@teselagen/ove 0.8.17 → 0.8.19

package/index.cjs.js

@@ -8349,6 +8349,15 @@ function baseLt(value, other) {
   return value < other;
 }
 __name(baseLt, "baseLt");
+function mapValues$1(object3, iteratee) {
+  var result = {};
+  iteratee = baseIteratee(iteratee);
+  baseForOwn(object3, function(value, key, object4) {
+    baseAssignValue(result, key, iteratee(value, key, object4));
+  });
+  return result;
+}
+__name(mapValues$1, "mapValues$1");
 function baseExtremum(array2, iteratee, comparator) {
   var index2 = -1, length = array2.length;
   while (++index2 < length) {
@@ -13213,12 +13222,12 @@ var getComputedStyleX;
 if (typeof window !== "undefined") {
   getComputedStyleX = window.getComputedStyle ? _getComputedStyle : _getComputedStyleIE;
 }
-function each$2(arr, fn4) {
+function each(arr, fn4) {
   for (var i = 0; i < arr.length; i++) {
     fn4(arr[i]);
   }
 }
-__name(each$2, "each$2");
+__name(each, "each");
 function isBorderBoxFn(elem) {
   return getComputedStyleX(elem, "boxSizing") === "border-box";
 }
@@ -13273,7 +13282,7 @@ function isWindow(obj) {
 }
 __name(isWindow, "isWindow");
 var domUtils = {};
-each$2(["Width", "Height"], function(name2) {
+each(["Width", "Height"], function(name2) {
   domUtils["doc".concat(name2)] = function(refWin) {
     var d2 = refWin.document;
     return Math.max(
@@ -13369,7 +13378,7 @@ function css(el, name2, v2) {
   return getComputedStyleX(el, name2);
 }
 __name(css, "css");
-each$2(["width", "height"], function(name2) {
+each(["width", "height"], function(name2) {
   var first = name2.charAt(0).toUpperCase() + name2.slice(1);
   domUtils["outer".concat(first)] = function(el, includeMargin) {
     return el && getWHIgnoreDisplay(el, name2, includeMargin ? MARGIN_INDEX : BORDER_INDEX);
@@ -13420,7 +13429,7 @@ var util$2 = _objectSpread2$2({
     }
   }, "offset"),
   isWindow,
-  each: each$2,
+  each,
   css,
   clone: /* @__PURE__ */ __name(function clone(obj) {
     var ret = {};
@@ -75209,17 +75218,25 @@ function tidyUpSequenceData(pSeqData, options = {}) {
   });
   if (!noTranslationData) {
     seqData.translations = flatMap(seqData.translations, (translation) => {
+      var _a2, _b2;
       if (noCdsTranslations && translation.translationType === "CDS Feature") {
         return [];
       }
-      if (!translation.aminoAcids && !seqData.noSequence) {
-        translation.aminoAcids = getAminoAcidDataForEachBaseOfDna(
+      const codonStart = ((_b2 = (_a2 = translation == null ? void 0 : translation.notes) == null ? void 0 : _a2.codon_start) == null ? void 0 : _b2[0]) - 1 || 0;
+      const expandedRange = expandOrContractRangeByLength(
+        translation,
+        -codonStart,
+        true,
+        seqData.sequence.length
+      );
+      if (!expandedRange.aminoAcids && !seqData.noSequence) {
+        expandedRange.aminoAcids = getAminoAcidDataForEachBaseOfDna(
           seqData.sequence,
-          translation.forward,
-          translation
+          expandedRange.forward,
+          expandedRange
         );
       }
-      return translation;
+      return expandedRange;
     });
   }
   if (annotationsAsObjects) {
@@ -97810,32 +97827,6 @@ const orfsSelector = createSelector(
   (state2) => state2.useAdditionalOrfStartCodons,
   findOrfsInPlasmid
 );
-var forEach_1;
-var hasRequiredForEach;
-function requireForEach() {
-  if (hasRequiredForEach) return forEach_1;
-  hasRequiredForEach = 1;
-  var arrayEach2 = require_arrayEach(), baseEach2 = require_baseEach(), castFunction2 = require_castFunction(), isArray2 = requireIsArray();
-  function forEach3(collection, iteratee) {
-    var func = isArray2(collection) ? arrayEach2 : baseEach2;
-    return func(collection, castFunction2(iteratee));
-  }
-  __name(forEach3, "forEach");
-  forEach_1 = forEach3;
-  return forEach_1;
-}
-__name(requireForEach, "requireForEach");
-var each$1;
-var hasRequiredEach;
-function requireEach() {
-  if (hasRequiredEach) return each$1;
-  hasRequiredEach = 1;
-  each$1 = requireForEach();
-  return each$1;
-}
-__name(requireEach, "requireEach");
-var eachExports = requireEach();
-const each = /* @__PURE__ */ getDefaultExportFromCjs(eachExports);
 function translationsRawSelector(sequenceData2) {
   return sequenceData2.translations;
 }
@@ -98002,14 +97993,22 @@ function translationsSelector(isCircular, translationSearchMatches, sequence2, o
     },
     {}
   ));
-  each(translationsToPass, function(translation) {
-    translation.aminoAcids = getAminoAcidDataForEachBaseOfDna(
+  return mapValues$1(translationsToPass, (translation) => {
+    var _a2, _b2;
+    const codonStart = ((_b2 = (_a2 = translation == null ? void 0 : translation.notes) == null ? void 0 : _a2.codon_start) == null ? void 0 : _b2[0]) - 1 || 0;
+    const expandedRange = expandOrContractRangeByLength(
+      translation,
+      -codonStart,
+      true,
+      sequence2.length
+    );
+    expandedRange.aminoAcids = getAminoAcidDataForEachBaseOfDna(
       sequence2,
-      translation.forward,
-      translation
+      expandedRange.forward,
+      expandedRange
     );
+    return expandedRange;
   });
-  return translationsToPass;
 }
 __name(translationsSelector, "translationsSelector");
 const translationsSelector$1 = createSelector(
@@ -109885,6 +109884,21 @@ function Orf(props) {
   );
 }
 __name(Orf, "Orf");
+var forEach_1;
+var hasRequiredForEach;
+function requireForEach() {
