Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,115 @@ | ||
| import React, { useEffect, useState } from 'react' | ||
| import { observer } from 'mobx-react' | ||
| import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui' | ||
| import { PluginContext } from 'molstar/lib/mol-plugin/context' | ||
| import domLoadScript from 'load-script' | ||
|
|
||
| // locals | ||
| import { JBrowsePluginProteinViewModel } from '../model' | ||
| import Header from './Header' | ||
|
|
||
| // hooks | ||
| import useProteinView from '../useProteinView' | ||
| import useProteinViewClickBehavior from '../useProteinViewClickBehavior' | ||
| import useProteinViewHoverBehavior from '../useProteinViewHoverBehavior' | ||
|
|
||
| // utils | ||
| import selectResidue from '../selectResidue' | ||
| import highlightResidue from '../highlightResidue' | ||
| import clearSelection from '../clearSelection' | ||
| import ProteinViewer from '../..' | ||
|
|
||
| function injectStylesheet(param: string) { | ||
| if (document?.head) { | ||
| const link = document.createElement('link') | ||
| link.type = 'text/css' | ||
| link.rel = 'stylesheet' | ||
|
|
||
| //link.href = 'http://fonts.googleapis.com/css?family=Oswald&effect=neon'; | ||
| document.head.appendChild(link) | ||
|
|
||
| link.href = param | ||
| } | ||
| } | ||
|
|
||
| injectStylesheet( | ||
| 'https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/jquery-ui.min.css', | ||
| ) | ||
|
|
||
| injectStylesheet('https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.css') | ||
|
|
||
| function promisifiedLoadScript(src: string) { | ||
| return new Promise((resolve, reject) => { | ||
| domLoadScript(src, (err, script) => { | ||
| if (err) { | ||
| reject(err) | ||
| } else { | ||
| resolve(script.src) | ||
| } | ||
| }) | ||
| }) | ||
| } | ||
|
|
||
| function Icn3dProteinPanel({ model }: { model: ProteinViewer }) { | ||
| const { url } = model | ||
| const [error, setError] = useState<unknown>() | ||
| useEffect(() => { | ||
| // eslint-disable-next-line @typescript-eslint/no-floating-promises | ||
| ;(async () => { | ||
| try { | ||
| const icn3dui = new icn3d.iCn3DUI({ | ||
| divid: 'viewer', | ||
| mobilemenu: true, | ||
| url: 'mmcif|' + url, | ||
| }) | ||
| await icn3dui.show3DStructure() | ||
| } catch (e) { | ||
| console.error(e) | ||
| setError(e) | ||
| } | ||
| })() | ||
| }, [url]) | ||
| return error ? <ErrorMessage error={error} /> : <div id="viewer" /> | ||
| } | ||
|
|
||
| const Icn3dProteinView = observer(function ({ | ||
| model, | ||
| }: { | ||
| model: JBrowsePluginProteinViewModel | ||
| }) { | ||
| const [error, setError] = useState<unknown>() | ||
| const [completed, setCompleted] = useState(false) | ||
| useEffect(() => { | ||
| // eslint-disable-next-line @typescript-eslint/no-floating-promises | ||
| ;(async () => { | ||
| try { | ||
| await promisifiedLoadScript( | ||
