jbrowse-plugin-msaview 2.8.2 → 2.10.0

package/dist/MsaViewPanel/components/LoadingBLAST.js

@@ -3,7 +3,7 @@ import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
 import { Typography } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
-import RIDLink from './RIDLink';
+import JobLink from './JobLink';
 const useStyles = makeStyles()(theme => ({
     margin: {
         padding: 20,
@@ -12,22 +12,15 @@ const useStyles = makeStyles()(theme => ({
         background: theme.palette.background.paper,
     },
 }));
-function RIDError({ baseUrl, rid, error, }) {
-    return (React.createElement("div", null,
-        rid ? React.createElement(RIDLink, { rid: rid, baseUrl: baseUrl }) : null,
-        React.createElement(ErrorMessage, { error: error })));
-}
-function RIDProgress({ baseUrl, rid, progress, }) {
-    const { classes } = useStyles();
-    return (React.createElement("div", { className: classes.loading },
-        rid ? React.createElement(RIDLink, { baseUrl: baseUrl, rid: rid }) : null,
-        React.createElement(Typography, null, progress)));
-}
-const LoadingBLAST = observer(function LoadingBLAST2({ model, baseUrl, }) {
+const LoadingBLAST = observer(function LoadingBLAST2({ model, }) {
     const { progress, rid, error } = model;
     const { classes } = useStyles();
     return (React.createElement("div", { className: classes.margin },
-        React.createElement(LoadingEllipses, { message: "Running NCBI BLAST", variant: "h5" }),
-        error ? (React.createElement(RIDError, { baseUrl: baseUrl, rid: rid, error: error })) : rid ? (React.createElement(RIDProgress, { baseUrl: baseUrl, rid: rid, progress: progress })) : (React.createElement(Typography, null, progress || 'Initializing BLAST query'))));
+        React.createElement(LoadingEllipses, { message: "Running EBI BLAST", variant: "h5" }),
+        error ? (React.createElement("div", null,
+            rid ? React.createElement(JobLink, { jobId: rid }) : null,
+            React.createElement(ErrorMessage, { error: error }))) : rid ? (React.createElement("div", { className: classes.loading },
+            React.createElement(JobLink, { jobId: rid }),
+            React.createElement(Typography, null, progress))) : (React.createElement(Typography, null, progress || 'Initializing BLAST query'))));
 });
 export default LoadingBLAST;

package/dist/MsaViewPanel/components/MsaViewPanel.js

@@ -14,7 +14,7 @@ const MsaViewPanel = observer(function MsaViewPanel2({ model, }) {
     const { classes } = useStyles();
     const { blastParams, loadingStoredData } = model;
     return (React.createElement(ErrorBoundary, null,
-        React.createElement("div", null, blastParams ? (React.createElement(LoadingBLAST, { model: model, baseUrl: blastParams.baseUrl })) : loadingStoredData ? (React.createElement("div", { className: classes.loadingContainer },
+        React.createElement("div", null, blastParams ? (React.createElement(LoadingBLAST, { model: model })) : loadingStoredData ? (React.createElement("div", { className: classes.loadingContainer },
             React.createElement(LoadingEllipses, { message: "Loading MSA data", variant: "h6" }))) : (React.createElement(MSAView, { model: model })))));
 });
 export default MsaViewPanel;

