protvista-uniprot 4.3.1 → 4.3.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (11) hide show
  1. package/dist/protvista-uniprot.mjs +45356 -62030
  2. package/dist/protvista-uniprot.mjs.map +1 -1
  3. package/package.json +40 -40
  4. package/src/.vscode/settings.json +3 -0
  5. package/src/adapters/__tests__/__snapshots__/structure-adapter.spec.ts.snap +36 -36
  6. package/src/adapters/interpro-adapter.ts +3 -3
  7. package/src/adapters/ptm-exchange-adapter.ts +0 -1
  8. package/src/adapters/structure-adapter.ts +0 -1
  9. package/src/adapters/variation-graph-adapter.ts +0 -2
  10. package/src/protvista-uniprot-structure.ts +3 -2
  11. package/src/protvista-uniprot.ts +0 -1
package/package.json CHANGED
@@ -1,7 +1,7 @@
1
1
  {
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  "name": "protvista-uniprot",
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  "description": "ProtVista tool for the UniProt website",
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- "version": "4.3.1",
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+ "version": "4.3.2",
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  "files": [
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  "dist",
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  "src"
@@ -29,53 +29,53 @@
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  "author": "Xavier Watkins <xwatkins@ebi.ac.uk>",
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  "license": "MIT",
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  "dependencies": {
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- "@nightingale-elements/nightingale-colored-sequence": "5.4.0",
33
- "@nightingale-elements/nightingale-filter": "5.4.0",
34
- "@nightingale-elements/nightingale-interpro-track": "5.5.0",
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- "@nightingale-elements/nightingale-linegraph-track": "5.4.0",
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- "@nightingale-elements/nightingale-manager": "5.4.0",
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- "@nightingale-elements/nightingale-navigation": "5.4.0",
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- "@nightingale-elements/nightingale-sequence": "5.4.0",
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- "@nightingale-elements/nightingale-sequence-heatmap": "5.4.0",
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- "@nightingale-elements/nightingale-structure": "5.4.0",
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- "@nightingale-elements/nightingale-track-canvas": "5.5.0",
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- "@nightingale-elements/nightingale-variation": "5.5.0",
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+ "@nightingale-elements/nightingale-colored-sequence": "5.6.0",
33
+ "@nightingale-elements/nightingale-filter": "5.6.0",
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+ "@nightingale-elements/nightingale-interpro-track": "5.6.0",
35
+ "@nightingale-elements/nightingale-linegraph-track": "5.6.0",
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+ "@nightingale-elements/nightingale-manager": "5.6.0",
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+ "@nightingale-elements/nightingale-navigation": "5.6.0",
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+ "@nightingale-elements/nightingale-sequence": "5.6.0",
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+ "@nightingale-elements/nightingale-sequence-heatmap": "5.6.0",
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+ "@nightingale-elements/nightingale-structure": "5.6.0",
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+ "@nightingale-elements/nightingale-track-canvas": "5.6.0",
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+ "@nightingale-elements/nightingale-variation": "5.6.0",
43
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  "color-hash": "2.0.2",
44
- "core-js": "3.13.0",
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+ "core-js": "3.42.0",
45
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  "lit": "3.1.3",
46
46
  "lodash-es": "4.17.21",
47
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  "protvista-datatable": "3.8.22",
48
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  "timing-functions": "2.0.1",
49
- "url-join": "4.0.1"
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+ "url-join": "5.0.0"
50
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  },
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  "devDependencies": {
52
- "@babel/core": "^7.14.3",
53
- "@babel/plugin-proposal-decorators": "^7.25.9",
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- "@babel/plugin-transform-runtime": "^7.14.3",
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- "@babel/preset-env": "^7.14.2",
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- "@babel/preset-typescript": "^7.13.0",
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- "@babel/runtime-corejs3": "^7.14.0",
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- "@originjs/vite-plugin-commonjs": "^1.0.1",
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- "@types/jest": "^29.5.14",
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- "@types/url-join": "^4.0.0",
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- "@typescript-eslint/eslint-plugin": "4.26.1",
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- "@typescript-eslint/parser": "4.26.1",
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- "babel-jest": "^29.7.0",
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- "babel-loader": "^9.2.1",
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- "concurrently": "^4.1.0",
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- "css-loader": "^5.2.6",
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- "eslint": "^7.27.0",
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- "eslint-config-prettier": "^8.3.0",
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- "jest": "^26.4.2",
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- "npm-run-all": "^4.1.5",
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- "style-loader": "^2.0.0",
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- "svg-inline-loader": "^0.8.0",
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- "typescript": "^5.6.3",
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- "vite": "^6.0.7",
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- "vite-plugin-dts": "^4.4.0",
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- "vite-plugin-env-compatible": "^2.0.1",
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+ "@babel/core": "7.27.1",
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+ "@babel/plugin-proposal-decorators": "7.27.1",
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+ "@babel/plugin-transform-runtime": "7.27.1",
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+ "@babel/preset-env": "7.27.1",
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+ "@babel/preset-typescript": "7.27.1",
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+ "@babel/runtime-corejs3": "7.27.1",
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+ "@eslint/js": "9.25.1",
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+ "@originjs/vite-plugin-commonjs": "1.0.3",
