@teselagen/ove 0.7.24 → 0.7.26

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.7.24",
+  "version": "0.7.26",
   "main": "./src/index.js",
   "type": "module",
   "exports": {
@@ -11,47 +11,28 @@
     "./*": "./*"
   },
   "dependencies": {
-    "@teselagen/sequence-utils": "0.3.28",
-    "@teselagen/range-utils": "0.3.10",
-    "@teselagen/ui": "0.7.23",
-    "@teselagen/file-utils": "0.3.18",
-    "@teselagen/bio-parsers": "0.4.24",
+    "@teselagen/sequence-utils": "file:../sequence-utils",
+    "@teselagen/range-utils": "file:../range-utils",
+    "@teselagen/ui": "file:../ui",
+    "@teselagen/file-utils": "file:../file-utils",
+    "@teselagen/bio-parsers": "file:../bio-parsers",
     "@blueprintjs/core": "3.54.0",
-    "@blueprintjs/datetime": "^3.24.1",
-    "@blueprintjs/icons": "3.33.0",
-    "@blueprintjs/select": "3.18.11",
-    "@dnd-kit/modifiers": "^7.0.0",
-    "@dnd-kit/sortable": "^8.0.0",
-    "@dnd-kit/utilities": "3.2.2",
     "@hello-pangea/dnd": "16.2.0",
     "@risingstack/react-easy-state": "^6.3.0",
     "@teselagen/react-list": "0.8.18",
-    "@teselagen/react-table": "6.10.16",
-    "bluebird": "3.7.2",
-    "bson-objectid": "2.0.4",
-    "buffer": "6.0.3",
-    "bufferpack": "0.0.6",
     "classnames": "^2.3.2",
     "color": "^3.2.1",
     "combokeys": "^3.0.1",
     "copy-to-clipboard": "^3.3.1",
     "deep-equal": "^1.1.1",
-    "dom-scroll-into-view": "^2.0.1",
     "dom-to-image": "^2.6.0",
     "downloadjs": "^1.4.7",
-    "escape-string-regexp": "5.0.0",
-    "fflate": "0.8.2",
     "file-saver": "^2.0.5",
-    "fuse.js": "^6.6.2",
-    "fuzzysearch": "^1.0.3",
     "html2canvas": "^1.4.1",
     "immer": "^9.0.15",
     "is-mobile": "^3.0.0",
-    "jsondiffpatch": "0.4.1",
-    "jszip": "^3.10.1",
     "lodash": "4.17.21",
     "lodash-es": "^4.17.21",
-    "math-expression-evaluator": "^1.3.7",
     "node-interval-tree": "^1.3.3",
     "papaparse": "5.3.2",
     "paths-js": "^0.4.11",
@@ -59,7 +40,6 @@
     "popper.js": "^1.16.1",
     "prop-types": "^15.6.2",
     "react": "^18.3.1",
-    "react-color": "^2.19.3",
     "react-dom": "^18.3.1",
     "react-draggable": "4.4.5",
     "react-dropzone": "^11.4.2",
@@ -67,7 +47,6 @@
     "react-measure": "^2.5.2",
     "react-redux": "^8.0.5",
     "react-sizeme": "^2.6.12",
-    "react-transition-group": "^2.4.0",
     "recompose": "npm:react-recompose@0.31.1",
     "redux": "^4.1.2",
     "redux-act": "^1.8.0",
@@ -76,13 +55,17 @@
     "remark-gfm": "^4.0.0",
     "reselect": "^4.1.7",
     "tg-use-local-storage-state": "^16.0.3",
-    "tippy.js": "^6.3.7",
     "to-regex-range": "5.0.1",
-    "url-join": "^4.0.1",
     "use-debounce": "^8.0.4",
-    "use-deep-compare-effect": "^1.6.1",
     "validate.io-nonnegative-integer-array": "^1.0.1",
-    "write-excel-file": "^1.4.25"
+    "cypress-real-events": "^1.13.0",
+    "biomsa": "^0.2.4",
+    "shortid": "2.2.16",
+    "@use-gesture/react": "10.3.0",
+    "vite": "^5.2.11",
+    "@vitejs/plugin-react": "^4.3.0",
+    "vite-plugin-libcss": "^1.1.1",
+    "vite-tsconfig-paths": "^4.3.2"
   },
   "license": "MIT"
 }

package/src/Editor/index.js

@@ -55,6 +55,8 @@ import { getClientX, getClientY } from "../utils/editorUtils";
 import PCRTool from "../PCRTool/PCRTool";
 import classNames from "classnames";
 
