jbrowse-plugin-msaview 3.7.0 → 3.8.0

package/dist/utils/unirefHomologs.js

@@ -19,7 +19,7 @@
 // pantherOrthologs.ts produce, so the launch, the labels and the aligner do not
 // know which source ran. `protein` is the UniProt accession, which is what the
 // CDD overlay reads through efetch (Swiss-Prot rows only; see the PANTHER note
-// in DEVELOPERS.md).
+// in docs/alignments-from-a-gene.md).
 import { handleFetch, jsonfetch } from './fetch';
 import { cleanGeneCandidate, dedupeLabels, defaultMaxSpecies, } from './ncbiOrthologs';
 const UNIPROT = 'https://rest.uniprot.org';

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "3.7.0";
+export declare const version = "3.8.0";

package/dist/version.js

@@ -1 +1 @@
-export const version = '3.7.0';
+export const version = '3.8.0';

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "3.7.0",
+  "version": "3.8.0",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "repository": {
@@ -46,7 +46,7 @@
     "jsdom": "^30.1.0",
     "mobx": "^7.0.3",
     "mobx-react": "^10.0.2",
-    "msa-parsers": "^8.1.0",
+    "msa-parsers": "^8.2.0",
     "oxfmt": "^0.68.0",
     "oxlint": "^1.83.0",
     "oxlint-tsgolint": "^7.0.2001",
@@ -56,7 +56,7 @@
     "puppeteer": "^25.11.0",
     "react": "^19.3.0",
     "react-dom": "^19.3.0",
-    "react-msaview": "^8.1.0",
+    "react-msaview": "^8.2.0",
     "rimraf": "^6.1.3",
     "rxjs": "^7.8.2",
     "serve": "^14.2.6",
@@ -87,10 +87,11 @@
     "test:setup:version": "node scripts/test-versions.mjs setup",
     "test:versions": "node scripts/test-versions.mjs run",
     "test:version": "node scripts/test-versions.mjs run",
+    "readme-figure": "node scripts/readme-figure.mjs",
     "host-compat": "node scripts/host-compat-probe.mjs --bundle dist/jbrowse-plugin-msaview.umd.production.min.js",
     "check-ci": "node scripts/require-green-ci.mjs",
     "preversion": "pnpm check-ci && pnpm check-host-dep-pins && pnpm lint && pnpm build && pnpm check-host-externals && pnpm host-compat",
-    "version": "node -e \"console.log('export const version = \\'' + require('./package.json').version + '\\'')\" > src/version.ts && git-cliff --tag v$npm_package_version --unreleased --prepend CHANGELOG.md && git add src/version.ts CHANGELOG.md",
+    "version": "node -e \"console.log('export const version = \\'' + require('./package.json').version + '\\'')\" > src/version.ts && git-cliff --tag v$npm_package_version --unreleased --prepend CHANGELOG.md && (pnpm readme-figure || echo 'WARNING: README figure not refreshed, see above') && git add src/version.ts CHANGELOG.md img/1.png",
     "postversion": "git push --follow-tags"
   }
 }

package/src/LaunchMsaView/launchTarget.test.ts

@@ -137,6 +137,20 @@ describe('launchTarget', () => {
     expect(target?.preferredTranscriptId).toBe(mrna.id())
   })
 
+  // the canvas host names the clicked isoform beside the gene it fetches, as
+  // its own Collapse introns dialog reads it
+  test('carries the isoform a canvas click landed on', () => {
+    const host = modernHost('gene')
+    const target = launchTarget({
+      ...host,
+      contextMenuInfo: {
+        ...host.contextMenuInfo,
+        subfeature: { featureId: 'mrna-2' },
+      },
+    })
+    expect(target?.preferredTranscriptId).toBe('mrna-2')
+  })
+
   // a host that has both shapes must not fall through to the legacy branch and
   // launch on a stale feature when the click was not on a gene
   test('a non-gene click on a host carrying both shapes offers nothing', () => {

package/src/LaunchMsaView/launchTarget.ts

@@ -3,12 +3,15 @@ import { geneLikeRoot, isGeneLikeType, isKnownNonCoding } from './codingFeature'
 import type { MenuItem } from '@jbrowse/core/ui'
 import type { Feature } from '@jbrowse/core/util'
 
