npm - jbrowse-plugin-msaview - Versions diffs - 2.3.5 → 2.3.8 - Mend

jbrowse-plugin-msaview 2.3.5 → 2.3.8

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 (62) hide show

package/README.md CHANGED Viewed

@@ -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 CHANGED Viewed

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

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"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 CHANGED Viewed

@@ -4,9 +4,22 @@ 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 { 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) {
@@ -21,6 +34,7 @@ function getResultDisplayName(result) {
     return parts.join(' - ');
 }
 const CachedBlastResults = observer(function ({ model, handleClose, feature, }) {
+    const { classes } = useStyles();
     const view = getContainingView(model);
     const [operationError, setOperationError] = useState();
     const geneIds = useMemo(() => getGeneIdentifiers(feature), [feature]);
@@ -44,12 +58,7 @@ const CachedBlastResults = observer(function ({ model, handleClose, feature, })
         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,
@@ -63,7 +72,7 @@ const CachedBlastResults = observer(function ({ model, handleClose, feature, })
                         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: async (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();
                     try {
                         setOperationError(undefined);

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

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

@@ -94,14 +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 CHANGED Viewed

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

@@ -20,6 +20,9 @@ const useStyles = makeStyles()({
         margin: 30,
         maxWidth: 600,
     },
+    infoText: {
+        marginTop: 20,
+    },
 });
 const NCBIBlastManualPanel = observer(function ({ handleClose, feature, model, children, baseUrl, }) {
     const { classes } = useStyles();
@@ -36,7 +39,7 @@ const NCBIBlastManualPanel = observer(function ({ handleClose, feature, model, c
             proteinSequence ? (React.createElement("div", { className: classes.ncbiLink },
                 "Link to NCBI BLAST: ",
                 React.createElement(ExternalLink, { href: link }, link2))) : null,
-            React.createElement(Typography, { style: { marginTop: 20 } }, "Click the link above and run your BLAST query, and once you have results, click \"Multiple Alignment\" at the top of the results page to be redirected to COBALT, NCBI's multiple sequence aligner. Once COBALT completes, you can download an MSA (.aln file) and optionally a Newick tree (.nh) and paste the results into JBrowse")),
+            React.createElement(Typography, { className: classes.infoText }, "Click the link above and run your BLAST query, and once you have results, click \"Multiple Alignment\" at the top of the results page to be redirected to COBALT, NCBI's multiple sequence aligner. Once COBALT completes, you can download an MSA (.aln file) and optionally a Newick tree (.nh) and paste the results into JBrowse")),
         React.createElement(DialogActions, null,
             React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
                     handleClose();

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

	@@ -1 +1 @@
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"}
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;IACD,QAAQ,EAAE;QACR,SAAS,EAAE,EAAE;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,SAAS,EAAE,OAAO,CAAC,QAAQ,2UAM1B,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/NCBIBlastPanel.js CHANGED Viewed

@@ -2,12 +2,18 @@ import React, { useState } from 'react';
 import { useLocalStorage } from '@jbrowse/core/util';
 import SettingsIcon from '@mui/icons-material/Settings';
 import { IconButton } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
 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 useStyles = makeStyles()({
+    settingsButton: {
+        float: 'right',
+    },
+});
 const panelMap = {
     automatic: NCBIBlastAutomaticPanel,
     rid: NCBIBlastRIDPanel,
@@ -17,9 +23,10 @@ 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 { classes } = useStyles();
     const Panel = panelMap[lookupMethod];
     return (React.createElement(React.Fragment, null,
-        React.createElement(IconButton, { style: { float: 'right' }, size: "small", onClick: () => {
+        React.createElement(IconButton, { className: classes.settingsButton, size: "small", onClick: () => {
                 setSettingsOpen(true);
             } },
             React.createElement(SettingsIcon, null)),

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;AAC1C,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,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,cAAc,EAAE;QACd,KAAK,EAAE,OAAO;KACf;CACF,CAAC,CAAA;AAEF,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;IACvD,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAE/B,MAAM,KAAK,GAAG,QAAQ,CAAC,YAAqC,CAAC,CAAA;IAE7D,OAAO,CACL;QACE,oBAAC,UAAU,IACT,SAAS,EAAE,OAAO,CAAC,cAAc,EACjC,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.js CHANGED Viewed

@@ -15,6 +15,15 @@ const useStyles = makeStyles()({
     dialogContent: {
         width: '80em',
     },
+    marginBottom: {
+        marginBottom: 16,
+    },
+    ridField: {
+        width: 150,
+    },
+    infoText: {
+        marginTop: 20,
+    },
 });
 const NCBIBlastRIDPanel = observer(function ({ handleClose, feature, model, children, baseUrl, }) {
     const { classes } = useStyles();
@@ -24,23 +33,22 @@ const NCBIBlastRIDPanel = observer(function ({ handleClose, feature, model, chil
     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 => {
+            React.createElement(Typography, { variant: "body2", className: classes.marginBottom }, "Enter the RID (Request ID) from a previously submitted NCBI BLAST query. You can find the RID in the BLAST results page URL or at the top of the results page. RIDs are typically valid for 24-36 hours after submission."),
+            React.createElement(TextField2, { variant: "outlined", label: "BLAST RID", placeholder: "e.g., ABC12345", fullWidth: true, className: classes.marginBottom, value: rid, onChange: event => {
                     setRid(event.target.value);
                 } }),
-            trimmedRid ? (React.createElement(Typography, { variant: "body2", style: { marginBottom: 16 } },
+            trimmedRid ? (React.createElement(Typography, { variant: "body2", className: classes.marginBottom },
                 React.createElement(ExternalLink, { href: `${baseUrl}?CMD=Get&RID=${trimmedRid}` }, "View BLAST results on NCBI"))) : null,
-            React.createElement(TextField2, { variant: "outlined", label: "MSA Algorithm", style: style, select: true, value: selectedMsaAlgorithm, onChange: event => {
+            React.createElement(TextField2, { variant: "outlined", label: "MSA Algorithm", className: classes.ridField, select: true, value: selectedMsaAlgorithm, onChange: event => {
                     setSelectedMsaAlgorithm(event.target.value);
                 } }, msaAlgorithms.map(val => (React.createElement(MenuItem, { value: val, key: val }, val)))),
             React.createElement(TranscriptSelector, { feature: feature, options: options, selectedId: selectedId, selectedTranscript: selectedTranscript, onTranscriptChange: setSelectedId, proteinSequence: proteinSequence }),
-            React.createElement(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(Typography, { className: classes.infoText }, "This will fetch the BLAST results for the provided RID and run them through a multiple sequence alignment. The protein sequence from the selected transcript will be added as the query sequence in the MSA.")),
         React.createElement(DialogActions, null,
             React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
                     try {
@@ -62,12 +70,12 @@ const NCBIBlastRIDPanel = observer(function ({ handleClose, feature, model, chil
                                 rid: trimmedRid,
                             },
                         });
+                        handleClose();
                     }
                     catch (e) {
                         console.error(e);
                         setLaunchViewError(e);
                     }
-                    handleClose();
                 }, disabled: !proteinSequence || !trimmedRid }, "Submit"),
             React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
                     handleClose();

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

	@@ -1 +1 @@
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