jbrowse-plugin-msaview 2.3.8 → 2.4.1

package/src/MsaViewPanel/structureConnection.ts

@@ -21,6 +21,13 @@ export function isProteinView(view: unknown): view is ProteinView {
   return v.type === 'ProteinView' && Array.isArray(v.structures)
 }
 
+/**
+ * Extract all ProteinView instances from a session's views array.
+ */
+export function getProteinViews(views: { type: string }[]): ProteinView[] {
+  return (views as unknown[]).filter(isProteinView)
+}
+
 /**
  * Represents a connection between the MSA view and a protein structure
  */
@@ -82,10 +89,3 @@ export function ungappedToGappedPosition(
   }
   return undefined
 }
-
-/**
- * Convert Map to plain object for MST frozen storage
- */
-export function mapToRecord(map: Map<number, number>): Record<number, number> {
-  return Object.fromEntries(map)
-}

package/src/MsaViewPanel/util.ts

@@ -5,13 +5,38 @@ export function checkHovered(hovered: unknown): hovered is {
   hoverPosition: { coord: number; refName: string }
 } {
   return (
+    !!hovered &&
     typeof hovered === 'object' &&
-    hovered !== null &&
     'hoverFeature' in hovered &&
-    'hoverPosition' in hovered
+    'hoverPosition' in hovered &&
+    !!hovered.hoverPosition
   )
 }
 
+interface AssemblyManagerLike {
+  get: (name: string) =>
+    | { getCanonicalRefName: (r: string) => string | undefined }
+    | undefined
+}
+
+export function getCanonicalRefName({
+  assemblyManager,
+  assemblyNames,
+  refName,
+}: {
+  assemblyManager: AssemblyManagerLike
+  assemblyNames: string[] | undefined
+  refName: string
+}) {
+  const assemblyName = assemblyNames?.[0]
+  if (assemblyName) {
+    return (
+      assemblyManager.get(assemblyName)?.getCanonicalRefName(refName) ?? refName
+    )
+  }
+  return refName
+}
+
 /**
  * Extracts UniProt ID from an AlphaFold URL
  * Examples:

package/src/utils/blastCache.ts

@@ -1,5 +1,11 @@
 import { openDB } from 'idb'
 
+import type {
+  BlastDatabase,
+  BlastProgram,
+  MsaAlgorithm,
+} from '../LaunchMsaView/components/NCBIBlastQuery/consts'
+
 const DB_NAME = 'jbrowse-msaview-blast-cache'
 const STORE_NAME = 'blast-results'
 const DB_VERSION = 2
@@ -7,9 +13,9 @@ const DB_VERSION = 2
 export interface CachedBlastResult {
   id: string
   proteinSequence: string
-  blastDatabase: string
-  blastProgram: string
-  msaAlgorithm: string
+  blastDatabase: BlastDatabase
+  blastProgram: BlastProgram
+  msaAlgorithm: MsaAlgorithm
   msa: string
   tree: string
   treeMetadata: string
@@ -36,8 +42,8 @@ async function getDB() {
 
 function createCacheKey(
   proteinSequence: string,
-  blastDatabase: string,
-  blastProgram: string,
+  blastDatabase: BlastDatabase,
+  blastProgram: BlastProgram,
   transcriptId?: string,
 ) {
   if (transcriptId) {
@@ -46,27 +52,6 @@ function createCacheKey(
   return `${blastDatabase}:${blastProgram}:${proteinSequence}`
 }
 
-export async function getCachedBlastResult({
-  proteinSequence,
-  blastDatabase,
-  blastProgram,
-  transcriptId,
-}: {
-  proteinSequence: string
-  blastDatabase: string
-  blastProgram: string
-  transcriptId?: string
-}) {
-  const db = await getDB()
-  const id = createCacheKey(
-    proteinSequence,
-    blastDatabase,
-    blastProgram,
-    transcriptId,
-  )
-  return db.get(STORE_NAME, id)
-}
-
 export async function saveBlastResult({
   proteinSequence,
   blastDatabase,
@@ -82,9 +67,9 @@ export async function saveBlastResult({
   geneName,
 }: {
   proteinSequence: string
-  blastDatabase: string
-  blastProgram: string
-  msaAlgorithm: string
+  blastDatabase: BlastDatabase
+  blastProgram: BlastProgram
+  msaAlgorithm: MsaAlgorithm
   msa: string
   tree: string
   treeMetadata: string
@@ -127,14 +112,6 @@ export async function getAllCachedResults() {
   return results.toSorted((a, b) => b.timestamp - a.timestamp)
 }
 