-// The canvas LinearBasicDisplay (JBrowse >=4.3) exposes the right-clicked
-// feature via contextMenuInfo + async fetchFullFeature. Hosts before that -- and
-// the v3.7.0 in the wild that shipped configs still name -- expose it
-// synchronously as contextMenuFeature, and only have that one.
+// The canvas LinearBasicDisplay (JBrowse 5; no release through v4.3.0 has it)
+// exposes the right-clicked feature via contextMenuInfo + async
+// fetchFullFeature. Hosts before that -- v4.3.0, and the v3.7.0 in the wild
+// that shipped configs still name -- expose it synchronously as
+// contextMenuFeature, and only have that one.
 export interface ContextMenuInfo {
   item: { featureId: string; type?: string }
+  // the isoform under the pointer when the click landed on a gene's child
+  subfeature?: { featureId: string }
   displayedRegionIndex: number
 }
 
@@ -86,6 +89,7 @@ export function launchTarget(self: DisplayModel): MenuTarget | undefined {
       ? {
           fetchFeature: () =>
             fetchFullFeature(info.item.featureId, info.displayedRegionIndex),
+          preferredTranscriptId: info.subfeature?.featureId,
         }
       : undefined
   }

package/src/LaunchMsaViewExtensionPoint/index.test.ts

@@ -88,3 +88,51 @@ test('one field set is enough to need init', () => {
     querySeqName: 'QUERY',
   })
 })
+
+test('msa and tree urls reach the plugin sources, query the query row', () => {
+  const snapshot = launch({
+    msa: 'https://example.com/p53.afa',
+    tree: 'https://example.com/p53.nh',
+    query: 'Human',
+  })
+  expect(snapshot.init).toMatchObject({
+    msaUrl: 'https://example.com/p53.afa',
+    querySeqName: 'Human',
+  })
+  expect(snapshot.treeFilehandle).toEqual({
+    uri: 'https://example.com/p53.nh',
+    locationType: 'UriLocation',
+  })
+  expect(snapshot.relativeTo).toBe('Human')
+  expect('msa' in snapshot || 'query' in snapshot).toBe(false)
+})
+
+test('inline msa and newick text become inline data', () => {
+  const snapshot = launch({ msa: '>a\nMEEP\n>b\nMEEP', tree: '(a,b);' })
+  expect(snapshot.data).toEqual({ msa: '>a\nMEEP\n>b\nMEEP', tree: '(a,b);' })
+  expect('init' in snapshot).toBe(false)
+})
+
+test('highlights, region and column tracks expand onto the query row', () => {
+  const snapshot = launch({
+    msa: 'https://example.com/p53.afa',
+    query: 'Human',
+    highlights: ['102-292 DNA-binding', 175],
+    region: '170-290',
+    columnTracks: [{ name: 'ClinVar', start: 3, values: [2, 1] }],
+  })
+  expect(snapshot.highlights).toEqual([
+    { row: 'Human', start: 102, end: 292, label: 'DNA-binding' },
+    { row: 'Human', start: 175, end: 175, label: '{residue}{position}' },
+  ])
+  expect(snapshot.region).toEqual({ row: 'Human', start: 170, end: 290 })
+  expect(snapshot.columnTracks).toEqual([
+    {
+      id: 'clinvar',
+      name: 'ClinVar',
+      kind: 'bar',
+      row: 'Human',
+      values: [0, 0, 2, 1],
+    },
+  ])
+})

package/src/LaunchMsaViewExtensionPoint/index.ts

@@ -1,3 +1,5 @@
+import { expandSpec } from 'react-msaview'
+
 import { launchMsaView } from '../utils/launchMsaView'
 
 import type { BlastParams, OrthologParams } from '../MsaViewPanel/model'
@@ -6,16 +8,25 @@ import type PluginManager from '@jbrowse/core/PluginManager'
 import type { AbstractSessionModel } from '@jbrowse/core/util'
 import type {
   Clade,
-  ColumnTrackSpec,
+  ColumnTrackShorthand,
   Encoding,
-  Highlight,
-  Region,
+  HighlightShorthand,
+  RegionShorthand,
   ResidueMapping,
   RowPanelSpec,
 } from 'react-msaview'
 
