@rcsb/rcsb-saguaro-app 6.3.2 → 6.3.4

package/lib/commonjs/RcsbAnnotationConfig/RcsbAnnotationConfig.d.ts

@@ -1,31 +0,0 @@
-import { AnnotationFeatures, Feature } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { RcsbFvDisplayTypes } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvDefaultConfigValues";
-import { AnnotationConfigInterface, RcsbAnnotationConfigInterface } from "./AnnotationConfigInterface";
-import { AnnotationRequestContext } from "../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
-export interface RcsbMergedTypesInterface {
-    merged_types: Array<string>;
-    title: string;
-    type: string;
-    display: RcsbFvDisplayTypes;
-}
-export declare class RcsbAnnotationConfig {
-    private readonly annotationConfigMap;
-    private readonly annotationMap;
-    private readonly annotationTypes;
-    private readonly mergedTypes;
-    constructor(acm?: AnnotationConfigInterface);
-    getConfig(type: string): RcsbAnnotationConfigInterface | undefined;
-    allTypes(): Set<string>;
-    uniprotOrder(): Array<string>;
-    instanceOrder(): Array<string>;
-    entityOrder(): Array<string>;
-    getAnnotationType(requestConfig: AnnotationRequestContext, ann: AnnotationFeatures, feature: Feature): Promise<string>;
-    isMergedType(type: string): boolean;
-    getMergeConfig(type: string): RcsbMergedTypesInterface | undefined;
-    private addNewType;
-    private checkAndIncludeNewType;
-    static randomRgba(str?: string): string;
-    private addProvenance;
-    addMultipleProvenance(type: string, provenanceList: Array<string>): void;
-    private initTypes;
-}

