npm - jbrowse-plugin-msaview - Versions diffs - 2.3.5 → 2.4.0 - Mend

jbrowse-plugin-msaview 2.3.5 → 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 (148) hide show

package/dist/LaunchMsaView/components/useSWRFeatureSequence.d.ts CHANGED Viewed

@@ -1,13 +1,12 @@
-import type { SeqState } from './types';
 import type { Feature } from '@jbrowse/core/util';
-export declare function useSWRFeatureSequence({ view, feature, upDownBp, forceLoad, }: {
+export declare function useSWRFeatureSequence({ view, feature, }: {
     view: {
         assemblyNames?: string[];
     } | undefined;
     feature?: Feature;
-    upDownBp?: number;
-    forceLoad?: boolean;
 }): {
-    sequence: SeqState | undefined;
+    sequence: {
+        seq: string;
+    } | undefined;
     error: any;
 };

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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package/dist/MsaViewPanel/afterCreateAutoruns.js CHANGED Viewed

@@ -2,12 +2,8 @@ import { getSession } from '@jbrowse/core/util';
 import { doLaunchBlast } from './doLaunchBlast';
 import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord';
 import { cleanupOldData, generateDataStoreId, retrieveMsaData, storeMsaData, } from './msaDataStore';
-import { gappedToUngappedPosition } from './structureConnection';
+import { gappedToUngappedPosition, getProteinViews, } from './structureConnection';
 import { getUniprotIdFromAlphaFoldUrl } from './util';
-function isProteinView(view) {
-    const v = view;
-    return v.type === 'ProteinView' && Array.isArray(v.structures);
-}
 export function loadStoredData(self) {
     const { dataStoreId, rows } = self;
     if (dataStoreId && rows.length === 0) {
@@ -38,8 +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;
@@ -154,7 +149,7 @@ export function highlightConnectedStructures(self) {
         return;
     }
     for (const conn of connectedProteinViews) {
-        const structure = conn.proteinView?.structures?.[conn.structureIdx];
+        const structure = conn.proteinView.structures[conn.structureIdx];
         if (!structure) {
             continue;
         }
@@ -181,18 +176,13 @@ export function highlightConnectedStructures(self) {
     }
 }
 export function autoConnectStructures(self) {
-    const { views } = getSession(self);
     const { connectedViewId, uniprotId, rows, connectedStructures } = self;
     if (!uniprotId || rows.length === 0) {
         return;
     }
-    for (const view of views) {
-        if (!isProteinView(view)) {
-            continue;
-        }
-        const v = view;
-        for (let structureIdx = 0; structureIdx < v.structures.length; structureIdx++) {
-            const structure = v.structures[structureIdx];
+    for (const view of getProteinViews(getSession(self).views)) {
+        for (let structureIdx = 0; structureIdx < view.structures.length; structureIdx++) {
+            const structure = view.structures[structureIdx];
             if (!structure) {
                 continue;
             }
@@ -202,7 +192,7 @@ export function autoConnectStructures(self) {
             if (structure.uniprotId !== uniprotId) {
                 continue;
             }
-            const alreadyConnected = connectedStructures.some(c => c.proteinViewId === v.id && c.structureIdx === structureIdx);
+            const alreadyConnected = connectedStructures.some(c => c.proteinViewId === view.id && c.structureIdx === structureIdx);
             if (alreadyConnected) {
                 continue;
             }
@@ -210,7 +200,7 @@ export function autoConnectStructures(self) {
                 continue;
             }
             try {
-                self.connectToStructure(v.id, structureIdx);
+                self.connectToStructure(view.id, structureIdx);
             }
             catch (e) {
                 console.error('Failed to auto-connect to ProteinView:', e);
@@ -219,18 +209,13 @@ export function autoConnectStructures(self) {
     }
 }
 export function observeProteinHighlights(self) {
-    const { views } = getSession(self);
     const { connectedViewId, transcriptToMsaMap, querySeqName } = self;
     if (!connectedViewId || !transcriptToMsaMap) {
         return;
     }
     const columns = new Set();
-    for (const view of views) {
-        if (!isProteinView(view)) {
-            continue;
-        }
-        const v = view;
-        for (const structure of v.structures) {
+    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 @@
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package/dist/MsaViewPanel/components/ConnectStructureDialog.js CHANGED Viewed