package/dist/MsaViewPanel/doLaunchBlast.js

@@ -1,32 +1,25 @@
 import { makeId, strip } from '../LaunchMsaView/components/util';
 import { cleanProteinSequence } from '../LaunchMsaView/util';
 import { saveBlastResult } from '../utils/blastCache';
+import { queryEbiBlast } from '../utils/ebiBlast';
 import { launchMSA } from '../utils/msa';
-import { queryBlast, queryBlastFromRid } from '../utils/ncbiBlast';
 import { fetchTaxonomyInfo } from '../utils/taxonomyNames';
 export async function doLaunchBlast({ self, }) {
-    const { baseUrl, blastDatabase, blastProgram, msaAlgorithm, proteinSequence, selectedTranscript, rid: existingRid, } = self.blastParams;
+    const { blastDatabase, msaAlgorithm, proteinSequence, selectedTranscript } = self.blastParams;
     const cleanedSeq = cleanProteinSequence(proteinSequence);
     const onProgress = (arg) => {
         self.setProgress(arg);
     };
-    if (existingRid) {
-        // publish it before the first poll so the view can link out to NCBI while
+    const { hits, rid } = await queryEbiBlast({
+        query: cleanedSeq,
+        blastDatabase,
+        onProgress,
+        // publish the job id before the first poll so the view can link out while
         // the job is still running
-        self.setRid(existingRid);
-    }
-    const { hits, rid } = existingRid
-        ? await queryBlastFromRid({ rid: existingRid, baseUrl, onProgress })
-        : await queryBlast({
-            query: cleanedSeq,
-            blastDatabase,
-            blastProgram,
-            baseUrl,
-            onProgress,
-            onRid: r => {
-                self.setRid(r);
-            },
-        });
+        onRid: r => {
+            self.setRid(r);
+        },
+    });
     self.setProgress('Fetching species taxonomy info...');
     const taxids = hits
         .map(h => h.description[0]?.taxid)
@@ -53,7 +46,6 @@ export async function doLaunchBlast({ self, }) {
     await saveBlastResult({
         proteinSequence: cleanedSeq,
         blastDatabase,
-        blastProgram,
         msaAlgorithm,
         msa: result.msa,
         tree: result.tree,

package/dist/MsaViewPanel/doLaunchOrthologs.js

@@ -1,6 +1,7 @@
 import { cleanProteinSequence } from '../LaunchMsaView/util';
 import { launchMSA } from '../utils/msa';
-import { COMMON_SPECIES, fetchOrthologRows, fetchProteinForGene, resolveGeneId, } from '../utils/ncbiOrthologs';
+import { dedupeLabels, fetchOrthologRows, fetchProteinForGene, resolveGeneId, } from '../utils/ncbiOrthologs';
+import { fetchTaxonomyInfo } from '../utils/taxonomyNames';
 /**
  * The no-search-job alternative to doLaunchBlast.
  *
@@ -17,7 +18,7 @@ import { COMMON_SPECIES, fetchOrthologRows, fetchProteinForGene, resolveGeneId,
  * excluded from the ortholog set rather than appearing twice.
  */
 export async function doLaunchOrthologs({ self, }) {
-    const { taxId, taxa, geneCandidates, msaAlgorithm, proteinSequence } = self.orthologParams;
+    const { taxId, taxa, maxSpecies, geneCandidates, msaAlgorithm, proteinSequence, } = self.orthologParams;
     const onProgress = (arg) => {
         self.setProgress(arg);
     };
@@ -39,20 +40,33 @@ export async function doLaunchOrthologs({ self, }) {
     if (!cleanedSeq) {
         throw new Error(`No query protein: none was supplied and NCBI returned no representative protein for gene ${resolved.geneId}.`);
     }