+  if (hasRequiredForEach) return forEach_1;
+  hasRequiredForEach = 1;
+  var arrayEach2 = require_arrayEach(), baseEach2 = require_baseEach(), castFunction2 = require_castFunction(), isArray2 = requireIsArray();
+  function forEach3(collection, iteratee) {
+    var func = isArray2(collection) ? arrayEach2 : baseEach2;
+    return func(collection, castFunction2(iteratee));
+  }
+  __name(forEach3, "forEach");
+  forEach_1 = forEach3;
+  return forEach_1;
+}
+__name(requireForEach, "requireForEach");
 var forEachExports = requireForEach();
 const forEach2 = /* @__PURE__ */ getDefaultExportFromCjs(forEachExports);
 var lib = {};
@@ -116640,7 +116654,7 @@ function showFileDialog({ multiple = false, onSelect }) {
   input.click();
 }
 __name(showFileDialog, "showFileDialog");
-const version = "0.8.16";
+const version = "0.8.18";
 const packageJson = {
   version
 };
@@ -124292,6 +124306,7 @@ const __LinearView = class __LinearView extends React.Component {
           RowItem$1,
           __spreadProps(__spreadValues({}, __spreadValues(__spreadProps(__spreadValues({}, rest), {
             editorName,
+            showAminoAcidUnitAsCodon,
             onScroll: /* @__PURE__ */ __name(() => {
               this.easyStore.viewportWidth = width;
               const row = this.linearView.querySelector(".veRowItemWrapper");
@@ -138096,7 +138111,7 @@ const PropertySidePanel = /* @__PURE__ */ __name(({ properties: properties2, set
         item: selection && selection.start > -1 ? /* @__PURE__ */ React.createElement("span", null, selection.start + 1, " - ", selection.end + 1) : /* @__PURE__ */ React.createElement("span", null, "1 - ", isProtein2 ? proteinSize : size),
         title: "Region"
       }
-    )), /* @__PURE__ */ React.createElement("h5", null, isProtein2 ? "Amino Acid" : "Base Pair", " Frequencies"), /* @__PURE__ */ React.createElement("div", { className: "sidebar-table" }, /* @__PURE__ */ React.createElement("div", { className: "sidebar-row" }, /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, "Amino Acid"), /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, "Count"), /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, "Percentage")), frequencyEntries.map(([aa, data], idx) => {
+    )), /* @__PURE__ */ React.createElement("h5", null, isProtein2 ? "Amino Acid" : "Base Pair", " Frequencies"), /* @__PURE__ */ React.createElement("div", { className: "sidebar-table" }, /* @__PURE__ */ React.createElement("div", { className: "sidebar-row" }, /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, isProtein2 ? "Amino Acid" : "Base"), /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, "Count"), /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, "Percentage")), frequencyEntries.map(([aa, data], idx) => {
       return /* @__PURE__ */ React.createElement("div", { className: `sidebar-row property-amino-acid-${idx}` }, /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, aa, " ", isProtein2 ? `(${aminoAcidShortNames[aa]})` : ""), /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, data.count), /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, data.percentage.toFixed(1), "%"));
     })));
   } else {
@@ -138596,7 +138611,11 @@ ${seqDataToCopy}\r
   }, [alignmentTracks, id2, store2]);
   React.useEffect(() => {
     const handleAlignmentCopy = /* @__PURE__ */ __name((event) => {
+      var _a3, _b2, _c;
       if (event.key === "c" && !event.shiftKey && (event.metaKey === true || event.ctrlKey === true)) {
+        if (!((_a3 = document.activeElement) == null ? void 0 : _a3.classList.contains("alignmentView"))) {
+          return;
+        }
         const input = document.createElement("textarea");
         document.body.appendChild(input);
         const seqDataToCopy = getAllAlignmentsFastaText();
@@ -138610,6 +138629,8 @@ ${seqDataToCopy}\r
         }
         document.body.removeChild(input);
         event.preventDefault();
+        (_b2 = document.activeElement) == null ? void 0 : _b2.blur();
+        (_c = document.querySelector(".alignmentView")) == null ? void 0 : _c.focus();
       }
     }, "handleAlignmentCopy");
     document.addEventListener("keydown", handleAlignmentCopy);
@@ -139768,6 +139789,7 @@ ${seqDataToCopy}\r
           position: "relative",
           overflowY: "auto"
         }, style2),
+        tabIndex: 0,
         className: "alignmentView"
       },
       /* @__PURE__ */ React.createElement(
@@ -143607,7 +143629,7 @@ const genericAnnotationProperties = /* @__PURE__ */ __name(({
       this.commands = getCommands(this);
     }
     render() {
-      var _a2, _b2;
+      var _a2, _b2, _c;
       const {
         readOnly: readOnly2,
         annotations = {},
@@ -143631,7 +143653,9 @@ const genericAnnotationProperties = /* @__PURE__ */ __name(({
         });
       });
       const keyedPartTags = (_a2 = getKeyedTagsAndTagOptions(allPartTags)) != null ? _a2 : {};
-      const additionalColumns = ((_b2 = PropertiesProps == null ? void 0 : PropertiesProps[annotationType]) == null ? void 0 : _b2.additionalColumns) || [];
+      const additionalColumns = ((_c = (_b2 = PropertiesProps == null ? void 0 : PropertiesProps.propertiesList) == null ? void 0 : _b2.find(
+        (p2) => (p2.name || p2) === (pluralize(annotationType) || "")
+      )) == null ? void 0 : _c.additionalColumns) || [];
       this.schema = {
         fields: [
           {

