npm - jbrowse-plugin-msaview - Versions diffs - 2.2.7 → 2.2.11 - Mend

jbrowse-plugin-msaview 2.2.7 → 2.2.11

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.

Files changed (65) hide show

package/dist/BgzipFastaMsaAdapter/configSchema.d.ts CHANGED Viewed

@@ -1,7 +1,7 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export default function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{
+export default function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     msaRegex: {
         type: string;
         defaultValue: string;
     };
-}, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration").AnyConfigurationSchemaType, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration").AnyConfigurationSchemaType, undefined>>;

package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js CHANGED Viewed

@@ -40,7 +40,7 @@ const EnsemblGeneTree = observer(function ({ model, feature, handleClose, }) {
                     "See ",
                     treeData.geneTreeId,
                     " at Ensembl"))) : null,
-            React.createElement(TranscriptSelector, { feature: feature, options: options, selectedTranscript: selectedTranscript, onTranscriptChange: setSelectedId, proteinSequence: proteinSequence })),
+            React.createElement(TranscriptSelector, { feature: feature, options: options, selectedId: selectedId, selectedTranscript: selectedTranscript, onTranscriptChange: setSelectedId, proteinSequence: proteinSequence })),
         React.createElement(DialogActions, null,
             React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
                     try {

package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"EnsemblGeneTree.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,YAAY,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAChE,OAAO,EAGL,iBAAiB,EACjB,UAAU,GACX,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,IAAI,EAAE,MAAM,eAAe,CAAA;AAC1E,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,EAAE,yBAAyB,EAAE,MAAM,6BAA6B,CAAA;AACvE,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAA;AAC3C,OAAO,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAA;AAC/C,OAAO,kBAAkB,MAAM,uBAAuB,CAAA;AACtD,OAAO,EAAE,sBAAsB,EAAE,MAAM,2BAA2B,CAAA;AAIlE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;QACb,OAAO,EAAE,MAAM;QACf,aAAa,EAAE,QAAQ;QACvB,GAAG,EAAE,EAAE;KACR;CACF,CAAC,CAAA;AAEF,MAAM,eAAe,GAAG,QAAQ,CAAC,UAAU,EACzC,KAAK,EACL,OAAO,EACP,WAAW,GAKZ;IACC,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAC9D,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,eAAe,EAAE,kBAAkB,CAAC,GAAG,QAAQ,EAAW,CAAA;IACjE,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,EAAE,QAAQ,EAAE,aAAa,EAAE,SAAS,EAAE,GAAG,WAAW,CAAC,UAAU,CAAC,CAAA;IAEtE,MAAM,cAAc,GAAG,aAAa;QAClC,CAAC,CAAC,yCAAyC;QAC3C,CAAC,CAAC,SAAS,CAAA;IACb,MAAM,CAAC,GAAG,SAAS,IAAI,eAAe,IAAI,oBAAoB,CAAA;IAE9D,OAAO,CACL;QACE,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,aAAa;YAC5C,CAAC,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,CAAC,GAAI,CAAC,CAAC,CAAC,IAAI;YACrC,cAAc,CAAC,CAAC,CAAC,oBAAC,eAAe,IAAC,OAAO,EAAE,cAAc,GAAI,CAAC,CAAC,CAAC,IAAI;YACpE,QAAQ,CAAC,CAAC,CAAC,CACV;gBACE;;oBAAsC,QAAQ,CAAC,UAAU,CAAO;gBAChE,oBAAC,IAAI,IACH,MAAM,EAAC,QAAQ,EACf,IAAI,EAAE,sDAAsD,QAAQ,CAAC,UAAU,EAAE;;oBAE5E,QAAQ,CAAC,UAAU;kCACnB,CACH,CACP,CAAC,CAAC,CAAC,IAAI;YAER,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,CACY;QAEhB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,IAAI,CAAC;wBACH,IAAI,CAAC,QAAQ,EAAE,CAAC;4BACd,OAAM;wBACR,CAAC;wBACD,kBAAkB,CAAC,SAAS,CAAC,CAAA;wBAE7B,yBAAyB,CAAC;4BACxB,OAAO;4BACP,IAAI;4BACJ,OAAO;4BACP,YAAY,EAAE,kBAAkB,CAAC,OAAO,CAAC;4BACzC,IAAI,EAAE,QAAQ;yBACf,CAAC,CAAA;wBACF,WAAW,EAAE,CAAA;oBACf,CAAC;oBAAC,OAAO,CAAC,EAAE,CAAC;wBACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;wBAChB,kBAAkB,CAAC,CAAC,CAAC,CAAA;oBACvB,CAAC;gBACH,CAAC,aAGM;YACT,oBAAC,MAAM,IACL,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,EAAE,CAAA;gBACf,CAAC,aAGM,CACK,CACf,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,eAAe,CAAA"}

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

@@ -28,7 +28,7 @@ const ManualMSALoader = observer(function PreLoadedMSA2({ model, feature, handle
     const [msaFileLocation, setMsaFileLocation] = useState();
     const [treeFileLocation, setTreeFileLocation] = useState();
     const [querySeqName, setQuerySeqName] = useState('');
-    const { options, setSelectedId, selectedTranscript, proteinSequence, error: error2, } = useTranscriptSelection({ feature, view });
+    const { options, selectedId, setSelectedId, selectedTranscript, proteinSequence, error: error2, } = useTranscriptSelection({ feature, view });
     const e = launchViewError ?? error2;
     return (React.createElement(React.Fragment, null,
         React.createElement(DialogContent, { className: classes.dialogContent },
@@ -48,7 +48,7 @@ const ManualMSALoader = observer(function PreLoadedMSA2({ model, feature, handle
                 React.createElement(TextField2, { variant: "outlined", name: "Tree", multiline: true, minRows: 5, maxRows: 10, fullWidth: true, placeholder: "Paste newick tree (optional)", value: treeText, onChange: event => {
                         setTreeText(event.target.value);
                     } })))),
-            React.createElement(TranscriptSelector, { feature: feature, options: options, selectedTranscript: selectedTranscript, onTranscriptChange: setSelectedId, proteinSequence: proteinSequence }),
+            React.createElement(TranscriptSelector, { feature: feature, options: options, selectedId: selectedId, selectedTranscript: selectedTranscript, onTranscriptChange: setSelectedId, proteinSequence: proteinSequence }),
             React.createElement(TextField2, { variant: "outlined", name: "MSA row name", fullWidth: true, required: true, style: { marginTop: 20 }, placeholder: "Row name in MSA that corresponds to the selected transcript", helperText: "Required: Specify the name of the row in your MSA that should be aligned with the selected transcript", value: querySeqName, onChange: event => {
                     setQuerySeqName(event.target.value);
                 } }),

