jbrowse-plugin-msaview 2.3.3 → 2.3.8

package/README.md

@@ -39,231 +39,30 @@ https://jbrowse.org/code/jb2/main/index.html?config=https://unpkg.com/jbrowse-pl
 - Clustal files (e.g. .aln file, uses clustal-js parser)
 - Newick (tree can be loaded separately as a .nh file)
 
-## Data persistence
+## Publication
 
-MSA datasets loaded from inline data (pasted text, local file uploads) are
-automatically stored in the browser's IndexedDB to enable persistence across
-page refreshes. This works around a limitation in react-msaview that strips
-large data from session snapshots.
+If you find this tool useful please cite our work
 
-### How it works
+Diesh, C., Stevens, G., Bridge, C., Hogue, G., Buels, R., Cain, S., Stein, L., &
+Holmes, I. (2026). Proteins in the Genome Browser: Integration of Phylogenies,
+Alignments, and Structures With Nucleotide-level Evidence in JBrowse 2. Journal
+of Molecular Biology, 169645. https://doi.org/10.1016/j.jmb.2026.169645
 
-1. When MSA data is loaded from inline sources (not URL-based files), it is
-   automatically stored in IndexedDB
-2. A reference ID (`dataStoreId`) is saved in the session snapshot instead of
-   the raw data
-3. On page reload, the plugin detects the `dataStoreId` and retrieves the data
-   from IndexedDB
-4. Old IndexedDB entries are automatically cleaned up after 7 days
+See also https://github.com/GMOD/proteinbrowser for overview
 
-Note: URL-based files (loaded via file selector with a URL) don't need IndexedDB
-storage as they can be reloaded directly from the URL.
+## Availability
 
-### Storage details
+This plugin is installed by default on https://genomes.jbrowse.org so you can
+use it on any species there
 
-- Database name: `jbrowse-msaview-data`
-- Stored data includes: MSA alignment, tree, and tree metadata
-- Each entry is timestamped for cleanup purposes
+## Programmatic usage
 
-This mechanism is transparent to users and requires no configuration.
+See [DEVELOPERS.md](DEVELOPERS.md)
 
-## LaunchView-MsaView extension point
+## Publishing
 
-This plugin registers a `LaunchView-MsaView` extension point that allows
-programmatic launching of an MsaView. This can be used via the JBrowse 2 session
-spec URL parameters (see https://jbrowse.org/jb2/docs/urlparams/#session-spec).
+just push a new tag using e.g.
 
