jbrowse-plugin-msaview 2.3.3 → 2.3.5
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js +2 -11
- package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js.map +1 -1
- package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.js +24 -47
- package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.js.map +1 -1
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js +5 -20
- package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js.map +1 -1
- package/dist/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.d.ts +7 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.js +29 -0
- package/dist/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.js.map +1 -0
- package/dist/LaunchMsaView/components/useTranscriptSelection.js +15 -14
- package/dist/LaunchMsaView/components/useTranscriptSelection.js.map +1 -1
- package/dist/MsaViewPanel/afterCreateAutoruns.js +14 -9
- package/dist/MsaViewPanel/afterCreateAutoruns.js.map +1 -1
- package/dist/MsaViewPanel/components/ErrorBoundary.d.ts +19 -0
- package/dist/MsaViewPanel/components/ErrorBoundary.js +22 -0
- package/dist/MsaViewPanel/components/ErrorBoundary.js.map +1 -0
- package/dist/MsaViewPanel/components/MsaViewPanel.js +4 -2
- package/dist/MsaViewPanel/components/MsaViewPanel.js.map +1 -1
- package/dist/MsaViewPanel/model.d.ts +0 -12
- package/dist/MsaViewPanel/model.js +1 -1
- package/dist/MsaViewPanel/model.js.map +1 -1
- package/dist/MsaViewPanel/pairwiseAlignment.js +9 -4
- package/dist/MsaViewPanel/pairwiseAlignment.js.map +1 -1
- package/dist/jbrowse-plugin-msaview.umd.production.min.js +26 -26
- package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +4 -4
- package/dist/utils/blastCache.js +2 -3
- package/dist/utils/blastCache.js.map +1 -1
- package/dist/version.d.ts +1 -1
- package/dist/version.js +1 -1
- package/package.json +35 -35
- package/src/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.ts +2 -11
- package/src/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.tsx +23 -49
- package/src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.tsx +6 -20
- package/src/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.ts +49 -0
- package/src/LaunchMsaView/components/useTranscriptSelection.ts +25 -17
- package/src/MsaViewPanel/afterCreateAutoruns.ts +26 -9
- package/src/MsaViewPanel/components/ErrorBoundary.tsx +40 -0
- package/src/MsaViewPanel/components/MsaViewPanel.tsx +14 -11
- package/src/MsaViewPanel/model.ts +32 -21
- package/src/MsaViewPanel/pairwiseAlignment.ts +9 -4
- package/src/utils/blastCache.ts +2 -3
- package/src/version.ts +1 -1
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@@ -33,24 +33,15 @@ export default class BgzipFastaMsaAdapter extends BaseAdapter {
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}
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async getMSAList() {
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const refNames = await this.getMSARefs();
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const list = new Set();
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const val = this.getConf('msaRegex');
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const re = new RegExp(val);
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list.add(refNames[i].split(re)[0]);
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}
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const list = new Set(refNames.map(name => name.split(re)[0]));
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return [...list];
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}
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async getMSA(id) {
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const adapter = await this.configure();
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const refNames = await adapter.getRefNames();
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const rows =
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for (let i = 0, l = refNames.length; i < l; i++) {
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const refName = refNames[i];
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if (refName.startsWith(id)) {
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rows.push(refName);
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}
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}
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const rows = refNames.filter(refName => refName.startsWith(id));
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return firstValueFrom(adapter
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.getFeaturesInMultipleRegions(rows.map(refName => ({
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refName,
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@@ -1 +1 @@
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-
{"version":3,"file":"BgzipFastaMsaAdapter.js","sourceRoot":"","sources":["../../src/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAC5D,OAAO,EAAE,WAAW,EAAE,MAAM,yCAAyC,CAAA;AACrE,OAAO,EAAE,cAAc,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAI9C,MAAM,CAAC,OAAO,OAAO,oBAAqB,SAAQ,WAAW;IAK3D,KAAK,CAAC,YAAY;QAChB,MAAM,aAAa,GAAG,IAAI,CAAC,aAAa,CAAA;QACxC,IAAI,aAAa,EAAE,CAAC;YAClB,MAAM,OAAO,GAAG,MAAM,aAAa,CAAC;gBAClC,GAAG,cAAc,CAAC,IAAI,CAAC,MAAM,CAAC;gBAC9B,IAAI,EAAE,mBAAmB;aAC1B,CAAC,CAAA;YAEF,OAAO,OAAO,CAAC,WAAqC,CAAA;QACtD,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,mBAAmB,CAAC,CAAA;QACtC,CAAC;IACH,CAAC;IACD,SAAS;QACP,IAAI,CAAC,UAAU,KAAK,IAAI,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;YAC3D,IAAI,CAAC,UAAU,GAAG,SAAS,CAAA;YAC3B,MAAM,CAAC,CAAA;QACT,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;IAED,KAAK,CAAC,UAAU;QACd,IAAI,CAAC,SAAS,KAAK,IAAI,CAAC,SAAS,EAAE;aAChC,IAAI,CAAC,OAAO,CAAC,EAAE,CAAC,OAAO,CAAC,WAAW,EAAE,CAAC;aACtC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;YACpB,IAAI,CAAC,SAAS,GAAG,SAAS,CAAA;YAC1B,MAAM,CAAC,CAAA;QACT,CAAC,CAAC,CAAA;QACJ,OAAO,IAAI,CAAC,SAAS,CAAA;IACvB,CAAC;IAED,KAAK,CAAC,UAAU;QACd,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,UAAU,EAAE,CAAA;QACxC,MAAM,
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{"version":3,"file":"BgzipFastaMsaAdapter.js","sourceRoot":"","sources":["../../src/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAC5D,OAAO,EAAE,WAAW,EAAE,MAAM,yCAAyC,CAAA;AACrE,OAAO,EAAE,cAAc,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAI9C,MAAM,CAAC,OAAO,OAAO,oBAAqB,SAAQ,WAAW;IAK3D,KAAK,CAAC,YAAY;QAChB,MAAM,aAAa,GAAG,IAAI,CAAC,aAAa,CAAA;QACxC,IAAI,aAAa,EAAE,CAAC;YAClB,MAAM,OAAO,GAAG,MAAM,aAAa,CAAC;gBAClC,GAAG,cAAc,CAAC,IAAI,CAAC,MAAM,CAAC;gBAC9B,IAAI,EAAE,mBAAmB;aAC1B,CAAC,CAAA;YAEF,OAAO,OAAO,CAAC,WAAqC,CAAA;QACtD,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,mBAAmB,CAAC,CAAA;QACtC,CAAC;IACH,CAAC;IACD,SAAS;QACP,IAAI,CAAC,UAAU,KAAK,IAAI,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;YAC3D,IAAI,CAAC,UAAU,GAAG,SAAS,CAAA;YAC3B,MAAM,CAAC,CAAA;QACT,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;IAED,KAAK,CAAC,UAAU;QACd,IAAI,CAAC,SAAS,KAAK,IAAI,CAAC,SAAS,EAAE;aAChC,IAAI,CAAC,OAAO,CAAC,EAAE,CAAC,OAAO,CAAC,WAAW,EAAE,CAAC;aACtC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;YACpB,IAAI,CAAC,SAAS,GAAG,SAAS,CAAA;YAC1B,MAAM,CAAC,CAAA;QACT,CAAC,CAAC,CAAA;QACJ,OAAO,IAAI,CAAC,SAAS,CAAA;IACvB,CAAC;IAED,KAAK,CAAC,UAAU;QACd,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,UAAU,EAAE,CAAA;QACxC,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,UAAU,CAAC,CAAA;QACpC,MAAM,EAAE,GAAG,IAAI,MAAM,CAAC,GAAG,CAAC,CAAA;QAC1B,MAAM,IAAI,GAAG,IAAI,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAC,CAAE,CAAC,CAAC,CAAA;QAC9D,OAAO,CAAC,GAAG,IAAI,CAAC,CAAA;IAClB,CAAC;IAED,KAAK,CAAC,MAAM,CAAC,EAAU;QACrB,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,MAAM,QAAQ,GAAG,MAAM,OAAO,CAAC,WAAW,EAAE,CAAA;QAC5C,MAAM,IAAI,GAAG,QAAQ,CAAC,MAAM,CAAC,OAAO,CAAC,EAAE,CAAC,OAAO,CAAC,UAAU,CAAC,EAAE,CAAC,CAAC,CAAA;QAC/D,OAAO,cAAc,CACnB,OAAO;aACJ,4BAA4B,CAC3B,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;YACnB,OAAO;YACP,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,aAAa;YAClB,YAAY,EAAE,EAAE;SACjB,CAAC,CAAC,CACJ;aACA,IAAI,CAAC,OAAO,EAAE,CAAC,CACnB,CAAA;IACH,CAAC;CACF"}
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@@ -1,11 +1,11 @@
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import React, {
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import React, { useMemo, useState } from 'react';
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import { ErrorMessage } from '@jbrowse/core/ui';