| 'https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/jquery.min.js', | ||
| ) | ||
| await promisifiedLoadScript( | ||
| 'https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/jquery-ui.min.js', | ||
| ) | ||
| await promisifiedLoadScript( | ||
| 'https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/threeClass.min.js', | ||
| ) | ||
| await promisifiedLoadScript( | ||
| 'https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.min.js', | ||
| ) | ||
| setCompleted(true) | ||
| } catch (e) { | ||
| console.error(e) | ||
| setError(e) | ||
| } | ||
| })() | ||
| }, []) | ||
|
|
||
| return error ? ( | ||
| <ErrorMessage error={error} /> | ||
| ) : completed ? ( | ||
| <Icn3dProteinPanel model={model} /> | ||
|
Check failure on line 109 in src/ProteinView/components/Icn3dProteinView.tsx
|
||
| ) : ( | ||
| <LoadingEllipses /> | ||
| ) | ||
| }) | ||
|
|
||
| export default Icn3dProteinView | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,9 @@ | ||
| import * as THREE from 'icn3d/three' | ||
| import $ from 'jquery' | ||
| import 'jquery-ui-bundle' | ||
|
|
||
| import 'jquery-ui-bundle/jquery-ui.min.css' | ||
|
|
||
| global.THREE = THREE | ||
| global.$ = $ | ||
| global.jQuery = $ |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -494,7 +494,7 @@ | |
| dependencies: | ||
| eslint-visitor-keys "^3.3.0" | ||
|
|
||
| "@eslint-community/regexpp@^4.10.0", "@eslint-community/regexpp@^4.11.0": | ||
| version "4.11.0" | ||
| resolved "https://registry.yarnpkg.com/@eslint-community/regexpp/-/regexpp-4.11.0.tgz#b0ffd0312b4a3fd2d6f77237e7248a5ad3a680ae" | ||
| integrity sha512-G/M/tIiMrTAxEWRfLfQJMmGNX28IxBg4PBz8XqQhqUHLFI6TL2htpIB1iQCj144V5ee/JaKyT9/WZ0MGZWfA7A== | ||
|
|
@@ -528,10 +528,10 @@ | |
| minimatch "^3.1.2" | ||
| strip-json-comments "^3.1.1" | ||
|
|
||
| "@eslint/js@9.7.0": | ||
| version "9.7.0" | ||
| resolved "https://registry.yarnpkg.com/@eslint/js/-/js-9.7.0.tgz#b712d802582f02b11cfdf83a85040a296afec3f0" | ||
| integrity sha512-ChuWDQenef8OSFnvuxv0TCVxEwmu3+hPNKvM9B34qpM0rDRbjL8t5QkQeHHeAfsKQjuH9wS82WeCi1J/owatng== | ||
|
|
||
| "@eslint/object-schema@^2.1.4": | ||
| version "2.1.4" | ||
|
|
@@ -1897,9 +1897,9 @@ camelcase@^6.2.0: | |
| integrity sha512-Gmy6FhYlCY7uOElZUSbxo2UCDH8owEk996gkbrpsgGtrJLM3J7jGxl9Ic7Qwwj4ivOE5AWZWRMecDdF7hqGjFA== | ||
|
|
||
| caniuse-lite@^1.0.30001640: | ||
| version "1.0.30001642" | ||
| resolved "https://registry.yarnpkg.com/caniuse-lite/-/caniuse-lite-1.0.30001642.tgz#6aa6610eb24067c246d30c57f055a9d0a7f8d05f" | ||
| integrity sha512-3XQ0DoRgLijXJErLSl+bLnJ+Et4KqV1PY6JJBGAFlsNsz31zeAIncyeZfLCabHK/jtSh+671RM9YMldxjUPZtA== | ||
|
|
||
| canvas-sequencer@^3.1.0: | ||
| version "3.1.0" | ||
|
|
@@ -2249,7 +2249,7 @@ define-data-property@^1.0.1, define-data-property@^1.1.4: | |
| es-errors "^1.3.0" | ||
| gopd "^1.0.1" | ||
|
|
||
| define-properties@^1.1.3, define-properties@^1.2.0, define-properties@^1.2.1: | ||
| version "1.2.1" | ||
