@teselagen/ove 0.3.30 → 0.3.43

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.3.30",
+  "version": "0.3.43",
   "main": "./src/index.js",
   "exports": {
     ".": {
@@ -13,12 +13,12 @@
     "node": "16.20.2"
   },
   "dependencies": {
-    "@teselagen/sequence-utils": "0.3.8",
+    "@teselagen/sequence-utils": "0.3.9",
     "@teselagen/range-utils": "0.3.7",
-    "@teselagen/ui": "0.3.29",
+    "@teselagen/ui": "0.3.32",
     "@teselagen/file-utils": "0.3.9",
     "@teselagen/bounce-loader": "0.3.11",
-    "@teselagen/bio-parsers": "0.3.10",
+    "@teselagen/bio-parsers": "0.4.1",
     "@blueprintjs/core": "3.52.0",
     "@blueprintjs/datetime": "3.23.19",
     "@blueprintjs/icons": "3.33.0",

package/src/RowItem/Sequence.js

@@ -90,7 +90,7 @@ class Sequence extends React.Component {
 
     let inner;
     const shared = {
-      ...isSafari ? { letterSpacing: "3px" } : {},
+      ...(isSafari ? { letterSpacing: "3px" } : {}),
       y: height - height / 4,
       className:
         "ve-monospace-font " + (isReverse ? " ve-sequence-reverse" : "")

package/src/helperComponents/AddOrEditPrimerDialog/index.js

@@ -6,11 +6,13 @@ import {
   generateField,
   RadioGroupField
 } from "@teselagen/ui";
-import { getReverseComplementSequenceString } from "@teselagen/sequence-utils";
+import {
+  filterSequenceString,
+  getReverseComplementSequenceString
+} from "@teselagen/sequence-utils";
 
 import AddOrEditAnnotationDialog from "../AddOrEditAnnotationDialog";
 import { convertRangeTo0Based } from "@teselagen/range-utils";
-import { getAcceptedChars } from "../../utils/editorUtils";
 import classNames from "classnames";
 import "./style.css";
 import { getSequenceWithinRange } from "@teselagen/range-utils";
@@ -42,14 +44,9 @@ const CustomContentEditable = generateField(function CustomContentEditable({
     const newVal = e.target.innerText;
     const savedCaretPosition = CaretPositioning.saveSelection(e.currentTarget);
     setCaretPosition(savedCaretPosition);
-    const acceptedChars = getAcceptedChars(sequenceData);
-    let newBases = "";
-    newVal.split("").forEach(letter => {
-      if (acceptedChars.includes(letter.toLowerCase())) {
-        newBases += letter;
-      }
-    });
-    if (newVal.length !== newBases.length) {
+    const [newBases, warnings] = filterSequenceString(newVal, sequenceData);
+
+    if (warnings.length) {
       setTempError(true);
       setTimeout(() => {
         setTempError(false);

package/src/utils/editorUtils.js

@@ -4,7 +4,6 @@ import { divideBy3 } from "./proteinUtils";
 import {
   getInsertBetweenVals,
   calculatePercentGC,
-  bioData,
   aliasedEnzymesByName
 } from "@teselagen/sequence-utils";
 import { get, sortBy } from "lodash";
@@ -172,24 +171,6 @@ export function getSelFromWrappedAddon(selectionLayer, sequenceLength) {
   return selToUse;
 }
 
