molstar 3.26.0 → 3.28.0

package/lib/commonjs/extensions/meshes/mesh-streaming/behavior.js

@@ -0,0 +1,379 @@
+"use strict";
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.MeshStreaming = exports.BACKGROUND_SEGMENT_VOLUME_THRESHOLD = exports.NO_SEGMENT = void 0;
+var tslib_1 = require("tslib");
+var rxjs_1 = require("rxjs");
+var cif_1 = require("../../../mol-io/reader/cif");
+var geometry_1 = require("../../../mol-math/geometry");
+var objects_1 = require("../../../mol-plugin-state/objects");
+var behavior_1 = require("../../../mol-plugin/behavior");
+var commands_1 = require("../../../mol-plugin/commands");
+var mol_util_1 = require("../../../mol-util");
+var assets_1 = require("../../../mol-util/assets");
+var names_1 = require("../../../mol-util/color/names");
+var param_definition_1 = require("../../../mol-util/param-definition");
+var choice_1 = require("../choice");
+var mesh_extension_1 = require("../mesh-extension");
+var metadata_1 = require("../metadata");
+var DEFAULT_SEGMENT_NAME = 'Untitled segment';
+var DEFAULT_SEGMENT_COLOR = names_1.ColorNames.lightgray;
+exports.NO_SEGMENT = -1;
+/** Maximum (worst) detail level available in GUI (TODO set actual maximum possible value) */
+var MAX_DETAIL = 10;
+var DEFAULT_DETAIL = 7; // TODO decide a reasonable default
+/** Segments whose bounding box volume is above this value (relative to the overall bounding box) are considered as background segments */
+exports.BACKGROUND_SEGMENT_VOLUME_THRESHOLD = 0.5;
+// const DEBUG_IGNORED_SEGMENTS = new Set([13, 15]); // TODO remove
+var DEBUG_IGNORED_SEGMENTS = new Set(); // TODO remove
+var MeshStreaming = /** @class */ (function (_super) {
+    tslib_1.__extends(MeshStreaming, _super);
+    function MeshStreaming() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
+    return MeshStreaming;
+}(objects_1.PluginStateObject.CreateBehavior({ name: 'Mesh Streaming' })));
+exports.MeshStreaming = MeshStreaming;
+(function (MeshStreaming) {
+    var Params;
+    (function (Params) {
+        Params.ViewTypeChoice = new choice_1.Choice({ off: 'Off', select: 'Select', all: 'All' }, 'select'); // TODO add camera target?
+        function create(options) {
+            return {
+                view: param_definition_1.ParamDefinition.MappedStatic('select', {
+                    'off': param_definition_1.ParamDefinition.Group({}),
+                    'select': param_definition_1.ParamDefinition.Group({
+                        baseDetail: param_definition_1.ParamDefinition.Numeric(DEFAULT_DETAIL, { min: 1, max: MAX_DETAIL, step: 1 }, { description: 'Detail level for the non-selected segments (lower number = better)' }),
+                        focusDetail: param_definition_1.ParamDefinition.Numeric(1, { min: 1, max: MAX_DETAIL, step: 1 }, { description: 'Detail level for the selected segment (lower number = better)' }),
+                        selectedSegment: param_definition_1.ParamDefinition.Numeric(exports.NO_SEGMENT, {}, { isHidden: true }),
+                    }, { isFlat: true }),
+                    'all': param_definition_1.ParamDefinition.Group({
+                        detail: param_definition_1.ParamDefinition.Numeric(DEFAULT_DETAIL, { min: 1, max: MAX_DETAIL, step: 1 }, { description: 'Detail level for all segments (lower number = better)' })
+                    }, { isFlat: true }),
+                }, { description: '"Off" hides all segments. \n"Select" shows all segments in lower detail, clicked segment in better detail. "All" shows all segment in the same level.' }),
+            };
+        }
+        Params.create = create;
+        function copyValues(params) {
+            return {
+                view: {
+                    name: params.view.name,
+                    params: tslib_1.__assign({}, params.view.params),
+                }
+            };
+        }
+        Params.copyValues = copyValues;
+        function valuesEqual(p, q) {
+            if (p.view.name !== q.view.name)
+                return false;
+            for (var key in p.view.params) {
+                if (p.view.params[key] !== q.view.params[key])
+                    return false;
+            }
+            return true;
+        }
+        Params.valuesEqual = valuesEqual;
+        function detailsEqual(p, q) {
