jbrowse-plugin-msaview 2.2.1 → 2.2.3

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

@@ -1,15 +1,19 @@
-import React, { useEffect, useState } from 'react';
-import { ErrorMessage } from '@jbrowse/core/ui';
-import { getContainingView, getSession, } from '@jbrowse/core/util';
-import { Button, DialogActions, DialogContent, Typography } from '@mui/material';
+import React, { useEffect, useMemo, useState } from 'react';
+import { readConfObject } from '@jbrowse/core/configuration';
+import { ErrorMessage, LoadingEllipses, SanitizedHTML } from '@jbrowse/core/ui';
+import { getContainingView, getEnv, getSession, } from '@jbrowse/core/util';
+import { Button, DialogActions, DialogContent, MenuItem } from '@mui/material';
 import { observer } from 'mobx-react';
+import useSWR from 'swr';
 import { makeStyles } from 'tss-react/mui';
-import { fetchGeneList } from './fetchGeneList';
-import { preCalculatedLaunchView } from './preCalculatedLaunchView';
-import ExternalLink from '../../../ExternalLink';
+import TextField2 from '../../../components/TextField2';
 import { getGeneDisplayName, getId, getTranscriptFeatures } from '../../util';
 import TranscriptSelector from '../TranscriptSelector';
 import { useFeatureSequence } from '../useFeatureSequence';
+import { swrFlags } from './consts';
+import { fetchMSA, fetchMSAList } from './fetchMSAData';
+import { findValidTranscriptId } from './findValidTranscriptId';
+import { preCalculatedLaunchView } from './preCalculatedLaunchView';
 const useStyles = makeStyles()({
     dialogContent: {
         width: '80em',
@@ -19,70 +23,90 @@ const PreLoadedMSA = observer(function PreLoadedMSA2({ model, feature, handleClo
     const session = getSession(model);
     const view = getContainingView(model);
     const { classes } = useStyles();
-    const [error1, setError] = useState();
-    const [geneNameList, setGeneNameList] = useState();
-    useEffect(() => {
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
-        ;
-        (async () => {
-            try {
-                const data = await fetchGeneList();
-                setGeneNameList(data);
-                const set = new Set(data);
-                const options = getTranscriptFeatures(feature);
-                const ret = options.find(val => set.has(getId(val)));
-                if (ret) {
-                    setUserSelection(getId(ret));
-                }
-            }
-            catch (e) {
-                console.error(e);
-                setError(e);
-            }
-        })();
-    }, [feature]);
-    const validSet = new Set(geneNameList);
-    const options = getTranscriptFeatures(feature);
-    const ret = options.find(val => validSet.has(getId(val)));
-    const [userSelection, setUserSelection] = useState(getId(options[0]));
-    const selectedTranscript = options.find(val => getId(val) === userSelection);
-    const { proteinSequence, error: error2 } = useFeatureSequence({
+    const { pluginManager } = getEnv(model);
+    const { assemblyNames } = view;
+    const transcripts = getTranscriptFeatures(feature);
+    const [selectedTranscriptId, setSelectedTranscriptId] = useState(getId(transcripts[0]));
+    const [viewError, setViewError] = useState();
+    const selectedTranscript = selectedTranscriptId
+        ? transcripts.find(val => getId(val) === selectedTranscriptId)
+        : undefined;
+    const { proteinSequence, error: proteinSequenceError } = useFeatureSequence({
         view,
         feature: selectedTranscript,
     });
-    const e = error1 ?? error2;
+    const { jbrowse } = session;
+    const datasets = readConfObject(jbrowse, ['msa', 'datasets']);
+    const [selectedDatasetId, setSelectedDatasetId] = useState(datasets?.[0]?.datasetId);
+    const selectedDataset = datasets?.find(d => d.datasetId === selectedDatasetId);
+    const { data: msaList, isLoading: msaListLoading, error: msaListFetchError, } = useSWR(selectedDatasetId ? `${selectedDatasetId}-msa-list` : 'none-msa-list', () => selectedDataset
+        ? fetchMSAList({
+            config: selectedDataset.adapter,
+            pluginManager,
+        })
+        : undefined, swrFlags);
+    const { data: msaData, isLoading: msaDataLoading, error: msaDataFetchError, } = useSWR(selectedTranscriptId && selectedDatasetId
+        ? `${selectedTranscriptId}-${selectedTranscriptId}-${msaList?.length}-msa`
+        : 'none-msa', () => selectedTranscriptId && selectedDataset && msaList
+        ? fetchMSA({
+            msaId: selectedTranscriptId,
+            config: selectedDataset.adapter,
+            pluginManager,
+        })
+        : undefined, swrFlags);
+    const validSet = useMemo(() => new Set(msaList), [msaList]);
+    // Update selectedTranscriptId when msaList changes
+    useEffect(() => {
+        if (msaList && msaList.length > 0) {
+            const validId = findValidTranscriptId({
