jbrowse-plugin-msaview 5.1.0 → 5.1.1

package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.d.ts

@@ -2,12 +2,11 @@ import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 export default class BgzipFastaMsaAdapter extends BaseAdapter {
     configureP: Promise<BaseFeatureDataAdapter> | undefined;
-    refNamesP: Promise<string[]> | undefined;
+    msaRowsP: Promise<Map<string, string[]>> | undefined;
     configurePre(): Promise<BaseFeatureDataAdapter<import("@jbrowse/core/configuration").AnyConfigurationModel>>;
     configure(): Promise<BaseFeatureDataAdapter<import("@jbrowse/core/configuration").AnyConfigurationModel>>;
-    getMSARefs(): Promise<string[]>;
-    getMsaRegex(): RegExp;
-    refNameToMsaId(refName: string): string;
+    groupRows(): Promise<Map<string, string[]>>;
+    getMSARows(): Promise<Map<string, string[]>>;
     getMSAList(): Promise<string[]>;
     getMSA(id: string): Promise<import("@jbrowse/core/util").Feature[]>;
 }

package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js

@@ -22,30 +22,35 @@ export default class BgzipFastaMsaAdapter extends BaseAdapter {
         });
         return this.configureP;
     }
-    async getMSARefs() {
-        this.refNamesP ??= this.configure()
-            .then(adapter => adapter.getRefNames())
-            .catch((e) => {
-            this.refNamesP = undefined;
+    async groupRows() {
+        const adapter = await this.configure();
+        const separator = new RegExp(this.getConf('msaRegex'));
+        const rows = new Map();
+        for (const refName of await adapter.getRefNames()) {
+            const msaId = refName.split(separator)[0];
+            const group = rows.get(msaId);
+            if (group) {
+                group.push(refName);
+            }
+            else {
+                rows.set(msaId, [refName]);
+            }
+        }
+        return rows;
+    }
+    getMSARows() {
+        this.msaRowsP ??= this.groupRows().catch((e) => {
+            this.msaRowsP = undefined;
             throw e;
         });
-        return this.refNamesP;
-    }
-    getMsaRegex() {
-        return new RegExp(this.getConf('msaRegex'));
-    }
-    refNameToMsaId(refName) {
-        return refName.split(this.getMsaRegex())[0];
+        return this.msaRowsP;
     }
     async getMSAList() {
-        const refNames = await this.getMSARefs();
-        const list = new Set(refNames.map(name => this.refNameToMsaId(name)));
-        return [...list];
+        return [...(await this.getMSARows()).keys()];
     }
     async getMSA(id) {
         const adapter = await this.configure();
-        const refNames = await this.getMSARefs();
-        const rows = refNames.filter(refName => this.refNameToMsaId(refName) === id);
+        const rows = (await this.getMSARows()).get(id) ?? [];
         return firstValueFrom(adapter
             .getFeaturesInMultipleRegions(rows.map(refName => ({
             refName,

package/dist/LaunchMsaView/components/BlastQuery/BlastAutomaticPanel.js

@@ -46,14 +46,14 @@ const BlastAutomaticPanel = observer(function ({ handleClose, feature, model, ch
     const hitCountValid = Number.isInteger(hitCount) && hitCount >= 1;
     const isPhmmer = search.program === 'phmmer';
     const geneIds = useMemo(() => getGeneIdentifiers(feature), [feature]);
-    const { results: cachedResults, error: cachedResultsError } = useCachedBlastResults(geneIds);
+    const cached = useCachedBlastResults(geneIds);
     const transcriptSelection = useTranscriptSelection({
         feature,
         view,
         preferredTranscriptId,
     });
     const { selectedTranscript, proteinSequence, sequenceStatus } = transcriptSelection;
-    const e = transcriptSelection.error ?? launchError ?? cachedResultsError;
+    const e = transcriptSelection.error ?? launchError ?? cached.error;
     return (React.createElement(React.Fragment, null,
         React.createElement(LaunchPanelContent, { error: e },
             children,
@@ -80,11 +80,11 @@ const BlastAutomaticPanel = observer(function ({ handleClose, feature, model, ch
                     : 'The hits come back from EBI and are then run through the chosen aligner.',
                 ' ',
                 "The EBI queue is the wait, and it runs from seconds to many minutes."),
-            cachedResults.length > 0 ? (React.createElement(Accordion, { className: classes.cachedResultsAccordion },
+            cached.results.length > 0 ? (React.createElement(Accordion, { className: classes.cachedResultsAccordion },
                 React.createElement(AccordionSummary, { expandIcon: React.createElement(ExpandMoreIcon, null) },
                     React.createElement(Typography, null, "Previous BLAST Results")),
                 React.createElement(AccordionDetails, null,
-                    React.createElement(CachedBlastResults, { model: model, handleClose: handleClose, feature: feature })))) : null),
+                    React.createElement(CachedBlastResults, { model: model, handleClose: handleClose, feature: feature, cached: cached })))) : null),
         React.createElement(SubmitCancelActions, { model: model, hint: React.createElement(SequenceStatusMessage, { status: sequenceStatus }), submitDisabled: !proteinSequence || !hitCountValid, onSubmit: placement => {
                 if (selectedTranscript) {
                     const blastParams = search.program === 'phmmer'

