jbrowse-plugin-msaview 2.4.3 → 2.4.5

package/dist/AddHighlightModel/GenomeMouseoverHighlight.js

@@ -2,9 +2,10 @@ import React from 'react';
 import { getSession } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
 import { hasHoverPosition, useStyles } from './util';
+import { isMsaView } from '../MsaViewPanel/model';
 const GenomeMouseoverHighlight = observer(function ({ model, }) {
     const { hovered, views } = getSession(model);
-    const hasMsaView = views.some(s => s.type === 'MsaView');
+    const hasMsaView = views.some(s => isMsaView(s) && s.connectedViewId === model.id);
     return hasMsaView && hasHoverPosition(hovered) ? (React.createElement(GenomeMouseoverHighlightRenderer, { model: model, hovered: hovered })) : null;
 });
 const GenomeMouseoverHighlightRenderer = observer(function ({ model, hovered, }) {
@@ -21,4 +22,3 @@ const GenomeMouseoverHighlightRenderer = observer(function ({ model, hovered, })
     return null;
 });
 export default GenomeMouseoverHighlight;
-//# sourceMappingURL=GenomeMouseoverHighlight.js.map

package/dist/AddHighlightModel/HighlightComponents.js

@@ -8,4 +8,3 @@ const HighlightComponents = observer(function HighlightComponents2({ model, }) {
         React.createElement(GenomeMouseoverHighlight, { model: model })));
 });
 export default HighlightComponents;
-//# sourceMappingURL=HighlightComponents.js.map

package/dist/AddHighlightModel/MsaToGenomeHighlight.js

@@ -2,14 +2,17 @@ import React from 'react';
 import { getSession } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
 import { hasHoverPosition, useStyles } from './util';
+import { isMsaView } from '../MsaViewPanel/model';
 import { getCanonicalRefName } from '../MsaViewPanel/util';
 const MsaToGenomeHighlight = observer(function MsaToGenomeHighlight2({ model, }) {
     const { views, hovered } = getSession(model);
-    const msaView = views.find(f => f.type === 'MsaView');
+    const msaView = views
+        .filter(isMsaView)
+        .find(v => v.connectedViewId === model.id);
     const highlights = msaView?.connectedHighlights;
     // Suppress codon highlight while hovering the LGV — GenomeMouseoverHighlight
     // handles the single-bp display in that case
-    return !hasHoverPosition(hovered) && highlights?.length ? (React.createElement(MsaToGenomeHighlightRenderer, { model: model, highlights: Array.from(highlights) })) : null;
+    return !hasHoverPosition(hovered) && highlights?.length ? (React.createElement(MsaToGenomeHighlightRenderer, { model: model, highlights: highlights })) : null;
 });
 // Inner component: handles the scroll-dependent rendering
 const MsaToGenomeHighlightRenderer = observer(function ({ model, highlights, }) {
@@ -33,4 +36,3 @@ const MsaToGenomeHighlightRenderer = observer(function ({ model, highlights, })
     })));
 });
 export default MsaToGenomeHighlight;
-//# sourceMappingURL=MsaToGenomeHighlight.js.map

package/dist/AddHighlightModel/index.js

@@ -1,13 +1,14 @@
 import React from 'react';
 import { getSession } from '@jbrowse/core/util';
 import HighlightComponents from './HighlightComponents';
+import { isMsaView } from '../MsaViewPanel/model';
 export default function AddHighlightComponentsModelF(pluginManager) {
     pluginManager.addToExtensionPoint('LinearGenomeView-TracksContainerComponent', 
     // @ts-expect-error
     (rest, { model }) => {
         // Quick check: don't add any components if no MSA view exists
         const { views } = getSession(model);
-        const hasMsaView = views.some(v => v.type === 'MsaView');
+        const hasMsaView = views.some(v => isMsaView(v) && v.connectedViewId === model.id);
         if (!hasMsaView) {
             return rest;
         }
@@ -17,4 +18,3 @@ export default function AddHighlightComponentsModelF(pluginManager) {
         ];
     });
 }
-//# sourceMappingURL=index.js.map

