jbrowse-plugin-protein3d 0.0.3 → 0.0.4

package/dist/test_data/gene.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "0.0.3",
+  "version": "0.0.4",
   "name": "jbrowse-plugin-protein3d",
   "keywords": [
     "jbrowse",
@@ -11,12 +11,13 @@
     "src"
   ],
   "scripts": {
-    "test": "jest",
+    "test": "vitest",
     "clean": "rimraf dist",
+    "format": "prettier --write .",
     "prebuild": "npm run clean",
     "start": "node esbuild.mjs",
     "build": "tsc && NODE_ENV=production node esbuild.mjs",
-    "lint": "eslint --report-unused-disable-directives --max-warnings 0  src/",
+    "lint": "eslint --report-unused-disable-directives --max-warnings 0",
     "prepack": "npm run build",
     "postversion": "git push --follow-tags"
   },
@@ -28,6 +29,7 @@
     "pako": "^2.1.0"
   },
   "devDependencies": {
+    "@emotion/react": "^11.13.0",
     "@eslint/compat": "^1.1.1",
     "@fal-works/esbuild-plugin-global-externals": "^2.1.2",
     "@jbrowse/core": "^2.0.0",
@@ -35,21 +37,20 @@
     "@mui/material": "^5.12.0",
     "@mui/system": "^5.12.0",
     "@mui/x-data-grid": "^7.3.0",
-    "@types/jest": "^29.5.12",
-    "@types/node": "^20.11.16",
+    "@types/node": "^22.5.0",
     "@types/pako": "^2.0.0",
     "@types/react": "^18.2.54",
-    "@typescript-eslint/eslint-plugin": "^7.0.1",
-    "@typescript-eslint/parser": "^7.0.1",
+    "@typescript-eslint/eslint-plugin": "^8.1.0",
+    "@typescript-eslint/parser": "^8.1.0",
     "esbuild": "^0.23.0",
     "eslint": "^9.0.0",
     "eslint-config-prettier": "^9.0.0",
     "eslint-plugin-prettier": "^5.0.0",
     "eslint-plugin-react": "^7.20.3",
-    "eslint-plugin-react-hooks": "^4.0.8",
-    "eslint-plugin-react-refresh": "^0.4.3",
-    "eslint-plugin-unicorn": "^54.0.0",
-    "jest": "^29.7.0",
+    "eslint-plugin-react-hooks": "^5.1.0-rc-eb3ad065-20240822",
+    "eslint-plugin-react-refresh": "^0.4.11",
+    "eslint-plugin-unicorn": "^55.0.0",
+    "fp-ts": "^2.16.9",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.1",
     "mobx-state-tree": "5.4.2",
@@ -58,12 +59,12 @@
     "pretty-bytes": "^6.1.1",
     "react": "^18.2.0",
     "react-dom": "^18.2.0",
-    "rimraf": "^5.0.0",
+    "rimraf": "^6.0.1",
     "rxjs": "^7.0.0",
-    "ts-jest": "^29.1.2",
-    "ts-node": "^10.3.0",
     "tss-react": "^4.9.4",
-    "typescript": "^5.3.3"
+    "typescript": "^5.3.3",
+    "typescript-eslint": "^8.1.0",
+    "vitest": "^2.0.5"
   },
   "author": "Colin <colin.diesh@gmail.com>",
   "license": "MIT"

package/src/AddHighlightModel/GenomeMouseoverHighlight.tsx

@@ -4,30 +4,17 @@ import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import { getSession } from '@jbrowse/core/util'
 // locals
 import Highlight from './Highlight'
+import { checkHovered } from '../ProteinView/util'
 