-    // Every species the panel offers, when a launch names none. A spec that wants
-    // a narrower comparison says so; one that just wants "this gene across
-    // species" should not have to enumerate the list the dialog would have
-    // checked for it.
-    const wantedTaxa = taxa ?? COMMON_SPECIES.map(s => s.taxId);
-    // the query species is represented by the query row above
-    const wanted = new Set(wantedTaxa.filter(t => t !== taxId));
+    // Every species NCBI has an ortholog for, when a launch names none, capped at
+    // maxSpecies. A launch that wants specific species lists them; one that just
+    // wants "this gene across species" gets NCBI's own order, which leads with the
+    // reference organisms.
     const rows = await fetchOrthologRows({
         geneId: resolved.geneId,
-        taxa: wanted,
+        taxa: taxa ? new Set(taxa) : undefined,
+        // the query species is represented by the query row above
+        exclude: taxId,
+        limit: maxSpecies,
         onProgress,
     });
+    // The query row is named for its species like every other row, with a suffix
+    // marking it as the one the genome view is linked to. A bare `QUERY` among
+    // ninety-nine named species reads as a row whose species failed to resolve,
+    // and there is nothing else in the picture saying which row the hover
+    // highlight travels through -- react-msaview has no notion of a query row, it
+    // only looks one up by name.
+    //
+    // Deduped against the ortholog labels rather than assumed unique: the query
+    // taxon is excluded from that set, but a subspecies can sanitize to the same
+    // token, and a collision would silently point the coordinate mapping at
+    // another animal's row.
+    const queryLabel = await queryRowLabel(taxId, rows);
+    self.setQuerySeqName(queryLabel);
     const treeMetadata = {
-        QUERY: buildQueryMetadata(self, resolved.geneId, cleanedSeq, representative),
+        [queryLabel]: buildQueryMetadata(self, resolved.geneId, cleanedSeq, representative),
     };
     for (const row of rows) {
         treeMetadata[row.label] = buildRowMetadata(row);
@@ -60,7 +74,7 @@ export async function doLaunchOrthologs({ self, }) {
     const result = await launchMSA({
         algorithm: msaAlgorithm,
         sequence: [
-            `>QUERY\n${cleanedSeq}`,
+            `>${queryLabel}\n${cleanedSeq}`,
             ...rows.map(r => `>${r.label}\n${r.sequence}`),
         ].join('\n'),
         onProgress,
@@ -70,6 +84,23 @@ export async function doLaunchOrthologs({ self, }) {
         treeMetadata: JSON.stringify(treeMetadata),
     };
 }
+/**
+ * `<species>_query`, unique against the ortholog labels. Falls back to the bare
+ * marker when NCBI cannot name the taxon, which is a naming failure and must not
+ * take down the launch.
+ */
+async function queryRowLabel(taxId, rows) {
+    let name;
+    try {
+        const info = (await fetchTaxonomyInfo([taxId])).get(taxId);
+        name = info?.commonName ?? info?.sciname;
+    }
+    catch (e) {
+        console.warn('[msaview-orthologs] taxonomy name lookup failed:', e);
+    }
+    return dedupeLabels([...rows.map(r => r.label), `${name ?? 'query'}_query`])
+        .at(-1);
+}
 /**
  * A failed lookup only costs the query row its domain overlay and, for a launch
  * that supplied no sequence of its own, the alignment — so it is reported by