package/index.es.js

@@ -8331,6 +8331,15 @@ function baseLt(value, other) {
   return value < other;
 }
 __name(baseLt, "baseLt");
+function mapValues$1(object3, iteratee) {
+  var result = {};
+  iteratee = baseIteratee(iteratee);
+  baseForOwn(object3, function(value, key, object4) {
+    baseAssignValue(result, key, iteratee(value, key, object4));
+  });
+  return result;
+}
+__name(mapValues$1, "mapValues$1");
 function baseExtremum(array2, iteratee, comparator) {
   var index2 = -1, length = array2.length;
   while (++index2 < length) {
@@ -13195,12 +13204,12 @@ var getComputedStyleX;
 if (typeof window !== "undefined") {
   getComputedStyleX = window.getComputedStyle ? _getComputedStyle : _getComputedStyleIE;
 }
-function each$2(arr, fn4) {
+function each(arr, fn4) {
   for (var i = 0; i < arr.length; i++) {
     fn4(arr[i]);
   }
 }
-__name(each$2, "each$2");
+__name(each, "each");
 function isBorderBoxFn(elem) {
   return getComputedStyleX(elem, "boxSizing") === "border-box";
 }
@@ -13255,7 +13264,7 @@ function isWindow(obj) {
 }
 __name(isWindow, "isWindow");
 var domUtils = {};
-each$2(["Width", "Height"], function(name2) {
+each(["Width", "Height"], function(name2) {
   domUtils["doc".concat(name2)] = function(refWin) {
     var d2 = refWin.document;
     return Math.max(
@@ -13351,7 +13360,7 @@ function css(el, name2, v2) {
   return getComputedStyleX(el, name2);
 }
 __name(css, "css");
-each$2(["width", "height"], function(name2) {
+each(["width", "height"], function(name2) {
   var first = name2.charAt(0).toUpperCase() + name2.slice(1);
   domUtils["outer".concat(first)] = function(el, includeMargin) {
     return el && getWHIgnoreDisplay(el, name2, includeMargin ? MARGIN_INDEX : BORDER_INDEX);
@@ -13402,7 +13411,7 @@ var util$2 = _objectSpread2$2({
     }
   }, "offset"),
   isWindow,
-  each: each$2,
+  each,
   css,
   clone: /* @__PURE__ */ __name(function clone(obj) {
     var ret = {};
@@ -75191,17 +75200,25 @@ function tidyUpSequenceData(pSeqData, options = {}) {
   });
   if (!noTranslationData) {
     seqData.translations = flatMap(seqData.translations, (translation) => {
+      var _a2, _b2;
       if (noCdsTranslations && translation.translationType === "CDS Feature") {
         return [];
       }
-      if (!translation.aminoAcids && !seqData.noSequence) {
-        translation.aminoAcids = getAminoAcidDataForEachBaseOfDna(
+      const codonStart = ((_b2 = (_a2 = translation == null ? void 0 : translation.notes) == null ? void 0 : _a2.codon_start) == null ? void 0 : _b2[0]) - 1 || 0;
+      const expandedRange = expandOrContractRangeByLength(
+        translation,
+        -codonStart,
+        true,
+        seqData.sequence.length
+      );
+      if (!expandedRange.aminoAcids && !seqData.noSequence) {
+        expandedRange.aminoAcids = getAminoAcidDataForEachBaseOfDna(
           seqData.sequence,
-          translation.forward,
-          translation
+          expandedRange.forward,
+          expandedRange
         );
       }
-      return translation;
+      return expandedRange;
     });
   }
   if (annotationsAsObjects) {
@@ -97792,32 +97809,6 @@ const orfsSelector = createSelector(
   (state2) => state2.useAdditionalOrfStartCodons,
   findOrfsInPlasmid
 );
-var forEach_1;
-var hasRequiredForEach;
-function requireForEach() {
-  if (hasRequiredForEach) return forEach_1;
-  hasRequiredForEach = 1;
-  var arrayEach2 = require_arrayEach(), baseEach2 = require_baseEach(), castFunction2 = require_castFunction(), isArray2 = requireIsArray();
-  function forEach3(collection, iteratee) {
-    var func = isArray2(collection) ? arrayEach2 : baseEach2;
-    return func(collection, castFunction2(iteratee));
-  }
-  __name(forEach3, "forEach");
-  forEach_1 = forEach3;
-  return forEach_1;
-}
-__name(requireForEach, "requireForEach");
-var each$1;
-var hasRequiredEach;
-function requireEach() {
-  if (hasRequiredEach) return each$1;
-  hasRequiredEach = 1;
-  each$1 = requireForEach();
-  return each$1;
-}
-__name(requireEach, "requireEach");
-var eachExports = requireEach();
-const each = /* @__PURE__ */ getDefaultExportFromCjs(eachExports);
 function translationsRawSelector(sequenceData2) {
   return sequenceData2.translations;
 }
@@ -97984,14 +97975,22 @@ function translationsSelector(isCircular, translationSearchMatches, sequence2, o
     },
     {}
   ));
-  each(translationsToPass, function(translation) {
-    translation.aminoAcids = getAminoAcidDataForEachBaseOfDna(
+  return mapValues$1(translationsToPass, (translation) => {
+    var _a2, _b2;
+    const codonStart = ((_b2 = (_a2 = translation == null ? void 0 : translation.notes) == null ? void 0 : _a2.codon_start) == null ? void 0 : _b2[0]) - 1 || 0;
+    const expandedRange = expandOrContractRangeByLength(
+      translation,
+      -codonStart,
+      true,
+      sequence2.length
+    );
+    expandedRange.aminoAcids = getAminoAcidDataForEachBaseOfDna(
       sequence2,
-      translation.forward,
-      translation
+      expandedRange.forward,
+      expandedRange
     );
+    return expandedRange;
   });
-  return translationsToPass;
 }
 __name(translationsSelector, "translationsSelector");
 const translationsSelector$1 = createSelector(
@@ -109867,6 +109866,21 @@ function Orf(props) {
   );
 }
 __name(Orf, "Orf");
+var forEach_1;
+var hasRequiredForEach;
+function requireForEach() {
+  if (hasRequiredForEach) return forEach_1;
+  hasRequiredForEach = 1;
+  var arrayEach2 = require_arrayEach(), baseEach2 = require_baseEach(), castFunction2 = require_castFunction(), isArray2 = requireIsArray();
