molstar
Version:
A comprehensive macromolecular library.
218 lines (217 loc) • 11.4 kB
JavaScript
"use strict";
/**
* Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Adam Midlik <midlik@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.MolViewSpec = void 0;
const behavior_1 = require("../../mol-plugin/behavior/behavior.js");
const mol_state_1 = require("../../mol-state/index.js");
const mol_task_1 = require("../../mol-task/index.js");
const file_1 = require("../../mol-util/file.js");
const param_definition_1 = require("../../mol-util/param-definition.js");
const annotation_color_theme_1 = require("./components/annotation-color-theme.js");
const representation_1 = require("./components/annotation-label/representation.js");
const annotation_prop_1 = require("./components/annotation-prop.js");
const annotation_tooltips_prop_1 = require("./components/annotation-tooltips-prop.js");
const representation_2 = require("./components/custom-label/representation.js");
const custom_tooltips_prop_1 = require("./components/custom-tooltips-prop.js");
const formats_1 = require("./components/formats.js");
const is_mvs_model_prop_1 = require("./components/is-mvs-model-prop.js");
const multilayer_color_theme_1 = require("./components/multilayer-color-theme.js");
const load_1 = require("./load.js");
const mvs_data_1 = require("./mvs-data.js");
/** Registers everything needed for loading MolViewSpec files */
exports.MolViewSpec = behavior_1.PluginBehavior.create({
name: 'molviewspec',
category: 'misc',
display: {
name: 'MolViewSpec',
description: 'MolViewSpec extension',
},
ctor: class extends behavior_1.PluginBehavior.Handler {
constructor() {
super(...arguments);
this.registrables = {
customModelProperties: [
is_mvs_model_prop_1.IsMVSModelProvider,
annotation_prop_1.MVSAnnotationsProvider,
],
customStructureProperties: [
custom_tooltips_prop_1.CustomTooltipsProvider,
annotation_tooltips_prop_1.MVSAnnotationTooltipsProvider,
],
representations: [
representation_2.CustomLabelRepresentationProvider,
representation_1.MVSAnnotationLabelRepresentationProvider,
],
colorThemes: [
annotation_color_theme_1.MVSAnnotationColorThemeProvider,
(0, multilayer_color_theme_1.makeMultilayerColorThemeProvider)(this.ctx.representation.structure.themes.colorThemeRegistry),
],
lociLabels: [
custom_tooltips_prop_1.CustomTooltipsLabelProvider,
annotation_tooltips_prop_1.MVSAnnotationTooltipsLabelProvider,
],
dragAndDropHandlers: [
MVSDragAndDropHandler,
],
dataFormats: [
{ name: 'MVSJ', provider: formats_1.MVSJFormatProvider },
{ name: 'MVSX', provider: formats_1.MVSXFormatProvider },
],
actions: [
formats_1.LoadMvsData,
]
};
}
register() {
var _a, _b, _c, _d, _e, _f, _g, _h;
for (const prop of (_a = this.registrables.customModelProperties) !== null && _a !== void 0 ? _a : []) {
this.ctx.customModelProperties.register(prop, this.params.autoAttach);
}
for (const prop of (_b = this.registrables.customStructureProperties) !== null && _b !== void 0 ? _b : []) {
this.ctx.customStructureProperties.register(prop, this.params.autoAttach);
}
for (const repr of (_c = this.registrables.representations) !== null && _c !== void 0 ? _c : []) {
this.ctx.representation.structure.registry.add(repr);
}
for (const theme of (_d = this.registrables.colorThemes) !== null && _d !== void 0 ? _d : []) {
this.ctx.representation.structure.themes.colorThemeRegistry.add(theme);
}
for (const provider of (_e = this.registrables.lociLabels) !== null && _e !== void 0 ? _e : []) {
this.ctx.managers.lociLabels.addProvider(provider);
}
for (const handler of (_f = this.registrables.dragAndDropHandlers) !== null && _f !== void 0 ? _f : []) {
this.ctx.managers.dragAndDrop.addHandler(handler.name, handler.handle);
}
for (const format of (_g = this.registrables.dataFormats) !== null && _g !== void 0 ? _g : []) {
this.ctx.dataFormats.add(format.name, format.provider);
}
for (const action of (_h = this.registrables.actions) !== null && _h !== void 0 ? _h : []) {
this.ctx.state.data.actions.add(action);
}
this.ctx.state.data.registerRefResolver('mvs', (state, ref) => {
const tagSearch = mol_state_1.StateTree.doPreOrder(state.tree, state.tree.root, { ref, ret: undefined }, (n, _, s) => {
var _a, _b;
if (!n.tags)
return;
for (const t of n.tags) {
if (t.startsWith('mvs-ref:') && t.substring(8) === ref) {
