@rcsb/rcsb-saguaro-app 6.3.2 → 6.3.4

package/lib/RcsbFvWeb/RcsbFvGroup/GroupTabs/GroupPfvApp.js

@@ -1,131 +0,0 @@
-import { __awaiter } from "tslib";
-import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
-import { RcsbFvUniprotBuilder } from "../../RcsbFvBuilder/RcsbFvUniprotBuilder";
-import { groupExternalTrackBuilder } from "../../../RcsbUtils/TrackGenerators/GroupExternalTrackBuilder";
-import { RcsbFvGroupBuilder } from "../../RcsbFvBuilder/RcsbFvGroupBuilder";
-import { FieldName, GroupReference, OperationType, SequenceReference, Source, Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { alignmentGlobalLigandBindingSite } from "../../../RcsbUtils/TrackGenerators/AlignmentGlobalBindingSite";
-import { RcsbTabs } from "../../RcsbFvComponents/RcsbTabs";
-import { GroupPfvUI } from "../../../RcsbFvUI/GroupPfvUI";
-import { ActionMethods } from "../../../RcsbFvUI/Helper/ActionMethods";
-import { PaginationItemComponent } from "../../../RcsbFvUI/Components/PaginationItemComponent";
-export var GroupPfvApp;
-(function (GroupPfvApp) {
-    function alignment(elementId, groupProvenanceId, groupId, entityCount, additionalConfig) {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e, _f, _g, _h, _j;
-            switch (groupProvenanceId) {
-                case GroupProvenanceId.ProvenanceMatchingUniprotAccession:
-                    return RcsbFvUniprotBuilder.buildUniprotMultipleEntitySequenceFv(elementId, elementId + RcsbTabs.SELECT_SUFFIX, groupId, {}, additionalConfig);
-                default:
-                    additionalConfig = Object.assign(Object.assign({}, additionalConfig), { externalTrackBuilder: groupExternalTrackBuilder() });
-                    // SequenceReference.PdbEntity && SequenceReference.Uniprot are needed to add row prefixes
-                    const pfvArgs = [
-                        getReferenceFromGroupProvenance(groupProvenanceId),
-                        groupId,
-                        SequenceReference.PdbEntity,
-                        SequenceReference.Uniprot
-                    ];
-                    const pfv = yield RcsbFvGroupBuilder.buildGroupAlignmentFv(elementId, ...pfvArgs, additionalConfig);
-                    const paginationCallback = ActionMethods.paginationCallback();
-                    const uiComp = {
-                        component: PaginationItemComponent,
-                        props: {
-                            count: entityCount,
-                            after: (_b = (_a = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page) === null || _a === void 0 ? void 0 : _a.after) !== null && _b !== void 0 ? _b : "0",
-                            first: (_d = (_c = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page) === null || _c === void 0 ? void 0 : _c.first) !== null && _d !== void 0 ? _d : 50,
-                            stateChange: (state, prevState) => {
-                                paginationCallback(elementId, pfv, RcsbFvGroupBuilder.buildGroupAlignmentFv, pfvArgs, Object.assign(Object.assign({}, additionalConfig), { page: {
-                                        first: state.first,
-                                        after: state.after.toString()
-                                    }, excludeLogo: true }));
-                            }
-                        }
-                    };
-                    GroupPfvUI.fvUI(GroupPfvUI.addBootstrapElement(elementId), (_f = (_e = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.externalUiComponents) === null || _e === void 0 ? void 0 : _e.replace) !== null && _f !== void 0 ? _f : (entityCount > ((_h = (_g = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.page) === null || _g === void 0 ? void 0 : _g.first) !== null && _h !== void 0 ? _h : 50) ? [uiComp] : []).concat(((_j = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.externalUiComponents) === null || _j === void 0 ? void 0 : _j.add) ? additionalConfig.externalUiComponents.add : []));
-                    return pfv;
-            }
-        });
-    }
-    GroupPfvApp.alignment = alignment;
-    function structure(elementId, groupProvenanceId, groupId, nTargets, additionalConfig) {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a;