-export async function getCachedResultsByGeneId(geneId: string) {
-  const db = await getDB()
-  const results = await db.getAll(STORE_NAME)
-  return results
-    .filter(r => r.geneId === geneId)
-    .toSorted((a, b) => b.timestamp - a.timestamp)
-}
-
 export async function deleteCachedResult(id: string) {
   const db = await getDB()
   await db.delete(STORE_NAME, id)

package/src/utils/msa.ts

@@ -1,9 +1,11 @@
 import { textfetch, timeout } from './fetch'
 
+import type { MsaAlgorithm } from '../LaunchMsaView/components/NCBIBlastQuery/consts'
+
 const base = `https://www.ebi.ac.uk/Tools/services/rest`
 
 const algorithms: Record<
-  string,
+  MsaAlgorithm,
   {
     params: Record<string, string>
     msaResult: string
@@ -38,7 +40,7 @@ async function wait({
   algorithm,
 }: {
   jobId: string
-  algorithm: string
+  algorithm: MsaAlgorithm
   onProgress: (arg: string) => void
 }) {
   // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
@@ -62,14 +64,11 @@ export async function launchMSA({
   sequence,
   onProgress,
 }: {
-  algorithm: string
+  algorithm: MsaAlgorithm
   sequence: string
   onProgress: (arg: string) => void
 }) {
   const config = algorithms[algorithm]
-  if (!config) {
-    throw new Error(`unknown algorithm: ${algorithm}`)
-  }
 
   onProgress(`Launching ${algorithm} MSA...`)
 

package/src/utils/ncbiBlast.ts

@@ -1,6 +1,10 @@
 import { jsonfetch, textfetch, timeout } from './fetch'
 
 import type { BlastResults } from './types'
+import type {
+  BlastDatabase,
+  BlastProgram,
+} from '../LaunchMsaView/components/NCBIBlastQuery/consts'
 
 export async function queryBlastFromRid({
   rid,
@@ -35,8 +39,8 @@ export async function queryBlast({
   onRid,
 }: {
   query: string
-  blastDatabase: string
-  blastProgram: string
+  blastDatabase: BlastDatabase
+  blastProgram: BlastProgram
   baseUrl: string
   onProgress: (arg: string) => void
   onRid: (arg: string) => void
@@ -59,8 +63,8 @@ async function initialQuery({
   baseUrl,
 }: {
   query: string
-  blastProgram: string
-  blastDatabase: string
+  blastProgram: BlastProgram
+  blastDatabase: BlastDatabase
   baseUrl: string
 }) {
   const res = await textfetch(baseUrl, {
@@ -70,7 +74,7 @@ async function initialQuery({
       PROGRAM: blastProgram === 'quick-blastp' ? 'blastp' : blastProgram,
       DATABASE: blastDatabase,
       QUERY: query,
-      ...(blastDatabase === 'nr_clustered_seq'
+      ...(blastDatabase === 'nr_cluster_seq'
         ? {
             CLUSTERED_DB: 'on',
             DB_TYPE: 'Experimental Databases',
@@ -117,25 +121,28 @@ async function waitForRid({
     const res = await textfetch(
       `${baseUrl}?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=${rid}`,
     )
-    const isWaiting = /\s+Status=WAITING/m.test(res)
-    const isFailed = /\s+Status=FAILED/m.test(res)
-    const isReady = /\s+Status=READY/m.test(res)
+    const statusMatch = /\s+Status=(\S+)/m.exec(res)
+    const status = statusMatch?.[1]
     const hasHits = /\s+ThereAreHits=yes/m.test(res)
 
-    if (isWaiting) {
+    if (status === 'WAITING') {
       continue
     }
 
-    if (isFailed) {
+    if (status === 'FAILED') {
       throw new Error(`BLAST ${rid} failed`)
     }
 
-    if (isReady) {
+    if (status === 'READY') {
       if (hasHits) {
         return true
       } else {
         throw new Error('No hits found')
       }
     }
+
+    throw new Error(
+      `BLAST ${rid} returned unexpected status: ${status ?? 'unknown'}`,
+    )
   }
 }

package/src/utils/taxonomyNames.ts

@@ -21,9 +21,16 @@ async function getDB() {
   })
 }
 
-async function getCachedCommonName(taxid: number) {
+async function getCachedTaxonomies(taxids: number[]) {
   const db = await getDB()
-  return db.get(STORE_NAME, taxid) as Promise<CachedTaxonomy | undefined>
+  const tx = db.transaction(STORE_NAME, 'readonly')
+  const results = await Promise.all(
+    taxids.map(
+      taxid => tx.store.get(taxid) as Promise<CachedTaxonomy | undefined>,
+    ),
+  )
+  await tx.done
+  return results
 }
 
 async function saveTaxonomyCache(entries: CachedTaxonomy[]) {
@@ -45,9 +52,11 @@ export async function fetchTaxonomyInfo(
 ): Promise<Map<number, TaxonomyInfo>> {
   const result = new Map<number, TaxonomyInfo>()
   const uncachedTaxids: number[] = []
+  const cachedResults = await getCachedTaxonomies(taxids)
 
