jbrowse-plugin-protein3d 0.0.2

package/README.md

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+# jbrowse-plugin-protein3d
+
+WIP for displaying 3D protein structure alongside the genome browser

package/dist/AddHighlightModel/GenomeMouseoverHighlight.d.ts

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+import React from 'react';
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+declare const GenomeMouseoverHighlight: ({ model, }: {
+    model: LinearGenomeViewModel;
+}) => React.JSX.Element | null;
+export default GenomeMouseoverHighlight;

package/dist/AddHighlightModel/GenomeMouseoverHighlight.js

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+import React from 'react';
+import { observer } from 'mobx-react';
+import { getSession } from '@jbrowse/core/util';
+// locals
+import Highlight from './Highlight';
+const GenomeMouseoverHighlight = observer(function ({ model, }) {
+    const { hovered } = getSession(model);
+    return hovered &&
+        typeof hovered === 'object' &&
+        'hoverPosition' in hovered ? (React.createElement(HoverHighlight, { model: model })) : null;
+});
+const HoverHighlight = observer(function ({ model, }) {
+    const session = getSession(model);
+    if (session.views.some(s => s.type === 'ProteinView')) {
+        const { hovered } = session;
+        const { assemblyNames } = model;
+        // @ts-expect-error
+        const { coord, refName } = hovered.hoverPosition;
+        return (React.createElement(Highlight, { model: model, start: coord - 1, end: coord, refName: refName, assemblyName: assemblyNames[0] }));
+    }
+    return null;
+});
+export default GenomeMouseoverHighlight;
+//# sourceMappingURL=GenomeMouseoverHighlight.js.map

package/dist/AddHighlightModel/GenomeMouseoverHighlight.js.map

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package/dist/AddHighlightModel/Highlight.d.ts

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+import React from 'react';
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+declare const Highlight: ({ assemblyName, start, end, refName, model, }: {
+    model: LinearGenomeViewModel;
+    assemblyName: string;
+    start: number;
+    end: number;
+    refName: string;
+}) => React.JSX.Element | null;
+export default Highlight;

package/dist/AddHighlightModel/Highlight.js

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+import React from 'react';
+import { observer } from 'mobx-react';
+import { getSession } from '@jbrowse/core/util';
+// locals
+import { useStyles } from './util';
+const Highlight = observer(function Highlight({ assemblyName, start, end, refName, model, }) {
+    const { cx, classes } = useStyles();
+    const { assemblyManager } = getSession(model);
+    const { offsetPx } = model;
+    const assembly = assemblyManager.get(assemblyName);
+    const ref = assembly?.getCanonicalRefName(refName) ?? refName;
+    const s = model.bpToPx({ refName: ref, coord: start });
+    const e = model.bpToPx({ refName: ref, coord: end });
+    if (s && e) {
+        const width = Math.max(Math.abs(e.offsetPx - s.offsetPx), 3);
+        const left = Math.min(s.offsetPx, e.offsetPx) - offsetPx;
+        return (React.createElement("div", { className: cx(classes.highlight, width <= 3 ? classes.thinborder : undefined), style: { left, width } }));
+    }
+    else {
+        return null;
+    }
+});
+export default Highlight;
+//# sourceMappingURL=Highlight.js.map