-            additionalConfig = Object.assign(Object.assign({}, additionalConfig), { filters: [...((_a = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.filters) !== null && _a !== void 0 ? _a : []), {
-                        field: FieldName.Type,
-                        values: [Type.HelixP, Type.Sheet, Type.Cath, Type.Scop],
-                        operation: OperationType.Equals,
-                        source: Source.PdbInstance
-                    }, {
-                        field: FieldName.Type,
-                        values: [Type.Pfam],
-                        operation: OperationType.Equals,
-                        source: Source.PdbEntity
-                    }], sources: [Source.PdbInstance, Source.PdbEntity], annotationProcessing: annotationPositionFrequencyProcessing(nTargets), externalTrackBuilder: groupExternalTrackBuilder() });
-            // SequenceReference.PdbEntity && SequenceReference.Uniprot are needed to add row prefixes
-            const pfvArgs = [
-                getReferenceFromGroupProvenance(groupProvenanceId),
-                groupId,
-                SequenceReference.PdbEntity,
-                SequenceReference.Uniprot
-            ];
-            return yield RcsbFvGroupBuilder.buildGroupAnnotationFv(elementId, ...pfvArgs, additionalConfig);
-        });
-    }
-    GroupPfvApp.structure = structure;
-    function bindingSites(elementId, groupProvenanceId, groupId, nTargets, additionalConfig) {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a;
-            additionalConfig = Object.assign(Object.assign({}, additionalConfig), { filters: [...((_a = additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.filters) !== null && _a !== void 0 ? _a : []), {
-                        field: FieldName.Type,
-                        values: [Type.BindingSite],
-                        operation: OperationType.Equals,
-                        source: Source.PdbInstance
-                    }], sources: [Source.PdbInstance], annotationProcessing: annotationPositionFrequencyProcessing(nTargets), externalTrackBuilder: alignmentGlobalLigandBindingSite() });
-            // SequenceReference.PdbEntity && SequenceReference.Uniprot are needed to add row prefixes
-            const pfvArgs = [
-                getReferenceFromGroupProvenance(groupProvenanceId),
-                groupId,
-                SequenceReference.PdbEntity,
-                SequenceReference.Uniprot
-            ];
-            return yield RcsbFvGroupBuilder.buildGroupAnnotationFv(elementId, ...pfvArgs, additionalConfig);
-        });
-    }
-    GroupPfvApp.bindingSites = bindingSites;
-})(GroupPfvApp || (GroupPfvApp = {}));
-function annotationPositionFrequencyProcessing(nTargets) {
-    const targets = new Map();
-    return {
-        getAnnotationValue: (feature) => {
-            var _a, _b, _c, _d;
-            if (!targets.has(feature.type)) {
-                if (feature.d.value)
-                    targets.set(feature.type, feature.d.value);
-                return (_b = (_a = feature.p.values) === null || _a === void 0 ? void 0 : _a[0]) !== null && _b !== void 0 ? _b : 0;
-            }
-            else {
-                return (_d = (_c = feature.p.values) === null || _c === void 0 ? void 0 : _c[0]) !== null && _d !== void 0 ? _d : 0;
-            }
-        },
-        computeAnnotationValue: (annotationTracks) => {
-            annotationTracks.forEach((at, type) => {
-                const N = (type.includes(Type.Cath) || type.includes(Type.Scop) || type.includes(Type.BindingSite) || type.includes(Type.Pfam)) ? targets.get(type) : nTargets;
-                at.forEach((ann, positionKey) => {
-                    if (ann.source != Source.PdbInterface)
-                        ann.value = Math.ceil(1000 * ann.value / (N !== null && N !== void 0 ? N : 1)) / 1000;
-                });
-            });
-        }
-    };
-}
-export function getReferenceFromGroupProvenance(groupProvenanceId) {
-    switch (groupProvenanceId) {
-        case GroupProvenanceId.ProvenanceMatchingDepositGroupId:
-            throw `Undefined reference for provenance ${groupProvenanceId}`;
-        case GroupProvenanceId.ProvenanceSequenceIdentity:
-            return GroupReference.SequenceIdentity;
-        case GroupProvenanceId.ProvenanceMatchingUniprotAccession:
-            return GroupReference.MatchingUniprotAccession;
-    }
-}

