npm - jbrowse-plugin-msaview - Versions diffs - 2.3.3 → 2.3.8 - Mend

jbrowse-plugin-msaview 2.3.3 → 2.3.8

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 (76) hide show

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 { isProteinView } 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 = session.views.filter(isProteinView);
     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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package/dist/MsaViewPanel/components/ErrorBoundary.d.ts ADDED Viewed

@@ -0,0 +1,19 @@
+import type { ReactNode } from 'react';
+import React, { Component } from 'react';
+interface Props {
+    children: ReactNode;
+}
+interface State {
+    hasError: boolean;
+    error: unknown;
+}
+export declare class ErrorBoundary extends Component<Props, State> {
+    constructor(props: Props);
+    static getDerivedStateFromError(error: unknown): {
+        hasError: boolean;
+        error: unknown;
+    };
+    componentDidCatch(error: unknown, info: React.ErrorInfo): void;
+    render(): string | number | bigint | boolean | React.JSX.Element | Iterable<ReactNode> | Promise<string | number | bigint | boolean | React.ReactPortal | React.ReactElement<unknown, string | React.JSXElementConstructor<any>> | Iterable<ReactNode> | null | undefined> | null | undefined;
+}
+export {};

package/dist/MsaViewPanel/components/ErrorBoundary.js ADDED Viewed

@@ -0,0 +1,22 @@
+import React, { Component } from 'react';
+import { ErrorMessage } from '@jbrowse/core/ui';
+export class ErrorBoundary extends Component {
+    constructor(props) {
+        super(props);
+        this.state = { hasError: false, error: null };
+    }
+    static getDerivedStateFromError(error) {
+        return { hasError: true, error };
+    }
+    componentDidCatch(error, info) {
+        console.error('MsaViewPanel error:', error, info.componentStack);
+    }
+    render() {
+        if (this.state.hasError) {
+            return (React.createElement("div", { style: { padding: 20 } },
+                React.createElement(ErrorMessage, { error: this.state.error })));
+        }
+        return this.props.children;
+    }
+}
+//# sourceMappingURL=ErrorBoundary.js.map

package/dist/MsaViewPanel/components/ErrorBoundary.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"ErrorBoundary.js","sourceRoot":"","sources":["../../../src/MsaViewPanel/components/ErrorBoundary.tsx"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,OAAO,CAAA;AAExC,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAW/C,MAAM,OAAO,aAAc,SAAQ,SAAuB;IACxD,YAAY,KAAY;QACtB,KAAK,CAAC,KAAK,CAAC,CAAA;QACZ,IAAI,CAAC,KAAK,GAAG,EAAE,QAAQ,EAAE,KAAK,EAAE,KAAK,EAAE,IAAI,EAAE,CAAA;IAC/C,CAAC;IAED,MAAM,CAAC,wBAAwB,CAAC,KAAc;QAC5C,OAAO,EAAE,QAAQ,EAAE,IAAI,EAAE,KAAK,EAAE,CAAA;IAClC,CAAC;IAED,iBAAiB,CAAC,KAAc,EAAE,IAAqB;QACrD,OAAO,CAAC,KAAK,CAAC,qBAAqB,EAAE,KAAK,EAAE,IAAI,CAAC,cAAc,CAAC,CAAA;IAClE,CAAC;IAED,MAAM;QACJ,IAAI,IAAI,CAAC,KAAK,CAAC,QAAQ,EAAE,CAAC;YACxB,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,EAAE,EAAE;gBACzB,oBAAC,YAAY,IAAC,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,KAAK,GAAI,CACrC,CACP,CAAA;QACH,CAAC;QAED,OAAO,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAA;IAC5B,CAAC;CACF"}

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

@@ -2,11 +2,20 @@ 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("div", null, blastParams ? (React.createElement(LoadingBLAST, { model: model, baseUrl: blastParams.baseUrl })) : loadingStoredData ? (React.createElement("div", { style: { padding: 20 } },
-        React.createElement(LoadingEllipses, { message: "Loading MSA data", variant: "h6" }))) : (React.createElement(MSAView, { model: model }))));
+    return (React.createElement(ErrorBoundary, null,
+        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;
 //# sourceMappingURL=MsaViewPanel.js.map