 interface LaunchMsaViewArgs {
   session: AbstractSessionModel
+  /**
+   * Shorthand, see react-msaview's docs/layers.md: `msa` and `tree` take a
+   * url or the text itself, and `query` names the row the spec is about, the
+   * `querySeqName` and the `row` of every highlight, region and column track
+   * that names none
+   */
+  msa?: string
+  tree?: string
+  query?: string
   data?: { msa: string; tree?: string }
   msaFileLocation?: { uri: string }
   msaIndexedLocation?: { uri: string }
@@ -54,15 +65,15 @@ interface LaunchMsaViewArgs {
    * for whole rows. Prefer this over `highlightColumns`: a residue range stays
    * put when `allowedGappyness` changes the visible columns.
    */
-  highlights?: Highlight[]
+  highlights?: HighlightShorthand[]
   /** per-column tracks supplied as data, see react-msaview's docs/layers.md */
-  columnTracks?: ColumnTrackSpec[]
+  columnTracks?: ColumnTrackShorthand[]
   /**
    * Where the view opens, in `highlights` coordinates: `{row, start, end}`
    * zooms onto residues of that row, `{start, end}` onto alignment columns.
    * Applied once the alignment has loaded, then dropped from the session.
    */
-  region?: Region
+  region?: RegionShorthand
   /**
    * Passed through untouched as react-msaview snapshot properties; see its
    * docs/layers.md. A bare `{ uri }` is enough for the two filehandles.
@@ -121,6 +132,30 @@ interface LaunchMsaViewArgs {
   placement?: MsaViewPlacement
 }
 
+/**
+ * `msa` and `tree` onto the plugin's own sources, so a url still goes through
+ * `init.msaUrl` and its format sniffing, and `query` onto `querySeqName`
+ */
+function withLongSources({ msa, tree, ...args }: LaunchMsaViewArgs) {
+  const inlineMsa = msa?.includes('\n') ? msa : undefined
+  const inlineTree = tree?.trimStart().startsWith('(') ? tree : undefined
+  const data =
+    inlineMsa || inlineTree
+      ? {
+          ...args.data,
+          ...(inlineMsa ? { msa: inlineMsa } : {}),
+          ...(inlineTree ? { tree: inlineTree } : {}),
+        }
+      : args.data
+  return {
+    ...args,
+    data: data as LaunchMsaViewArgs['data'],
+    ...(msa && !inlineMsa ? { msaFileLocation: { uri: msa } } : {}),
+    ...(tree && !inlineTree ? { treeFileLocation: { uri: tree } } : {}),
+    querySeqName: args.querySeqName ?? args.query,
+  }
+}
+
 export default function LaunchMsaViewExtensionPointF(
   pluginManager: PluginManager,
 ) {
@@ -129,6 +164,7 @@ export default function LaunchMsaViewExtensionPointF(
     (args: LaunchMsaViewArgs) => {
       const {
         session,
+        query,
         data,
         msaFileLocation,
         msaIndexedLocation,
@@ -137,7 +173,7 @@ export default function LaunchMsaViewExtensionPointF(
         querySeqName,
         searchParams,
         ...rest
-      } = args
+      } = withLongSources(args)
 
       // `orthologParams` and `searchParams` name no alignment at all — the
       // view builds one at launch, which is the dialog's Orthologs and BLAST
@@ -169,7 +205,7 @@ export default function LaunchMsaViewExtensionPointF(
         querySeqName,
       }
       launchMsaView(session, {
-        ...rest,
+        ...expandSpec({ ...rest, query }),
         ...(searchParams ? { blastParams: searchParams } : {}),
         data,
         ...(treeFileLocation

package/src/MsaViewPanel/model.ts

@@ -20,7 +20,6 @@ import {
   storeDataToIndexedDB,
   syncGenomeHoverToMsaColumn,
 } from './afterCreateAutoruns'
-import { applyRegion } from './applyRegion'
 import {
   msaCoordToGenomeCoord,
   msaCoordToGenomeRegions,
@@ -40,7 +39,6 @@ import type { TranscriptRef } from './util'
 import type { MenuItem } from '@jbrowse/core/ui'
 import type { Instance } from '@jbrowse/mobx-state-tree'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-import type { Region } from 'react-msaview'
 
 type LGV = LinearGenomeViewModel
 
@@ -246,14 +244,6 @@ export default function stateModelFactory() {
          * #property
          */
         mafRegion: types.frozen<MafRegion | undefined>(),
-
-        /**
-         * #property
-         * where the view opens: 1-based residues of `row`, or alignment
-         * columns without one. Zoomed onto once and then cleared, so a
-         * reloaded session keeps the reader's own scroll.
-         */
-        region: types.frozen<Region | undefined>(),
       }),
     )
 