package/dist/AddHighlightModel/util.d.ts

@@ -1,9 +1,4 @@
-export declare function hasHoverPosition(hovered: unknown): hovered is {
-    hoverPosition: {
-        coord: number;
-        refName: string;
-    };
-};
+export { hasHoverPosition } from '../MsaViewPanel/util';
 export declare const useStyles: (params: void, muiStyleOverridesParams?: {
     props: Record<string, unknown>;
     ownerState?: Record<string, unknown> | undefined;

package/dist/AddHighlightModel/util.js

@@ -1,10 +1,5 @@
 import { makeStyles } from 'tss-react/mui';
-export function hasHoverPosition(hovered) {
-    return (!!hovered &&
-        typeof hovered === 'object' &&
-        'hoverPosition' in hovered &&
-        !!hovered.hoverPosition);
-}
+export { hasHoverPosition } from '../MsaViewPanel/util';
 export const useStyles = makeStyles()({
     highlight: {
         height: '100%',
@@ -17,4 +12,3 @@ export const useStyles = makeStyles()({
         overflow: 'hidden',
     },
 });
-//# sourceMappingURL=util.js.map

package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js

@@ -56,4 +56,3 @@ export default class BgzipFastaMsaAdapter extends BaseAdapter {
             .pipe(toArray()));
     }
 }
-//# sourceMappingURL=BgzipFastaMsaAdapter.js.map

package/dist/BgzipFastaMsaAdapter/configSchema.js

@@ -10,4 +10,3 @@ export default function configSchemaF(pluginManager) {
         baseConfiguration: base?.configSchema,
     });
 }
-//# sourceMappingURL=configSchema.js.map

package/dist/BgzipFastaMsaAdapter/index.js

@@ -12,4 +12,3 @@ export default function BgzipFastaMsaAdapterF(pluginManager) {
         });
     });
 }
-//# sourceMappingURL=index.js.map

package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js

@@ -26,4 +26,3 @@ export default function LaunchMsaViewDialog({ handleClose, feature, model, }) {
         React.createElement(TabPanel, { value: value, index: "manual_msa" },
             React.createElement(ManualMSALoader, { model: model, feature: feature, handleClose: handleClose }))));
 }
-//# sourceMappingURL=LaunchMsaViewDialog.js.map

package/dist/LaunchMsaView/components/LaunchPanelContent.js

@@ -13,4 +13,3 @@ export default function LaunchPanelContent({ error, children, }) {
         error ? React.createElement(ErrorMessage, { error: error }) : null,
         children));
 }
-//# sourceMappingURL=LaunchPanelContent.js.map

package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js

@@ -101,4 +101,3 @@ const ManualMSALoader = observer(function PreLoadedMSA2({ model, feature, handle
             }, onCancel: handleClose })));
 });
 export default ManualMSALoader;
-//# sourceMappingURL=ManualMSALoader.js.map

package/dist/LaunchMsaView/components/ManualMSALoader/fetchGeneList.js

@@ -9,4 +9,3 @@ export async function fetchGeneList() {
         .map(f => f.trim())
         .filter(f => !!f);
 }
-//# sourceMappingURL=fetchGeneList.js.map

package/dist/LaunchMsaView/components/ManualMSALoader/launchView.js

@@ -10,4 +10,3 @@ export function launchView({ session, newViewTitle, view, feature, msaFilehandle
         data,
     });
 }
-//# sourceMappingURL=launchView.js.map

package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.js

@@ -77,4 +77,3 @@ const CachedBlastResults = observer(function ({ model, handleClose, feature, })
                 React.createElement(ListItemText, { primary: `${getResultDisplayName(result)} - ${result.blastDatabase}/${result.blastProgram} (${result.msaAlgorithm})`, secondary: `${new Date(result.timestamp).toLocaleString()} - Seq: ${result.proteinSequence.slice(0, 30)}...` }))))))));
 });
 export default CachedBlastResults;
-//# sourceMappingURL=CachedBlastResults.js.map