package/dist/LaunchMsaView/components/BlastQuery/BlastPanel.js

@@ -24,7 +24,7 @@ export default function BlastPanel({ handleClose, model, feature, preferredTrans
     const { classes } = useStyles();
     const Panel = panelMap[lookupMethod];
     return (React.createElement(React.Fragment, null,
-        React.createElement(Tooltip, { title: `EBI settings — jobs are submitted with ${ebiEmail}` },
+        React.createElement(Tooltip, { title: `EBI settings — jobs are submitted with ${ebiEmail.trim() || DEFAULT_EBI_EMAIL}` },
             React.createElement(IconButton, { className: classes.settingsButton, "aria-label": "EBI settings", size: "small", onClick: () => {
                     setSettingsOpen(true);
                 } },

package/dist/LaunchMsaView/components/BlastQuery/CachedBlastResults.d.ts

@@ -1,5 +1,6 @@
 import React from 'react';
 import type { CachedBlastResult } from '../../../utils/blastCache';
+import type { useCachedBlastResults } from './useCachedBlastResults';
 import type { AbstractTrackModel, Feature } from '@jbrowse/core/util';
 /**
  * How the row was produced: `uniprotkb_swissprot / blastp / clustalo`, or
@@ -12,9 +13,11 @@ import type { AbstractTrackModel, Feature } from '@jbrowse/core/util';
  * queried NCBI directly and blastp/quick-blastp was a real choice.
  */
 export declare function describeSearch(result: CachedBlastResult): string;
-declare const CachedBlastResults: ({ model, handleClose, feature, }: {
+declare const CachedBlastResults: ({ model, handleClose, feature, cached: { results, handleDelete, handleClearAll }, }: {
     model: AbstractTrackModel;
     handleClose: () => void;
     feature: Feature;
+    /** the panel's own listing, so clearing it here empties it there too */
+    cached: ReturnType<typeof useCachedBlastResults>;
 }) => React.JSX.Element;
 export default CachedBlastResults;

package/dist/LaunchMsaView/components/BlastQuery/CachedBlastResults.js

@@ -1,13 +1,12 @@
-import React, { useMemo, useState } from 'react';
+import React, { useState } from 'react';
 import { ErrorMessage } from '@jbrowse/core/ui';
 import DeleteIcon from '@mui/icons-material/Delete';
 import { Button, IconButton, List, ListItem, ListItemButton, ListItemText, Typography, } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
-import { featureMatchesId, getGeneIdentifiers, getLinearGenomeView, getSortedTranscriptFeatures, } from '../../util';
+import { featureMatchesId, getLinearGenomeView, getSortedTranscriptFeatures, } from '../../util';
 import { builtAlignmentLook, launchConnectedView } from '../launchConnectedView';
 import { useLaunchPlacement } from '../launchPlacement';
-import { useCachedBlastResults } from './useCachedBlastResults';
 const useStyles = makeStyles()({
     header: {
         display: 'flex',
@@ -50,13 +49,11 @@ export function describeSearch(result) {
         .filter(Boolean)
         .join(' / ');
 }
-const CachedBlastResults = observer(function ({ model, handleClose, feature, }) {
+const CachedBlastResults = observer(function ({ model, handleClose, feature, cached: { results, handleDelete, handleClearAll }, }) {
     const { classes } = useStyles();
     const view = getLinearGenomeView(model);
     const [operationError, setOperationError] = useState();
     const [sideBySide] = useLaunchPlacement();
-    const geneIds = useMemo(() => getGeneIdentifiers(feature), [feature]);
-    const { results, error, isLoading, handleDelete, handleClearAll } = useCachedBlastResults(geneIds);
     const handleUseCached = (cached) => {
         // the cached query row is the plugin's default `QUERY`, translated from
         // the transcript stored as transcriptId, so that transcript relinks it
@@ -75,8 +72,8 @@ const CachedBlastResults = observer(function ({ model, handleClose, feature, })
             setOperationError(e);
         });
     };
-    const displayError = error ?? operationError;
-    return displayError ? (React.createElement(ErrorMessage, { error: displayError })) : isLoading ? (React.createElement(Typography, null, "Loading cached results...")) : results.length === 0 ? (React.createElement(Typography, { color: "textSecondary" }, "No cached BLAST results found for this gene. Run a BLAST query to cache results.")) : (React.createElement("div", null,
+    return (React.createElement("div", null,
+        operationError ? React.createElement(ErrorMessage, { error: operationError }) : null,
         React.createElement("div", { className: classes.header },
             React.createElement(Typography, { variant: "subtitle1" },
                 "Cached BLAST Results (",

