jbrowse-plugin-msaview 2.2.2 → 2.2.4

package/CHANGELOG.md

@@ -46,7 +46,7 @@
 
 # v1.0.7
 
-- Move npm run build script to prepare script in package.jsom
+- Move yarn build script to prepare script in package.jsom
 
 # v1.0.6
 

package/README.md

@@ -38,3 +38,232 @@ https://jbrowse.org/code/jb2/main/index.html?config=https://unpkg.com/jbrowse-pl
   alignments embedded in a single file)
 - Clustal files (e.g. .aln file, uses clustal-js parser)
 - Newick (tree can be loaded separately as a .nh file)
+
+## Data persistence
+
+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.
+
+### How it works
+
+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
+
+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.
+
+### Storage details
+
+- Database name: `jbrowse-msaview-data`
+- Stored data includes: MSA alignment, tree, and tree metadata
+- Each entry is timestamped for cleanup purposes
+
+This mechanism is transparent to users and requires no configuration.
+
+## LaunchView-MsaView extension point
+
+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).
+
+### 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)         │
+          └─────────────────────────────────────────┘
+```
+
+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

@@ -3,26 +3,31 @@ import { getSession } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
 import { useStyles } from './util';
 const GenomeMouseoverHighlight = observer(function ({ model, }) {
-    const { hovered } = getSession(model);
-    return hovered &&
-        typeof hovered === 'object' &&
-        'hoverPosition' in hovered ? (React.createElement(GenomeMouseoverHighlightPostNullCheck, { model: model })) : null;
+    const session = getSession(model);
+    const { hovered, views } = session;
+    // Early return if no MSA view exists
+    const hasMsaView = views.some(s => s.type === 'MsaView');
+    if (!hasMsaView) {
+        return null;
+    }
+    // Early return if no hover position
+    if (!hovered ||
+        typeof hovered !== 'object' ||
+        !('hoverPosition' in hovered)) {
+        return null;
+    }
+    return React.createElement(GenomeMouseoverHighlightRenderer, { model: model, hovered: hovered });
 });
-const GenomeMouseoverHighlightPostNullCheck = observer(function ({ model, }) {
+const GenomeMouseoverHighlightRenderer = observer(function ({ model, hovered, }) {
     const { classes } = useStyles();
-    const session = getSession(model);
-    if (session.views.some(s => s.type === 'MsaView')) {
-        const { hovered } = session;
-        const { offsetPx } = model;
-        // @ts-expect-error
-        const { coord, refName } = hovered.hoverPosition;
-        const s = model.bpToPx({ refName, coord: coord - 1 });
-        const e = model.bpToPx({ refName, coord: coord });
-        if (s && e) {
-            const width = Math.max(Math.abs(e.offsetPx - s.offsetPx), 4);
-            const left = Math.min(s.offsetPx, e.offsetPx) - offsetPx;
-            return React.createElement("div", { className: classes.highlight, style: { left, width } });
-        }
+    const { offsetPx } = model;
+    const { coord, refName } = hovered.hoverPosition;
+    const s = model.bpToPx({ refName, coord: coord - 1 });
+    const e = model.bpToPx({ refName, coord: coord });
+    if (s && e) {
+        const width = Math.max(Math.abs(e.offsetPx - s.offsetPx), 4);
+        const left = Math.min(s.offsetPx, e.offsetPx) - offsetPx;
+        return React.createElement("div", { className: classes.highlight, style: { left, width } });
     }
     return null;
 });

package/dist/AddHighlightModel/GenomeMouseoverHighlight.js.map

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package/dist/AddHighlightModel/MsaToGenomeHighlight.js

