@teselagen/ove 0.8.36 → 0.8.38

package/helperComponents/PropertiesDialog/utils.d.ts

@@ -1,6 +1,6 @@
-export function sizeSchema(isProtein: any): {
+export function sizeSchema(): {
     path: string;
     type: string;
-    render: (val: any, _record: any) => import("react/jsx-runtime").JSX.Element;
+    render: (val: any, record: any) => import("react/jsx-runtime").JSX.Element;
 };
 export function getMemoOrfs(editorState: any): any;

package/index.cjs.js

@@ -20258,6 +20258,23 @@ function applyWhereClause(records, where) {
               if (!isString$1(value) || !new RegExp(conditionValue.replace(/%/g, ".*")).test(value))
                 return false;
               break;
+            case "_in":
+              if (!some(conditionValue, (item) => isEqual$3(value, item)))
+                return false;
+              break;
+            case "_nin":
+              if (some(conditionValue, (item) => isEqual$3(value, item)))
+                return false;
+              break;
+            case "_regex": {
+              try {
+                if (!isString$1(value) || !new RegExp(conditionValue).test(value))
+                  return false;
+              } catch (e) {
+                return false;
+              }
+              break;
+            }
             default:
               if (operator.startsWith("_")) {
                 console.warn(`Unsupported operator: ${operator}`);
@@ -50812,7 +50829,7 @@ const FilterAndSortMenu = /* @__PURE__ */ __name(({
       filterValToUse = false;
     } else if (ccSelectedFilter2 === "inList" || ccSelectedFilter2 === "notInList") {
       if (dataType === "number") {
-        filterValToUse = filterValue && filterValue.map((val2) => parseFloat(val2.replaceAll(",", "")));
+        filterValToUse = filterValue && filterValue.map((val2) => parseFloat(`${val2}`.replaceAll(",", "")));
       }
     }
     if (isInvalidFilterValue(filterValToUse)) {
@@ -50918,7 +50935,7 @@ const FilterInput = /* @__PURE__ */ __name(({
           multi: true,
           creatable: true,
           value: (filterValue || []).map((val2) => ({
-            label: val2,
+            label: `${val2}`,
             value: val2
           })),
           onChange: /* @__PURE__ */ __name((selectedOptions) => {
@@ -95178,7 +95195,44 @@ function getCurrentDateString() {
   return day2 + "-" + month + "-" + year;
 }
 __name(getCurrentDateString, "getCurrentDateString");
+const standardLineLength = 79;
 function featureNoteInDataToGenbankString(name2, value, options) {
+  const valueString = mangleOrStripUrls(value, options);
+  if (valueString.length > standardLineLength - 25 - name2.length) {
+    const lines = [];
+    let currentIndex = 0;
+    while (currentIndex < valueString.length) {
+      if (currentIndex === 0) {
+        const chunk = valueString.substring(
+          currentIndex,
+          currentIndex + standardLineLength - name2.length - 24
+        );
+        lines.push(
+          StringUtil.lpad("/", " ", 22) + name2 + '="' + chunk + (currentIndex + standardLineLength - 22 - name2.length >= valueString.length ? '"' : "")
+        );
+        currentIndex += standardLineLength - name2.length - 24;
+      } else {
+        const chunk = valueString.substring(
+          currentIndex,
+          currentIndex + standardLineLength - 21
+        );
+        if (currentIndex + standardLineLength - 21 >= valueString.length) {
+          const lineString = " ".repeat(21) + chunk;
+          if (lineString.length === standardLineLength) {
+            lines.push(lineString);
+            lines.push(" ".repeat(21) + '"');
+          } else {
+            lines.push(lineString + '"');
+          }
+        } else {
+          const lineString = " ".repeat(21) + chunk;
+          lines.push(lineString);
+        }
+        currentIndex += standardLineLength - 21;
+      }
+    }
+    return lines.join("\r\n");
+  }
   return StringUtil.lpad("/", " ", 22) + name2 + '="' + mangleOrStripUrls(value, options) + '"';
 }
 __name(featureNoteInDataToGenbankString, "featureNoteInDataToGenbankString");
@@ -117191,7 +117245,7 @@ function showFileDialog({ multiple = false, onSelect }) {
   input.click();
 }
 __name(showFileDialog, "showFileDialog");
-const version = "0.8.36";
+const version = "0.8.38";
 const packageJson = {
   version
 };
@@ -127692,14 +127746,13 @@ const _ComponentToPrint = class _ComponentToPrint extends React.Component {
 };
 __name(_ComponentToPrint, "ComponentToPrint");
 let ComponentToPrint = _ComponentToPrint;
-const sizeSchema = /* @__PURE__ */ __name((isProtein2) => ({
+const sizeSchema = /* @__PURE__ */ __name(() => ({
   path: "size",
   type: "number",
-  render: /* @__PURE__ */ __name((val2, _record) => {
-    const record = isProtein2 ? convertDnaCaretPositionOrRangeToAA(_record) : _record;
+  render: /* @__PURE__ */ __name((val2, record) => {
     const base1Range = convertRangeTo1Based(record);
     const hasJoinedLocations = record.locations && record.locations.length > 1;
-    return /* @__PURE__ */ React.createElement("span", null, isProtein2 ? Math.floor(val2 / 3) : val2, " ", /* @__PURE__ */ React.createElement("span", { style: { fontSize: 10 } }, hasJoinedLocations ? record.locations.map((loc, i) => {