package/dist/AddHighlightModel/Highlight.js.map

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+{"version":3,"file":"Highlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/Highlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE/C,SAAS;AACT,OAAO,EAAE,SAAS,EAAE,MAAM,QAAQ,CAAA;AAElC,MAAM,SAAS,GAAG,QAAQ,CAAC,SAAS,SAAS,CAAC,EAC5C,YAAY,EACZ,KAAK,EACL,GAAG,EACH,OAAO,EACP,KAAK,GAON;IACC,MAAM,EAAE,EAAE,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IACnC,MAAM,EAAE,eAAe,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IAC7C,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAC1B,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;IAClD,MAAM,GAAG,GAAG,QAAQ,EAAE,mBAAmB,CAAC,OAAO,CAAC,IAAI,OAAO,CAAA;IAC7D,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAA;IACtD,MAAM,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,EAAE,CAAC,CAAA;IACpD,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;QACX,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAA;QAC5D,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,QAAQ,CAAA;QACxD,OAAO,CACL,6BACE,SAAS,EAAE,EAAE,CACX,OAAO,CAAC,SAAS,EACjB,KAAK,IAAI,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,UAAU,CAAC,CAAC,CAAC,SAAS,CAC5C,EACD,KAAK,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,GACtB,CACH,CAAA;IACH,CAAC;SAAM,CAAC;QACN,OAAO,IAAI,CAAA;IACb,CAAC;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,SAAS,CAAA"}

package/dist/AddHighlightModel/HighlightComponents.d.ts

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+import React from 'react';
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+type LGV = LinearGenomeViewModel;
+declare const HighlightComponents: ({ model, }: {
+    model: LGV;
+}) => React.JSX.Element;
+export default HighlightComponents;

package/dist/AddHighlightModel/HighlightComponents.js

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+import React from 'react';
+import { observer } from 'mobx-react';
+// locals
+import ProteinToGenomeClickHighlight from './ProteinToGenomeClickHighlight';
+import ProteinToGenomeHoverHighlight from './ProteinToGenomeHoverHighlight';
+import GenomeMouseoverHighlight from './GenomeMouseoverHighlight';
+const HighlightComponents = observer(function Highlight({ model, }) {
+    return (React.createElement(React.Fragment, null,
+        React.createElement(ProteinToGenomeClickHighlight, { model: model }),
+        React.createElement(ProteinToGenomeHoverHighlight, { model: model }),
+        React.createElement(GenomeMouseoverHighlight, { model: model })));
+});
+export default HighlightComponents;
+//# sourceMappingURL=HighlightComponents.js.map

package/dist/AddHighlightModel/HighlightComponents.js.map

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+{"version":3,"file":"HighlightComponents.js","sourceRoot":"","sources":["../../src/AddHighlightModel/HighlightComponents.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAGrC,SAAS;AACT,OAAO,6BAA6B,MAAM,iCAAiC,CAAA;AAC3E,OAAO,6BAA6B,MAAM,iCAAiC,CAAA;AAC3E,OAAO,wBAAwB,MAAM,4BAA4B,CAAA;AAIjE,MAAM,mBAAmB,GAAG,QAAQ,CAAC,SAAS,SAAS,CAAC,EACtD,KAAK,GAGN;IACC,OAAO,CACL;QACE,oBAAC,6BAA6B,IAAC,KAAK,EAAE,KAAK,GAAI;QAC/C,oBAAC,6BAA6B,IAAC,KAAK,EAAE,KAAK,GAAI;QAC/C,oBAAC,wBAAwB,IAAC,KAAK,EAAE,KAAK,GAAI,CACzC,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,mBAAmB,CAAA"}

package/dist/AddHighlightModel/ProteinToGenomeClickHighlight.d.ts

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+import React from 'react';
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+type LGV = LinearGenomeViewModel;
+declare const ProteinToGenomeClickHighlight: ({ model, }: {
+    model: LGV;
+}) => React.JSX.Element | null;
+export default ProteinToGenomeClickHighlight;

package/dist/AddHighlightModel/ProteinToGenomeClickHighlight.js

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+import React from 'react';
+import { observer } from 'mobx-react';
+import { getSession } from '@jbrowse/core/util';
+import Highlight from './Highlight';
+const ProteinToGenomeClickHighlight = observer(function ({ model, }) {
+    const { assemblyManager, views } = getSession(model);
+    const { assemblyNames } = model;
+    const p = views.find(f => f.type === 'ProteinView');
+    const assembly = assemblyManager.get(assemblyNames[0]);
+    return assembly ? (React.createElement(React.Fragment, null, p?.clickGenomeHighlights.map((r, idx) => (React.createElement(Highlight, { key: `${JSON.stringify(r)}-${idx}}`, start: r.start, end: r.end, refName: r.refName, assemblyName: assemblyNames[0], model: model }))))) : null;
+});
+export default ProteinToGenomeClickHighlight;
+//# sourceMappingURL=ProteinToGenomeClickHighlight.js.map

