jbrowse-plugin-msaview 2.4.2 → 2.4.4

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastRIDPanel.js

@@ -1,20 +1,17 @@
 import React, { useState } from 'react';
-import { ErrorMessage } from '@jbrowse/core/ui';
-import { getContainingView } from '@jbrowse/core/util';
-import { Button, DialogActions, DialogContent, MenuItem, Typography, } from '@mui/material';
+import { Typography } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
+import MsaAlgorithmSelect from './MsaAlgorithmSelect';
 import { blastLaunchView } from './blastLaunchView';
-import { msaAlgorithms } from './consts';
 import ExternalLink from '../../../components/ExternalLink';
 import TextField2 from '../../../components/TextField2';
-import { getGeneDisplayName, getTranscriptDisplayName } from '../../util';
+import { getBlastViewTitle, getLinearGenomeView } from '../../util';
+import LaunchPanelContent from '../LaunchPanelContent';
+import SubmitCancelActions from '../SubmitCancelActions';
 import TranscriptSelector from '../TranscriptSelector';
 import { useTranscriptSelection } from '../useTranscriptSelection';
 const useStyles = makeStyles()({
-    dialogContent: {
-        width: '80em',
-    },
     marginBottom: {
         marginBottom: 16,
     },
@@ -27,39 +24,34 @@ const useStyles = makeStyles()({
 });
 const NCBIBlastRIDPanel = observer(function ({ handleClose, feature, model, children, baseUrl, }) {
     const { classes } = useStyles();
-    const view = getContainingView(model);
+    const view = getLinearGenomeView(model);
     const [launchViewError, setLaunchViewError] = useState();
     const [rid, setRid] = useState('');
     const [selectedMsaAlgorithm, setSelectedMsaAlgorithm] = useState('clustalo');
-    const { options, selectedId, setSelectedId, selectedTranscript, proteinSequence, error: proteinSequenceError, } = useTranscriptSelection({ feature, view });
-    const e = proteinSequenceError ?? launchViewError;
+    const transcriptSelection = useTranscriptSelection({ feature, view });
+    const { selectedTranscript, proteinSequence } = transcriptSelection;
+    const e = transcriptSelection.error ?? launchViewError;
     const trimmedRid = rid.trim();
     return (React.createElement(React.Fragment, null,
-        React.createElement(DialogContent, { className: classes.dialogContent },
+        React.createElement(LaunchPanelContent, { error: e },
             children,
-            e ? React.createElement(ErrorMessage, { error: e }) : null,
             React.createElement(Typography, { variant: "body2", className: classes.marginBottom }, "Enter the RID (Request ID) from a previously submitted NCBI BLAST query. You can find the RID in the BLAST results page URL or at the top of the results page. RIDs are typically valid for 24-36 hours after submission."),
             React.createElement(TextField2, { variant: "outlined", label: "BLAST RID", placeholder: "e.g., ABC12345", fullWidth: true, className: classes.marginBottom, value: rid, onChange: event => {
                     setRid(event.target.value);
                 } }),
             trimmedRid ? (React.createElement(Typography, { variant: "body2", className: classes.marginBottom },
                 React.createElement(ExternalLink, { href: `${baseUrl}?CMD=Get&RID=${trimmedRid}` }, "View BLAST results on NCBI"))) : null,
-            React.createElement(TextField2, { variant: "outlined", label: "MSA Algorithm", className: classes.ridField, select: true, value: selectedMsaAlgorithm, onChange: event => {
-                    setSelectedMsaAlgorithm(event.target.value);
-                } }, msaAlgorithms.map(val => (React.createElement(MenuItem, { value: val, key: val }, val)))),
-            React.createElement(TranscriptSelector, { feature: feature, options: options, selectedId: selectedId, selectedTranscript: selectedTranscript, onTranscriptChange: setSelectedId, proteinSequence: proteinSequence }),
+            React.createElement(MsaAlgorithmSelect, { className: classes.ridField, value: selectedMsaAlgorithm, onChange: setSelectedMsaAlgorithm }),
+            React.createElement(TranscriptSelector, { feature: feature, ...transcriptSelection }),
             React.createElement(Typography, { className: classes.infoText }, "This will fetch the BLAST results for the provided RID and run them through a multiple sequence alignment. The protein sequence from the selected transcript will be added as the query sequence in the MSA.")),
-        React.createElement(DialogActions, null,
-            React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
-                    try {
-                        if (!selectedTranscript || !trimmedRid) {
-                            return;
-                        }
+        React.createElement(SubmitCancelActions, { submitDisabled: !proteinSequence || !trimmedRid, onSubmit: () => {
+                try {
+                    if (selectedTranscript && trimmedRid) {
                         setLaunchViewError(undefined);
                         blastLaunchView({
                             feature: selectedTranscript,
                             view,
-                            newViewTitle: `BLAST - ${getGeneDisplayName(feature)} - ${getTranscriptDisplayName(selectedTranscript)}`,
+                            newViewTitle: getBlastViewTitle(feature, selectedTranscript),
                             blastParams: {
                                 baseUrl,
                                 blastProgram: 'blastp',
@@ -72,14 +64,12 @@ const NCBIBlastRIDPanel = observer(function ({ handleClose, feature, model, chil
                         });
                         handleClose();
                     }
-                    catch (e) {
-                        console.error(e);
-                        setLaunchViewError(e);
-                    }
-                }, disabled: !proteinSequence || !trimmedRid }, "Submit"),
-            React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
-                    handleClose();
-                } }, "Cancel"))));
+                }
+                catch (e) {
+                    console.error(e);
+                    setLaunchViewError(e);
+                }
+            }, onCancel: handleClose })));
 });
 export default NCBIBlastRIDPanel;
 //# sourceMappingURL=NCBIBlastRIDPanel.js.map