package/dist/LaunchMsaView/components/NCBIBlastQuery/MsaAlgorithmSelect.js

@@ -7,4 +7,3 @@ export default function MsaAlgorithmSelect({ value, onChange, className, }) {
             onChange(event.target.value);
         } }, msaAlgorithms.map(val => (React.createElement(MenuItem, { value: val, key: val }, val)))));
 }
-//# sourceMappingURL=MsaAlgorithmSelect.js.map

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js

@@ -94,4 +94,3 @@ const NCBIBlastAutomaticPanel = observer(function ({ handleClose, feature, model
             }, onCancel: handleClose })));
 });
 export default NCBIBlastAutomaticPanel;
-//# sourceMappingURL=NCBIBlastAutomaticPanel.js.map

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js

@@ -40,4 +40,3 @@ const NCBIBlastManualPanel = observer(function ({ handleClose, feature, model, c
                 } }, "Close"))));
 });
 export default NCBIBlastManualPanel;
-//# sourceMappingURL=NCBIBlastManualPanel.js.map

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastMethodSelector.js

@@ -9,4 +9,3 @@ export default function NCBIBlastMethodSelector({ lookupMethod, setLookupMethod,
             React.createElement(FormControlLabel, { value: "rid", control: React.createElement(Radio, null), label: "Load from RID" }),
             React.createElement(FormControlLabel, { value: "manual", control: React.createElement(Radio, null), label: "Manual" }))));
 }
-//# sourceMappingURL=NCBIBlastMethodSelector.js.map

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.js

@@ -39,4 +39,3 @@ export default function NCBIBlastPanel({ handleClose, model, feature, }) {
                 setSettingsOpen(false);
             } })) : null));
 }
-//# sourceMappingURL=NCBIBlastPanel.js.map

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastRIDPanel.js

@@ -72,4 +72,3 @@ const NCBIBlastRIDPanel = observer(function ({ handleClose, feature, model, chil
             }, onCancel: handleClose })));
 });
 export default NCBIBlastRIDPanel;
-//# sourceMappingURL=NCBIBlastRIDPanel.js.map

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.js

@@ -30,4 +30,3 @@ export default function NCBISettingsDialog({ handleClose, baseUrl, }) {
                     handleClose(tempBaseUrl);
                 } }, "Save"))));
 }
-//# sourceMappingURL=NCBISettingsDialog.js.map

package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.js

@@ -26,4 +26,3 @@ export function blastLaunchViewFromCache({ newViewTitle, view, cached, }) {
         },
     });
 }
-//# sourceMappingURL=blastLaunchView.js.map

package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.js

@@ -2,4 +2,3 @@ export const BASE_BLAST_URL = 'https://blast.ncbi.nlm.nih.gov/Blast.cgi';
 export const msaAlgorithms = ['clustalo', 'muscle', 'kalign', 'mafft'];
 export const blastDatabaseOptions = ['nr', 'nr_cluster_seq'];
 export const blastPrograms = ['blastp', 'quick-blastp'];
-//# sourceMappingURL=consts.js.map

package/dist/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.js

@@ -22,4 +22,3 @@ export function useCachedBlastResults(geneIds) {
         handleClearAll,
     };
 }
-//# sourceMappingURL=useCachedBlastResults.js.map

package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js

@@ -84,4 +84,3 @@ const PreLoadedMSA = observer(function ({ model, feature, handleClose, }) {
             }, onCancel: handleClose })));
 });
 export default PreLoadedMSA;
-//# sourceMappingURL=PreLoadedMSADataPanel.js.map

package/dist/LaunchMsaView/components/PreLoadedMSA/fetchMSAData.js

@@ -11,4 +11,3 @@ export async function fetchMSA({ config, pluginManager, msaId, }) {
     const adapter = await getMsaAdapter(pluginManager, config);
     return adapter.getMSA(msaId);
 }
-//# sourceMappingURL=fetchMSAData.js.map

package/dist/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.js

@@ -16,4 +16,3 @@ export function preCalculatedLaunchView({ session, newViewTitle, view, feature,
         connectedFeature: feature.toJSON(),
     });
 }
-//# sourceMappingURL=preCalculatedLaunchView.js.map