 const GenomeMouseoverHighlight = observer(function ({
   model,
 }: {
   model: LinearGenomeViewModel
-}) {
-  const { hovered } = getSession(model)
-  return hovered &&
-    typeof hovered === 'object' &&
-    'hoverPosition' in hovered ? (
-    <HoverHighlight model={model} />
-  ) : null
-})
-
-const HoverHighlight = observer(function ({
-  model,
-}: {
-  model: LinearGenomeViewModel
 }) {
   const session = getSession(model)
-  if (session.views.some(s => s.type === 'ProteinView')) {
-    const { hovered } = session
+  const { views, hovered } = session
+  if (checkHovered(hovered) && views.some(s => s.type === 'ProteinView')) {
     const { assemblyNames } = model
-    // @ts-expect-error
     const { coord, refName } = hovered.hoverPosition
     return (
       <Highlight
@@ -35,7 +22,7 @@ const HoverHighlight = observer(function ({
         start={coord - 1}
         end={coord}
         refName={refName}
-        assemblyName={assemblyNames[0]}
+        assemblyName={assemblyNames[0]!}
       />
     )
   }

package/src/AddHighlightModel/ProteinToGenomeClickHighlight.tsx

@@ -16,22 +16,25 @@ const ProteinToGenomeClickHighlight = observer(function ({
 }) {
   const { assemblyManager, views } = getSession(model)
   const { assemblyNames } = model
-  const p = views.find(
-    f => f.type === 'ProteinView',
-  ) as JBrowsePluginProteinViewModel
-  const assembly = assemblyManager.get(assemblyNames[0])
+  const proteinView = views.find(f => f.type === 'ProteinView') as
+    | JBrowsePluginProteinViewModel
+    | undefined
+  const assemblyName = assemblyNames[0]!
+  const assembly = assemblyManager.get(assemblyName)
   return assembly ? (
     <>
-      {p?.clickGenomeHighlights.map((r, idx) => (
-        <Highlight
-          key={`${JSON.stringify(r)}-${idx}}`}
-          start={r.start}
-          end={r.end}
-          refName={r.refName}
-          assemblyName={assemblyNames[0]}
-          model={model}
-        />
-      ))}
+      {proteinView?.structures.map(structure =>
+        structure.clickGenomeHighlights.map((r, idx) => (
+          <Highlight
+            key={`${JSON.stringify(r)}-${idx}}`}
+            start={r.start}
+            end={r.end}
+            refName={r.refName}
+            assemblyName={assemblyName}
+            model={model}
+          />
+        )),
+      )}
     </>
   ) : null
 })

package/src/AddHighlightModel/ProteinToGenomeHoverHighlight.tsx

@@ -7,31 +7,32 @@ import { getSession } from '@jbrowse/core/util'
 import { JBrowsePluginProteinViewModel } from '../ProteinView/model'
 import Highlight from './Highlight'
 
-type LGV = LinearGenomeViewModel
-
 const ProteinToGenomeHoverHighlight = observer(function ({
   model,
 }: {
-  model: LGV
+  model: LinearGenomeViewModel
 }) {
   const { assemblyManager, views } = getSession(model)
   const { assemblyNames } = model
-  const p = views.find(
-    f => f.type === 'ProteinView',
-  ) as JBrowsePluginProteinViewModel
-  const assembly = assemblyManager.get(assemblyNames[0])
+  const proteinView = views.find(f => f.type === 'ProteinView') as
+    | JBrowsePluginProteinViewModel
+    | undefined
+  const assemblyName = assemblyNames[0]!
+  const assembly = assemblyManager.get(assemblyName)
   return assembly ? (
     <>
-      {p?.hoverGenomeHighlights.map((r, idx) => (
-        <Highlight
-          key={`${JSON.stringify(r)}-${idx}`}
-          start={r.start}
-          end={r.end}
-          refName={r.refName}
-          assemblyName={assemblyNames[0]}
-          model={model}
-        />
-      ))}
+      {proteinView?.structures.map(structure =>
+        structure.hoverGenomeHighlights.map((r, idx) => (
+          <Highlight
+            key={`${JSON.stringify(r)}-${idx}`}
+            start={r.start}
+            end={r.end}
+            refName={r.refName}
+            assemblyName={assemblyName}
+            model={model}
+          />
+        )),
+      )}
     </>
   ) : null
 })