package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js

@@ -22,13 +22,14 @@ import { useTranscriptSelection } from '../useTranscriptSelection';
  */
 function useMsaFileText(location) {
     const debounced = useDebounced(location, 500);
-    const { data } = useFetch(debounced ? [JSON.stringify(debounced), 'msa-file-text'] : null, () => openLocation(debounced).readFile('utf8'));
-    return data ?? '';
+    const { data, error, isLoading } = useFetch(debounced ? [JSON.stringify(debounced), 'msa-file-text'] : null, () => openLocation(debounced).readFile('utf8'));
+    return {
+        text: data ?? '',
+        error,
+        isLoading: isLoading || debounced !== location,
+    };
 }
 const useStyles = makeStyles()({
-    textAreaFont: {
-        fontFamily: 'Courier New',
-    },
     inputContainer: {
         marginBottom: 30,
     },
@@ -54,9 +55,9 @@ const ManualMSALoader = observer(function PreLoadedMSA2({ model, feature, handle
         preferredTranscriptId,
     });
     const { selectedTranscript, proteinSequence, error, sequenceStatus } = transcriptSelection;
-    const msaFileText = useMsaFileText(inputMethod === 'file' ? msaFileLocation : undefined);
-    const queryRow = useQueryRowName(inputMethod === 'file' ? msaFileText : msaText, proteinSequence);
-    const e = launchError ?? error;
+    const msaFile = useMsaFileText(inputMethod === 'file' ? msaFileLocation : undefined);
+    const queryRow = useQueryRowName(inputMethod === 'file' ? msaFile.text : msaText, proteinSequence);
+    const e = launchError ?? error ?? msaFile.error;
     return (React.createElement(React.Fragment, null,
         React.createElement(LaunchPanelContent, { error: e },
             React.createElement(FormControl, { component: "fieldset" },
@@ -77,7 +78,7 @@ const ManualMSALoader = observer(function PreLoadedMSA2({ model, feature, handle
             React.createElement(TranscriptSelector, { feature: feature, ...transcriptSelection }),
             React.createElement(QueryRowSelector, { ...queryRow })),
         React.createElement(SubmitCancelActions, { model: model, hint: React.createElement(SequenceStatusMessage, { status: sequenceStatus }), submitDisabled: !selectedTranscript ||
-                (inputMethod === 'file' && !msaFileLocation) ||
+                (inputMethod === 'file' && (!msaFileLocation || msaFile.isLoading)) ||
                 (inputMethod === 'text' && !msaText.trim()), onSubmit: placement => {
                 if (selectedTranscript) {
                     submit(() => launchConnectedView({

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

@@ -8,7 +8,16 @@ async function describeTaxon(query, signal) {
     if (!taxId) {
         throw new Error(`No NCBI taxon matches "${query}"`);
     }
-    const info = (await fetchTaxonomyInfo([taxId], signal)).get(taxId);
+    const failures = [];
+    const info = (await fetchTaxonomyInfo([taxId], signal, e => {
+        failures.push(e);
+    })).get(taxId);
+    // a throttle would otherwise read as a taxon NCBI has no name for
+    if (!info && failures.length > 0) {
+        throw new Error(`NCBI did not answer for the name of taxon ${taxId}`, {
+            cause: failures[0],
+        });
+    }
     const label = [info?.sciname, info?.commonName && `(${info.commonName})`]
         .filter(Boolean)
         .join(' ');