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+ "@types/jest": "29.5.14",
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+ "@typescript-eslint/eslint-plugin": "8.31.1",
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+ "@typescript-eslint/parser": "8.31.1",
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+ "babel-jest": "29.7.0",
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+ "eslint": "9.25.1",
65
+ "eslint-config-prettier": "10.1.2",
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+ "eslint-plugin-prettier": "5.2.6",
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+ "globals": "16.0.0",
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+ "jest": "29.7.0",
69
+ "npm-run-all": "4.1.5",
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+ "rollup-plugin-visualizer": "5.14.0",
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+ "svg-inline-loader": "0.8.2",
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+ "typescript": "5.8.3",
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+ "typescript-eslint": "8.31.1",
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+ "vite": "6.3.4",
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+ "vite-plugin-dts": "4.5.3",
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+ "vite-plugin-env-compatible": "2.0.1",
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  "vite-plugin-html": "3.2.2",
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- "vite-plugin-svgo": "^1.6.2"
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+ "vite-plugin-svgo": "1.6.2"
79
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  },
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  "jest": {
81
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  "testRegex": "(/__tests__/.*|(\\.|/))spec\\.ts$",
package/src/.vscode/settings.json ADDED
@@ -0,0 +1,3 @@
1
+ {
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+ "window.title": "${rootPath}${separator}[new-ptm-builds]"
3
+ }
package/src/adapters/__tests__/__snapshots__/structure-adapter.spec.ts.snap CHANGED
@@ -1,16 +1,16 @@
1
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  // Jest Snapshot v1, https://goo.gl/fbAQLP
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3
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  exports[`structure data should merge Overlapping Intervals 1`] = `
4
- Array [
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- Object {
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+ [
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+ {
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  "category": "STRUCTURE_COVERAGE",
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  "end": 0,
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  "start": 0,
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- "structures": Array [
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- Object {
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+ "structures": [
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+ {
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  "description": "Method: X-ray. Resolution: 1.50 A. ",
12
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  "end": 0,
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- "source": Object {
13
+ "source": {
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  "id": "1AAP",
15
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  "url": "http://www.ebi.ac.uk/pdbe-srv/view/entry/1AAP",
16
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  },
@@ -19,42 +19,42 @@ Array [
19
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  ],
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  "type": "PDBE_COVER",
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  },
22
- Object {
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+ {
23
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  "category": "STRUCTURE_COVERAGE",
24
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  "end": 711,
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  "start": 672,
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- "structures": Array [
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- Object {
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+ "structures": [
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+ {
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  "description": "Method: NMR. Chains: A=672-699. ",
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  "end": 699,
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- "source": Object {
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+ "source": {
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  "id": "1AMB",
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  "url": "http://www.ebi.ac.uk/pdbe-srv/view/entry/1AMB",
33
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  },
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  "start": 672,
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  },
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- Object {
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+ {
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  "description": "Method: NMR. Chains: A=672-699. ",
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  "end": 699,
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- "source": Object {
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+ "source": {
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  "id": "1AMC",
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  "url": "http://www.ebi.ac.uk/pdbe-srv/view/entry/1AMC",
42
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  },
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  "start": 672,
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  },
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- Object {
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+ {
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  "description": "Method: NMR. Chains: A=672-711. ",
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  "end": 711,
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- "source": Object {
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+ "source": {
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  "id": "1AML",
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  "url": "http://www.ebi.ac.uk/pdbe-srv/view/entry/1AML",
51
51
  },
52
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  "start": 672,
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53
  },
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- Object {
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+ {
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  "description": "Method: NMR. Chains: A=672-711. ",
56
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  "end": 711,
57
- "source": Object {
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+ "source": {
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  "id": "1BA4",
59
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  "url": "http://www.ebi.ac.uk/pdbe-srv/view/entry/1BA4",
60
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  },
@@ -67,16 +67,16 @@ Array [
67
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  `;
68
68
 
