npm - jbrowse-plugin-msaview - Versions diffs - 2.3.8 → 2.4.0 - Mend

jbrowse-plugin-msaview 2.3.8 → 2.4.0

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 (120) hide show

package/dist/LaunchMsaView/components/useSWRFeatureSequence.js CHANGED Viewed

@@ -1,46 +1,27 @@
 import { getSession } from '@jbrowse/core/util';
 import useSWR from 'swr';
 import { fetchSeq } from './fetchSeq';
-async function featureSequenceFetcher({ feature, assemblyName, upDownBp, view, }) {
+async function featureSequenceFetcher({ feature, assemblyName, view, }) {
     const session = getSession(view);
     const { start, end, refName } = feature.toJSON();
-    const b = start - upDownBp;
-    const e = end + upDownBp;
-    const [seq, upstream, downstream] = await Promise.all([
-        fetchSeq({
-            start,
-            end,
-            refName,
-            assemblyName,
-            session,
-        }),
-        fetchSeq({
-            start: Math.max(0, b),
-            end: start,
-            refName,
-            assemblyName,
-            session,
-        }),
-        fetchSeq({
-            start: end,
-            end: e,
-            refName,
-            assemblyName,
-            session,
-        }),
-    ]);
-    return { seq, upstream, downstream };
+    const seq = await fetchSeq({
+        start,
+        end,
+        refName,
+        assemblyName,
+        session,
+    });
+    return { seq };
 }
-export function useSWRFeatureSequence({ view, feature, upDownBp = 0, forceLoad = true, }) {
+export function useSWRFeatureSequence({ view, feature, }) {
     const assemblyName = view?.assemblyNames?.[0];
     const { data, error } = useSWR(
     // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     feature && assemblyName && view
-        ? [feature.id(), assemblyName, upDownBp, forceLoad, 'feature-sequence']
+        ? [feature.id(), assemblyName, 'feature-sequence']
         : null, () => featureSequenceFetcher({
         feature: feature,
         assemblyName: assemblyName,
-        upDownBp,
         view: view,
     }), {
         revalidateOnFocus: false,

package/dist/LaunchMsaView/components/useSWRFeatureSequence.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"useSWRFeatureSequence.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/useSWRFeatureSequence.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,MAAM,MAAM,KAAK,CAAA;AAExB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,KAAK,UAAU,sBAAsB,CAAC,EACpC,OAAO,EACP,YAAY,EACZ,IAAI,GAKL;IACC,MAAM,OAAO,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;IAChC,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,OAAO,CAAC,MAAM,EAI7C,CAAA;IACD,MAAM,GAAG,GAAG,MAAM,QAAQ,CAAC;QACzB,KAAK;QACL,GAAG;QACH,OAAO;QACP,YAAY;QACZ,OAAO;KACR,CAAC,CAAA;IACF,OAAO,EAAE,GAAG,EAAE,CAAA;AAChB,CAAC;AAED,MAAM,UAAU,qBAAqB,CAAC,EACpC,IAAI,EACJ,OAAO,GAIR;IACC,MAAM,YAAY,GAAG,IAAI,EAAE,aAAa,EAAE,CAAC,CAAC,CAAC,CAAA;IAC7C,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,MAAM;IAC5B,uEAAuE;IACvE,OAAO,IAAI,YAAY,IAAI,IAAI;QAC7B,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,EAAE,EAAE,YAAY,EAAE,kBAAkB,CAAC;QAClD,CAAC,CAAC,IAAI,EACR,GAAG,EAAE,CACH,sBAAsB,CAAC;QACrB,OAAO,EAAE,OAAQ;QACjB,YAAY,EAAE,YAAa;QAC3B,IAAI,EAAE,IAAK;KACZ,CAAC,EACJ;QACE,iBAAiB,EAAE,KAAK;QACxB,qBAAqB,EAAE,KAAK;QAC5B,iBAAiB,EAAE,KAAK;KACzB,CACF,CAAA;IAED,OAAO;QACL,QAAQ,EAAE,IAAI;QACd,KAAK;KACN,CAAA;AACH,CAAC"}