+    return /* @__PURE__ */ React.createElement("span", null, val2, " ", /* @__PURE__ */ React.createElement("span", { style: { fontSize: 10 } }, hasJoinedLocations ? record.locations.map((loc, i) => {
       const base1Range2 = convertRangeTo1Based(loc);
       return /* @__PURE__ */ React.createElement("span", { key: i }, "(", base1Range2.start, "-", base1Range2.end, ")");
     }) : /* @__PURE__ */ React.createElement("span", null, "(", base1Range.start, "-", base1Range.end, ")")));
@@ -127709,11 +127762,7 @@ const getMemoOrfs = /* @__PURE__ */ (() => {
   let lastDeps;
   let lastResult;
   return (editorState) => {
-    const {
-      sequenceData: sequenceData2,
-      minimumOrfSize: minimumOrfSize2,
-      useAdditionalOrfStartCodons: useAdditionalOrfStartCodons2
-    } = editorState;
+    const { sequenceData: sequenceData2, minimumOrfSize: minimumOrfSize2, useAdditionalOrfStartCodons: useAdditionalOrfStartCodons2 } = editorState;
     const { sequence: sequence2, circular: circular2 } = sequenceData2;
     const deps = {
       sequence: sequence2,
@@ -133730,6 +133779,7 @@ const RemoveDuplicatesDialog = /* @__PURE__ */ __name((props) => {
   const ignoreName = useFormValue(dialogFormName, "ignoreName");
   const ignoreStartAndEnd = useFormValue(dialogFormName, "ignoreStartAndEnd");
   const ignoreStrand = useFormValue(dialogFormName, "ignoreStrand");
+  const isProteinSeq = isProtein2 || sequenceData2.isProtein;
   const recomputeDups = React.useCallback(
     (values3) => {
       const ignoreName2 = values3 == null ? void 0 : values3.ignoreName;
@@ -133738,17 +133788,20 @@ const RemoveDuplicatesDialog = /* @__PURE__ */ __name((props) => {
       const annotations = sequenceData2[type2];
       const newDups = [];
       const seqsHashByStartEndStrandName = {};
-      forEach$1(annotations, (a2) => {
-        const hash2 = `${ignoreStartAndEnd2 ? "" : a2.start}&${ignoreStartAndEnd2 ? "" : a2.end}&${ignoreStrand2 ? "" : a2.strand}&${ignoreName2 ? "" : a2.name}`;
+      forEach$1(annotations, (_annotation) => {
+        const annotation = isProteinSeq ? convertDnaCaretPositionOrRangeToAA(_annotation) : _annotation;
+        const hash2 = `${ignoreStartAndEnd2 ? "" : annotation.start}&${ignoreStartAndEnd2 ? "" : annotation.end}&${ignoreStrand2 ? "" : annotation.strand}&${ignoreName2 ? "" : annotation.name}`;
         if (seqsHashByStartEndStrandName[hash2]) {
-          newDups.push(__spreadProps(__spreadValues({}, a2), { size: getRangeLength(a2, sequenceLength) }));
+          newDups.push(__spreadProps(__spreadValues({}, annotation), {
+            size: getRangeLength(annotation, sequenceLength)
+          }));
         } else {
           seqsHashByStartEndStrandName[hash2] = true;
         }
       });
       return newDups;
     },
-    [sequenceData2, sequenceLength, type2]
+    [sequenceData2, sequenceLength, type2, isProteinSeq]
   );
   const [dups, setDups] = React.useState(recomputeDups);
   const selectedIds = React.useMemo(() => dups.map((d2) => d2.id), [dups]);
@@ -133770,11 +133823,11 @@ const RemoveDuplicatesDialog = /* @__PURE__ */ __name((props) => {
       fields: [
         { path: "name", type: "string" },
         // ...(noType ? [] : [{ path: "type", type: "string" }]),
-        sizeSchema(isProtein2),
+        sizeSchema(),
         { path: "strand", type: "string" }
       ]
     }),
-    [isProtein2]
+    []
   );
   return /* @__PURE__ */ React.createElement("div", { className: classNames(core.Classes.DIALOG_BODY, "tg-min-width-dialog") }, /* @__PURE__ */ React.createElement(
     WrappedDT,
@@ -144235,14 +144288,15 @@ const genericAnnotationProperties = /* @__PURE__ */ __name(({
     const annotationPropertiesSelectedEntities = _annotationPropertiesSelectedEntities.filter((a2) => annotations[a2.id]);
     const deleteAnnotation = props[`delete${annotationTypeUpper}`];
     const annotationsToUse = React.useMemo(
-      () => map$3(annotations, (annotation) => {
+      () => map$3(annotations, (_annotation) => {
+        const annotation = isProtein2 ? convertDnaCaretPositionOrRangeToAA(_annotation) : _annotation;
         return __spreadProps(__spreadValues(__spreadValues({}, annotation), annotation.strand === void 0 && {
           strand: annotation.forward ? 1 : -1
         }), {
           size: getRangeLength(annotation, sequenceLength)
         });
       }),
-      [annotations, sequenceLength]
+      [annotations, sequenceLength, isProtein2]
     );
     const keyedPartTags = (_a2 = getKeyedTagsAndTagOptions(allPartTags)) != null ? _a2 : {};
     const additionalColumns = ((_c = (_b2 = PropertiesProps == null ? void 0 : PropertiesProps.propertiesList) == null ? void 0 : _b2.find(
@@ -144312,7 +144366,7 @@ const genericAnnotationProperties = /* @__PURE__ */ __name(({
               }, "render")
             }
           ],
-          sizeSchema(isProtein2),
+          sizeSchema(),
           ...withTags && allPartTags ? [
             {
               path: "tags",
@@ -144806,7 +144860,7 @@ const _OrfProperties = class _OrfProperties extends React.Component {
               displayName: "Size (aa)",
               type: "number"
             },
-            sizeSchema(this.props.isProtein),
+            sizeSchema(),
             { path: "frame", type: "number" },
             { path: "strand", type: "number" }
           ]