package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.js CHANGED Viewed

@@ -1,29 +1,52 @@
-import React, { useEffect, useState } from 'react';
+import React, { useEffect, useMemo, useState } from 'react';
 import { getContainingView } from '@jbrowse/core/util';
 import DeleteIcon from '@mui/icons-material/Delete';
 import { Button, IconButton, List, ListItem, ListItemButton, ListItemText, Typography, } from '@mui/material';
 import { observer } from 'mobx-react';
 import { blastLaunchViewFromCache } from './blastLaunchView';
 import { clearAllCachedResults, deleteCachedResult, getAllCachedResults, } from '../../../utils/blastCache';
+function getGeneIdentifiers(feature) {
+    const ids = [
+        feature.id(),
+        feature.get('id'),
+        feature.get('name'),
+        feature.get('gene_id'),
+        feature.get('gene_name'),
+    ].filter((id) => !!id);
+    return [...new Set(ids)];
+}
+function getResultDisplayName(result) {
+    const parts = [];
+    if (result.geneName) {
+        parts.push(result.geneName);
+    }
+    if (result.transcriptName && result.transcriptName !== result.geneName) {
+        parts.push(result.transcriptName);
+    }
+    if (parts.length === 0) {
+        parts.push(result.geneId ?? result.transcriptId ?? 'Unknown');
+    }
+    return parts.join(' - ');
+}
 const CachedBlastResults = observer(function ({ model, handleClose, feature, }) {
     const [results, setResults] = useState([]);
     const [loading, setLoading] = useState(true);
     const view = getContainingView(model);
-    const geneId = feature.get('id');
+    const geneIds = useMemo(() => getGeneIdentifiers(feature), [feature]);
     useEffect(() => {
         // eslint-disable-next-line @typescript-eslint/no-floating-promises
         ;
         (async () => {
             try {
                 const cached = await getAllCachedResults();
-                setResults(cached.filter(r => r.geneId === geneId));
+                setResults(cached.filter(r => r.geneId && geneIds.includes(r.geneId)));
                 setLoading(false);
             }
             catch (e) {
                 console.error(e);
             }
         })();
-    }, [geneId]);
+    }, [geneIds]);
     const handleDelete = async (id) => {
         await deleteCachedResult(id);
         setResults(r => r.filter(result => result.id !== id));
@@ -36,7 +59,7 @@ const CachedBlastResults = observer(function ({ model, handleClose, feature, })
         blastLaunchViewFromCache({
             view,
             cached,
-            newViewTitle: `BLAST - ${cached.geneId ?? cached.transcriptId ?? 'Unknown gene'}`,
+            newViewTitle: `BLAST - ${getResultDisplayName(cached)}`,
         });
         handleClose();
     };
@@ -70,7 +93,7 @@ const CachedBlastResults = observer(function ({ model, handleClose, feature, })
             React.createElement(ListItemButton, { onClick: () => {
                     handleUseCached(result);
                 } },
-                React.createElement(ListItemText, { primary: `${result.geneId ?? result.transcriptId ?? 'Unknown'} - ${result.blastDatabase}/${result.blastProgram} (${result.msaAlgorithm})`, secondary: `${new Date(result.timestamp).toLocaleString()} - Seq: ${result.proteinSequence.slice(0, 30)}...` }))))))));
+                React.createElement(ListItemText, { primary: `${getResultDisplayName(result)} - ${result.blastDatabase}/${result.blastProgram} (${result.msaAlgorithm})`, secondary: `${new Date(result.timestamp).toLocaleString()} - Seq: ${result.proteinSequence.slice(0, 30)}...` }))))))));
 });
 export default CachedBlastResults;
 //# sourceMappingURL=CachedBlastResults.js.map