-### Parameters
-
-| Parameter          | Required                    | Description                                     |
-| ------------------ | --------------------------- | ----------------------------------------------- |
-| `data`             | One of data/msaFileLocation | `{ msa: string, tree?: string }`                |
-| `msaFileLocation`  | One of data/msaFileLocation | `{ uri: string }` for MSA file                  |
-| `treeFileLocation` | No                          | `{ uri: string }` for tree file                 |
-| `connectedViewId`  | No                          | ID of connected LinearGenomeView                |
-| `connectedFeature` | No                          | Feature for cross-linking                       |
-| `displayName`      | No                          | Custom view display name                        |
-| `colorSchemeName`  | No                          | Color scheme (e.g., 'percent_identity_dynamic') |
-| `colWidth`         | No                          | Column width in pixels                          |
-| `rowHeight`        | No                          | Row height in pixels                            |
-| `treeAreaWidth`    | No                          | Tree area width                                 |
-| `treeWidth`        | No                          | Tree width                                      |
-| `drawNodeBubbles`  | No                          | Show node bubbles on tree                       |
-| `labelsAlignRight` | No                          | Align labels to the right                       |
-| `showBranchLen`    | No                          | Show branch lengths                             |
-| `querySeqName`     | No                          | Name for query sequence                         |
-
-### URL example
-
-```
-https://jbrowse.org/code/jb2/main/?config=config.json&session=spec-{"views":[{"type":"MsaView","msaFileLocation":{"uri":"https://example.com/alignment.fa"}}]}
-```
-
-### Programmatic usage
-
-```typescript
-pluginManager.evaluateExtensionPoint('LaunchView-MsaView', {
-  session,
-  data: { msa: clustalOutput, tree: newickTree },
-  displayName: 'My MSA',
-  colorSchemeName: 'percent_identity_dynamic',
-})
-```
-
-## Inter-plugin communication
-
-This plugin supports bidirectional communication with both the Linear Genome
-View and jbrowse-plugin-protein3d for synchronized highlighting and navigation.
-
-### Communication with Linear Genome View
-
-The MSA view can be connected to a Linear Genome View to enable cross-linking
-between MSA columns and genome coordinates.
-
-#### Connection mechanism
-
-When launching an MSA view from a gene feature (via right-click context menu),
-the plugin stores:
-
-- `connectedViewId`: The ID of the Linear Genome View
-- `connectedFeature`: The gene/transcript feature for coordinate mapping
-
-#### Coordinate mapping
-
-The plugin uses the `transcriptToMsaMap` (generated by g2p_mapper) to convert
-between MSA positions and genome coordinates:
-
-1. MSA column (gapped) → ungapped position
-2. Ungapped position → protein position
-3. Protein position → genome coordinate (via p2g mapping)
-
-Key files:
-
-- `src/MsaViewPanel/msaCoordToGenomeCoord.ts` - MSA to genome conversion
-- `src/MsaViewPanel/genomeToMSA.ts` - Genome to MSA conversion
-
-#### Click navigation
-
-Clicking on an MSA column navigates the connected Linear Genome View to the
-corresponding genome position. The `handleMsaClick()` action in
-`src/MsaViewPanel/model.ts:364-382` handles this.
-
-#### Bidirectional highlighting
-
-- **MSA → Genome**: When hovering over MSA columns, the corresponding genome
-  region is highlighted in the Linear Genome View via the
-  `LinearGenomeView-TracksContainerComponent` extension point
-  (`src/AddHighlightModel/MsaToGenomeHighlight.tsx`)
-
-- **Genome → MSA**: When hovering over the genome view, the corresponding MSA
-  column is highlighted (`src/AddHighlightModel/GenomeMouseoverHighlight.tsx`)
-
-### Communication with jbrowse-plugin-protein3d
-
-The MSA view can connect to protein structures displayed in
-jbrowse-plugin-protein3d for synchronized highlighting between sequence
-alignment and 3D structure.
-
