jbrowse-plugin-msaview 2.8.0 → 2.8.2

package/dist/LaunchMsaViewExtensionPoint/index.js

@@ -1,12 +1,19 @@
 export default function LaunchMsaViewExtensionPointF(pluginManager) {
     pluginManager.addToExtensionPoint('LaunchView-MsaView', (args) => {
         const { session, data, msaFileLocation, msaIndexedLocation, msaName, treeFileLocation, querySeqName, ...rest } = args;
-        if (!data && !msaFileLocation && !msaIndexedLocation) {
-            throw new Error('No MSA data or file location provided when launching MSA view');
+        // `orthologParams` is a fourth source, and unlike the other three it names
+        // no alignment at all — the view builds one from NCBI at launch, which is
+        // the dialog's Orthologs tab reached declaratively.
+        if (!data &&
+            !msaFileLocation &&
+            !msaIndexedLocation &&
+            !rest.orthologParams) {
+            throw new Error('No MSA data, file location or orthologParams provided when launching MSA view');
         }
         // inline data and the tree URL are native react-msaview snapshot props, set
-        // directly. Only sources needing launch-time resolution go through `init`:
-        // msaUrl (AlphaFold sniff) and the name-indexed bgzip block (no native loader).
+        // directly, and so is orthologParams (the model's own autorun picks it up).
+        // Only sources needing launch-time resolution go through `init`: msaUrl
+        // (AlphaFold sniff) and the name-indexed bgzip block (no native loader).
         session.addView('MsaView', {
             type: 'MsaView',
             ...rest,

package/dist/MsaViewPanel/doLaunchOrthologs.js

@@ -1,6 +1,6 @@
 import { cleanProteinSequence } from '../LaunchMsaView/util';
 import { launchMSA } from '../utils/msa';
-import { fetchOrthologRows, fetchProteinForGene, resolveGeneId, } from '../utils/ncbiOrthologs';
+import { COMMON_SPECIES, fetchOrthologRows, fetchProteinForGene, resolveGeneId, } from '../utils/ncbiOrthologs';
 /**
  * The no-search-job alternative to doLaunchBlast.
  *
@@ -18,7 +18,6 @@ import { fetchOrthologRows, fetchProteinForGene, resolveGeneId, } from '../utils
  */
 export async function doLaunchOrthologs({ self, }) {
     const { taxId, taxa, geneCandidates, msaAlgorithm, proteinSequence } = self.orthologParams;
-    const cleanedSeq = cleanProteinSequence(proteinSequence);
     const onProgress = (arg) => {
         self.setProgress(arg);
     };
@@ -27,15 +26,33 @@ export async function doLaunchOrthologs({ self, }) {
     if (!resolved) {
         throw new Error(`Could not resolve any of ${geneCandidates.join(', ')} to an NCBI gene in taxon ${taxId}. Try the NCBI BLAST tab, which needs no gene identifier.`);
     }
-    // the query species is represented by the user's own transcript below
-    const wanted = new Set(taxa.filter(t => t !== taxId));
+    // The query row. The dialog always supplies it — it is the user's OWN
+    // selected transcript, which is what makes `connectedFeature` map genome
+    // coordinates through this row. A launch that has no transcript to translate
+    // (a session spec naming only a gene) falls back to NCBI's representative
+    // protein for the resolved gene, which is the same choice made for every
+    // other row, so the alignment is the one NCBI would build for that gene.
+    const representative = await fetchRepresentativeQueryProtein(resolved.geneId);
+    const cleanedSeq = proteinSequence
+        ? cleanProteinSequence(proteinSequence)
+        : representative?.sequence;
+    if (!cleanedSeq) {
+        throw new Error(`No query protein: none was supplied and NCBI returned no representative protein for gene ${resolved.geneId}.`);
+    }
+    // Every species the panel offers, when a launch names none. A spec that wants
+    // a narrower comparison says so; one that just wants "this gene across
+    // species" should not have to enumerate the list the dialog would have
+    // checked for it.
+    const wantedTaxa = taxa ?? COMMON_SPECIES.map(s => s.taxId);
+    // the query species is represented by the query row above
+    const wanted = new Set(wantedTaxa.filter(t => t !== taxId));
     const rows = await fetchOrthologRows({
         geneId: resolved.geneId,
         taxa: wanted,
         onProgress,
     });
     const treeMetadata = {
-        QUERY: await buildQueryMetadata(self, resolved.geneId, cleanedSeq),
+        QUERY: buildQueryMetadata(self, resolved.geneId, cleanedSeq, representative),
     };
     for (const row of rows) {
         treeMetadata[row.label] = buildRowMetadata(row);
@@ -54,31 +71,37 @@ export async function doLaunchOrthologs({ self, }) {
     };
 }
 /**
- * The query row is the user's own translated transcript, so it carries an
- * Accession — which is what drives the automatic CDD overlay
- * (afterCreateAutoruns.autoLoadProteinDomains -> loadProteinDomains) — ONLY
- * when its sequence is byte-identical to the RefSeq protein that accession
+ * A failed lookup only costs the query row its domain overlay and, for a launch
+ * that supplied no sequence of its own, the alignment — so it is reported by
+ * returning nothing rather than by throwing here.
+ */
+async function fetchRepresentativeQueryProtein(geneId) {
+    try {
+        return await fetchProteinForGene(geneId);
+    }
+    catch (e) {
+        console.warn('[msaview-orthologs] query protein lookup failed:', e);
+        return undefined;
+    }
+}
+/**
+ * The query row carries an Accession — which is what drives the automatic CDD
+ * overlay (afterCreateAutoruns.autoLoadProteinDomains -> loadProteinDomains) —
+ * ONLY when its sequence is byte-identical to the RefSeq protein that accession
  * names. Attaching it unconditionally would put every domain box at an offset
  * whenever the user picked a non-representative isoform, which is a silently
- * wrong figure rather than a missing one.
+ * wrong figure rather than a missing one. A launch that took the representative
+ * protein as its query row passes that test by construction.
  */
-async function buildQueryMetadata(self, geneId, proteinSequence) {
+function buildQueryMetadata(self, geneId, proteinSequence, representative) {
     const transcript = self.orthologParams?.selectedTranscript;
     const metadata = { 'Gene ID': geneId };
     const name = transcript?.get('name') ?? transcript?.get('id');
     if (name) {
         metadata.Transcript = name;
     }
-    try {
-        const representative = await fetchProteinForGene(geneId);
-        if (representative?.sequence === proteinSequence) {
-            metadata.Accession = representative.accession;
-        }
-    }
-    catch (e) {
-        // a failed lookup only costs the query row its domain overlay, so it must
-        // not take down an alignment that is otherwise complete
-        console.warn('[msaview-orthologs] query protein lookup failed:', e);
+    if (representative?.sequence === proteinSequence) {
+        metadata.Accession = representative.accession;
     }
     return metadata;
 }

