jbrowse-plugin-protein3d 0.0.2

package/dist/ProteinView/util.d.ts

@@ -0,0 +1,19 @@
+import { Feature } from '@jbrowse/core/util';
+import { Structure } from 'molstar/lib/mol-model/structure';
+export declare function checkHovered(hovered: unknown): hovered is {
+    hoverFeature: Feature;
+    hoverPosition: {
+        coord: number;
+        refName: string;
+    };
+};
+export declare function getMolstarStructureSelection({ structure, selectedResidue, }: {
+    structure: Structure;
+    selectedResidue: number;
+}): import("molstar/lib/mol-model/structure").StructureSelection;
+export declare function toStr(r: {
+    structureSeqPos: number;
+    code?: string;
+    chain?: string;
+}): string;
+export declare function invertMap(arg: Record<number, number | undefined>): any;

package/dist/ProteinView/util.js

@@ -0,0 +1,32 @@
+import { Script } from 'molstar/lib/mol-script/script';
+import { proteinAbbreviationMapping } from './proteinAbbreviationMapping';
+export function checkHovered(hovered) {
+    return (!!hovered &&
+        typeof hovered == 'object' &&
+        'hoverFeature' in hovered &&
+        'hoverPosition' in hovered);
+}
+export function getMolstarStructureSelection({ structure, selectedResidue, }) {
+    return Script.getStructureSelection(Q => Q.struct.generator.atomGroups({
+        'residue-test': Q.core.rel.eq([
+            Q.struct.atomProperty.macromolecular.label_seq_id(),
+            selectedResidue,
+        ]),
+        'group-by': Q.struct.atomProperty.macromolecular.residueKey(),
+    }), structure);
+}
+export function toStr(r) {
+    return [
+        `Position: ${r.structureSeqPos}`,
+        r.code
+            ? `Letter: ${r.code} (${proteinAbbreviationMapping[r.code]?.singleLetterCode})`
+            : '',
+        r.chain ? `Chain: ${r.chain}` : '',
+    ]
+        .filter(f => !!f)
+        .join(', ');
+}
+export function invertMap(arg) {
+    return Object.fromEntries(Object.entries(arg).map(([a, b]) => [b, a]));
+}
+//# sourceMappingURL=util.js.map

package/dist/ProteinView/util.js.map

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package/dist/fetchUtils.d.ts

@@ -0,0 +1,5 @@
+export declare function myfetch(url: string, args?: RequestInit): Promise<Response>;
+export declare function textfetch(url: string, args?: RequestInit): Promise<string>;
+export declare function jsonfetch(url: string, args?: RequestInit): Promise<any>;
+export declare function abfetch(url: string): Promise<ArrayBuffer>;
+export declare function timeout(time: number): Promise<unknown>;

package/dist/fetchUtils.js

@@ -0,0 +1,23 @@
+export async function myfetch(url, args) {
+    const response = await fetch(url, args);
+    if (!response.ok) {
+        throw new Error(`HTTP ${response.status} fetching ${url} ${await response.text()}`);
+    }
+    return response;
+}
+export async function textfetch(url, args) {
+    const response = await myfetch(url, args);
+    return response.text();
+}
+export async function jsonfetch(url, args) {
+    const response = await myfetch(url, args);
+    return response.json();
+}
+export async function abfetch(url) {
+    const res = await myfetch(url);
+    return res.arrayBuffer();
+}
+export function timeout(time) {
+    return new Promise(res => setTimeout(res, time));
+}
+//# sourceMappingURL=fetchUtils.js.map

package/dist/fetchUtils.js.map

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package/dist/genomeToTranscriptMapping.d.ts

@@ -0,0 +1,7 @@
+import { Feature } from '@jbrowse/core/util';
+export declare function genomeToTranscriptMapping(feature: Feature): {
+    g2p: Record<number, number | undefined>;
+    p2g: Record<number, number | undefined>;
+    refName: string;
+    strand: number;
+};

package/dist/genomeToTranscriptMapping.js

@@ -0,0 +1,36 @@
+// see similar function in msaview plugin
+export function genomeToTranscriptMapping(feature) {
+    const strand = feature.get('strand');
+    const refName = feature.get('refName');
+    const subs = feature.children() ?? [];
+    const cds = subs
+        .filter(f => f.get('type') === 'CDS')
+        .sort((a, b) => strand * (a.get('start') - b.get('start')));
+    const g2p = {};
+    const p2g = {};
+    let proteinCounter = 0;
+    if (strand !== -1) {
+        for (const f of cds) {
+            for (let genomePos = f.get('start'); genomePos < f.get('end'); genomePos++) {
+                const proteinPos = Math.floor(proteinCounter++ / 3);
+                g2p[genomePos] = proteinPos;
+                if (!p2g[proteinPos]) {
+                    p2g[proteinPos] = genomePos;
+                }
+            }
+        }
+    }
+    else {
+        for (const f of cds) {
+            for (let genomePos = f.get('end'); genomePos > f.get('start'); genomePos--) {
+                const proteinPos = Math.floor(proteinCounter++ / 3);
+                g2p[genomePos] = proteinPos;
+                if (!p2g[proteinPos]) {
+                    p2g[proteinPos] = genomePos;
+                }
+            }
+        }
+    }
+    return { g2p, p2g, refName, strand };
+}
+//# sourceMappingURL=genomeToTranscriptMapping.js.map

package/dist/genomeToTranscriptMapping.js.map

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package/dist/index.d.ts

@@ -0,0 +1,8 @@
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default class ProteinViewer extends Plugin {
+    name: string;
+    version: any;
+    install(pluginManager: PluginManager): void;
+    configure(_pluginManager: PluginManager): void;
+}

package/dist/index.js

@@ -0,0 +1,26 @@
+import Plugin from '@jbrowse/core/Plugin';
+import { types } from 'mobx-state-tree';
+// locals
+import { version } from '../package.json';
+import ProteinViewF from './ProteinView';
+import LaunchProteinViewF from './LaunchProteinView';
+import AddHighlightModelF from './AddHighlightModel';
+import ProteinModelSessionExtension from './ProteinModelSessionExtension';
+export default class ProteinViewer extends Plugin {
+    name = 'ProteinViewer';
+    version = version;
+    install(pluginManager) {
+        ProteinViewF(pluginManager);
+        LaunchProteinViewF(pluginManager);
+        AddHighlightModelF(pluginManager);
+        pluginManager.addToExtensionPoint('Core-extendSession', session => {
+            return types.compose(types.model({
+                proteinModel: types.optional(ProteinModelSessionExtension, {}),
+            }), 
+            // @ts-expect-error
+            session);
+        });
+    }
+    configure(_pluginManager) { }
+}
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

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