package/index.es.js

@@ -20240,6 +20240,23 @@ function applyWhereClause(records, where) {
               if (!isString$1(value) || !new RegExp(conditionValue.replace(/%/g, ".*")).test(value))
                 return false;
               break;
+            case "_in":
+              if (!some(conditionValue, (item) => isEqual$3(value, item)))
+                return false;
+              break;
+            case "_nin":
+              if (some(conditionValue, (item) => isEqual$3(value, item)))
+                return false;
+              break;
+            case "_regex": {
+              try {
+                if (!isString$1(value) || !new RegExp(conditionValue).test(value))
+                  return false;
+              } catch (e) {
+                return false;
+              }
+              break;
+            }
             default:
               if (operator.startsWith("_")) {
                 console.warn(`Unsupported operator: ${operator}`);
@@ -50794,7 +50811,7 @@ const FilterAndSortMenu = /* @__PURE__ */ __name(({
       filterValToUse = false;
     } else if (ccSelectedFilter2 === "inList" || ccSelectedFilter2 === "notInList") {
       if (dataType === "number") {
-        filterValToUse = filterValue && filterValue.map((val2) => parseFloat(val2.replaceAll(",", "")));
+        filterValToUse = filterValue && filterValue.map((val2) => parseFloat(`${val2}`.replaceAll(",", "")));
       }
     }
     if (isInvalidFilterValue(filterValToUse)) {
@@ -50900,7 +50917,7 @@ const FilterInput = /* @__PURE__ */ __name(({
           multi: true,
           creatable: true,
           value: (filterValue || []).map((val2) => ({
-            label: val2,
+            label: `${val2}`,
             value: val2
           })),
           onChange: /* @__PURE__ */ __name((selectedOptions) => {
@@ -95160,7 +95177,44 @@ function getCurrentDateString() {
   return day2 + "-" + month + "-" + year;
 }
 __name(getCurrentDateString, "getCurrentDateString");
+const standardLineLength = 79;
 function featureNoteInDataToGenbankString(name2, value, options) {
+  const valueString = mangleOrStripUrls(value, options);
+  if (valueString.length > standardLineLength - 25 - name2.length) {
+    const lines = [];
+    let currentIndex = 0;
+    while (currentIndex < valueString.length) {
+      if (currentIndex === 0) {
+        const chunk = valueString.substring(
+          currentIndex,
+          currentIndex + standardLineLength - name2.length - 24
+        );
+        lines.push(
+          StringUtil.lpad("/", " ", 22) + name2 + '="' + chunk + (currentIndex + standardLineLength - 22 - name2.length >= valueString.length ? '"' : "")
+        );
+        currentIndex += standardLineLength - name2.length - 24;
+      } else {
+        const chunk = valueString.substring(
+          currentIndex,
+          currentIndex + standardLineLength - 21
+        );
+        if (currentIndex + standardLineLength - 21 >= valueString.length) {
+          const lineString = " ".repeat(21) + chunk;
+          if (lineString.length === standardLineLength) {
+            lines.push(lineString);
+            lines.push(" ".repeat(21) + '"');
+          } else {
+            lines.push(lineString + '"');
+          }
+        } else {
+          const lineString = " ".repeat(21) + chunk;
+          lines.push(lineString);
+        }
+        currentIndex += standardLineLength - 21;
+      }
+    }
+    return lines.join("\r\n");
+  }
   return StringUtil.lpad("/", " ", 22) + name2 + '="' + mangleOrStripUrls(value, options) + '"';
 }
 __name(featureNoteInDataToGenbankString, "featureNoteInDataToGenbankString");
@@ -117173,7 +117227,7 @@ function showFileDialog({ multiple = false, onSelect }) {
   input.click();
 }
 __name(showFileDialog, "showFileDialog");
-const version = "0.8.36";
+const version = "0.8.38";
 const packageJson = {
   version
 };
@@ -127674,14 +127728,13 @@ const _ComponentToPrint = class _ComponentToPrint extends React__default.Compone
 };
 __name(_ComponentToPrint, "ComponentToPrint");
 let ComponentToPrint = _ComponentToPrint;
-const sizeSchema = /* @__PURE__ */ __name((isProtein2) => ({
+const sizeSchema = /* @__PURE__ */ __name(() => ({
   path: "size",
   type: "number",
-  render: /* @__PURE__ */ __name((val2, _record) => {
-    const record = isProtein2 ? convertDnaCaretPositionOrRangeToAA(_record) : _record;
+  render: /* @__PURE__ */ __name((val2, record) => {
     const base1Range = convertRangeTo1Based(record);
     const hasJoinedLocations = record.locations && record.locations.length > 1;
-    return /* @__PURE__ */ React__default.createElement("span", null, isProtein2 ? Math.floor(val2 / 3) : val2, " ", /* @__PURE__ */ React__default.createElement("span", { style: { fontSize: 10 } }, hasJoinedLocations ? record.locations.map((loc, i) => {
+    return /* @__PURE__ */ React__default.createElement("span", null, val2, " ", /* @__PURE__ */ React__default.createElement("span", { style: { fontSize: 10 } }, hasJoinedLocations ? record.locations.map((loc, i) => {
       const base1Range2 = convertRangeTo1Based(loc);