+                transcriptsList: transcripts,
+                validMsaList: msaList,
+            });
+            if (validId && validId !== selectedTranscriptId) {
+                setSelectedTranscriptId(validId);
+            }
+        }
+    }, [msaList, transcripts, selectedTranscriptId]);
+    const e = msaListFetchError ?? msaDataFetchError ?? proteinSequenceError ?? viewError;
+    if (e) {
+        console.error(e);
+    }
     return (React.createElement(React.Fragment, null,
         React.createElement(DialogContent, { className: classes.dialogContent },
             e ? React.createElement(ErrorMessage, { error: e }) : null,
-            React.createElement(Typography, null,
-                "The source data for these multiple sequence alignments is from",
-                ' ',
-                React.createElement(ExternalLink, { href: "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz100way/alignments/" }, "knownCanonical.multiz100way.protAA.fa.gz")),
-            geneNameList && !ret ? (React.createElement(Typography, { color: "error" }, "No MSA data for this gene found")) : null,
-            React.createElement(TranscriptSelector, { feature: feature, options: options, selectedTranscriptId: userSelection, onTranscriptChange: setUserSelection, proteinSequence: proteinSequence, validSet: validSet })),
+            React.createElement(TextField2, { select: true, label: "Select MSA dataset", value: selectedDatasetId, onChange: event => {
+                    setSelectedDatasetId(event.target.value);
+                } }, datasets && datasets.length > 0 ? (datasets.map(d => (React.createElement(MenuItem, { key: d.datasetId, value: d.datasetId }, d.name)))) : (React.createElement(MenuItem, null, "No MSA datasets found"))),
+            selectedDataset ? (React.createElement("div", { style: { marginTop: 50 } },
+                !msaListLoading && msaDataLoading ? (React.createElement(LoadingEllipses, { variant: "h6", message: `Loading MSA for (${selectedTranscriptId})` })) : null,
+                msaListLoading ? (React.createElement(LoadingEllipses, { variant: "h6", message: `Loading available MSAs for (${selectedDataset.name})` })) : null,
+                msaList ? (React.createElement("div", null,
+                    React.createElement(SanitizedHTML, { html: selectedDataset.description }),
+                    React.createElement(TranscriptSelector, { feature: feature, options: transcripts, selectedTranscriptId: selectedTranscriptId, onTranscriptChange: setSelectedTranscriptId, proteinSequence: proteinSequence, validSet: validSet }))) : null)) : null),
         React.createElement(DialogActions, null,
-            React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
-                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
-                    ;
-                    (async () => {
-                        try {
-                            if (!ret) {
-                                return;
-                            }
-                            await preCalculatedLaunchView({
-                                userSelection,
-                                session,
-                                newViewTitle: getGeneDisplayName(ret),
-                                view,
-                                feature: ret,
-                            });
-                            handleClose();
-                        }
-                        catch (e) {
-                            console.error(e);
-                            setError(e);
+            React.createElement(Button, { color: "primary", variant: "contained", disabled: !selectedTranscript || !msaData?.length, onClick: () => {
+                    try {
+                        if (!selectedTranscript || !msaData) {
+                            return;
                         }
-                    })();
+                        const querySeqName = `${selectedTranscriptId}_${assemblyNames[0]}`;
+                        preCalculatedLaunchView({
+                            session,
+                            newViewTitle: getGeneDisplayName(selectedTranscript),
+                            view,
+                            querySeqName,
+                            feature: selectedTranscript,
+                            data: {
+                                msa: msaData
+                                    .map(r => `>${r.get('refName')}\n${r.get('seq')}`)
+                                    .join('\n'),
+                            },
+                        });
+                        handleClose();
+                    }
+                    catch (e) {
+                        setViewError(e);
+                    }
                 } }, "Submit"),
             React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
                     handleClose();