package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"CachedBlastResults.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;~~AAElD~~,OAAO,EAAW,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AAC/D,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,EACL,qBAAqB,EACrB,kBAAkB,EAClB,mBAAmB,GACpB,MAAM,2BAA2B,CAAA;AAMlC,MAAM,kBAAkB,GAAG,QAAQ,CAAC,UAAU,EAC5C,KAAK,EACL,WAAW,EACX,OAAO,GAKR;IACC,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,CAAsB,EAAE,CAAC,CAAA;IAC/D,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IAC5C,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAE9D,MAAM,~~MAAM~~,GAAG,OAAO,CAAC,GAAG,CAAC,~~IAAI~~,CAAC,CAAA;~~IAChC~~,SAAS,CAAC,GAAG,EAAE;QACb,mEAAmE;QACnE,CAAC;QAAA,CAAC,KAAK,IAAI,EAAE;YACX,IAAI,CAAC;gBACH,MAAM,MAAM,GAAG,MAAM,mBAAmB,EAAE,CAAA;gBAC1C,UAAU,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,~~KAAK~~,MAAM,CAAC,CAAC,CAAA;~~gBACnD~~,UAAU,CAAC,KAAK,CAAC,CAAA;YACnB,CAAC;YAAC,OAAO,CAAC,EAAE,CAAC;gBACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YAClB,CAAC;QACH,CAAC,CAAC,EAAE,CAAA;IACN,CAAC,EAAE,CAAC,~~MAAM~~,CAAC,CAAC,CAAA;~~IAEZ~~,MAAM,YAAY,GAAG,KAAK,EAAE,EAAU,EAAE,EAAE;QACxC,MAAM,kBAAkB,CAAC,EAAE,CAAC,CAAA;QAC5B,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC,MAAM,CAAC,EAAE,KAAK,EAAE,CAAC,CAAC,CAAA;IACvD,CAAC,CAAA;IAED,MAAM,cAAc,GAAG,KAAK,IAAI,EAAE;QAChC,MAAM,qBAAqB,EAAE,CAAA;QAC7B,UAAU,CAAC,EAAE,CAAC,CAAA;IAChB,CAAC,CAAA;IAED,MAAM,eAAe,GAAG,CAAC,MAAyB,EAAE,EAAE;QACpD,wBAAwB,CAAC;YACvB,IAAI;YACJ,MAAM;YACN,YAAY,EAAE,WAAW,~~MAAM~~,CAAC,MAAM,~~IAAI,MAAM,~~CAAC,~~YAAY,IAAI,cAAc,~~EAAE;~~SAClF~~,CAAC,CAAA;QACF,WAAW,EAAE,CAAA;IACf,CAAC,CAAA;IAED,IAAI,OAAO,EAAE,CAAC;QACZ,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,GAAG,EAAE;oBACZ,mEAAmE;oBACnE,cAAc,EAAE,CAAA;gBAClB,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,CAAC,CAAC,EAAE;oBACX,CAAC,CAAC,eAAe,EAAE,CAAA;oBACnB,mEAAmE;oBACnE,YAAY,CAAC,MAAM,CAAC,EAAE,CAAC,CAAA;gBACzB,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,~~MAAM~~,CAAC,MAAM,~~IAAI,MAAM,~~CAAC,~~YAAY,IAAI,SAAS,~~MAAM,MAAM,CAAC,aAAa,IAAI,MAAM,CAAC,YAAY,KAAK,MAAM,CAAC,YAAY,GAAG,~~EACzI~~,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"}
1	+ {"version":3,"file":"CachedBlastResults.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,OAAO,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAE3D,OAAO,EAAW,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AAC/D,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,EACL,qBAAqB,EACrB,kBAAkB,EAClB,mBAAmB,GACpB,MAAM,2BAA2B,CAAA;AAMlC,SAAS,kBAAkB,CAAC,OAAgB;IAC1C,MAAM,GAAG,GAAG;QACV,OAAO,CAAC,EAAE,EAAE;QACZ,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC;QACjB,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC;QACnB,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC;QACtB,OAAO,CAAC,GAAG,CAAC,WAAW,CAAC;KACzB,CAAC,MAAM,CAAC,CAAC,EAAE,EAAgB,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAA;IACpC,OAAO,CAAC,GAAG,IAAI,GAAG,CAAC,GAAG,CAAC,CAAC,CAAA;AAC1B,CAAC;AAED,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,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,CAAsB,EAAE,CAAC,CAAA;IAC/D,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IAC5C,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAE9D,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,EAAE,CAAC,kBAAkB,CAAC,OAAO,CAAC,EAAE,CAAC,OAAO,CAAC,CAAC,CAAA;IAErE,SAAS,CAAC,GAAG,EAAE;QACb,mEAAmE;QACnE,CAAC;QAAA,CAAC,KAAK,IAAI,EAAE;YACX,IAAI,CAAC;gBACH,MAAM,MAAM,GAAG,MAAM,mBAAmB,EAAE,CAAA;gBAC1C,UAAU,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,IAAI,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAA;gBACtE,UAAU,CAAC,KAAK,CAAC,CAAA;YACnB,CAAC;YAAC,OAAO,CAAC,EAAE,CAAC;gBACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YAClB,CAAC;QACH,CAAC,CAAC,EAAE,CAAA;IACN,CAAC,EAAE,CAAC,OAAO,CAAC,CAAC,CAAA;IAEb,MAAM,YAAY,GAAG,KAAK,EAAE,EAAU,EAAE,EAAE;QACxC,MAAM,kBAAkB,CAAC,EAAE,CAAC,CAAA;QAC5B,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC,MAAM,CAAC,EAAE,KAAK,EAAE,CAAC,CAAC,CAAA;IACvD,CAAC,CAAA;IAED,MAAM,cAAc,GAAG,KAAK,IAAI,EAAE;QAChC,MAAM,qBAAqB,EAAE,CAAA;QAC7B,UAAU,CAAC,EAAE,CAAC,CAAA;IAChB,CAAC,CAAA;IAED,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,IAAI,OAAO,EAAE,CAAC;QACZ,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,GAAG,EAAE;oBACZ,mEAAmE;oBACnE,cAAc,EAAE,CAAA;gBAClB,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,CAAC,CAAC,EAAE;oBACX,CAAC,CAAC,eAAe,EAAE,CAAA;oBACnB,mEAAmE;oBACnE,YAAY,CAAC,MAAM,CAAC,EAAE,CAAC,CAAA;gBACzB,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"}

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js CHANGED Viewed

@@ -1,4 +1,4 @@
-import React, { useEffect, useState } from 'react';
+import React, { useEffect, useMemo, useState } from 'react';
 import { ErrorMessage } from '@jbrowse/core/ui';
 import { getContainingView, } from '@jbrowse/core/util';
 import ExpandMoreIcon from '@mui/icons-material/ExpandMore';
@@ -12,6 +12,16 @@ import { getAllCachedResults } from '../../../utils/blastCache';
 import { getGeneDisplayName, getTranscriptDisplayName } from '../../util';
 import TranscriptSelector from '../TranscriptSelector';
 import { useTranscriptSelection } from '../useTranscriptSelection';
+function getGeneIdentifiers(feature) {
+    const ids = [
+        feature.id(),
+        feature.get('id'),
+        feature.get('name'),
+        feature.get('gene_id'),
+        feature.get('gene_name'),
+    ].filter((id) => !!id);
+    return [...new Set(ids)];
+}
 const useStyles = makeStyles()({
     dialogContent: {
         width: '80em',
@@ -32,22 +42,22 @@ const NCBIBlastAutomaticPanel = observer(function ({ handleClose, feature, model
     const [selectedBlastProgram, setSelectedBlastProgram] = useState('quick-blastp');
     const [hasCachedResults, setHasCachedResults] = useState(false);
     const [error, setError] = useState();
-    const geneId = feature.get('id');
+    const geneIds = useMemo(() => getGeneIdentifiers(feature), [feature]);
     useEffect(() => {
         // eslint-disable-next-line @typescript-eslint/no-floating-promises
         ;
         (async () => {
             try {
                 const results = await getAllCachedResults();
-                setHasCachedResults(results.some(r => r.geneId === geneId));
+                setHasCachedResults(results.some(r => r.geneId && geneIds.includes(r.geneId)));
             }
             catch (e) {
                 console.error(e);
                 setError(e);
             }
         })();
-    }, [geneId]);
-    const { options, setSelectedId, selectedTranscript, proteinSequence, error: proteinSequenceError, } = useTranscriptSelection({ feature, view });
+    }, [geneIds]);
+    const { options, selectedId, setSelectedId, selectedTranscript, proteinSequence, error: proteinSequenceError, } = useTranscriptSelection({ feature, view });
     useEffect(() => {
         if (selectedBlastDatabase === 'nr_cluster_seq') {
             setSelectedBlastProgram('blastp');
@@ -73,7 +83,7 @@ const NCBIBlastAutomaticPanel = observer(function ({ handleClose, feature, model
                         marginLeft: 4,
                         alignContent: 'center',
                     } }, "Can only use blastp on nr_cluster_seq")) : null),
-            React.createElement(TranscriptSelector, { feature: feature, options: options, selectedTranscript: selectedTranscript, onTranscriptChange: setSelectedId, proteinSequence: proteinSequence }),
+            React.createElement(TranscriptSelector, { feature: feature, options: options, selectedId: selectedId, selectedTranscript: selectedTranscript, onTranscriptChange: setSelectedId, proteinSequence: proteinSequence }),
             React.createElement(Typography, { style: { marginTop: 20 } }, "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"),
             hasCachedResults ? (React.createElement(Accordion, { style: { marginTop: 20 } },
                 React.createElement(AccordionSummary, { expandIcon: React.createElement(ExpandMoreIcon, null) },