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import { getContainingView } from '@jbrowse/core/util';
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import DeleteIcon from '@mui/icons-material/Delete';
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import { Button, IconButton, List, ListItem, ListItemButton, ListItemText, Typography, } from '@mui/material';
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import { observer } from 'mobx-react';
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import { blastLaunchViewFromCache } from './blastLaunchView';
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import {
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import { useCachedBlastResults } from './useCachedBlastResults';
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import { getGeneIdentifiers } from '../../util';
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function getResultDisplayName(result) {
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const parts = [];
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return parts.join(' - ');
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}
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const CachedBlastResults = observer(function ({ model, handleClose, feature, }) {
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const [results, setResults] = useState([]);
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const [loading, setLoading] = useState(true);
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const [error, setError] = useState();
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const view = getContainingView(model);
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const [operationError, setOperationError] = useState();
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const geneIds = useMemo(() => getGeneIdentifiers(feature), [feature]);
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// eslint-disable-next-line @typescript-eslint/no-floating-promises
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;
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(async () => {
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try {
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const cached = await getAllCachedResults();
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setResults(cached.filter(r => r.geneId && geneIds.includes(r.geneId)));
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setLoading(false);
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}
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catch (e) {
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console.error(e);
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setError(e);
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}
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})();
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}, [geneIds]);
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const handleDelete = async (id) => {
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try {
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await deleteCachedResult(id);
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setResults(r => r.filter(result => result.id !== id));
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}
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catch (e) {
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setError(e);
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}
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};
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const handleClearAll = async () => {
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try {
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await clearAllCachedResults();
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setResults([]);
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}
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catch (e) {
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setError(e);
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}
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};
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const { results, error, isLoading, handleDelete, handleClearAll } = useCachedBlastResults(geneIds);
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const handleUseCached = (cached) => {
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blastLaunchViewFromCache({
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handleClose();
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};
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const displayError = error ?? operationError;
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if (displayError) {
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return React.createElement(ErrorMessage, { error: displayError });
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}
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if (
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if (isLoading) {
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return React.createElement(Typography, null, "Loading cached results...");
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}
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"Cached BLAST Results (",
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")"),
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React.createElement(Button, { size: "small", color: "error", onClick: () => {
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React.createElement(Button, { size: "small", color: "error", onClick: async () => {
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try {
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setOperationError(undefined);
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await handleClearAll();
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}
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catch (e) {
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setOperationError(e);
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}
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} }, "Clear All")),
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React.createElement(List, { dense: true, style: { maxHeight: 300, overflow: 'auto' } }, results.map(result => (React.createElement(ListItem, { key: result.id, disablePadding: true, secondaryAction: React.createElement(IconButton, { edge: "end", size: "small", onClick: e => {
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React.createElement(List, { dense: true, style: { maxHeight: 300, overflow: 'auto' } }, results.map(result => (React.createElement(ListItem, { key: result.id, disablePadding: true, secondaryAction: React.createElement(IconButton, { edge: "end", size: "small", onClick: async (e) => {
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e.stopPropagation();
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try {
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setOperationError(undefined);
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await handleDelete(result.id);
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}
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catch (err) {
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setOperationError(err);
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}
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} },
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React.createElement(DeleteIcon, { fontSize: "small" })) },
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React.createElement(ListItemButton, { onClick: () => {
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{"version":3,"file":"CachedBlastResults.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,