@@ -2,27 +2,37 @@ import React from 'react';
 import { getSession } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
 import { useStyles } from './util';
-function getCanonicalName(assembly, s) {
-    return assembly.getCanonicalRefName(s) ?? s;
-}
+// Outer component: only re-renders when MSA view or highlights change
 const MsaToGenomeHighlight = observer(function MsaToGenomeHighlight2({ model, }) {
+    const { views } = getSession(model);
+    const msaView = views.find(f => f.type === 'MsaView');
+    const highlights = msaView?.connectedHighlights;
+    // Early return if no highlights - avoid all other work
+    if (!highlights || highlights.length === 0) {
+        return null;
+    }
+    return React.createElement(MsaToGenomeHighlightRenderer, { model: model, highlights: highlights });
+});
+// Inner component: handles the scroll-dependent rendering
+const MsaToGenomeHighlightRenderer = observer(function ({ model, highlights, }) {
     const { classes } = useStyles();
-    const { assemblyManager, views } = getSession(model);
-    const p = views.find(f => f.type === 'MsaView');
+    const { assemblyManager } = getSession(model);
     const assembly = assemblyManager.get(model.assemblyNames[0]);
-    return assembly ? (React.createElement(React.Fragment, null, p?.connectedHighlights.map((r, idx) => {
-        const refName = getCanonicalName(assembly, r.refName);
+    const { offsetPx } = model;
+    if (!assembly) {
+        return null;
+    }
+    return (React.createElement(React.Fragment, null, highlights.map((r, idx) => {
+        const refName = assembly.getCanonicalRefName(r.refName) ?? r.refName;
         const s = model.bpToPx({ refName, coord: r.start });
         const e = model.bpToPx({ refName, coord: r.end });
         if (s && e) {
             const width = Math.max(Math.abs(e.offsetPx - s.offsetPx), 4);
-            const left = Math.min(s.offsetPx, e.offsetPx) - model.offsetPx;
-            return (React.createElement("div", { key: `${JSON.stringify(r)}-${idx}`, className: classes.highlight, style: { left, width } }));
-        }
-        else {
-            return null;
+            const left = Math.min(s.offsetPx, e.offsetPx) - offsetPx;
+            return (React.createElement("div", { key: `${r.refName}-${r.start}-${r.end}-${idx}`, className: classes.highlight, style: { left, width } }));
         }
-    }))) : null;
+        return null;
+    })));
 });
 export default MsaToGenomeHighlight;
 //# sourceMappingURL=MsaToGenomeHighlight.js.map

package/dist/AddHighlightModel/MsaToGenomeHighlight.js.map

@@ -1 +1 @@
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+{"version":3,"file":"MsaToGenomeHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/MsaToGenomeHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,SAAS,EAAE,MAAM,QAAQ,CAAA;AAOlC,sEAAsE;AACtE,MAAM,oBAAoB,GAAG,QAAQ,CAAC,SAAS,qBAAqB,CAAC,EACnE,KAAK,GAGN;IACC,MAAM,EAAE,KAAK,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACnC,MAAM,OAAO,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,SAAS,CAEvC,CAAA;IAEb,MAAM,UAAU,GAAG,OAAO,EAAE,mBAAmB,CAAA;IAE/C,uDAAuD;IACvD,IAAI,CAAC,UAAU,IAAI,UAAU,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAC3C,OAAO,IAAI,CAAA;IACb,CAAC;IAED,OAAO,oBAAC,4BAA4B,IAAC,KAAK,EAAE,KAAK,EAAE,UAAU,EAAE,UAAU,GAAI,CAAA;AAC/E,CAAC,CAAC,CAAA;AAEF,0DAA0D;AAC1D,MAAM,4BAA4B,GAAG,QAAQ,CAAC,UAAU,EACtD,KAAK,EACL,UAAU,GAIX;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,eAAe,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IAC7C,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,KAAK,CAAC,aAAa,CAAC,CAAC,CAAE,CAAC,CAAA;IAC7D,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAE1B,IAAI,CAAC,QAAQ,EAAE,CAAC;QACd,OAAO,IAAI,CAAA;IACb,CAAC;IAED,OAAO,CACL,0CACG,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;QACzB,MAAM,OAAO,GAAG,QAAQ,CAAC,mBAAmB,CAAC,CAAC,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,OAAO,CAAA;QACpE,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAA;QACnD,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC,GAAG,EAAE,CAAC,CAAA;QACjD,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACX,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAA;YAC5D,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,QAAQ,CAAA;YACxD,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,CAAC,CAAC,OAAO,IAAI,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,GAAG,IAAI,GAAG,EAAE,EAC9C,SAAS,EAAE,OAAO,CAAC,SAAS,EAC5B,KAAK,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,GACtB,CACH,CAAA;QACH,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC,CAAC,CACD,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,oBAAoB,CAAA"}

