jbrowse-plugin-msaview 2.2.3 → 2.2.4

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

@@ -1 +1 @@
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package/dist/LaunchMsaView/components/PreLoadedMSA/consts.d.ts

@@ -1,6 +1,7 @@
 export declare const swrFlags: {
     revalidateOnFocus: boolean;
     revalidateOnReconnect: boolean;
+    revalidateIfStale: boolean;
     refreshWhenHidden: boolean;
     refreshWhenOffline: boolean;
     shouldRetryOnError: boolean;

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

@@ -1,6 +1,7 @@
 export const swrFlags = {
     revalidateOnFocus: false,
     revalidateOnReconnect: false,
+    revalidateIfStale: false,
     refreshWhenHidden: false,
     refreshWhenOffline: false,
     shouldRetryOnError: false,

package/dist/LaunchMsaView/components/PreLoadedMSA/consts.js.map

@@ -1 +1 @@
-{"version":3,"file":"consts.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/PreLoadedMSA/consts.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,QAAQ,GAAG;IACtB,iBAAiB,EAAE,KAAK;IACxB,qBAAqB,EAAE,KAAK;IAC5B,iBAAiB,EAAE,KAAK;IACxB,kBAAkB,EAAE,KAAK;IACzB,kBAAkB,EAAE,KAAK;CAC1B,CAAA"}
+{"version":3,"file":"consts.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/PreLoadedMSA/consts.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,QAAQ,GAAG;IACtB,iBAAiB,EAAE,KAAK;IACxB,qBAAqB,EAAE,KAAK;IAC5B,iBAAiB,EAAE,KAAK;IACxB,iBAAiB,EAAE,KAAK;IACxB,kBAAkB,EAAE,KAAK;IACzB,kBAAkB,EAAE,KAAK;CAC1B,CAAA"}

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

@@ -1,6 +1,6 @@
 import React from 'react';
 export default function TabPanel({ children, value, index, ...other }: {
     children?: React.ReactNode;
-    index: number;
-    value: number;
+    index: number | string;
+    value: number | string;
 }): React.JSX.Element;

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

@@ -1,9 +1,9 @@
 import React from 'react';
 import { Feature } from '@jbrowse/core/util';
-export default function TranscriptSelector({ feature, options, selectedTranscriptId, onTranscriptChange, proteinSequence, validSet, }: {
+export default function TranscriptSelector({ feature, options, selectedTranscript, onTranscriptChange, proteinSequence, validSet, }: {
     feature: Feature;
     options: Feature[];
-    selectedTranscriptId: string;
+    selectedTranscript: Feature | undefined;
     onTranscriptChange: (transcriptId: string) => void;
     proteinSequence: string | undefined;
     validSet?: Set<string>;

package/dist/LaunchMsaView/components/TranscriptSelector.js

@@ -12,17 +12,14 @@ const useStyles = makeStyles()({
         minWidth: 300,
     },
 });
-export default function TranscriptSelector({ feature, options, selectedTranscriptId, onTranscriptChange, proteinSequence, validSet, }) {
+export default function TranscriptSelector({ feature, options, selectedTranscript, onTranscriptChange, proteinSequence, validSet, }) {
     const { classes } = useStyles();
     const [showSequence, setShowSequence] = useState(false);
-    const selectedTranscript = options.find(val => getId(val) === selectedTranscriptId);
     return (React.createElement(React.Fragment, null,
         React.createElement("div", { className: classes.flex },
-            React.createElement(TextField2, { variant: "outlined", label: `Choose isoform of ${getGeneDisplayName(feature)}`, select: true, className: classes.minWidth, value: selectedTranscriptId, onChange: event => {
+            React.createElement(TextField2, { variant: "outlined", label: `Choose isoform of ${getGeneDisplayName(feature)}`, select: true, className: classes.minWidth, value: getId(selectedTranscript), onChange: event => {
                     onTranscriptChange(event.target.value);
-                } }, options
-                .toSorted((a, b) => getTranscriptLength(b).len - getTranscriptLength(a).len)
-                .map(val => {
+                } }, options.map(val => {
                 const inSet = validSet ? validSet.has(getId(val)) : true;
                 const { len, mod } = getTranscriptLength(val);
                 return (React.createElement(MenuItem, { value: getId(val), key: val.id(), disabled: !inSet },