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastRIDPanel.js.map

@@ -1 +1 @@
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package/dist/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.js

@@ -1,18 +1,11 @@
 import useSWR from 'swr';
 import { clearAllCachedResults, deleteCachedResult, getAllCachedResults, } from '../../../utils/blastCache';
-const swrConfig = {
-    revalidateOnFocus: false,
-    revalidateOnReconnect: false,
-    revalidateIfStale: false,
-    refreshWhenHidden: false,
-    refreshWhenOffline: false,
-    shouldRetryOnError: false,
-};
+import { staticSwrConfig } from '../../../utils/swrConfig';
 export function useCachedBlastResults(geneIds) {
     const { data: results, error, mutate, } = useSWR(`cached-blast-${geneIds.join(',')}`, async () => {
         const cached = await getAllCachedResults();
         return cached.filter(r => r.geneId && geneIds.includes(r.geneId));
-    }, swrConfig);
+    }, staticSwrConfig);
     const handleDelete = async (id) => {
         await deleteCachedResult(id);
         await mutate(results => results?.filter(result => result.id !== id) ?? [], false);

package/dist/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.js.map

@@ -1 +1 @@
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+{"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;AAClC,OAAO,EAAE,eAAe,EAAE,MAAM,0BAA0B,CAAA;AAE1D,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,eAAe,CAChB,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"}