-  for (const taxid of taxids) {
-    const cached = await getCachedCommonName(taxid)
+  for (let i = 0; i < taxids.length; i++) {
+    const taxid = taxids[i]!
+    const cached = cachedResults[i]
     if (cached) {
       result.set(taxid, {
         sciname: cached.sciname,
@@ -126,8 +135,6 @@ export async function fetchTaxonomyInfo(
           const sci = sciName?.[1] ?? ''
           result.set(taxid, { sciname: sci, commonName: name })
           toCache.push({ taxid, sciname: sci, commonName: name })
-        } else {
-          toCache.push({ taxid, sciname: '', commonName: undefined })
         }
       }
     } catch (error) {

package/src/version.ts

@@ -1 +1 @@
-export const version = '2.3.8'
+export const version = '2.4.1'

package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.d.ts

@@ -1,8 +0,0 @@
-import React from 'react';
-import type { AbstractTrackModel, Feature } from '@jbrowse/core/util';
-declare const EnsemblGeneTree: ({ model, feature, handleClose, }: {
-    model: AbstractTrackModel;
-    feature: Feature;
-    handleClose: () => void;
-}) => React.JSX.Element;
-export default EnsemblGeneTree;

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

@@ -1,70 +0,0 @@
-import React, { useState } from 'react';
-import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
-import { getContainingView, getSession } from '@jbrowse/core/util';
-import { Button, DialogActions, DialogContent, Link } from '@mui/material';
-import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
-import { ensemblGeneTreeLaunchView } from './ensemblGeneTreeLaunchView';
-import { useGeneTree } from './useGeneTree';
-import { getGeneDisplayName } from '../../util';
-import TranscriptSelector from '../TranscriptSelector';
-import { useTranscriptSelection } from '../useTranscriptSelection';
-const useStyles = makeStyles()({
-    dialogContent: {
-        width: '80em',
-        display: 'flex',
-        flexDirection: 'column',
-        gap: 16,
-    },
-});
-const EnsemblGeneTree = observer(function ({ model, feature, handleClose, }) {
-    const session = getSession(model);
-    const view = getContainingView(model);
-    const { classes } = useStyles();
-    const [launchViewError, setLaunchViewError] = useState();
-    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;
-    const e = treeError ?? launchViewError ?? featureSequenceError;
-    return (React.createElement(React.Fragment, null,
-        React.createElement(DialogContent, { className: classes.dialogContent },
-            e ? React.createElement(ErrorMessage, { error: e }) : null,
-            loadingMessage ? React.createElement(LoadingEllipses, { message: loadingMessage }) : null,
-            treeData ? (React.createElement("div", null,
-                React.createElement("div", null,
-                    "Found Ensembl Compara GeneTree: ",
-                    treeData.geneTreeId),
-                React.createElement(Link, { target: "_blank", href: `https://useast.ensembl.org/Multi/GeneTree/Image?gt=${treeData.geneTreeId}` },
-                    "See ",
-                    treeData.geneTreeId,
-                    " at Ensembl"))) : null,
-            React.createElement(TranscriptSelector, { feature: feature, options: options, selectedId: selectedId, selectedTranscript: selectedTranscript, onTranscriptChange: setSelectedId, proteinSequence: proteinSequence })),
-        React.createElement(DialogActions, null,
-            React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
-                    try {
-                        if (!treeData) {
-                            return;
-                        }
-                        setLaunchViewError(undefined);
-                        ensemblGeneTreeLaunchView({
-                            feature,
-                            view,
-                            session,
-                            newViewTitle: getGeneDisplayName(feature),
-                            data: treeData,
-                        });
-                        handleClose();
-                    }
-                    catch (e) {
-                        console.error(e);
-                        setLaunchViewError(e);
-                    }
-                } }, "Submit"),
-            React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
-                    handleClose();
-                } }, "Cancel"))));
-});
-export default EnsemblGeneTree;
-//# sourceMappingURL=EnsemblGeneTree.js.map

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

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package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.d.ts

@@ -1,13 +0,0 @@
-import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-export declare function ensemblGeneTreeLaunchView({ session, newViewTitle, view, feature, data, }: {
-    session: AbstractSessionModel;
-    newViewTitle: string;
-    view: LinearGenomeViewModel;
-    feature: Feature;
-    data: {
-        tree: string;
-        msa: string;
-        treeMetadata: string;
-    };
-}): void;

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

@@ -1,12 +0,0 @@
-export function ensemblGeneTreeLaunchView({ session, newViewTitle, view, feature, data, }) {
-    session.addView('MsaView', {
-        type: 'MsaView',
-        displayName: newViewTitle,
-        colWidth: 10,
-        rowHeight: 12,
-        data,
-        connectedViewId: view.id,
-        connectedFeature: feature.toJSON(),
-    });
-}
-//# sourceMappingURL=ensemblGeneTreeLaunchView.js.map

