@opencloning/ui 1.3.1 → 1.3.2

package/CHANGELOG.md

@@ -1,5 +1,15 @@
 # @opencloning/ui
 
+## 1.3.2
+
+### Patch Changes
+
+- [#605](https://github.com/manulera/OpenCloning_frontend/pull/605) [`ff60c18`](https://github.com/manulera/OpenCloning_frontend/commit/ff60c18c1500e8b9046f0810cbd69fe1a65c550c) Thanks [@manulera](https://github.com/manulera)! - Fix how syntaxes are imported to adapt to syntaxes repository change
+
+- Updated dependencies []:
+  - @opencloning/store@1.3.2
+  - @opencloning/utils@1.3.2
+
 ## 1.3.1
 
 ### Patch Changes

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@opencloning/ui",
-  "version": "1.3.1",
+  "version": "1.3.2",
   "type": "module",
   "main": "./src/index.js",
   "scripts": {
@@ -25,8 +25,8 @@
     "@emotion/styled": "^11.14.0",
     "@mui/icons-material": "^5.15.17",
     "@mui/material": "^5.15.17",
-    "@opencloning/store": "1.3.1",
-    "@opencloning/utils": "1.3.1",
+    "@opencloning/store": "1.3.2",
+    "@opencloning/utils": "1.3.2",
     "@teselagen/bio-parsers": "^0.4.32",
     "@teselagen/ove": "^0.8.30",
     "@teselagen/range-utils": "^0.3.13",

package/src/components/assembler/Assembler.jsx

@@ -263,7 +263,7 @@ function LoadSyntaxButton({ setSyntax, addPlasmids }) {
   const [existingSyntaxDialogOpen, setExistingSyntaxDialogOpen] = React.useState(false)
   const onSyntaxSelect = React.useCallback((syntax, plasmids) => {
     setSyntax(syntax)
-    addPlasmids(plasmids.filter((plasmid) => plasmid.appData.correspondingParts.length === 1).map(formatPlasmid))
+    addPlasmids(plasmids)
   }, [setSyntax, addPlasmids])
   return <>
     <Button color="success" onClick={() => setExistingSyntaxDialogOpen(true)}>Load Syntax</Button>

package/src/components/assembler/assembler_utils.js

@@ -101,6 +101,11 @@ export function getSimplifiedDigestFragments(sequenceData, enzymes) {
 }
 
 export function assignSequenceToSyntaxPart(sequenceData, enzymes, graph) {
+  // Something that is important to understand here is the meaning of forward and reverse.
+  // It does not mean whether the overhang is 5' or 3', the value on the top strand is always
+  // used, which is convenient for classification within the syntax.
+  // Instead, forward means whether the recognition site was forward or reverse when producing that cut.
+  // see the test called "shows the meaning of forward and reverse" for more details.
   const simplifiedDigestFragments = getSimplifiedDigestFragments(sequenceData, enzymes);
   const foundParts = [];
   simplifiedDigestFragments

package/src/components/assembler/assembler_utils.test.js

@@ -28,6 +28,46 @@ describe('reverseComplementSimplifiedDigestFragment', () => {
   });
 });
 
+it('shows the meaning of forward and reverse', () => {
+  const sequence = 'aaGGTCTCaTACTaaa'
+  const digestFragments = getDigestFragmentsForRestrictionEnzymes(
+    sequence,
+    false,
+    aliasedEnzymesByName["bsai"],
+  );
+
+  // This does not denote whether the overhang is 5' or 3',
+  // but the orientation of the recognition site.
+  expect(digestFragments[0].cut2.overhangBps).toBe('TACT');
+  expect(digestFragments[0].cut2.forward).toBe(true);
+  expect(digestFragments[1].cut1.overhangBps).toBe('TACT');
+  expect(digestFragments[1].cut1.forward).toBe(true);
+
+  // See how for a fragment with the same overhangs, the forward
+  // value is different
+  const sequence2 = 'aTACTcGAGACCaaa'
+  const digestFragments2 = getDigestFragmentsForRestrictionEnzymes(
+    sequence2,
+    false,
+    aliasedEnzymesByName["bsai"],
+  );
+  expect(digestFragments2[0].cut2.overhangBps).toBe('TACT');
+  expect(digestFragments2[0].cut2.forward).toBe(false);
+  expect(digestFragments2[1].cut1.overhangBps).toBe('TACT');
+  expect(digestFragments2[1].cut1.forward).toBe(false);
+
+  // For EcoRI, it's always forward
+  const sequenceEcoRI = 'aaaGAATTCaaaGAATTCaaaa'
+  const digestFragmentsEcoRI = getDigestFragmentsForRestrictionEnzymes(
+    sequenceEcoRI,
+    true,
+    aliasedEnzymesByName["ecori"],
+  );
+  expect(digestFragmentsEcoRI[0].cut2.overhangBps).toBe('AATT');
+  expect(digestFragmentsEcoRI[0].cut2.forward).toBe(true);
+  expect(digestFragmentsEcoRI[0].cut1.overhangBps).toBe('AATT');
+  expect(digestFragmentsEcoRI[0].cut1.forward).toBe(true);
+});
 
 describe('assignSequenceToSyntaxPart', () => {
   it('works', () => {

package/src/version.js

@@ -1,2 +1,2 @@
 // Version placeholder - replaced at publish time via prepack script
-export const version = "1.3.1";
+export const version = "1.3.2";