       return /* @__PURE__ */ React__default.createElement("span", { key: i }, "(", base1Range2.start, "-", base1Range2.end, ")");
     }) : /* @__PURE__ */ React__default.createElement("span", null, "(", base1Range.start, "-", base1Range.end, ")")));
@@ -127691,11 +127744,7 @@ const getMemoOrfs = /* @__PURE__ */ (() => {
   let lastDeps;
   let lastResult;
   return (editorState) => {
-    const {
-      sequenceData: sequenceData2,
-      minimumOrfSize: minimumOrfSize2,
-      useAdditionalOrfStartCodons: useAdditionalOrfStartCodons2
-    } = editorState;
+    const { sequenceData: sequenceData2, minimumOrfSize: minimumOrfSize2, useAdditionalOrfStartCodons: useAdditionalOrfStartCodons2 } = editorState;
     const { sequence: sequence2, circular: circular2 } = sequenceData2;
     const deps = {
       sequence: sequence2,
@@ -133712,6 +133761,7 @@ const RemoveDuplicatesDialog = /* @__PURE__ */ __name((props) => {
   const ignoreName = useFormValue(dialogFormName, "ignoreName");
   const ignoreStartAndEnd = useFormValue(dialogFormName, "ignoreStartAndEnd");
   const ignoreStrand = useFormValue(dialogFormName, "ignoreStrand");
+  const isProteinSeq = isProtein2 || sequenceData2.isProtein;
   const recomputeDups = useCallback$1(
     (values3) => {
       const ignoreName2 = values3 == null ? void 0 : values3.ignoreName;
@@ -133720,17 +133770,20 @@ const RemoveDuplicatesDialog = /* @__PURE__ */ __name((props) => {
       const annotations = sequenceData2[type2];
       const newDups = [];
       const seqsHashByStartEndStrandName = {};
-      forEach$1(annotations, (a2) => {
-        const hash2 = `${ignoreStartAndEnd2 ? "" : a2.start}&${ignoreStartAndEnd2 ? "" : a2.end}&${ignoreStrand2 ? "" : a2.strand}&${ignoreName2 ? "" : a2.name}`;
+      forEach$1(annotations, (_annotation) => {
+        const annotation = isProteinSeq ? convertDnaCaretPositionOrRangeToAA(_annotation) : _annotation;
+        const hash2 = `${ignoreStartAndEnd2 ? "" : annotation.start}&${ignoreStartAndEnd2 ? "" : annotation.end}&${ignoreStrand2 ? "" : annotation.strand}&${ignoreName2 ? "" : annotation.name}`;
         if (seqsHashByStartEndStrandName[hash2]) {
-          newDups.push(__spreadProps(__spreadValues({}, a2), { size: getRangeLength(a2, sequenceLength) }));
+          newDups.push(__spreadProps(__spreadValues({}, annotation), {
+            size: getRangeLength(annotation, sequenceLength)
+          }));
         } else {
           seqsHashByStartEndStrandName[hash2] = true;
         }
       });
       return newDups;
     },
-    [sequenceData2, sequenceLength, type2]
+    [sequenceData2, sequenceLength, type2, isProteinSeq]
   );
   const [dups, setDups] = useState(recomputeDups);
   const selectedIds = useMemo$1(() => dups.map((d2) => d2.id), [dups]);
@@ -133752,11 +133805,11 @@ const RemoveDuplicatesDialog = /* @__PURE__ */ __name((props) => {
       fields: [
         { path: "name", type: "string" },
         // ...(noType ? [] : [{ path: "type", type: "string" }]),
-        sizeSchema(isProtein2),
+        sizeSchema(),
         { path: "strand", type: "string" }
       ]
     }),
-    [isProtein2]
+    []
   );
   return /* @__PURE__ */ React__default.createElement("div", { className: classNames(Classes.DIALOG_BODY, "tg-min-width-dialog") }, /* @__PURE__ */ React__default.createElement(
     WrappedDT,
@@ -144217,14 +144270,15 @@ const genericAnnotationProperties = /* @__PURE__ */ __name(({
     const annotationPropertiesSelectedEntities = _annotationPropertiesSelectedEntities.filter((a2) => annotations[a2.id]);
     const deleteAnnotation = props[`delete${annotationTypeUpper}`];
     const annotationsToUse = React__default.useMemo(
-      () => map$3(annotations, (annotation) => {
+      () => map$3(annotations, (_annotation) => {
+        const annotation = isProtein2 ? convertDnaCaretPositionOrRangeToAA(_annotation) : _annotation;
         return __spreadProps(__spreadValues(__spreadValues({}, annotation), annotation.strand === void 0 && {
           strand: annotation.forward ? 1 : -1
         }), {
           size: getRangeLength(annotation, sequenceLength)
         });
       }),
-      [annotations, sequenceLength]
+      [annotations, sequenceLength, isProtein2]
     );
     const keyedPartTags = (_a2 = getKeyedTagsAndTagOptions(allPartTags)) != null ? _a2 : {};
     const additionalColumns = ((_c = (_b2 = PropertiesProps == null ? void 0 : PropertiesProps.propertiesList) == null ? void 0 : _b2.find(
@@ -144294,7 +144348,7 @@ const genericAnnotationProperties = /* @__PURE__ */ __name(({
               }, "render")
             }
           ],
-          sizeSchema(isProtein2),
+          sizeSchema(),
           ...withTags && allPartTags ? [
             {
               path: "tags",
@@ -144788,7 +144842,7 @@ const _OrfProperties = class _OrfProperties extends React__default.Component {
               displayName: "Size (aa)",
               type: "number"
             },
-            sizeSchema(this.props.isProtein),
+            sizeSchema(),
             { path: "frame", type: "number" },
             { path: "strand", type: "number" }
           ]