+  function forEach3(collection, iteratee) {
+    var func = isArray2(collection) ? arrayEach2 : baseEach2;
+    return func(collection, castFunction2(iteratee));
+  }
+  __name(forEach3, "forEach");
+  forEach_1 = forEach3;
+  return forEach_1;
+}
+__name(requireForEach, "requireForEach");
 var forEachExports = requireForEach();
 const forEach2 = /* @__PURE__ */ getDefaultExportFromCjs(forEachExports);
 var lib = {};
@@ -116622,7 +116636,7 @@ function showFileDialog({ multiple = false, onSelect }) {
   input.click();
 }
 __name(showFileDialog, "showFileDialog");
-const version = "0.8.16";
+const version = "0.8.18";
 const packageJson = {
   version
 };
@@ -124274,6 +124288,7 @@ const __LinearView = class __LinearView extends React__default.Component {
           RowItem$1,
           __spreadProps(__spreadValues({}, __spreadValues(__spreadProps(__spreadValues({}, rest), {
             editorName,
+            showAminoAcidUnitAsCodon,
             onScroll: /* @__PURE__ */ __name(() => {
               this.easyStore.viewportWidth = width;
               const row = this.linearView.querySelector(".veRowItemWrapper");
@@ -138078,7 +138093,7 @@ const PropertySidePanel = /* @__PURE__ */ __name(({ properties: properties2, set
         item: selection && selection.start > -1 ? /* @__PURE__ */ React__default.createElement("span", null, selection.start + 1, " - ", selection.end + 1) : /* @__PURE__ */ React__default.createElement("span", null, "1 - ", isProtein2 ? proteinSize : size),
         title: "Region"
       }
-    )), /* @__PURE__ */ React__default.createElement("h5", null, isProtein2 ? "Amino Acid" : "Base Pair", " Frequencies"), /* @__PURE__ */ React__default.createElement("div", { className: "sidebar-table" }, /* @__PURE__ */ React__default.createElement("div", { className: "sidebar-row" }, /* @__PURE__ */ React__default.createElement("div", { className: "sidebar-cell" }, "Amino Acid"), /* @__PURE__ */ React__default.createElement("div", { className: "sidebar-cell" }, "Count"), /* @__PURE__ */ React__default.createElement("div", { className: "sidebar-cell" }, "Percentage")), frequencyEntries.map(([aa, data], idx) => {
+    )), /* @__PURE__ */ React__default.createElement("h5", null, isProtein2 ? "Amino Acid" : "Base Pair", " Frequencies"), /* @__PURE__ */ React__default.createElement("div", { className: "sidebar-table" }, /* @__PURE__ */ React__default.createElement("div", { className: "sidebar-row" }, /* @__PURE__ */ React__default.createElement("div", { className: "sidebar-cell" }, isProtein2 ? "Amino Acid" : "Base"), /* @__PURE__ */ React__default.createElement("div", { className: "sidebar-cell" }, "Count"), /* @__PURE__ */ React__default.createElement("div", { className: "sidebar-cell" }, "Percentage")), frequencyEntries.map(([aa, data], idx) => {
       return /* @__PURE__ */ React__default.createElement("div", { className: `sidebar-row property-amino-acid-${idx}` }, /* @__PURE__ */ React__default.createElement("div", { className: "sidebar-cell" }, aa, " ", isProtein2 ? `(${aminoAcidShortNames[aa]})` : ""), /* @__PURE__ */ React__default.createElement("div", { className: "sidebar-cell" }, data.count), /* @__PURE__ */ React__default.createElement("div", { className: "sidebar-cell" }, data.percentage.toFixed(1), "%"));
     })));
   } else {
@@ -138578,7 +138593,11 @@ ${seqDataToCopy}\r
   }, [alignmentTracks, id2, store2]);
   useEffect(() => {
     const handleAlignmentCopy = /* @__PURE__ */ __name((event) => {
+      var _a3, _b2, _c;
       if (event.key === "c" && !event.shiftKey && (event.metaKey === true || event.ctrlKey === true)) {
+        if (!((_a3 = document.activeElement) == null ? void 0 : _a3.classList.contains("alignmentView"))) {
+          return;
+        }
         const input = document.createElement("textarea");
         document.body.appendChild(input);
         const seqDataToCopy = getAllAlignmentsFastaText();
@@ -138592,6 +138611,8 @@ ${seqDataToCopy}\r
         }
         document.body.removeChild(input);
         event.preventDefault();
+        (_b2 = document.activeElement) == null ? void 0 : _b2.blur();
+        (_c = document.querySelector(".alignmentView")) == null ? void 0 : _c.focus();
       }
     }, "handleAlignmentCopy");
     document.addEventListener("keydown", handleAlignmentCopy);
@@ -139750,6 +139771,7 @@ ${seqDataToCopy}\r
           position: "relative",
           overflowY: "auto"
         }, style2),
+        tabIndex: 0,
         className: "alignmentView"
       },
       /* @__PURE__ */ React__default.createElement(
@@ -143589,7 +143611,7 @@ const genericAnnotationProperties = /* @__PURE__ */ __name(({
       this.commands = getCommands(this);
     }
     render() {
-      var _a2, _b2;
+      var _a2, _b2, _c;
       const {
         readOnly: readOnly2,
         annotations = {},
@@ -143613,7 +143635,9 @@ const genericAnnotationProperties = /* @__PURE__ */ __name(({
         });
       });
       const keyedPartTags = (_a2 = getKeyedTagsAndTagOptions(allPartTags)) != null ? _a2 : {};
-      const additionalColumns = ((_b2 = PropertiesProps == null ? void 0 : PropertiesProps[annotationType]) == null ? void 0 : _b2.additionalColumns) || [];
+      const additionalColumns = ((_c = (_b2 = PropertiesProps == null ? void 0 : PropertiesProps.propertiesList) == null ? void 0 : _b2.find(
+        (p2) => (p2.name || p2) === (pluralize(annotationType) || "")
+      )) == null ? void 0 : _c.additionalColumns) || [];
       this.schema = {
         fields: [
           {