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ {"version":3,"file":"NCBIBlastAutomaticPanel.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,OAAO,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAE3D,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAGL,iBAAiB,GAClB,MAAM,oBAAoB,CAAA;AAC3B,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,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,EAAE,mBAAmB,EAAE,MAAM,2BAA2B,CAAA;AAC/D,OAAO,EAAE,kBAAkB,EAAE,wBAAwB,EAAE,MAAM,YAAY,CAAA;AACzE,OAAO,kBAAkB,MAAM,uBAAuB,CAAA;AACtD,OAAO,EAAE,sBAAsB,EAAE,MAAM,2BAA2B,CAAA;AAIlE,SAAS,kBAAkB,CAAC,OAAgB;IAC1C,MAAM,GAAG,GAAG;QACV,OAAO,CAAC,EAAE,EAAE;QACZ,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC;QACjB,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC;QACnB,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC;QACtB,OAAO,CAAC,GAAG,CAAC,WAAW,CAAC;KACzB,CAAC,MAAM,CAAC,CAAC,EAAE,EAAgB,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAA;IACpC,OAAO,CAAC,GAAG,IAAI,GAAG,CAAC,GAAG,CAAC,CAAC,CAAA;AAC1B,CAAC;AAED,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;IACD,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;KAC1B;CACF,CAAC,CAAA;AAEF,MAAM,oBAAoB,GAAG,CAAC,IAAI,EAAE,gBAAgB,CAAU,CAAA;AAC9D,MAAM,aAAa,GAAG,CAAC,UAAU,EAAE,QAAQ,EAAE,QAAQ,EAAE,OAAO,CAAU,CAAA;AACxE,MAAM,aAAa,GAAG,CAAC,QAAQ,EAAE,cAAc,CAAU,CAAA;AAMzD,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,CAAiB,UAAU,CAAC,CAAA;IACtC,MAAM,CAAC,oBAAoB,EAAE,uBAAuB,CAAC,GACnD,QAAQ,CAAiB,cAAc,CAAC,CAAA;IAC1C,MAAM,CAAC,gBAAgB,EAAE,mBAAmB,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAC/D,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAE7C,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,EAAE,CAAC,kBAAkB,CAAC,OAAO,CAAC,EAAE,CAAC,OAAO,CAAC,CAAC,CAAA;IACrE,SAAS,CAAC,GAAG,EAAE;QACb,mEAAmE;QACnE,CAAC;QAAA,CAAC,KAAK,IAAI,EAAE;YACX,IAAI,CAAC;gBACH,MAAM,OAAO,GAAG,MAAM,mBAAmB,EAAE,CAAA;gBAC3C,mBAAmB,CACjB,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,IAAI,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAC1D,CAAA;YACH,CAAC;YAAC,OAAO,CAAC,EAAE,CAAC;gBACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;gBAChB,QAAQ,CAAC,CAAC,CAAC,CAAA;YACb,CAAC;QACH,CAAC,CAAC,EAAE,CAAA;IACN,CAAC,EAAE,CAAC,OAAO,CAAC,CAAC,CAAA;IAEb,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;IAE7C,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,qBAAqB,KAAK,gBAAgB,EAAE,CAAC;YAC/C,uBAAuB,CAAC,QAAQ,CAAC,CAAA;QACnC,CAAC;IACH,CAAC,EAAE,CAAC,qBAAqB,CAAC,CAAC,CAAA;IAC3B,MAAM,CAAC,GAAG,oBAAoB,IAAI,eAAe,IAAI,KAAK,CAAA;IAC1D,MAAM,KAAK,GAAG,EAAE,KAAK,EAAE,GAAG,EAAE,CAAA;IAC5B,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,KAAK,EAAE,KAAK,EACZ,MAAM,QACN,KAAK,EAAE,qBAAqB,EAC5B,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,wBAAwB,CACtB,KAAK,CAAC,MAAM,CAAC,KAA8C,CAC5D,CAAA;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,KAAK,EAAE,KAAK,EACZ,MAAM,QACN,KAAK,EAAE,oBAAoB,EAC3B,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,uBAAuB,CACrB,KAAK,CAAC,MAAM,CAAC,KAAuC,CACrD,CAAA;gBACH,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,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;gBAC7B,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,KAAK,EAAC,eAAe,EACrB,QAAQ,EAAE,qBAAqB,KAAK,gBAAgB,EACpD,KAAK,EAAE,KAAK,EACZ,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,KAAK,EAAE;wBACL,UAAU,EAAE,CAAC;wBACb,YAAY,EAAE,QAAQ;qBACvB,4CAGU,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,KAAK,EAAE,EAAE,SAAS,EAAE,EAAE,EAAE,kiBASvB;YAEZ,gBAAgB,CAAC,CAAC,CAAC,CAClB,oBAAC,SAAS,IAAC,KAAK,EAAE,EAAE,SAAS,EAAE,EAAE,EAAE;gBACjC,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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package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js CHANGED Viewed

@@ -24,7 +24,7 @@ const useStyles = makeStyles()({
 const NCBIBlastManualPanel = observer(function ({ handleClose, feature, model, children, baseUrl, }) {
     const { classes } = useStyles();
     const view = getContainingView(model);
-    const { options, setSelectedId, selectedTranscript, proteinSequence, error } = useTranscriptSelection({ feature, view });
+    const { options, selectedId, setSelectedId, selectedTranscript, proteinSequence, error, } = useTranscriptSelection({ feature, view });
     const s2 = cleanProteinSequence(proteinSequence);
     const link = `${baseUrl}?PAGE_TYPE=BlastSearch&PAGE=Proteins&PROGRAM=blastp&QUERY=${s2}`;
     const link2 = `${baseUrl}?PAGE_TYPE=BlastSearch&PAGE=Proteins&PROGRAM=blastp&QUERY=${shorten2(s2, 10)}`;
@@ -32,7 +32,7 @@ const NCBIBlastManualPanel = observer(function ({ handleClose, feature, model, c
         React.createElement(DialogContent, { className: classes.dialogContent },
             children,
             error ? React.createElement(ErrorMessage, { error: error }) : null,
-            React.createElement(TranscriptSelector, { feature: feature, options: options, selectedTranscript: selectedTranscript, onTranscriptChange: setSelectedId, proteinSequence: proteinSequence }),
+            React.createElement(TranscriptSelector, { feature: feature, options: options, selectedId: selectedId, selectedTranscript: selectedTranscript, onTranscriptChange: setSelectedId, proteinSequence: proteinSequence }),
             proteinSequence ? (React.createElement("div", { className: classes.ncbiLink },
                 "Link to NCBI BLAST: ",
                 React.createElement(ExternalLink, { href: link }, link2))) : null,