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

@@ -2,4 +2,3 @@ import { readConfObject } from '@jbrowse/core/configuration';
 export function readMsaDatasets(jbrowse) {
     return readConfObject(jbrowse, ['msa', 'datasets']);
 }
-//# sourceMappingURL=types.js.map

package/dist/LaunchMsaView/components/SubmitCancelActions.js

@@ -9,4 +9,3 @@ export default function SubmitCancelActions({ onSubmit, onCancel, submitDisabled
                 onCancel();
             } }, cancelLabel)));
 }
-//# sourceMappingURL=SubmitCancelActions.js.map

package/dist/LaunchMsaView/components/TabPanel.js

@@ -1,6 +1,5 @@
 import React from 'react';
 // this is from MUI example
 export default function TabPanel({ children, value, index, ...other }) {
-    return (React.createElement("div", { role: "tabpanel", hidden: value !== index, ...other }, value === index ? React.createElement("div", null, children) : null));
+    return (React.createElement("div", { role: "tabpanel", hidden: value !== index, ...other }, value === index ? children : null));
 }
-//# sourceMappingURL=TabPanel.js.map

package/dist/LaunchMsaView/components/TranscriptSelector.js

@@ -44,4 +44,3 @@ export default function TranscriptSelector({ feature, options, selectedId, selec
                 ? `>${getTranscriptDisplayName(selectedTranscript)}\n${proteinSequence}`
                 : 'Loading...' })) : null));
 }
-//# sourceMappingURL=TranscriptSelector.js.map

package/dist/LaunchMsaView/components/calculateProteinSequence.js

@@ -36,4 +36,3 @@ export function getProteinSequenceFromFeature({ feature, seq, }) {
         codonTable: generateCodonTable(defaultCodonTable),
     });
 }
-//# sourceMappingURL=calculateProteinSequence.js.map

package/dist/LaunchMsaView/components/fetchSeq.js

@@ -20,4 +20,3 @@ export async function fetchSeq({ start, end, refName, session, assemblyName, })
     }));
     return feats[0]?.get('seq') ?? '';
 }
-//# sourceMappingURL=fetchSeq.js.map

package/dist/LaunchMsaView/components/types.js

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

package/dist/LaunchMsaView/components/useFeatureSequence.js

@@ -17,4 +17,3 @@ export function useFeatureSequence({ view, feature, }) {
         error,
     };
 }
-//# sourceMappingURL=useFeatureSequence.js.map

package/dist/LaunchMsaView/components/useSWRFeatureSequence.js

@@ -23,4 +23,3 @@ export function useSWRFeatureSequence({ view, feature, }) {
         error,
     };
 }
-//# sourceMappingURL=useSWRFeatureSequence.js.map

package/dist/LaunchMsaView/components/useTranscriptSelection.js

@@ -32,4 +32,3 @@ export function useTranscriptSelection({ feature, view, validIds, }) {
         validIds,
     };
 }
-//# sourceMappingURL=useTranscriptSelection.js.map

package/dist/LaunchMsaView/components/util.js

@@ -14,4 +14,3 @@ export function makeId(h, taxonomyInfo) {
 export function strip(s) {
     return s.replaceAll('-', '');
 }
-//# sourceMappingURL=util.js.map

package/dist/LaunchMsaView/index.js

@@ -46,4 +46,3 @@ export default function LaunchMsaViewF(pluginManager) {
         return elt;
     });
 }
-//# sourceMappingURL=index.js.map