+
+
 // if (process.env.NODE_ENV !== 'production') {
 //   const {whyDidYouUpdate} = require('why-did-you-update');
 //   whyDidYouUpdate(React);

package/src/commands/index.js

@@ -265,8 +265,7 @@ const fileCommandDefs = {
       props.exportSequenceToFile(isProtein(props) ? "genpept" : "genbank")
   },
   exportDNASequenceAsFasta: {
-    name: props =>
-      `Download ${props.sequenceData.isProtein ? "DNA " : ""}FASTA File`,
+    name: props => `Download ${isProtein(props) ? "DNA " : ""}FASTA File`,
     isHidden: props => !props.sequenceData.sequence,
     handler: props =>
       props.exportSequenceToFile("fasta", {
@@ -418,7 +417,12 @@ const editCommandDefs = {
     hotkey: "mod+x"
   },
   createNewFromSubsequence: {
-    name: "New Sequence From Selected Range",
+    name: props =>
+      isProtein(props)
+        ? "Create New AA Sequence From Selection"
+        : isOligo(props)
+          ? "Create New Oligo From Selection"
+          : "Create New DNA Sequence From Selection",
     isDisabled: props =>
       props.sequenceLength === 0 || props.selectionLayer.start === -1,
     isHidden: props => !props.onCreateNewFromSubsequence,
@@ -1190,11 +1194,6 @@ const annotationToggleCommandDefs = {};
       );
     }
   },
-  // {
-  //   type: "aminoAcidNumbers",
-  //   isHidden: (p, c) =>
-  //     (c.isDnaMenu && p.isProtein) || (!c.isDnaMenu && !p.isProtein)
-  // },
   { type: "aminoAcidNumbers" },
   "axisNumbers",
   {
@@ -1288,7 +1287,7 @@ const additionalAnnotationCommandsDefs = {
   showAll: {
     handler: props => {
       annotationTypes.forEach(type => {
-        if (props.isProtein) {
+        if (isProtein(props)) {
           if (type === "translations" || type === "cutsites")
             return props.annotationVisibilityHide(type);
         }
@@ -1306,10 +1305,6 @@ const additionalAnnotationCommandsDefs = {
   showAllLabels: {
     handler: props => {
       annotationTypes.forEach(type => {
-        // if (props.isProtein) {
-        //   if (type === "translations" || type === "cutsites")
-        //     return props.annotationVisibilityHide(type);
-        // }
         props.annotationLabelVisibilityShow(type);
       });
     }

package/src/index.js

@@ -52,3 +52,4 @@ export { default as EnzymeViewer } from "./EnzymeViewer";
 export { default as AlignmentView } from "./AlignmentView";
 export { default as getOveHotkeyDefs } from "./commands/getOveHotkeyDefs";
 export { getStructuredBases } from "./RowItem/StackedAnnotations/getStructuredBases";
+export { divideBy3 } from "./utils/proteinUtils";

package/fileUtils.d.ts

@@ -1,12 +0,0 @@
-export const allowedCsvFileTypes: string[];
-export function isZipFile(file: any): boolean;
-export function getExt(file: any): any;
-export function isExcelFile(file: any): boolean;
-export function isCsvFile(file: any): boolean;
-export function isTextFile(file: any): boolean;
-export function parseCsvFile(csvFile: any, parserOptions?: {}): Promise<any>;
-export function parseCsvString(csvString: any, parserOptions?: {}): void;
-export function cleanCommaSeparatedCell(cellData: any): any;
-export function cleanCsvExport(rows: any): any;
-export function validateCSVRequiredHeaders(fields: any, requiredHeaders: any, filename: any): string | undefined;
-export function validateCSVRow(row: any, requiredHeaders: any, index: any): string | undefined;