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

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package/dist/LaunchMsaView/components/PreLoadedMSA/consts.d.ts

@@ -0,0 +1,7 @@
+export declare const swrFlags: {
+    revalidateOnFocus: boolean;
+    revalidateOnReconnect: boolean;
+    refreshWhenHidden: boolean;
+    refreshWhenOffline: boolean;
+    shouldRetryOnError: boolean;
+};

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

@@ -0,0 +1,8 @@
+export const swrFlags = {
+    revalidateOnFocus: false,
+    revalidateOnReconnect: false,
+    refreshWhenHidden: false,
+    refreshWhenOffline: false,
+    shouldRetryOnError: false,
+};
+//# sourceMappingURL=consts.js.map

package/dist/LaunchMsaView/components/PreLoadedMSA/consts.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"consts.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/PreLoadedMSA/consts.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,QAAQ,GAAG;IACtB,iBAAiB,EAAE,KAAK;IACxB,qBAAqB,EAAE,KAAK;IAC5B,iBAAiB,EAAE,KAAK;IACxB,kBAAkB,EAAE,KAAK;IACzB,kBAAkB,EAAE,KAAK;CAC1B,CAAA"}

package/dist/LaunchMsaView/components/PreLoadedMSA/fetchMSAData.d.ts

@@ -0,0 +1,12 @@
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { Feature } from '@jbrowse/core/util';
+import type PluginManager from '@jbrowse/core/PluginManager';
+export declare function fetchMSAList({ config, pluginManager, }: {
+    config: AnyConfigurationModel;
+    pluginManager: PluginManager;
+}): Promise<string[]>;
+export declare function fetchMSA({ config, pluginManager, msaId, }: {
+    config: AnyConfigurationModel;
+    pluginManager: PluginManager;
+    msaId: string;
+}): Promise<Feature[]>;

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

@@ -0,0 +1,12 @@
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
+export async function fetchMSAList({ config, pluginManager, }) {
+    const result = await getAdapter(pluginManager, 'msa', config);
+    // @ts-expect-error
+    return result.dataAdapter.getMSAList();
+}
+export async function fetchMSA({ config, pluginManager, msaId, }) {
+    const result = await getAdapter(pluginManager, 'msa', config);
+    // @ts-expect-error
+    return result.dataAdapter.getMSA(msaId);
+}
+//# sourceMappingURL=fetchMSAData.js.map

package/dist/LaunchMsaView/components/PreLoadedMSA/fetchMSAData.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"fetchMSAData.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/PreLoadedMSA/fetchMSAData.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,UAAU,EAAE,MAAM,8CAA8C,CAAA;AAKzE,MAAM,CAAC,KAAK,UAAU,YAAY,CAAC,EACjC,MAAM,EACN,aAAa,GAId;IACC,MAAM,MAAM,GAAG,MAAM,UAAU,CAAC,aAAa,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;IAE7D,mBAAmB;IACnB,OAAO,MAAM,CAAC,WAAW,CAAC,UAAU,EAAE,CAAA;AACxC,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,QAAQ,CAAC,EAC7B,MAAM,EACN,aAAa,EACb,KAAK,GAKN;IACC,MAAM,MAAM,GAAG,MAAM,UAAU,CAAC,aAAa,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;IAE7D,mBAAmB;IACnB,OAAO,MAAM,CAAC,WAAW,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;AACzC,CAAC"}