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"NCBIBlastManualPanel.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAAE,iBAAiB,EAAE,QAAQ,EAAE,MAAM,oBAAoB,CAAA;AAChE,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAChF,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,YAAY,MAAM,kCAAkC,CAAA;AAC3D,OAAO,EAAE,oBAAoB,EAAE,MAAM,YAAY,CAAA;AACjD,OAAO,kBAAkB,MAAM,uBAAuB,CAAA;AACtD,OAAO,EAAE,sBAAsB,EAAE,MAAM,2BAA2B,CAAA;AAKlE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;IACD,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;KAC1B;IACD,QAAQ,EAAE;QACR,SAAS,EAAE,WAAW;QACtB,MAAM,EAAE,EAAE;QACV,QAAQ,EAAE,GAAG;KACd;CACF,CAAC,CAAA;AAEF,MAAM,oBAAoB,GAAG,QAAQ,CAAC,UAAU,EAC9C,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,EACJ,OAAO,EACP,UAAU,EACV,aAAa,EACb,kBAAkB,EAClB,eAAe,EACf,KAAK,GACN,GAAG,sBAAsB,CAAC,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAA;IAE7C,MAAM,EAAE,GAAG,oBAAoB,CAAC,eAAe,CAAC,CAAA;IAChD,MAAM,IAAI,GAAG,GAAG,OAAO,6DAA6D,EAAE,EAAE,CAAA;IACxF,MAAM,KAAK,GAAG,GAAG,OAAO,6DAA6D,QAAQ,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAA;IAEvG,OAAO,CACL;QACE,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,aAAa;YAC5C,QAAQ;YACR,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;YAE9C,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;YAED,eAAe,CAAC,CAAC,CAAC,CACjB,6BAAK,SAAS,EAAE,OAAO,CAAC,QAAQ;;gBACV,oBAAC,YAAY,IAAC,IAAI,EAAE,IAAI,IAAG,KAAK,CAAgB,CAChE,CACP,CAAC,CAAC,CAAC,IAAI;YAER,oBAAC,UAAU,IAAC,KAAK,EAAE,EAAE,SAAS,EAAE,EAAE,EAAE,2UAMvB,CACC;QAEhB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,EAAE,CAAA;gBACf,CAAC,aAGM;YACT,oBAAC,MAAM,IACL,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,EAAE,CAAA;gBACf,CAAC,YAGM,CACK,CACf,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,oBAAoB,CAAA"}

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastMethodSelector.js CHANGED Viewed

@@ -5,7 +5,8 @@ export default function NCBIBlastMethodSelector({ lookupMethod, setLookupMethod,
         React.createElement(RadioGroup, { row: true, value: lookupMethod, onChange: event => {
                 setLookupMethod(event.target.value);
             } },
-            React.createElement(FormControlLabel, { value: "automatic", control: React.createElement(Radio, null), label: "Run NCBI BLAST and load results automatically" }),
-            React.createElement(FormControlLabel, { value: "manual", control: React.createElement(Radio, null), label: "Link to NCBI BLAST and import results manually" }))));
+            React.createElement(FormControlLabel, { value: "automatic", control: React.createElement(Radio, null), label: "Automatic" }),
+            React.createElement(FormControlLabel, { value: "rid", control: React.createElement(Radio, null), label: "Load from RID" }),
+            React.createElement(FormControlLabel, { value: "manual", control: React.createElement(Radio, null), label: "Manual" }))));
 }
 //# sourceMappingURL=NCBIBlastMethodSelector.js.map

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastMethodSelector.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"NCBIBlastMethodSelector.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastMethodSelector.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,WAAW,EAAE,gBAAgB,EAAE,KAAK,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAEhF,MAAM,CAAC,OAAO,UAAU,uBAAuB,CAAC,EAC9C,YAAY,EACZ,eAAe,GAIhB;IACC,OAAO,CACL,oBAAC,WAAW,IAAC,SAAS,EAAC,UAAU;QAC/B,oBAAC,UAAU,IACT,GAAG,QACH,KAAK,EAAE,YAAY,EACnB,QAAQ,EAAE,KAAK,CAAC,EAAE;gBAChB,eAAe,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;YACrC,CAAC;YAED,oBAAC,gBAAgB,IACf,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,KAAK,EAAC,WAAW,GACjB;YACF,oBAAC,gBAAgB,IACf,KAAK,EAAC,KAAK,EACX,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,KAAK,EAAC,eAAe,GACrB;YACF,oBAAC,gBAAgB,IAAC,KAAK,EAAC,QAAQ,EAAC,OAAO,EAAE,oBAAC,KAAK,OAAG,EAAE,KAAK,EAAC,QAAQ,GAAG,CAC3D,CACD,CACf,CAAA;AACH,CAAC"}

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.js CHANGED Viewed

@@ -5,15 +5,19 @@ import { IconButton } from '@mui/material';
 import NCBIBlastAutomaticPanel from './NCBIBlastAutomaticPanel';
 import NCBIBlastManualPanel from './NCBIBlastManualPanel';
 import NCBIBlastMethodSelector from './NCBIBlastMethodSelector';
+import NCBIBlastRIDPanel from './NCBIBlastRIDPanel';
 import NCBISettingsDialog from './NCBISettingsDialog';
 import { BASE_BLAST_URL } from './consts';
+const panelMap = {
+    automatic: NCBIBlastAutomaticPanel,
+    rid: NCBIBlastRIDPanel,
+    manual: NCBIBlastManualPanel,
+};
 export default function NCBIBlastPanel({ handleClose, model, feature, }) {
     const [lookupMethod, setLookupMethod] = useState('automatic');
     const [baseUrl, setBaseUrl] = useLocalStorage('msa-blastRootUrl', BASE_BLAST_URL);
     const [settingsOpen, setSettingsOpen] = useState(false);
-    const Panel = lookupMethod === 'automatic'
-        ? NCBIBlastAutomaticPanel
-        : NCBIBlastManualPanel;
+    const Panel = panelMap[lookupMethod];
     return (React.createElement(React.Fragment, null,
         React.createElement(IconButton, { style: { float: 'right' }, size: "small", onClick: () => {
                 setSettingsOpen(true);