package/index.umd.js

@@ -46511,6 +46511,23 @@ ${latestSubscriptionCallbackError.current.stack}
                 if (!isString$1(value) || !new RegExp(conditionValue.replace(/%/g, ".*")).test(value))
                   return false;
                 break;
+              case "_in":
+                if (!some(conditionValue, (item) => isEqual$3(value, item)))
+                  return false;
+                break;
+              case "_nin":
+                if (some(conditionValue, (item) => isEqual$3(value, item)))
+                  return false;
+                break;
+              case "_regex": {
+                try {
+                  if (!isString$1(value) || !new RegExp(conditionValue).test(value))
+                    return false;
+                } catch (e2) {
+                  return false;
+                }
+                break;
+              }
               default:
                 if (operator.startsWith("_")) {
                   console.warn(`Unsupported operator: ${operator}`);
@@ -79843,7 +79860,7 @@ ${latestSubscriptionCallbackError.current.stack}
         filterValToUse = false;
       } else if (ccSelectedFilter2 === "inList" || ccSelectedFilter2 === "notInList") {
         if (dataType === "number") {
-          filterValToUse = filterValue && filterValue.map((val2) => parseFloat(val2.replaceAll(",", "")));
+          filterValToUse = filterValue && filterValue.map((val2) => parseFloat(`${val2}`.replaceAll(",", "")));
         }
       }
       if (isInvalidFilterValue(filterValToUse)) {
@@ -79949,7 +79966,7 @@ ${latestSubscriptionCallbackError.current.stack}
             multi: true,
             creatable: true,
             value: (filterValue || []).map((val2) => ({
-              label: val2,
+              label: `${val2}`,
               value: val2
             })),
             onChange: /* @__PURE__ */ __name((selectedOptions) => {
@@ -124079,7 +124096,44 @@ ${seq.sequence}
     return day2 + "-" + month + "-" + year;
   }
   __name(getCurrentDateString, "getCurrentDateString");
+  const standardLineLength = 79;
   function featureNoteInDataToGenbankString(name2, value, options) {
+    const valueString = mangleOrStripUrls(value, options);
+    if (valueString.length > standardLineLength - 25 - name2.length) {
+      const lines = [];
+      let currentIndex = 0;
+      while (currentIndex < valueString.length) {
+        if (currentIndex === 0) {
+          const chunk = valueString.substring(
+            currentIndex,
+            currentIndex + standardLineLength - name2.length - 24
+          );
+          lines.push(
+            StringUtil.lpad("/", " ", 22) + name2 + '="' + chunk + (currentIndex + standardLineLength - 22 - name2.length >= valueString.length ? '"' : "")
+          );
+          currentIndex += standardLineLength - name2.length - 24;
+        } else {
+          const chunk = valueString.substring(
+            currentIndex,
+            currentIndex + standardLineLength - 21
+          );
+          if (currentIndex + standardLineLength - 21 >= valueString.length) {
+            const lineString = " ".repeat(21) + chunk;
+            if (lineString.length === standardLineLength) {
+              lines.push(lineString);
+              lines.push(" ".repeat(21) + '"');
+            } else {
+              lines.push(lineString + '"');
+            }
+          } else {
+            const lineString = " ".repeat(21) + chunk;
+            lines.push(lineString);
+          }
+          currentIndex += standardLineLength - 21;
+        }
+      }
+      return lines.join("\r\n");
+    }
     return StringUtil.lpad("/", " ", 22) + name2 + '="' + mangleOrStripUrls(value, options) + '"';
   }
   __name(featureNoteInDataToGenbankString, "featureNoteInDataToGenbankString");
@@ -145289,7 +145343,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
     input.click();
   }
   __name(showFileDialog, "showFileDialog");
-  const version = "0.8.36";
+  const version = "0.8.38";
   const packageJson = {
     version
   };
@@ -154188,14 +154242,13 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
   };
   __name(_ComponentToPrint, "ComponentToPrint");
   let ComponentToPrint = _ComponentToPrint;
-  const sizeSchema = /* @__PURE__ */ __name((isProtein2) => ({
+  const sizeSchema = /* @__PURE__ */ __name(() => ({
     path: "size",
     type: "number",
-    render: /* @__PURE__ */ __name((val2, _record) => {
-      const record = isProtein2 ? convertDnaCaretPositionOrRangeToAA(_record) : _record;
+    render: /* @__PURE__ */ __name((val2, record) => {
       const base1Range = convertRangeTo1Based(record);
       const hasJoinedLocations = record.locations && record.locations.length > 1;
-      return /* @__PURE__ */ React.createElement("span", null, isProtein2 ? Math.floor(val2 / 3) : val2, " ", /* @__PURE__ */ React.createElement("span", { style: { fontSize: 10 } }, hasJoinedLocations ? record.locations.map((loc, i2) => {
+      return /* @__PURE__ */ React.createElement("span", null, val2, " ", /* @__PURE__ */ React.createElement("span", { style: { fontSize: 10 } }, hasJoinedLocations ? record.locations.map((loc, i2) => {