package/index.umd.js

@@ -35432,6 +35432,15 @@ ${latestSubscriptionCallbackError.current.stack}
     return value < other;
   }
   __name(baseLt, "baseLt");
+  function mapValues$1(object2, iteratee) {
+    var result = {};
+    iteratee = baseIteratee(iteratee);
+    baseForOwn(object2, function(value, key, object3) {
+      baseAssignValue(result, key, iteratee(value, key, object3));
+    });
+    return result;
+  }
+  __name(mapValues$1, "mapValues$1");
   function baseExtremum(array, iteratee, comparator) {
     var index2 = -1, length = array.length;
     while (++index2 < length) {
@@ -40254,12 +40263,12 @@ ${latestSubscriptionCallbackError.current.stack}
   if (typeof window !== "undefined") {
     getComputedStyleX = window.getComputedStyle ? _getComputedStyle : _getComputedStyleIE;
   }
-  function each$2(arr, fn2) {
+  function each(arr, fn2) {
     for (var i2 = 0; i2 < arr.length; i2++) {
       fn2(arr[i2]);
     }
   }
-  __name(each$2, "each$2");
+  __name(each, "each");
   function isBorderBoxFn(elem) {
     return getComputedStyleX(elem, "boxSizing") === "border-box";
   }
@@ -40314,7 +40323,7 @@ ${latestSubscriptionCallbackError.current.stack}
   }
   __name(isWindow, "isWindow");
   var domUtils = {};
-  each$2(["Width", "Height"], function(name2) {
+  each(["Width", "Height"], function(name2) {
     domUtils["doc".concat(name2)] = function(refWin) {
       var d2 = refWin.document;
       return Math.max(
@@ -40410,7 +40419,7 @@ ${latestSubscriptionCallbackError.current.stack}
     return getComputedStyleX(el, name2);
   }
   __name(css, "css");
-  each$2(["width", "height"], function(name2) {
+  each(["width", "height"], function(name2) {
     var first = name2.charAt(0).toUpperCase() + name2.slice(1);
     domUtils["outer".concat(first)] = function(el, includeMargin) {
       return el && getWHIgnoreDisplay(el, name2, includeMargin ? MARGIN_INDEX : BORDER_INDEX);
@@ -40461,7 +40470,7 @@ ${latestSubscriptionCallbackError.current.stack}
       }
     }, "offset"),
     isWindow,
-    each: each$2,
+    each,
     css,
     clone: /* @__PURE__ */ __name(function clone2(obj) {
       var ret = {};
@@ -104112,17 +104121,25 @@ ${latestSubscriptionCallbackError.current.stack}
     });
     if (!noTranslationData) {
       seqData.translations = flatMap(seqData.translations, (translation) => {
+        var _a2, _b2;
         if (noCdsTranslations && translation.translationType === "CDS Feature") {
           return [];
         }
-        if (!translation.aminoAcids && !seqData.noSequence) {
-          translation.aminoAcids = getAminoAcidDataForEachBaseOfDna(
+        const codonStart = ((_b2 = (_a2 = translation == null ? void 0 : translation.notes) == null ? void 0 : _a2.codon_start) == null ? void 0 : _b2[0]) - 1 || 0;
+        const expandedRange = expandOrContractRangeByLength(
+          translation,
+          -codonStart,
+          true,
+          seqData.sequence.length
+        );
+        if (!expandedRange.aminoAcids && !seqData.noSequence) {
+          expandedRange.aminoAcids = getAminoAcidDataForEachBaseOfDna(
             seqData.sequence,
-            translation.forward,
-            translation
+            expandedRange.forward,
+            expandedRange
           );
         }
-        return translation;
+        return expandedRange;
       });
     }
     if (annotationsAsObjects) {
@@ -125958,32 +125975,6 @@ ${seq.sequence}
     (state2) => state2.useAdditionalOrfStartCodons,
     findOrfsInPlasmid
   );
-  var forEach_1;
-  var hasRequiredForEach;
-  function requireForEach() {
-    if (hasRequiredForEach) return forEach_1;
-    hasRequiredForEach = 1;
-    var arrayEach2 = require_arrayEach(), baseEach2 = require_baseEach(), castFunction2 = require_castFunction(), isArray2 = requireIsArray();
-    function forEach2(collection, iteratee) {
-      var func = isArray2(collection) ? arrayEach2 : baseEach2;
-      return func(collection, castFunction2(iteratee));
-    }
-    __name(forEach2, "forEach");
-    forEach_1 = forEach2;
-    return forEach_1;
-  }
-  __name(requireForEach, "requireForEach");
-  var each$1;
-  var hasRequiredEach;
-  function requireEach() {
-    if (hasRequiredEach) return each$1;
-    hasRequiredEach = 1;
-    each$1 = requireForEach();
-    return each$1;
-  }
-  __name(requireEach, "requireEach");
-  var eachExports = requireEach();
-  const each = /* @__PURE__ */ getDefaultExportFromCjs(eachExports);
   function translationsRawSelector(sequenceData2) {
     return sequenceData2.translations;
   }
@@ -126150,14 +126141,22 @@ ${seq.sequence}
       },
       {}
     ));
-    each(translationsToPass, function(translation) {
-      translation.aminoAcids = getAminoAcidDataForEachBaseOfDna(
+    return mapValues$1(translationsToPass, (translation) => {
+      var _a2, _b2;
+      const codonStart = ((_b2 = (_a2 = translation == null ? void 0 : translation.notes) == null ? void 0 : _a2.codon_start) == null ? void 0 : _b2[0]) - 1 || 0;
+      const expandedRange = expandOrContractRangeByLength(
+        translation,
+        -codonStart,
+        true,
+        sequence2.length
+      );
+      expandedRange.aminoAcids = getAminoAcidDataForEachBaseOfDna(
         sequence2,
-        translation.forward,
-        translation
+        expandedRange.forward,
+        expandedRange
       );
+      return expandedRange;
     });
-    return translationsToPass;
   }
   __name(translationsSelector, "translationsSelector");
   const translationsSelector$1 = createSelector(
@@ -138033,6 +138032,21 @@ ${seq.sequence}