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{"version":3,"file":"CachedBlastResults.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,OAAO,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEhD,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AACtD,OAAO,UAAU,MAAM,4BAA4B,CAAA;AACnD,OAAO,EACL,MAAM,EACN,UAAU,EACV,IAAI,EACJ,QAAQ,EACR,cAAc,EACd,YAAY,EACZ,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,wBAAwB,EAAE,MAAM,mBAAmB,CAAA;AAC5D,OAAO,EAAE,qBAAqB,EAAE,MAAM,yBAAyB,CAAA;AAC/D,OAAO,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAA;AAM/C,SAAS,oBAAoB,CAAC,MAAyB;IACrD,MAAM,KAAK,GAAG,EAAE,CAAA;IAChB,IAAI,MAAM,CAAC,QAAQ,EAAE,CAAC;QACpB,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAA;IAC7B,CAAC;IACD,IAAI,MAAM,CAAC,cAAc,IAAI,MAAM,CAAC,cAAc,KAAK,MAAM,CAAC,QAAQ,EAAE,CAAC;QACvE,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,cAAc,CAAC,CAAA;IACnC,CAAC;IACD,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACvB,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,IAAI,MAAM,CAAC,YAAY,IAAI,SAAS,CAAC,CAAA;IAC/D,CAAC;IACD,OAAO,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;AAC1B,CAAC;AAED,MAAM,kBAAkB,GAAG,QAAQ,CAAC,UAAU,EAC5C,KAAK,EACL,WAAW,EACX,OAAO,GAKR;IACC,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAC9D,MAAM,CAAC,cAAc,EAAE,iBAAiB,CAAC,GAAG,QAAQ,EAAW,CAAA;IAE/D,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,EAAE,CAAC,kBAAkB,CAAC,OAAO,CAAC,EAAE,CAAC,OAAO,CAAC,CAAC,CAAA;IAErE,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,SAAS,EAAE,YAAY,EAAE,cAAc,EAAE,GAC/D,qBAAqB,CAAC,OAAO,CAAC,CAAA;IAEhC,MAAM,eAAe,GAAG,CAAC,MAAyB,EAAE,EAAE;QACpD,wBAAwB,CAAC;YACvB,IAAI;YACJ,MAAM;YACN,YAAY,EAAE,WAAW,oBAAoB,CAAC,MAAM,CAAC,EAAE;SACxD,CAAC,CAAA;QACF,WAAW,EAAE,CAAA;IACf,CAAC,CAAA;IAED,MAAM,YAAY,GAAG,KAAK,IAAI,cAAc,CAAA;IAC5C,IAAI,YAAY,EAAE,CAAC;QACjB,OAAO,oBAAC,YAAY,IAAC,KAAK,EAAE,YAAY,GAAI,CAAA;IAC9C,CAAC;IAED,IAAI,SAAS,EAAE,CAAC;QACd,OAAO,oBAAC,UAAU,oCAAuC,CAAA;IAC3D,CAAC;IAED,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACzB,OAAO,CACL,oBAAC,UAAU,IAAC,KAAK,EAAC,eAAe,uFAGpB,CACd,CAAA;IACH,CAAC;IAED,OAAO,CACL;QACE,6BACE,KAAK,EAAE;gBACL,OAAO,EAAE,MAAM;gBACf,cAAc,EAAE,eAAe;gBAC/B,UAAU,EAAE,QAAQ;gBACpB,YAAY,EAAE,CAAC;aAChB;YAED,oBAAC,UAAU,IAAC,OAAO,EAAC,WAAW;;gBACN,OAAO,CAAC,MAAM;oBAC1B;YACb,oBAAC,MAAM,IACL,IAAI,EAAC,OAAO,EACZ,KAAK,EAAC,OAAO,EACb,OAAO,EAAE,KAAK,IAAI,EAAE;oBAClB,IAAI,CAAC;wBACH,iBAAiB,CAAC,SAAS,CAAC,CAAA;wBAC5B,MAAM,cAAc,EAAE,CAAA;oBACxB,CAAC;oBAAC,OAAO,CAAC,EAAE,CAAC;wBACX,iBAAiB,CAAC,CAAC,CAAC,CAAA;oBACtB,CAAC;gBACH,CAAC,gBAGM,CACL;QACN,oBAAC,IAAI,IAAC,KAAK,QAAC,KAAK,EAAE,EAAE,SAAS,EAAE,GAAG,EAAE,QAAQ,EAAE,MAAM,EAAE,IACpD,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,CACrB,oBAAC,QAAQ,IACP,GAAG,EAAE,MAAM,CAAC,EAAE,EACd,cAAc,QACd,eAAe,EACb,oBAAC,UAAU,IACT,IAAI,EAAC,KAAK,EACV,IAAI,EAAC,OAAO,EACZ,OAAO,EAAE,KAAK,EAAC,CAAC,EAAC,EAAE;oBACjB,CAAC,CAAC,eAAe,EAAE,CAAA;oBACnB,IAAI,CAAC;wBACH,iBAAiB,CAAC,SAAS,CAAC,CAAA;wBAC5B,MAAM,YAAY,CAAC,MAAM,CAAC,EAAE,CAAC,CAAA;oBAC/B,CAAC;oBAAC,OAAO,GAAG,EAAE,CAAC;wBACb,iBAAiB,CAAC,GAAG,CAAC,CAAA;oBACxB,CAAC;gBACH,CAAC;gBAED,oBAAC,UAAU,IAAC,QAAQ,EAAC,OAAO,GAAG,CACpB;YAGf,oBAAC,cAAc,IACb,OAAO,EAAE,GAAG,EAAE;oBACZ,eAAe,CAAC,MAAM,CAAC,CAAA;gBACzB,CAAC;gBAED,oBAAC,YAAY,IACX,OAAO,EAAE,GAAG,oBAAoB,CAAC,MAAM,CAAC,MAAM,MAAM,CAAC,aAAa,IAAI,MAAM,CAAC,YAAY,KAAK,MAAM,CAAC,YAAY,GAAG,EACpH,SAAS,EAAE,GAAG,IAAI,IAAI,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC,cAAc,EAAE,WAAW,MAAM,CAAC,eAAe,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,KAAK,GAC5G,CACa,CACR,CACZ,CAAC,CACG,CACH,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,kBAAkB,CAAA"}
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@@ -1,4 +1,4 @@
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1
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-
import React, {
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1
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+
import React, { useMemo, useState } from 'react';
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2
2
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import { ErrorMessage } from '@jbrowse/core/ui';
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3
3
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import { getContainingView } from '@jbrowse/core/util';
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4
4
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import ExpandMoreIcon from '@mui/icons-material/ExpandMore';
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@@ -8,8 +8,8 @@ import { makeStyles } from 'tss-react/mui';
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8
8
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import CachedBlastResults from './CachedBlastResults';
|
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9
9
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import { blastLaunchView } from './blastLaunchView';
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10
10
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import { msaAlgorithms } from './consts';
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11
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+
import { useCachedBlastResults } from './useCachedBlastResults';
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11
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import TextField2 from '../../../components/TextField2';
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-
import { getAllCachedResults } from '../../../utils/blastCache';
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13
13
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import { getGeneDisplayName, getGeneIdentifiers, getTranscriptDisplayName, } from '../../util';
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14
14
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import TranscriptSelector from '../TranscriptSelector';
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15
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import { useTranscriptSelection } from '../useTranscriptSelection';
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@@ -43,25 +43,10 @@ const NCBIBlastAutomaticPanel = observer(function ({ handleClose, feature, model
|
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43
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const [selectedBlastDatabase, setSelectedBlastDatabase] = useState('nr');
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44
44
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const [selectedMsaAlgorithm, setSelectedMsaAlgorithm] = useState('clustalo');
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45
45
|
const [selectedBlastProgram, setSelectedBlastProgram] = useState('quick-blastp');
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46
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-
const [hasCachedResults, setHasCachedResults] = useState(false);
|
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47
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-
const [error, setError] = useState();
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48
46
|
const geneIds = useMemo(() => getGeneIdentifiers(feature), [feature]);
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49
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-
|
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50
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// eslint-disable-next-line @typescript-eslint/no-floating-promises
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-
;
|
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52
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-
(async () => {
|
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53
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-
try {
|
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54
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-
const results = await getAllCachedResults();
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55
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-
setHasCachedResults(results.some(r => r.geneId && geneIds.includes(r.geneId)));
|
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56
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-
}
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57
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-
catch (e) {
|
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58
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-
console.error(e);
|
|
59
|
-
setError(e);
|
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60
|
-
}
|
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61
|
-
})();
|
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62
|
-
}, [geneIds]);
|
|
47
|
+
const { results: cachedResults, error: cachedResultsError } = useCachedBlastResults(geneIds);
|
|
63
48
|
const { options, selectedId, setSelectedId, selectedTranscript, proteinSequence, error: proteinSequenceError, } = useTranscriptSelection({ feature, view });
|
|
64
|
-
const e = proteinSequenceError ?? launchViewError ??