package/dist/LaunchMsaView/components/PreLoadedMSA/findValidTranscriptId.d.ts

@@ -0,0 +1,5 @@
+import type { Feature } from '@jbrowse/core/util';
+export declare function findValidTranscriptId({ transcriptsList, validMsaList, }: {
+    transcriptsList: Feature[];
+    validMsaList?: string[];
+}): string | null;

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

@@ -0,0 +1,16 @@
+import { getId } from '../../util';
+// Function to find a valid transcript ID that exists in the MSA list
+export function findValidTranscriptId({ transcriptsList, validMsaList, }) {
+    if (!validMsaList || validMsaList.length === 0) {
+        return null;
+    }
+    // Try to find a transcript ID that exists in the MSA list
+    for (const transcript of transcriptsList) {
+        const id = getId(transcript);
+        if (id && validMsaList.includes(id)) {
+            return id;
+        }
+    }
+    return null;
+}
+//# sourceMappingURL=findValidTranscriptId.js.map

package/dist/LaunchMsaView/components/PreLoadedMSA/findValidTranscriptId.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"findValidTranscriptId.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/PreLoadedMSA/findValidTranscriptId.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,YAAY,CAAA;AAIlC,qEAAqE;AACrE,MAAM,UAAU,qBAAqB,CAAC,EACpC,eAAe,EACf,YAAY,GAIb;IACC,IAAI,CAAC,YAAY,IAAI,YAAY,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAC/C,OAAO,IAAI,CAAA;IACb,CAAC;IAED,0DAA0D;IAC1D,KAAK,MAAM,UAAU,IAAI,eAAe,EAAE,CAAC;QACzC,MAAM,EAAE,GAAG,KAAK,CAAC,UAAU,CAAC,CAAA;QAC5B,IAAI,EAAE,IAAI,YAAY,CAAC,QAAQ,CAAC,EAAE,CAAC,EAAE,CAAC;YACpC,OAAO,EAAE,CAAA;QACX,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}

package/dist/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.d.ts

@@ -1,9 +1,12 @@
 import { AbstractSessionModel, Feature } from '@jbrowse/core/util';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-export declare function preCalculatedLaunchView({ userSelection, session, newViewTitle, view, feature, }: {
+export declare function preCalculatedLaunchView({ session, newViewTitle, view, feature, data, querySeqName, }: {
+    data: {
+        msa: string;
+    };
     session: AbstractSessionModel;
-    userSelection: string;
     newViewTitle: string;
     view: LinearGenomeViewModel;
     feature: Feature;
-}): Promise<void>;
+    querySeqName: string;
+}): void;

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

@@ -1,18 +1,9 @@
-import { ungzip } from 'pako';
-async function myfetch(url) {
-    const res = await fetch(url);
-    if (!res.ok) {
-        throw new Error(`HTTP ${res.status} fetching ${await res.text()}`);
-    }
-    const data = await res.arrayBuffer();
-    return new TextDecoder().decode(ungzip(data));
-}
-export async function preCalculatedLaunchView({ userSelection, session, newViewTitle, view, feature, }) {
-    const d = await myfetch(`https://jbrowse.org/demos/msaview/knownCanonical/${userSelection}.mfa.gz`);
+export function preCalculatedLaunchView({ session, newViewTitle, view, feature, data, querySeqName, }) {
     session.addView('MsaView', {
         type: 'MsaView',
         displayName: newViewTitle,
         treeAreaWidth: 200,
+        querySeqName,
         treeWidth: 100,
         drawNodeBubbles: false,
         labelsAlignRight: true,
@@ -20,15 +11,7 @@ export async function preCalculatedLaunchView({ userSelection, session, newViewT
         colWidth: 10,
         rowHeight: 12,
         colorSchemeName: 'percent_identity_dynamic',
-        treeFilehandle: {
-            uri: 'https://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz100way/hg38.100way.nh',
-        },
-        treeMetadataFilehandle: {
-            uri: 'https://s3.amazonaws.com/jbrowse.org/demos/app/species.json',
-        },
-        data: {
-            msa: d,
-        },
+        data,
         connectedViewId: view.id,
         connectedFeature: feature.toJSON(),
     });