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"NCBIBlastPanel.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAA;AACpD,OAAO,YAAY,MAAM,8BAA8B,CAAA;AACvD,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,uBAAuB,MAAM,2BAA2B,CAAA;AAC/D,OAAO,oBAAoB,MAAM,wBAAwB,CAAA;AACzD,OAAO,uBAAuB,MAAM,2BAA2B,CAAA;AAC/D,OAAO,iBAAiB,MAAM,qBAAqB,CAAA;AACnD,OAAO,kBAAkB,MAAM,sBAAsB,CAAA;AACrD,OAAO,EAAE,cAAc,EAAE,MAAM,UAAU,CAAA;AAIzC,MAAM,QAAQ,GAAG;IACf,SAAS,EAAE,uBAAuB;IAClC,GAAG,EAAE,iBAAiB;IACtB,MAAM,EAAE,oBAAoB;CACpB,CAAA;AAEV,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,EACrC,WAAW,EACX,KAAK,EACL,OAAO,GAKR;IACC,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,WAAW,CAAC,CAAA;IAC7D,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,eAAe,CAC3C,kBAAkB,EAClB,cAAc,CACf,CAAA;IACD,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAEvD,MAAM,KAAK,GAAG,QAAQ,CAAC,YAAqC,CAAC,CAAA;IAE7D,OAAO,CACL;QACE,oBAAC,UAAU,IACT,KAAK,EAAE,EAAE,KAAK,EAAE,OAAO,EAAE,EACzB,IAAI,EAAC,OAAO,EACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,eAAe,CAAC,IAAI,CAAC,CAAA;YACvB,CAAC;YAED,oBAAC,YAAY,OAAG,CACL;QAEb,oBAAC,KAAK,IACJ,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,OAAO,EAChB,WAAW,EAAE,WAAW,EACxB,OAAO,EAAE,OAAO;YAEhB,oBAAC,uBAAuB,IACtB,YAAY,EAAE,YAAY,EAC1B,eAAe,EAAE,eAAe,GAChC,CACI;QAEP,YAAY,CAAC,CAAC,CAAC,CACd,oBAAC,kBAAkB,IACjB,OAAO,EAAE,OAAO,EAChB,WAAW,EAAE,MAAM,CAAC,EAAE;gBACpB,IAAI,MAAM,EAAE,CAAC;oBACX,UAAU,CAAC,MAAM,CAAC,CAAA;gBACpB,CAAC;gBACD,eAAe,CAAC,KAAK,CAAC,CAAA;YACxB,CAAC,GACD,CACH,CAAC,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC"}

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastRIDPanel.d.ts ADDED Viewed

@@ -0,0 +1,10 @@
+import React from 'react';
+import { AbstractTrackModel, Feature } from '@jbrowse/core/util';
+declare const NCBIBlastRIDPanel: ({ handleClose, feature, model, children, baseUrl, }: {
+    model: AbstractTrackModel;
+    feature: Feature;
+    baseUrl: string;
+    handleClose: () => void;
+    children: React.ReactNode;
+}) => React.JSX.Element;
+export default NCBIBlastRIDPanel;

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

@@ -0,0 +1,77 @@
+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 { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+import { blastLaunchView } from './blastLaunchView';
+import ExternalLink from '../../../components/ExternalLink';
+import TextField2 from '../../../components/TextField2';
+import { getGeneDisplayName, getTranscriptDisplayName } from '../../util';
+import TranscriptSelector from '../TranscriptSelector';
+import { useTranscriptSelection } from '../useTranscriptSelection';
+const useStyles = makeStyles()({
+    dialogContent: {
+        width: '80em',
+    },
+});
+const msaAlgorithms = ['clustalo', 'muscle', 'kalign', 'mafft'];
+const NCBIBlastRIDPanel = observer(function ({ handleClose, feature, model, children, baseUrl, }) {
+    const { classes } = useStyles();
+    const view = getContainingView(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 style = { width: 150 };
+    const trimmedRid = rid.trim();
+    return (React.createElement(React.Fragment, null,
+        React.createElement(DialogContent, { className: classes.dialogContent },
+            children,
+            e ? React.createElement(ErrorMessage, { error: e }) : null,
+            React.createElement(Typography, { variant: "body2", style: { marginBottom: 16 } }, "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, style: { marginBottom: 16 }, value: rid, onChange: event => {
+                    setRid(event.target.value);
+                } }),
+            trimmedRid ? (React.createElement(Typography, { variant: "body2", style: { marginBottom: 16 } },
+                React.createElement(ExternalLink, { href: `${baseUrl}?CMD=Get&RID=${trimmedRid}` }, "View BLAST results on NCBI"))) : null,
+            React.createElement(TextField2, { variant: "outlined", label: "MSA Algorithm", style: style, 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(Typography, { style: { marginTop: 20 } }, "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;
+                        }
+                        setLaunchViewError(undefined);
+                        blastLaunchView({
+                            feature: selectedTranscript,
+                            view,
+                            newViewTitle: `BLAST - ${getGeneDisplayName(feature)} - ${getTranscriptDisplayName(selectedTranscript)}`,
+                            blastParams: {
+                                baseUrl,
+                                blastProgram: 'blastp',
+                                blastDatabase: 'nr',
+                                msaAlgorithm: selectedMsaAlgorithm,
+                                selectedTranscript,
+                                proteinSequence,
+                                rid: trimmedRid,
+                            },
+                        });
+                    }
+                    catch (e) {
+                        console.error(e);
+                        setLaunchViewError(e);
+                    }
+                    handleClose();
+                }, disabled: !proteinSequence || !trimmedRid }, "Submit"),
+            React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
+                    handleClose();
+                } }, "Cancel"))));
+});
+export default NCBIBlastRIDPanel;
+//# sourceMappingURL=NCBIBlastRIDPanel.js.map

