRadius: radius
@@ -179454,6 +179546,7 @@ ${seqDataToCopy}\r
         hideStatusBar,
         hoveredId,
         isFullscreen,
+        maxInsertSize,
         maxAnnotationsToDisplay,
         minHeight = 400,
         onlyShowLabelsThatDoNotFit = true,
@@ -179641,6 +179734,7 @@ ${seqDataToCopy}\r
             doubleClickOverrides: this.props.doubleClickOverrides
           }), panelPropsToSpread), {
             editorName,
+            maxInsertSize,
             isProtein: sequenceData2.isProtein,
             onlyShowLabelsThatDoNotFit,
             tabHeight,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.7.34",
+  "version": "0.7.36",
   "main": "./src/index.js",
   "type": "module",
   "exports": {
@@ -19,7 +19,7 @@
     "@teselagen/range-utils": "0.3.13",
     "@teselagen/react-list": "0.8.18",
     "@teselagen/sequence-utils": "0.3.32",
-    "@teselagen/ui": "0.9.4",
+    "@teselagen/ui": "0.9.6",
     "@use-gesture/react": "10.3.0",
     "biomsa": "^0.2.4",
     "classnames": "^2.3.2",

package/src/CircularView/SelectionLayer.js

@@ -103,6 +103,7 @@ function SelectionLayer({
           onClick={onClick ? noop : preventDefaultStopPropagation}
           selectionMessage={selectionMessage}
           caretPosition={start}
+          isProtein={isProtein}
           sequenceLength={sequenceLength}
           innerRadius={innerRadius}
           outerRadius={radius}
@@ -120,6 +121,7 @@ function SelectionLayer({
           onClick={onClick ? noop : preventDefaultStopPropagation}
           selectionMessage={selectionMessage}
           caretPosition={end + 1}
+          isProtein={isProtein}
           sequenceLength={sequenceLength}
           innerRadius={innerRadius}
           outerRadius={radius}

package/src/Editor/index.js

@@ -360,6 +360,7 @@ export class Editor extends React.Component {
       hideStatusBar,
       hoveredId,
       isFullscreen,
+      maxInsertSize,
       maxAnnotationsToDisplay,
       minHeight = 400,
       onlyShowLabelsThatDoNotFit = true,
@@ -592,6 +593,7 @@ export class Editor extends React.Component {
           doubleClickOverrides={this.props.doubleClickOverrides}
           {...panelPropsToSpread}
           editorName={editorName}
+          maxInsertSize={maxInsertSize}
           isProtein={sequenceData.isProtein}
           onlyShowLabelsThatDoNotFit={onlyShowLabelsThatDoNotFit}
           tabHeight={tabHeight}

package/src/RowItem/Chromatograms/Chromatogram.js

@@ -63,7 +63,8 @@ export default function Chromatogram(props) {
         noQualityScores: !showChromQualScores
       })}
       style={{
-        position: "relative"
+        position: "relative",
+        textAlign: "left"
       }}
       onContextMenu={e => {
         showContextMenu([chromatogramMenu], undefined, e);

package/src/RowItem/SelectionLayer/index.js

@@ -107,6 +107,7 @@ function SelectionLayer(props) {
                   <Caret
                     key={key + "caret1"}
                     {...{
+                      isProtein,
                       leftMargin,
                       onClick: _onClick || preventDefaultStopPropagation,
                       onRightClick: onSelectionContextMenu,
@@ -129,6 +130,7 @@ function SelectionLayer(props) {
                   <Caret
                     key={key + "caret2"}
                     {...{
+                      isProtein,
                       leftMargin,
                       onClick: _onClick || preventDefaultStopPropagation,
                       onRightClick: onSelectionContextMenu,

package/src/RowItem/index.js

@@ -618,6 +618,7 @@ export default function RowItem(props) {
         {caretPosition > -1 && (
           <Caret
             caretPosition={caretPosition}
+            isProtein={isProtein}
             {...{ ...annotationCommonProps, ...{ getGaps: undefined } }}
             row={
               alignmentData

package/src/withEditorInteractions/createSequenceInputPopup.js

@@ -65,7 +65,8 @@ class SequenceInputNoHotkeys extends React.Component {
     }
     const seqToInsert = isProtein
       ? {
-          proteinSequence: charsToInsert
+          proteinSequence: charsToInsert,
+          isProtein: true
         }
       : {
           sequence: charsToInsert
@@ -153,10 +154,9 @@ class SequenceInputNoHotkeys extends React.Component {
                 });
               }, 200);
             }
-            if (maxInsertSize && sanitizedVal.lenth > maxInsertSize) {
+            if (maxInsertSize && sanitizedVal.length > maxInsertSize) {
               return window.toastr.error(
-                "Sorry, your insert is greater than ",
-                maxInsertSize
+                `Sorry, your insert is greater than ${maxInsertSize}`,
               );
             }
             e.target.value = sanitizedVal;

package/src/withEditorInteractions/index.js

@@ -211,7 +211,8 @@ function VectorInteractionHOC(Component /* options */) {
         readOnly,
         onPaste,
         disableBpEditing,
-        sequenceData
+        sequenceData,
+        maxInsertSize
       } = this.props;
 
       if (disableBpEditing) {
@@ -241,6 +242,16 @@ function VectorInteractionHOC(Component /* options */) {
         seqDataToInsert.proteinSequence = seqDataToInsert.sequence;
       }
 
+      if (
+        maxInsertSize &&
+        (seqDataToInsert.proteinSequence || seqDataToInsert.sequence).length >
+          maxInsertSize
+      ) {
+        return window.toastr.error(
+          `Sorry, the pasted sequence exceeds the maximum allowed length of ${maxInsertSize}`
+        );
+      }
+
       seqDataToInsert = tidyUpSequenceData(seqDataToInsert, {
         topLevelSeqData: sequenceData,
         provideNewIdsForAnnotations: true,
@@ -387,7 +398,8 @@ function VectorInteractionHOC(Component /* options */) {
         selectionLayer = { start: -1, end: -1 },
         sequenceData = { sequence: "" },
         readOnly,
-        disableBpEditing
+        disableBpEditing,
+        maxInsertSize
         // updateSequenceData,
         // wrappedInsertSequenceDataAtPositionOrRange
         // handleInsert
@@ -408,6 +420,7 @@ function VectorInteractionHOC(Component /* options */) {
           selectionLayer,
           sequenceLength,
           caretPosition,
+          maxInsertSize,
           handleInsert: async seqDataToInsert => {
             await insertAndSelectHelper({
               props: this.props,
@@ -602,6 +615,7 @@ function VectorInteractionHOC(Component /* options */) {
       const { sequenceData, readOnly, disableBpEditing, selectionLayer } =
         this.props;
       const { isProtein } = sequenceData;
+
       // Add the appropriate listener
       document.body.addEventListener("copy", this.handleCopy, { once: true });
       document.body.addEventListener("cut", this.handleCut, { once: true });
@@ -827,6 +841,8 @@ function VectorInteractionHOC(Component /* options */) {
           [this.commandEnhancer],
           e,
           () => {
+            document.body.removeEventListener("cut", this.handleCut);
+            document.body.removeEventListener("copy", this.handleCopy);
             if (lastFocusedEl) {
               lastFocusedEl.focus();
             }