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

@@ -1 +1 @@
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+{"version":3,"file":"TranscriptSelector.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/TranscriptSelector.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAGvC,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAChD,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,kBAAkB,MAAM,qCAAqC,CAAA;AACpE,OAAO,UAAU,MAAM,6BAA6B,CAAA;AACpD,OAAO,EACL,kBAAkB,EAClB,KAAK,EACL,wBAAwB,EACxB,mBAAmB,GACpB,MAAM,SAAS,CAAA;AAEhB,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,IAAI,EAAE;QACJ,OAAO,EAAE,MAAM;KAChB;IACD,QAAQ,EAAE;QACR,QAAQ,EAAE,GAAG;KACd;CACF,CAAC,CAAA;AAEF,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,EACzC,OAAO,EACP,OAAO,EACP,kBAAkB,EAClB,kBAAkB,EAClB,eAAe,EACf,QAAQ,GAQT;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAEvD,OAAO,CACL;QACE,6BAAK,SAAS,EAAE,OAAO,CAAC,IAAI;YAC1B,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,KAAK,EAAE,qBAAqB,kBAAkB,CAAC,OAAO,CAAC,EAAE,EACzD,MAAM,QACN,SAAS,EAAE,OAAO,CAAC,QAAQ,EAC3B,KAAK,EAAE,KAAK,CAAC,kBAAkB,CAAC,EAChC,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,kBAAkB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBACxC,CAAC,IAEA,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE;gBACjB,MAAM,KAAK,GAAG,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;gBACxD,MAAM,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,mBAAmB,CAAC,GAAG,CAAC,CAAA;gBAC7C,OAAO,CACL,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,EAAE,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE,EAAE,QAAQ,EAAE,CAAC,KAAK;oBACzD,wBAAwB,CAAC,GAAG,CAAC;;oBAAI,GAAG;;oBAAM,GAAG;oBAC7C,GAAG,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,EAAE;oBACjC,QAAQ,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,EAAE,CAC9C,CACZ,CAAA;YACH,CAAC,CAAC,CACS;YACb,6BAAK,KAAK,EAAE,EAAE,YAAY,EAAE,QAAQ,EAAE,UAAU,EAAE,EAAE,EAAE;gBACpD,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;wBACZ,eAAe,CAAC,CAAC,YAAY,CAAC,CAAA;oBAChC,CAAC,IAEA,YAAY,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,eAAe,CAC1C,CACL,CACF;QAEL,YAAY,IAAI,CACf,oBAAC,kBAAkB,IACjB,KAAK,EACH,eAAe;gBACb,CAAC,CAAC,IAAI,wBAAwB,CAAC,kBAAkB,CAAC,KAAK,eAAe,EAAE;gBACxE,CAAC,CAAC,YAAY,GAElB,CACH,CACA,CACJ,CAAA;AACH,CAAC"}

package/dist/LaunchMsaView/components/useSWRFeatureSequence.js

@@ -1,8 +1,7 @@
 import { getSession } from '@jbrowse/core/util';
 import useSWR from 'swr';
 import { fetchSeq } from './fetchSeq';
-const BPLIMIT = 500_000;
-async function featureSequenceFetcher({ feature, assemblyName, upDownBp, view, forceLoad, }) {
+async function featureSequenceFetcher({ feature, assemblyName, upDownBp, view, }) {
     const session = getSession(view);
     const { start, end, refName } = feature.toJSON();
     const b = start - upDownBp;
@@ -43,8 +42,11 @@ export function useSWRFeatureSequence({ view, feature, upDownBp = 0, forceLoad =
         assemblyName: assemblyName,
         upDownBp,
         view: view,
-        forceLoad,
-    }));
+    }), {
+        revalidateOnFocus: false,
+        revalidateOnReconnect: false,
+        revalidateIfStale: false,
+    });
     return {
         sequence: data,
         error,