package/dist/MsaViewPanel/afterCreateAutoruns.js CHANGED Viewed

@@ -2,7 +2,7 @@ import { getSession } from '@jbrowse/core/util';
 import { doLaunchBlast } from './doLaunchBlast';
 import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord';
 import { cleanupOldData, generateDataStoreId, retrieveMsaData, storeMsaData, } from './msaDataStore';
-import { gappedToUngappedPosition, isProteinView } from './structureConnection';
+import { gappedToUngappedPosition, getProteinViews, } from './structureConnection';
 import { getUniprotIdFromAlphaFoldUrl } from './util';
 export function loadStoredData(self) {
     const { dataStoreId, rows } = self;
@@ -34,8 +34,7 @@ export function loadStoredData(self) {
 export function storeDataToIndexedDB(self) {
     const { rows, dataStoreId } = self;
     if (rows.length > 0 && !dataStoreId) {
-        const hasFilehandle = !!(self.msaFilehandle ?? self.treeFilehandle);
-        if (hasFilehandle) {
+        if (self.msaFilehandle || self.treeFilehandle) {
             return;
         }
         const msaData = self.data.msa;
@@ -177,15 +176,11 @@ export function highlightConnectedStructures(self) {
     }
 }
 export function autoConnectStructures(self) {
-    const views = getSession(self).views;
     const { connectedViewId, uniprotId, rows, connectedStructures } = self;
     if (!uniprotId || rows.length === 0) {
         return;
     }
-    for (const view of views) {
-        if (!isProteinView(view)) {
-            continue;
-        }
+    for (const view of getProteinViews(getSession(self).views)) {
         for (let structureIdx = 0; structureIdx < view.structures.length; structureIdx++) {
             const structure = view.structures[structureIdx];
             if (!structure) {
@@ -214,16 +209,12 @@ export function autoConnectStructures(self) {
     }
 }
 export function observeProteinHighlights(self) {
-    const views = getSession(self).views;
     const { connectedViewId, transcriptToMsaMap, querySeqName } = self;
     if (!connectedViewId || !transcriptToMsaMap) {
         return;
     }
     const columns = new Set();
-    for (const view of views) {
-        if (!isProteinView(view)) {
-            continue;
-        }
+    for (const view of getProteinViews(getSession(self).views)) {
         for (const structure of view.structures) {
             if (structure.connectedViewId !== connectedViewId) {
                 continue;

package/dist/MsaViewPanel/afterCreateAutoruns.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/MsaViewPanel/components/ConnectStructureDialog.js CHANGED Viewed

@@ -4,7 +4,7 @@ import { getSession } from '@jbrowse/core/util';
 import { Button, DialogActions, DialogContent, FormControl, InputLabel, MenuItem, Select, Typography, } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
-import { isProteinView } from '../structureConnection';
+import { getProteinViews } from '../structureConnection';
 const useStyles = makeStyles()(theme => ({
     formControl: {
         marginBottom: theme.spacing(2),
@@ -17,7 +17,7 @@ const ConnectStructureDialog = observer(function ConnectStructureDialog({ model,
     const [selectedStructureIdx, setSelectedStructureIdx] = useState(0);
     const [selectedMsaRow, setSelectedMsaRow] = useState(model.querySeqName);
     const [error, setError] = useState();
-    const proteinViews = session.views.filter(isProteinView);
+    const proteinViews = getProteinViews(session.views);
     const selectedView = proteinViews.find(v => v.id === selectedViewId);
     const structures = selectedView?.structures ?? [];
     const msaRowNames = model.rows.map(r => r[0]);

package/dist/MsaViewPanel/components/ConnectStructureDialog.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/MsaViewPanel/components/LoadingBLAST.js CHANGED Viewed

@@ -24,12 +24,11 @@ function RIDProgress({ baseUrl, rid, progress, }) {
         React.createElement(Typography, null, progress)));
 }
 const LoadingBLAST = observer(function LoadingBLAST2({ model, baseUrl, }) {
-    const { progress, rid, error, processing } = model;
+    const { progress, rid, error } = model;
     const { classes } = useStyles();
     return (React.createElement("div", { className: classes.margin },
         React.createElement(LoadingEllipses, { message: "Running NCBI BLAST", variant: "h5" }),
-        error ? (React.createElement(RIDError, { baseUrl: baseUrl, rid: rid, error: error })) : rid ? (React.createElement(RIDProgress, { baseUrl: baseUrl, rid: rid, progress: progress })) : null,
-        React.createElement(Typography, null, processing || 'Initializing BLAST query')));
+        error ? (React.createElement(RIDError, { baseUrl: baseUrl, rid: rid, error: error })) : rid ? (React.createElement(RIDProgress, { baseUrl: baseUrl, rid: rid, progress: progress })) : (React.createElement(Typography, null, progress || 'Initializing BLAST query'))));
 });
 export default LoadingBLAST;
 //# sourceMappingURL=LoadingBLAST.js.map

package/dist/MsaViewPanel/components/LoadingBLAST.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/MsaViewPanel/model.d.ts CHANGED Viewed