+            switch (p.view.name) {
+                case 'off':
+                    return q.view.name === 'off';
+                case 'select':
+                    return q.view.name === 'select' && p.view.params.baseDetail === q.view.params.baseDetail && p.view.params.focusDetail === q.view.params.focusDetail;
+                case 'all':
+                    return q.view.name === 'all' && p.view.params.detail === q.view.params.detail;
+                default:
+                    throw new Error('Not implemented');
+            }
+        }
+        Params.detailsEqual = detailsEqual;
+    })(Params = MeshStreaming.Params || (MeshStreaming.Params = {}));
+    var VisualInfo;
+    (function (VisualInfo) {
+        VisualInfo.DetailTypes = ['low', 'high'];
+        function tagFor(segmentId, detail) {
+            return "".concat(detail, "-").concat(segmentId);
+        }
+        VisualInfo.tagFor = tagFor;
+    })(VisualInfo = MeshStreaming.VisualInfo || (MeshStreaming.VisualInfo = {}));
+    var Behavior = /** @class */ (function (_super) {
+        tslib_1.__extends(Behavior, _super);
+        function Behavior(plugin, data, params) {
+            var _this = _super.call(this, plugin, params) || this;
+            _this.ref = '';
+            _this.backgroundSegments = {};
+            _this.focusObservable = _this.plugin.behaviors.interaction.click.pipe(// QUESTION is this OK way to get focused segment?
+            (0, rxjs_1.map)(function (evt) { return evt.current.loci; }), (0, rxjs_1.map)(function (loci) { return (loci.kind === 'group-loci') ? loci.shape.sourceData : null; }), (0, rxjs_1.map)(function (data) { return ((data === null || data === void 0 ? void 0 : data.ownerId) === _this.id) ? data : null; }), // do not process shapes created by others
+            (0, rxjs_1.distinctUntilChanged)(function (old, current) { return (old === null || old === void 0 ? void 0 : old.segmentId) === (current === null || current === void 0 ? void 0 : current.segmentId); }));
+            _this.focusSubscription = undefined;
+            _this.backgroundSegmentsInitialized = false;
+            _this.id = mol_util_1.UUID.create22();
+            _this.parentData = data;
+            return _this;
+        }
+        Behavior.prototype.register = function (ref) {
+            this.ref = ref;
+        };
+        Behavior.prototype.unregister = function () {
+            if (this.focusSubscription) {
+                this.focusSubscription.unsubscribe();
+                this.focusSubscription = undefined;
+            }
+            // TODO empty cache here (if used)
+        };
+        Behavior.prototype.selectSegment = function (segmentId) {
+            if (this.params.view.name === 'select') {
+                if (this.params.view.params.selectedSegment === segmentId)
+                    return;
+                var newParams = Params.copyValues(this.params);
+                if (newParams.view.name === 'select') {
+                    newParams.view.params.selectedSegment = segmentId;
+                }
+                var state = this.plugin.state.data;
+                var update = state.build().to(this.ref).update(newParams);
+                commands_1.PluginCommands.State.Update(this.plugin, { state: state, tree: update, options: { doNotUpdateCurrent: true } });
+            }
+        };
+        Behavior.prototype.update = function (params) {
+            return tslib_1.__awaiter(this, void 0, void 0, function () {
+                var oldParams, response, _a, _b;
+                var _this = this;
+                return tslib_1.__generator(this, function (_c) {
+                    switch (_c.label) {
+                        case 0:
+                            oldParams = this.params;
+                            this.params = params;
+                            if (!!this.metadata) return [3 /*break*/, 3];
+                            return [4 /*yield*/, fetch(this.getMetadataUrl())];
+                        case 1:
+                            response = _c.sent();
+                            _a = this;
+                            return [4 /*yield*/, response.json()];
+                        case 2:
+                            _a.metadata = _c.sent();
+                            _c.label = 3;