         const base1Range2 = convertRangeTo1Based(loc);
         return /* @__PURE__ */ React.createElement("span", { key: i2 }, "(", base1Range2.start, "-", base1Range2.end, ")");
       }) : /* @__PURE__ */ React.createElement("span", null, "(", base1Range.start, "-", base1Range.end, ")")));
@@ -154205,11 +154258,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
     let lastDeps;
     let lastResult;
     return (editorState) => {
-      const {
-        sequenceData: sequenceData2,
-        minimumOrfSize: minimumOrfSize2,
-        useAdditionalOrfStartCodons: useAdditionalOrfStartCodons2
-      } = editorState;
+      const { sequenceData: sequenceData2, minimumOrfSize: minimumOrfSize2, useAdditionalOrfStartCodons: useAdditionalOrfStartCodons2 } = editorState;
       const { sequence: sequence2, circular: circular2 } = sequenceData2;
       const deps = {
         sequence: sequence2,
@@ -160226,6 +160275,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
     const ignoreName = useFormValue(dialogFormName, "ignoreName");
     const ignoreStartAndEnd = useFormValue(dialogFormName, "ignoreStartAndEnd");
     const ignoreStrand = useFormValue(dialogFormName, "ignoreStrand");
+    const isProteinSeq = isProtein2 || sequenceData2.isProtein;
     const recomputeDups = reactExports.useCallback(
       (values2) => {
         const ignoreName2 = values2 == null ? void 0 : values2.ignoreName;
@@ -160234,17 +160284,20 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
         const annotations = sequenceData2[type2];
         const newDups = [];
         const seqsHashByStartEndStrandName = {};
-        forEach$1(annotations, (a2) => {
-          const hash2 = `${ignoreStartAndEnd2 ? "" : a2.start}&${ignoreStartAndEnd2 ? "" : a2.end}&${ignoreStrand2 ? "" : a2.strand}&${ignoreName2 ? "" : a2.name}`;
+        forEach$1(annotations, (_annotation) => {
+          const annotation = isProteinSeq ? convertDnaCaretPositionOrRangeToAA(_annotation) : _annotation;
+          const hash2 = `${ignoreStartAndEnd2 ? "" : annotation.start}&${ignoreStartAndEnd2 ? "" : annotation.end}&${ignoreStrand2 ? "" : annotation.strand}&${ignoreName2 ? "" : annotation.name}`;
           if (seqsHashByStartEndStrandName[hash2]) {
-            newDups.push(__spreadProps(__spreadValues({}, a2), { size: getRangeLength(a2, sequenceLength) }));
+            newDups.push(__spreadProps(__spreadValues({}, annotation), {
+              size: getRangeLength(annotation, sequenceLength)
+            }));
           } else {
             seqsHashByStartEndStrandName[hash2] = true;
           }
         });
         return newDups;
       },
-      [sequenceData2, sequenceLength, type2]
+      [sequenceData2, sequenceLength, type2, isProteinSeq]
     );
     const [dups, setDups] = reactExports.useState(recomputeDups);
     const selectedIds = reactExports.useMemo(() => dups.map((d2) => d2.id), [dups]);
@@ -160266,11 +160319,11 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
         fields: [
           { path: "name", type: "string" },
           // ...(noType ? [] : [{ path: "type", type: "string" }]),
-          sizeSchema(isProtein2),
+          sizeSchema(),
           { path: "strand", type: "string" }
         ]
       }),
-      [isProtein2]
+      []
     );
     return /* @__PURE__ */ React.createElement("div", { className: classNames$1(DIALOG_BODY, "tg-min-width-dialog") }, /* @__PURE__ */ React.createElement(
       WrappedDT,
@@ -170731,14 +170784,15 @@ ${seqDataToCopy}\r
       const annotationPropertiesSelectedEntities = _annotationPropertiesSelectedEntities.filter((a2) => annotations[a2.id]);
       const deleteAnnotation = props[`delete${annotationTypeUpper}`];
       const annotationsToUse = React.useMemo(
-        () => map$3(annotations, (annotation) => {
+        () => map$3(annotations, (_annotation) => {
+          const annotation = isProtein2 ? convertDnaCaretPositionOrRangeToAA(_annotation) : _annotation;
           return __spreadProps(__spreadValues(__spreadValues({}, annotation), annotation.strand === void 0 && {
             strand: annotation.forward ? 1 : -1
           }), {
             size: getRangeLength(annotation, sequenceLength)
           });
         }),
-        [annotations, sequenceLength]
+        [annotations, sequenceLength, isProtein2]
       );
       const keyedPartTags = (_a2 = getKeyedTagsAndTagOptions(allPartTags)) != null ? _a2 : {};
       const additionalColumns = ((_c2 = (_b2 = PropertiesProps == null ? void 0 : PropertiesProps.propertiesList) == null ? void 0 : _b2.find(
@@ -170808,7 +170862,7 @@ ${seqDataToCopy}\r
                 }, "render")
               }
             ],
-            sizeSchema(isProtein2),
+            sizeSchema(),
             ...withTags && allPartTags ? [
               {
                 path: "tags",
@@ -171302,7 +171356,7 @@ ${seqDataToCopy}\r
                 displayName: "Size (aa)",
                 type: "number"
               },
-              sizeSchema(this.props.isProtein),
+              sizeSchema(),
               { path: "frame", type: "number" },
               { path: "strand", type: "number" }
             ]