package/lib/commonjs/RcsbAnnotationConfig/RcsbAnnotationConfig.js

@@ -1,187 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.RcsbAnnotationConfig = void 0;
-const tslib_1 = require("tslib");
-const acm = tslib_1.__importStar(require("./RcsbAnnotationConfig.ac.json"));
-const string_to_color_1 = tslib_1.__importDefault(require("string-to-color"));
-const Assertions_1 = require("../RcsbUtils/Helpers/Assertions");
-var assertDefined = Assertions_1.Assertions.assertDefined;
-const uniqid_1 = tslib_1.__importDefault(require("uniqid"));
-const annotationConfigMap = acm;
-class RcsbAnnotationConfig {
-    constructor(acm) {
-        this.annotationMap = new Map();
-        this.annotationTypes = {
-            instance: new Map(),
-            entity: new Map(),
-            external: new Map()
-        };
-        this.mergedTypes = new Map();
-        this.annotationConfigMap = acm !== null && acm !== void 0 ? acm : annotationConfigMap;
-        this.annotationConfigMap.config.forEach(m => {
-            //TODO move provenance list from configuration to TrackManager
-            m.provenanceList = new Set();
-            this.annotationMap.set(m.type, m);
-        });
-        this.initTypes();
-    }
-    getConfig(type) {
-        return this.annotationMap.get(type);
-    }
-    allTypes() {
-        const concat = this.uniprotOrder().concat(this.instanceOrder()).concat(this.entityOrder());
-        return new Set(concat);
-    }
-    uniprotOrder() {
-        return Array.from(this.annotationTypes.external.entries()).map(e => e[1].sort((a, b) => a.localeCompare(b))).flat();
-    }
-    instanceOrder() {
-        return Array.from(this.annotationTypes.instance.entries()).map(e => e[1].sort((a, b) => a.localeCompare(b))).flat();
-    }
-    entityOrder() {
-        return Array.from(this.annotationTypes.entity.entries()).map(e => e[1].sort((a, b) => a.localeCompare(b))).flat();
-    }
-    //TODO refactor how title and type are defined. Can this be split in two different methods ?
-    getAnnotationType(requestConfig, ann, feature) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c;
-            const trackTitle = typeof requestConfig.trackTitle === "function" ? (yield requestConfig.trackTitle(ann, feature)) : undefined;
-            const titleSuffix = typeof requestConfig.titleSuffix === "function" ? (yield requestConfig.titleSuffix(ann, feature)) : undefined;
-            const typeSuffix = typeof requestConfig.typeSuffix === "function" ? (yield requestConfig.typeSuffix(ann, feature)) : undefined;
-            const type = feature.type;
-            assertDefined(type);
-            const a = feature;
-            const addToTypeSuffix = new ArraySuffix();
-            const ac = this.annotationMap.get(type);
-            if (titleSuffix)
-                addToTypeSuffix.push(titleSuffix);
-            if (typeSuffix)
-                addToTypeSuffix.push(typeSuffix);
-            if (Array.isArray(ac === null || ac === void 0 ? void 0 : ac.addToType)) {
-                (_a = ac === null || ac === void 0 ? void 0 : ac.addToType) === null || _a === void 0 ? void 0 : _a.forEach(field => {
-                    if (a[field] != null)
-                        addToTypeSuffix.push(a[field]);
-                });
-            }
-            let newType;
-            if (ac && ac.key != null && a[ac.key]) {
-                addToTypeSuffix.unshift(a[ac.key]);
-                newType = type + addToTypeSuffix.join(".");
-                if (!this.annotationMap.has(newType)) {
-                    const title = a[ac.key] != null ? a[ac.key] : "";
-                    this.annotationMap.set(newType, Object.assign(Object.assign({}, ac), { type: newType, color: typeof ac.color === "string" ? RcsbAnnotationConfig.randomRgba(title) : Object.assign(Object.assign({}, ac.color), { colors: RcsbAnnotationConfig.randomRgba(title) }), prefix: trackTitle !== null && trackTitle !== void 0 ? trackTitle : ac.title, title: title, provenanceList: new Set() }));
-                    this.addNewType(newType, type);
-                }
-            }
-            else if (titleSuffix != null) {
-                newType = type + addToTypeSuffix.join(".");
-                if (!this.annotationMap.has(newType)) {
-                    this.annotationMap.set(newType, Object.assign(Object.assign({ display: (_b = ac === null || ac === void 0 ? void 0 : ac.display) !== null && _b !== void 0 ? _b : "block" /* RcsbFvDisplayTypes.BLOCK */ }, ac), { type: newType, prefix: trackTitle !== null && trackTitle !== void 0 ? trackTitle : ac === null || ac === void 0 ? void 0 : ac.title, title: titleSuffix, provenanceList: new Set() }));
-                    this.addNewType(newType, type, titleSuffix);
-                }
-            }
-            else if (trackTitle != null) {
-                newType = type + addToTypeSuffix.join(".");
-                if (!this.annotationMap.has(newType)) {
-                    this.annotationMap.set(newType, Object.assign(Object.assign({ display: "block" /* RcsbFvDisplayTypes.BLOCK */, type: (0, uniqid_1.default)("type-") }, ac), { title: trackTitle, provenanceList: new Set() }));
-                    this.addNewType(newType, type);
-                }
-            }
-            else {
-                newType = type + addToTypeSuffix.join(".");
-                if (!this.annotationMap.has(newType) || this.mergedTypes.has(type)) {
-                    this.addNewType(newType, type);
-                }
-            }
-            this.addProvenance(newType, (_c = feature.provenance_source) !== null && _c !== void 0 ? _c : "N/A");
-            return newType;
-        });
-    }
-    isMergedType(type) {
-        return this.mergedTypes.has(type);
-    }
-    getMergeConfig(type) {
-        return this.mergedTypes.get(type);
-    }
-    addNewType(newType, type, titleSuffix) {
-        const mt = this.mergedTypes.get(type);
-        if (mt) {
-            const mergedType = titleSuffix ? mt.type + "." + titleSuffix : mt.type;
-            if (newType != type)
-                this.mergedTypes.set(newType, {
-                    merged_types: mt.merged_types,
-                    display: mt.display,
-                    type: mergedType,
-                    title: mt.title,
-                });
-            this.annotationMap.set(mergedType, {
-                type: mergedType,
-                display: mt.display,
-                title: titleSuffix !== null && titleSuffix !== void 0 ? titleSuffix : mt.title,
-                prefix: titleSuffix ? mt.title : undefined,
-                provenanceList: new Set()
-            });
-            this.checkAndIncludeNewType(mergedType, mt.type);
-        }
-        else {
-            this.checkAndIncludeNewType(newType, type);
-        }
-    }
-    checkAndIncludeNewType(newType, type) {
-        var _a, _b, _c, _d, _e, _f;
-        if (type === newType)
-            return;
-        if (this.annotationTypes.instance.has(type) && !((_a = this.annotationTypes.instance.get(type)) === null || _a === void 0 ? void 0 : _a.includes(newType)))
-            (_b = this.annotationTypes.instance.get(type)) === null || _b === void 0 ? void 0 : _b.push(newType);
-        if (this.annotationTypes.entity.has(type) && !((_c = this.annotationTypes.entity.get(type)) === null || _c === void 0 ? void 0 : _c.includes(newType)))
-            (_d = this.annotationTypes.entity.get(type)) === null || _d === void 0 ? void 0 : _d.push(newType);
-        if (this.annotationTypes.external.has(type) && !((_e = this.annotationTypes.external.get(type)) === null || _e === void 0 ? void 0 : _e.includes(newType)))
-            (_f = this.annotationTypes.external.get(type)) === null || _f === void 0 ? void 0 : _f.push(newType);
-    }
-    static randomRgba(str) {
-        return (0, string_to_color_1.default)(str);
-    }
-    addProvenance(type, provenanceName) {
-        var _a;
-        if (this.annotationMap.has(type))
-            (_a = this.annotationMap.get(type)) === null || _a === void 0 ? void 0 : _a.provenanceList.add(provenanceName);
-    }
-    addMultipleProvenance(type, provenanceList) {
-        provenanceList.forEach(p => {
-            this.addProvenance(type, p);
-        });
-    }
-    initTypes() {
-        var _a, _b, _c, _d;
-        (_a = this.annotationConfigMap.external_data_order) === null || _a === void 0 ? void 0 : _a.forEach(type => {
-            this.annotationTypes.external.set(type, [type]);
-        });
-        (_b = this.annotationConfigMap.instance_order) === null || _b === void 0 ? void 0 : _b.forEach(type => {
-            this.annotationTypes.instance.set(type, [type]);
-        });
-        (_c = this.annotationConfigMap.entity_order) === null || _c === void 0 ? void 0 : _c.forEach(type => {
-            this.annotationTypes.entity.set(type, [type]);
-        });
-        (_d = this.annotationConfigMap.merge) === null || _d === void 0 ? void 0 : _d.forEach(m => {
-            m.merged_types.forEach(type => {
-                this.mergedTypes.set(type, m);
-            });
-        });
-    }
-}
-exports.RcsbAnnotationConfig = RcsbAnnotationConfig;
-class ArraySuffix extends Array {
-    join(separator) {
-        if (this.length == 0)
-            return "";
-        else
-            return ":" + super.join(separator);
-    }
-    push(...items) {
-        items.forEach(i => {
-            if (i)
-                super.push(i);
-        });
-        return this.length;
-    }
-}