s.ret = (_b = (_a = state.cells.get(n.ref)) === null || _a === void 0 ? void 0 : _a.obj) === null || _b === void 0 ? void 0 : _b.data;
return false;
}
}
});
return tagSearch.ret;
});
this.ctx.managers.markdownExtensions.registerRefResolver('mvs', (plugin, refs) => {
const mvsRefs = new Set(refs.map(ref => `mvs-ref:${ref}`));
return mol_state_1.StateTree.doPreOrder(plugin.state.data.tree, plugin.state.data.tree.root, { mvsRefs, plugin, cells: [] }, (n, _, s) => {
if (!n.tags)
return;
for (const tag of n.tags) {
if (!s.mvsRefs.has(tag))
continue;
const cell = s.plugin.state.data.cells.get(n.ref);
if (cell) {
s.cells.push(cell);
break;
}
}
}).cells;
});
this.ctx.managers.markdownExtensions.registerUriResolver('mvs', (plugin, uri) => {
const { assets } = plugin.managers.asset;
const asset = assets.find(a => a.file.name === uri);
if (!asset) {
return undefined;
}
try {
return (0, file_1.fileToDataUri)(asset.file);
}
catch (e) {
console.error(`MVS: Failed to convert asset file to data URI for '${uri}'`, e);
return undefined;
}
});
}
update(p) {
var _a, _b;
const updated = this.params.autoAttach !== p.autoAttach;
this.params.autoAttach = p.autoAttach;
for (const prop of (_a = this.registrables.customModelProperties) !== null && _a !== void 0 ? _a : []) {
this.ctx.customModelProperties.setDefaultAutoAttach(prop.descriptor.name, this.params.autoAttach);
}
for (const prop of (_b = this.registrables.customStructureProperties) !== null && _b !== void 0 ? _b : []) {
this.ctx.customStructureProperties.setDefaultAutoAttach(prop.descriptor.name, this.params.autoAttach);
}
return updated;
}
unregister() {
var _a, _b, _c, _d, _e, _f, _g, _h;
for (const prop of (_a = this.registrables.customModelProperties) !== null && _a !== void 0 ? _a : []) {
this.ctx.customModelProperties.unregister(prop.descriptor.name);
}
for (const prop of (_b = this.registrables.customStructureProperties) !== null && _b !== void 0 ? _b : []) {
this.ctx.customStructureProperties.unregister(prop.descriptor.name);
}
for (const repr of (_c = this.registrables.representations) !== null && _c !== void 0 ? _c : []) {
this.ctx.representation.structure.registry.remove(repr);
}
for (const theme of (_d = this.registrables.colorThemes) !== null && _d !== void 0 ? _d : []) {
this.ctx.representation.structure.themes.colorThemeRegistry.remove(theme);
}
for (const labelProvider of (_e = this.registrables.lociLabels) !== null && _e !== void 0 ? _e : []) {
this.ctx.managers.lociLabels.removeProvider(labelProvider);
}
for (const handler of (_f = this.registrables.dragAndDropHandlers) !== null && _f !== void 0 ? _f : []) {
this.ctx.managers.dragAndDrop.removeHandler(handler.name);
}
for (const format of (_g = this.registrables.dataFormats) !== null && _g !== void 0 ? _g : []) {
this.ctx.dataFormats.remove(format.name);
}
for (const action of (_h = this.registrables.actions) !== null && _h !== void 0 ? _h : []) {
this.ctx.state.data.actions.remove(action);
}
this.ctx.state.data.removeRefResolver('mvs');
this.ctx.managers.markdownExtensions.removeRefResolver('mvs');
}
},
params: () => ({
autoAttach: param_definition_1.ParamDefinition.Boolean(false),
})
});
/** DragAndDropHandler handler for `.mvsj` and `.mvsx` files */
const MVSDragAndDropHandler = {
name: 'mvs-mvsj-mvsx',
/** Load .mvsj and .mvsx files. Delete previous plugin state before loading.
* If multiple files are provided, merge their MVS data into one state.
* Return `true` if at least one file has been loaded. */
async handle(files, plugin) {
let applied = false;
for (const file of files) {
if (file.name.toLowerCase().endsWith('.mvsj')) {
const task = mol_task_1.Task.create('Load MVSJ file', async (ctx) => {
const data = await file.text();
const mvsData = mvs_data_1.MVSData.fromMVSJ(data);
await (0, load_1.loadMVS)(plugin, mvsData, { sanityChecks: true, appendSnapshots: applied, sourceUrl: undefined });
});
await plugin.runTask(task);
applied = true;
}
if (file.name.toLowerCase().endsWith('.mvsx')) {
const task = mol_task_1.Task.create('Load MVSX file', async (ctx) => {
const buffer = await file.arrayBuffer();
const array = new Uint8Array(buffer);
const parsed = await (0, formats_1.loadMVSX)(plugin, ctx, array);
await (0, load_1.loadMVS)(plugin, parsed.mvsData, { sanityChecks: true, appendSnapshots: applied, sourceUrl: parsed.sourceUrl });
});
await plugin.runTask(task);
applied = true;
}
}
return applied;
},
};