package/dist/AddHighlightModel/index.js

@@ -1,9 +1,16 @@
 import React from 'react';
+import { getSession } from '@jbrowse/core/util';
 import HighlightComponents from './HighlightComponents';
 export default function AddHighlightComponentsModelF(pluginManager) {
     pluginManager.addToExtensionPoint('LinearGenomeView-TracksContainerComponent', 
     // @ts-expect-error
-    (rest = [], { model }) => {
+    (rest, { model }) => {
+        // Quick check: don't add any components if no MSA view exists
+        const { views } = getSession(model);
+        const hasMsaView = views.some(v => v.type === 'MsaView');
+        if (!hasMsaView) {
+            return rest;
+        }
         return [
             ...rest,
             React.createElement(HighlightComponents, { key: "highlight_protein_viewer_msaview", model: model }),

package/dist/AddHighlightModel/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AddHighlightModel/index.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAIzB,OAAO,mBAAmB,MAAM,uBAAuB,CAAA;AAIvD,MAAM,CAAC,OAAO,UAAU,4BAA4B,CAClD,aAA4B;IAE5B,aAAa,CAAC,mBAAmB,CAC/B,2CAA2C;IAC3C,mBAAmB;IACnB,CACE,OAA0B,EAAE,EAC5B,EAAE,KAAK,EAAoC,EAC3C,EAAE;QACF,OAAO;YACL,GAAG,IAAI;YACP,oBAAC,mBAAmB,IAClB,GAAG,EAAC,kCAAkC,EACtC,KAAK,EAAE,KAAK,GACZ;SACH,CAAA;IACH,CAAC,CACF,CAAA;AACH,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AddHighlightModel/index.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAGzB,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE/C,OAAO,mBAAmB,MAAM,uBAAuB,CAAA;AAIvD,MAAM,CAAC,OAAO,UAAU,4BAA4B,CAClD,aAA4B;IAE5B,aAAa,CAAC,mBAAmB,CAC/B,2CAA2C;IAC3C,mBAAmB;IACnB,CAAC,IAAuB,EAAE,EAAE,KAAK,EAAoC,EAAE,EAAE;QACvE,8DAA8D;QAC9D,MAAM,EAAE,KAAK,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;QACnC,MAAM,UAAU,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,SAAS,CAAC,CAAA;QACxD,IAAI,CAAC,UAAU,EAAE,CAAC;YAChB,OAAO,IAAI,CAAA;QACb,CAAC;QAED,OAAO;YACL,GAAG,IAAI;YACP,oBAAC,mBAAmB,IAClB,GAAG,EAAC,kCAAkC,EACtC,KAAK,EAAE,KAAK,GACZ;SACH,CAAA;IACH,CAAC,CACF,CAAA;AACH,CAAC"}

package/dist/AddHighlightModel/util.d.ts

@@ -4,6 +4,6 @@ export declare const useStyles: (params: void, muiStyleOverridesParams?: {
 } | undefined) => {
     classes: Record<"highlight", string>;
     theme: import("@mui/material").Theme;
-    css: import("tss-react/types").Css;
-    cx: import("tss-react/types").Cx;
+    css: import("tss-react").Css;
+    cx: import("tss-react").Cx;
 };