     );
   }
   __name(Orf, "Orf");
+  var forEach_1;
+  var hasRequiredForEach;
+  function requireForEach() {
+    if (hasRequiredForEach) return forEach_1;
+    hasRequiredForEach = 1;
+    var arrayEach2 = require_arrayEach(), baseEach2 = require_baseEach(), castFunction2 = require_castFunction(), isArray2 = requireIsArray();
+    function forEach2(collection, iteratee) {
+      var func = isArray2(collection) ? arrayEach2 : baseEach2;
+      return func(collection, castFunction2(iteratee));
+    }
+    __name(forEach2, "forEach");
+    forEach_1 = forEach2;
+    return forEach_1;
+  }
+  __name(requireForEach, "requireForEach");
   var forEachExports = requireForEach();
   const forEach = /* @__PURE__ */ getDefaultExportFromCjs(forEachExports);
   var lib = {};
@@ -144738,7 +144752,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
     input.click();
   }
   __name(showFileDialog, "showFileDialog");
-  const version = "0.8.16";
+  const version = "0.8.18";
   const packageJson = {
     version
   };
@@ -150788,6 +150802,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
             RowItem$1,
             __spreadProps(__spreadValues({}, __spreadValues(__spreadProps(__spreadValues({}, rest), {
               editorName,
+              showAminoAcidUnitAsCodon,
               onScroll: /* @__PURE__ */ __name(() => {
                 this.easyStore.viewportWidth = width;
                 const row = this.linearView.querySelector(".veRowItemWrapper");
@@ -164592,7 +164607,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
           item: selection && selection.start > -1 ? /* @__PURE__ */ React.createElement("span", null, selection.start + 1, " - ", selection.end + 1) : /* @__PURE__ */ React.createElement("span", null, "1 - ", isProtein2 ? proteinSize : size2),
           title: "Region"
         }
-      )), /* @__PURE__ */ React.createElement("h5", null, isProtein2 ? "Amino Acid" : "Base Pair", " Frequencies"), /* @__PURE__ */ React.createElement("div", { className: "sidebar-table" }, /* @__PURE__ */ React.createElement("div", { className: "sidebar-row" }, /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, "Amino Acid"), /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, "Count"), /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, "Percentage")), frequencyEntries.map(([aa, data], idx) => {
+      )), /* @__PURE__ */ React.createElement("h5", null, isProtein2 ? "Amino Acid" : "Base Pair", " Frequencies"), /* @__PURE__ */ React.createElement("div", { className: "sidebar-table" }, /* @__PURE__ */ React.createElement("div", { className: "sidebar-row" }, /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, isProtein2 ? "Amino Acid" : "Base"), /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, "Count"), /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, "Percentage")), frequencyEntries.map(([aa, data], idx) => {
         return /* @__PURE__ */ React.createElement("div", { className: `sidebar-row property-amino-acid-${idx}` }, /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, aa, " ", isProtein2 ? `(${aminoAcidShortNames[aa]})` : ""), /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, data.count), /* @__PURE__ */ React.createElement("div", { className: "sidebar-cell" }, data.percentage.toFixed(1), "%"));
       })));
     } else {
@@ -165092,7 +165107,11 @@ ${seqDataToCopy}\r
     }, [alignmentTracks, id2, store2]);
     reactExports.useEffect(() => {
       const handleAlignmentCopy = /* @__PURE__ */ __name((event) => {
+        var _a3, _b2, _c2;
         if (event.key === "c" && !event.shiftKey && (event.metaKey === true || event.ctrlKey === true)) {
+          if (!((_a3 = document.activeElement) == null ? void 0 : _a3.classList.contains("alignmentView"))) {
+            return;
+          }
           const input = document.createElement("textarea");
           document.body.appendChild(input);
           const seqDataToCopy = getAllAlignmentsFastaText();
@@ -165106,6 +165125,8 @@ ${seqDataToCopy}\r
           }
           document.body.removeChild(input);
           event.preventDefault();
+          (_b2 = document.activeElement) == null ? void 0 : _b2.blur();
+          (_c2 = document.querySelector(".alignmentView")) == null ? void 0 : _c2.focus();
         }
       }, "handleAlignmentCopy");
       document.addEventListener("keydown", handleAlignmentCopy);
@@ -166264,6 +166285,7 @@ ${seqDataToCopy}\r
             position: "relative",
             overflowY: "auto"
           }, style2),
+          tabIndex: 0,
           className: "alignmentView"
         },
         /* @__PURE__ */ React.createElement(
@@ -170103,7 +170125,7 @@ ${seqDataToCopy}\r
         this.commands = getCommands(this);
       }
       render() {
-        var _a2, _b2;
+        var _a2, _b2, _c2;
         const {
           readOnly: readOnly2,
           annotations = {},
@@ -170127,7 +170149,9 @@ ${seqDataToCopy}\r
           });
         });
         const keyedPartTags = (_a2 = getKeyedTagsAndTagOptions(allPartTags)) != null ? _a2 : {};
-        const additionalColumns = ((_b2 = PropertiesProps == null ? void 0 : PropertiesProps[annotationType]) == null ? void 0 : _b2.additionalColumns) || [];
+        const additionalColumns = ((_c2 = (_b2 = PropertiesProps == null ? void 0 : PropertiesProps.propertiesList) == null ? void 0 : _b2.find(
+          (p2) => (p2.name || p2) === (pluralize(annotationType) || "")
+        )) == null ? void 0 : _c2.additionalColumns) || [];
         this.schema = {
           fields: [
             {