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

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

package/dist/MsaViewPanel/doLaunchOrthologs.test.js

@@ -0,0 +1,201 @@
+import { beforeEach, describe, expect, test, vi } from 'vitest';
+import { doLaunchOrthologs } from './doLaunchOrthologs';
+import { launchMSA } from '../utils/msa';
+import { defaultMaxSpecies, fetchOrthologRows, fetchProteinForGene, resolveGeneId, } from '../utils/ncbiOrthologs';
+import { fetchTaxonomyInfo } from '../utils/taxonomyNames';
+// Every network call is mocked and nothing else is. What is under test is the
+// argument shaping either side of those calls -- which species get asked for,
+// what becomes the QUERY row, and whether the row earns the Accession that
+// drives the CDD overlay -- so the real cleanProteinSequence stays in the
+// picture.
+vi.mock('../utils/ncbiOrthologs', async (importOriginal) => ({
+    ...(await importOriginal()),
+    resolveGeneId: vi.fn(),
+    fetchProteinForGene: vi.fn(),
+    fetchOrthologRows: vi.fn(),
+}));
+vi.mock('../utils/msa', () => ({ launchMSA: vi.fn() }));
+vi.mock('../utils/taxonomyNames', () => ({ fetchTaxonomyInfo: vi.fn() }));
+const mockResolveGeneId = vi.mocked(resolveGeneId);
+const mockFetchProtein = vi.mocked(fetchProteinForGene);
+const mockFetchRows = vi.mocked(fetchOrthologRows);
+const mockLaunchMSA = vi.mocked(launchMSA);
+const mockFetchTaxonomy = vi.mocked(fetchTaxonomyInfo);
+const HUMAN = 9606;
+const GENE_ID = '22861';
+const REPRESENTATIVE = { accession: 'NP_127497.1', sequence: 'MAGGAWGRLACY' };
+const setQuerySeqName = vi.fn();
+function makeModel(orthologParams) {
+    return {
+        orthologParams,
+        setProgress: () => { },
+        setQuerySeqName,
+    };
+}
+function params(extra = {}) {
+    return {
+        taxId: HUMAN,
+        geneCandidates: ['NLRP1'],
+        msaAlgorithm: 'clustalo',
+        ...extra,
+    };
+}
+// What fetchOrthologRows was asked for, which is the only place the species
+// defaults are observable.
+function rowRequest() {
+    const { taxa, exclude, limit } = mockFetchRows.mock.calls[0][0];
+    return {
+        taxa: taxa && [...taxa].sort((a, b) => a - b),
+        exclude,
+        limit,
+    };
+}
+// The QUERY row as it went to the aligner, read back out of the FASTA rather
+// than out of an intermediate, since the FASTA is what the alignment is of.
+function queryRowSent() {
+    return mockLaunchMSA.mock.calls[0][0].sequence.split('\n')[1];
+}
+// Keyed by the row's own label, which has to be the name the FASTA header
+// carries -- the tree comes back from the aligner naming its leaves that way,
+// and the metadata is paired to a leaf by name.
+function queryMetadata(result) {
+    return JSON.parse(result.treeMetadata)[queryRowName()];
+}
+function queryRowName() {
+    return mockLaunchMSA.mock.calls[0][0].sequence.split('\n')[0].slice(1);
+}
+beforeEach(() => {
+    vi.clearAllMocks();
+    mockResolveGeneId.mockResolvedValue({ geneId: GENE_ID, matched: 'NLRP1' });
+    mockFetchProtein.mockResolvedValue(REPRESENTATIVE);
+    mockFetchRows.mockResolvedValue([]);
+    mockLaunchMSA.mockResolvedValue({ msa: '', tree: '' });
+    mockFetchTaxonomy.mockResolvedValue(new Map([[HUMAN, { sciname: 'Homo sapiens', commonName: 'human' }]]));
+});
+describe('which species become rows', () => {
+    test('omitted taxa asks for no restriction at all, which is every ortholog NCBI has', async () => {
+        await doLaunchOrthologs({ self: makeModel(params()) });
+        expect(rowRequest().taxa).toBeUndefined();
+    });
+    test('given taxa is taken as written', async () => {
+        await doLaunchOrthologs({
+            self: makeModel(params({ taxa: [HUMAN, 10090, 9615] })),
+        });
+        expect(rowRequest().taxa).toEqual([9606, 9615, 10090]);
+    });
+    // Not folded into the taxa list before the call, so that "restrict to these"
+    // and "the query row already covers this one" stay separable -- an unrestricted
+    // launch still has to drop the query species.
+    test('the query species is excluded whether or not taxa was given', async () => {
+        await doLaunchOrthologs({ self: makeModel(params()) });
+        expect(rowRequest().exclude).toBe(HUMAN);
+        vi.clearAllMocks();
+        mockResolveGeneId.mockResolvedValue({ geneId: GENE_ID, matched: 'NLRP1' });
+        mockFetchProtein.mockResolvedValue(REPRESENTATIVE);
+        mockFetchRows.mockResolvedValue([]);
+        mockLaunchMSA.mockResolvedValue({ msa: '', tree: '' });
+        await doLaunchOrthologs({
+            self: makeModel(params({ taxa: [HUMAN, 10090] })),
+        });
+        expect(rowRequest().exclude).toBe(HUMAN);
+    });
+    test('an empty list is a request for no rows, not a request for all of them', async () => {
+        await doLaunchOrthologs({ self: makeModel(params({ taxa: [] })) });
+        expect(rowRequest().taxa).toEqual([]);
+    });
+});
+// The cap is the only thing standing between a launch and a 7 minute EBI job:
+// NCBI publishes 865 orthologs for CFTR and the aligner runs at roughly half a
+// second a row.
+describe('the row cap', () => {
+    test('is passed through when given', async () => {
+        await doLaunchOrthologs({ self: makeModel(params({ maxSpecies: 12 })) });
+        expect(rowRequest().limit).toBe(12);
+    });
+    test('omitted leaves the default to fetchOrthologGenes rather than sending Infinity', async () => {
+        await doLaunchOrthologs({ self: makeModel(params()) });
+        expect(rowRequest().limit).toBeUndefined();
+        expect(defaultMaxSpecies).toBeGreaterThan(2);
+    });
+});
+// The row's name is load bearing three times over: it is the FASTA header, it
+// is therefore the tree leaf the aligner returns, and it is what
+// `seqPosToVisibleCol` looks up to turn a genome hover into a column. So the
+// model's querySeqName and the header have to be the same string.
+describe('the query row name', () => {
+    test('is the species, marked, rather than a bare QUERY among named rows', async () => {
+        await doLaunchOrthologs({ self: makeModel(params()) });
+        expect(queryRowName()).toBe('human_query');
+        expect(setQuerySeqName).toHaveBeenCalledWith('human_query');
+    });
+    test('cannot collide with an ortholog row that sanitizes to the same token', async () => {
+        mockFetchRows.mockResolvedValue([
+            { label: 'human_query', sequence: 'MM' },
+        ]);
+        await doLaunchOrthologs({ self: makeModel(params()) });
+        expect(queryRowName()).toBe('human_query_2');
+        expect(setQuerySeqName).toHaveBeenCalledWith('human_query_2');
+    });
+    test('falls back rather than throwing when NCBI cannot name the taxon', async () => {
+        vi.spyOn(console, 'warn').mockImplementation(() => { });
+        mockFetchTaxonomy.mockRejectedValue(new Error('429'));
+        await doLaunchOrthologs({ self: makeModel(params()) });
+        expect(queryRowName()).toBe('query_query');
+    });
+    test('the metadata that drives the domain overlay is keyed to that same name', async () => {
+        const result = await doLaunchOrthologs({ self: makeModel(params()) });
+        expect(Object.keys(JSON.parse(result.treeMetadata))).toContain('human_query');
+    });
+});
+describe('the query row sequence', () => {
+    test('omitted proteinSequence falls back to the representative protein', async () => {
+        await doLaunchOrthologs({ self: makeModel(params()) });
+        expect(queryRowSent()).toBe(REPRESENTATIVE.sequence);
+    });
+    test('a supplied sequence is used, and is cleaned first', async () => {
+        await doLaunchOrthologs({
+            self: makeModel(params({ proteinSequence: 'MAGG*AWGR&' })),
+        });
+        expect(queryRowSent()).toBe('MAGGAWGR');
+    });
+    test('throws when neither a sequence nor a representative is available', async () => {
+        mockFetchProtein.mockResolvedValue(undefined);
+        await expect(doLaunchOrthologs({ self: makeModel(params()) })).rejects.toThrow(/No query protein/);
+        expect(mockLaunchMSA).not.toHaveBeenCalled();
+    });
+    test('a failed representative lookup does not take down a launch that brought its own sequence', async () => {
+        vi.spyOn(console, 'warn').mockImplementation(() => { });
+        mockFetchProtein.mockRejectedValue(new Error('429'));
+        await doLaunchOrthologs({
+            self: makeModel(params({ proteinSequence: REPRESENTATIVE.sequence })),
+        });
+        expect(queryRowSent()).toBe(REPRESENTATIVE.sequence);
+    });
+});
+// The Accession is what afterCreateAutoruns.autoLoadProteinDomains keys the CDD
+// overlay off, and attaching it to a row that is NOT the protein it names draws
+// every domain box at an offset. So the byte-identity guard is the assertion
+// here, in both directions.
+describe('the Accession that drives the domain overlay', () => {
+    test('is attached when the query row IS the representative protein', async () => {
+        const result = await doLaunchOrthologs({ self: makeModel(params()) });
+        expect(queryMetadata(result)).toMatchObject({
+            'Gene ID': GENE_ID,
+            Accession: REPRESENTATIVE.accession,
+        });
+    });
+    test('is withheld from a non-representative isoform', async () => {
+        const result = await doLaunchOrthologs({
+            self: makeModel(params({ proteinSequence: 'MDIFFERENTISOFORM' })),
+        });
+        expect(queryMetadata(result).Accession).toBeUndefined();
+    });
+    test('is withheld when the representative lookup failed', async () => {
+        vi.spyOn(console, 'warn').mockImplementation(() => { });
+        mockFetchProtein.mockRejectedValue(new Error('429'));
+        const result = await doLaunchOrthologs({
+            self: makeModel(params({ proteinSequence: REPRESENTATIVE.sequence })),
+        });
+        expect(queryMetadata(result).Accession).toBeUndefined();
+    });
+});