package/dist/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.js.map

@@ -1 +1 @@
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+{"version":3,"file":"preCalculatedLaunchView.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.ts"],"names":[],"mappings":"AAIA,MAAM,UAAU,uBAAuB,CAAC,EACtC,OAAO,EACP,YAAY,EACZ,IAAI,EACJ,OAAO,EACP,IAAI,EACJ,YAAY,GAQb;IACC,OAAO,CAAC,OAAO,CAAC,SAAS,EAAE;QACzB,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,YAAY;QACzB,aAAa,EAAE,GAAG;QAClB,YAAY;QACZ,SAAS,EAAE,GAAG;QACd,eAAe,EAAE,KAAK;QACtB,gBAAgB,EAAE,IAAI;QACtB,aAAa,EAAE,KAAK;QACpB,QAAQ,EAAE,EAAE;QACZ,SAAS,EAAE,EAAE;QACb,eAAe,EAAE,0BAA0B;QAC3C,IAAI;QACJ,eAAe,EAAE,IAAI,CAAC,EAAE;QACxB,gBAAgB,EAAE,OAAO,CAAC,MAAM,EAAE;KACnC,CAAC,CAAA;AACJ,CAAC"}

package/dist/LaunchMsaView/components/PreLoadedMSA/types.d.ts

@@ -0,0 +1,7 @@
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export interface Dataset {
+    datasetId: string;
+    name: string;
+    description?: string;
+    adapter: AnyConfigurationModel;
+}

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

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=types.js.map

package/dist/LaunchMsaView/components/PreLoadedMSA/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/PreLoadedMSA/types.ts"],"names":[],"mappings":""}

package/dist/LaunchMsaView/components/TranscriptSelector.js

@@ -1,8 +1,8 @@
 import React, { useState } from 'react';
 import { Button, MenuItem } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
-import ReadOnlyTextField2 from '../../ReadOnlyTextField2';
-import TextField2 from '../../TextField2';
+import ReadOnlyTextField2 from '../../components/ReadOnlyTextField2';
+import TextField2 from '../../components/TextField2';
 import { getGeneDisplayName, getId, getTranscriptDisplayName, getTranscriptLength, } from '../util';
 const useStyles = makeStyles()({
     flex: {