package/lib/commonjs/RcsbAnnotationConfig/RcsbAnnotationConstants.d.ts

@@ -1,15 +0,0 @@
-export declare const RcsbAnnotationConstants: {
-    provenanceColorCode: {
-        rcsbLink: string;
-        rcsbPdb: string;
-        external: string;
-        csm: string;
-    };
-    provenanceName: {
-        pdb: string;
-        csm: string;
-        mmseqs: string;
-        promotif: string;
-        userInput: string;
-    };
-};

package/lib/commonjs/RcsbAnnotationConfig/RcsbAnnotationConstants.js

@@ -1,21 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.RcsbAnnotationConstants = void 0;
-const tslib_1 = require("tslib");
-const acm = tslib_1.__importStar(require("./RcsbAnnotationConfig.ac.json"));
-const annotationConfigMap = acm;
-exports.RcsbAnnotationConstants = {
-    provenanceColorCode: {
-        rcsbLink: annotationConfigMap.provenance_color_code.rcsb_link,
-        rcsbPdb: annotationConfigMap.provenance_color_code.rcsb_pdb,
-        external: annotationConfigMap.provenance_color_code.external,
-        csm: annotationConfigMap.provenance_color_code.csm,
-    },
-    provenanceName: {
-        pdb: "PDB",
-        csm: "CSM",
-        mmseqs: "MMseqs",
-        promotif: "PROMOTIF",
-        userInput: "USER INPUT"
-    }
-};

