jbrowse-plugin-msaview 2.9.0 → 2.10.0

package/dist/LaunchMsaView/components/OrthologQuery/OrthologPanel.js

@@ -1,10 +1,11 @@
 import React, { useMemo, useState } from 'react';
-import { Checkbox, FormControlLabel, MenuItem, Typography } from '@mui/material';
+import { Typography } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
+import QuerySpeciesSelect from './QuerySpeciesSelect';
 import { orthologLaunchView } from './orthologLaunchView';
 import TextField2 from '../../../components/TextField2';
-import { COMMON_SPECIES } from '../../../utils/ncbiOrthologs';
+import { defaultMaxSpecies } from '../../../utils/ncbiOrthologs';
 import { getGeneDisplayName, getGeneIdentifiers, getLinearGenomeView, getTranscriptDisplayName, } from '../../util';
 import MsaAlgorithmSelect from '../BlastQuery/MsaAlgorithmSelect';
 import LaunchPanelContent from '../LaunchPanelContent';
@@ -15,23 +16,6 @@ const useStyles = makeStyles()({
     selectField: {
         width: 180,
     },
-    // A GRID, not a wrapping flex row of fixed-width items. The old form was three
-    // 160px columns inside a 560px box, which is five rows for thirteen species and
-    // eight for twenty-three -- and the checkbox list is the tallest thing in the
-    // dialog, so those rows are the dialog's height. Five auto-fitted columns is
-    // five rows for twenty-three, i.e. more species in less space, and it reflows
-    // rather than being pinned to a width the dialog may not have.
-    speciesBox: {
-        display: 'grid',
-        gridTemplateColumns: 'repeat(auto-fit, minmax(130px, 1fr))',
-        maxWidth: 700,
-        marginTop: 4,
-    },
-    // The label carries the row height; the default control padding is what makes
-    // 23 rows of it tall.
-    species: {
-        marginRight: 0,
-    },
 });
 const OrthologPanel = observer(function ({ handleClose, feature, model, }) {
     const { classes } = useStyles();
@@ -39,28 +23,24 @@ const OrthologPanel = observer(function ({ handleClose, feature, model, }) {
     const [launchViewError, setLaunchViewError] = useState();
     const [taxId, setTaxId] = useState(9606);
     const [msaAlgorithm, setMsaAlgorithm] = useState('clustalo');
-    const [excluded, setExcluded] = useState([]);
+    const [maxSpecies, setMaxSpecies] = useState(String(defaultMaxSpecies));
     const geneCandidates = useMemo(() => getGeneIdentifiers(feature), [feature]);
     const transcriptSelection = useTranscriptSelection({ feature, view });
     const { selectedTranscript, proteinSequence } = transcriptSelection;
     const e = transcriptSelection.error ?? launchViewError;
-    const taxa = COMMON_SPECIES.map(s => s.taxId).filter(t => !excluded.includes(t));
+    const rowCount = Number(maxSpecies);
+    const rowCountValid = Number.isInteger(rowCount) && rowCount >= 2;
     return (React.createElement(React.Fragment, null,
         React.createElement(LaunchPanelContent, { error: e },
-            React.createElement(Typography, { variant: "body2" }, "NCBI's precomputed orthologs, one gene per species, aligned at EBI in seconds rather than the 10+ minutes BLAST takes."),
+            React.createElement(Typography, { variant: "body2" }, "NCBI's precomputed orthologs, one gene per species, looked up rather than searched for. No BLAST job to queue."),
             React.createElement("div", null,
-                React.createElement(TextField2, { variant: "outlined", label: "Query species", className: classes.selectField, select: true, value: taxId, onChange: event => {
-                        setTaxId(Number(event.target.value));
-                    }, helperText: "the species this gene is from" }, COMMON_SPECIES.map(s => (React.createElement(MenuItem, { value: s.taxId, key: s.taxId }, s.label)))),
-                React.createElement(MsaAlgorithmSelect, { className: classes.selectField, value: msaAlgorithm, onChange: setMsaAlgorithm })),
-            React.createElement(Typography, { variant: "subtitle2", style: { marginTop: 8 } }, "Species to include (those without an ortholog are skipped)"),
-            React.createElement("div", { className: classes.speciesBox }, COMMON_SPECIES.map(s => (React.createElement(FormControlLabel, { className: classes.species, key: s.taxId, control: React.createElement(Checkbox, { checked: !excluded.includes(s.taxId), onChange: event => {
-                        setExcluded(event.target.checked
-                            ? excluded.filter(t => t !== s.taxId)
-                            : [...excluded, s.taxId]);
-                    } }), label: s.label })))),
+                React.createElement(QuerySpeciesSelect, { className: classes.selectField, value: taxId, onChange: setTaxId }),
+                React.createElement(MsaAlgorithmSelect, { className: classes.selectField, value: msaAlgorithm, onChange: setMsaAlgorithm }),
+                React.createElement(TextField2, { variant: "outlined", label: "Rows to align", className: classes.selectField, type: "number", value: maxSpecies, onChange: event => {
+                        setMaxSpecies(event.target.value);
+                    }, error: !rowCountValid, helperText: "the closest N species NCBI has" })),
             React.createElement(TranscriptSelector, { feature: feature, ...transcriptSelection })),
-        React.createElement(SubmitCancelActions, { submitDisabled: !proteinSequence || taxa.length < 2, onSubmit: () => {
+        React.createElement(SubmitCancelActions, { submitDisabled: !proteinSequence || !rowCountValid, onSubmit: () => {
                 try {
                     if (selectedTranscript) {
                         setLaunchViewError(undefined);
@@ -70,7 +50,7 @@ const OrthologPanel = observer(function ({ handleClose, feature, model, }) {
                             newViewTitle: `Orthologs - ${getGeneDisplayName(feature)} - ${getTranscriptDisplayName(selectedTranscript)}`,
                             orthologParams: {
                                 taxId,
-                                taxa,
+                                maxSpecies: rowCount,
                                 geneCandidates,
                                 msaAlgorithm,
                                 selectedTranscript,