@@ -1,20 +1,25 @@
 import React, { useState } from 'react';
-import { Dialog } from '@jbrowse/core/ui';
+import { Dialog, ErrorMessage } from '@jbrowse/core/ui';
 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 { getProteinViews } from '../structureConnection';
+const useStyles = makeStyles()(theme => ({
+    formControl: {
+        marginBottom: theme.spacing(2),
+    },
+}));
 const ConnectStructureDialog = observer(function ConnectStructureDialog({ model, handleClose, }) {
+    const { classes } = useStyles();
     const session = getSession(model);
     const [selectedViewId, setSelectedViewId] = useState('');
     const [selectedStructureIdx, setSelectedStructureIdx] = useState(0);
     const [selectedMsaRow, setSelectedMsaRow] = useState(model.querySeqName);
     const [error, setError] = useState();
-    // Find all ProteinViews in the session
-    const proteinViews = session.views.filter((v) => v.type === 'ProteinView');
-    // Get structures for the selected view
+    const proteinViews = getProteinViews(session.views);
     const selectedView = proteinViews.find(v => v.id === selectedViewId);
     const structures = selectedView?.structures ?? [];
-    // Get MSA row names
     const msaRowNames = model.rows.map(r => r[0]);
     const handleConnect = () => {
         if (!selectedViewId) {
@@ -31,23 +36,23 @@ const ConnectStructureDialog = observer(function ConnectStructureDialog({ model,
     };
     return (React.createElement(Dialog, { maxWidth: "sm", title: "Connect to Protein Structure", open: true, onClose: handleClose },
         React.createElement(DialogContent, null, proteinViews.length === 0 ? (React.createElement(Typography, { color: "textSecondary" }, "No protein views are currently open. Please open a protein structure view first.")) : (React.createElement(React.Fragment, null,
-            React.createElement(FormControl, { fullWidth: true, sx: { mb: 2 } },
+            React.createElement(FormControl, { fullWidth: true, className: classes.formControl },
                 React.createElement(InputLabel, null, "Protein View"),
                 React.createElement(Select, { value: selectedViewId, label: "Protein View", onChange: e => {
                         setSelectedViewId(e.target.value);
                         setSelectedStructureIdx(0);
                     } }, proteinViews.map(view => (React.createElement(MenuItem, { key: view.id, value: view.id }, view.displayName ?? `ProteinView ${view.id}`))))),
-            structures.length > 1 && (React.createElement(FormControl, { fullWidth: true, sx: { mb: 2 } },
+            structures.length > 1 ? (React.createElement(FormControl, { fullWidth: true, className: classes.formControl },
                 React.createElement(InputLabel, null, "Structure"),
                 React.createElement(Select, { value: selectedStructureIdx, label: "Structure", onChange: e => {
                         setSelectedStructureIdx(e.target.value);
-                    } }, structures.map((structure, idx) => (React.createElement(MenuItem, { key: idx, value: idx }, structure.url ?? `Structure ${idx + 1}`)))))),
-            React.createElement(FormControl, { fullWidth: true, sx: { mb: 2 } },
+                    } }, structures.map((structure, idx) => (React.createElement(MenuItem, { key: idx, value: idx }, structure.url ?? `Structure ${idx + 1}`)))))) : null,
+            React.createElement(FormControl, { fullWidth: true, className: classes.formControl },
                 React.createElement(InputLabel, null, "MSA Row"),
                 React.createElement(Select, { value: selectedMsaRow, label: "MSA Row", onChange: e => {
                         setSelectedMsaRow(e.target.value);
                     } }, msaRowNames.map(name => (React.createElement(MenuItem, { key: name, value: name }, name))))),
-            error && (React.createElement(Typography, { color: "error", sx: { mt: 1 } }, error))))),
+            error ? React.createElement(ErrorMessage, { error: error }) : null))),
         React.createElement(DialogActions, null,
             React.createElement(Button, { onClick: handleClose }, "Cancel"),
             React.createElement(Button, { onClick: handleConnect, variant: "contained", disabled: proteinViews.length === 0 || !selectedViewId }, "Connect"))));