package/dist/LaunchMsaView/components/TranscriptSelector.js.map

@@ -1 +1 @@
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+{"version":3,"file":"TranscriptSelector.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/TranscriptSelector.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAGvC,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAChD,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,kBAAkB,MAAM,qCAAqC,CAAA;AACpE,OAAO,UAAU,MAAM,6BAA6B,CAAA;AACpD,OAAO,EACL,kBAAkB,EAClB,KAAK,EACL,wBAAwB,EACxB,mBAAmB,GACpB,MAAM,SAAS,CAAA;AAEhB,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,IAAI,EAAE;QACJ,OAAO,EAAE,MAAM;KAChB;IACD,QAAQ,EAAE;QACR,QAAQ,EAAE,GAAG;KACd;CACF,CAAC,CAAA;AAEF,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,EACzC,OAAO,EACP,OAAO,EACP,oBAAoB,EACpB,kBAAkB,EAClB,eAAe,EACf,QAAQ,GAQT;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IACvD,MAAM,kBAAkB,GAAG,OAAO,CAAC,IAAI,CACrC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,oBAAoB,CAC1C,CAAA;IAEF,OAAO,CACL;QACE,6BAAK,SAAS,EAAE,OAAO,CAAC,IAAI;YAC1B,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,KAAK,EAAE,qBAAqB,kBAAkB,CAAC,OAAO,CAAC,EAAE,EACzD,MAAM,QACN,SAAS,EAAE,OAAO,CAAC,QAAQ,EAC3B,KAAK,EAAE,oBAAoB,EAC3B,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,kBAAkB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBACxC,CAAC,IAEA,OAAO;iBACL,QAAQ,CACP,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,mBAAmB,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,mBAAmB,CAAC,CAAC,CAAC,CAAC,GAAG,CAClE;iBACA,GAAG,CAAC,GAAG,CAAC,EAAE;gBACT,MAAM,KAAK,GAAG,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;gBACxD,MAAM,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,mBAAmB,CAAC,GAAG,CAAC,CAAA;gBAC7C,OAAO,CACL,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,EAAE,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE,EAAE,QAAQ,EAAE,CAAC,KAAK;oBACzD,wBAAwB,CAAC,GAAG,CAAC;;oBAAI,GAAG;;oBAAM,GAAG;oBAC7C,GAAG,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,EAAE;oBACjC,QAAQ,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,EAAE,CAC9C,CACZ,CAAA;YACH,CAAC,CAAC,CACO;YACb,6BAAK,KAAK,EAAE,EAAE,YAAY,EAAE,QAAQ,EAAE,UAAU,EAAE,EAAE,EAAE;gBACpD,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;wBACZ,eAAe,CAAC,CAAC,YAAY,CAAC,CAAA;oBAChC,CAAC,IAEA,YAAY,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,eAAe,CAC1C,CACL,CACF;QAEL,YAAY,IAAI,CACf,oBAAC,kBAAkB,IACjB,KAAK,EACH,eAAe;gBACb,CAAC,CAAC,IAAI,wBAAwB,CAAC,kBAAkB,CAAC,KAAK,eAAe,EAAE;gBACxE,CAAC,CAAC,YAAY,GAElB,CACH,CACA,CACJ,CAAA;AACH,CAAC"}

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

@@ -11,7 +11,7 @@ export declare function revlist(list: Feat[], seqlen: number): {
     end: number;
     type?: string;
 }[];
-export declare function getProteinSequenceFromFeature({ selectedTranscript, seq, }: {
+export declare function getProteinSequenceFromFeature({ feature, seq, }: {
     seq: string;
-    selectedTranscript: Feature;
+    feature: Feature;
 }): string;

package/dist/LaunchMsaView/components/calculateProteinSequence.js

@@ -20,8 +20,8 @@ export function revlist(list, seqlen) {
     }))
         .toSorted((a, b) => a.start - b.start);
 }
-export function getProteinSequenceFromFeature({ selectedTranscript, seq, }) {
-    const { subfeatures, start, strand } = selectedTranscript.toJSON();
+export function getProteinSequenceFromFeature({ feature, seq, }) {
+    const { subfeatures, start, strand } = feature.toJSON();
     const cds = dedupe(subfeatures
         ?.toSorted((a, b) => a.start - b.start)
         .map(sub => ({