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

@@ -1,29 +1,28 @@
 import React, { useState } from 'react';
-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 { LoadingEllipses, SanitizedHTML } from '@jbrowse/core/ui';
+import { getEnv, getSession } from '@jbrowse/core/util';
+import { MenuItem } from '@mui/material';
 import { observer } from 'mobx-react';
 import useSWR from 'swr';
 import { makeStyles } from 'tss-react/mui';
 import TextField2 from '../../../components/TextField2';
-import { getGeneDisplayName } from '../../util';
+import { staticSwrConfig } from '../../../utils/swrConfig';
+import { getGeneDisplayName, getLinearGenomeView } from '../../util';
+import LaunchPanelContent from '../LaunchPanelContent';
+import SubmitCancelActions from '../SubmitCancelActions';
 import TranscriptSelector from '../TranscriptSelector';
 import { useTranscriptSelection } from '../useTranscriptSelection';
-import { swrFlags } from './consts';
 import { fetchMSA, fetchMSAList } from './fetchMSAData';
 import { preCalculatedLaunchView } from './preCalculatedLaunchView';
 import { readMsaDatasets } from './types';
 const useStyles = makeStyles()({
-    dialogContent: {
-        width: '80em',
-    },
     selectedContainer: {
         marginTop: 50,
     },
 });
 const PreLoadedMSA = observer(function ({ model, feature, handleClose, }) {
     const session = getSession(model);
-    const view = getContainingView(model);
+    const view = getLinearGenomeView(model);
     const { classes } = useStyles();
     const { pluginManager } = getEnv(model);
     const { assemblyNames } = view;
@@ -31,19 +30,26 @@ const PreLoadedMSA = observer(function ({ model, feature, handleClose, }) {
     const datasets = readMsaDatasets(session.jbrowse);
     const [selectedDatasetId, setSelectedDatasetId] = useState(datasets?.[0]?.datasetId);
     const selectedDataset = datasets?.find(d => d.datasetId === selectedDatasetId);
-    const { data: msaList, isLoading: msaListLoading, error: msaListFetchError, } = useSWR(selectedDataset ? `${selectedDataset.datasetId}-msa-list` : null, () => fetchMSAList({ config: selectedDataset.adapter, pluginManager }), swrFlags);
-    const { options: transcripts, selectedId, setSelectedId, selectedTranscript, proteinSequence, error: proteinSequenceError, } = useTranscriptSelection({ feature, view, validIds: msaList });
+    const { data: msaList, isLoading: msaListLoading, error: msaListFetchError, } = useSWR(selectedDataset ? `${selectedDataset.datasetId}-msa-list` : null, () => fetchMSAList({ config: selectedDataset.adapter, pluginManager }), staticSwrConfig);
+    const transcriptSelection = useTranscriptSelection({
+        feature,
+        view,
+        validIds: msaList,
+    });
+    const { selectedId, selectedTranscript } = transcriptSelection;
     const { data: msaData, isLoading: msaDataLoading, error: msaDataFetchError, } = useSWR(selectedId && selectedDataset && msaList
         ? `${selectedDataset.datasetId}-${selectedId}-${msaList.length}-msa`
         : null, () => fetchMSA({
         msaId: selectedId,
         config: selectedDataset.adapter,
         pluginManager,
-    }), swrFlags);
-    const e = msaListFetchError ?? msaDataFetchError ?? proteinSequenceError ?? viewError;
+    }), staticSwrConfig);
+    const e = msaListFetchError ??
+        msaDataFetchError ??
+        transcriptSelection.error ??
+        viewError;
     return (React.createElement(React.Fragment, null,