+                        case 3:
+                            if (!this.visuals) {
+                                this.initVisualInfos();
+                            }
+                            else if (!Params.detailsEqual(this.params, oldParams)) {
+                                this.updateVisualInfoDetails();
+                            }
+                            _b = params.view.name;
+                            switch (_b) {
+                                case 'off': return [3 /*break*/, 4];
+                                case 'select': return [3 /*break*/, 6];
+                                case 'all': return [3 /*break*/, 8];
+                            }
+                            return [3 /*break*/, 10];
+                        case 4: return [4 /*yield*/, this.disableVisuals()];
+                        case 5:
+                            _c.sent();
+                            return [3 /*break*/, 11];
+                        case 6: return [4 /*yield*/, this.enableVisuals(params.view.params.selectedSegment)];
+                        case 7:
+                            _c.sent();
+                            return [3 /*break*/, 11];
+                        case 8: return [4 /*yield*/, this.enableVisuals()];
+                        case 9:
+                            _c.sent();
+                            return [3 /*break*/, 11];
+                        case 10: throw new Error('Not implemented');
+                        case 11:
+                            if (params.view.name !== 'off' && !this.backgroundSegmentsInitialized) {
+                                this.guessBackgroundSegments();
+                                this.backgroundSegmentsInitialized = true;
+                            }
+                            if (params.view.name === 'select' && !this.focusSubscription) {
+                                this.focusSubscription = this.subscribeObservable(this.focusObservable, function (data) { var _a; _this.selectSegment((_a = data === null || data === void 0 ? void 0 : data.segmentId) !== null && _a !== void 0 ? _a : exports.NO_SEGMENT); });
+                            }
+                            else if (params.view.name !== 'select' && this.focusSubscription) {
+                                this.focusSubscription.unsubscribe();
+                                this.focusSubscription = undefined;
+                            }
+                            return [2 /*return*/, true];
+                    }
+                });
+            });
+        };
+        Behavior.prototype.getMetadataUrl = function () {
+            return "".concat(this.parentData.serverUrl, "/").concat(this.parentData.source, "/").concat(this.parentData.entryId, "/metadata");
+        };
+        Behavior.prototype.getMeshUrl = function (segment, detail) {
+            return "".concat(this.parentData.serverUrl, "/").concat(this.parentData.source, "/").concat(this.parentData.entryId, "/mesh_bcif/").concat(segment, "/").concat(detail);
+        };
+        Behavior.prototype.initVisualInfos = function () {
+            var _a, _b, _c, _d;
+            var namesAndColors = metadata_1.Metadata.namesAndColorsBySegment(this.metadata);
+            var visuals = {};
+            for (var _i = 0, _e = metadata_1.Metadata.meshSegments(this.metadata); _i < _e.length; _i++) {
+                var segid = _e[_i];
+                if (DEBUG_IGNORED_SEGMENTS.has(segid))
+                    continue;
+                var name_1 = (_b = (_a = namesAndColors[segid]) === null || _a === void 0 ? void 0 : _a.name) !== null && _b !== void 0 ? _b : DEFAULT_SEGMENT_NAME;
+                var color = (_d = (_c = namesAndColors[segid]) === null || _c === void 0 ? void 0 : _c.color) !== null && _d !== void 0 ? _d : DEFAULT_SEGMENT_COLOR;
+                for (var _f = 0, _g = VisualInfo.DetailTypes; _f < _g.length; _f++) {
+                    var detailType = _g[_f];
+                    var visual = {
+                        tag: VisualInfo.tagFor(segid, detailType),
+                        segmentId: segid,
+                        segmentName: name_1,
+                        detailType: detailType,
+                        detail: -1,
+                        color: color,