package/dist/LaunchMsaView/components/calculateProteinSequence.js.map

@@ -1 +1 @@
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+{"version":3,"file":"calculateProteinSequence.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/calculateProteinSequence.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,MAAM,EACN,iBAAiB,EACjB,kBAAkB,EAClB,MAAM,GACP,MAAM,oBAAoB,CAAA;AAK3B,MAAM,UAAU,MAAM,CAAC,QAAgB,EAAE,QAAgB;IACvD,OAAO,QAAQ,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;AACzE,CAAC;AAED,MAAM,UAAU,wBAAwB,CAAC,EACvC,GAAG,EACH,QAAQ,EACR,UAAU,GAKX;IACC,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAA;IACjC,IAAI,OAAO,GAAG,EAAE,CAAA;IAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QACvC,qDAAqD;QACrD,OAAO,IAAI,UAAU,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,GAAG,CAAA;IACnD,CAAC;IACD,OAAO,OAAO,CAAA;AAChB,CAAC;AAED,MAAM,UAAU,OAAO,CAAC,IAAY,EAAE,MAAc;IAClD,OAAO,IAAI;SACR,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QACX,GAAG,GAAG;QACN,KAAK,EAAE,MAAM,GAAG,GAAG,CAAC,GAAG;QACvB,GAAG,EAAE,MAAM,GAAG,GAAG,CAAC,KAAK;KACxB,CAAC,CAAC;SACF,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAA;AAC1C,CAAC;AAED,MAAM,UAAU,6BAA6B,CAAC,EAC5C,OAAO,EACP,GAAG,GAIJ;IACC,MAAM,EAAE,WAAW,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC,MAAM,EAAE,CAAA;IACvD,MAAM,GAAG,GAAG,MAAM,CAChB,WAAW;QACT,EAAE,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC;SACtC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QACX,GAAG,GAAG;QACN,KAAK,EAAE,GAAG,CAAC,KAAK,GAAG,KAAK;QACxB,GAAG,EAAE,GAAG,CAAC,GAAG,GAAG,KAAK;KACrB,CAAC,CAAC;SACF,MAAM,CAAC,UAAU,CAAC,EAAE,CAAC,UAAU,CAAC,IAAI,KAAK,KAAK,CAAC,IAAI,EAAE,EACxD,IAAI,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,GAAG,EAAE,CACpC,CAAA;IAED,OAAO,wBAAwB,CAAC;QAC9B,GAAG,EAAE,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG;QACnD,QAAQ,EAAE,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG;QAC3C,UAAU,EAAE,kBAAkB,CAAC,iBAAiB,CAAC;KAClD,CAAC,CAAA;AACJ,CAAC"}

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

@@ -7,4 +7,5 @@ export interface SeqState {
     seq: string;
     upstream?: string;
     downstream?: string;
+    error?: unknown;
 }

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

@@ -1,17 +1,13 @@
-import type { SeqState } from './types';
 import type { Feature } from '@jbrowse/core/util';
-export interface ErrorState {
-    error: string;
-}
 export declare function useFeatureSequence({ view, feature, upDownBp, forceLoad, }: {
     view: {
         assemblyNames?: string[];
     } | undefined;
-    feature: Feature;
+    feature?: Feature;
     upDownBp?: number;
     forceLoad?: boolean;
 }): {
     proteinSequence: string;
-    sequence: SeqState | ErrorState | undefined;
-    error: unknown;
+    sequence: import("./types").SeqState | undefined;
+    error: any;
 };