package/lib/RcsbFvWeb/RcsbFvGroup/RcsbFvGroupTabsBuilder.d.ts

@@ -1,6 +0,0 @@
-import { GroupProvenanceId } from "@rcsb/rcsb-api-tools/build/RcsbDw/Types/DwEnums";
-import { SearchQuery } from "@rcsb/rcsb-api-tools/build/RcsbSearch/Types/SearchQueryInterface";
-import { RcsbFvAdditionalConfig } from "../RcsbFvModule/RcsbFvModuleInterface";
-export declare class RcsbFvGroupTabsBuilder {
-    static buildGroupTabs(elementId: string, groupProvenanceId: GroupProvenanceId, groupId: string, query?: SearchQuery, additionalConfig?: RcsbFvAdditionalConfig): void;
-}

package/lib/RcsbFvWeb/RcsbFvGroup/RcsbFvGroupTabsBuilder.js

@@ -1,12 +0,0 @@
-import { jsx as _jsx } from "react/jsx-runtime";
-import { GroupPfvTabs } from "./GroupPfvTabs";
-import { createRoot } from "react-dom/client";
-import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
-var assertDefined = Assertions.assertDefined;
-export class RcsbFvGroupTabsBuilder {
-    static buildGroupTabs(elementId, groupProvenanceId, groupId, query, additionalConfig) {
-        const element = document.getElementById(elementId);
-        assertDefined(element);
-        createRoot(element).render(_jsx(GroupPfvTabs, { groupProvenanceId: groupProvenanceId, groupId: groupId, searchQuery: query, additionalConfig: additionalConfig }));
-    }
-}

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvAbstractModule.d.ts

@@ -1,47 +0,0 @@
-import { RcsbFv } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFv";
-import { RcsbFvBoardConfigInterface, RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-import { AlignmentCollectorInterface } from "../../RcsbCollectTools/AlignmentCollector/AlignmentCollectorInterface";
-import { AnnotationRequestContext, AnnotationCollectorInterface } from "../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
-import { RcsbFvModuleBuildInterface, RcsbFvModuleInterface } from "./RcsbFvModuleInterface";
-import { AlignmentResponse, AnnotationFeatures, Feature, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { TrackFactoryInterface } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryInterface";
-import { AlignmentRequestContextType } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AlignmentTrackFactory";
-import { AnnotationConfigInterface } from "../../RcsbAnnotationConfig/AnnotationConfigInterface";
-export declare abstract class RcsbFvAbstractModule implements RcsbFvModuleInterface {
-    protected readonly rcsbFv: RcsbFv;
-    protected readonly elementId: string;
-    protected boardConfigData: RcsbFvBoardConfigInterface;
-    protected rowConfigData: Array<RcsbFvRowConfigInterface>;
-    protected polymerEntityInstance: PolymerEntityInstanceTranslate;
-    protected alignmentCollector: AlignmentCollectorInterface;
-    protected annotationCollector: AnnotationCollectorInterface;
-    protected referenceTrack: RcsbFvRowConfigInterface;
-    protected alignmentTracks: Array<RcsbFvRowConfigInterface>;
-    protected annotationTracks: Array<RcsbFvRowConfigInterface>;
-    protected buildConfig: RcsbFvModuleBuildInterface;
-    private rcsbFvRowUpdatePromise;
-    private activeDisplayFlag;
-    constructor(elementId: string, rcsbFv: RcsbFv);
-    setPolymerEntityInstanceTranslator(polymerEntityInstance: PolymerEntityInstanceTranslate): void;
-    getPolymerEntityInstanceTranslator(): PolymerEntityInstanceTranslate;
-    display(): Promise<void>;
-    activeDisplay(): boolean;
-    getFv(): RcsbFv;
-    getTargets(): Promise<Array<string>>;
-    getAlignmentResponse(): Promise<AlignmentResponse>;
-    getFeatures(): Promise<Array<Feature>>;
-    getAnnotationConfigData(): Promise<Array<RcsbFvRowConfigInterface>>;
-    build(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
-    wait(): Promise<void>;
-    protected abstract protectedBuild(): Promise<void>;
-    protected abstract concatAlignmentAndAnnotationTracks(): void;
-    protected buildAlignmentTracks(alignmentRequestContext: AlignmentRequestContextType, alignmentResponse: AlignmentResponse, trackFactories?: {
-        alignmentTrackFactory?: TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]>;
-        sequenceTrackFactory?: TrackFactoryInterface<[AlignmentRequestContextType, string]>;
-    }): Promise<void>;
-    protected buildAnnotationsTrack(annotationsRequestContext: AnnotationRequestContext, annotationsFeatures: AnnotationFeatures[], annotationConfigMap?: AnnotationConfigInterface): Promise<void>;
-    protected getBoardConfig(): Promise<RcsbFvBoardConfigInterface>;
-    protected getRowsConfig(): Promise<Array<RcsbFvRowConfigInterface>>;
-    private buildExternalTracks;
-}