package/dist/AddHighlightModel/ProteinToGenomeClickHighlight.js.map

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+{"version":3,"file":"ProteinToGenomeClickHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/ProteinToGenomeClickHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAI/C,OAAO,SAAS,MAAM,aAAa,CAAA;AAInC,MAAM,6BAA6B,GAAG,QAAQ,CAAC,UAAU,EACvD,KAAK,GAGN;IACC,MAAM,EAAE,eAAe,EAAE,KAAK,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACpD,MAAM,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAC/B,MAAM,CAAC,GAAG,KAAK,CAAC,IAAI,CAClB,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,aAAa,CACG,CAAA;IAClC,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,CAAA;IACtD,OAAO,QAAQ,CAAC,CAAC,CAAC,CAChB,0CACG,CAAC,EAAE,qBAAqB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE,CAAC,CACxC,oBAAC,SAAS,IACR,GAAG,EAAE,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,GAAG,GAAG,EACnC,KAAK,EAAE,CAAC,CAAC,KAAK,EACd,GAAG,EAAE,CAAC,CAAC,GAAG,EACV,OAAO,EAAE,CAAC,CAAC,OAAO,EAClB,YAAY,EAAE,aAAa,CAAC,CAAC,CAAC,EAC9B,KAAK,EAAE,KAAK,GACZ,CACH,CAAC,CACD,CACJ,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,6BAA6B,CAAA"}

package/dist/AddHighlightModel/ProteinToGenomeHoverHighlight.d.ts

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+import React from 'react';
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+type LGV = LinearGenomeViewModel;
+declare const ProteinToGenomeHoverHighlight: ({ model, }: {
+    model: LGV;
+}) => React.JSX.Element | null;
+export default ProteinToGenomeHoverHighlight;

package/dist/AddHighlightModel/ProteinToGenomeHoverHighlight.js

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+import React from 'react';
+import { observer } from 'mobx-react';
+import { getSession } from '@jbrowse/core/util';
+import Highlight from './Highlight';
+const ProteinToGenomeHoverHighlight = observer(function ({ model, }) {
+    const { assemblyManager, views } = getSession(model);
+    const { assemblyNames } = model;
+    const p = views.find(f => f.type === 'ProteinView');
+    const assembly = assemblyManager.get(assemblyNames[0]);
+    return assembly ? (React.createElement(React.Fragment, null, p?.hoverGenomeHighlights.map((r, idx) => (React.createElement(Highlight, { key: `${JSON.stringify(r)}-${idx}`, start: r.start, end: r.end, refName: r.refName, assemblyName: assemblyNames[0], model: model }))))) : null;
+});
+export default ProteinToGenomeHoverHighlight;
+//# sourceMappingURL=ProteinToGenomeHoverHighlight.js.map

package/dist/AddHighlightModel/ProteinToGenomeHoverHighlight.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"ProteinToGenomeHoverHighlight.js","sourceRoot":"","sources":["../../src/AddHighlightModel/ProteinToGenomeHoverHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAI/C,OAAO,SAAS,MAAM,aAAa,CAAA;AAInC,MAAM,6BAA6B,GAAG,QAAQ,CAAC,UAAU,EACvD,KAAK,GAGN;IACC,MAAM,EAAE,eAAe,EAAE,KAAK,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACpD,MAAM,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAC/B,MAAM,CAAC,GAAG,KAAK,CAAC,IAAI,CAClB,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,aAAa,CACG,CAAA;IAClC,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,CAAA;IACtD,OAAO,QAAQ,CAAC,CAAC,CAAC,CAChB,0CACG,CAAC,EAAE,qBAAqB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE,CAAC,CACxC,oBAAC,SAAS,IACR,GAAG,EAAE,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,GAAG,EAAE,EAClC,KAAK,EAAE,CAAC,CAAC,KAAK,EACd,GAAG,EAAE,CAAC,CAAC,GAAG,EACV,OAAO,EAAE,CAAC,CAAC,OAAO,EAClB,YAAY,EAAE,aAAa,CAAC,CAAC,CAAC,EAC9B,KAAK,EAAE,KAAK,GACZ,CACH,CAAC,CACD,CACJ,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,6BAA6B,CAAA"}