package/dist/BgzipFastaMsaAdapter/configSchema.d.ts

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

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

@@ -6,9 +6,9 @@ import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 import { ensemblGeneTreeLaunchView } from './ensemblGeneTreeLaunchView';
 import { useGeneTree } from './useGeneTree';
-import { getGeneDisplayName, getId, getTranscriptFeatures } from '../../util';
+import { getGeneDisplayName } from '../../util';
 import TranscriptSelector from '../TranscriptSelector';
-import { useFeatureSequence } from '../useFeatureSequence';
+import { useTranscriptSelection } from '../useTranscriptSelection';
 const useStyles = makeStyles()({
     dialogContent: {
         width: '80em',
@@ -22,14 +22,8 @@ const EnsemblGeneTree = observer(function ({ model, feature, handleClose, }) {
     const view = getContainingView(model);
     const { classes } = useStyles();
     const [launchViewError, setLaunchViewError] = useState();
-    const options = getTranscriptFeatures(feature);
-    const [userSelection, setUserSelection] = useState(getId(options[0]));
-    const { treeData, isTreeLoading, treeError } = useGeneTree(userSelection);
-    const selectedTranscript = options.find(val => getId(val) === userSelection);
-    const { proteinSequence, error: featureSequenceError } = useFeatureSequence({
-        view,
-        feature: selectedTranscript,
-    });
+    const { options, selectedId, setSelectedId, selectedTranscript, proteinSequence, error: featureSequenceError, } = useTranscriptSelection({ feature, view });
+    const { treeData, isTreeLoading, treeError } = useGeneTree(selectedId);
     const loadingMessage = isTreeLoading
         ? 'Loading tree data from Ensembl GeneTree'
         : undefined;
@@ -46,7 +40,7 @@ const EnsemblGeneTree = observer(function ({ model, feature, handleClose, }) {
                     "See ",
                     treeData.geneTreeId,
                     " at Ensembl"))) : null,
-            React.createElement(TranscriptSelector, { feature: feature, options: options, selectedTranscriptId: userSelection, onTranscriptChange: setUserSelection, proteinSequence: proteinSequence })),
+            React.createElement(TranscriptSelector, { feature: feature, options: options, 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

@@ -1 +1 @@
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package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.js

@@ -1,7 +1,11 @@
 import useSWR from 'swr';
 import { geneTreeFetcher } from './ensemblGeneTreeUtils';
 export function useGeneTree(geneId) {
-    const { data, error, isLoading } = useSWR(() => (geneId ? ['geneTree', geneId] : null), ([, geneId]) => geneTreeFetcher(geneId));
+    const { data, error, isLoading } = useSWR(() => (geneId ? ['geneTree', geneId] : null), ([, geneId]) => geneTreeFetcher(geneId), {
+        revalidateOnFocus: false,
+        revalidateOnReconnect: false,
+        revalidateIfStale: false,
+    });
     return { treeData: data, isTreeLoading: isLoading, treeError: error };
 }
 //# sourceMappingURL=useGeneTree.js.map

package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.js.map

@@ -1 +1 @@
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+{"version":3,"file":"useGeneTree.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,KAAK,CAAA;AAExB,OAAO,EAAE,eAAe,EAAE,MAAM,wBAAwB,CAAA;AAExD,MAAM,UAAU,WAAW,CAAC,MAAc;IACxC,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,SAAS,EAAE,GAAG,MAAM,CACvC,GAAG,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,UAAU,EAAE,MAAM,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,EAC5C,CAAC,CAAC,EAAE,MAAM,CAAC,EAAE,EAAE,CAAC,eAAe,CAAC,MAAM,CAAC,EACvC;QACE,iBAAiB,EAAE,KAAK;QACxB,qBAAqB,EAAE,KAAK;QAC5B,iBAAiB,EAAE,KAAK;KACzB,CACF,CAAA;IAED,OAAO,EAAE,QAAQ,EAAE,IAAI,EAAE,aAAa,EAAE,SAAS,EAAE,SAAS,EAAE,KAAK,EAAE,CAAA;AACvE,CAAC"}