-        React.createElement(DialogContent, { className: classes.dialogContent },
-            e ? React.createElement(ErrorMessage, { error: e }) : null,
+        React.createElement(LaunchPanelContent, { error: e },
             React.createElement(TextField2, { select: true, label: "Select MSA dataset", value: selectedDatasetId, onChange: event => {
                     setSelectedDatasetId(event.target.value);
                 } }, datasets?.map(d => (React.createElement(MenuItem, { key: d.datasetId, value: d.datasetId }, d.name)))),
@@ -52,13 +58,10 @@ const PreLoadedMSA = observer(function ({ model, feature, handleClose, }) {
                 msaListLoading ? (React.createElement(LoadingEllipses, { variant: "h6", message: `Loading available MSAs for (${selectedDataset.name})` })) : null,
                 msaList ? (React.createElement("div", null,
                     React.createElement(SanitizedHTML, { html: selectedDataset.description }),
-                    React.createElement(TranscriptSelector, { feature: feature, options: transcripts, selectedId: selectedId, selectedTranscript: selectedTranscript, onTranscriptChange: setSelectedId, proteinSequence: proteinSequence, validIds: msaList }))) : null)) : null),
-        React.createElement(DialogActions, null,
-            React.createElement(Button, { color: "primary", variant: "contained", disabled: !selectedTranscript || !msaData?.length, onClick: () => {
-                    try {
-                        if (!selectedTranscript || !msaData) {
-                            return;
-                        }
+                    React.createElement(TranscriptSelector, { feature: feature, ...transcriptSelection }))) : null)) : null),
+        React.createElement(SubmitCancelActions, { submitDisabled: !selectedTranscript || !msaData?.length, onSubmit: () => {
+                try {
+                    if (selectedTranscript && msaData) {
                         const querySeqName = `${selectedId}_${assemblyNames[0]}`;
                         preCalculatedLaunchView({
                             session,
@@ -74,13 +77,11 @@ const PreLoadedMSA = observer(function ({ model, feature, handleClose, }) {
                         });
                         handleClose();
                     }
-                    catch (e) {
-                        setViewError(e);
-                    }
-                } }, "Submit"),
-            React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
-                    handleClose();
-                } }, "Cancel"))));
+                }
+                catch (e) {
+                    setViewError(e);
+                }
+            }, onCancel: handleClose })));
 });
 export default PreLoadedMSA;
 //# sourceMappingURL=PreLoadedMSADataPanel.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"PreLoadedMSADataPanel.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,eAAe,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAA;AACjE,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AACvD,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AACxC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,MAAM,MAAM,KAAK,CAAA;AACxB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,EAAE,eAAe,EAAE,MAAM,0BAA0B,CAAA;AAC1D,OAAO,EAAE,kBAAkB,EAAE,mBAAmB,EAAE,MAAM,YAAY,CAAA;AACpE,OAAO,kBAAkB,MAAM,uBAAuB,CAAA;AACtD,OAAO,mBAAmB,MAAM,wBAAwB,CAAA;AACxD,OAAO,kBAAkB,MAAM,uBAAuB,CAAA;AACtD,OAAO,EAAE,sBAAsB,EAAE,MAAM,2BAA2B,CAAA;AAClE,OAAO,EAAE,QAAQ,EAAE,YAAY,EAAE,MAAM,gBAAgB,CAAA;AACvD,OAAO,EAAE,uBAAuB,EAAE,MAAM,2BAA2B,CAAA;AACnE,OAAO,EAAE,eAAe,EAAE,MAAM,SAAS,CAAA;AAIzC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,iBAAiB,EAAE;QACjB,SAAS,EAAE,EAAE;KACd;CACF,CAAC,CAAA;AAEF,MAAM,YAAY,GAAG,QAAQ,CAAC,UAAU,EACtC,KAAK,EACL,OAAO,EACP,WAAW,GAKZ;IACC,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,IAAI,GAAG,mBAAmB,CAAC,KAAK,CAAC,CAAA;IACvC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,aAAa,EAAE,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IACvC,MAAM,EAAE,aAAa,EAAE,GAAG,IAAI,CAAA;IAC9B,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,EAAW,CAAA;IAErD,MAAM,QAAQ,GAAG,eAAe,CAAC,OAAO,CAAC,OAAO,CAAC,CAAA;IACjD,MAAM,CAAC,iBAAiB,EAAE,oBAAoB,CAAC,GAAG,QAAQ,CACxD,QAAQ,EAAE,CAAC,CAAC,CAAC,EAAE,SAAS,CACzB,CAAA;IACD,MAAM,eAAe,GAAG,QAAQ,EAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,SAAS,KAAK,iBAAiB,CAAC,CAAA;IAC9E,MAAM,EACJ,IAAI,EAAE,OAAO,EACb,SAAS,EAAE,cAAc,EACzB,KAAK,EAAE,iBAAiB,GACzB,GAAG,MAAM,CACR,eAAe,CAAC,CAAC,CAAC,GAAG,eAAe,CAAC,SAAS,WAAW,CAAC,CAAC,CAAC,IAAI,EAChE,GAAG,EAAE,CAAC,YAAY,CAAC,EAAE,MAAM,EAAE,eAAgB,CAAC,OAAO,EAAE,aAAa,EAAE,CAAC,EACvE,eAAe,CAChB,CAAA;IAED,MAAM,mBAAmB,GAAG,sBAAsB,CAAC;QACjD,OAAO;QACP,IAAI;QACJ,QAAQ,EAAE,OAAO;KAClB,CAAC,CAAA;IACF,MAAM,EAAE,UAAU,EAAE,kBAAkB,EAAE,GAAG,mBAAmB,CAAA;IAE9D,MAAM,EACJ,IAAI,EAAE,OAAO,EACb,SAAS,EAAE,cAAc,EACzB,KAAK,EAAE,iBAAiB,GACzB,GAAG,MAAM,CACR,UAAU,IAAI,eAAe,IAAI,OAAO;QACtC,CAAC,CAAC,GAAG,eAAe,CAAC,SAAS,IAAI,UAAU,IAAI,OAAO,CAAC,MAAM,MAAM;QACpE,CAAC,CAAC,IAAI,EACR,GAAG,EAAE,CACH,QAAQ,CAAC;QACP,KAAK,EAAE,UAAU;QACjB,MAAM,EAAE,eAAgB,CAAC,OAAO;QAChC,aAAa;KACd,CAAC,EACJ,eAAe,CAChB,CAAA;IAED,MAAM,CAAC,GACL,iBAAiB;QACjB,iBAAiB;QACjB,mBAAmB,CAAC,KAAK;QACzB,SAAS,CAAA;IACX,OAAO,CACL;QACE,oBAAC,kBAAkB,IAAC,KAAK,EAAE,CAAC;YAC1B,oBAAC,UAAU,IACT,MAAM,QACN,KAAK,EAAC,oBAAoB,EAC1B,KAAK,EAAE,iBAAiB,EACxB,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,oBAAoB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAC1C,CAAC,IAEA,QAAQ,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAClB,oBAAC,QAAQ,IAAC,GAAG,EAAE,CAAC,CAAC,SAAS,EAAE,KAAK,EAAE,CAAC,CAAC,SAAS,IAC3C,CAAC,CAAC,IAAI,CACE,CACZ,CAAC,CACS;YAEZ,eAAe,CAAC,CAAC,CAAC,CACjB,6BAAK,SAAS,EAAE,OAAO,CAAC,iBAAiB;gBACtC,CAAC,cAAc,IAAI,cAAc,CAAC,CAAC,CAAC,CACnC,oBAAC,eAAe,IACd,OAAO,EAAC,IAAI,EACZ,OAAO,EAAE,oBAAoB,UAAU,GAAG,GAC1C,CACH,CAAC,CAAC,CAAC,IAAI;gBACP,cAAc,CAAC,CAAC,CAAC,CAChB,oBAAC,eAAe,IACd,OAAO,EAAC,IAAI,EACZ,OAAO,EAAE,+BAA+B,eAAe,CAAC,IAAI,GAAG,GAC/D,CACH,CAAC,CAAC,CAAC,IAAI;gBAEP,OAAO,CAAC,CAAC,CAAC,CACT;oBACE,oBAAC,aAAa,IAAC,IAAI,EAAE,eAAe,CAAC,WAAW,GAAI;oBACpD,oBAAC,kBAAkB,IACjB,OAAO,EAAE,OAAO,KACZ,mBAAmB,GACvB,CACE,CACP,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAC,CAAC,CAAC,IAAI,CACW;QAErB,oBAAC,mBAAmB,IAClB,cAAc,EAAE,CAAC,kBAAkB,IAAI,CAAC,OAAO,EAAE,MAAM,EACvD,QAAQ,EAAE,GAAG,EAAE;gBACb,IAAI,CAAC;oBACH,IAAI,kBAAkB,IAAI,OAAO,EAAE,CAAC;wBAClC,MAAM,YAAY,GAAG,GAAG,UAAU,IAAI,aAAa,CAAC,CAAC,CAAC,EAAE,CAAA;wBACxD,uBAAuB,CAAC;4BACtB,OAAO;4BACP,YAAY,EAAE,kBAAkB,CAAC,kBAAkB,CAAC;4BACpD,IAAI;4BACJ,YAAY;4BACZ,OAAO,EAAE,kBAAkB;4BAC3B,IAAI,EAAE;gCACJ,GAAG,EAAE,OAAO;qCACT,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC;qCACjD,IAAI,CAAC,IAAI,CAAC;6BACd;yBACF,CAAC,CAAA;wBACF,WAAW,EAAE,CAAA;oBACf,CAAC;gBACH,CAAC;gBAAC,OAAO,CAAC,EAAE,CAAC;oBACX,YAAY,CAAC,CAAC,CAAC,CAAA;gBACjB,CAAC;YACH,CAAC,EACD,QAAQ,EAAE,WAAW,GACrB,CACD,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,YAAY,CAAA"}