|
|
49
|
+
const e = proteinSequenceError ?? launchViewError ?? cachedResultsError;
|
|
65
50
|
return (React.createElement(React.Fragment, null,
|
|
66
51
|
React.createElement(DialogContent, { className: classes.dialogContent },
|
|
67
52
|
children,
|
|
@@ -84,7 +69,7 @@ const NCBIBlastAutomaticPanel = observer(function ({ handleClose, feature, model
|
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|
84
69
|
selectedBlastDatabase === 'nr_cluster_seq' ? (React.createElement(Typography, { variant: "subtitle2", className: classes.clusterSeqMessage }, "Can only use blastp on nr_cluster_seq")) : null),
|
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85
70
|
React.createElement(TranscriptSelector, { feature: feature, options: options, selectedId: selectedId, selectedTranscript: selectedTranscript, onTranscriptChange: setSelectedId, proteinSequence: proteinSequence }),
|
|
86
71
|
React.createElement(Typography, { className: classes.infoText }, "This panel will automatically submit a query to NCBI. Using blastp can take 10+ minutes to run, quick-blastp is generally a lot faster but is not available for the clustered database. After completion, all the hits will be run through a multiple sequence alignment. Note: we are not able to currently run NCBI COBALT automatically on the BLAST results, even though that is the method NCBI uses on their website. If you need a COBALT alignment, please use the manual approach of submitting BLAST yourself and downloading the resulting files"),
|
|
87
|
-
|
|
72
|
+
cachedResults.length > 0 ? (React.createElement(Accordion, { className: classes.cachedResultsAccordion },
|
|
88
73
|
React.createElement(AccordionSummary, { expandIcon: React.createElement(ExpandMoreIcon, null) },
|
|
89
74
|
React.createElement(Typography, null, "Previous BLAST Results")),
|
|
90
75
|
React.createElement(AccordionDetails, null,
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@@ -1 +1 @@
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|
1
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-
{"version":3,"file":"NCBIBlastAutomaticPanel.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,
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1
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+
{"version":3,"file":"NCBIBlastAutomaticPanel.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,OAAO,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEhD,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AACtD,OAAO,cAAc,MAAM,gCAAgC,CAAA;AAC3D,OAAO,EACL,SAAS,EACT,gBAAgB,EAChB,gBAAgB,EAChB,MAAM,EACN,aAAa,EACb,aAAa,EACb,QAAQ,EACR,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,kBAAkB,MAAM,sBAAsB,CAAA;AACrD,OAAO,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAA;AACnD,OAAO,EAAE,aAAa,EAAE,MAAM,UAAU,CAAA;AACxC,OAAO,EAAE,qBAAqB,EAAE,MAAM,yBAAyB,CAAA;AAC/D,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,EACL,kBAAkB,EAClB,kBAAkB,EAClB,wBAAwB,GACzB,MAAM,YAAY,CAAA;AACnB,OAAO,kBAAkB,MAAM,uBAAuB,CAAA;AACtD,OAAO,EAAE,sBAAsB,EAAE,MAAM,2BAA2B,CAAA;AAMlE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;IACD,WAAW,EAAE;QACX,KAAK,EAAE,GAAG;KACX;IACD,sBAAsB,EAAE;QACtB,OAAO,EAAE,MAAM;KAChB;IACD,iBAAiB,EAAE;QACjB,UAAU,EAAE,CAAC;QACb,YAAY,EAAE,QAAQ;KACvB;IACD,sBAAsB,EAAE;QACtB,SAAS,EAAE,EAAE;KACd;IACD,QAAQ,EAAE;QACR,SAAS,EAAE,EAAE;KACd;CACF,CAAC,CAAA;AAEF,MAAM,oBAAoB,GAAG,CAAC,IAAI,EAAE,gBAAgB,CAAU,CAAA;AAC9D,MAAM,aAAa,GAAG,CAAC,QAAQ,EAAE,cAAc,CAAU,CAAA;AAKzD,MAAM,uBAAuB,GAAG,QAAQ,CAAC,UAAU,EACjD,WAAW,EACX,OAAO,EACP,KAAK,EACL,QAAQ,EACR,OAAO,GAOR;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAC9D,MAAM,CAAC,eAAe,EAAE,kBAAkB,CAAC,GAAG,QAAQ,EAAW,CAAA;IACjE,MAAM,CAAC,qBAAqB,EAAE,wBAAwB,CAAC,GACrD,QAAQ,CAAwB,IAAI,CAAC,CAAA;IACvC,MAAM,CAAC,oBAAoB,EAAE,uBAAuB,CAAC,GACnD,QAAQ,CAAe,UAAU,CAAC,CAAA;IACpC,MAAM,CAAC,oBAAoB,EAAE,uBAAuB,CAAC,GACnD,QAAQ,CAAiB,cAAc,CAAC,CAAA;IAE1C,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,EAAE,CAAC,kBAAkB,CAAC,OAAO,CAAC,EAAE,CAAC,OAAO,CAAC,CAAC,CAAA;IACrE,MAAM,EAAE,OAAO,EAAE,aAAa,EAAE,KAAK,EAAE,kBAAkB,EAAE,GACzD,qBAAqB,CAAC,OAAO,CAAC,CAAA;IAEhC,MAAM,EACJ,OAAO,EACP,UAAU,EACV,aAAa,EACb,kBAAkB,EAClB,eAAe,EACf,KAAK,EAAE,oBAAoB,GAC5B,GAAG,sBAAsB,CAAC,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAA;IAC7C,MAAM,CAAC,GAAG,oBAAoB,IAAI,eAAe,IAAI,kBAAkB,CAAA;IACvE,OAAO,CACL;QACE,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,aAAa;YAC5C,QAAQ;YACR,CAAC,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,CAAC,GAAI,CAAC,CAAC,CAAC,IAAI;YACtC,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,KAAK,EAAC,gBAAgB,EACtB,SAAS,EAAE,OAAO,CAAC,WAAW,EAC9B,MAAM,QACN,KAAK,EAAE,qBAAqB,EAC5B,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,MAAM,KAAK,GAAG,KAAK,CAAC,MAAM;yBACvB,KAA8C,CAAA;oBACjD,wBAAwB,CAAC,KAAK,CAAC,CAAA;oBAC/B,IAAI,KAAK,KAAK,gBAAgB,EAAE,CAAC;wBAC/B,uBAAuB,CAAC,QAAQ,CAAC,CAAA;oBACnC,CAAC;gBACH,CAAC,IAEA,oBAAoB,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAC/B,oBAAC,QAAQ,IAAC,KAAK,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,IAC3B,GAAG,CACK,CACZ,CAAC,CACS;YAEb,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,KAAK,EAAC,eAAe,EACrB,SAAS,EAAE,OAAO,CAAC,WAAW,EAC9B,MAAM,QACN,KAAK,EAAE,oBAAoB,EAC3B,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,uBAAuB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAqB,CAAC,CAAA;gBAC7D,CAAC,IAEA,aAAa,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CACxB,oBAAC,QAAQ,IAAC,KAAK,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,IAC3B,GAAG,CACK,CACZ,CAAC,CACS;YAEb,6BAAK,SAAS,EAAE,OAAO,CAAC,sBAAsB;gBAC5C,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,KAAK,EAAC,eAAe,EACrB,QAAQ,EAAE,qBAAqB,KAAK,gBAAgB,EACpD,SAAS,EAAE,OAAO,CAAC,WAAW,EAC9B,MAAM,QACN,KAAK,EAAE,oBAAoB,EAC3B,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,uBAAuB,CACrB,KAAK,CAAC,MAAM,CAAC,KAAuC,CACrD,CAAA;oBACH,CAAC,IAEA,aAAa,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CACxB,oBAAC,QAAQ,IAAC,KAAK,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,IAC3B,GAAG,CACK,CACZ,CAAC,CACS;gBACZ,qBAAqB,KAAK,gBAAgB,CAAC,CAAC,CAAC,CAC5C,oBAAC,UAAU,IACT,OAAO,EAAC,WAAW,EACnB,SAAS,EAAE,OAAO,CAAC,iBAAiB,4CAGzB,CACd,CAAC,CAAC,CAAC,IAAI,CACJ;YAEN,oBAAC,kBAAkB,IACjB,OAAO,EAAE,OAAO,EAChB,OAAO,EAAE,OAAO,EAChB,UAAU,EAAE,UAAU,EACtB,kBAAkB,EAAE,kBAAkB,EACtC,kBAAkB,EAAE,aAAa,EACjC,eAAe,EAAE,eAAe,GAChC;YAEF,oBAAC,UAAU,IAAC,SAAS,EAAE,OAAO,CAAC,QAAQ,kiBAS1B;YAEZ,aAAa,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CAC1B,oBAAC,SAAS,IAAC,SAAS,EAAE,OAAO,CAAC,sBAAsB;gBAClD,oBAAC,gBAAgB,IAAC,UAAU,EAAE,oBAAC,cAAc,OAAG;oBAC9C,oBAAC,UAAU,iCAAoC,CAC9B;gBACnB,oBAAC,gBAAgB;oBACf,oBAAC,kBAAkB,IACjB,KAAK,EAAE,KAAK,EACZ,WAAW,EAAE,WAAW,EACxB,OAAO,EAAE,OAAO,GAChB,CACe,CACT,CACb,CAAC,CAAC,CAAC,IAAI,CACM;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,IAAI,CAAC;wBACH,IAAI,CAAC,kBAAkB,EAAE,CAAC;4BACxB,OAAM;wBACR,CAAC;wBACD,kBAAkB,CAAC,SAAS,CAAC,CAAA;wBAC7B,eAAe,CAAC;4BACd,OAAO,EAAE,kBAAkB;4BAC3B,IAAI;4BACJ,YAAY,EAAE,WAAW,kBAAkB,CAAC,OAAO,CAAC,MAAM,wBAAwB,CAAC,kBAAkB,CAAC,EAAE;4BACxG,WAAW,EAAE;gCACX,OAAO;gCACP,YAAY,EAAE,oBAAoB;gCAClC,aAAa,EAAE,qBAAqB;gCACpC,YAAY,EAAE,oBAAoB;gCAClC,kBAAkB;gCAClB,eAAe;6BAChB;yBACF,CAAC,CAAA;oBACJ,CAAC;oBAAC,OAAO,CAAC,EAAE,CAAC;wBACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;wBAChB,kBAAkB,CAAC,CAAC,CAAC,CAAA;oBACvB,CAAC;oBAED,WAAW,EAAE,CAAA;gBACf,CAAC,EACD,QAAQ,EAAE,CAAC,eAAe,aAGnB;YACT,oBAAC,MAAM,IAAC,KAAK,EAAC,WAAW,EAAC,OAAO,EAAC,WAAW,EAAC,OAAO,EAAE,WAAW,aAEzD,CACK,CACf,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,uBAAuB,CAAA"}