package/dist/AddHighlightModel/index.d.ts

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+import PluginManager from '@jbrowse/core/PluginManager';
+export default function AddHighlightModelF(pluginManager: PluginManager): void;

package/dist/AddHighlightModel/index.js

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+import React from 'react';
+// locals
+import HighlightComponents from './HighlightComponents';
+export default function AddHighlightModelF(pluginManager) {
+    pluginManager.addToExtensionPoint('LinearGenomeView-TracksContainerComponent', 
+    // @ts-expect-error
+    (rest = [], { model }) => {
+        return [
+            ...rest,
+            React.createElement(HighlightComponents, { key: "highlight_protein_viewer_protein3d", model: model }),
+        ];
+    });
+}
+//# sourceMappingURL=index.js.map

package/dist/AddHighlightModel/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AddHighlightModel/index.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAIzB,SAAS;AACT,OAAO,mBAAmB,MAAM,uBAAuB,CAAA;AAEvD,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,aAA4B;IACrE,aAAa,CAAC,mBAAmB,CAC/B,2CAA2C;IAC3C,mBAAmB;IACnB,CACE,OAA0B,EAAE,EAC5B,EAAE,KAAK,EAAoC,EAC3C,EAAE;QACF,OAAO;YACL,GAAG,IAAI;YACP,oBAAC,mBAAmB,IAClB,GAAG,EAAC,oCAAoC,EACxC,KAAK,EAAE,KAAK,GACZ;SACH,CAAA;IACH,CAAC,CACF,CAAA;AACH,CAAC"}

package/dist/AddHighlightModel/util.d.ts

@@ -0,0 +1,9 @@
+export declare const useStyles: (params: void, muiStyleOverridesParams?: {
+    props: Record<string, unknown>;
+    ownerState?: Record<string, unknown> | undefined;
+} | undefined) => {
+    classes: Record<"highlight" | "thinborder", string>;
+    theme: import("@mui/material").Theme;
+    css: import("tss-react").Css;
+    cx: import("tss-react").Cx;
+};

package/dist/AddHighlightModel/util.js

@@ -0,0 +1,17 @@
+import { makeStyles } from 'tss-react/mui';
+export const useStyles = makeStyles()({
+    highlight: {
+        height: '100%',
+        background: 'rgba(255,255,0,0.2)',
+        border: '1px solid rgba(50,50,0,0.2)',
+        position: 'absolute',
+        zIndex: 1000,
+        textAlign: 'center',
+        pointerEvents: 'none',
+        overflow: 'hidden',
+    },
+    thinborder: {
+        border: '1px solid black',
+    },
+});
+//# sourceMappingURL=util.js.map

package/dist/AddHighlightModel/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/AddHighlightModel/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,CAAC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IACpC,SAAS,EAAE;QACT,MAAM,EAAE,MAAM;QACd,UAAU,EAAE,qBAAqB;QACjC,MAAM,EAAE,6BAA6B;QACrC,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,IAAI;QACZ,SAAS,EAAE,QAAQ;QACnB,aAAa,EAAE,MAAM;QACrB,QAAQ,EAAE,QAAQ;KACnB;IACD,UAAU,EAAE;QACV,MAAM,EAAE,iBAAiB;KAC1B;CACF,CAAC,CAAA"}