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.8.36",
+  "version": "0.8.38",
   "main": "./src/index.js",
   "type": "module",
   "repository": "https://github.com/TeselaGen/tg-oss",
@@ -15,12 +15,12 @@
     "@blueprintjs/core": "3.54.0",
     "@hello-pangea/dnd": "16.2.0",
     "@risingstack/react-easy-state": "^6.3.0",
-    "@teselagen/bio-parsers": "0.4.35",
+    "@teselagen/bio-parsers": "0.4.36",
     "@teselagen/file-utils": "0.3.23",
     "@teselagen/range-utils": "0.3.20",
     "@teselagen/react-list": "0.8.18",
     "@teselagen/sequence-utils": "0.3.42",
-    "@teselagen/ui": "0.10.19",
+    "@teselagen/ui": "0.10.20",
     "@use-gesture/react": "10.3.0",
     "classnames": "^2.3.2",
     "clipboard": "^2.0.11",

package/src/helperComponents/PropertiesDialog/GenericAnnotationProperties.js

@@ -11,6 +11,7 @@ import {
   removeDuplicatesIcon,
   useMemoDeepEqual
 } from "@teselagen/ui";
+import { convertDnaCaretPositionOrRangeToAA } from "@teselagen/sequence-utils";
 import { map, upperFirst, pick, startCase, isFunction } from "lodash-es";
 import {
   AnchorButton,
@@ -86,7 +87,10 @@ const genericAnnotationProperties = ({
 
     const annotationsToUse = React.useMemo(
       () =>
-        map(annotations, annotation => {
+        map(annotations, _annotation => {
+          const annotation = isProtein
+            ? convertDnaCaretPositionOrRangeToAA(_annotation)
+            : _annotation;
           return {
             ...annotation,
             ...(annotation.strand === undefined && {
@@ -95,7 +99,7 @@ const genericAnnotationProperties = ({
             size: getRangeLength(annotation, sequenceLength)
           };
         }),
-      [annotations, sequenceLength]
+      [annotations, sequenceLength, isProtein]
     );
 