+                        visible: false,
+                        data: undefined,
+                    };
+                    visuals[visual.tag] = visual;
+                }
+            }
+            this.visuals = visuals;
+            this.updateVisualInfoDetails();
+        };
+        Behavior.prototype.updateVisualInfoDetails = function () {
+            var highDetail;
+            var lowDetail;
+            switch (this.params.view.name) {
+                case 'off':
+                    lowDetail = undefined;
+                    highDetail = undefined;
+                    break;
+                case 'select':
+                    lowDetail = this.params.view.params.baseDetail;
+                    highDetail = this.params.view.params.focusDetail;
+                    break;
+                case 'all':
+                    lowDetail = this.params.view.params.detail;
+                    highDetail = undefined;
+                    break;
+            }
+            for (var tag in this.visuals) {
+                var visual = this.visuals[tag];
+                var preferredDetail = (visual.detailType === 'high') ? highDetail : lowDetail;
+                if (preferredDetail !== undefined) {
+                    visual.detail = metadata_1.Metadata.getSufficientDetail(this.metadata, visual.segmentId, preferredDetail);
+                }
+            }
+        };
+        Behavior.prototype.enableVisuals = function (highDetailSegment) {
+            return tslib_1.__awaiter(this, void 0, void 0, function () {
+                var _a, _b, _c, _i, tag, visual, requiredDetailType, _d;
+                return tslib_1.__generator(this, function (_e) {
+                    switch (_e.label) {
+                        case 0:
+                            _a = this.visuals;
+                            _b = [];
+                            for (_c in _a)
+                                _b.push(_c);
+                            _i = 0;
+                            _e.label = 1;
+                        case 1:
+                            if (!(_i < _b.length)) return [3 /*break*/, 5];
+                            _c = _b[_i];
+                            if (!(_c in _a)) return [3 /*break*/, 4];
+                            tag = _c;
+                            visual = this.visuals[tag];
+                            requiredDetailType = visual.segmentId === highDetailSegment ? 'high' : 'low';
+                            if (!(visual.detailType === requiredDetailType)) return [3 /*break*/, 3];
+                            _d = visual;
+                            return [4 /*yield*/, this.getMeshData(visual)];
+                        case 2:
+                            _d.data = _e.sent();
+                            visual.visible = true;
+                            return [3 /*break*/, 4];
+                        case 3:
+                            visual.visible = false;
+                            _e.label = 4;
+                        case 4:
+                            _i++;
+                            return [3 /*break*/, 1];
+                        case 5: return [2 /*return*/];
+                    }
+                });
+            });
+        };
+        Behavior.prototype.disableVisuals = function () {
+            return tslib_1.__awaiter(this, void 0, void 0, function () {
+                var tag, visual;
+                return tslib_1.__generator(this, function (_a) {
+                    for (tag in this.visuals) {
+                        visual = this.visuals[tag];
+                        visual.visible = false;
+                    }
+                    return [2 /*return*/];
+                });
+            });
+        };
+        /** Fetch data in current `visual.detail`, or return already fetched data (if available in the correct detail). */
+        Behavior.prototype.getMeshData = function (visual) {
+            return tslib_1.__awaiter(this, void 0, void 0, function () {
+                var url, urlAsset, asset, parsed, meshlistData;
+                return tslib_1.__generator(this, function (_a) {
+                    switch (_a.label) {
+                        case 0:
+                            if (visual.data && visual.data.detail === visual.detail) {