package/dist/LaunchProteinView/calculateProteinSequence.d.ts

@@ -0,0 +1,28 @@
+import { Feature } from '@jbrowse/core/util';
+export interface Feat {
+    start: number;
+    end: number;
+    type: string;
+}
+export declare function stitch(subfeats: Feat[], sequence: string): string;
+export declare function calculateProteinSequence({ cds, sequence, codonTable, }: {
+    cds: Feat[];
+    sequence: string;
+    codonTable: Record<string, string>;
+}): string;
+export declare function revlist(list: Feat[], seqlen: number): {
+    start: number;
+    end: number;
+    type: string;
+}[];
+export declare function dedupe(list: Feat[]): Feat[];
+export declare function getProteinSequence({ feature, seq, }: {
+    seq: string;
+    feature: Feature;
+}): string;
+export declare function fetchProteinSeq({ feature, view, }: {
+    feature: Feature;
+    view: {
+        assemblyNames?: string[];
+    } | undefined;
+}): Promise<string | undefined>;

package/dist/LaunchProteinView/calculateProteinSequence.js

@@ -0,0 +1,77 @@
+import { getConf } from '@jbrowse/core/configuration';
+import { defaultCodonTable, generateCodonTable, getSession, revcom, } from '@jbrowse/core/util';
+export function stitch(subfeats, sequence) {
+    return subfeats.map(sub => sequence.slice(sub.start, sub.end)).join('');
+}
+export function calculateProteinSequence({ cds, sequence, codonTable, }) {
+    const str = stitch(cds, sequence);
+    let protein = '';
+    for (let i = 0; i < str.length; i += 3) {
+        // use & symbol for undefined codon, or partial slice
+        protein += codonTable[str.slice(i, i + 3)] || '&';
+    }
+    return protein;
+}
+export function revlist(list, seqlen) {
+    return list
+        .map(sub => ({
+        ...sub,
+        start: seqlen - sub.end,
+        end: seqlen - sub.start,
+    }))
+        .sort((a, b) => a.start - b.start);
+}
+// filter items if they have the same "ID" or location
+function getItemId(feat) {
+    return `${feat.start}-${feat.end}`;
+}
+// filters if successive elements share same start/end
+export function dedupe(list) {
+    return list.filter((item, pos, ary) => !pos || getItemId(item) !== getItemId(ary[pos - 1]));
+}
+export function getProteinSequence({ feature, seq, }) {
+    // @ts-expect-error
+    const f = feature.toJSON();
+    const cds = dedupe(f.subfeatures
+        .sort((a, b) => a.start - b.start)
+        .map(sub => ({
+        ...sub,
+        start: sub.start - f.start,
+        end: sub.end - f.start,
+    }))
+        .filter(f => f.type === 'CDS'));
+    return calculateProteinSequence({
+        cds: f.strand === -1 ? revlist(cds, seq.length) : cds,
+        sequence: f.strand === -1 ? revcom(seq) : seq,
+        codonTable: generateCodonTable(defaultCodonTable),
+    });
+}
+export async function fetchProteinSeq({ feature, view, }) {
+    const start = feature.get('start');
+    const end = feature.get('end');
+    const refName = feature.get('refName');
+    const session = getSession(view);
+    const { assemblyManager, rpcManager } = session;
+    const [assemblyName] = view?.assemblyNames ?? [];
+    const assembly = await assemblyManager.waitForAssembly(assemblyName);
+    if (!assembly) {
+        throw new Error('assembly not found');
+    }
+    const sessionId = 'getSequence';
+    const feats = await rpcManager.call(sessionId, 'CoreGetFeatures', {
+        adapterConfig: getConf(assembly, ['sequence', 'adapter']),
+        sessionId,
+        regions: [
+            {
+                start,
+                end,
+                refName: assembly.getCanonicalRefName(refName),
+                assemblyName,
+            },
+        ],
+    });
+    const [feat] = feats;
+    const seq = feat?.get('seq');
+    return seq ? getProteinSequence({ seq, feature }) : undefined;
+}
+//# sourceMappingURL=calculateProteinSequence.js.map

package/dist/LaunchProteinView/calculateProteinSequence.js.map

@@ -0,0 +1 @@
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package/dist/LaunchProteinView/components/AlphaFoldDBSearch.d.ts