package/dist/LaunchMsaView/util.js

@@ -79,4 +79,3 @@ export function getGeneIdentifiers(feature) {
         feature.get('gene_name'),
     ]);
 }
-//# sourceMappingURL=util.js.map

package/dist/LaunchMsaViewExtensionPoint/index.js

@@ -28,4 +28,3 @@ export default function LaunchMsaViewExtensionPointF(pluginManager) {
         });
     });
 }
-//# sourceMappingURL=index.js.map

package/dist/MsaViewPanel/afterCreateAutoruns.d.ts

@@ -3,7 +3,6 @@ export declare function loadStoredData(self: JBrowsePluginMsaViewModel): void;
 export declare function storeDataToIndexedDB(self: JBrowsePluginMsaViewModel): void;
 export declare function launchBlastIfNeeded(self: JBrowsePluginMsaViewModel): void;
 export declare function processInit(self: JBrowsePluginMsaViewModel): void;
-export declare function updateGenomeHighlights(self: JBrowsePluginMsaViewModel): void;
 export declare function highlightConnectedStructures(self: JBrowsePluginMsaViewModel): void;
 export declare function autoConnectStructures(self: JBrowsePluginMsaViewModel): void;
 export declare function observeProteinHighlights(self: JBrowsePluginMsaViewModel): void;

package/dist/MsaViewPanel/afterCreateAutoruns.js

@@ -1,15 +1,12 @@
 import { getSession } from '@jbrowse/core/util';
 import { doLaunchBlast } from './doLaunchBlast';
-import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord';
 import { cleanupOldData, generateDataStoreId, retrieveMsaData, storeMsaData, } from './msaDataStore';
 import { gappedToUngappedPosition, getProteinViews, } from './structureConnection';
 import { getUniprotIdFromAlphaFoldUrl } from './util';
 export function loadStoredData(self) {
     const { dataStoreId, rows } = self;
     if (dataStoreId && rows.length === 0) {
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
-        ;
-        (async () => {
+        void (async () => {
             try {
                 self.setLoadingStoredData(true);
                 const storedData = await retrieveMsaData(dataStoreId);
@@ -44,7 +41,7 @@ export function storeDataToIndexedDB(self) {
             // data observables change while the write is pending) don't kick off a
             // duplicate write and leave an orphan IndexedDB entry
             self.setIsStoringData(true);
-            (async () => {
+            void (async () => {
                 try {
                     const newId = generateDataStoreId();
                     const success = await storeMsaData(newId, {
@@ -68,9 +65,7 @@ export function storeDataToIndexedDB(self) {
 }
 export function launchBlastIfNeeded(self) {
     if (self.blastParams) {
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
-        ;
-        (async () => {
+        void (async () => {
             try {
                 self.setProgress('Submitting query');
                 self.setError(undefined);
@@ -91,9 +86,7 @@ export function launchBlastIfNeeded(self) {
 export function processInit(self) {
     const { init } = self;
     if (init) {
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
-        ;
-        (async () => {
+        void (async () => {
             try {
                 self.setError(undefined);
                 const { msaData, msaUrl, treeData, treeUrl, querySeqName } = init;
@@ -138,16 +131,6 @@ export function processInit(self) {
         })();
     }
 }
-export function updateGenomeHighlights(self) {
-    const { mouseCol, mouseClickCol } = self;
-    const r1 = mouseCol === undefined
-        ? undefined
-        : msaCoordToGenomeCoord({ model: self, coord: mouseCol });
-    const r2 = mouseClickCol === undefined
-        ? undefined
-        : msaCoordToGenomeCoord({ model: self, coord: mouseClickCol });
-    self.setConnectedHighlights([r1, r2].filter(f => !!f));
-}
 export function highlightConnectedStructures(self) {
     const { mouseCol, connectedProteinViews } = self;
     if (connectedProteinViews.length === 0) {
@@ -250,4 +233,3 @@ export function runCleanup() {
         console.error('Failed to cleanup old MSA data:', e);
     });
 }
-//# sourceMappingURL=afterCreateAutoruns.js.map