69
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  exports[`structure data should turn structures into features 1`] = `
70
- Array [
71
- Object {
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+ [
71
+ {
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  "category": "STRUCTURE_COVERAGE",
73
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  "end": 0,
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  "start": 0,
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- "structures": Array [
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- Object {
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+ "structures": [
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+ {
77
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  "description": "Method: X-ray. Resolution: 1.50 A. ",
78
78
  "end": 0,
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- "source": Object {
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+ "source": {
80
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  "id": "1AAP",
81
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  "url": "http://www.ebi.ac.uk/pdbe-srv/view/entry/1AAP",
82
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  },
@@ -85,15 +85,15 @@ Array [
85
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  ],
86
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  "type": "PDBE_COVER",
87
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  },
88
- Object {
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+ {
89
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  "category": "STRUCTURE_COVERAGE",
90
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  "end": 699,
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  "start": 672,
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- "structures": Array [
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- Object {
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+ "structures": [
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+ {
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  "description": "Method: NMR. Chains: A=672-699. ",
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  "end": 699,
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- "source": Object {
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+ "source": {
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  "id": "1AMB",
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  "url": "http://www.ebi.ac.uk/pdbe-srv/view/entry/1AMB",
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  },
@@ -102,15 +102,15 @@ Array [
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  ],
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  "type": "PDBE_COVER",
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  },
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- Object {
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+ {
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  "category": "STRUCTURE_COVERAGE",
107
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  "end": 699,
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  "start": 672,
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- "structures": Array [
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- Object {
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+ "structures": [
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+ {
111
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  "description": "Method: NMR. Chains: A=672-699. ",
112
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  "end": 699,
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- "source": Object {
113
+ "source": {
114
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  "id": "1AMC",
115
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  "url": "http://www.ebi.ac.uk/pdbe-srv/view/entry/1AMC",
116
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  },
@@ -119,15 +119,15 @@ Array [
119
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  ],
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  "type": "PDBE_COVER",
121
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  },
122
- Object {
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+ {
123
123
  "category": "STRUCTURE_COVERAGE",
124
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  "end": 711,
125
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  "start": 672,
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- "structures": Array [
127
- Object {
126
+ "structures": [
127
+ {
128
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  "description": "Method: NMR. Chains: A=672-711. ",
129
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  "end": 711,
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- "source": Object {
130
+ "source": {
131
131
  "id": "1AML",
132
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  "url": "http://www.ebi.ac.uk/pdbe-srv/view/entry/1AML",
133
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  },
@@ -136,15 +136,15 @@ Array [
136
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  ],
137
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  "type": "PDBE_COVER",
138
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  },
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- Object {
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+ {
140
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  "category": "STRUCTURE_COVERAGE",
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  "end": 711,
142
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  "start": 672,
143
- "structures": Array [
144
- Object {
143
+ "structures": [
144
+ {
145
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  "description": "Method: NMR. Chains: A=672-711. ",
146
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  "end": 711,
147
- "source": Object {
147
+ "source": {
148
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  "id": "1BA4",
149
149
  "url": "http://www.ebi.ac.uk/pdbe-srv/view/entry/1BA4",
150
150
  },
package/src/adapters/interpro-adapter.ts CHANGED
@@ -24,9 +24,9 @@ const transformData = (data: InterProProteinSearch): TransformedInterPro => {
24
24
 