package/src/AddHighlightModel/util.ts

@@ -6,7 +6,7 @@ export const useStyles = makeStyles()({
     background: 'rgba(255,255,0,0.2)',
     border: '1px solid rgba(50,50,0,0.2)',
     position: 'absolute',
-    zIndex: 1000,
+    zIndex: 99,
     textAlign: 'center',
     pointerEvents: 'none',
     overflow: 'hidden',

package/src/AlphaFoldConfidenceAdapter/AlphaFoldConfidenceAdapter.ts

@@ -0,0 +1,63 @@
+import {
+  BaseFeatureDataAdapter,
+  BaseOptions,
+} from '@jbrowse/core/data_adapters/BaseAdapter'
+import { openLocation } from '@jbrowse/core/util/io'
+import { ObservableCreate } from '@jbrowse/core/util/rxjs'
+import {
+  Region,
+  Feature,
+  doesIntersect2,
+  SimpleFeature,
+} from '@jbrowse/core/util'
+
+export default class AlphaFoldConfidenceAdapter extends BaseFeatureDataAdapter {
+  public static capabilities = ['getFeatures', 'getRefNames']
+
+  public feats:
+    | Promise<{ uniqueId: string; start: number; end: number; score: number }[]>
+    | undefined
+
+  private async loadDataP() {
+    const scores = JSON.parse(
+      await openLocation(this.getConf('location')).readFile('utf8'),
+    ) as { residueNumber: number[]; confidenceScore: number[] }
+
+    return scores.residueNumber.map((value, idx) => ({
+      uniqueId: `feat-${idx}`,
+      start: value,
+      end: value + 1,
+      score: scores.confidenceScore[idx]!,
+    }))
+  }
+
+  private async loadData(_opts: BaseOptions = {}) {
+    if (!this.feats) {
+      this.feats = this.loadDataP().catch((e: unknown) => {
+        this.feats = undefined
+        throw e
+      })
+    }
+
+    return this.feats
+  }
+
+  public async getRefNames(_opts: BaseOptions = {}) {
+    return []
+  }
+
+  public getFeatures(query: Region, opts: BaseOptions = {}) {
+    return ObservableCreate<Feature>(async observer => {
+      const { start, end, refName } = query
+      const data = await this.loadData()
+      for (const f of data) {
+        if (doesIntersect2(f.start, f.end, start, end)) {
+          observer.next(new SimpleFeature({ ...f, refName }))
+        }
+      }
+      observer.complete()
+    }, opts.signal)
+  }
+
+  public freeResources(): void {}
+}

package/src/AlphaFoldConfidenceAdapter/configSchema.ts

@@ -0,0 +1,21 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+
+/**
+ * #config AlphaFoldConfidenceAdapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const AlphaFoldConfidenceAdapter = ConfigurationSchema(
+  'AlphaFoldConfidenceAdapter',
+  {
+    /**
+     * #slot
+     */
+    location: {
+      type: 'fileLocation',
+      defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
+    },
+  },
+  { explicitlyTyped: true },
+)
+export default AlphaFoldConfidenceAdapter

package/src/AlphaFoldConfidenceAdapter/index.ts

@@ -0,0 +1,19 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
+
+import configSchema from './configSchema'
+
+export default function AlphaFoldConfidenceAdapterF(
+  pluginManager: PluginManager,
+) {
+  pluginManager.addAdapterType(
+    () =>
+      new AdapterType({
+        name: 'AlphaFoldConfidenceAdapter',
+        displayName: 'AlphaFoldConfidence adapter',
+        configSchema,
+        getAdapterClass: () =>
+          import('./AlphaFoldConfidenceAdapter').then(r => r.default),
+      }),
+  )
+}

package/src/AlphaMissensePathogenicityAdapter/AlphaMissensePathogenicityAdapter.ts