package/dist/MsaViewPanel/blosum62.js

@@ -625,4 +625,3 @@ const BLOSUM62 = {
     },
 };
 export default BLOSUM62;
-//# sourceMappingURL=blosum62.js.map

package/dist/MsaViewPanel/components/ConnectStructureDialog.js

@@ -58,4 +58,3 @@ const ConnectStructureDialog = observer(function ConnectStructureDialog({ model,
             React.createElement(Button, { onClick: handleConnect, variant: "contained", disabled: proteinViews.length === 0 || !selectedViewId }, "Connect"))));
 });
 export default ConnectStructureDialog;
-//# sourceMappingURL=ConnectStructureDialog.js.map

package/dist/MsaViewPanel/components/ErrorBoundary.d.ts

@@ -14,6 +14,6 @@ export declare class ErrorBoundary extends Component<Props, State> {
         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;
+    render(): string | number | bigint | boolean | Iterable<ReactNode> | Promise<string | number | bigint | boolean | React.ReactPortal | React.ReactElement<unknown, string | React.JSXElementConstructor<any>> | Iterable<ReactNode> | null | undefined> | React.JSX.Element | null | undefined;
 }
 export {};

package/dist/MsaViewPanel/components/ErrorBoundary.js

@@ -19,4 +19,3 @@ export class ErrorBoundary extends Component {
         return this.props.children;
     }
 }
-//# sourceMappingURL=ErrorBoundary.js.map

package/dist/MsaViewPanel/components/LoadingBLAST.js

@@ -31,4 +31,3 @@ const LoadingBLAST = observer(function LoadingBLAST2({ model, baseUrl, }) {
         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/MsaViewPanel.js

@@ -18,4 +18,3 @@ const MsaViewPanel = observer(function MsaViewPanel2({ model, }) {
             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/RIDLink.js

@@ -10,4 +10,3 @@ function RIDLink({ baseUrl, rid }) {
         ")"));
 }
 export default RIDLink;
-//# sourceMappingURL=RIDLink.js.map

package/dist/MsaViewPanel/doLaunchBlast.js

@@ -102,4 +102,3 @@ function buildRowMetadata(desc, taxonomyInfo) {
     }
     return metadata;
 }
-//# sourceMappingURL=doLaunchBlast.js.map

package/dist/MsaViewPanel/genomeToMSA.d.ts

@@ -1,10 +1,4 @@
 import type { JBrowsePluginMsaViewModel } from './model';
-/**
- * Convert a genome coordinate from session.hovered to a visible MSA column.
- *
- * @param model - The MSA view model
- * @returns The visible column index, or undefined if no mapping exists
- */
 export declare function genomeToMSA({ model }: {
     model: JBrowsePluginMsaViewModel;
 }): number | undefined;