@@ -0,0 +1,8 @@
+import React from 'react';
+import { AbstractTrackModel, Feature } from '@jbrowse/core/util';
+declare const AlphaFoldDBSearch: ({ feature, model, handleClose, }: {
+    feature: Feature;
+    model: AbstractTrackModel;
+    handleClose: () => void;
+}) => React.JSX.Element;
+export default AlphaFoldDBSearch;

package/dist/LaunchProteinView/components/AlphaFoldDBSearch.js

@@ -0,0 +1,71 @@
+import React, { useEffect, useState } from 'react';
+import { observer } from 'mobx-react';
+import { Button, DialogActions, DialogContent } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import { getContainingView, getSession, } from '@jbrowse/core/util';
+import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
+// locals
+import { getDisplayName, getGeneDisplayName, getId, getTranscriptDisplayName, getTranscriptFeatures, } from '../util';
+import TranscriptSelector from './TranscriptSelector';
+import HelpButton from './HelpButton';
+// hooks
+import useMyGeneInfo from '../useMyGeneInfo';
+import useAllSequences from '../useProteinSequences';
+import { useCheckAlphaFoldDBExistence } from './useCheckAlphaFoldDBExistence';
+import AlphaFoldDBSearchStatus from './AlphaFoldDBSearchStatus';
+const useStyles = makeStyles()(theme => ({
+    dialogContent: {
+        marginTop: theme.spacing(6),
+        width: '80em',
+    },
+}));
+const AlphaFoldDBSearch = observer(function AlphaFoldDBSearch({ feature, model, handleClose, }) {
+    const { classes } = useStyles();
+    const session = getSession(model);
+    // 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 options = getTranscriptFeatures(feature);
+    const [userSelection, setUserSelection] = useState();
+    const view = getContainingView(model);
+    const selectedTranscript = options.find(val => getId(val) === userSelection);
+    const { seqs, error: error2 } = useAllSequences({ feature, view });
+    const protein = seqs?.[userSelection ?? ''];
+    const { result: foundStructureId, error } = useMyGeneInfo({
+        id: selectedTranscript ? getDisplayName(selectedTranscript) : '',
+    });
+    useEffect(() => {
+        if (userSelection === undefined && seqs !== undefined) {
+            setUserSelection(options.find(f => !!seqs[f.id()])?.id());
+        }
+    }, [options, userSelection, seqs]);
+    const { success, loading, error: error3, } = useCheckAlphaFoldDBExistence({
+        foundStructureId,
+    });
+    const e = error || error2 || error3;
+    const url = `https://alphafold.ebi.ac.uk/files/AF-${foundStructureId}-F1-model_v4.cif`;
+    return (React.createElement(React.Fragment, null,
+        React.createElement(DialogContent, { className: classes.dialogContent },
+            e ? React.createElement(ErrorMessage, { error: e }) : null,
+            React.createElement("div", null,
+                "Look up AlphaFoldDB structure for given transcript ",
+                React.createElement(HelpButton, null)),
+            seqs ? (React.createElement(React.Fragment, null,
+                React.createElement(TranscriptSelector, { val: userSelection ?? '', setVal: setUserSelection, options: options, feature: feature, seqs: seqs }),
+                selectedTranscript ? (React.createElement(AlphaFoldDBSearchStatus, { foundStructureId: foundStructureId, selectedTranscript: selectedTranscript, success: success, loading: loading })) : null)) : (React.createElement("div", { style: { margin: 20 } },
+                React.createElement(LoadingEllipses, { message: "Loading protein sequences", variant: "h6" })))),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"),
+            React.createElement(Button, { variant: "contained", color: "primary", disabled: !foundStructureId || !protein || !selectedTranscript, onClick: () => {
+                    session.addView('ProteinView', {
+                        type: 'ProteinView',
+                        url,
+                        seq2: protein,
+                        feature: selectedTranscript?.toJSON(),
+                        connectedViewId: view.id,
+                        displayName: `Protein view ${getGeneDisplayName(feature)} - ${getTranscriptDisplayName(selectedTranscript)}`,
+                    });
+                    handleClose();
+                } }, "Submit"))));
+});
+export default AlphaFoldDBSearch;
+//# sourceMappingURL=AlphaFoldDBSearch.js.map