-export function getAcceptedChars({
-  isOligo,
-  isProtein,
-  isRna,
-  isMixedRnaAndDna
-} = {}) {
-  return isProtein
-    ? bioData.extended_protein_letters.toLowerCase()
-    : isOligo
-    ? bioData.ambiguous_rna_letters.toLowerCase() + "t"
-    : isRna
-    ? bioData.ambiguous_rna_letters.toLowerCase()
-    : isMixedRnaAndDna
-    ? bioData.ambiguous_rna_letters.toLowerCase() +
-      bioData.ambiguous_dna_letters.toLowerCase()
-    : //just plain old dna
-      bioData.ambiguous_dna_letters.toLowerCase();
-}
 export function getStripedPattern({ color }) {
   return (
     <pattern

package/src/withEditorInteractions/createSequenceInputPopup.js

@@ -6,7 +6,8 @@ import Popper from "popper.js";
 
 import {
   getInsertBetweenVals,
-  convertDnaCaretPositionOrRangeToAA
+  convertDnaCaretPositionOrRangeToAA,
+  filterSequenceString
 } from "@teselagen/sequence-utils";
 import React from "react";
 import { divideBy3 } from "../utils/proteinUtils";
@@ -77,9 +78,8 @@ class SequenceInputNoHotkeys extends React.Component {
       selectionLayer,
       sequenceLength,
       isProtein,
-      replaceChars,
       caretPosition,
-      acceptedChars,
+      sequenceData,
       maxInsertSize
     } = this.props;
     const { charsToInsert, hasTempError } = this.state;
@@ -136,19 +136,14 @@ class SequenceInputNoHotkeys extends React.Component {
           autoFocus
           style={hasTempError ? { borderColor: "red" } : {}}
           onChange={e => {
-            let sanitizedVal = "";
-            e.target.value.split("").forEach(letter => {
-              const lowerLetter = letter.toLowerCase();
-              if (replaceChars && replaceChars[lowerLetter]) {
-                const isUpper = lowerLetter !== letter;
-                sanitizedVal += isUpper
-                  ? replaceChars[lowerLetter].toUpperCase()
-                  : replaceChars[lowerLetter];
-              } else if (acceptedChars.includes(lowerLetter)) {
-                sanitizedVal += letter;
+            const [sanitizedVal, warnings] = filterSequenceString(
+              e.target.value,
+              {
+                ...sequenceData,
+                name: undefined
               }
-            });
-            if (e.target.value.length !== sanitizedVal.length) {
+            );
+            if (warnings.length) {
               this.setState({
                 hasTempError: true
               });
@@ -165,7 +160,6 @@ class SequenceInputNoHotkeys extends React.Component {
               );
             }
             e.target.value = sanitizedVal;
-
             this.setState({ charsToInsert: sanitizedVal });
           }}
         />

package/src/withEditorInteractions/index.js

@@ -41,11 +41,7 @@ import {
   createNewAnnotationMenu
 } from "../MenuBar/defaultConfig";
 import { fullSequenceTranslationMenu } from "../MenuBar/viewSubmenu";
-import {
-  getAcceptedChars,
-  getNodeToRefocus,
-  getSelFromWrappedAddon
-} from "../utils/editorUtils";
+import { getNodeToRefocus, getSelFromWrappedAddon } from "../utils/editorUtils";
 
 import {
   showAddOrEditAnnotationDialog,
@@ -212,7 +208,8 @@ function VectorInteractionHOC(Component /* options */) {
         selectionLayer = { start: -1, end: -1 },
         readOnly,
         onPaste,
-        disableBpEditing
+        disableBpEditing,
+        sequenceData
       } = this.props;
 
       if (disableBpEditing) {
@@ -240,6 +237,7 @@ function VectorInteractionHOC(Component /* options */) {
       }
 
       seqDataToInsert = tidyUpSequenceData(seqDataToInsert, {
+        topLevelSeqData: sequenceData,
         provideNewIdsForAnnotations: true,
         annotationsAsObjects: true,
         removeUnwantedChars: true,
@@ -360,8 +358,7 @@ function VectorInteractionHOC(Component /* options */) {
         createSequenceInputPopup({
           useEventPositioning,
           isReplace,
-          replaceChars: sequenceData.isRna ? { t: "u" } : undefined,
-          acceptedChars: getAcceptedChars(sequenceData),
+          sequenceData,
           isProtein: sequenceData.isProtein,
           selectionLayer,
           sequenceLength,