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

@@ -0,0 +1 @@

+ {"version":3,"file":"NCBIBlastRIDPanel.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastRIDPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAGL,iBAAiB,GAClB,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EACL,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,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAA;AACnD,OAAO,YAAY,MAAM,kCAAkC,CAAA;AAC3D,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,EAAE,kBAAkB,EAAE,wBAAwB,EAAE,MAAM,YAAY,CAAA;AACzE,OAAO,kBAAkB,MAAM,uBAAuB,CAAA;AACtD,OAAO,EAAE,sBAAsB,EAAE,MAAM,2BAA2B,CAAA;AAIlE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;CACF,CAAC,CAAA;AAEF,MAAM,aAAa,GAAG,CAAC,UAAU,EAAE,QAAQ,EAAE,QAAQ,EAAE,OAAO,CAAU,CAAA;AAIxE,MAAM,iBAAiB,GAAG,QAAQ,CAAC,UAAU,EAC3C,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,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IAClC,MAAM,CAAC,oBAAoB,EAAE,uBAAuB,CAAC,GACnD,QAAQ,CAAiB,UAAU,CAAC,CAAA;IAEtC,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;IAE7C,MAAM,CAAC,GAAG,oBAAoB,IAAI,eAAe,CAAA;IACjD,MAAM,KAAK,GAAG,EAAE,KAAK,EAAE,GAAG,EAAE,CAAA;IAC5B,MAAM,UAAU,GAAG,GAAG,CAAC,IAAI,EAAE,CAAA;IAE7B,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;YAEtC,oBAAC,UAAU,IAAC,OAAO,EAAC,OAAO,EAAC,KAAK,EAAE,EAAE,YAAY,EAAE,EAAE,EAAE,gOAK1C;YAEb,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,KAAK,EAAC,WAAW,EACjB,WAAW,EAAC,gBAAgB,EAC5B,SAAS,QACT,KAAK,EAAE,EAAE,YAAY,EAAE,EAAE,EAAE,EAC3B,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAC5B,CAAC,GACD;YAED,UAAU,CAAC,CAAC,CAAC,CACZ,oBAAC,UAAU,IAAC,OAAO,EAAC,OAAO,EAAC,KAAK,EAAE,EAAE,YAAY,EAAE,EAAE,EAAE;gBACrD,oBAAC,YAAY,IAAC,IAAI,EAAE,GAAG,OAAO,gBAAgB,UAAU,EAAE,iCAE3C,CACJ,CACd,CAAC,CAAC,CAAC,IAAI;YAER,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,KAAK,EAAC,eAAe,EACrB,KAAK,EAAE,KAAK,EACZ,MAAM,QACN,KAAK,EAAE,oBAAoB,EAC3B,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,uBAAuB,CACrB,KAAK,CAAC,MAAM,CAAC,KAAuC,CACrD,CAAA;gBACH,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,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,KAAK,EAAE,EAAE,SAAS,EAAE,EAAE,EAAE,mNAIvB,CACC;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,IAAI,CAAC,UAAU,EAAE,CAAC;4BACvC,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,QAAQ;gCACtB,aAAa,EAAE,IAAI;gCACnB,YAAY,EAAE,oBAAoB;gCAClC,kBAAkB;gCAClB,eAAe;gCACf,GAAG,EAAE,UAAU;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,IAAI,CAAC,UAAU,aAGlC;YACT,oBAAC,MAAM,IACL,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,EAAE,CAAA;gBACf,CAAC,aAGM,CACK,CACf,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,iBAAiB,CAAA"}

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

@@ -60,7 +60,7 @@ const PreLoadedMSA = observer(function PreLoadedMSA2({ model, feature, handleClo
                 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, selectedTranscript: selectedTranscript, onTranscriptChange: setSelectedId, proteinSequence: proteinSequence, validSet: validSet }))) : null)) : null),
+                    React.createElement(TranscriptSelector, { feature: feature, options: transcripts, selectedId: selectedId, selectedTranscript: selectedTranscript, onTranscriptChange: setSelectedId, proteinSequence: proteinSequence, validSet: validSet }))) : null)) : null),
         React.createElement(DialogActions, null,
             React.createElement(Button, { color: "primary", variant: "contained", disabled: !selectedTranscript || !msaData?.length, onClick: () => {
                     try {

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

	@@ -1 +1 @@
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1	+ {"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,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAC5D,OAAO,EAAE,YAAY,EAAE,eAAe,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAA;AAC/E,OAAO,EAGL,iBAAiB,EACjB,MAAM,EACN,UAAU,GACX,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC9E,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,kBAAkB,EAAE,MAAM,YAAY,CAAA;AAC/C,OAAO,kBAAkB,MAAM,uBAAuB,CAAA;AACtD,OAAO,EAAE,sBAAsB,EAAE,MAAM,2BAA2B,CAAA;AAClE,OAAO,EAAE,QAAQ,EAAE,MAAM,UAAU,CAAA;AACnC,OAAO,EAAE,QAAQ,EAAE,YAAY,EAAE,MAAM,gBAAgB,CAAA;AACvD,OAAO,EAAE,uBAAuB,EAAE,MAAM,2BAA2B,CAAA;AAKnE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;CACF,CAAC,CAAA;AAEF,MAAM,YAAY,GAAG,QAAQ,CAAC,SAAS,aAAa,CAAC,EACnD,KAAK,EACL,OAAO,EACP,WAAW,GAKZ;IACC,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAC9D,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,EAAE,OAAO,EAAE,GAAG,OAAO,CAAA;IAC3B,MAAM,QAAQ,GAAG,cAAc,CAAC,OAAO,EAAE,CAAC,KAAK,EAAE,UAAU,CAAC,CAE/C,CAAA;IACb,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,iBAAiB,CAAC,CAAC,CAAC,GAAG,iBAAiB,WAAW,CAAC,CAAC,CAAC,eAAe,EACrE,GAAG,EAAE,CACH,eAAe;QACb,CAAC,CAAC,YAAY,CAAC;YACX,MAAM,EAAE,eAAe,CAAC,OAAO;YAC/B,aAAa;SACd,CAAC;QACJ,CAAC,CAAC,SAAS,EACf,QAAQ,CACT,CAAA;IAED,MAAM,EACJ,OAAO,EAAE,WAAW,EACpB,UAAU,EACV,aAAa,EACb,kBAAkB,EAClB,eAAe,EACf,KAAK,EAAE,oBAAoB,EAC3B,QAAQ,GACT,GAAG,sBAAsB,CAAC,EAAE,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,OAAO,EAAE,CAAC,CAAA;IAEhE,MAAM,EACJ,IAAI,EAAE,OAAO,EACb,SAAS,EAAE,cAAc,EACzB,KAAK,EAAE,iBAAiB,GACzB,GAAG,MAAM,CACR,UAAU,IAAI,iBAAiB;QAC7B,CAAC,CAAC,GAAG,UAAU,IAAI,UAAU,IAAI,OAAO,EAAE,MAAM,MAAM;QACtD,CAAC,CAAC,UAAU,EACd,GAAG,EAAE,CACH,UAAU,IAAI,eAAe,IAAI,OAAO;QACtC,CAAC,CAAC,QAAQ,CAAC;YACP,KAAK,EAAE,UAAU;YACjB,MAAM,EAAE,eAAe,CAAC,OAAO;YAC/B,aAAa;SACd,CAAC;QACJ,CAAC,CAAC,SAAS,EACf,QAAQ,CACT,CAAA;IAED,MAAM,CAAC,GACL,iBAAiB,IAAI,iBAAiB,IAAI,oBAAoB,IAAI,SAAS,CAAA;IAC7E,IAAI,CAAC,EAAE,CAAC;QACN,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;IAClB,CAAC;IACD,OAAO,CACL;QACE,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,aAAa;YAC5C,CAAC,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,CAAC,GAAI,CAAC,CAAC,CAAC,IAAI;YAEtC,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,KAAK,EAAE,EAAE,SAAS,EAAE,EAAE,EAAE;gBAC1B,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,EAChB,OAAO,EAAE,WAAW,EACpB,UAAU,EAAE,UAAU,EACtB,kBAAkB,EAAE,kBAAkB,EACtC,kBAAkB,EAAE,aAAa,EACjC,eAAe,EAAE,eAAe,EAChC,QAAQ,EAAE,QAAQ,GAClB,CACE,CACP,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAC,CAAC,CAAC,IAAI,CACM;QAEhB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,QAAQ,EAAE,CAAC,kBAAkB,IAAI,CAAC,OAAO,EAAE,MAAM,EACjD,OAAO,EAAE,GAAG,EAAE;oBACZ,IAAI,CAAC;wBACH,IAAI,CAAC,kBAAkB,IAAI,CAAC,OAAO,EAAE,CAAC;4BACpC,OAAM;wBACR,CAAC;wBACD,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;oBAAC,OAAO,CAAC,EAAE,CAAC;wBACX,YAAY,CAAC,CAAC,CAAC,CAAA;oBACjB,CAAC;gBACH,CAAC,aAGM;YACT,oBAAC,MAAM,IACL,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,EAAE,CAAA;gBACf,CAAC,aAGM,CACK,CACf,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,YAAY,CAAA"}