package/dist/LaunchProteinView/components/AlphaFoldDBSearch.js.map

@@ -0,0 +1 @@
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package/dist/LaunchProteinView/components/AlphaFoldDBSearchStatus.d.ts

@@ -0,0 +1,8 @@
+import React from 'react';
+import { Feature } from '@jbrowse/core/util';
+export default function AlphaFoldDBSearchStatus({ foundStructureId, selectedTranscript, success, loading, }: {
+    foundStructureId?: string;
+    selectedTranscript: Feature;
+    success: boolean;
+    loading: boolean;
+}): React.JSX.Element;

package/dist/LaunchProteinView/components/AlphaFoldDBSearchStatus.js

@@ -0,0 +1,19 @@
+import React from 'react';
+import { Link, Typography } from '@mui/material';
+import { LoadingEllipses } from '@jbrowse/core/ui';
+// locals
+import { getDisplayName } from '../util';
+export default function AlphaFoldDBSearchStatus({ foundStructureId, selectedTranscript, success, loading, }) {
+    return !foundStructureId ? (React.createElement(Typography, null,
+        "Searching ",
+        getDisplayName(selectedTranscript),
+        " for UniProt ID")) : (React.createElement(React.Fragment, null,
+        React.createElement(Typography, null,
+            "Found Uniprot ID: ",
+            foundStructureId),
+        loading ? (React.createElement(LoadingEllipses, { title: "Looking up structure in AlphaFoldDB" })) : success ? (React.createElement(Typography, null, "Found structure in AlphaFoldDB")) : (React.createElement(Typography, null,
+            "No structure found for this UniProtID in AlphaFoldDB",
+            ' ',
+            React.createElement(Link, { target: "_blank", href: `https://alphafold.ebi.ac.uk/search/text/${foundStructureId}` }, "(search for results)")))));
+}
+//# sourceMappingURL=AlphaFoldDBSearchStatus.js.map

package/dist/LaunchProteinView/components/AlphaFoldDBSearchStatus.js.map

@@ -0,0 +1 @@
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package/dist/LaunchProteinView/components/HelpButton.d.ts

@@ -0,0 +1,2 @@
+import React from 'react';
+export default function HelpButton(): React.JSX.Element;

package/dist/LaunchProteinView/components/HelpButton.js

@@ -0,0 +1,15 @@
+import React, { Suspense, lazy, useState } from 'react';
+import { IconButton } from '@mui/material';
+// icons
+import Help from '@mui/icons-material/Help';
+// lazies
+const HelpDialog = lazy(() => import('./HelpDialog'));
+export default function HelpButton() {
+    const [show, setShow] = useState(false);
+    return (React.createElement(React.Fragment, null,
+        React.createElement(IconButton, { onClick: () => setShow(true) },
+            React.createElement(Help, null)),
+        show ? (React.createElement(Suspense, { fallback: null },
+            React.createElement(HelpDialog, { handleClose: () => setShow(false) }))) : null));
+}
+//# sourceMappingURL=HelpButton.js.map

package/dist/LaunchProteinView/components/HelpButton.js.map

@@ -0,0 +1 @@
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package/dist/LaunchProteinView/components/HelpDialog.d.ts