@@ -1,5 +1,6 @@
 import type { ProteinView, StructureConnection } from './structureConnection';
 import type { MafRegion, MsaViewInitState } from './types';
+import type { BlastDatabase, BlastProgram, MsaAlgorithm } from '../LaunchMsaView/components/NCBIBlastQuery/consts';
 import type { Feature } from '@jbrowse/core/util';
 import type { Instance } from '@jbrowse/mobx-state-tree';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
@@ -12,9 +13,9 @@ export interface IRegion {
 }
 export interface BlastParams {
     baseUrl: string;
-    blastDatabase: string;
-    msaAlgorithm: string;
-    blastProgram: string;
+    blastDatabase: BlastDatabase;
+    msaAlgorithm: MsaAlgorithm;
+    blastProgram: BlastProgram;
     selectedTranscript?: Feature;
     proteinSequence: string;
     rid?: string;
@@ -632,10 +633,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         refName: string;
         strand: number;
     } | undefined;
-    /**
-     * #getter
-     */
-    readonly processing: boolean;
     /**
      * #getter
      */
@@ -656,10 +653,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * #getter
      */
     readonly mouseCol2: number | undefined;
-    /**
-     * #getter
-     */
-    readonly clickCol2: undefined;
 } & {
     /**
      * #action

package/dist/MsaViewPanel/model.js CHANGED Viewed

@@ -9,7 +9,7 @@ import { autoConnectStructures, highlightConnectedStructures, launchBlastIfNeede
 import { genomeToMSA } from './genomeToMSA';
 import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord';
 import { buildAlignmentMaps, runPairwiseAlignment } from './pairwiseAlignment';
-import { isProteinView, mapToRecord, ungappedToGappedPosition, } from './structureConnection';
+import { getProteinViews, ungappedToGappedPosition, } from './structureConnection';
 const ConnectStructureDialog = lazy(() => import('./components/ConnectStructureDialog'));
 /**
  * #stateModel MsaViewPlugin
@@ -109,12 +109,6 @@ export default function stateModelFactory() {
                 ? genomeToTranscriptSeqMapping(self.connectedFeature)
                 : undefined;
         },
-        /**
-         * #getter
-         */
-        get processing() {
-            return !!self.progress;
-        },
         /**
          * #getter
          */
@@ -126,11 +120,10 @@ export default function stateModelFactory() {
          * #getter
          */
         get connectedProteinViews() {
-            const { views } = getSession(self);
-            const unknownViews = views;
+            const proteinViews = getProteinViews(getSession(self).views);
             const result = [];
             for (const conn of self.connectedStructures) {
-                const proteinView = unknownViews.find((v) => isProteinView(v) && v.id === conn.proteinViewId);
+                const proteinView = proteinViews.find(v => v.id === conn.proteinViewId);
                 if (proteinView) {
                     result.push({ ...conn, proteinView });
                 }
@@ -173,12 +166,6 @@ export default function stateModelFactory() {
             }
             return genomeToMSA({ model: self });
         },
-        /**
-         * #getter
-         */
-        get clickCol2() {
-            return undefined;
-        },
     }))
         .actions(self => ({
         /**
@@ -295,8 +282,7 @@ export default function stateModelFactory() {
                 throw new Error(`MSA row "${rowName}" not found`);
             }
             const ungappedMsaSequence = msaSequence.replaceAll('-', '');
-            const { views } = getSession(self);
-            const proteinView = views.find((v) => isProteinView(v) && v.id === proteinViewId);
+            const proteinView = getProteinViews(getSession(self).views).find(v => v.id === proteinViewId);
             if (!proteinView) {
                 throw new Error(`ProteinView "${proteinViewId}" not found`);
             }
@@ -314,8 +300,8 @@ export default function stateModelFactory() {
                 proteinViewId,
                 structureIdx,
                 msaRowName: rowName,
-                msaToStructure: mapToRecord(seq1ToSeq2),
-                structureToMsa: mapToRecord(seq2ToSeq1),
+                msaToStructure: Object.fromEntries(seq1ToSeq2),
+                structureToMsa: Object.fromEntries(seq2ToSeq1),
             };
             self.connectedStructures.push(connection);
         },

package/dist/MsaViewPanel/model.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/MsaViewPanel/msaDataStore.d.ts CHANGED Viewed