package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js

@@ -1,35 +1,35 @@
 import React, { useState } from 'react';
+import { readConfObject } from '@jbrowse/core/configuration';
 import { Dialog } from '@jbrowse/core/ui';
+import { getSession } from '@jbrowse/core/util';
 import { Tab, Tabs } from '@mui/material';
 import EnsemblGeneTree from './EnsemblGeneTree/EnsemblGeneTree';
 import ManualMSALoader from './ManualMSALoader/ManualMSALoader';
 import NCBIBlastPanel from './NCBIBlastQuery/NCBIBlastPanel';
 import PreLoadedMSA from './PreLoadedMSA/PreLoadedMSADataPanel';
 import TabPanel from './TabPanel';
-const TABS = {
-    NCBI_BLAST: 0,
-    PRELOADED_MSA: 1,
-    ENSEMBL_GENETREE: 2,
-    MANUAL_MSA: 3,
-};
 export default function LaunchMsaViewDialog({ handleClose, feature, model, }) {
-    const [value, setValue] = useState(TABS.NCBI_BLAST);
+    const session = getSession(model);
+    const { jbrowse } = session;
+    const datasets = readConfObject(jbrowse, ['msa', 'datasets']);
+    const hasPreloadedDatasets = datasets && datasets.length > 0;
+    const [value, setValue] = useState('ncbi_blast');
     const handleChange = (_event, newValue) => {
         setValue(newValue);
     };
     return (React.createElement(Dialog, { maxWidth: "xl", title: "Launch MSA view", open: true, onClose: handleClose },
         React.createElement(Tabs, { value: value, onChange: handleChange },
-            React.createElement(Tab, { label: "NCBI BLAST query", value: TABS.NCBI_BLAST }),
-            React.createElement(Tab, { label: "Pre-loaded MSA datasets", value: TABS.PRELOADED_MSA }),
-            React.createElement(Tab, { label: "Ensembl GeneTree", value: TABS.ENSEMBL_GENETREE }),
-            React.createElement(Tab, { label: "Manually open MSA dataset", value: TABS.MANUAL_MSA })),
-        React.createElement(TabPanel, { value: value, index: TABS.NCBI_BLAST },
+            React.createElement(Tab, { label: "NCBI BLAST query", value: "ncbi_blast" }),
+            hasPreloadedDatasets ? (React.createElement(Tab, { label: "Pre-loaded MSA datasets", value: "preloaded_msa" })) : null,
+            React.createElement(Tab, { label: "Ensembl GeneTree", value: "ensembl_genetree" }),
+            React.createElement(Tab, { label: "Manual upload", value: "manual_msa" })),
+        React.createElement(TabPanel, { value: value, index: "ncbi_blast" },
             React.createElement(NCBIBlastPanel, { handleClose: handleClose, feature: feature, model: model })),
-        React.createElement(TabPanel, { value: value, index: TABS.PRELOADED_MSA },
-            React.createElement(PreLoadedMSA, { model: model, feature: feature, handleClose: handleClose })),
-        React.createElement(TabPanel, { value: value, index: TABS.ENSEMBL_GENETREE },
+        hasPreloadedDatasets ? (React.createElement(TabPanel, { value: value, index: "preloaded_msa" },
+            React.createElement(PreLoadedMSA, { model: model, feature: feature, handleClose: handleClose }))) : null,
+        React.createElement(TabPanel, { value: value, index: "ensembl_genetree" },
             React.createElement(EnsemblGeneTree, { model: model, feature: feature, handleClose: handleClose })),
-        React.createElement(TabPanel, { value: value, index: TABS.MANUAL_MSA },
+        React.createElement(TabPanel, { value: value, index: "manual_msa" },
             React.createElement(ManualMSALoader, { model: model, feature: feature, handleClose: handleClose }))));
 }
 //# sourceMappingURL=LaunchMsaViewDialog.js.map

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

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