package/dist/MsaViewPanel/model.d.ts

@@ -1,6 +1,6 @@
 export type { MSAFormat } from 'msa-parsers';
 import type { MafRegion, MsaViewInitState } from './types';
-import type { BlastDatabase, BlastProgram, MsaAlgorithm } from '../LaunchMsaView/components/NCBIBlastQuery/consts';
+import type { BlastDatabase, MsaAlgorithm } from '../LaunchMsaView/components/BlastQuery/consts';
 import type { Feature } from '@jbrowse/core/util';
 import type { Instance } from '@jbrowse/mobx-state-tree';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
@@ -12,23 +12,27 @@ export interface IRegion {
     end: number;
 }
 export interface BlastParams {
-    baseUrl: string;
     blastDatabase: BlastDatabase;
     msaAlgorithm: MsaAlgorithm;
-    blastProgram: BlastProgram;
     selectedTranscript?: Feature;
     proteinSequence: string;
-    rid?: string;
 }
 export interface OrthologParams {
     /** NCBI taxon id of the assembly the query gene came from */
     taxId: number;
     /**
      * taxon ids to include as rows (the query taxon is represented by QUERY).
-     * Omitted means every species the launch dialog offers, which is what a
-     * launch that just wants "this gene across species" wants.
+     * Omitted means every species NCBI has an ortholog for, in its report order,
+     * which is what a launch that just wants "this gene across species" wants.
      */
     taxa?: number[];
+    /**
+     * how many ortholog rows to align, `defaultMaxSpecies` when omitted. The
+     * aligner is what this bounds: EBI runs at roughly half a second per row for
+     * a ~1400aa protein, so a gene with 865 orthologs is a 7 minute job at no
+     * cap.
+     */
+    maxSpecies?: number;
     /** candidate gene identifiers off the feature, tried in order */
     geneCandidates: string[];
     msaAlgorithm: MsaAlgorithm;
@@ -51,7 +55,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     minimized: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-}, "height" | "id" | "type" | "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawTree" | "labelsAlignRight" | "showBranchLen" | "treeAreaWidth" | "treeWidth" | "bgColor" | "colorSchemeName" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "colWidth" | "collapsed" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "hideGaps" | "highlightColumns" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawTree" | "labelsAlignRight" | "showBranchLen" | "treeAreaWidth" | "treeWidth"> & {
+}, "height" | "id" | "type" | "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawTree" | "labelsAlignRight" | "showBranchLen" | "treeAreaWidth" | "treeWidth" | "bgColor" | "colorSchemeName" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "colWidth" | "collapsed" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "hideGaps" | "highlightColumns" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawTree" | "labelsAlignRight" | "showBranchLen" | "treeAreaWidth" | "treeWidth"> & {
     drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -64,10 +68,11 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("react-msaview").MSAFormat>>;
-}, "height" | "id" | "type" | "allowedGappyness" | "colWidth" | "collapsed" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "hideGaps" | "highlightColumns" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks"> & {
+    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
+}, "height" | "id" | "type" | "allowedGappyness" | "colWidth" | "collapsed" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "hideGaps" | "highlightColumns" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showDomainLegend: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     hideGaps: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     allowedGappyness: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     subFeatureRows: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -518,7 +523,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setColorSchemeName(name: string): void;
     setBgColor(arg: boolean): void;
     setShowColumnStats(arg: boolean): void;
-    setMSAFormat(arg?: import("react-msaview").MSAFormat): void;
+    setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
 } & {
     headerHeight: number;
     status: {
@@ -559,6 +564,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setMousePos(col?: number, row?: number): void;
     setHighlightedColumns(columns?: number[]): void;
     setShowDomains(arg: boolean): void;
+    setShowDomainLegend(arg: boolean): void;
     setSubFeatureRows(arg: boolean): void;
     setMouseClickPos(col?: number, row?: number): void;
     setRowHeight(n: number): void;
@@ -605,7 +611,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly noDomains: boolean;
     menuItems(): never[];
     readonly treeMetadata: Record<string, Record<string, string> | undefined>;
-    readonly MSA: import("react-msaview").MSAParserType | null;
+    readonly MSA: import("msa-parsers").MSAParserType | null;
     readonly numColumns: number;
     readonly tree: import("react-msaview").NodeWithIds;
     readonly rowNames: string[];
@@ -967,7 +973,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     bgColor: boolean;
     colorSchemeName: string;
     showColumnStats: boolean;
-    msaFormat: import("react-msaview").MSAFormat | undefined;
+    msaFormat: import("msa-parsers").MSAFormat | undefined;
     drawLabels: boolean;
     labelsAlignRight: boolean;
     treeAreaWidth: number;
@@ -978,6 +984,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     autoTreeAreaWidth: boolean;
     id: string;
     showDomains: boolean;
+    showDomainLegend: boolean;
     hideGaps: boolean;
     allowedGappyness: number;
     subFeatureRows: boolean;
@@ -1080,6 +1087,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         tree?: string | undefined;
         msa?: string | undefined;
         treeMetadata?: string | undefined;
+        gff?: string | undefined;
     };
 } & import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export type JBrowsePluginMsaViewStateModel = ReturnType<typeof stateModelFactory>;