package/ove.css

@@ -11260,6 +11260,12 @@ path.partWithSelectedTag {
   height: 100% !important;
   overflow: hidden;
 }
+.alignmentView .veAlignmentSelectionLayer.veRowViewSelectionLayer {
+  background: gray;
+}
+.alignmentView:focus .veAlignmentSelectionLayer.veRowViewSelectionLayer {
+  background: #0099ff;
+}
 .alignmentView .veSelectionLayer {
   top: 0;
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.8.17",
+  "version": "0.8.19",
   "main": "./src/index.js",
   "type": "module",
   "exports": {

package/selectors/translationsSelector.d.ts

@@ -1,4 +1,6 @@
-declare const _default: ((state: any) => any) & import('reselect').OutputSelectorFields<(args_0: any, args_1: unknown, args_2: any, args_3: {
+declare const _default: ((state: any) => {
+    [x: string]: any;
+}) & import('reselect').OutputSelectorFields<(args_0: any, args_1: unknown, args_2: any, args_3: {
     start: number;
     end: number;
     length: number;
@@ -8,7 +10,9 @@ declare const _default: ((state: any) => any) & import('reselect').OutputSelecto
     annotationTypePlural: string;
     isOrf: boolean;
     id: any;
-}[], args_4: any, args_5: any, args_6: any[], args_7: any, args_8: any, args_9: any, args_10: any, args_11: any, args_12: any) => any, {
+}[], args_4: any, args_5: any, args_6: any[], args_7: any, args_8: any, args_9: any, args_10: any, args_11: any, args_12: any) => {
+    [x: string]: any;
+}, {
     clearCache: () => void;
 }> & {
     clearCache: () => void;