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

@@ -1,12 +1,14 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
-export async function fetchMSAList({ config, pluginManager, }) {
+async function getMsaAdapter(pluginManager, config) {
     const result = await getAdapter(pluginManager, 'msa', config);
-    // @ts-expect-error
-    return result.dataAdapter.getMSAList();
+    return result.dataAdapter;
+}
+export async function fetchMSAList({ config, pluginManager, }) {
+    const adapter = await getMsaAdapter(pluginManager, config);
+    return adapter.getMSAList();
 }
 export async function fetchMSA({ config, pluginManager, msaId, }) {
-    const result = await getAdapter(pluginManager, 'msa', config);
-    // @ts-expect-error
-    return result.dataAdapter.getMSA(msaId);
+    const adapter = await getMsaAdapter(pluginManager, config);
+    return adapter.getMSA(msaId);
 }
 //# sourceMappingURL=fetchMSAData.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"fetchMSAData.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/PreLoadedMSA/fetchMSAData.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,8CAA8C,CAAA;AAMzE,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"}
+{"version":3,"file":"fetchMSAData.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/PreLoadedMSA/fetchMSAData.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,8CAA8C,CAAA;AAWzE,KAAK,UAAU,aAAa,CAC1B,aAA4B,EAC5B,MAA6B;IAE7B,MAAM,MAAM,GAAG,MAAM,UAAU,CAAC,aAAa,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;IAC7D,OAAO,MAAM,CAAC,WAAwC,CAAA;AACxD,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,YAAY,CAAC,EACjC,MAAM,EACN,aAAa,GAId;IACC,MAAM,OAAO,GAAG,MAAM,aAAa,CAAC,aAAa,EAAE,MAAM,CAAC,CAAA;IAC1D,OAAO,OAAO,CAAC,UAAU,EAAE,CAAA;AAC7B,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,QAAQ,CAAC,EAC7B,MAAM,EACN,aAAa,EACb,KAAK,GAKN;IACC,MAAM,OAAO,GAAG,MAAM,aAAa,CAAC,aAAa,EAAE,MAAM,CAAC,CAAA;IAC1D,OAAO,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;AAC9B,CAAC"}

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

@@ -0,0 +1,8 @@
+import React from 'react';
+export default function SubmitCancelActions({ onSubmit, onCancel, submitDisabled, submitLabel, cancelLabel, }: {
+    onSubmit: () => void;
+    onCancel: () => void;
+    submitDisabled?: boolean;
+    submitLabel?: string;
+    cancelLabel?: string;
+}): React.JSX.Element;

package/dist/LaunchMsaView/components/SubmitCancelActions.js

@@ -0,0 +1,12 @@
+import React from 'react';
+import { Button, DialogActions } from '@mui/material';
+export default function SubmitCancelActions({ onSubmit, onCancel, submitDisabled, submitLabel = 'Submit', cancelLabel = 'Cancel', }) {
+    return (React.createElement(DialogActions, null,
+        React.createElement(Button, { color: "primary", variant: "contained", disabled: submitDisabled, onClick: () => {
+                onSubmit();
+            } }, submitLabel),
+        React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
+                onCancel();
+            } }, cancelLabel)));
+}
+//# sourceMappingURL=SubmitCancelActions.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"SubmitCancelActions.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/SubmitCancelActions.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,MAAM,eAAe,CAAA;AAErD,MAAM,CAAC,OAAO,UAAU,mBAAmB,CAAC,EAC1C,QAAQ,EACR,QAAQ,EACR,cAAc,EACd,WAAW,GAAG,QAAQ,EACtB,WAAW,GAAG,QAAQ,GAOvB;IACC,OAAO,CACL,oBAAC,aAAa;QACZ,oBAAC,MAAM,IACL,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,QAAQ,EAAE,cAAc,EACxB,OAAO,EAAE,GAAG,EAAE;gBACZ,QAAQ,EAAE,CAAA;YACZ,CAAC,IAEA,WAAW,CACL;QACT,oBAAC,MAAM,IACL,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;gBACZ,QAAQ,EAAE,CAAA;YACZ,CAAC,IAEA,WAAW,CACL,CACK,CACjB,CAAA;AACH,CAAC"}

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

@@ -1,11 +1,11 @@
 import React from 'react';
 import type { Feature } from '@jbrowse/core/util';
-export default function TranscriptSelector({ feature, options, selectedId, selectedTranscript, onTranscriptChange, proteinSequence, validIds, }: {
+export default function TranscriptSelector({ feature, options, selectedId, selectedTranscript, setSelectedId, proteinSequence, validIds, }: {
     feature: Feature;
     options: Feature[];
     selectedId: string;
     selectedTranscript: Feature | undefined;
-    onTranscriptChange: (transcriptId: string) => void;
+    setSelectedId: (transcriptId: string) => void;
     proteinSequence: string | undefined;
     validIds?: string[];
 }): React.JSX.Element;