|
|
@@ -0,0 +1,29 @@
|
|
|
1
|
+
import useSWR from 'swr';
|
|
2
|
+
import { clearAllCachedResults, deleteCachedResult, getAllCachedResults, } from '../../../utils/blastCache';
|
|
3
|
+
const swrConfig = {
|
|
4
|
+
revalidateOnFocus: false,
|
|
5
|
+
revalidateOnReconnect: false,
|
|
6
|
+
revalidateIfStale: false,
|
|
7
|
+
};
|
|
8
|
+
export function useCachedBlastResults(geneIds) {
|
|
9
|
+
const { data: results, error, mutate, } = useSWR(`cached-blast-${geneIds.join(',')}`, async () => {
|
|
10
|
+
const cached = await getAllCachedResults();
|
|
11
|
+
return cached.filter(r => r.geneId && geneIds.includes(r.geneId));
|
|
12
|
+
}, swrConfig);
|
|
13
|
+
const handleDelete = async (id) => {
|
|
14
|
+
await deleteCachedResult(id);
|
|
15
|
+
await mutate(results => results?.filter(result => result.id !== id) ?? [], false);
|
|
16
|
+
};
|
|
17
|
+
const handleClearAll = async () => {
|
|
18
|
+
await clearAllCachedResults();
|
|
19
|
+
await mutate([], false);
|
|
20
|
+
};
|
|
21
|
+
return {
|
|
22
|
+
results: results ?? [],
|
|
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|
+
error,
|
|
24
|
+
isLoading: !results && !error,
|
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|
+
handleDelete,
|
|
26
|
+
handleClearAll,
|
|
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|
+
};
|
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|
+
}
|
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29
|
+
//# sourceMappingURL=useCachedBlastResults.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"useCachedBlastResults.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,KAAK,CAAA;AAExB,OAAO,EACL,qBAAqB,EACrB,kBAAkB,EAClB,mBAAmB,GACpB,MAAM,2BAA2B,CAAA;AAElC,MAAM,SAAS,GAAG;IAChB,iBAAiB,EAAE,KAAK;IACxB,qBAAqB,EAAE,KAAK;IAC5B,iBAAiB,EAAE,KAAK;CACzB,CAAA;AAED,MAAM,UAAU,qBAAqB,CAAC,OAAiB;IACrD,MAAM,EACJ,IAAI,EAAE,OAAO,EACb,KAAK,EACL,MAAM,GACP,GAAG,MAAM,CACR,gBAAgB,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,EACnC,KAAK,IAAI,EAAE;QACT,MAAM,MAAM,GAAG,MAAM,mBAAmB,EAAE,CAAA;QAC1C,OAAO,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,IAAI,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAA;IACnE,CAAC,EACD,SAAS,CACV,CAAA;IAED,MAAM,YAAY,GAAG,KAAK,EAAE,EAAU,EAAE,EAAE;QACxC,MAAM,kBAAkB,CAAC,EAAE,CAAC,CAAA;QAC5B,MAAM,MAAM,CACV,OAAO,CAAC,EAAE,CAAC,OAAO,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC,MAAM,CAAC,EAAE,KAAK,EAAE,CAAC,IAAI,EAAE,EAC5D,KAAK,CACN,CAAA;IACH,CAAC,CAAA;IAED,MAAM,cAAc,GAAG,KAAK,IAAI,EAAE;QAChC,MAAM,qBAAqB,EAAE,CAAA;QAC7B,MAAM,MAAM,CAAC,EAAE,EAAE,KAAK,CAAC,CAAA;IACzB,CAAC,CAAA;IAED,OAAO;QACL,OAAO,EAAE,OAAO,IAAI,EAAE;QACtB,KAAK;QACL,SAAS,EAAE,CAAC,OAAO,IAAI,CAAC,KAAK;QAC7B,YAAY;QACZ,cAAc;KACf,CAAA;AACH,CAAC"}
|
|
@@ -1,31 +1,32 @@
|
|
|
1
|
-
import {
|
|
1
|
+
import { useMemo, useState } from 'react';
|
|
2
2
|
import { featureMatchesId, getId, getSortedTranscriptFeatures } from '../util';
|
|
3
3
|
import { useFeatureSequence } from './useFeatureSequence';
|
|
4
4
|
function featureInValidIds(feature, validIds) {
|
|
5
5
|
return validIds.some(id => featureMatchesId(feature, id));
|
|
6
6
|
}
|
|
7
|
+
function findValidSelection(currentId, options, validIds) {
|
|
8
|
+
if (!validIds || validIds.length === 0) {
|
|
9
|
+
return undefined;
|
|
10
|
+
}
|
|
11
|
+
const currentFeature = options.find(opt => getId(opt) === currentId);
|
|
12
|
+
if (!currentFeature || featureInValidIds(currentFeature, validIds)) {
|
|
13
|
+
return undefined;
|
|
14
|
+
}
|
|
15
|
+
const validOption = options.find(opt => featureInValidIds(opt, validIds));
|
|
16
|
+
return validOption ? getId(validOption) : undefined;
|
|
17
|
+
}
|
|
7
18
|
export function useTranscriptSelection({ feature, view, validIds, }) {
|
|
8
19
|
const options = useMemo(() => getSortedTranscriptFeatures(feature), [feature]);
|
|
9
20
|
const [selectedId, setSelectedId] = useState(() => getId(options[0]));
|
|
10
|
-
const
|
|
21
|
+
const validatedSelectedId = findValidSelection(selectedId, options, validIds) || selectedId;
|
|
22
|
+
const selectedTranscript = options.find(val => getId(val) === validatedSelectedId);
|
|
11
23
|
const { proteinSequence, error } = useFeatureSequence({
|
|
12
24
|
view,
|
|
13
25
|
feature: selectedTranscript,
|
|
14
26
|
});
|
|
15
|
-
useEffect(() => {
|
|
16
|
-
if (validIds && validIds.length > 0) {
|
|
17
|
-
const currentFeature = options.find(opt => getId(opt) === selectedId);
|
|
18
|
-
if (currentFeature && !featureInValidIds(currentFeature, validIds)) {
|
|
19
|
-
const validOption = options.find(opt => featureInValidIds(opt, validIds));
|
|
20
|
-
if (validOption) {
|
|
21
|
-
setSelectedId(getId(validOption));
|
|
22
|
-
}
|
|
23
|
-
}
|
|
24
|
-
}
|
|
25
|
-
}, [validIds, options, selectedId]);
|
|
26
27
|
return {
|
|
27
28
|
options,
|
|
28
|
-
selectedId,
|
|
29
|
+
selectedId: validatedSelectedId,
|
|
29
30
|
setSelectedId,
|
|
30
31
|
selectedTranscript,
|
|
31
32
|
proteinSequence,
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"useTranscriptSelection.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/useTranscriptSelection.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,
|
|
1
|
+
{"version":3,"file":"useTranscriptSelection.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/useTranscriptSelection.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEzC,OAAO,EAAE,gBAAgB,EAAE,KAAK,EAAE,2BAA2B,EAAE,MAAM,SAAS,CAAA;AAC9E,OAAO,EAAE,kBAAkB,EAAE,MAAM,sBAAsB,CAAA;AAIzD,SAAS,iBAAiB,CAAC,OAAgB,EAAE,QAAkB;IAC7D,OAAO,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,gBAAgB,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,CAAA;AAC3D,CAAC;AAED,SAAS,kBAAkB,CACzB,SAAiB,EACjB,OAAkB,EAClB,QAA8B;IAE9B,IAAI,CAAC,QAAQ,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACvC,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,MAAM,cAAc,GAAG,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,SAAS,CAAC,CAAA;IACpE,IAAI,CAAC,cAAc,IAAI,iBAAiB,CAAC,cAAc,EAAE,QAAQ,CAAC,EAAE,CAAC;QACnE,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,MAAM,WAAW,GAAG,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,iBAAiB,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAC,CAAA;IACzE,OAAO,WAAW,CAAC,CAAC,CAAC,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;AACrD,CAAC;AAED,MAAM,UAAU,sBAAsB,CAAC,EACrC,OAAO,EACP,IAAI,EACJ,QAAQ,GAKT;IACC,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,EAAE,CAAC,2BAA2B,CAAC,OAAO,CAAC,EAAE,CAAC,OAAO,CAAC,CAAC,CAAA;IAC9E,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,QAAQ,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrE,MAAM,mBAAmB,GACvB,kBAAkB,CAAC,UAAU,EAAE,OAAO,EAAE,QAAQ,CAAC,IAAI,UAAU,CAAA;IACjE,MAAM,kBAAkB,GAAG,OAAO,CAAC,IAAI,CACrC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,mBAAmB,CAC1C,CAAA;IACD,MAAM,EAAE,eAAe,EAAE,KAAK,EAAE,GAAG,kBAAkB,CAAC;QACpD,IAAI;QACJ,OAAO,EAAE,kBAAkB;KAC5B,CAAC,CAAA;IAEF,OAAO;QACL,OAAO;QACP,UAAU,EAAE,mBAAmB;QAC/B,aAAa;QACb,kBAAkB;QAClB,eAAe;QACf,KAAK;QACL,QAAQ;KACT,CAAA;AACH,CAAC"}