@@ -433,12 +423,6 @@ export default function stateModelFactory() {
       setQuerySeqName(arg: string) {
         self.querySeqName = arg
       },
-      /**
-       * #action
-       */
-      setQuerySeqOffset(arg: number) {
-        self.querySeqOffset = arg
-      },
       /**
        * #action
        */
@@ -457,18 +441,6 @@ export default function stateModelFactory() {
       setLaunchCompleted(arg: boolean) {
         self.launchCompleted = arg
       },
-      /**
-       * #action
-       */
-      setMafRegion(arg?: MafRegion) {
-        self.mafRegion = arg
-      },
-      /**
-       * #action
-       */
-      setRegion(arg?: Region) {
-        self.region = arg
-      },
       /**
        * #action
        */
@@ -671,12 +643,6 @@ export default function stateModelFactory() {
         // so they're factories returning the autorun body rather than plain fns
         addDisposer(self, autorun(syncGenomeHoverToMsaColumn(self)))
         addDisposer(self, autorun(observeProteinHighlights(self)))
-        addDisposer(
-          self,
-          autorun(() => {
-            applyRegion(self)
-          }),
-        )
       },
     }))
 }

package/src/utils/unirefHomologs.ts

@@ -19,7 +19,7 @@
 // pantherOrthologs.ts produce, so the launch, the labels and the aligner do not
 // know which source ran. `protein` is the UniProt accession, which is what the
 // CDD overlay reads through efetch (Swiss-Prot rows only; see the PANTHER note
-// in DEVELOPERS.md).
+// in docs/alignments-from-a-gene.md).
 
 import { handleFetch, jsonfetch } from './fetch'
 import {

package/src/version.ts

@@ -1 +1 @@
-export const version = '3.7.0'
+export const version = '3.8.0'

package/dist/MsaViewPanel/applyRegion.d.ts

@@ -1,23 +0,0 @@
-import type { Region } from 'react-msaview';
-interface RegionModel {
-    region?: Region;
-    viewInitialized: boolean;
-    numColumns: number;
-    treeFilehandle?: unknown;
-    data: {
-        tree?: string;
-    };
-    zoomToRegion: (region: Region) => void;
-    setRegion: (region?: Region) => void;
-}
-/**
- * Zoom onto the launch's `region` once, then forget it, so a reloaded session
- * opens where the reader left it rather than back on the region.
- *
- * zoomToRegion is a no-op until the view has a width, and it resolves residues
- * through the visible columns, so it waits for the alignment and for a tree
- * file too: a clade the tree collapses hides columns and would move the
- * target after the zoom.
- */
-export declare function applyRegion(self: RegionModel): void;
-export {};

package/dist/MsaViewPanel/applyRegion.js

@@ -1,19 +0,0 @@
-/**
- * Zoom onto the launch's `region` once, then forget it, so a reloaded session
- * opens where the reader left it rather than back on the region.
- *
- * zoomToRegion is a no-op until the view has a width, and it resolves residues
- * through the visible columns, so it waits for the alignment and for a tree
- * file too: a clade the tree collapses hides columns and would move the
- * target after the zoom.
- */
-export function applyRegion(self) {
-    const { region } = self;
-    if (region &&
-        self.viewInitialized &&
-        self.numColumns > 0 &&
-        !(self.treeFilehandle && !self.data.tree)) {
-        self.zoomToRegion(region);
-        self.setRegion(undefined);
-    }
-}

package/dist/MsaViewPanel/applyRegion.test.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/MsaViewPanel/applyRegion.test.js