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

@@ -1,8 +1,9 @@
 import React from 'react';
 import { Feature } from '@jbrowse/core/util';
-export default function TranscriptSelector({ feature, options, selectedTranscript, onTranscriptChange, proteinSequence, validSet, }: {
+export default function TranscriptSelector({ feature, options, selectedId, selectedTranscript, onTranscriptChange, proteinSequence, validSet, }: {
     feature: Feature;
     options: Feature[];
+    selectedId: string;
     selectedTranscript: Feature | undefined;
     onTranscriptChange: (transcriptId: string) => void;
     proteinSequence: string | undefined;

package/dist/LaunchMsaView/components/TranscriptSelector.js CHANGED Viewed

@@ -1,9 +1,8 @@
 import React, { useState } from 'react';
-import { Button, MenuItem } from '@mui/material';
+import { Button, MenuItem, TextField } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
 import ReadOnlyTextField2 from '../../components/ReadOnlyTextField2';
-import TextField2 from '../../components/TextField2';
-import { getGeneDisplayName, getId, getTranscriptDisplayName, getTranscriptLength, } from '../util';
+import { featureMatchesId, getGeneDisplayName, getId, getTranscriptDisplayName, getTranscriptLength, } from '../util';
 const useStyles = makeStyles()({
     flex: {
         display: 'flex',
@@ -12,15 +11,17 @@ const useStyles = makeStyles()({
         minWidth: 300,
     },
 });
-export default function TranscriptSelector({ feature, options, selectedTranscript, onTranscriptChange, proteinSequence, validSet, }) {
+export default function TranscriptSelector({ feature, options, selectedId, selectedTranscript, onTranscriptChange, proteinSequence, validSet, }) {
     const { classes } = useStyles();
     const [showSequence, setShowSequence] = useState(false);
     return (React.createElement(React.Fragment, null,
         React.createElement("div", { className: classes.flex },
-            React.createElement(TextField2, { variant: "outlined", label: `Choose isoform of ${getGeneDisplayName(feature)}`, select: true, className: classes.minWidth, value: getId(selectedTranscript), onChange: event => {
+            React.createElement(TextField, { variant: "outlined", label: `Choose isoform of ${getGeneDisplayName(feature)}`, select: true, className: classes.minWidth, value: selectedId, onChange: event => {
                     onTranscriptChange(event.target.value);
                 } }, options.map(val => {
-                const inSet = validSet ? validSet.has(getId(val)) : true;
+                const inSet = validSet
+                    ? [...validSet].some(id => featureMatchesId(val, id))
+                    : true;
                 const { len, mod } = getTranscriptLength(val);
                 return (React.createElement(MenuItem, { value: getId(val), key: val.id(), disabled: !inSet },
                     getTranscriptDisplayName(val),

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

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

@@ -1,9 +1,12 @@
 import { useEffect, useMemo, useState } from 'react';
-import { getId, getSortedTranscriptFeatures } from '../util';
+import { featureMatchesId, getId, getSortedTranscriptFeatures } from '../util';
 import { useFeatureSequence } from './useFeatureSequence';
+function featureInValidIds(feature, validIds) {
+    return validIds.some(id => featureMatchesId(feature, id));
+}
 export function useTranscriptSelection({ feature, view, validIds, }) {
-    const options = getSortedTranscriptFeatures(feature);
-    const [selectedId, setSelectedId] = useState(getId(options[0]));
+    const options = useMemo(() => getSortedTranscriptFeatures(feature), [feature]);
+    const [selectedId, setSelectedId] = useState(() => getId(options[0]));
     const selectedTranscript = options.find(val => getId(val) === selectedId);
     const { proteinSequence, error } = useFeatureSequence({
         view,
@@ -11,10 +14,13 @@ export function useTranscriptSelection({ feature, view, validIds, }) {
     });
     const validSet = useMemo(() => (validIds ? new Set(validIds) : undefined), [validIds]);
     useEffect(() => {
-        if (validIds && validIds.length > 0 && !validIds.includes(selectedId)) {
-            const validOption = options.find(opt => validIds.includes(getId(opt)));
-            if (validOption) {
-                setSelectedId(getId(validOption));
+        if (validIds && validIds.length > 0) {
+            const currentFeature = options.find(opt => getId(opt) === selectedId);
+            if (currentFeature && !featureInValidIds(currentFeature, validIds)) {
+                const validOption = options.find(opt => featureInValidIds(opt, validIds));
+                if (validOption) {
+                    setSelectedId(getId(validOption));
+                }
             }
         }
     }, [validIds, options, selectedId]);

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