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

@@ -1 +1 @@
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+{"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;AAKrC,KAAK,UAAU,sBAAsB,CAAC,EACpC,OAAO,EACP,YAAY,EACZ,QAAQ,EACR,IAAI,GAML;IACC,MAAM,OAAO,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;IAChC,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,OAAO,CAAC,MAAM,EAI7C,CAAA;IAED,MAAM,CAAC,GAAG,KAAK,GAAG,QAAQ,CAAA;IAC1B,MAAM,CAAC,GAAG,GAAG,GAAG,QAAQ,CAAA;IACxB,MAAM,CAAC,GAAG,EAAE,QAAQ,EAAE,UAAU,CAAC,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC;QACpD,QAAQ,CAAC;YACP,KAAK;YACL,GAAG;YACH,OAAO;YACP,YAAY;YACZ,OAAO;SACR,CAAC;QACF,QAAQ,CAAC;YACP,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC;YACrB,GAAG,EAAE,KAAK;YACV,OAAO;YACP,YAAY;YACZ,OAAO;SACR,CAAC;QACF,QAAQ,CAAC;YACP,KAAK,EAAE,GAAG;YACV,GAAG,EAAE,CAAC;YACN,OAAO;YACP,YAAY;YACZ,OAAO;SACR,CAAC;KACH,CAAC,CAAA;IACF,OAAO,EAAE,GAAG,EAAE,QAAQ,EAAE,UAAU,EAAE,CAAA;AACtC,CAAC;AAED,MAAM,UAAU,qBAAqB,CAAC,EACpC,IAAI,EACJ,OAAO,EACP,QAAQ,GAAG,CAAC,EACZ,SAAS,GAAG,IAAI,GAMjB;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,QAAQ,EAAE,SAAS,EAAE,kBAAkB,CAAC;QACvE,CAAC,CAAC,IAAI,EACR,GAAG,EAAE,CACH,sBAAsB,CAAC;QACrB,OAAO,EAAE,OAAQ;QACjB,YAAY,EAAE,YAAa;QAC3B,QAAQ;QACR,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/LaunchMsaView/components/useTranscriptSelection.d.ts

@@ -0,0 +1,16 @@
+import type { Feature } from '@jbrowse/core/util';
+export declare function useTranscriptSelection({ feature, view, validIds, }: {
+    feature: Feature;
+    view: {
+        assemblyNames?: string[];
+    } | undefined;
+    validIds?: string[];
+}): {
+    options: Feature[];
+    selectedId: string;
+    setSelectedId: import("react").Dispatch<import("react").SetStateAction<string>>;
+    selectedTranscript: Feature | undefined;
+    proteinSequence: string;
+    error: any;
+    validSet: Set<string> | undefined;
+};

package/dist/LaunchMsaView/components/useTranscriptSelection.js

@@ -0,0 +1,31 @@
+import { useEffect, useMemo, useState } from 'react';
+import { getId, getSortedTranscriptFeatures } from '../util';
+import { useFeatureSequence } from './useFeatureSequence';
+export function useTranscriptSelection({ feature, view, validIds, }) {
+    const options = getSortedTranscriptFeatures(feature);
+    const [selectedId, setSelectedId] = useState(getId(options[0]));
+    const selectedTranscript = options.find(val => getId(val) === selectedId);
+    const { proteinSequence, error } = useFeatureSequence({
+        view,
+        feature: selectedTranscript,
+    });
+    const validSet = useMemo(() => (validIds ? new Set(validIds) : undefined), [validIds]);
+    useEffect(() => {
+        if (validIds && validIds.length > 0 && !validIds.includes(selectedId)) {
+            const validOption = options.find(opt => validIds.includes(getId(opt)));
+            if (validOption) {
+                setSelectedId(getId(validOption));
+            }
+        }
+    }, [validIds, options, selectedId]);
+    return {
+        options,
+        selectedId,
+        setSelectedId,
+        selectedTranscript,
+        proteinSequence,
+        error,
+        validSet,
+    };
+}
+//# sourceMappingURL=useTranscriptSelection.js.map