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"ConnectStructureDialog.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/ConnectStructureDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AACvD,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,WAAW,EACX,UAAU,EACV,QAAQ,EACR,MAAM,EACN,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,EAAE,eAAe,EAAE,MAAM,wBAAwB,CAAA;AAIxD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,WAAW,EAAE;QACX,YAAY,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KAC/B;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,sBAAsB,GAAG,QAAQ,CAAC,SAAS,sBAAsB,CAAC,EACtE,KAAK,EACL,WAAW,GAIZ;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,CAAC,cAAc,EAAE,iBAAiB,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IACxD,MAAM,CAAC,oBAAoB,EAAE,uBAAuB,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;IACnE,MAAM,CAAC,cAAc,EAAE,iBAAiB,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,YAAY,CAAC,CAAA;IACxE,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAU,CAAA;IAE5C,MAAM,YAAY,GAAG,eAAe,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;IAEnD,MAAM,YAAY,GAAG,YAAY,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,KAAK,cAAc,CAAC,CAAA;IACpE,MAAM,UAAU,GAAG,YAAY,EAAE,UAAU,IAAI,EAAE,CAAA;IAEjD,MAAM,WAAW,GAAG,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAE7C,MAAM,aAAa,GAAG,GAAG,EAAE;QACzB,IAAI,CAAC,cAAc,EAAE,CAAC;YACpB,QAAQ,CAAC,8BAA8B,CAAC,CAAA;YACxC,OAAM;QACR,CAAC;QAED,IAAI,CAAC;YACH,KAAK,CAAC,kBAAkB,CACtB,cAAc,EACd,oBAAoB,EACpB,cAAc,CACf,CAAA;YACD,WAAW,EAAE,CAAA;QACf,CAAC;QAAC,OAAO,CAAC,EAAE,CAAC;YACX,QAAQ,CAAC,CAAC,YAAY,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;QACtD,CAAC;IACH,CAAC,CAAA;IAED,OAAO,CACL,oBAAC,MAAM,IACL,QAAQ,EAAC,IAAI,EACb,KAAK,EAAC,8BAA8B,EACpC,IAAI,QACJ,OAAO,EAAE,WAAW;QAEpB,oBAAC,aAAa,QACX,YAAY,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAC3B,oBAAC,UAAU,IAAC,KAAK,EAAC,eAAe,uFAGpB,CACd,CAAC,CAAC,CAAC,CACF;YACE,oBAAC,WAAW,IAAC,SAAS,QAAC,SAAS,EAAE,OAAO,CAAC,WAAW;gBACnD,oBAAC,UAAU,uBAA0B;gBACrC,oBAAC,MAAM,IACL,KAAK,EAAE,cAAc,EACrB,KAAK,EAAC,cAAc,EACpB,QAAQ,EAAE,CAAC,CAAC,EAAE;wBACZ,iBAAiB,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;wBACjC,uBAAuB,CAAC,CAAC,CAAC,CAAA;oBAC5B,CAAC,IAEA,YAAY,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CACxB,oBAAC,QAAQ,IAAC,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE,KAAK,EAAE,IAAI,CAAC,EAAE,IACnC,IAAI,CAAC,WAAW,IAAI,eAAe,IAAI,CAAC,EAAE,EAAE,CACpC,CACZ,CAAC,CACK,CACG;YAEb,UAAU,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CACvB,oBAAC,WAAW,IAAC,SAAS,QAAC,SAAS,EAAE,OAAO,CAAC,WAAW;gBACnD,oBAAC,UAAU,oBAAuB;gBAClC,oBAAC,MAAM,IACL,KAAK,EAAE,oBAAoB,EAC3B,KAAK,EAAC,WAAW,EACjB,QAAQ,EAAE,CAAC,CAAC,EAAE;wBACZ,uBAAuB,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBACzC,CAAC,IAEA,UAAU,CAAC,GAAG,CAAC,CAAC,SAAS,EAAE,GAAG,EAAE,EAAE,CAAC,CAClC,oBAAC,QAAQ,IAAC,GAAG,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,IAC3B,SAAS,CAAC,GAAG,IAAI,aAAa,GAAG,GAAG,CAAC,EAAE,CAC/B,CACZ,CAAC,CACK,CACG,CACf,CAAC,CAAC,CAAC,IAAI;YAER,oBAAC,WAAW,IAAC,SAAS,QAAC,SAAS,EAAE,OAAO,CAAC,WAAW;gBACnD,oBAAC,UAAU,kBAAqB;gBAChC,oBAAC,MAAM,IACL,KAAK,EAAE,cAAc,EACrB,KAAK,EAAC,SAAS,EACf,QAAQ,EAAE,CAAC,CAAC,EAAE;wBACZ,iBAAiB,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBACnC,CAAC,IAEA,WAAW,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CACvB,oBAAC,QAAQ,IAAC,GAAG,EAAE,IAAI,EAAE,KAAK,EAAE,IAAI,IAC7B,IAAI,CACI,CACZ,CAAC,CACK,CACG;YAEb,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI,CAC7C,CACJ,CACa;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IAAC,OAAO,EAAE,WAAW,aAAiB;YAC7C,oBAAC,MAAM,IACL,OAAO,EAAE,aAAa,EACtB,OAAO,EAAC,WAAW,EACnB,QAAQ,EAAE,YAAY,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,cAAc,cAG/C,CACK,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,sBAAsB,CAAA"}