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

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

@@ -1,4 +1,4 @@
-import type { StructureConnection } from './structureConnection';
+import type { ProteinView, StructureConnection } from './structureConnection';
 import type { MafRegion, MsaViewInitState } from './types';
 import type { Feature } from '@jbrowse/core/util';
 import type { Instance } from '@jbrowse/mobx-state-tree';
@@ -609,21 +609,9 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     fitHorizontally(): void;
     afterCreate(): void;
 } & {
-    /**
-     * #volatile
-     */
     rid: string | undefined;
-    /**
-     * #volatile
-     */
     progress: string;
-    /**
-     * #volatile
-     */
     error: unknown;
-    /**
-     * #volatile
-     */
     loadingStoredData: boolean;
 } & {
     /**
@@ -656,7 +644,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * #getter
      */
     readonly connectedProteinViews: (StructureConnection & {
-        proteinView: any;
+        proteinView: ProteinView;
     })[];
 } & {
     /**

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 { isProteinView, mapToRecord, ungappedToGappedPosition, } from './structureConnection';
 const ConnectStructureDialog = lazy(() => import('./components/ConnectStructureDialog'));
 /**
  * #stateModel MsaViewPlugin
@@ -127,12 +127,15 @@ export default function stateModelFactory() {
          */
         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);
+            const unknownViews = views;
+            const result = [];
+            for (const conn of self.connectedStructures) {
+                const proteinView = unknownViews.find((v) => isProteinView(v) && v.id === conn.proteinViewId);
+                if (proteinView) {
+                    result.push({ ...conn, proteinView });
+                }
+            }
+            return result;
         },
     }))
         .views(self => ({
@@ -141,7 +144,7 @@ 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];
@@ -293,11 +296,11 @@ export default function stateModelFactory() {
             }
             const ungappedMsaSequence = msaSequence.replaceAll('-', '');
             const { views } = getSession(self);
-            const proteinView = views.find((v) => v.id === proteinViewId);
+            const proteinView = views.find((v) => isProteinView(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`);
             }

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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;
@@ -53,10 +53,11 @@ export function needlemanWunsch(seq1, seq2, gapOpen = GAP_OPEN, gapExtend = GAP_
             const matchScore = getScore(seq1[i - 1], seq2[j - 1]);
             const prevM = M[i - 1][j - 1];
             const prevIx = Ix[i - 1][j - 1];
-            if (M[i][j] === prevM + matchScore) {
+            const currentScore = M[i][j];
+            if (currentScore === prevM + matchScore) {
                 currentMatrix = 'M';
             }
-            else if (M[i][j] === prevIx + matchScore) {
+            else if (currentScore === prevIx + matchScore) {
                 currentMatrix = 'Ix';
             }
             else {
@@ -68,13 +69,17 @@ export function needlemanWunsch(seq1, seq2, gapOpen = GAP_OPEN, gapExtend = GAP_
         else if (currentMatrix === 'Ix' && i > 0) {
             alignedSeq1 = seq1[i - 1] + alignedSeq1;
             alignedSeq2 = '-' + alignedSeq2;
-            currentMatrix = Ix[i][j] === M[i - 1][j] + gapOpen ? 'M' : 'Ix';
+            const ixScore = Ix[i][j];
+            const mScore = M[i - 1][j] + gapOpen;
+            currentMatrix = ixScore === mScore ? 'M' : 'Ix';
             i--;
         }
         else if (j > 0) {
             alignedSeq1 = '-' + alignedSeq1;
             alignedSeq2 = seq2[j - 1] + alignedSeq2;
-            currentMatrix = Iy[i][j] === M[i][j - 1] + gapOpen ? 'M' : 'Iy';
+            const iyScore = Iy[i][j];
+            const mScore = M[i][j - 1] + gapOpen;
+            currentMatrix = iyScore === mScore ? 'M' : 'Iy';
             j--;
         }
         else {

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

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

@@ -1,3 +1,25 @@
+export interface ProteinViewStructure {
+    url?: string;
+    connectedViewId?: string;
+    uniprotId?: string;
+    structureSequences?: string[];
+    hoverGenomeHighlights?: {
+        start: number;
+        end: number;
+    }[];
+    hoverPosition?: {
+        structureSeqPos?: number;
+    };
+    clearHighlightFromExternal?: () => void;
+    highlightFromExternal?: (pos: number) => void;
+}
+export interface ProteinView {
+    type: 'ProteinView';
+    id: string;
+    displayName?: string;
+    structures: ProteinViewStructure[];
+}
+export declare function isProteinView(view: unknown): view is ProteinView;
 /**
  * Represents a connection between the MSA view and a protein structure
  */

package/dist/MsaViewPanel/structureConnection.js CHANGED Viewed

@@ -1,3 +1,7 @@
+export function isProteinView(view) {
+    const v = view;
+    return v.type === 'ProteinView' && Array.isArray(v.structures);
+}
 /**
  * Helper to convert gapped MSA column to ungapped position for a specific row
  */

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

	@@ -1 +1 @@
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