-#### Auto-connection
-
-The plugin automatically discovers and connects to compatible ProteinViews based
-on:
-
-1. Matching `connectedViewId` (both views connected to the same genome view)
-2. Matching `uniprotId` between MSA row and protein structure
-
-This logic is in `src/MsaViewPanel/model.ts:625-685`.
-
-#### Manual connection
-
-Users can manually connect to protein structures via the menu: **Menu → "Connect
-to protein structure..."**
-
-The `ConnectStructureDialog`
-(`src/MsaViewPanel/components/ConnectStructureDialog.tsx`) allows selecting:
-
-- Which ProteinView to connect to
-- Which structure (if multiple)
-- Which MSA row to align with the structure sequence
-
-#### Pairwise alignment
-
-When connecting to a structure, the plugin performs a Needleman-Wunsch pairwise
-alignment between the MSA row sequence and the structure's sequence to create
-coordinate mappings. This handles cases where sequences may differ slightly.
-
-Key file: `src/MsaViewPanel/pairwiseAlignment.ts`
-
-#### Connection data structure
-
-Each structure connection stores:
-
-```typescript
-interface StructureConnection {
-  proteinViewId: string
-  structureIdx: number
-  msaRowName: string
-  msaToStructure: Record<number, number> // MSA ungapped → structure position
-  structureToMsa: Record<number, number> // structure position → MSA ungapped
-}
 ```
-
-#### Bidirectional highlighting
-
-- **MSA → Structure**: When hovering over MSA columns, the corresponding residue
-  is highlighted in the 3D structure via `structure.highlightFromExternal()`
-
-- **Structure → MSA**: When hovering over residues in the 3D structure, the
-  corresponding MSA column is highlighted. This works via two mechanisms:
-  1. Direct mapping via `structureHoverCol` getter (requires explicit
-     connection)
-  2. Indirect via genome coordinates: the MSA view observes protein3d's
-     `hoverGenomeHighlights` and maps back to MSA columns using `g2p` mapping.
-     This works automatically when both views share the same `connectedViewId`.
-
-### Three-way synchronization
-
-When all three views are connected (Linear Genome View, MSA View, and Protein
-View), hovering over any one view will highlight the corresponding positions in
-the other two views, creating a fully synchronized visualization experience.
-
-```
-┌─────────────────────┐
-│  Linear Genome View │◄────────────────────────────┐
-│    (genome coords)  │                             │
-└─────────┬───────────┘                             │
-          │                                         │
-          │ connectedViewId + connectedFeature      │ hoverGenomeHighlights
-          │ (uses p2g/g2p mapping)                  │ (genome coords)
-          ▼                                         │
-┌─────────────────────┐                   ┌─────────┴───────────┐
-│      MSA View       │◄──────────────────│    Protein View     │
-│   (aligned seqs)    │  observes genome  │   (3D structure)    │
-└─────────┬───────────┘  highlights       └───────────────────────┘
-          │                                         ▲
-          │ pairwise alignment mapping              │
-          │ (msaToStructure/structureToMsa)         │
-          └─────────────────────────────────────────┘
+pnpm version minor
 ```
-
-The MSA view can receive highlights from protein3d via two paths:
-
-1. **Direct**: MSA observes `structure.hoverPosition` (requires explicit
-   connection with matching `uniprotId`)
-2. **Indirect**: MSA observes `structure.hoverGenomeHighlights` and maps genome
-   coords back to MSA columns (works when both share `connectedViewId`)
-
-### Launch mechanisms
-
-The MSA view can be launched from the Linear Genome View via right-click context
-menu on gene/mRNA/transcript features. This provides several data source
-options:
-
-1. **NCBI BLAST Query**: Submit protein sequence to NCBI BLAST and display
-   results
-2. **Pre-loaded MSA Datasets**: Use pre-calculated alignments from configuration
-3. **Ensembl Gene Tree**: Fetch orthologous sequences from Ensembl
-4. **Manual MSA Loader**: Load MSA/tree files directly
-
-Each launch method automatically sets up the genome view connection for
-coordinate mapping and highlighting.