package/src/AlignmentView/index.js

@@ -211,6 +211,9 @@ export const AlignmentView = props => {
         !event.shiftKey &&
         (event.metaKey === true || event.ctrlKey === true)
       ) {
+        if (!document.activeElement?.classList.contains("alignmentView")) {
+          return; //stop early if we're not focused on the alignment view
+        }
         const input = document.createElement("textarea");
         document.body.appendChild(input);
         const seqDataToCopy = getAllAlignmentsFastaText();
@@ -224,6 +227,8 @@ export const AlignmentView = props => {
         }
         document.body.removeChild(input);
         event.preventDefault();
+        document.activeElement?.blur();
+        document.querySelector(".alignmentView")?.focus();
       }
     };
 
@@ -1584,6 +1589,7 @@ export const AlignmentView = props => {
               ...style
               // borderTop: "1px solid black"
             }}
+            tabIndex={0}
             className="alignmentView"
           >
             <DragDropContext

package/src/AlignmentView/style.css

@@ -73,6 +73,12 @@
   height: 100% !important;
   overflow: hidden;
 }
+.alignmentView .veAlignmentSelectionLayer.veRowViewSelectionLayer {
+  background: gray;
+}
+.alignmentView:focus .veAlignmentSelectionLayer.veRowViewSelectionLayer {
+  background: #0099ff;
+}
 .alignmentView .veSelectionLayer {
   top: 0;
 }

package/src/LinearView/index.js

@@ -327,6 +327,7 @@ class _LinearView extends React.Component {
               {...{
                 ...rest,
                 editorName,
+                showAminoAcidUnitAsCodon,
                 onScroll: () => {
                   this.easyStore.viewportWidth = width;
                   const row =

package/src/PropertySidePanel/index.js

@@ -149,7 +149,9 @@ export default ({ properties, setProperties, style }) => {
         <h5>{isProtein ? "Amino Acid" : "Base Pair"} Frequencies</h5>
         <div className="sidebar-table">
           <div className="sidebar-row">
-            <div className="sidebar-cell">Amino Acid</div>
+            <div className="sidebar-cell">
+              {isProtein ? "Amino Acid" : "Base"}
+            </div>
             <div className="sidebar-cell">Count</div>
             <div className="sidebar-cell">Percentage</div>
           </div>

package/src/helperComponents/PropertiesDialog/GenericAnnotationProperties.js

@@ -20,6 +20,7 @@ import {
   Tooltip
 } from "@blueprintjs/core";
 import { getRangeLength } from "@teselagen/range-utils";
+import pluralize from "pluralize";
 // import { Popover } from "@blueprintjs/core";
 // import ColorPicker from "./ColorPicker";
 import { connectToEditor } from "../../withEditorProps";
@@ -87,9 +88,10 @@ const genericAnnotationProperties = ({
       });
 
       const keyedPartTags = getKeyedTagsAndTagOptions(allPartTags) ?? {};
-
       const additionalColumns =
-        PropertiesProps?.[annotationType]?.additionalColumns || [];
+        PropertiesProps?.propertiesList?.find(
+          p => (p.name || p) === (pluralize(annotationType) || "")
+        )?.additionalColumns || [];
 
       this.schema = {
         fields: [

package/src/selectors/translationsSelector.js

@@ -1,14 +1,16 @@
-import { reduce } from "lodash-es";
+import { reduce, mapValues } from "lodash-es";
 import uuid from "shortid";
 import sequenceSelector from "./sequenceSelector";
 import orfsSelector from "./orfsSelector";
 import { createSelector } from "reselect";
 
 import { getAminoAcidDataForEachBaseOfDna } from "@teselagen/sequence-utils";
-import each from "lodash/each";
 import translationsRawSelector from "./translationsRawSelector";
 import translationSearchMatchesSelector from "./translationSearchMatchesSelector";
-import { normalizePositionByRangeLength } from "@teselagen/range-utils";
+import {
+  expandOrContractRangeByLength,
+  normalizePositionByRangeLength
+} from "@teselagen/range-utils";
 import cdsFeaturesSelector from "./cdsFeaturesSelector";
 import circularSelector from "./circularSelector";
 
@@ -109,14 +111,21 @@ function translationsSelector(
       {}
     )
   };
-  each(translationsToPass, function (translation) {
-    translation.aminoAcids = getAminoAcidDataForEachBaseOfDna(
+  return mapValues(translationsToPass, translation => {
+    const codonStart = translation?.notes?.codon_start?.[0] - 1 || 0;
+    const expandedRange = expandOrContractRangeByLength(
+      translation,
+      -codonStart,
+      true,
+      sequence.length
+    );
+    expandedRange.aminoAcids = getAminoAcidDataForEachBaseOfDna(
       sequence,
-      translation.forward,
-      translation
+      expandedRange.forward,
+      expandedRange
     );
+    return expandedRange;
   });
-  return translationsToPass;
 }
 
 export default createSelector(