package/dist/MsaViewPanel/genomeToMSA.js

@@ -1,48 +1,26 @@
 import { getSession } from '@jbrowse/core/util';
-import { checkHovered } from './util';
-/**
- * Convert a genome coordinate from session.hovered to a visible MSA column.
- *
- * @param model - The MSA view model
- * @returns The visible column index, or undefined if no mapping exists
- */
+import { hasHoverPosition } from './util';
 export function genomeToMSA({ model }) {
     const { hovered } = getSession(model);
     const { querySeqName, transcriptToMsaMap, connectedView, mafRegion } = model;
-    if (!connectedView?.initialized || !checkHovered(hovered)) {
+    if (!connectedView?.initialized || !hasHoverPosition(hovered)) {
         return undefined;
     }
     const { coord: hoverCoord, refName } = hovered.hoverPosition;
-    // Handle MAF region mapping
     if (mafRegion) {
-        // Check if the hover is on the same refName as the MAF region
-        if (refName !== mafRegion.refName) {
+        if (refName !== mafRegion.refName ||
+            !connectedView.assemblyNames.includes(mafRegion.assemblyName) ||
+            hoverCoord < mafRegion.start ||
+            hoverCoord >= mafRegion.end) {
             return undefined;
         }
-        // Check if we're on the same assembly (if assembly info is available)
-        const viewAssemblies = connectedView.assemblyNames;
-        if (!viewAssemblies.includes(mafRegion.assemblyName)) {
-            return undefined;
-        }
-        // Check if the hover coordinate is within the MAF region
-        if (hoverCoord < mafRegion.start || hoverCoord >= mafRegion.end) {
-            return undefined;
-        }
-        // Calculate the ungapped position relative to the region start
-        const ungappedPos = hoverCoord - mafRegion.start;
-        // Convert to visible column using the query sequence
-        return model.seqPosToVisibleCol(querySeqName, ungappedPos);
+        return model.seqPosToVisibleCol(querySeqName, hoverCoord - mafRegion.start);
     }
-    // Handle transcript mapping (original behavior)
     if (transcriptToMsaMap) {
-        const { g2p } = transcriptToMsaMap;
-        // g2p maps genome coordinate to sequence position (0-based)
-        const seqPos = g2p[hoverCoord];
+        const seqPos = transcriptToMsaMap.g2p[hoverCoord];
         if (seqPos !== undefined) {
-            // Convert sequence position to visible column
             return model.seqPosToVisibleCol(querySeqName, seqPos);
         }
     }
     return undefined;
 }
-//# sourceMappingURL=genomeToMSA.js.map

package/dist/MsaViewPanel/genomeToMSA.test.js

@@ -241,4 +241,3 @@ describe('genomeToMSA', () => {
         expect(result).toBeUndefined();
     });
 });
-//# sourceMappingURL=genomeToMSA.test.js.map

package/dist/MsaViewPanel/index.js

@@ -12,4 +12,3 @@ export default function MsaViewF(pluginManager) {
         });
     });
 }
-//# sourceMappingURL=index.js.map

package/dist/MsaViewPanel/model.d.ts

@@ -330,11 +330,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
 } & {
     connectedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     connectedFeature: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
-    connectedHighlights: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
-        refName: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
-        start: import("@jbrowse/mobx-state-tree").ISimpleType<number>;
-        end: import("@jbrowse/mobx-state-tree").ISimpleType<number>;
-    }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     blastParams: import("@jbrowse/mobx-state-tree").IType<BlastParams | undefined, BlastParams | undefined, BlastParams | undefined>;
     querySeqName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
     uniprotId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -631,6 +626,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly transcriptToMsaMap: {
         g2p: Record<number, number>;
         p2g: Record<number, number>;
+        p2gCodon: Record<number, number[]>;
         refName: string;
         strand: number;
     } | undefined;
@@ -654,6 +650,10 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * #getter
      */
     readonly mouseCol2: number | undefined;
+    /**
+     * #getter
+     */
+    readonly connectedHighlights: IRegion[];
 } & {
     /**
      * #action
@@ -671,18 +671,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * #action
      */
     setRid(arg: string): void;
-    /**
-     * #action
-     */
-    setConnectedHighlights(r: IRegion[]): void;
-    /**
-     * #action
-     */
-    addToConnectedHighlights(r: IRegion): void;
-    /**
-     * #action
-     */
-    clearConnectedHighlights(): void;
     /**
      * #action
      */
@@ -757,7 +745,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     id: string;
     displayName: string | undefined;
     minimized: boolean;
-} & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & Omit<import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+} & import("@jbrowse/mobx-state-tree").NonEmptyObject & Omit<import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
     drawLabels: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -1059,3 +1047,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
 export type JBrowsePluginMsaViewStateModel = ReturnType<typeof stateModelFactory>;
 export type JBrowsePluginMsaViewModel = Instance<JBrowsePluginMsaViewStateModel>;
 export { type MafRegion, type MsaViewInitState } from './types';
+export declare function isMsaView(view: {
+    type: string;
+}): view is JBrowsePluginMsaViewModel;