package/lib/commonjs/RcsbAnnotationConfig/RcsbDistributionConfig.d.ts

@@ -1,12 +0,0 @@
-import { RcsbDistributionConfigInterface, RcsbTrackBlockConfigInterface, RcsbTrackConfigInterface } from "./AnnotationConfigInterface";
-export declare class RcsbDistributionConfig {
-    private readonly distributionConfig;
-    private trackToBlockType;
-    private trackConfig;
-    private blockConfig;
-    constructor(dcm?: RcsbDistributionConfigInterface);
-    getBlockType(trackType: string): string | undefined;
-    getBlockConfig(type: string): RcsbTrackBlockConfigInterface | undefined;
-    getTrackConfig(type: string): RcsbTrackConfigInterface | undefined;
-    private processConfig;
-}

package/lib/commonjs/RcsbAnnotationConfig/RcsbDistributionConfig.dc.json

@@ -1,59 +0,0 @@
-{
-    "blockConfig": [{
-            "type": "MA_QA_METRIC_LOCAL_TYPE_PLDDT",
-            "trackType": ["MA_QA_METRIC_LOCAL_TYPE_PLDDT"],
-            "sort": ["VERY_LOW", "LOW", "CONFIDENT", "VERY_HIGH"],
-            "contentType": "numerical",
-            "axisLabel": "Number of Residues",
-            "undefTrack": {
-                "label": "N/A",
-                "id": "UNDEF",
-                "color": "#cccccc"
-            }
-        }, {
-            "type": "SECONDARY_STRUCTURE",
-            "title": "Secondary Structure Distribution",
-            "trackType": ["HELIX", "SHEET", "TURN"],
-            "contentType": "binary",
-            "undefTrack": {
-                "label": "Undef",
-                "id": "UNDEF",
-                "color": "#cccccc"
-            }
-        }],
-    "trackConfig": [{
-            "type": "MA_QA_METRIC_LOCAL_TYPE_PLDDT",
-            "numericalCategories": {
-                "categories": [{
-                        "color": "#ff7d45",
-                        "label": "Very Low",
-                        "id": "VERY_LOW"
-                    }, {
-                        "color": "#ffdb13",
-                        "label": "Low",
-                        "id": "LOW"
-                    }, {
-                        "color": "#65cbf3",
-                        "label": "Confident",
-                        "id": "CONFIDENT"
-                    }, {
-                        "color": "#0053d6",
-                        "label": "Very High",
-                        "id": "VERY_HIGH"
-                    }],
-                "thresholds": [50, 70, 90]
-            }
-        }, {
-            "type": "HELIX",
-            "label": "Helix",
-            "color": "#e43372"
-        }, {
-            "type": "SHEET",
-            "label": "Sheet",
-            "color": "#f1d23b"
-        }, {
-            "type": "TURN",
-            "label": "Turn",
-            "color": "#0053d6"
-        }]
-}

package/lib/commonjs/RcsbAnnotationConfig/RcsbDistributionConfig.js

@@ -1,36 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.RcsbDistributionConfig = void 0;
-const tslib_1 = require("tslib");
-const dcm = tslib_1.__importStar(require("./RcsbDistributionConfig.dc.json"));
-const distributionConfig = dcm;
-class RcsbDistributionConfig {
-    constructor(dcm = distributionConfig) {
-        this.trackToBlockType = new Map();
-        this.trackConfig = new Map();
-        this.blockConfig = new Map();
-        this.distributionConfig = dcm;
-        this.processConfig();
-    }
-    getBlockType(trackType) {
-        return this.trackToBlockType.get(trackType);
-    }
-    getBlockConfig(type) {
-        return this.blockConfig.get(type);
-    }
-    getTrackConfig(type) {
-        return this.trackConfig.get(type);
-    }
-    processConfig() {
-        this.distributionConfig.blockConfig.forEach(bc => {
-            this.blockConfig.set(bc.type, bc);
-            bc.trackType.forEach(type => {
-                this.trackToBlockType.set(type, bc.type);
-            });
-        });
-        this.distributionConfig.trackConfig.forEach(tc => {
-            this.trackConfig.set(tc.type, tc);
-        });
-    }
-}
-exports.RcsbDistributionConfig = RcsbDistributionConfig;