package/dist/AddHighlightModel/GenomeMouseoverHighlight.js.map

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package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js

@@ -33,24 +33,15 @@ export default class BgzipFastaMsaAdapter extends BaseAdapter {
     }
     async getMSAList() {
         const refNames = await this.getMSARefs();
-        const list = new Set();
         const val = this.getConf('msaRegex');
         const re = new RegExp(val);
-        for (let i = 0, l = refNames.length; i < l; i++) {
-            list.add(refNames[i].split(re)[0]);
-        }
+        const list = new Set(refNames.map(name => name.split(re)[0]));
         return [...list];
     }
     async getMSA(id) {
         const adapter = await this.configure();
         const refNames = await adapter.getRefNames();
-        const rows = [];
-        for (let i = 0, l = refNames.length; i < l; i++) {
-            const refName = refNames[i];
-            if (refName.startsWith(id)) {
-                rows.push(refName);
-            }
-        }
+        const rows = refNames.filter(refName => refName.startsWith(id));
         return firstValueFrom(adapter
             .getFeaturesInMultipleRegions(rows.map(refName => ({
             refName,

package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js.map

@@ -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,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"}

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

@@ -16,6 +16,21 @@ const useStyles = makeStyles()({
     textAreaFont: {
         fontFamily: 'Courier New',
     },
+    inputContainer: {
+        marginBottom: 30,
+    },
+    fileContainer: {
+        maxWidth: 500,
+    },
+    msaInput: {
+        marginBottom: 20,
+    },
+    queryNameInput: {
+        marginTop: 20,
+    },
+    warningAlert: {
+        marginTop: 10,
+    },
 });
 const ManualMSALoader = observer(function PreLoadedMSA2({ model, feature, handleClose, }) {
     const session = getSession(model);
@@ -39,20 +54,20 @@ const ManualMSALoader = observer(function PreLoadedMSA2({ model, feature, handle
                     } },
                     React.createElement(FormControlLabel, { value: "file", control: React.createElement(Radio, null), label: "Open files" }),
                     React.createElement(FormControlLabel, { value: "text", control: React.createElement(Radio, null), label: "Paste text" }))),
-            React.createElement("div", { style: { marginBottom: 30 } }, inputMethod === 'file' ? (React.createElement("div", { style: { maxWidth: 500 } },
+            React.createElement("div", { className: classes.inputContainer }, inputMethod === 'file' ? (React.createElement("div", { className: classes.fileContainer },
                 React.createElement(FileSelector, { name: "MSA File .aln (Clustal), .fa/.mfa (aligned FASTA), .stock (Stockholm), etc)", inline: true, location: msaFileLocation, setLocation: setMsaFileLocation }),
                 React.createElement(FileSelector, { name: "Tree file .nh (Newick) or .asn (NCBI COBALT ASN.1)", inline: true, location: treeFileLocation, setLocation: setTreeFileLocation }))) : (React.createElement(React.Fragment, null,
-                React.createElement(TextField2, { variant: "outlined", name: "MSA", multiline: true, minRows: 5, style: { marginBottom: '20px' }, maxRows: 10, fullWidth: true, placeholder: "Paste MSA here", value: msaText, onChange: event => {
+                React.createElement(TextField2, { variant: "outlined", name: "MSA", multiline: true, minRows: 5, className: classes.msaInput, maxRows: 10, fullWidth: true, placeholder: "Paste MSA here", value: msaText, onChange: event => {
                         setMsaText(event.target.value);
                     } }),
                 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, 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 => {
+            React.createElement(TextField2, { variant: "outlined", name: "MSA row name", fullWidth: true, required: true, className: classes.queryNameInput, 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);
                 } }),
-            !querySeqName.trim() && (React.createElement(Alert, { severity: "warning", style: { marginTop: 10 } }, "Without specifying the MSA row name, clicking on the MSA will not navigate to the corresponding genome position, and hovering highlights will not work."))),
+            !querySeqName.trim() ? (React.createElement(Alert, { severity: "warning", className: classes.warningAlert }, "Without specifying the MSA row name, clicking on the MSA will not navigate to the corresponding genome position, and hovering highlights will not work.")) : null),
         React.createElement(DialogActions, null,
             React.createElement(Button, { color: "primary", variant: "contained", disabled: !selectedTranscript ||
                     (inputMethod === 'file' && !msaFileLocation) ||