+                                // Do not recreate
+                                return [2 /*return*/, visual.data];
+                            }
+                            url = this.getMeshUrl(visual.segmentId, visual.detail);
+                            urlAsset = assets_1.Asset.getUrlAsset(this.plugin.managers.asset, url);
+                            return [4 /*yield*/, this.plugin.runTask(this.plugin.managers.asset.resolve(urlAsset, 'binary'))];
+                        case 1:
+                            asset = _a.sent();
+                            return [4 /*yield*/, this.plugin.runTask(cif_1.CIF.parseBinary(asset.data))];
+                        case 2:
+                            parsed = _a.sent();
+                            if (parsed.isError) {
+                                throw new Error("Failed parsing CIF file from ".concat(url));
+                            }
+                            return [4 /*yield*/, mesh_extension_1.MeshlistData.fromCIF(parsed.result, visual.segmentId, visual.segmentName, visual.detail)];
+                        case 3:
+                            meshlistData = _a.sent();
+                            meshlistData.ownerId = this.id;
+                            // const bbox = MeshlistData.bbox(meshlistData);
+                            // const bboxVolume = bbox ? MS.Box3D.volume(bbox) : 0.0;
+                            // console.log(`BBox ${visual.segmentId}: ${Math.round(bboxVolume! / 1e6)} M`, bbox); // DEBUG
+                            return [2 /*return*/, meshlistData];
+                    }
+                });
+            });
+        };
+        Behavior.prototype.guessBackgroundSegments = function () {
+            return tslib_1.__awaiter(this, void 0, void 0, function () {
+                var bboxes, tag, visual, bbox, totalBbox, totalVolume, isBgSegment, segid, bbox, bboxVolume;
+                return tslib_1.__generator(this, function (_a) {
+                    bboxes = {};
+                    for (tag in this.visuals) {
+                        visual = this.visuals[tag];
+                        if (visual.detailType === 'low' && visual.data) {
+                            bbox = mesh_extension_1.MeshlistData.bbox(visual.data);
+                            if (bbox) {
+                                bboxes[visual.segmentId] = bbox;
+                            }
+                        }
+                    }
+                    totalBbox = mesh_extension_1.MeshlistData.combineBBoxes(Object.values(bboxes));
+                    totalVolume = totalBbox ? geometry_1.Box3D.volume(totalBbox) : 0.0;
+                    isBgSegment = {};
+                    for (segid in bboxes) {
+                        bbox = bboxes[segid];
+                        bboxVolume = geometry_1.Box3D.volume(bbox);
+                        isBgSegment[segid] = (bboxVolume > totalVolume * exports.BACKGROUND_SEGMENT_VOLUME_THRESHOLD);
+                        // console.log(`BBox ${segid}: ${Math.round(bboxVolume! / 1e6)} M, ${bboxVolume / totalVolume}`, bbox); // DEBUG
+                    }
+                    this.backgroundSegments = isBgSegment;
+                    return [2 /*return*/];
+                });
+            });
+        };
+        Behavior.prototype.getDescription = function () {
+            return Params.ViewTypeChoice.prettyName(this.params.view.name);
+        };
+        return Behavior;
+    }(behavior_1.PluginBehavior.WithSubscribers));
+    MeshStreaming.Behavior = Behavior;
+})(MeshStreaming = exports.MeshStreaming || (exports.MeshStreaming = {}));
+exports.MeshStreaming = MeshStreaming;

package/lib/commonjs/extensions/meshes/mesh-streaming/server-info.d.ts

@@ -0,0 +1,54 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+import { PluginStateObject } from '../../../mol-plugin-state/objects';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { Choice } from '../choice';
+export declare const DEFAULT_MESH_SERVER = "http://localhost:9000/v2";
+declare const MeshServerInfo_base: {
+    new (data: PD.Values<{
+        serverUrl: PD.Text<string>;
+        source: PD.Select<"emdb" | "empiar">;
+        entryId: PD.Text<string>;
+    }>, props?: {
+        label: string;
+        description?: string | undefined;