package/dist/LaunchMsaView/components/TranscriptSelector.js

@@ -15,13 +15,13 @@ const useStyles = makeStyles()({
         marginLeft: 20,
     },
 });
-export default function TranscriptSelector({ feature, options, selectedId, selectedTranscript, onTranscriptChange, proteinSequence, validIds, }) {
+export default function TranscriptSelector({ feature, options, selectedId, selectedTranscript, setSelectedId, proteinSequence, validIds, }) {
     const { classes } = useStyles();
     const [showSequence, setShowSequence] = useState(false);
     return (React.createElement(React.Fragment, null,
         React.createElement("div", { className: classes.flex },
             React.createElement(TextField, { variant: "outlined", label: `Choose isoform of ${getGeneDisplayName(feature)}`, select: true, className: classes.minWidth, value: selectedId, onChange: event => {
-                    onTranscriptChange(event.target.value);
+                    setSelectedId(event.target.value);
                 } }, options.map(val => {
                 const inSet = validIds
                     ? validIds.some(id => featureMatchesId(val, id))

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

@@ -1 +1 @@
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package/dist/LaunchMsaView/components/useSWRFeatureSequence.js

@@ -1,6 +1,7 @@
 import { getSession } from '@jbrowse/core/util';
 import useSWR from 'swr';
 import { fetchSeq } from './fetchSeq';
+import { staticSwrConfig } from '../../utils/swrConfig';
 async function featureSequenceFetcher({ feature, assemblyName, view, }) {
     const session = getSession(view);
     const { start, end, refName } = feature.toJSON();
@@ -15,19 +16,8 @@ async function featureSequenceFetcher({ feature, assemblyName, view, }) {
 }
 export function useSWRFeatureSequence({ view, feature, }) {
     const assemblyName = view?.assemblyNames?.[0];
-    const { data, error } = useSWR(
-    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-    feature && assemblyName && view
-        ? [feature.id(), assemblyName, 'feature-sequence']
-        : null, () => featureSequenceFetcher({
-        feature: feature,
-        assemblyName: assemblyName,
-        view: view,
-    }), {
-        revalidateOnFocus: false,
-        revalidateOnReconnect: false,
-        revalidateIfStale: false,
-    });
+    const args = feature && assemblyName ? { feature, assemblyName, view } : undefined;
+    const { data, error } = useSWR(args ? [args.feature.id(), args.assemblyName, 'feature-sequence'] : null, () => featureSequenceFetcher(args), staticSwrConfig);
     return {
         sequence: data,
         error,

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

@@ -1 +1 @@
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package/dist/LaunchMsaView/components/useTranscriptSelection.js

@@ -1,24 +1,22 @@
 import { useMemo, useState } from 'react';
 import { featureMatchesId, getId, getSortedTranscriptFeatures } from '../util';
 import { useFeatureSequence } from './useFeatureSequence';
-function featureInValidIds(feature, validIds) {
-    return validIds.some(id => featureMatchesId(feature, id));
-}
 function findValidSelection(currentId, options, validIds) {
-    if (!validIds || validIds.length === 0) {
-        return undefined;
-    }
-    const currentFeature = options.find(opt => getId(opt) === currentId);
-    if (!currentFeature || featureInValidIds(currentFeature, validIds)) {
-        return undefined;
+    if (validIds && validIds.length > 0) {
+        const currentFeature = options.find(opt => getId(opt) === currentId);
+        const currentIsValid = currentFeature &&
+            validIds.some(id => featureMatchesId(currentFeature, id));
+        if (currentFeature && !currentIsValid) {
+            const validOption = options.find(opt => validIds.some(id => featureMatchesId(opt, id)));
+            return validOption ? getId(validOption) : undefined;
+        }
     }
-    const validOption = options.find(opt => featureInValidIds(opt, validIds));
-    return validOption ? getId(validOption) : undefined;
+    return undefined;
 }
 export function useTranscriptSelection({ feature, view, validIds, }) {
     const options = useMemo(() => getSortedTranscriptFeatures(feature), [feature]);
     const [selectedId, setSelectedId] = useState(() => getId(options[0]));
-    const validatedSelectedId = findValidSelection(selectedId, options, validIds) || selectedId;
+    const validatedSelectedId = findValidSelection(selectedId, options, validIds) ?? selectedId;
     const selectedTranscript = options.find(val => getId(val) === validatedSelectedId);
     const { proteinSequence, error } = useFeatureSequence({
         view,