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

@@ -1 +0,0 @@
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package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.d.ts

@@ -1,6 +0,0 @@
-export declare function geneTreeFetcher(id2: string): Promise<{
-    geneTreeId: string;
-    tree: string;
-    msa: string;
-    treeMetadata: string;
-}>;

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

@@ -1,25 +0,0 @@
-import { gatherSequencesFromTree } from './gatherSequencesFromTree';
-import { fetchWithLocalStorageCache, jsonfetch, textfetch } from './util';
-const base = 'https://rest.ensembl.org';
-export async function geneTreeFetcher(id2) {
-    const id = id2.replace(/\..*/, '');
-    const { species } = await fetchWithLocalStorageCache(`${id}-ensembl`, () => jsonfetch(`${base}/lookup/id/${id}?content-type=application/json`));
-    const treeBase = `${base}/genetree/member/id/${species}/${id}`;
-    const geneTreeResult = await fetchWithLocalStorageCache(`${id}-msa`, () => jsonfetch(`${treeBase}?content-type=application/json;aligned=1;sequence=pep`));
-    // we query again to get newick format tree. could probably extract from json
-    // as alternative
-    const tree = await fetchWithLocalStorageCache(`${id}-tree`, () => textfetch(`${treeBase}?nh_format=simple;content-type=text/x-nh`));
-    const res = gatherSequencesFromTree(geneTreeResult.tree);
-    return {
-        geneTreeId: geneTreeResult.id,
-        tree,
-        msa: res.map(r => `>${r.id}\n${r.seq}`).join('\n'),
-        treeMetadata: JSON.stringify(Object.fromEntries(res.map(r => [
-            r.id,
-            {
-                genome: r.species,
-            },
-        ]))),
-    };
-}
-//# sourceMappingURL=ensemblGeneTreeUtils.js.map

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

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package/dist/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.d.ts

@@ -1,2 +0,0 @@
-import type { TreeNode, TreeRow } from './types';
-export declare function gatherSequencesFromTree(tree: TreeNode, arr?: TreeRow[]): TreeRow[];

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

@@ -1,20 +0,0 @@
-export function gatherSequencesFromTree(tree, arr = []) {
-    if (tree.children) {
-        for (const child of tree.children) {
-            if (child.sequence) {
-                const id = child.sequence.id[0]?.accession;
-                if (id) {
-                    arr.push({
-                        id,
-                        seq: child.sequence.mol_seq.seq,
-                        species: child.taxonomy.common_name || child.taxonomy.scientific_name,
-                        genomicLocString: child.sequence.mol_seq.location,
-                    });
-                }
-            }
-            gatherSequencesFromTree(child, arr);
-        }
-    }
-    return arr;
-}
-//# sourceMappingURL=gatherSequencesFromTree.js.map

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

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package/dist/LaunchMsaView/components/EnsemblGeneTree/types.d.ts

@@ -1,24 +0,0 @@
-export interface TreeNodeSequence {
-    mol_seq: {
-        seq: string;
-        location?: string;
-    };
-    id: {
-        accession: string;
-    }[];
-}
-export interface TreeNodeTaxonomy {
-    common_name: string;
-    scientific_name: string;
-}
-export interface TreeNode {
-    children?: TreeNode[];
-    sequence?: TreeNodeSequence;
-    taxonomy: TreeNodeTaxonomy;
-}
-export interface TreeRow {
-    id: string;
-    seq: string;
-    species: string;
-    genomicLocString?: string;
-}

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

@@ -1,2 +0,0 @@
-export {};
-//# sourceMappingURL=types.js.map

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

@@ -1 +0,0 @@
-{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/EnsemblGeneTree/types.ts"],"names":[],"mappings":""}

package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.d.ts

@@ -1,10 +0,0 @@
-export declare function useGeneTree(geneId: string): {
-    treeData: {
-        geneTreeId: string;
-        tree: string;
-        msa: string;
-        treeMetadata: string;
-    } | undefined;
-    isTreeLoading: boolean;
-    treeError: any;
-};

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

@@ -1,11 +0,0 @@
-import useSWR from 'swr';
-import { geneTreeFetcher } from './ensemblGeneTreeUtils';
-export function useGeneTree(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

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package/dist/LaunchMsaView/components/EnsemblGeneTree/util.d.ts

@@ -1 +0,0 @@
-export { fetchWithLocalStorageCache, jsonfetch, textfetch, unzipfetch, } from '../../../utils/fetch';

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

@@ -1,2 +0,0 @@
-export { fetchWithLocalStorageCache, jsonfetch, textfetch, unzipfetch, } from '../../../utils/fetch';
-//# sourceMappingURL=util.js.map

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

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