| resolved "https://registry.yarnpkg.com/define-properties/-/define-properties-1.2.1.tgz#10781cc616eb951a80a034bafcaa7377f6af2b6c" | ||
| integrity sha512-8QmQKqEASLd5nx0U1B1okLElbUuuttJ/AnYmRXbbbGDWh6uS208EjD4Xqq/I9wK7u0v6O08XhTWnt5XtEbR6Dg== | ||
|
|
@@ -2381,7 +2381,7 @@ error-ex@^1.3.1: | |
| dependencies: | ||
| is-arrayish "^0.2.1" | ||
|
|
||
| es-abstract@^1.17.5, es-abstract@^1.22.1, es-abstract@^1.22.3, es-abstract@^1.23.0, es-abstract@^1.23.1, es-abstract@^1.23.2, es-abstract@^1.23.3: | ||
| version "1.23.3" | ||
| resolved "https://registry.yarnpkg.com/es-abstract/-/es-abstract-1.23.3.tgz#8f0c5a35cd215312573c5a27c87dfd6c881a0aa0" | ||
| integrity sha512-e+HfNH61Bj1X9/jLc5v1owaLYuHdeHHSQlkhCBiTK8rBvKaULl/beGMxwrMXjpYrv4pz22BlY570vVePA2ho4A== | ||
|
|
@@ -2591,9 +2591,9 @@ eslint-plugin-react-refresh@^0.4.3: | |
| integrity sha512-MIKAclwaDFIiYtVBLzDdm16E+Ty4GwhB6wZlCAG1R3Ur+F9Qbo6PRxpA5DK7XtDgm+WlCoAY2WxAwqhmIDHg6Q== | ||
|
|
||
| eslint-plugin-react@^7.20.3: | ||
| version "7.34.4" | ||
| resolved "https://registry.yarnpkg.com/eslint-plugin-react/-/eslint-plugin-react-7.34.4.tgz#1f0dc313a0937db7ce15fd1f6c3d77e70f3e02fb" | ||
| integrity sha512-Np+jo9bUwJNxCsT12pXtrGhJgT3T44T1sHhn1Ssr42XFn8TES0267wPGo5nNrMHi8qkyimDAX2BUmkf9pSaVzA== | ||
| dependencies: | ||
| array-includes "^3.1.8" | ||
| array.prototype.findlast "^1.2.5" | ||
|
|
@@ -2603,16 +2603,17 @@ eslint-plugin-react@^7.20.3: | |
| doctrine "^2.1.0" | ||
| es-iterator-helpers "^1.0.19" | ||
| estraverse "^5.3.0" | ||
| hasown "^2.0.2" | ||
| jsx-ast-utils "^2.4.1 || ^3.0.0" | ||
| minimatch "^3.1.2" | ||
| object.entries "^1.1.8" | ||
| object.fromentries "^2.0.8" | ||
| object.values "^1.2.0" | ||
| prop-types "^15.8.1" | ||
| resolve "^2.0.0-next.5" | ||
| semver "^6.3.1" | ||
| string.prototype.matchall "^4.0.11" | ||
| string.prototype.repeat "^1.0.0" | ||
|
|
||
| eslint-plugin-unicorn@^54.0.0: | ||
| version "54.0.0" | ||
|
|
@@ -2636,10 +2637,10 @@ eslint-plugin-unicorn@^54.0.0: | |
| semver "^7.6.1" | ||
| strip-indent "^3.0.0" | ||
|
|
||
| eslint-scope@^8.0.2: | ||
| version "8.0.2" | ||
| resolved "https://registry.yarnpkg.com/eslint-scope/-/eslint-scope-8.0.2.tgz#5cbb33d4384c9136083a71190d548158fe128f94" | ||
| integrity sha512-6E4xmrTw5wtxnLA5wYL3WDfhZ/1bUBGOXV0zQvVRDOtrR8D0p6W7fs3JweNYhwRYeGvd/1CKX2se0/2s7Q/nJA== | ||
| dependencies: | ||
| esrecurse "^4.3.0" | ||
| estraverse "^5.2.0" | ||
|
|
@@ -2655,15 +2656,15 @@ eslint-visitor-keys@^4.0.0: | |
| integrity sha512-OtIRv/2GyiF6o/d8K7MYKKbXrOUBIK6SfkIRM4Z0dY3w+LiQ0vy3F57m0Z71bjbyeiWFiHJ8brqnmE6H6/jEuw== | ||
|
|
||
| eslint@^9.0.0: | ||
| version "9.7.0" | ||
| resolved "https://registry.yarnpkg.com/eslint/-/eslint-9.7.0.tgz#bedb48e1cdc2362a0caaa106a4c6ed943e8b09e4" | ||
| integrity sha512-FzJ9D/0nGiCGBf8UXO/IGLTgLVzIxze1zpfA8Ton2mjLovXdAPlYDv+MQDcqj3TmrhAGYfOpz9RfR+ent0AgAw== | ||
| dependencies: | ||
| "@eslint-community/eslint-utils" "^4.2.0" | ||