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

@@ -1 +1 @@
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package/dist/LaunchMsaView/util.d.ts

@@ -1,4 +1,6 @@
-import type { Feature } from '@jbrowse/core/util';
+import type { AbstractTrackModel, Feature } from '@jbrowse/core/util';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+export declare function getLinearGenomeView(model: AbstractTrackModel): LinearGenomeViewModel;
 export declare function getTranscriptFeatures(feature: Feature): Feature[];
 export declare function getTranscriptLength(feature: Feature): {
     len: number;
@@ -9,6 +11,7 @@ export declare function getMatchableIds(val?: Feature): string[];
 export declare function featureMatchesId(feature: Feature, id: string): boolean;
 export declare function getTranscriptDisplayName(val?: Feature): string;
 export declare function getGeneDisplayName(val?: Feature): string;
+export declare function getBlastViewTitle(feature: Feature, transcript: Feature): string;
 export declare function getSortedTranscriptFeatures(feature: Feature): Feature[];
 export declare function cleanProteinSequence(seq: string): string;
 export declare function getGeneIdentifiers(feature: Feature): string[];

package/dist/LaunchMsaView/util.js

@@ -1,4 +1,13 @@
-import { sum } from '@jbrowse/core/util';
+import { getContainingView, sum } from '@jbrowse/core/util';
+export function getLinearGenomeView(model) {
+    return getContainingView(model);
+}
+function uniqueDefined(vals) {
+    return [...new Set(vals.filter((v) => !!v))];
+}
+function joinDefined(sep, parts) {
+    return parts.filter((p) => !!p).join(sep);
+}
 export function getTranscriptFeatures(feature) {
     // check if we are looking at a 'two-level' or 'three-level' feature by
     // finding exon/CDS subfeatures. we want to select from transcript names
@@ -28,34 +37,31 @@ export function getId(val) {
     return val?.id() ?? '';
 }
 export function getMatchableIds(val) {
-    if (!val) {
-        return [];
-    }
-    const ids = [
-        val.id(),
-        val.get('name'),
-        val.get('id'),
-        val.get('transcript_id'),
-    ].filter((id) => !!id);
-    return [...new Set(ids)];
+    return val
+        ? uniqueDefined([
+            val.id(),
+            val.get('name'),
+            val.get('id'),
+            val.get('transcript_id'),
+        ])
+        : [];
 }
 export function featureMatchesId(feature, id) {
     return getMatchableIds(feature).includes(id);
 }
 export function getTranscriptDisplayName(val) {
-    return val === undefined
-        ? ''
-        : [val.get('name'), val.get('id')].filter(f => !!f).join(' ');
+    return val ? joinDefined(' ', [val.get('name'), val.get('id')]) : '';
 }
 export function getGeneDisplayName(val) {
-    return val === undefined
-        ? ''
-        : [
+    return val
+        ? joinDefined(' ', [
             val.get('gene_name') ?? val.get('name'),
-            val.get('id') ? `(${val.get('id')})` : '',
-        ]
-            .filter(f => !!f)
-            .join(' ');
+            val.get('id') ? `(${val.get('id')})` : undefined,
+        ])
+        : '';
+}
+export function getBlastViewTitle(feature, transcript) {
+    return `BLAST - ${getGeneDisplayName(feature)} - ${getTranscriptDisplayName(transcript)}`;
 }
 export function getSortedTranscriptFeatures(feature) {
     const transcripts = getTranscriptFeatures(feature);
@@ -65,13 +71,12 @@ export function cleanProteinSequence(seq) {
     return seq.replaceAll('*', '').replaceAll('&', '');
 }
 export function getGeneIdentifiers(feature) {
-    const ids = [
+    return uniqueDefined([
         feature.id(),
         feature.get('id'),
         feature.get('name'),
         feature.get('gene_id'),
         feature.get('gene_name'),
-    ].filter((id) => !!id);
-    return [...new Set(ids)];
+    ]);
 }
 //# sourceMappingURL=util.js.map

package/dist/LaunchMsaView/util.js.map

@@ -1 +1 @@
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package/dist/MsaViewPanel/model.d.ts

@@ -631,6 +631,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly transcriptToMsaMap: {
         g2p: Record<number, number>;
         p2g: Record<number, number>;
+        p2gCodon: Record<number, number[]>;
         refName: string;
         strand: number;
     } | undefined;