+    } | undefined): {
+        id: import("../../../mol-util/uuid").UUID;
+        type: PluginStateObject.TypeInfo;
+        label: string;
+        description?: string | undefined;
+        data: PD.Values<{
+            serverUrl: PD.Text<string>;
+            source: PD.Select<"emdb" | "empiar">;
+            entryId: PD.Text<string>;
+        }>;
+    };
+    type: PluginStateObject.TypeInfo;
+    is(obj?: import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>> | undefined): obj is {
+        id: import("../../../mol-util/uuid").UUID;
+        type: PluginStateObject.TypeInfo;
+        label: string;
+        description?: string | undefined;
+        data: PD.Values<{
+            serverUrl: PD.Text<string>;
+            source: PD.Select<"emdb" | "empiar">;
+            entryId: PD.Text<string>;
+        }>;
+    };
+};
+export declare class MeshServerInfo extends MeshServerInfo_base {
+}
+export declare namespace MeshServerInfo {
+    const MeshSourceChoice: Choice<"emdb" | "empiar", "empiar">;
+    type MeshSource = Choice.Values<typeof MeshSourceChoice>;
+    const Params: {
+        serverUrl: PD.Text<string>;
+        source: PD.Select<"emdb" | "empiar">;
+        entryId: PD.Text<string>;
+    };
+    type Data = PD.Values<typeof Params>;
+}
+export {};

package/lib/commonjs/extensions/meshes/mesh-streaming/server-info.js

@@ -0,0 +1,30 @@
+"use strict";
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.MeshServerInfo = exports.DEFAULT_MESH_SERVER = void 0;
+var tslib_1 = require("tslib");
+var objects_1 = require("../../../mol-plugin-state/objects");
+var param_definition_1 = require("../../../mol-util/param-definition");
+var choice_1 = require("../choice");
+exports.DEFAULT_MESH_SERVER = 'http://localhost:9000/v2';
+var MeshServerInfo = /** @class */ (function (_super) {
+    tslib_1.__extends(MeshServerInfo, _super);
+    function MeshServerInfo() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
+    return MeshServerInfo;
+}(objects_1.PluginStateObject.Create({ name: 'Volume Server', typeClass: 'Object' })));
+exports.MeshServerInfo = MeshServerInfo;
+(function (MeshServerInfo) {
+    MeshServerInfo.MeshSourceChoice = new choice_1.Choice({ empiar: 'EMPIAR', emdb: 'EMDB' }, 'empiar');
+    MeshServerInfo.Params = {
+        serverUrl: param_definition_1.ParamDefinition.Text(exports.DEFAULT_MESH_SERVER),
+        source: MeshServerInfo.MeshSourceChoice.PDSelect(),
+        entryId: param_definition_1.ParamDefinition.Text(''),
+    };
+})(MeshServerInfo = exports.MeshServerInfo || (exports.MeshServerInfo = {}));
+exports.MeshServerInfo = MeshServerInfo;

package/lib/commonjs/extensions/meshes/mesh-streaming/transformers.d.ts

@@ -0,0 +1,42 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+import { PluginStateObject } from '../../../mol-plugin-state/objects';
+import { StateAction, StateTransformer } from '../../../mol-state';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { MeshStreaming } from './behavior';
+import { MeshServerInfo } from './server-info';
+export declare const BACKGROUND_OPACITY = 0.2;
+export declare const FOREROUND_OPACITY = 1;
+export declare const MeshServerTransformer: StateTransformer<PluginStateObject.Root, MeshServerInfo, PD.Normalize<{
+    serverUrl: string;
+    source: "emdb" | "empiar";
+    entryId: string;
+}>>;
+export declare const MeshStreamingTransformer: StateTransformer<MeshServerInfo, MeshStreaming, PD.Normalize<{
+    view: PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
+        detail: any;
+    }>, "all"> | PD.NamedParams<PD.Normalize<{
+        baseDetail: any;
+        focusDetail: any;
+        selectedSegment: any;
+    }>, "select">;
+}>>;
+export declare const MeshVisualGroupTransformer: StateTransformer<MeshStreaming, PluginStateObject.Group, PD.Normalize<{
+    label: string;
+    description: string;
+    segmentId: number;
+    opacity: number;
+}>>;
+export declare const MeshVisualTransformer: StateTransformer<MeshStreaming, PluginStateObject.Shape.Representation3D, PD.Normalize<{
+    ref: string;
+    tag: string;
+    opacity: number;
+}>>;
+export declare const InitMeshStreaming: StateAction<PluginStateObject.Root, void, PD.Normalize<{
+    serverUrl: string;
+    source: "emdb" | "empiar";
+    entryId: string;
+}>>;