| "@eslint-community/regexpp" "^4.11.0" | ||
| "@eslint/config-array" "^0.17.0" | ||
| "@eslint/eslintrc" "^3.1.0" | ||
| "@eslint/js" "9.7.0" | ||
| "@humanwhocodes/module-importer" "^1.0.1" | ||
| "@humanwhocodes/retry" "^0.3.0" | ||
| "@nodelib/fs.walk" "^1.2.8" | ||
|
|
@@ -2672,7 +2673,7 @@ eslint@^9.0.0: | |
| cross-spawn "^7.0.2" | ||
| debug "^4.3.2" | ||
| escape-string-regexp "^4.0.0" | ||
| eslint-scope "^8.0.2" | ||
| eslint-visitor-keys "^4.0.0" | ||
| espree "^10.1.0" | ||
| esquery "^1.5.0" | ||
|
|
@@ -4561,11 +4562,16 @@ micromatch@^4.0.4: | |
| braces "^3.0.3" | ||
| picomatch "^2.3.1" | ||
|
|
||
| [email protected]: | ||
| version "1.52.0" | ||
| resolved "https://registry.yarnpkg.com/mime-db/-/mime-db-1.52.0.tgz#bbabcdc02859f4987301c856e3387ce5ec43bf70" | ||
| integrity sha512-sPU4uV7dYlvtWJxwwxHD0PuihVNiE7TyAbQ5SWxDCB9mUYvOgroQOwYQQOKPJ8CIbE+1ETVlOoK1UC2nU3gYvg== | ||
|
|
||
| "mime-db@>= 1.43.0 < 2": | ||
| version "1.53.0" | ||
| resolved "https://registry.yarnpkg.com/mime-db/-/mime-db-1.53.0.tgz#3cb63cd820fc29896d9d4e8c32ab4fcd74ccb447" | ||
| integrity sha512-oHlN/w+3MQ3rba9rqFr6V/ypF10LSkdwUysQL7GkXoTgIWeV+tcXGA852TBxH+gsh8UWoyhR1hKcoMJTuWflpg== | ||
|
|
||
| mime-types@^2.1.12, mime-types@~2.1.24, mime-types@~2.1.34: | ||
| version "2.1.35" | ||
| resolved "https://registry.yarnpkg.com/mime-types/-/mime-types-2.1.35.tgz#381a871b62a734450660ae3deee44813f70d959a" | ||
|
|
@@ -4808,15 +4814,6 @@ object.getownpropertydescriptors@^2.1.6: | |
| gopd "^1.0.1" | ||
| safe-array-concat "^1.1.2" | ||
|
|
||
| object.values@^1.1.6, object.values@^1.2.0: | ||
| version "1.2.0" | ||
| resolved "https://registry.yarnpkg.com/object.values/-/object.values-1.2.0.tgz#65405a9d92cee68ac2d303002e0b8470a4d9ab1b" | ||
|
|
@@ -5061,9 +5058,9 @@ prettier-linter-helpers@^1.0.0: | |
| fast-diff "^1.1.2" | ||
|
|
||
| prettier@^3.2.5: | ||
| version "3.3.3" | ||
| resolved "https://registry.yarnpkg.com/prettier/-/prettier-3.3.3.tgz#30c54fe0be0d8d12e6ae61dbb10109ea00d53105" | ||
| integrity sha512-i2tDNA0O5IrMO757lfrdQZCc2jPNDVntV0m/+4whiDfWaTKfMNgR7Qz0NAeGz/nRqF4m5/6CLzbP4/liHt12Ew== | ||
|
|
||
| pretty-bytes@^6.1.1: | ||
| version "6.1.1" | ||
|
|
@@ -5693,6 +5690,14 @@ string.prototype.padend@^3.0.0: | |
| es-abstract "^1.23.2" | ||
| es-object-atoms "^1.0.0" | ||
|
|
||
| string.prototype.repeat@^1.0.0: | ||
| version "1.0.0" | ||
| resolved "https://registry.yarnpkg.com/string.prototype.repeat/-/string.prototype.repeat-1.0.0.tgz#e90872ee0308b29435aa26275f6e1b762daee01a" | ||
| integrity sha512-0u/TldDbKD8bFCQ/4f5+mNRrXwZ8hg2w7ZR8wa16e8z9XpePWl3eGEcUD0OXpEH/VJH/2G3gjUtR3ZOiBe2S/w== | ||
| dependencies: | ||
| define-properties "^1.1.3" | ||
| es-abstract "^1.17.5" | ||
|
|
||
| string.prototype.trim@^1.2.9: | ||
| version "1.2.9" | ||
| resolved "https://registry.yarnpkg.com/string.prototype.trim/-/string.prototype.trim-1.2.9.tgz#b6fa326d72d2c78b6df02f7759c73f8f6274faa4" | ||
|
|
||