package/dist/MsaViewPanel/model.d.ts

@@ -23,13 +23,24 @@ export interface BlastParams {
 export interface OrthologParams {
     /** NCBI taxon id of the assembly the query gene came from */
     taxId: number;
-    /** taxon ids to include as rows (the query taxon is represented by QUERY) */
-    taxa: number[];
+    /**
+     * taxon ids to include as rows (the query taxon is represented by QUERY).
+     * Omitted means every species the launch dialog offers, which is what a
+     * launch that just wants "this gene across species" wants.
+     */
+    taxa?: number[];
     /** candidate gene identifiers off the feature, tried in order */
     geneCandidates: string[];
     msaAlgorithm: MsaAlgorithm;
     selectedTranscript?: Feature;
-    proteinSequence: string;
+    /**
+     * The QUERY row. The launch dialog always supplies it, translated from the
+     * transcript the user picked, which is what `connectedFeature` maps genome
+     * coordinates through. Omitted — a session spec naming a gene and nothing
+     * else — the query row becomes NCBI's representative protein for the resolved
+     * gene, the same choice every other row makes.
+     */
+    proteinSequence?: string;
 }
 /**
  * #stateModel MsaViewPlugin
@@ -53,7 +64,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
+    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("react-msaview").MSAFormat>>;
 }, "height" | "id" | "type" | "allowedGappyness" | "colWidth" | "collapsed" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "hideGaps" | "highlightColumns" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -507,7 +518,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setColorSchemeName(name: string): void;
     setBgColor(arg: boolean): void;
     setShowColumnStats(arg: boolean): void;
-    setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
+    setMSAFormat(arg?: import("react-msaview").MSAFormat): void;
 } & {
     headerHeight: number;
     status: {
@@ -594,7 +605,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly noDomains: boolean;
     menuItems(): never[];
     readonly treeMetadata: Record<string, Record<string, string> | undefined>;
-    readonly MSA: import("msa-parsers").MSAParserType | null;
+    readonly MSA: import("react-msaview").MSAParserType | null;
     readonly numColumns: number;
     readonly tree: import("react-msaview").NodeWithIds;
     readonly rowNames: string[];
@@ -956,7 +967,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     bgColor: boolean;
     colorSchemeName: string;
     showColumnStats: boolean;
-    msaFormat: import("msa-parsers").MSAFormat | undefined;
+    msaFormat: import("react-msaview").MSAFormat | undefined;
     drawLabels: boolean;
     labelsAlignRight: boolean;
     treeAreaWidth: number;