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

@@ -1 +1 @@
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+{"version":3,"file":"ManualMSALoader.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,YAAY,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC7D,OAAO,EAAE,iBAAiB,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAClE,OAAO,EACL,KAAK,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,WAAW,EACX,gBAAgB,EAChB,KAAK,EACL,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,EAAE,UAAU,EAAE,MAAM,cAAc,CAAA;AACzC,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;AASlE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;IACD,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;KAC1B;IACD,cAAc,EAAE;QACd,YAAY,EAAE,EAAE;KACjB;IACD,aAAa,EAAE;QACb,QAAQ,EAAE,GAAG;KACd;IACD,QAAQ,EAAE;QACR,YAAY,EAAE,EAAE;KACjB;IACD,cAAc,EAAE;QACd,SAAS,EAAE,EAAE;KACd;IACD,YAAY,EAAE;QACZ,SAAS,EAAE,EAAE;KACd;CACF,CAAC,CAAA;AAEF,MAAM,eAAe,GAAG,QAAQ,CAAC,SAAS,aAAa,CAAC,EACtD,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,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,QAAQ,CAAkB,MAAM,CAAC,CAAA;IACvE,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IAC1C,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IAC5C,MAAM,CAAC,eAAe,EAAE,kBAAkB,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACtE,MAAM,CAAC,gBAAgB,EAAE,mBAAmB,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACxE,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IACpD,MAAM,EACJ,OAAO,EACP,UAAU,EACV,aAAa,EACb,kBAAkB,EAClB,eAAe,EACf,KAAK,EAAE,MAAM,GACd,GAAG,sBAAsB,CAAC,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAA;IAE7C,MAAM,CAAC,GAAG,eAAe,IAAI,MAAM,CAAA;IACnC,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;YACtC,oBAAC,WAAW,IAAC,SAAS,EAAC,UAAU;gBAC/B,oBAAC,UAAU,IACT,GAAG,QACH,KAAK,EAAE,WAAW,EAClB,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,cAAc,CAAC,KAAK,CAAC,MAAM,CAAC,KAAwB,CAAC,CAAA;oBACvD,CAAC;oBAED,oBAAC,gBAAgB,IACf,KAAK,EAAC,MAAM,EACZ,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,KAAK,EAAC,YAAY,GAClB;oBACF,oBAAC,gBAAgB,IACf,KAAK,EAAC,MAAM,EACZ,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,KAAK,EAAC,YAAY,GAClB,CACS,CACD;YAEd,6BAAK,SAAS,EAAE,OAAO,CAAC,cAAc,IACnC,WAAW,KAAK,MAAM,CAAC,CAAC,CAAC,CACxB,6BAAK,SAAS,EAAE,OAAO,CAAC,aAAa;gBACnC,oBAAC,YAAY,IACX,IAAI,EAAC,6EAA6E,EAClF,MAAM,QACN,QAAQ,EAAE,eAAe,EACzB,WAAW,EAAE,kBAAkB,GAC/B;gBACF,oBAAC,YAAY,IACX,IAAI,EAAC,oDAAoD,EACzD,MAAM,QACN,QAAQ,EAAE,gBAAgB,EAC1B,WAAW,EAAE,mBAAmB,GAChC,CACE,CACP,CAAC,CAAC,CAAC,CACF;gBACE,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,IAAI,EAAC,KAAK,EACV,SAAS,QACT,OAAO,EAAE,CAAC,EACV,SAAS,EAAE,OAAO,CAAC,QAAQ,EAC3B,OAAO,EAAE,EAAE,EACX,SAAS,QACT,WAAW,EAAC,gBAAgB,EAC5B,KAAK,EAAE,OAAO,EACd,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,UAAU,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBAChC,CAAC,GACD;gBACF,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,IAAI,EAAC,MAAM,EACX,SAAS,QACT,OAAO,EAAE,CAAC,EACV,OAAO,EAAE,EAAE,EACX,SAAS,QACT,WAAW,EAAC,8BAA8B,EAC1C,KAAK,EAAE,QAAQ,EACf,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,WAAW,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBACjC,CAAC,GACD,CACD,CACJ,CACG;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,IACT,OAAO,EAAC,UAAU,EAClB,IAAI,EAAC,cAAc,EACnB,SAAS,QACT,QAAQ,QACR,SAAS,EAAE,OAAO,CAAC,cAAc,EACjC,WAAW,EAAC,6DAA6D,EACzE,UAAU,EAAC,uGAAuG,EAClH,KAAK,EAAE,YAAY,EACnB,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,eAAe,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBACrC,CAAC,GACD;YAED,CAAC,YAAY,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CACtB,oBAAC,KAAK,IAAC,QAAQ,EAAC,SAAS,EAAC,SAAS,EAAE,OAAO,CAAC,YAAY,8JAIjD,CACT,CAAC,CAAC,CAAC,IAAI,CACM;QAEhB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,QAAQ,EACN,CAAC,kBAAkB;oBACnB,CAAC,WAAW,KAAK,MAAM,IAAI,CAAC,eAAe,CAAC;oBAC5C,CAAC,WAAW,KAAK,MAAM,IAAI,CAAC,OAAO,CAAC,IAAI,EAAE,CAAC,EAE7C,OAAO,EAAE,GAAG,EAAE;oBACZ,IAAI,CAAC;wBACH,IAAI,CAAC,kBAAkB,EAAE,CAAC;4BACxB,OAAM;wBACR,CAAC;wBAED,kBAAkB,CAAC,SAAS,CAAC,CAAA;wBAC7B,UAAU,CAAC;4BACT,OAAO;4BACP,YAAY,EAAE,kBAAkB,CAAC,kBAAkB,CAAC;4BACpD,IAAI;4BACJ,OAAO,EAAE,kBAAkB;4BAC3B,YAAY,EAAE,YAAY,CAAC,IAAI,EAAE,IAAI,SAAS;4BAC9C,GAAG,CAAC,WAAW,KAAK,MAAM;gCACxB,CAAC,CAAC;oCACE,aAAa,EAAE,eAAe;oCAC9B,cAAc,EAAE,gBAAgB;iCACjC;gCACH,CAAC,CAAC;oCACE,IAAI,EAAE;wCACJ,GAAG,EAAE,OAAO;wCACZ,IAAI,EAAE,QAAQ,IAAI,SAAS;qCAC5B;iCACF,CAAC;yBACP,CAAC,CAAA;wBAEF,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/NCBIBlastQuery/CachedBlastResults.js