package/dist/LaunchMsaView/components/OrthologQuery/QuerySpeciesSelect.d.ts

@@ -0,0 +1,15 @@
+import React from 'react';
+/**
+ * The species the query gene came from, as free text resolved against NCBI's
+ * taxonomy rather than picked from a fixed list.
+ *
+ * The resolved taxon is shown back as helper text, which is the whole point of
+ * resolving on a debounce instead of on submit: a typo resolves to some other
+ * organism rather than to nothing, and the only place that surfaces is the gene
+ * lookup, as "could not resolve NLRP1 in taxon 9986".
+ */
+export default function QuerySpeciesSelect({ value, onChange, className, }: {
+    value: number;
+    onChange: (taxId: number) => void;
+    className?: string;
+}): React.JSX.Element;

package/dist/LaunchMsaView/components/OrthologQuery/QuerySpeciesSelect.js

@@ -0,0 +1,67 @@
+import React, { useEffect, useState } from 'react';
+import TextField2 from '../../../components/TextField2';
+import { resolveTaxId } from '../../../utils/ncbiTaxonomy';
+import { fetchTaxonomyInfo } from '../../../utils/taxonomyNames';
+/**
+ * The species the query gene came from, as free text resolved against NCBI's
+ * taxonomy rather than picked from a fixed list.
+ *
+ * The resolved taxon is shown back as helper text, which is the whole point of
+ * resolving on a debounce instead of on submit: a typo resolves to some other
+ * organism rather than to nothing, and the only place that surfaces is the gene
+ * lookup, as "could not resolve NLRP1 in taxon 9986".
+ */
+export default function QuerySpeciesSelect({ value, onChange, className, }) {
+    const [text, setText] = useState('human');
+    const [resolved, setResolved] = useState();
+    const [error, setError] = useState();
+    useEffect(() => {
+        // read through a call rather than as a property: the cleanup writes it from
+        // another turn of the loop, and a bare `run.live` narrows to true after the
+        // first check, which reads to the compiler as a redundant second one
+        const run = { live: true };
+        const cancelled = () => !run.live;
+        async function lookup() {
+            try {
+                setError(undefined);
+                const taxId = await resolveTaxId(text);
+                if (cancelled()) {
+                    return;
+                }
+                if (!taxId) {
+                    setResolved(undefined);
+                    setError(new Error(`No NCBI taxon matches "${text}"`));
+                    return;
+                }
+                const info = (await fetchTaxonomyInfo([taxId])).get(taxId);
+                if (cancelled()) {
+                    return;
+                }
+                setResolved([info?.sciname, info?.commonName && `(${info.commonName})`]
+                    .filter(Boolean)
+                    .join(' ') || `taxon ${taxId}`);
+                onChange(taxId);
+            }
+            catch (e) {
+                if (!cancelled()) {
+                    setError(e);
+                }
+            }
+        }
+        const timer = setTimeout(() => {
+            void lookup();
+        }, 400);
+        return () => {
+            run.live = false;
+            clearTimeout(timer);
+        };
+        // onChange is a setState updater from the parent and stable in practice;
+        // including it would re-run the lookup on every parent render
+        // eslint-disable-next-line react-hooks/exhaustive-deps
+    }, [text]);
+    return (React.createElement(TextField2, { variant: "outlined", label: "Query species", className: className, value: text, onChange: event => {
+            setText(event.target.value);
+        }, error: !!error, helperText: error
+            ? `${error}`
+            : (resolved ?? `the species this gene is from (taxon ${value})`) }));
+}