package/dist/LaunchMsaView/components/useFeatureSequence.js

@@ -1,69 +1,16 @@
-import { useEffect, useState } from 'react';
-import { getSession } from '@jbrowse/core/util';
 import { getProteinSequenceFromFeature } from './calculateProteinSequence';
-import { fetchSeq } from './fetchSeq';
-const BPLIMIT = 500_000;
+import { useSWRFeatureSequence } from './useSWRFeatureSequence';
 export function useFeatureSequence({ view, feature, upDownBp = 0, forceLoad = true, }) {
-    const [sequence, setSequence] = useState();
-    const [error, setError] = useState();
-    const assemblyName = view?.assemblyNames?.[0];
-    useEffect(() => {
-        if (view) {
-            // eslint-disable-next-line @typescript-eslint/no-floating-promises
-            ;
-            (async () => {
-                try {
-                    setError(undefined);
-                    setSequence(undefined);
-                    const session = getSession(view);
-                    const { start, end, refName } = feature.toJSON();
-                    if (!assemblyName) {
-                        throw new Error('No assembly found');
-                    }
-                    if (!forceLoad && end - start > BPLIMIT) {
-                        setSequence({
-                            error: `Genomic sequence larger than ${BPLIMIT}bp, use "force load" button to display`,
-                        });
-                    }
-                    else {
-                        const b = start - upDownBp;
-                        const e = end + upDownBp;
-                        setSequence({
-                            seq: await fetchSeq({
-                                start,
-                                end,
-                                refName,
-                                assemblyName,
-                                session,
-                            }),
-                            upstream: await fetchSeq({
-                                start: Math.max(0, b),
-                                end: start,
-                                refName,
-                                assemblyName,
-                                session,
-                            }),
-                            downstream: await fetchSeq({
-                                start: end,
-                                end: e,
-                                refName,
-                                assemblyName,
-                                session,
-                            }),
-                        });
-                    }
-                }
-                catch (e) {
-                    console.error(e);
-                    setError(e);
-                }
-            })();
-        }
-    }, [feature, view, upDownBp, assemblyName, forceLoad]);
-    const proteinSequence = sequence && !('error' in sequence)
+    const { sequence, error } = useSWRFeatureSequence({
+        view,
+        feature,
+        upDownBp,
+        forceLoad,
+    });
+    const proteinSequence = sequence && !('error' in sequence) && feature
         ? getProteinSequenceFromFeature({
             seq: sequence.seq,
-            selectedTranscript: feature,
+            feature,
         })
         : '';
     return {

package/dist/LaunchMsaView/components/useFeatureSequence.js.map

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

@@ -0,0 +1,13 @@
+import type { SeqState } from './types';
+import type { Feature } from '@jbrowse/core/util';
+export declare function useSWRFeatureSequence({ view, feature, upDownBp, forceLoad, }: {
+    view: {
+        assemblyNames?: string[];
+    } | undefined;
+    feature?: Feature;
+    upDownBp?: number;
+    forceLoad?: boolean;
+}): {
+    sequence: SeqState | undefined;
+    error: any;
+};

package/dist/LaunchMsaView/components/useSWRFeatureSequence.js

@@ -0,0 +1,53 @@
+import { getSession } from '@jbrowse/core/util';
+import useSWR from 'swr';
+import { fetchSeq } from './fetchSeq';
+const BPLIMIT = 500_000;
+async function featureSequenceFetcher({ feature, assemblyName, upDownBp, view, forceLoad, }) {
+    const session = getSession(view);
+    const { start, end, refName } = feature.toJSON();
+    const b = start - upDownBp;
+    const e = end + upDownBp;
+    const [seq, upstream, downstream] = await Promise.all([
+        fetchSeq({
+            start,
+            end,
+            refName,
+            assemblyName,
+            session,
+        }),
+        fetchSeq({
+            start: Math.max(0, b),
+            end: start,
+            refName,
+            assemblyName,
+            session,
+        }),
+        fetchSeq({
+            start: end,
+            end: e,
+            refName,
+            assemblyName,
+            session,
+        }),
+    ]);
+    return { seq, upstream, downstream };
+}
+export function useSWRFeatureSequence({ view, feature, upDownBp = 0, forceLoad = true, }) {
+    const assemblyName = view?.assemblyNames?.[0];
+    const { data, error } = useSWR(
+    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+    feature && assemblyName && view
+        ? [feature.id(), assemblyName, upDownBp, forceLoad, 'feature-sequence']
+        : null, () => featureSequenceFetcher({
+        feature: feature,
+        assemblyName: assemblyName,
+        upDownBp,
+        view: view,
+        forceLoad,
+    }));
+    return {
+        sequence: data,
+        error,
+    };
+}
+//# sourceMappingURL=useSWRFeatureSequence.js.map