@@ -1,12 +1,25 @@
-import React, { useEffect, useMemo, useState } from 'react';
+import React, { useMemo, useState } from 'react';
 import { ErrorMessage } from '@jbrowse/core/ui';
 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 { makeStyles } from 'tss-react/mui';
 import { blastLaunchViewFromCache } from './blastLaunchView';
-import { clearAllCachedResults, deleteCachedResult, getAllCachedResults, } from '../../../utils/blastCache';
+import { useCachedBlastResults } from './useCachedBlastResults';
 import { getGeneIdentifiers } from '../../util';
+const useStyles = makeStyles()({
+    header: {
+        display: 'flex',
+        justifyContent: 'space-between',
+        alignItems: 'center',
+        marginBottom: 8,
+    },
+    resultList: {
+        maxHeight: 300,
+        overflow: 'auto',
+    },
+});
 function getResultDisplayName(result) {
     const parts = [];
     if (result.geneName) {
@@ -21,44 +34,11 @@ function getResultDisplayName(result) {
     return parts.join(' - ');
 }
 const CachedBlastResults = observer(function ({ model, handleClose, feature, }) {
-    const [results, setResults] = useState([]);
-    const [loading, setLoading] = useState(true);
-    const [error, setError] = useState();
+    const { classes } = useStyles();
     const view = getContainingView(model);
+    const [operationError, setOperationError] = useState();
     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 && geneIds.includes(r.geneId)));
-                setLoading(false);
-            }
-            catch (e) {
-                console.error(e);
-                setError(e);
-            }
-        })();
-    }, [geneIds]);
-    const handleDelete = async (id) => {
-        try {
-            await deleteCachedResult(id);
-            setResults(r => r.filter(result => result.id !== id));
-        }
-        catch (e) {
-            setError(e);
-        }
-    };
-    const handleClearAll = async () => {
-        try {
-            await clearAllCachedResults();
-            setResults([]);
-        }
-        catch (e) {
-            setError(e);
-        }
-    };
+    const { results, error, isLoading, handleDelete, handleClearAll } = useCachedBlastResults(geneIds);
     const handleUseCached = (cached) => {
         blastLaunchViewFromCache({
             view,
@@ -67,34 +47,40 @@ const CachedBlastResults = observer(function ({ model, handleClose, feature, })
         });
         handleClose();
     };
-    if (error) {
-        return React.createElement(ErrorMessage, { error: error });
+    const displayError = error ?? operationError;
+    if (displayError) {
+        return React.createElement(ErrorMessage, { error: displayError });
     }
-    if (loading) {
+    if (isLoading) {
         return React.createElement(Typography, null, "Loading cached results...");
     }
     if (results.length === 0) {
         return (React.createElement(Typography, { color: "textSecondary" }, "No cached BLAST results found for this gene. Run a BLAST query to cache results."));
     }
     return (React.createElement("div", null,
-        React.createElement("div", { style: {
-                display: 'flex',
-                justifyContent: 'space-between',
-                alignItems: 'center',
-                marginBottom: 8,
-            } },
+        React.createElement("div", { className: classes.header },
             React.createElement(Typography, { variant: "subtitle1" },
                 "Cached BLAST Results (",
                 results.length,
                 ")"),
-            React.createElement(Button, { size: "small", color: "error", onClick: () => {
-                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
-                    handleClearAll();
+            React.createElement(Button, { size: "small", color: "error", onClick: async () => {
+                    try {
+                        setOperationError(undefined);
+                        await handleClearAll();
+                    }
+                    catch (e) {
+                        setOperationError(e);
+                    }
                 } }, "Clear All")),
-        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 => {
+        React.createElement(List, { dense: true, className: classes.resultList }, results.map(result => (React.createElement(ListItem, { key: result.id, disablePadding: true, secondaryAction: React.createElement(IconButton, { edge: "end", size: "small", onClick: async (e) => {
                     e.stopPropagation();
-                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
-                    handleDelete(result.id);
+                    try {
+                        setOperationError(undefined);
+                        await handleDelete(result.id);
+                    }
+                    catch (err) {
+                        setOperationError(err);
+                    }
                 } },
                 React.createElement(DeleteIcon, { fontSize: "small" })) },
             React.createElement(ListItemButton, { onClick: () => {

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

@@ -1 +1 @@
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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;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,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,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,MAAM,EAAE;QACN,OAAO,EAAE,MAAM;QACf,cAAc,EAAE,eAAe;QAC/B,UAAU,EAAE,QAAQ;QACpB,YAAY,EAAE,CAAC;KAChB;IACD,UAAU,EAAE;QACV,SAAS,EAAE,GAAG;QACd,QAAQ,EAAE,MAAM;KACjB;CACF,CAAC,CAAA;AAEF,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,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,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,6BAAK,SAAS,EAAE,OAAO,CAAC,MAAM;YAC5B,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,SAAS,EAAE,OAAO,CAAC,UAAU,IACtC,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"}