package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js

@@ -7,7 +7,7 @@ import { makeStyles } from 'tss-react/mui';
 import TextField2 from '../../../components/TextField2';
 import { useFetch } from '../../../utils/useFetch';
 import { resolveQueryRowName, useQueryRowName } from '../../useQueryRowName';
-import { getGeneDisplayName, getLinearGenomeView, getTranscriptDisplayName, } from '../../util';
+import { featureMatchesId, getGeneDisplayName, getLinearGenomeView, getTranscriptDisplayName, } from '../../util';
 import LaunchPanelContent from '../LaunchPanelContent';
 import QueryRowSelector from '../QueryRowSelector';
 import SequenceStatusMessage from '../SequenceStatus';
@@ -39,11 +39,16 @@ const PreLoadedMSA = observer(function ({ model, feature, handleClose, preferred
         validIds: msaList,
         preferredTranscriptId,
     });
-    const { selectedId, selectedTranscript, proteinSequence, sequenceStatus } = transcriptSelection;
-    const { data: msaData, isLoading: msaDataLoading, error: msaDataFetchError, } = useFetch(selectedId && selectedDataset && msaList
-        ? `${selectedDataset.datasetId}-${selectedId}-msa`
+    const { selectedTranscript, proteinSequence, sequenceStatus } = transcriptSelection;
+    // the dataset's name for this transcript, which a track is free not to use
+    // as the feature's own id
+    const msaId = selectedTranscript
+        ? msaList?.find(id => featureMatchesId(selectedTranscript, id))
+        : undefined;
+    const { data: msaData, isLoading: msaDataLoading, error: msaDataFetchError, } = useFetch(msaId && selectedDataset
+        ? `${selectedDataset.datasetId}-${msaId}-msa`
         : null, () => fetchMSA({
-        msaId: selectedId,
+        msaId: msaId,
         config: selectedDataset.adapter,
         pluginManager,
     }));
@@ -59,7 +64,7 @@ const PreLoadedMSA = observer(function ({ model, feature, handleClose, preferred
     // that convention does carry the row, so it is worth falling back to when the
     // residues do not match closely enough to find it -- but only when the
     // alignment really has it, which is the check the old code never made.
-    const querySeqName = resolveQueryRowName(queryRow, `${selectedId}_${assemblyNames[0] ?? ''}`);
+    const querySeqName = resolveQueryRowName(queryRow, `${msaId ?? ''}_${assemblyNames[0] ?? ''}`);
     const e = msaListFetchError ??
         msaDataFetchError ??
         transcriptSelection.error ??
@@ -70,7 +75,7 @@ const PreLoadedMSA = observer(function ({ model, feature, handleClose, preferred
                     setSelectedDatasetId(event.target.value);
                 } }, datasets?.map(d => (React.createElement(MenuItem, { key: d.datasetId, value: d.datasetId }, d.name)))),
             selectedDataset ? (React.createElement("div", { className: classes.selectedContainer },
-                !msaListLoading && msaDataLoading ? (React.createElement(LoadingEllipses, { variant: "h6", message: `Loading MSA for ${getTranscriptDisplayName(selectedTranscript) || selectedId}` })) : null,
+                !msaListLoading && msaDataLoading ? (React.createElement(LoadingEllipses, { variant: "h6", message: `Loading MSA for ${getTranscriptDisplayName(selectedTranscript) || msaId}` })) : null,
                 msaListLoading ? (React.createElement(LoadingEllipses, { variant: "h6", message: `Loading available MSAs for (${selectedDataset.name})` })) : null,
                 msaList ? (React.createElement("div", null,
                     React.createElement(SanitizedHTML, { html: selectedDataset.description }),

package/dist/LaunchMsaView/components/SubmitCancelActions.d.ts

@@ -1,7 +1,7 @@
 import React from 'react';
 import type { MsaViewPlacement } from '../../utils/workspaces';
 import type { AbstractTrackModel } from '@jbrowse/core/util';
-export default function SubmitCancelActions({ onSubmit, onCancel, submitDisabled, hint, submitLabel, cancelLabel, model, }: {
+export default function SubmitCancelActions({ onSubmit, onCancel, submitDisabled, hint, submitLabel, model, }: {
     /** handed the placement the box states, so no launch re-reads storage */
     onSubmit: (placement: MsaViewPlacement) => void;
     onCancel: () => void;
@@ -9,7 +9,6 @@ export default function SubmitCancelActions({ onSubmit, onCancel, submitDisabled
     /** why Submit is grey, shown beside it */
     hint?: React.ReactNode;
     submitLabel?: string;
-    cancelLabel?: string;
     /** omitted by a panel that submits something other than a view launch */
     model?: AbstractTrackModel;
 }): React.JSX.Element;