@@ -0,0 +1,4 @@
+import React from 'react';
+export default function HelpDialog({ handleClose, }: {
+    handleClose: () => void;
+}): React.JSX.Element;

package/dist/LaunchProteinView/components/HelpDialog.js

@@ -0,0 +1,16 @@
+import React from 'react';
+import { Button, DialogActions, DialogContent, Divider, Typography, } from '@mui/material';
+import { Dialog } from '@jbrowse/core/ui';
+function Typography2({ children }) {
+    return React.createElement(Typography, { style: { margin: 4 } }, children);
+}
+export default function HelpDialog({ handleClose, }) {
+    return (React.createElement(Dialog, { open: true, maxWidth: "lg", onClose: handleClose, title: "Protein alignment" },
+        React.createElement(DialogContent, null,
+            React.createElement(Typography2, null, "This process searches mygene.info for the transcript ID, in order to retrieve the UniProt ID associated with a given transcript ID. Then, it uses that UniProt ID to lookup the structure in AlphaFoldDB because every UniProt ID has been processed by AlphaFold."),
+            React.createElement(Typography2, null, "If you run into challenges with this workflow e.g. your transcripts are not being found in mygene.info and you are interested in using this plugin, contact colin.diesh@gmail.com")),
+        React.createElement(Divider, null),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { onClick: () => handleClose(), color: "primary" }, "Close"))));
+}
+//# sourceMappingURL=HelpDialog.js.map

package/dist/LaunchProteinView/components/HelpDialog.js.map

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package/dist/LaunchProteinView/components/LaunchProteinViewDialog.d.ts

@@ -0,0 +1,7 @@
+import React from 'react';
+import { AbstractTrackModel, Feature } from '@jbrowse/core/util';
+export default function LaunchProteinViewDialog({ handleClose, feature, model, }: {
+    handleClose: () => void;
+    feature: Feature;
+    model: AbstractTrackModel;
+}): React.JSX.Element;

package/dist/LaunchProteinView/components/LaunchProteinViewDialog.js

@@ -0,0 +1,23 @@
+import React, { useState } from 'react';
+import { Dialog } from '@jbrowse/core/ui';
+import { Tab, Tabs } from '@mui/material';
+// locals
+import PreLoadedStructureMapping from './PreLoadedStructureMapping';
+import AlphaFoldDBSearch from './AlphaFoldDBSearch';
+import UserProvidedStructure from './UserProvidedStructure';
+import TabPanel from './TabPanel';
+export default function LaunchProteinViewDialog({ handleClose, feature, model, }) {
+    const [choice, setChoice] = useState(0);
+    return (React.createElement(Dialog, { maxWidth: "xl", title: "Launch protein view", onClose: () => handleClose(), open: true },
+        React.createElement(Tabs, { value: choice, onChange: (_, val) => setChoice(val) },
+            React.createElement(Tab, { value: 0, label: "AlphaFoldDB search" }),
+            React.createElement(Tab, { value: 1, label: "Manual" }),
+            React.createElement(Tab, { value: 2, label: "Pre-configured" })),
+        React.createElement(TabPanel, { value: choice, index: 0 },
+            React.createElement(AlphaFoldDBSearch, { model: model, feature: feature, handleClose: handleClose })),
+        React.createElement(TabPanel, { value: choice, index: 1 },
+            React.createElement(UserProvidedStructure, { model: model, feature: feature, handleClose: handleClose })),
+        React.createElement(TabPanel, { value: choice, index: 2 },
+            React.createElement(PreLoadedStructureMapping, { feature: feature, model: model, handleClose: handleClose }))));
+}
+//# sourceMappingURL=LaunchProteinViewDialog.js.map

package/dist/LaunchProteinView/components/LaunchProteinViewDialog.js.map

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package/dist/LaunchProteinView/components/PreLoadedStructureMapping.d.ts

@@ -0,0 +1,8 @@
+import React from 'react';
+import { AbstractTrackModel, Feature } from '@jbrowse/core/util';
+declare const AutoForm: ({ model, feature, handleClose, }: {
+    model: AbstractTrackModel;
+    feature: Feature;
+    handleClose: () => void;
+}) => React.JSX.Element;
+export default AutoForm;