@@ -9,5 +9,4 @@ export declare function retrieveMsaData(id: string): Promise<{
     tree: string | undefined;
     treeMetadata: string | undefined;
 } | undefined>;
-export declare function deleteMsaData(id: string): Promise<void>;
 export declare function cleanupOldData(maxAgeMs?: number): Promise<number>;

package/dist/MsaViewPanel/msaDataStore.js CHANGED Viewed

@@ -51,15 +51,6 @@ export async function retrieveMsaData(id) {
         return undefined;
     }
 }
-export async function deleteMsaData(id) {
-    try {
-        const db = await getDB();
-        await db.delete(STORE_NAME, id);
-    }
-    catch (e) {
-        console.warn('Failed to delete MSA data:', e);
-    }
-}
 export async function cleanupOldData(maxAgeMs = 7 * 24 * 60 * 60 * 1000) {
     try {
         const db = await getDB();

package/dist/MsaViewPanel/msaDataStore.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/MsaViewPanel/structureConnection.d.ts CHANGED Viewed

@@ -20,6 +20,12 @@ export interface ProteinView {
     structures: ProteinViewStructure[];
 }
 export declare function isProteinView(view: unknown): view is ProteinView;
+/**
+ * Extract all ProteinView instances from a session's views array.
+ */
+export declare function getProteinViews(views: {
+    type: string;
+}[]): ProteinView[];
 /**
  * Represents a connection between the MSA view and a protein structure
  */
@@ -43,7 +49,3 @@ export declare function gappedToUngappedPosition(sequence: string, gappedPositio
  * Helper to convert ungapped position to gapped MSA column for a specific row
  */
 export declare function ungappedToGappedPosition(sequence: string, ungappedPosition: number): number | undefined;
-/**
- * Convert Map to plain object for MST frozen storage
- */
-export declare function mapToRecord(map: Map<number, number>): Record<number, number>;

package/dist/MsaViewPanel/structureConnection.js CHANGED Viewed

@@ -2,6 +2,12 @@ export function isProteinView(view) {
     const v = view;
     return v.type === 'ProteinView' && Array.isArray(v.structures);
 }
+/**
+ * Extract all ProteinView instances from a session's views array.
+ */
+export function getProteinViews(views) {
+    return views.filter(isProteinView);
+}
 /**
  * Helper to convert gapped MSA column to ungapped position for a specific row
  */
@@ -37,10 +43,4 @@ export function ungappedToGappedPosition(sequence, ungappedPosition) {
     }
     return undefined;
 }
-/**
- * Convert Map to plain object for MST frozen storage
- */
-export function mapToRecord(map) {
-    return Object.fromEntries(map);
-}
 //# sourceMappingURL=structureConnection.js.map

package/dist/MsaViewPanel/structureConnection.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/MsaViewPanel/structureConnection.test.js CHANGED Viewed

@@ -1,5 +1,5 @@
 import { describe, expect, test } from 'vitest';
-import { gappedToUngappedPosition, mapToRecord, ungappedToGappedPosition, } from './structureConnection';
+import { gappedToUngappedPosition, ungappedToGappedPosition, } from './structureConnection';
 describe('gappedToUngappedPosition', () => {
     test('returns correct ungapped position for non-gap character', () => {
         const seq = 'M-KA-A';
@@ -101,22 +101,4 @@ describe('gappedToUngappedPosition and ungappedToGappedPosition are inverses', (
         }
     });
 });
-describe('mapToRecord', () => {
-    test('converts Map to Record', () => {
-        const map = new Map([
-            [0, 5],
-            [1, 10],
-            [2, 15],
-        ]);
-        const record = mapToRecord(map);
-        expect(record[0]).toBe(5);
-        expect(record[1]).toBe(10);
-        expect(record[2]).toBe(15);
-    });
-    test('handles empty Map', () => {
-        const map = new Map();
-        const record = mapToRecord(map);
-        expect(Object.keys(record)).toHaveLength(0);
-    });
-});
 //# sourceMappingURL=structureConnection.test.js.map

package/dist/MsaViewPanel/structureConnection.test.js.map CHANGED Viewed

	@@ -1 +1 @@
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