|
|
@@ -4,6 +4,10 @@ import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord';
|
|
|
4
4
|
import { cleanupOldData, generateDataStoreId, retrieveMsaData, storeMsaData, } from './msaDataStore';
|
|
5
5
|
import { gappedToUngappedPosition } from './structureConnection';
|
|
6
6
|
import { getUniprotIdFromAlphaFoldUrl } from './util';
|
|
7
|
+
function isProteinView(view) {
|
|
8
|
+
const v = view;
|
|
9
|
+
return v.type === 'ProteinView' && Array.isArray(v.structures);
|
|
10
|
+
}
|
|
7
11
|
export function loadStoredData(self) {
|
|
8
12
|
const { dataStoreId, rows } = self;
|
|
9
13
|
if (dataStoreId && rows.length === 0) {
|
|
@@ -183,12 +187,15 @@ export function autoConnectStructures(self) {
|
|
|
183
187
|
return;
|
|
184
188
|
}
|
|
185
189
|
for (const view of views) {
|
|
186
|
-
|
|
187
|
-
if (v.type !== 'ProteinView' || !v.structures) {
|
|
190
|
+
if (!isProteinView(view)) {
|
|
188
191
|
continue;
|
|
189
192
|
}
|
|
193
|
+
const v = view;
|
|
190
194
|
for (let structureIdx = 0; structureIdx < v.structures.length; structureIdx++) {
|
|
191
195
|
const structure = v.structures[structureIdx];
|
|
196
|
+
if (!structure) {
|
|
197
|
+
continue;
|
|
198
|
+
}
|
|
192
199
|
if (structure.connectedViewId !== connectedViewId) {
|
|
193
200
|
continue;
|
|
194
201
|
}
|
|
@@ -217,12 +224,12 @@ export function observeProteinHighlights(self) {
|
|
|
217
224
|
if (!connectedViewId || !transcriptToMsaMap) {
|
|
218
225
|
return;
|
|
219
226
|
}
|
|
220
|
-
const columns =
|
|
227
|
+
const columns = new Set();
|
|
221
228
|
for (const view of views) {
|
|
222
|
-
|
|
223
|
-
if (v.type !== 'ProteinView' || !v.structures) {
|
|
229
|
+
if (!isProteinView(view)) {
|
|
224
230
|
continue;
|
|
225
231
|
}
|
|
232
|
+
const v = view;
|
|
226
233
|
for (const structure of v.structures) {
|
|
227
234
|
if (structure.connectedViewId !== connectedViewId) {
|
|
228
235
|
continue;
|
|
@@ -237,15 +244,13 @@ export function observeProteinHighlights(self) {
|
|
|
237
244
|
const proteinPos = g2p[coord];
|
|
238
245
|
if (proteinPos !== undefined) {
|
|
239
246
|
const col = self.seqPosToGlobalCol(querySeqName, proteinPos);
|
|
240
|
-
|
|
241
|
-
columns.push(col);
|
|
242
|
-
}
|
|
247
|
+
columns.add(col);
|
|
243
248
|
}
|
|
244
249
|
}
|
|
245
250
|
}
|
|
246
251
|
}
|
|
247
252
|
}
|
|
248
|
-
const visibleColumns = columns
|
|
253
|
+
const visibleColumns = Array.from(columns)
|
|
249
254
|
.map(col => self.globalColToVisibleCol(col))
|
|
250
255
|
.filter((col) => col !== undefined);
|
|
251
256
|
self.setHighlightedColumns(visibleColumns.length > 0 ? visibleColumns : undefined);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"afterCreateAutoruns.js","sourceRoot":"","sources":["../../src/MsaViewPanel/afterCreateAutoruns.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE/C,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAA;AAC/C,OAAO,EAAE,qBAAqB,EAAE,MAAM,yBAAyB,CAAA;AAC/D,OAAO,EACL,cAAc,EACd,mBAAmB,EACnB,eAAe,EACf,YAAY,GACb,MAAM,gBAAgB,CAAA;AACvB,OAAO,EAAE,wBAAwB,EAAE,MAAM,uBAAuB,CAAA;AAChE,OAAO,EAAE,4BAA4B,EAAE,MAAM,QAAQ,CAAA;
|
|
1
|
+
{"version":3,"file":"afterCreateAutoruns.js","sourceRoot":"","sources":["../../src/MsaViewPanel/afterCreateAutoruns.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE/C,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAA;AAC/C,OAAO,EAAE,qBAAqB,EAAE,MAAM,yBAAyB,CAAA;AAC/D,OAAO,EACL,cAAc,EACd,mBAAmB,EACnB,eAAe,EACf,YAAY,GACb,MAAM,gBAAgB,CAAA;AACvB,OAAO,EAAE,wBAAwB,EAAE,MAAM,uBAAuB,CAAA;AAChE,OAAO,EAAE,4BAA4B,EAAE,MAAM,QAAQ,CAAA;AAerD,SAAS,aAAa,CAAC,IAAa;IAClC,MAAM,CAAC,GAAG,IAA+B,CAAA;IACzC,OAAO,CAAC,CAAC,IAAI,KAAK,aAAa,IAAI,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,UAAU,CAAC,CAAA;AAChE,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,IAA+B;IAC5D,MAAM,EAAE,WAAW,EAAE,IAAI,EAAE,GAAG,IAAI,CAAA;IAClC,IAAI,WAAW,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACrC,mEAAmE;QACnE,CAAC;QAAA,CAAC,KAAK,IAAI,EAAE;YACX,IAAI,CAAC;gBACH,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,CAAA;gBAC/B,MAAM,UAAU,GAAG,MAAM,eAAe,CAAC,WAAW,CAAC,CAAA;gBACrD,IAAI,UAAU,EAAE,CAAC;oBACf,IAAI,UAAU,CAAC,GAAG,EAAE,CAAC;wBACnB,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,GAAG,CAAC,CAAA;oBAC7B,CAAC;oBACD,IAAI,UAAU,CAAC,IAAI,EAAE,CAAC;wBACpB,IAAI,CAAC,OAAO,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;oBAC/B,CAAC;gBACH,CAAC;YACH,CAAC;YAAC,OAAO,CAAC,EAAE,CAAC;gBACX,OAAO,CAAC,KAAK,CAAC,yCAAyC,EAAE,CAAC,CAAC,CAAA;YAC7D,CAAC;oBAAS,CAAC;gBACT,IAAI,CAAC,oBAAoB,CAAC,KAAK,CAAC,CAAA;YAClC,CAAC;QACH,CAAC,CAAC,EAAE,CAAA;IACN,CAAC;AACH,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,IAA+B;IAClE,MAAM,EAAE,IAAI,EAAE,WAAW,EAAE,GAAG,IAAI,CAAA;IAClC,IAAI,IAAI,CAAC,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,CAAC;QACpC,MAAM,aAAa,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,cAAc,CAAC,CAAA;QACnE,IAAI,aAAa,EAAE,CAAC;YAClB,OAAM;QACR,CAAC;QAED,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,CAAA;QAC7B,MAAM,QAAQ,GAAG,IAAI,CAAC,IAAI,CAAC,IAAI,CAAA;QAE/B,IAAI,OAAO,IAAI,QAAQ,EAAE,CAAC;YACxB,mEAAmE;YACnE,CAAC;YAAA,CAAC,KAAK,IAAI,EAAE;gBACX,IAAI,CAAC;oBACH,MAAM,KAAK,GAAG,mBAAmB,EAAE,CAAA;oBACnC,MAAM,OAAO,GAAG,MAAM,YAAY,CAAC,KAAK,EAAE;wBACxC,GAAG,EAAE,OAAO;wBACZ,IAAI,EAAE,QAAQ;wBACd,YAAY,EAAE,IAAI,CAAC,IAAI,CAAC,YAAY;qBACrC,CAAC,CAAA;oBACF,IAAI,OAAO,EAAE,CAAC;wBACZ,IAAI,CAAC,cAAc,CAAC,KAAK,CAAC,CAAA;oBAC5B,CAAC;gBACH,CAAC;gBAAC,OAAO,CAAC,EAAE,CAAC;oBACX,OAAO,CAAC,KAAK,CAAC,wCAAwC,EAAE,CAAC,CAAC,CAAA;gBAC5D,CAAC;YACH,CAAC,CAAC,EAAE,CAAA;QACN,CAAC;IACH,CAAC;AACH,CAAC;AAED,MAAM,UAAU,mBAAmB,CAAC,IAA+B;IACjE,IAAI,IAAI,CAAC,WAAW,EAAE,CAAC;QACrB,mEAAmE;QACnE,CAAC;QAAA,CAAC,KAAK,IAAI,EAAE;YACX,IAAI,CAAC;gBACH,IAAI,CAAC,WAAW,CAAC,kBAAkB,CAAC,CAAA;gBACpC,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAA;gBACxB,MAAM,IAAI,GAAG,MAAM,aAAa,CAAC,EAAE,IAAI,EAAE,CAAC,CAAA;gBAC1C,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;gBAClB,IAAI,CAAC,cAAc,CAAC,SAAS,CAAC,CAAA;YAChC,CAAC;YAAC,OAAO,CAAC,EAAE,CAAC;gBACX,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;gBAChB,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YAClB,CAAC;oBAAS,CAAC;gBACT,IAAI,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;YACtB,CAAC;QACH,CAAC,CAAC,EAAE,CAAA;IACN,CAAC;AACH,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,IAA+B;IACzD,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAA;IACrB,IAAI,IAAI,EAAE,CAAC;QACT,mEAAmE;QACnE,CAAC;QAAA,CAAC,KAAK,IAAI,EAAE;YACX,IAAI,CAAC;gBACH,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAA;gBACxB,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,YAAY,EAAE,GAAG,IAAI,CAAA;gBAEjE,IAAI,MAAM,EAAE,CAAC;oBACX,MAAM,EAAE,GAAG,4BAA4B,CAAC,MAAM,CAAC,CAAA;oBAC/C,IAAI,EAAE,EAAE,CAAC;wBACP,IAAI,CAAC,YAAY,CAAC,EAAE,CAAC,CAAA;wBACrB,IAAI,CAAC,eAAe,CAAC,OAAO,CAAC,CAAA;oBAC/B,CAAC;gBACH,CAAC;gBAED,IAAI,YAAY,EAAE,CAAC;oBACjB,IAAI,CAAC,eAAe,CAAC,YAAY,CAAC,CAAA;gBACpC,CAAC;gBAED,IAAI,OAAO,EAAE,CAAC;oBACZ,IAAI,CAAC,MAAM,CAAC,OAAO,CAAC,CAAA;gBACtB,CAAC;qBAAM,IAAI,MAAM,EAAE,CAAC;oBAClB,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC,CAAA;oBACpC,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;wBACjB,MAAM,IAAI,KAAK,CAAC,wBAAwB,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAA;oBAC5D,CAAC;oBACD,MAAM,IAAI,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAA;oBAClC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;gBACnB,CAAC;gBAED,IAAI,QAAQ,EAAE,CAAC;oBACb,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAA;gBACxB,CAAC;qBAAM,IAAI,OAAO,EAAE,CAAC;oBACnB,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,OAAO,CAAC,CAAA;oBACrC,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;wBACjB,MAAM,IAAI,KAAK,CAAC,yBAAyB,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAA;oBAC7D,CAAC;oBACD,MAAM,IAAI,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAA;oBAClC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;gBACpB,CAAC;gBAED,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,CAAA;YACzB,CAAC;YAAC,OAAO,CAAC,EAAE,CAAC;gBACX,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;gBAChB,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YAClB,CAAC;QACH,CAAC,CAAC,EAAE,CAAA;IACN,CAAC;AACH,CAAC;AAED,MAAM,UAAU,sBAAsB,CAAC,IAA+B;IACpE,MAAM,EAAE,QAAQ,EAAE,aAAa,EAAE,GAAG,IAAI,CAAA;IACxC,MAAM,EAAE,GACN,QAAQ,KAAK,SAAS;QACpB,CAAC,CAAC,SAAS;QACX,CAAC,CAAC,qBAAqB,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,KAAK,EAAE,QAAQ,EAAE,CAAC,CAAA;IAC7D,MAAM,EAAE,GACN,aAAa,KAAK,SAAS;QACzB,CAAC,CAAC,SAAS;QACX,CAAC,CAAC,qBAAqB,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,KAAK,EAAE,aAAa,EAAE,CAAC,CAAA;IAElE,IAAI,CAAC,sBAAsB,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AACxD,CAAC;AAED,MAAM,UAAU,4BAA4B,CAAC,IAA+B;IAC1E,MAAM,EAAE,QAAQ,EAAE,qBAAqB,EAAE,GAAG,IAAI,CAAA;IAChD,IAAI,qBAAqB,CAAC,MAAM,KAAK,CAAC,E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import type { ReactNode } from 'react';
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import React, { Component } from 'react';
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interface Props {
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children: ReactNode;
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}
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interface State {
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hasError: boolean;
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error: unknown;
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}
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export declare class ErrorBoundary extends Component<Props, State> {
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constructor(props: Props);
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static getDerivedStateFromError(error: unknown): {
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hasError: boolean;
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error: unknown;
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};
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componentDidCatch(error: unknown, info: React.ErrorInfo): void;
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render(): string | number | bigint | boolean | React.JSX.Element | Iterable<ReactNode> | Promise<string | number | bigint | boolean | React.ReactPortal | React.ReactElement<unknown, string | React.JSXElementConstructor<any>> | Iterable<ReactNode> | null | undefined> | null | undefined;
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}
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export {};
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@@ -0,0 +1,22 @@
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import React, { Component } from 'react';
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import { ErrorMessage } from '@jbrowse/core/ui';
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export class ErrorBoundary extends Component {
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constructor(props) {
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super(props);
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this.state = { hasError: false, error: null };
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}
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static getDerivedStateFromError(error) {
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return { hasError: true, error };
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}
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componentDidCatch(error, info) {
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console.error('MsaViewPanel error:', error, info.componentStack);
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}
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render() {
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if (this.state.hasError) {
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return (React.createElement("div", { style: { padding: 20 } },
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React.createElement(ErrorMessage, { error: this.state.error })));
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}
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return this.props.children;
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}
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}
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//# sourceMappingURL=ErrorBoundary.js.map
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@@ -0,0 +1 @@
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1
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{"version":3,"file":"ErrorBoundary.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/ErrorBoundary.tsx"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,OAAO,CAAA;AAExC,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAW/C,MAAM,OAAO,aAAc,SAAQ,SAAuB;IACxD,YAAY,KAAY;QACtB,KAAK,CAAC,KAAK,CAAC,CAAA;QACZ,IAAI,CAAC,KAAK,GAAG,EAAE,QAAQ,EAAE,KAAK,EAAE,KAAK,EAAE,IAAI,EAAE,CAAA;IAC/C,CAAC;IAED,MAAM,CAAC,wBAAwB,CAAC,KAAc;QAC5C,OAAO,EAAE,QAAQ,EAAE,IAAI,EAAE,KAAK,EAAE,CAAA;IAClC,CAAC;IAED,iBAAiB,CAAC,KAAc,EAAE,IAAqB;QACrD,OAAO,CAAC,KAAK,CAAC,qBAAqB,EAAE,KAAK,EAAE,IAAI,CAAC,cAAc,CAAC,CAAA;IAClE,CAAC;IAED,MAAM;QACJ,IAAI,IAAI,CAAC,KAAK,CAAC,QAAQ,EAAE,CAAC;YACxB,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,EAAE,EAAE;gBACzB,oBAAC,YAAY,IAAC,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,KAAK,GAAI,CACrC,CACP,CAAA;QACH,CAAC;QAED,OAAO,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAA;IAC5B,CAAC;CACF"}