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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1	+ {"version":3,"file":"LoadingBLAST.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/LoadingBLAST.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,YAAY,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAChE,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,OAAO,MAAM,WAAW,CAAA;AAI/B,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,MAAM,EAAE;QACN,OAAO,EAAE,EAAE;KACZ;IACD,OAAO,EAAE;QACP,UAAU,EAAE,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,KAAK;KAC3C;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,QAAQ,CAAC,EAChB,OAAO,EACP,GAAG,EACH,KAAK,GAKN;IACC,OAAO,CACL;QACG,GAAG,CAAC,CAAC,CAAC,oBAAC,OAAO,IAAC,GAAG,EAAE,GAAG,EAAE,OAAO,EAAE,OAAO,GAAI,CAAC,CAAC,CAAC,IAAI;QACrD,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAC1B,CACP,CAAA;AACH,CAAC;AAED,SAAS,WAAW,CAAC,EACnB,OAAO,EACP,GAAG,EACH,QAAQ,GAKT;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,6BAAK,SAAS,EAAE,OAAO,CAAC,OAAO;QAC5B,GAAG,CAAC,CAAC,CAAC,oBAAC,OAAO,IAAC,OAAO,EAAE,OAAO,EAAE,GAAG,EAAE,GAAG,GAAI,CAAC,CAAC,CAAC,IAAI;QACrD,oBAAC,UAAU,QAAE,QAAQ,CAAc,CAC/B,CACP,CAAA;AACH,CAAC;AAED,MAAM,YAAY,GAAG,QAAQ,CAAC,SAAS,aAAa,CAAC,EACnD,KAAK,EACL,OAAO,GAIR;IACC,MAAM,EAAE,QAAQ,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACtC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,6BAAK,SAAS,EAAE,OAAO,CAAC,MAAM;QAC5B,oBAAC,eAAe,IAAC,OAAO,EAAC,oBAAoB,EAAC,OAAO,EAAC,IAAI,GAAG;QAC5D,KAAK,CAAC,CAAC,CAAC,CACP,oBAAC,QAAQ,IAAC,OAAO,EAAE,OAAO,EAAE,GAAG,EAAE,GAAG,EAAE,KAAK,EAAE,KAAK,GAAI,CACvD,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CACR,oBAAC,WAAW,IAAC,OAAO,EAAE,OAAO,EAAE,GAAG,EAAE,GAAG,EAAE,QAAQ,EAAE,QAAQ,GAAI,CAChE,CAAC,CAAC,CAAC,CACF,oBAAC,UAAU,QAAE,QAAQ,IAAI,0BAA0B,CAAc,CAClE,CACG,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,YAAY,CAAA"}

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

@@ -2,12 +2,19 @@ import React from 'react';
 import { LoadingEllipses } from '@jbrowse/core/ui';
 import { observer } from 'mobx-react';
 import { MSAView } from 'react-msaview';
+import { makeStyles } from 'tss-react/mui';
 import { ErrorBoundary } from './ErrorBoundary';
 import LoadingBLAST from './LoadingBLAST';
+const useStyles = makeStyles()({
+    loadingContainer: {
+        padding: 20,
+    },
+});
 const MsaViewPanel = observer(function MsaViewPanel2({ model, }) {
+    const { classes } = useStyles();
     const { blastParams, loadingStoredData } = model;
     return (React.createElement(ErrorBoundary, null,
-        React.createElement("div", null, blastParams ? (React.createElement(LoadingBLAST, { model: model, baseUrl: blastParams.baseUrl })) : loadingStoredData ? (React.createElement("div", { style: { padding: 20 } },
+        React.createElement("div", null, blastParams ? (React.createElement(LoadingBLAST, { model: model, baseUrl: blastParams.baseUrl })) : loadingStoredData ? (React.createElement("div", { className: classes.loadingContainer },
             React.createElement(LoadingEllipses, { message: "Loading MSA data", variant: "h6" }))) : (React.createElement(MSAView, { model: model })))));
 });
 export default MsaViewPanel;

