@teselagen/ove 0.7.27 → 0.7.29

package/{style.css → ove.css}

@@ -9676,7 +9676,7 @@ body:not(.drag-active)
   display: flex;
   flex-wrap: wrap;
   align-items: center;
-  margin-top: 20px;
+  margin-top: 10px;
 }
 
 .ReactTable {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.7.27",
+  "version": "0.7.29",
   "main": "./src/index.js",
   "type": "module",
   "exports": {
@@ -11,11 +11,11 @@
     "./*": "./*"
   },
   "dependencies": {
-    "@teselagen/sequence-utils": "0.3.30",
+    "@teselagen/sequence-utils": "0.3.31",
     "@teselagen/range-utils": "0.3.13",
-    "@teselagen/ui": "0.7.26",
+    "@teselagen/ui": "0.8.6-beta.23",
     "@teselagen/file-utils": "0.3.20",
-    "@teselagen/bio-parsers": "0.4.27",
+    "@teselagen/bio-parsers": "0.4.28",
     "@blueprintjs/core": "3.54.0",
     "@hello-pangea/dnd": "16.2.0",
     "@risingstack/react-easy-state": "^6.3.0",
@@ -62,10 +62,7 @@
     "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"
+    "@playwright/test": "^1.44.1"
   },
   "license": "MIT"
 }

package/selectors/annotationSearchSelector.d.ts

@@ -1,5 +1,5 @@
 export const searchableTypes: string[];
-declare const _default: ((state: any) => any[][]) & import('reselect').OutputSelectorFields<(args_0: any, args_1: any, ...args_2: any[]) => any[][], {
+declare const _default: ((state: any) => any[][]) & import('reselect').OutputSelectorFields<(args_0: any, args_1: any, ...args: any[]) => any[][], {
     clearCache: () => void;
 }> & {
     clearCache: () => void;

package/src/Editor/DropHandler.js

@@ -28,7 +28,8 @@ export default class DropHandler extends React.Component {
           ".dna",
           ".prot",
           ".ab1",
-          ".json"
+          ".json",
+          ".fastq"
         ]}
         onDropRejected={() => {
           window.toastr.error("Error: Incorrect File Type");

package/src/Editor/index.js

@@ -55,8 +55,6 @@ 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/RowItem/StackedAnnotations/getStructuredBases.js

@@ -28,11 +28,25 @@ export function getStructuredBases({
       }
     }
   }
-  const aRange = {
-    //tnr: this probably needs to be changed in case annotation wraps origin
-    start: annotationRange.start - start,
-    end: annotationRange.end - start
-  };
+
+  const wrapsOrigin = start > end;
+  let aRange;
+  if (!wrapsOrigin) {
+    aRange = {
+      //tnr: this probably needs to be changed in case annotation wraps origin
+      start: annotationRange.start - start,
+      end: annotationRange.end - start
+    };
+  } else {
+    aRange = {
+      start: annotationRange.start === 0 ? sequenceLength - start : 0,
+      end:
+        annotationRange.start === 0
+          ? annLen - 1
+          : getRangeLength(annotationRange) - 1
+    };
+  }
+
   const r = {
     aRange,
     basesNoInserts: basesToUse,
@@ -63,7 +77,7 @@ export function getStructuredBases({
     forward ? r.basesNoInserts : r.basesNoInserts.split("").reverse().join("")
   );
   r.basesNoInsertsWithMetaData = basesForRange.split("").map((b, i) => {
-    const indexOfBase = i + annotationRange.start;
+    const indexOfBase = (i + annotationRange.start) % sequenceLength;
     let seqForBase = (fullSequence && fullSequence[indexOfBase]) || "";
     if (!forward) {
       seqForBase = getComplementSequenceString(seqForBase);

package/src/ToolBar/cutsiteTool.js

@@ -69,7 +69,7 @@ function CutsiteToolDropDown({
         onChangeHook={function () {
           annotationVisibilityShow("cutsites");
         }}
-        closeDropDown={toggleDropdown}
+        closeDropDown={() => toggleDropdown({ forceClose: true })}
       />
       {withDigestTool && (
         <Button

package/src/helperComponents/PropertiesDialog/TranslationProperties.js

@@ -44,7 +44,8 @@ class TranslationProperties extends React.Component {
     const translationsToUse = map(translations, translation => {
       let aaString = "";
       for (let i = 0; i < translation.aminoAcids.length; i++) {
-        aaString += translation.aminoAcids[i].aminoAcid.value;
+        // sometimes the `translation.aminoAcids[i].aminoAcid` is null
+        aaString += translation.aminoAcids[i].aminoAcid?.value || "";
       }
       return {
         ...translation,

package/updateEditor.d.ts

@@ -1,3 +1 @@
-export default function updateEditor(store: any, editorName: any, initialValues?: {}, extraMeta?: {}, { convertAnnotationsFromAAIndices }?: {
-    convertAnnotationsFromAAIndices: any;
-}): void;
+export default function updateEditor(store: any, editorName: any, initialValues?: {}, extraMeta?: {}, { convertAnnotationsFromAAIndices }?: {}): void;

package/utils/getAnnotationNameAndStartStopString.d.ts

@@ -7,8 +7,4 @@ export default function getAnnotationNameAndStartStopString({ name, start, end,
     annotationTypePlural: any;
     overlapsSelf: any;
     isWrappedAddon: any;
-}, { startText, isProtein, readOnly }?: {
-    startText: any;
-    isProtein: any;
-    readOnly: any;
-}): string;
+}, { startText, isProtein, readOnly }?: {}): string;

package/utils/selectionLayer.d.ts

@@ -1,5 +1,5 @@
 export function getAllSelectionLayers({ additionalSelectionLayers, searchLayers, selectionLayer }: {
-    additionalSelectionLayers?: any[] | undefined;
-    searchLayers?: any[] | undefined;
+    additionalSelectionLayers?: never[] | undefined;
+    searchLayers?: never[] | undefined;
     selectionLayer: any;
 }): any[];

package/withEditorInteractions/getBpsPerRow.d.ts

@@ -1,9 +1,7 @@
 export default function getBpsPerRow({ charWidth, width, dimensions: { width: width2 }, marginWidth, sequenceData }: {
     charWidth?: number | undefined;
     width?: number | undefined;
-    dimensions?: {
-        width: any;
-    } | undefined;
+    dimensions?: {} | undefined;
     marginWidth?: number | undefined;
     sequenceData: any;
 }): number;