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

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

@@ -1,5 +1,7 @@
+import type { TaxonomyInfo } from '../../utils/taxonomyNames';
 export declare function makeId(h: {
     accession: string;
     sciname: string;
-}): string;
+    taxid?: number;
+}, taxonomyInfo?: Map<number, TaxonomyInfo>): string;
 export declare function strip(s: string): string;

package/dist/LaunchMsaView/components/util.js

@@ -1,5 +1,15 @@
-export function makeId(h) {
-    return `${h.accession}-${h.sciname.replaceAll(' ', '_')}`;
+export function makeId(h, taxonomyInfo) {
+    let speciesName = h.sciname.replaceAll(' ', '_');
+    if (h.taxid && taxonomyInfo?.has(h.taxid)) {
+        const info = taxonomyInfo.get(h.taxid);
+        if (info.commonName) {
+            speciesName = info.commonName
+                .split(' ')
+                .map(word => word.charAt(0).toUpperCase() + word.slice(1).toLowerCase())
+                .join('_');
+        }
+    }
+    return `${h.accession}-${speciesName}`;
 }
 export function strip(s) {
     return s.replace('-', '');

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

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/util.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,MAAM,CACpB,CAAyD,EACzD,YAAwC;IAExC,IAAI,WAAW,GAAG,CAAC,CAAC,OAAO,CAAC,UAAU,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;IAChD,IAAI,CAAC,CAAC,KAAK,IAAI,YAAY,EAAE,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;QAC1C,MAAM,IAAI,GAAG,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,CAAE,CAAA;QACvC,IAAI,IAAI,CAAC,UAAU,EAAE,CAAC;YACpB,WAAW,GAAG,IAAI,CAAC,UAAU;iBAC1B,KAAK,CAAC,GAAG,CAAC;iBACV,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,WAAW,EAAE,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,WAAW,EAAE,CAAC;iBACvE,IAAI,CAAC,GAAG,CAAC,CAAA;QACd,CAAC;IACH,CAAC;IACD,OAAO,GAAG,CAAC,CAAC,SAAS,IAAI,WAAW,EAAE,CAAA;AACxC,CAAC;AAED,MAAM,UAAU,KAAK,CAAC,CAAS;IAC7B,OAAO,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,CAAC,CAAA;AAC3B,CAAC"}

package/dist/LaunchMsaView/util.d.ts

@@ -7,3 +7,5 @@ export declare function getTranscriptLength(feature: Feature): {
 export declare function getId(val?: Feature): string;
 export declare function getTranscriptDisplayName(val?: Feature): string;
 export declare function getGeneDisplayName(val?: Feature): string;
+export declare function getSortedTranscriptFeatures(feature: Feature): Feature[];
+export declare function cleanProteinSequence(seq: string): string;

package/dist/LaunchMsaView/util.js

@@ -3,10 +3,16 @@ export function getTranscriptFeatures(feature) {
     // check if we are looking at a 'two-level' or 'three-level' feature by
     // finding exon/CDS subfeatures. we want to select from transcript names
     const subfeatures = feature.get('subfeatures') ?? [];
-    return subfeatures.some(f => f.get('type') === 'CDS')
-        ? [feature]
-        : // filter out non-coding by finding subfeatures with CDS subfeatures
-            subfeatures.filter(f => f.get('subfeatures')?.some(f => f.get('type') === 'CDS'));
+    // Check for mRNA/transcript subfeatures (three-level: gene → mRNA → CDS)
+    // Filter to only those that have CDS subfeatures (i.e. are coding)
+    const transcripts = subfeatures.filter((f) => (f.get('type') === 'mRNA' || f.get('type') === 'transcript') &&
+        f.get('subfeatures')?.some((s) => s.get('type') === 'CDS'));
+    if (transcripts.length > 0) {
+        return transcripts;
+    }
+    // Has direct CDS children, treat feature itself as the transcript
+    // (two-level: gene → CDS or mRNA → CDS)
+    return [feature];
 }
 export function getTranscriptLength(feature) {
     const cdsLen = sum(feature
@@ -36,4 +42,10 @@ export function getGeneDisplayName(val) {
             .filter(f => !!f)
             .join(' ');
 }
+export function getSortedTranscriptFeatures(feature) {
+    return getTranscriptFeatures(feature).toSorted((a, b) => getTranscriptLength(b).len - getTranscriptLength(a).len);
+}
+export function cleanProteinSequence(seq) {
+    return seq.replaceAll('*', '').replaceAll('&', '');
+}
 //# sourceMappingURL=util.js.map

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package/dist/LaunchMsaViewExtensionPoint/index.d.ts