package/dist/LaunchMsaView/index.js

@@ -4,6 +4,24 @@ import LaunchMsaViewDialog from './components/LaunchMsaViewDialog';
 function isDisplay(elt) {
     return elt.name === 'LinearBasicDisplay';
 }
+// Read off the clicked item rather than off the display.
+//
+// LinearBasicDisplay used to publish an `isGeneLike` getter and this gated on
+// it. jbrowse-components 684142b3 (2026-08-16) inlined that getter into its own
+// `contextMenuItems`, and every host built after it returns `undefined` here --
+// so the gate was never satisfied, `onClick` stayed undefined, and the item
+// silently left the right-click menu on every gene track. Nothing failed loudly:
+// the display still had contextMenuInfo and fetchFullFeature, and the menu still
+// opened with its own items in it.
+//
+// A predicate over the type we were already given cannot go the same way, and it
+// costs one comparison. Deliberately the same loose case-insensitive test the
+// host applies (`isGeneLikeType` in collapseIntronsMenu.ts): real GFFs carry
+// 'mRNA', 'lnc_RNA', 'protein_coding_gene', 'transcript'.
+function isGeneLikeType(type) {
+    const t = (type ?? '').toLowerCase();
+    return t.includes('gene') || t.includes('rna') || t.includes('transcript');
+}
 const GENE_LIKE_TYPES = new Set(['gene', 'mRNA', 'transcript']);
 function extendStateModel(stateModel) {
     return stateModel.views((self) => {
@@ -21,7 +39,7 @@ function extendStateModel(stateModel) {
                 const info = self.contextMenuInfo;
                 const fetchFullFeature = self.fetchFullFeature;
                 const legacyFeature = self.contextMenuFeature;
-                const onClick = info && fetchFullFeature && self.isGeneLike
+                const onClick = info && fetchFullFeature && isGeneLikeType(info.item.type)
                     ? () => {
                         fetchFullFeature(info.item.featureId, info.displayedRegionIndex)
                             .then(feature => {

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.js

@@ -1,12 +1,13 @@
 import { beforeEach, describe, expect, test, vi } from 'vitest';
 import { doLaunchOrthologs } from './doLaunchOrthologs';
 import { launchMSA } from '../utils/msa';
-import { COMMON_SPECIES, fetchOrthologRows, fetchProteinForGene, resolveGeneId, } from '../utils/ncbiOrthologs';
+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 taxa get asked for, what
-// becomes the QUERY row, and whether the row earns the Accession that drives the
-// CDD overlay -- so the real COMMON_SPECIES list and the real
-// cleanProteinSequence stay in the picture.
+// 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(),
@@ -14,17 +15,21 @@ vi.mock('../utils/ncbiOrthologs', async (importOriginal) => ({
     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 = {}) {
@@ -35,18 +40,29 @@ function params(extra = {}) {
         ...extra,
     };
 }
-// What fetchOrthologRows was asked for, which is the only place the taxa
-// default is observable.
-function taxaAskedFor() {
-    return [...mockFetchRows.mock.calls[0][0].taxa].sort((a, b) => a - b);
+// 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).QUERY;
+    return JSON.parse(result.treeMetadata)[queryRowName()];
+}
+function queryRowName() {
+    return mockLaunchMSA.mock.calls[0][0].sequence.split('\n')[0].slice(1);
 }
 beforeEach(() => {
     vi.clearAllMocks();
@@ -54,26 +70,84 @@ beforeEach(() => {
     mockFetchProtein.mockResolvedValue(REPRESENTATIVE);
     mockFetchRows.mockResolvedValue([]);
     mockLaunchMSA.mockResolvedValue({ msa: '', tree: '' });
+    mockFetchTaxonomy.mockResolvedValue(new Map([[HUMAN, { sciname: 'Homo sapiens', commonName: 'human' }]]));
 });
-describe('taxa', () => {
-    test('omitted asks for every species the dialog offers, less the query', async () => {
+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(taxaAskedFor()).toEqual(COMMON_SPECIES.map(s => s.taxId)
-            .filter(t => t !== HUMAN)
-            .sort((a, b) => a - b));
+        expect(rowRequest().taxa).toBeUndefined();
     });
-    test('given is taken as written, less the query', async () => {
+    test('given taxa is taken as written', async () => {
         await doLaunchOrthologs({
             self: makeModel(params({ taxa: [HUMAN, 10090, 9615] })),
         });
-        expect(taxaAskedFor()).toEqual([9615, 10090]);
+        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(taxaAskedFor()).toEqual([]);
+        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', () => {
+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);

package/dist/MsaViewPanel/model.d.ts

@@ -22,10 +22,17 @@ export interface OrthologParams {
     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;
@@ -48,7 +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]>;
@@ -61,10 +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]>;
@@ -515,7 +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: {
@@ -556,6 +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;
@@ -602,7 +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[];
@@ -964,7 +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;
@@ -975,6 +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;
@@ -1077,6 +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>;