@@ -0,0 +1,109 @@
+import {
+  BaseFeatureDataAdapter,
+  BaseOptions,
+} from '@jbrowse/core/data_adapters/BaseAdapter'
+import { openLocation } from '@jbrowse/core/util/io'
+import { ObservableCreate } from '@jbrowse/core/util/rxjs'
+import {
+  Region,
+  Feature,
+  doesIntersect2,
+  SimpleFeature,
+  max,
+  min,
+} from '@jbrowse/core/util'
+
+export default class AlphaMissensePathogenicityAdapter extends BaseFeatureDataAdapter {
+  public static capabilities = ['getFeatures', 'getRefNames']
+
+  public feats:
+    | Promise<
+        {
+          uniqueId: string
+          start: number
+          end: number
+          score: number
+          ref: string
+          variant: string
+          am_class: string
+        }[]
+      >
+    | undefined
+
+  private async loadDataP() {
+    const scores = await openLocation(this.getConf('location')).readFile('utf8')
+    return scores
+      .split('\n')
+      .slice(1)
+      .map(f => f.trim())
+      .filter(f => !!f)
+      .map((row, idx) => {
+        const [protein_variant, score, am_class] = row.split(',')
+        const ref = protein_variant![0]
+        const variant = protein_variant!.at(-1)
+        const coord = protein_variant!.slice(1, -1)
+        return {
+          uniqueId: `feat-${idx}`,
+          ref: ref!,
+          variant: variant!,
+          start: +coord,
+          end: +coord + 1,
+          score: +score!,
+          am_class: am_class!,
+        }
+      })
+  }
+
+  private async loadData(_opts: BaseOptions = {}) {
+    if (!this.feats) {
+      this.feats = this.loadDataP().catch((e: unknown) => {
+        this.feats = undefined
+        throw e
+      })
+    }
+
+    return this.feats
+  }
+
+  public async getGlobalStats(_opts?: BaseOptions) {
+    const data = await this.loadData()
+    const scoreMin = min(data.map(s => s.score))
+    const scoreMax = max(data.map(s => s.score))
+    return { scoreMin, scoreMax }
+  }
+
+  // always render bigwig instead of calculating a feature density for it
+  async getMultiRegionFeatureDensityStats(_regions: Region[]) {
+    return { featureDensity: 0 }
+  }
+  public async getRefNames(_opts: BaseOptions = {}) {
+    return []
+  }
+
+  public getFeatures(query: Region, opts: BaseOptions = {}) {
+    return ObservableCreate<Feature>(async observer => {
+      const { start, end, refName } = query
+      const data = await this.loadData()
+      for (const f of data) {
+        if (doesIntersect2(f.start, f.end, start, end)) {
+          observer.next(new SimpleFeature({ ...f, refName, source: f.variant }))
+        }
+      }
+      observer.complete()
+    }, opts.signal)
+  }
+
+  public async getSources() {
+    const sources = new Set<string>()
+    const data = await this.loadData()
+    for (const f of data) {
+      sources.add(f.variant)
+    }
+    return [...sources].map(s => ({
+      name: s,
+      __name: s,
+    }))
+  }
+
+  public freeResources(): void {}
+}

package/src/AlphaMissensePathogenicityAdapter/configSchema.ts

@@ -0,0 +1,21 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+
+/**
+ * #config AlphaMissensePathogenicityAdapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const AlphaMissensePathogenicityAdapter = ConfigurationSchema(
+  'AlphaMissensePathogenicityAdapter',
+  {
+    /**
+     * #slot
+     */
+    location: {
+      type: 'fileLocation',
+      defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
+    },
+  },
+  { explicitlyTyped: true },
+)
+export default AlphaMissensePathogenicityAdapter

package/src/AlphaMissensePathogenicityAdapter/index.ts

@@ -0,0 +1,19 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
+
+import configSchema from './configSchema'
+
+export default function AlphaMissensePathogenicityAdapterF(
+  pluginManager: PluginManager,
+) {
+  pluginManager.addAdapterType(
+    () =>
+      new AdapterType({
+        name: 'AlphaMissensePathogenicityAdapter',
+        displayName: 'AlphaMissensePathogenicity adapter',
+        configSchema,
+        getAdapterClass: () =>
+          import('./AlphaMissensePathogenicityAdapter').then(r => r.default),
+      }),
+  )
+}