@@ -0,0 +1,2 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function LaunchMsaViewExtensionPointF(pluginManager: PluginManager): void;

package/dist/LaunchMsaViewExtensionPoint/index.js

@@ -0,0 +1,31 @@
+export default function LaunchMsaViewExtensionPointF(pluginManager) {
+    pluginManager.addToExtensionPoint('LaunchView-MsaView', 
+    // @ts-expect-error
+    ({ session, data, msaFileLocation, treeFileLocation, connectedViewId, connectedFeature, displayName, colorSchemeName, colWidth, rowHeight, treeAreaWidth, treeWidth, drawNodeBubbles, labelsAlignRight, showBranchLen, querySeqName, }) => {
+        if (!data && !msaFileLocation) {
+            throw new Error('No MSA data or file location provided when launching MSA view');
+        }
+        session.addView('MsaView', {
+            type: 'MsaView',
+            displayName,
+            connectedViewId,
+            connectedFeature,
+            colorSchemeName,
+            colWidth,
+            rowHeight,
+            treeAreaWidth,
+            treeWidth,
+            drawNodeBubbles,
+            labelsAlignRight,
+            showBranchLen,
+            init: {
+                msaData: data?.msa,
+                treeData: data?.tree,
+                msaUrl: msaFileLocation?.uri,
+                treeUrl: treeFileLocation?.uri,
+                querySeqName,
+            },
+        });
+    });
+}
+//# sourceMappingURL=index.js.map

package/dist/LaunchMsaViewExtensionPoint/index.js.map

@@ -0,0 +1 @@
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package/dist/MsaViewPanel/components/ConnectStructureDialog.d.ts

@@ -0,0 +1,7 @@
+import React from 'react';
+import type { JBrowsePluginMsaViewModel } from '../model';
+declare const ConnectStructureDialog: ({ model, handleClose, }: {
+    model: JBrowsePluginMsaViewModel;
+    handleClose: () => void;
+}) => React.JSX.Element;
+export default ConnectStructureDialog;

package/dist/MsaViewPanel/components/ConnectStructureDialog.js

@@ -0,0 +1,56 @@
+import React, { useState } from 'react';
+import { Dialog } 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';
+const ConnectStructureDialog = observer(function ConnectStructureDialog({ model, handleClose, }) {
+    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 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) {
+            setError('Please select a protein view');
+            return;
+        }
+        try {
+            model.connectToStructure(selectedViewId, selectedStructureIdx, selectedMsaRow);
+            handleClose();
+        }
+        catch (e) {
+            setError(e instanceof Error ? e.message : String(e));
+        }
+    };
+    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(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 } },
+                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 } },
+                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))))),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { onClick: handleClose }, "Cancel"),
+            React.createElement(Button, { onClick: handleConnect, variant: "contained", disabled: proteinViews.length === 0 || !selectedViewId }, "Connect"))));
+});
+export default ConnectStructureDialog;
+//# sourceMappingURL=ConnectStructureDialog.js.map

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

@@ -0,0 +1 @@
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package/dist/MsaViewPanel/components/MsaViewPanel.js

@@ -1,10 +1,12 @@
 import React from 'react';
+import { LoadingEllipses } from '@jbrowse/core/ui';
 import { observer } from 'mobx-react';
 import { MSAView } from 'react-msaview';
 import LoadingBLAST from './LoadingBLAST';
 const MsaViewPanel = observer(function MsaViewPanel2({ model, }) {
-    const { blastParams } = model;
-    return (React.createElement("div", null, blastParams ? (React.createElement(LoadingBLAST, { model: model, baseUrl: blastParams.baseUrl })) : (React.createElement(MSAView, { model: model }))));
+    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 }))));
 });
 export default MsaViewPanel;
 //# sourceMappingURL=MsaViewPanel.js.map

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

@@ -1 +1 @@
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package/dist/MsaViewPanel/doLaunchBlast.d.ts