25
25
  const end = proteins[0].entry_protein_locations
26
26
  ? Math.max(
27
- ...proteins[0].entry_protein_locations?.map((location) =>
27
+ ...(proteins[0].entry_protein_locations?.map((location) =>
28
28
  Math.max(...location.fragments.map((fragment) => fragment.end))
29
- )
29
+ ) || [])
30
30
  )
31
31
  : '';
32
32
 
@@ -43,7 +43,7 @@ const transformData = (data: InterProProteinSearch): TransformedInterPro => {
43
43
  };
44
44
  });
45
45
  } catch (error) {
46
- throw new Error('Failed transforming the data');
46
+ throw new Error(`Failed transforming the data: ${error}`);
47
47
  }
48
48
  };
49
49
 
package/src/adapters/ptm-exchange-adapter.ts CHANGED
@@ -110,7 +110,6 @@ const transformData = (data: ProteomicsPtm) => {
110
110
  ptm.position
111
111
  } - 1`
112
112
  );
113
- // eslint-disable-next-line no-continue
114
113
  continue;
115
114
  }
116
115
  const aa = feature.peptide[ptm.position - 1];
package/src/adapters/structure-adapter.ts CHANGED
@@ -95,7 +95,6 @@ const transformData = (data) => {
95
95
  transformedData = mergeOverlappingIntervals(allFeatureStructures);
96
96
 
97
97
  transformedData.forEach((feature) => {
98
- /* eslint-disable no-param-reassign */
99
98
  feature.tooltipContent = formatTooltip(feature);
100
99
  });
101
100
  }
package/src/adapters/variation-graph-adapter.ts CHANGED
@@ -12,12 +12,10 @@ const transformData = (data) => {
12
12
  for (const { start, association } of variants) {
13
13
  const index = +start;
14
14
  // skip if the variant is outside of bounds
15
- // eslint-disable-next-line no-continue
16
15
  if (index < 1 || index > data.sequence.length) continue;
17
16
 
18
17
  total[index] += 1;
19
18
 
20
- // eslint-disable-next-line no-continue
21
19
  if (!association) continue;
22
20
  const hasDisease = association.find(
23
21
  (association) => association.disease === true
package/src/protvista-uniprot-structure.ts CHANGED
@@ -1,5 +1,4 @@
1
1
  import { LitElement, html, svg, TemplateResult, css, nothing } from 'lit';
2
- // eslint-disable-next-line @typescript-eslint/no-unused-vars
3
2
  import { customElement } from 'lit/decorators.js';
4
3
  import { unsafeHTML } from 'lit/directives/unsafe-html.js';
5
4
  import NightingaleStructure, {
@@ -338,7 +337,9 @@ class ProtvistaUniprotStructure extends LitElement {
338
337
  @click=${(e) => this.toggleColorTheme(e)}
339
338
  disabled=${this.alphamissenseAvailable ? nothing : 'true'}
340
339
  />
341
- <label for="alphamissense" title=${this.alphamissenseAvailable
340
+ <label
341
+ for="alphamissense"
342
+ title=${this.alphamissenseAvailable
342
343
  ? ''
343
344
  : 'Color by pathogenicity is disabled as there are no AlphaMissense predictions available for this model'}
344
345
  >Pathogenicity
package/src/protvista-uniprot.ts CHANGED
@@ -1,5 +1,4 @@
1
1
  import { LitElement, html, svg } from 'lit';
2
- // eslint-disable-next-line @typescript-eslint/no-unused-vars
3
2
  import { customElement } from 'lit/decorators.js';
4
3
  import { unsafeHTML } from 'lit/directives/unsafe-html.js';
5
4
  import { frame } from 'timing-functions';