@@ -1,45 +0,0 @@
-import { expect, test, vi } from 'vitest';
-import { applyRegion } from './applyRegion';
-const REGION = { row: 'Human', start: 245, end: 249 };
-function makeModel(over = {}) {
-    const model = {
-        region: REGION,
-        viewInitialized: true,
-        numColumns: 400,
-        treeFilehandle: undefined,
-        data: {},
-        zoomToRegion: vi.fn(),
-        setRegion: vi.fn((arg) => {
-            model.region = arg;
-        }),
-        ...over,
-    };
-    return model;
-}
-test('zooms onto the region once, then forgets it', () => {
-    const model = makeModel();
-    applyRegion(model);
-    applyRegion(model);
-    expect(model.zoomToRegion).toHaveBeenCalledTimes(1);
-    expect(model.zoomToRegion).toHaveBeenCalledWith(REGION);
-    expect(model.region).toBeUndefined();
-});
-test('waits for the view to have a width', () => {
-    const model = makeModel({ viewInitialized: false });
-    applyRegion(model);
-    expect(model.zoomToRegion).not.toHaveBeenCalled();
-    expect(model.region).toEqual(REGION);
-});
-test('waits for the alignment', () => {
-    const model = makeModel({ numColumns: 0 });
-    applyRegion(model);
-    expect(model.zoomToRegion).not.toHaveBeenCalled();
-});
-test('waits for a tree file, whose collapsed clades move the columns', () => {
-    const model = makeModel({ treeFilehandle: { uri: 'x.nh' } });
-    applyRegion(model);
-    expect(model.zoomToRegion).not.toHaveBeenCalled();
-    model.data.tree = '(a,b);';
-    applyRegion(model);
-    expect(model.zoomToRegion).toHaveBeenCalledTimes(1);
-});

package/src/MsaViewPanel/applyRegion.test.ts

@@ -1,55 +0,0 @@
-import { expect, test, vi } from 'vitest'
-
-import { applyRegion } from './applyRegion'
-
-import type { Region } from 'react-msaview'
-
-const REGION: Region = { row: 'Human', start: 245, end: 249 }
-
-function makeModel(over: Record<string, unknown> = {}) {
-  const model = {
-    region: REGION as Region | undefined,
-    viewInitialized: true,
-    numColumns: 400,
-    treeFilehandle: undefined as unknown,
-    data: {} as { tree?: string },
-    zoomToRegion: vi.fn(),
-    setRegion: vi.fn((arg?: Region) => {
-      model.region = arg
-    }),
-    ...over,
-  }
-  return model
-}
-
-test('zooms onto the region once, then forgets it', () => {
-  const model = makeModel()
-  applyRegion(model)
-  applyRegion(model)
-  expect(model.zoomToRegion).toHaveBeenCalledTimes(1)
-  expect(model.zoomToRegion).toHaveBeenCalledWith(REGION)
-  expect(model.region).toBeUndefined()
-})
-
-test('waits for the view to have a width', () => {
-  const model = makeModel({ viewInitialized: false })
-  applyRegion(model)
-  expect(model.zoomToRegion).not.toHaveBeenCalled()
-  expect(model.region).toEqual(REGION)
-})
-
-test('waits for the alignment', () => {
-  const model = makeModel({ numColumns: 0 })
-  applyRegion(model)
-  expect(model.zoomToRegion).not.toHaveBeenCalled()
-})
-
-test('waits for a tree file, whose collapsed clades move the columns', () => {
-  const model = makeModel({ treeFilehandle: { uri: 'x.nh' } })
-  applyRegion(model)
-  expect(model.zoomToRegion).not.toHaveBeenCalled()
-
-  model.data.tree = '(a,b);'
-  applyRegion(model)
-  expect(model.zoomToRegion).toHaveBeenCalledTimes(1)
-})

package/src/MsaViewPanel/applyRegion.ts

@@ -1,33 +0,0 @@
-import type { Region } from 'react-msaview'
-
-interface RegionModel {
-  region?: Region
-  viewInitialized: boolean
-  numColumns: number
-  treeFilehandle?: unknown
-  data: { tree?: string }
-  zoomToRegion: (region: Region) => void
-  setRegion: (region?: Region) => void
-}
-
-/**
- * Zoom onto the launch's `region` once, then forget it, so a reloaded session
- * opens where the reader left it rather than back on the region.
- *
- * zoomToRegion is a no-op until the view has a width, and it resolves residues
- * through the visible columns, so it waits for the alignment and for a tree
- * file too: a clade the tree collapses hides columns and would move the
- * target after the zoom.
- */
-export function applyRegion(self: RegionModel) {
-  const { region } = self
-  if (
-    region &&
-    self.viewInitialized &&
-    self.numColumns > 0 &&
-    !(self.treeFilehandle && !self.data.tree)
-  ) {
-    self.zoomToRegion(region)
-    self.setRegion(undefined)
-  }
-}