@@ -2,6 +2,7 @@ import { JBrowsePluginMsaViewModel } from './model';
 export declare function doLaunchBlast({ self, }: {
     self: JBrowsePluginMsaViewModel;
 }): Promise<{
+    treeMetadata: string;
     msa: string;
     tree: string;
 }>;

package/dist/MsaViewPanel/doLaunchBlast.js

@@ -1,38 +1,84 @@
 import { makeId, strip } from '../LaunchMsaView/components/util';
+import { cleanProteinSequence } from '../LaunchMsaView/util';
+import { saveBlastResult } from '../utils/blastCache';
 import { launchMSA } from '../utils/msa';
 import { queryBlast } from '../utils/ncbiBlast';
+import { fetchTaxonomyInfo } from '../utils/taxonomyNames';
 export async function doLaunchBlast({ self, }) {
-    const { baseUrl, blastDatabase, blastProgram, msaAlgorithm, proteinSequence, } = self.blastParams;
-    const { hits } = await queryBlast({
-        query: proteinSequence.replaceAll('*', '').replaceAll('&', ''),
+    const { baseUrl, blastDatabase, blastProgram, msaAlgorithm, proteinSequence, selectedTranscript, } = self.blastParams;
+    const cleanedSeq = cleanProteinSequence(proteinSequence);
+    const { hits, rid } = await queryBlast({
+        query: cleanedSeq,
         blastDatabase,
         blastProgram,
         baseUrl,
         onProgress: arg => {
             self.setProgress(arg);
         },
-        onRid: rid => {
-            self.setRid(rid);
+        onRid: r => {
+            self.setRid(r);
         },
     });
-    return launchMSA({
+    self.setProgress('Fetching species taxonomy info...');
+    const taxids = hits
+        .map(h => h.description[0]?.taxid)
+        .filter((t) => t !== undefined);
+    const taxonomyInfo = await fetchTaxonomyInfo(taxids);
+    const treeMetadata = {};
+    const sequences = hits.map(h => {
+        const desc = h.description[0] ?? {
+            accession: 'unknown',
+            id: 'unknown',
+            sciname: 'unknown',
+        };
+        const rowName = makeId(desc, taxonomyInfo);
+        const seq = strip(h.hsps[0]?.hseq ?? '');
+        treeMetadata[rowName] = buildRowMetadata(desc, taxonomyInfo);
+        return `>${rowName}\n${seq}`;
+    });
+    const result = await launchMSA({
         algorithm: msaAlgorithm,
-        sequence: [
-            `>QUERY\n${proteinSequence.replaceAll('*', '').replaceAll('&', '')}`,
-            ...hits
-                .map(h => [
-                makeId(h.description[0] ?? {
-                    accession: 'unknown',
-                    id: 'unknown',
-                    sciname: 'unknown',
-                }),
-                strip(h.hsps[0]?.hseq ?? ''),
-            ])
-                .map(([id, seq]) => `>${id}\n${seq}`),
-        ].join('\n'),
+        sequence: [`>QUERY\n${cleanedSeq}`, ...sequences].join('\n'),
         onProgress: arg => {
             self.setProgress(arg);
         },
     });
+    const treeMetadataJson = JSON.stringify(treeMetadata);
+    await saveBlastResult({
+        proteinSequence: cleanedSeq,
+        blastDatabase,
+        blastProgram,
+        msaAlgorithm,
+        msa: result.msa,
+        tree: result.tree,
+        treeMetadata: treeMetadataJson,
+        rid,
+        geneId: selectedTranscript?.get('parentId'),
+        transcriptId: selectedTranscript?.get('id'),
+    });
+    return {
+        ...result,
+        treeMetadata: treeMetadataJson,
+    };
+}
+function buildRowMetadata(desc, taxonomyInfo) {
+    const metadata = {};
+    const taxInfo = desc.taxid ? taxonomyInfo.get(desc.taxid) : undefined;
+    if (taxInfo?.sciname) {
+        metadata['Scientific name'] = taxInfo.sciname;
+    }
+    if (taxInfo?.commonName) {
+        metadata['Common name'] = taxInfo.commonName;
+    }
+    if (desc.accession) {
+        metadata.Accession = desc.accession;
+    }
+    if (desc.id) {
+        metadata.ID = desc.id;
+    }
+    if (desc.title) {
+        metadata.Description = desc.title;
+    }
+    return metadata;
 }
 //# sourceMappingURL=doLaunchBlast.js.map

package/dist/MsaViewPanel/doLaunchBlast.js.map

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package/dist/MsaViewPanel/genomeToMSA.d.ts

@@ -1,4 +1,10 @@
 import { 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;