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

@@ -1,4 +1,4 @@
-import React, { useEffect, useMemo, useState } from 'react';
+import React, { useMemo, useState } from 'react';
 import { ErrorMessage } from '@jbrowse/core/ui';
 import { getContainingView } from '@jbrowse/core/util';
 import ExpandMoreIcon from '@mui/icons-material/ExpandMore';
@@ -8,8 +8,8 @@ import { makeStyles } from 'tss-react/mui';
 import CachedBlastResults from './CachedBlastResults';
 import { blastLaunchView } from './blastLaunchView';
 import { msaAlgorithms } from './consts';
+import { useCachedBlastResults } from './useCachedBlastResults';
 import TextField2 from '../../../components/TextField2';
-import { getAllCachedResults } from '../../../utils/blastCache';
 import { getGeneDisplayName, getGeneIdentifiers, getTranscriptDisplayName, } from '../../util';
 import TranscriptSelector from '../TranscriptSelector';
 import { useTranscriptSelection } from '../useTranscriptSelection';
@@ -43,25 +43,10 @@ const NCBIBlastAutomaticPanel = observer(function ({ handleClose, feature, model
     const [selectedBlastDatabase, setSelectedBlastDatabase] = useState('nr');
     const [selectedMsaAlgorithm, setSelectedMsaAlgorithm] = useState('clustalo');
     const [selectedBlastProgram, setSelectedBlastProgram] = useState('quick-blastp');
-    const [hasCachedResults, setHasCachedResults] = useState(false);
-    const [error, setError] = useState();
     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 && geneIds.includes(r.geneId)));
-            }
-            catch (e) {
-                console.error(e);
-                setError(e);
-            }
-        })();
-    }, [geneIds]);
+    const { results: cachedResults, error: cachedResultsError } = useCachedBlastResults(geneIds);
     const { options, selectedId, setSelectedId, selectedTranscript, proteinSequence, error: proteinSequenceError, } = useTranscriptSelection({ feature, view });
-    const e = proteinSequenceError ?? launchViewError ?? error;
+    const e = proteinSequenceError ?? launchViewError ?? cachedResultsError;
     return (React.createElement(React.Fragment, null,
         React.createElement(DialogContent, { className: classes.dialogContent },
             children,
@@ -84,7 +69,7 @@ const NCBIBlastAutomaticPanel = observer(function ({ handleClose, feature, model
                 selectedBlastDatabase === 'nr_cluster_seq' ? (React.createElement(Typography, { variant: "subtitle2", className: classes.clusterSeqMessage }, "Can only use blastp on nr_cluster_seq")) : null),
             React.createElement(TranscriptSelector, { feature: feature, options: options, selectedId: selectedId, selectedTranscript: selectedTranscript, onTranscriptChange: setSelectedId, proteinSequence: proteinSequence }),
             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"),
-            hasCachedResults ? (React.createElement(Accordion, { className: classes.cachedResultsAccordion },
+            cachedResults.length > 0 ? (React.createElement(Accordion, { className: classes.cachedResultsAccordion },
                 React.createElement(AccordionSummary, { expandIcon: React.createElement(ExpandMoreIcon, null) },
                     React.createElement(Typography, null, "Previous BLAST Results")),
                 React.createElement(AccordionDetails, null,
@@ -109,14 +94,16 @@ const NCBIBlastAutomaticPanel = observer(function ({ handleClose, feature, model
                                 proteinSequence,
                             },
                         });
+                        handleClose();
                     }
                     catch (e) {
                         console.error(e);
                         setLaunchViewError(e);
                     }
-                    handleClose();
                 }, disabled: !proteinSequence }, "Submit"),
-            React.createElement(Button, { color: "secondary", variant: "contained", onClick: handleClose }, "Cancel"))));
+            React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
+                    handleClose();
+                } }, "Cancel"))));
 });
 export default NCBIBlastAutomaticPanel;
 //# sourceMappingURL=NCBIBlastAutomaticPanel.js.map

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

@@ -1 +1 @@
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