     const keyedPartTags = getKeyedTagsAndTagOptions(allPartTags) ?? {};
@@ -180,7 +184,7 @@ const genericAnnotationProperties = ({
                   }
                 }
               ]),
-          sizeSchema(isProtein),
+          sizeSchema(),
           ...(withTags && allPartTags
             ? [
                 {

package/src/helperComponents/PropertiesDialog/OrfProperties.js

@@ -79,7 +79,7 @@ class OrfProperties extends React.Component {
                 displayName: "Size (aa)",
                 type: "number"
               },
-              sizeSchema(this.props.isProtein),
+              sizeSchema(),
               { path: "frame", type: "number" },
               { path: "strand", type: "number" }
             ]

package/src/helperComponents/PropertiesDialog/utils.js

@@ -1,22 +1,18 @@
 import React from "react";
 import { isEqual } from "lodash-es";
-import { convertDnaCaretPositionOrRangeToAA } from "@teselagen/sequence-utils";
 import { convertRangeTo1Based } from "@teselagen/range-utils";
 import selectors from "../../selectors";
 
-export const sizeSchema = isProtein => ({
+export const sizeSchema = () => ({
   path: "size",
   type: "number",
-  render: (val, _record) => {
-    const record = isProtein
-      ? convertDnaCaretPositionOrRangeToAA(_record)
-      : _record;
+  render: (val, record) => {
     const base1Range = convertRangeTo1Based(record);
     const hasJoinedLocations = record.locations && record.locations.length > 1;
 
     return (
       <span>
-        {isProtein ? Math.floor(val / 3) : val}{" "}
+        {val}{" "}
         <span style={{ fontSize: 10 }}>
           {hasJoinedLocations ? (
             record.locations.map((loc, i) => {
@@ -41,12 +37,9 @@ export const sizeSchema = isProtein => ({
 export const getMemoOrfs = (() => {
   let lastDeps;
   let lastResult;
-  return (editorState) => {
-    const {
-      sequenceData,
-      minimumOrfSize,
-      useAdditionalOrfStartCodons
-    } = editorState;
+  return editorState => {
+    const { sequenceData, minimumOrfSize, useAdditionalOrfStartCodons } =
+      editorState;
 
     const { sequence, circular } = sequenceData;
 

package/src/helperComponents/RemoveDuplicates/index.js

@@ -14,6 +14,7 @@ import { forEach, camelCase, startCase } from "lodash-es";
 import { sizeSchema } from "../PropertiesDialog/utils";
 import { getRangeLength } from "@teselagen/range-utils";
 import { useFormValue } from "../../utils/useFormValue";
+import { convertDnaCaretPositionOrRangeToAA } from "@teselagen/sequence-utils";
 
 const dialogFormName = "RemoveDuplicatesDialog";
 const dataTableFormName = "duplicatesToRemove";
@@ -33,6 +34,7 @@ const RemoveDuplicatesDialog = props => {
   const ignoreName = useFormValue(dialogFormName, "ignoreName");
   const ignoreStartAndEnd = useFormValue(dialogFormName, "ignoreStartAndEnd");
   const ignoreStrand = useFormValue(dialogFormName, "ignoreStrand");
+  const isProteinSeq = isProtein || sequenceData.isProtein;
 
   const recomputeDups = useCallback(
     values => {
@@ -42,19 +44,25 @@ const RemoveDuplicatesDialog = props => {
       const annotations = sequenceData[type];
       const newDups = [];
       const seqsHashByStartEndStrandName = {};
-      forEach(annotations, a => {
-        const hash = `${ignoreStartAndEnd ? "" : a.start}&${
-          ignoreStartAndEnd ? "" : a.end
-        }&${ignoreStrand ? "" : a.strand}&${ignoreName ? "" : a.name}`;
+      forEach(annotations, _annotation => {
+        const annotation = isProteinSeq
+          ? convertDnaCaretPositionOrRangeToAA(_annotation)
+          : _annotation;
+        const hash = `${ignoreStartAndEnd ? "" : annotation.start}&${
+          ignoreStartAndEnd ? "" : annotation.end
+        }&${ignoreStrand ? "" : annotation.strand}&${ignoreName ? "" : annotation.name}`;
         if (seqsHashByStartEndStrandName[hash]) {
-          newDups.push({ ...a, size: getRangeLength(a, sequenceLength) });
+          newDups.push({
+            ...annotation,
+            size: getRangeLength(annotation, sequenceLength)
+          });
         } else {
           seqsHashByStartEndStrandName[hash] = true;
         }
       });
       return newDups;
     },
-    [sequenceData, sequenceLength, type]
+    [sequenceData, sequenceLength, type, isProteinSeq]
   );
 
   const [dups, setDups] = useState(recomputeDups);
@@ -79,11 +87,11 @@ const RemoveDuplicatesDialog = props => {
       fields: [
         { path: "name", type: "string" },
         // ...(noType ? [] : [{ path: "type", type: "string" }]),
-        sizeSchema(isProtein),
+        sizeSchema(),
         { path: "strand", type: "string" }
       ]
     }),
-    [isProtein]
+    []
   );
 
   return (