package/dist/LaunchMsaView/components/SubmitCancelActions.js

@@ -19,7 +19,7 @@ function PlacementToggle({ checked, onChange, }) {
                 onChange(event.target.checked);
             } }) }));
 }
-export default function SubmitCancelActions({ onSubmit, onCancel, submitDisabled, hint, submitLabel = 'Submit', cancelLabel = 'Cancel', model, }) {
+export default function SubmitCancelActions({ onSubmit, onCancel, submitDisabled, hint, submitLabel = 'Submit', model, }) {
     const [sideBySide, setSideBySide] = useLaunchPlacement();
     // The stored value is what the next dialog opens on, so it is written on
     // submit rather than on the click: a dialog the user backed out of must not
@@ -46,5 +46,5 @@ export default function SubmitCancelActions({ onSubmit, onCancel, submitDisabled
                 } }, submitLabel),
             React.createElement(Button, { sx: { flexShrink: 0 }, color: "secondary", variant: "contained", onClick: () => {
                     onCancel();
-                } }, cancelLabel))));
+                } }, "Cancel"))));
 }

package/dist/LaunchMsaView/components/TabPanel.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-export default function TabPanel({ children, value, index, ...other }: {
+export default function TabPanel({ children, value, index, }: {
     children?: React.ReactNode;
     index: number | string;
     value: number | string;

package/dist/LaunchMsaView/components/TabPanel.js

@@ -7,11 +7,11 @@ import React, { useState } from 'react';
 // Lazy on first visit rather than mounted up front, because a panel mounts
 // fetches of its own: rendering all four on open would query the MSA dataset
 // adapter and the BLAST cache for tabs nobody looked at.
-export default function TabPanel({ children, value, index, ...other }) {
+export default function TabPanel({ children, value, index, }) {
     const active = value === index;
     const [visited, setVisited] = useState(active);
     if (active && !visited) {
         setVisited(true);
     }
-    return (React.createElement("div", { role: "tabpanel", hidden: !active, ...other }, visited || active ? children : null));
+    return (React.createElement("div", { role: "tabpanel", hidden: !active }, visited || active ? children : null));
 }

package/dist/LaunchMsaView/components/TranscriptSelector.js

@@ -50,5 +50,7 @@ export default function TranscriptSelector({ feature, options, selectedId, selec
                 ? `>${getTranscriptDisplayName(selectedTranscript)}\n${proteinSequence}`
                 : sequenceStatus === 'missing'
                     ? 'This transcript has no coding sequence, so there is nothing to translate.'
-                    : 'Loading...' })) : null));
+                    : sequenceStatus === 'error'
+                        ? 'The sequence could not be fetched.'
+                        : 'Loading...' })) : null));
 }

package/dist/LaunchMsaView/components/launchConnectedView.js

@@ -1,4 +1,4 @@
-import { useState } from 'react';
+import { useRef, useState } from 'react';
 import { getSession } from '@jbrowse/core/util';
 import { launchMsaView } from '../../utils/launchMsaView';
 /** how a view whose alignment the plugin builds opens */
@@ -22,11 +22,18 @@ export function launchConnectedView({ view, feature, placement, ...snapshot }) {
 /** runs a panel's launch, closing the dialog on success and keeping the error */
 export function useLaunchSubmit(handleClose) {
     const [launchError, setLaunchError] = useState();
+    // the first launch loads the view's chunk, which is long enough to click twice
+    const launching = useRef(false);
     return {
         launchError,
         submit: (launch) => {
+            if (launching.current) {
+                return;
+            }
+            launching.current = true;
             setLaunchError(undefined);
             launch().then(handleClose, (e) => {
+                launching.current = false;
                 console.error(e);
                 setLaunchError(e);
             });