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

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

@@ -1,5 +1,6 @@
-import type { StructureConnection } from './structureConnection';
+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
      */
@@ -644,7 +641,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * #getter
      */
     readonly connectedProteinViews: (StructureConnection & {
-        proteinView: any;
+        proteinView: ProteinView;
     })[];
 } & {
     /**
@@ -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 { 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
          */
@@ -126,13 +120,15 @@ export default function stateModelFactory() {
          * #getter
          */
         get connectedProteinViews() {
-            const { views } = getSession(self);
-            return self.connectedStructures
-                .map(conn => {
-                const proteinView = views.find((v) => v.id === conn.proteinViewId);
-                return proteinView ? { ...conn, proteinView } : undefined;
-            })
-                .filter((c) => c !== undefined);
+            const proteinViews = getProteinViews(getSession(self).views);
+            const result = [];
+            for (const conn of self.connectedStructures) {
+                const proteinView = proteinViews.find(v => v.id === conn.proteinViewId);
+                if (proteinView) {
+                    result.push({ ...conn, proteinView });
+                }
+            }
+            return result;
         },
     }))
         .views(self => ({
@@ -141,7 +137,7 @@ export default function stateModelFactory() {
          */
         get structureHoverCol() {
             for (const conn of self.connectedProteinViews) {
-                const structure = conn.proteinView?.structures?.[conn.structureIdx];
+                const structure = conn.proteinView.structures[conn.structureIdx];
                 const structurePos = structure?.hoverPosition?.structureSeqPos;
                 if (structurePos !== undefined) {
                     const msaUngapped = conn.structureToMsa[structurePos];
@@ -170,12 +166,6 @@ export default function stateModelFactory() {
             }
             return genomeToMSA({ model: self });
         },
-        /**
-         * #getter
-         */
-        get clickCol2() {
-            return undefined;
-        },
     }))
         .actions(self => ({
         /**
@@ -292,12 +282,11 @@ export default function stateModelFactory() {
                 throw new Error(`MSA row "${rowName}" not found`);
             }
             const ungappedMsaSequence = msaSequence.replaceAll('-', '');
-            const { views } = getSession(self);
-            const proteinView = views.find((v) => v.id === proteinViewId);
+            const proteinView = getProteinViews(getSession(self).views).find(v => v.id === proteinViewId);
             if (!proteinView) {
                 throw new Error(`ProteinView "${proteinViewId}" not found`);
             }
-            const structure = proteinView.structures?.[structureIdx];
+            const structure = proteinView.structures[structureIdx];
             if (!structure) {
                 throw new Error(`Structure at index ${structureIdx} not found`);
             }
@@ -311,8 +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);
         },

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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/pairwiseAlignment.js CHANGED Viewed

@@ -1,8 +1,6 @@
 import BLOSUM62 from './blosum62';
 function getScore(a, b) {
-    const upper_a = a.toUpperCase();
-    const upper_b = b.toUpperCase();
-    return BLOSUM62[upper_a]?.[upper_b] ?? -4;
+    return BLOSUM62[a.toUpperCase()]?.[b.toUpperCase()] ?? -4;
 }
 const GAP_OPEN = -10;
 const GAP_EXTEND = -0.5;
@@ -43,9 +41,11 @@ export function needlemanWunsch(seq1, seq2, gapOpen = GAP_OPEN, gapExtend = GAP_
     let alignedSeq2 = '';
     let i = m;
     let j = n;
-    const finalScores = [M[m][n], Ix[m][n], Iy[m][n]];
-    const score = Math.max(...finalScores);
-    let currentMatrix = score === M[m][n] ? 'M' : score === Ix[m][n] ? 'Ix' : 'Iy';
+    const mScore = M[m][n];
+    const ixScore = Ix[m][n];
+    const iyScore = Iy[m][n];
+    const score = Math.max(mScore, ixScore, iyScore);
+    let currentMatrix = score === mScore ? 'M' : score === ixScore ? 'Ix' : 'Iy';
     while (i > 0 || j > 0) {
         if (currentMatrix === 'M' && i > 0 && j > 0) {
             alignedSeq1 = seq1[i - 1] + alignedSeq1;