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@@ -2,11 +2,13 @@ import React from 'react';
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2
2
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import { LoadingEllipses } from '@jbrowse/core/ui';
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3
3
|
import { observer } from 'mobx-react';
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4
4
|
import { MSAView } from 'react-msaview';
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5
|
+
import { ErrorBoundary } from './ErrorBoundary';
|
|
5
6
|
import LoadingBLAST from './LoadingBLAST';
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|
6
7
|
const MsaViewPanel = observer(function MsaViewPanel2({ model, }) {
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7
8
|
const { blastParams, loadingStoredData } = model;
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8
|
-
return (React.createElement(
|
|
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-
React.createElement(
|
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9
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+
return (React.createElement(ErrorBoundary, null,
|
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React.createElement("div", null, blastParams ? (React.createElement(LoadingBLAST, { model: model, baseUrl: blastParams.baseUrl })) : loadingStoredData ? (React.createElement("div", { style: { padding: 20 } },
|
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11
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+
React.createElement(LoadingEllipses, { message: "Loading MSA data", variant: "h6" }))) : (React.createElement(MSAView, { model: model })))));
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10
12
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});
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11
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export default MsaViewPanel;
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//# sourceMappingURL=MsaViewPanel.js.map
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@@ -1 +1 @@
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1
|
-
{"version":3,"file":"MsaViewPanel.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/MsaViewPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,OAAO,EAAE,MAAM,eAAe,CAAA;AAEvC,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAIzC,MAAM,YAAY,GAAG,QAAQ,CAAC,SAAS,aAAa,CAAC,EACnD,KAAK,GAGN;IACC,MAAM,EAAE,WAAW,EAAE,iBAAiB,EAAE,GAAG,KAAK,CAAA;IAChD,OAAO,CACL,iCACG,WAAW,CAAC,CAAC,CAAC,CACb,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,EAAE,OAAO,EAAE,WAAW,CAAC,OAAO,GAAI,CAC7D,CAAC,CAAC,CAAC,iBAAiB,CAAC,CAAC,CAAC,CACtB,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,EAAE,EAAE;
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1
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+
{"version":3,"file":"MsaViewPanel.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/MsaViewPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,OAAO,EAAE,MAAM,eAAe,CAAA;AAEvC,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAA;AAC/C,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAIzC,MAAM,YAAY,GAAG,QAAQ,CAAC,SAAS,aAAa,CAAC,EACnD,KAAK,GAGN;IACC,MAAM,EAAE,WAAW,EAAE,iBAAiB,EAAE,GAAG,KAAK,CAAA;IAChD,OAAO,CACL,oBAAC,aAAa;QACZ,iCACG,WAAW,CAAC,CAAC,CAAC,CACb,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,EAAE,OAAO,EAAE,WAAW,CAAC,OAAO,GAAI,CAC7D,CAAC,CAAC,CAAC,iBAAiB,CAAC,CAAC,CAAC,CACtB,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,EAAE,EAAE;YACzB,oBAAC,eAAe,IAAC,OAAO,EAAC,kBAAkB,EAAC,OAAO,EAAC,IAAI,GAAG,CACvD,CACP,CAAC,CAAC,CAAC,CACF,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI,CAC1B,CACG,CACQ,CACjB,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,YAAY,CAAA"}
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@@ -609,21 +609,9 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
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fitHorizontally(): void;
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afterCreate(): void;
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611
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} & {
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-
/**
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613
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-
* #volatile
|
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-
*/
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rid: string | undefined;
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616
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-
/**
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617
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-
* #volatile
|
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618
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-
*/
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619
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|
progress: string;
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/**
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621
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-
* #volatile
|
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622
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-
*/
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623
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error: unknown;
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-
/**
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625
|
-
* #volatile
|
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626
|
-
*/
|
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627
615
|
loadingStoredData: boolean;
|
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628
616
|
} & {
|
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629
617
|
/**
|
|
@@ -132,7 +132,7 @@ export default function stateModelFactory() {
|
|
|
132
132
|
const proteinView = views.find((v) => v.id === conn.proteinViewId);
|
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133
133
|
return proteinView ? { ...conn, proteinView } : undefined;
|
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134
134
|
})
|
|
135
|
-
.filter((c) =>
|
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135
|
+
.filter((c) => c !== undefined);
|
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136
136
|
},
|
|
137
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|
}))
|
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138
138
|
.views(self => ({
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
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