package/dist/LaunchMsaView/components/useFeatureSequence.js

@@ -1,3 +1,4 @@
+import { useMemo } from 'react';
 import { getSession } from '@jbrowse/core/util';
 import { translateTranscript } from '@jbrowse/core/util/translateTranscript';
 import { useFetch } from '../../utils/useFetch';
@@ -16,11 +17,12 @@ export function useFeatureSequence({ view, feature, }) {
             session: getSession(view),
         });
     });
+    const proteinSequence = useMemo(() => sequence && feature
+        ? (translateTranscript({ transcript: feature, ...sequence })?.protein ??
+            '')
+        : '', [sequence, feature]);
     return {
-        proteinSequence: sequence && feature
-            ? (translateTranscript({ transcript: feature, ...sequence })?.protein ??
-                '')
-            : '',
+        proteinSequence,
         sequence,
         error,
         isLoading,

package/dist/LaunchMsaView/useQueryRowName.js

@@ -24,7 +24,11 @@ export function useQueryRowName(msaText, proteinSequence) {
     // parsing runs on every keystroke in the paste box otherwise, and an
     // alignment of a few hundred rows is not free
     const { names, match } = useMemo(() => findQueryRow(msaText, proteinSequence), [msaText, proteinSequence]);
-    const querySeqName = override ?? match?.name ?? '';
+    // a row picked from one alignment says nothing about the next one pasted
+    const picked = override !== undefined && (names.length === 0 || names.includes(override))
+        ? override
+        : undefined;
+    const querySeqName = picked ?? match?.name ?? '';
     return {
         detected: match,
         names,
@@ -33,6 +37,6 @@ export function useQueryRowName(msaText, proteinSequence) {
         // taken at face value, residue 1 to residue 1
         querySeqOffset: querySeqName === match?.name ? match.offset : 0,
         setQuerySeqName: setOverride,
-        isAutoDetected: override === undefined && !!match,
+        isAutoDetected: picked === undefined && !!match,
     };
 }

package/dist/LaunchMsaView/useQueryRowName.test.js

@@ -20,6 +20,17 @@ describe('useQueryRowName', () => {
         expect(result.current.querySeqName).toBe('other');
         expect(result.current.querySeqOffset).toBe(0);
     });
+    // the pick outlived the alignment it was made in, and the launch then named
+    // a row the new one does not have
+    test('a picked row is dropped once the alignment no longer has it', () => {
+        const { result, rerender } = renderHook(({ msa }) => useQueryRowName(msa, protein), { initialProps: { msa: trimmed } });
+        act(() => {
+            result.current.setQuerySeqName('other');
+        });
+        rerender({ msa: trimmed.replace('>other', '>renamed') });
+        expect(result.current.querySeqName).toBe('aligned_query');
+        expect(result.current.isAutoDetected).toBe(true);
+    });
 });
 // a pre-loaded dataset names its rows by a convention of its own, and the
 // residues can be too diverged for detection to find the row that is right

package/dist/MsaViewPanel/afterCreateAutoruns.d.ts

@@ -8,22 +8,12 @@ export declare function loadStoredData(self: JBrowsePluginMsaViewModel): void;
  * refusing IndexedDB fails once rather than in a loop.
  */
 export declare function storeDataToIndexedDB(self: JBrowsePluginMsaViewModel): void;
-/**
- * Same shape as launchBlastIfNeeded, for the ortholog path: the params ARE the
- * request, and `launchCompleted` is what marks it done. They are left in place
- * either way -- on failure so the error stays attributable to a specific
- * request, and on success because they are the only durable statement of what
- * the view is, which is what a stored alignment that expired is rebuilt from.
- * The autorun tracks those two reads alone, so nothing refires until a new
- * request replaces them or a retry clears the mark.
- */
 export declare function launchOrthologsIfNeeded(self: JBrowsePluginMsaViewModel): void;
 export declare function launchBlastIfNeeded(self: JBrowsePluginMsaViewModel): void;
 /**
- * Once an accession-bearing alignment is present (fresh from BLAST or restored
- * from cache), fetch NCBI CDD domains for those accessions and overlay them.
- * Runs once per view; the domainsRequested guard prevents refiring when NCBI
- * returns no domains (which leaves the annotation list empty).
+ * Once an alignment whose rows carry accessions is present, fetch NCBI CDD
+ * domains for them and overlay them. `domainsRequested` makes this once per
+ * view, so NCBI returning no domains does not refire it.
  */
 export declare function autoLoadProteinDomains(self: JBrowsePluginMsaViewModel): void;
 export declare function processInit(self: JBrowsePluginMsaViewModel): void;