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvAbstractModule.js

@@ -1,143 +0,0 @@
-import { __awaiter } from "tslib";
-import { AnnotationCollector } from "../../RcsbCollectTools/AnnotationCollector/AnnotationCollector";
-import { ComponentsManager } from "../RcsbFvComponents/ComponentsManager";
-import { SingletonMap } from "../../RcsbUtils/Helpers/SingletonMap";
-import { AlignmentCollector } from "../../RcsbCollectTools/AlignmentCollector/AlignmentCollector";
-import { AlignmentTrackFactory } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AlignmentTrackFactory";
-import { SequenceTrackFactory } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/SequenceTrackFactory";
-import { AlignmentBlockFactory } from "../RcsbFvFactories/RcsbFvBlockFactory/AlignmentBlockFactory";
-import { AnnotationsBlockFactory } from "../RcsbFvFactories/RcsbFvBlockFactory/AnnotationsBlockFactory";
-import { AnnotationsTrackFactory } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AnnotationsTrackFactory";
-import * as acm from "../../RcsbAnnotationConfig/RcsbAnnotationConfig.ac.json";
-import { AnnotationBlockManager } from "../RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationBlockManager";
-import { RcsbAnnotationConfig } from "../../RcsbAnnotationConfig/RcsbAnnotationConfig";
-import { AnnotationTrackManagerFactory } from "../RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationTrackManager";
-export class RcsbFvAbstractModule {
-    constructor(elementId, rcsbFv) {
-        this.boardConfigData = {
-            length: 0
-        };
-        this.rowConfigData = new Array();
-        this.alignmentCollector = new AlignmentCollector();
-        this.annotationCollector = new AnnotationCollector();
-        this.alignmentTracks = [];
-        this.annotationTracks = [];
-        this.activeDisplayFlag = false;
-        this.rcsbFv = rcsbFv;
-        this.elementId = elementId;
-        ComponentsManager.buildLoaderSpinner(elementId);
-    }
-    setPolymerEntityInstanceTranslator(polymerEntityInstance) {
-        this.polymerEntityInstance = polymerEntityInstance;
-    }
-    getPolymerEntityInstanceTranslator() {
-        return this.polymerEntityInstance;
-    }
-    display() {
-        return __awaiter(this, void 0, void 0, function* () {
-            console.info(`Starting display ${this.elementId}`);
-            yield this.rcsbFv.updateBoardConfig({
-                boardConfigData: yield this.getBoardConfig(),
-                rowConfigData: []
-            });
-            ComponentsManager.unmountLoaderSpinner(this.elementId);
-            console.info(`Rendering tracks ${this.elementId}`);
-            this.rcsbFvRowUpdatePromise = this.rcsbFv.updateBoardConfig({
-                rowConfigData: yield this.getRowsConfig()
-            });
-            this.activeDisplayFlag = true;
-            return void 0;
-        });
-    }
-    activeDisplay() {
-        return this.activeDisplayFlag;
-    }
-    getFv() {
-        return this.rcsbFv;
-    }
-    getTargets() {
-        return __awaiter(this, void 0, void 0, function* () {
-            return yield this.alignmentCollector.getTargets();
-        });
-    }
-    getAlignmentResponse() {
-        return __awaiter(this, void 0, void 0, function* () {
-            return yield this.alignmentCollector.getAlignment();
-        });
-    }
-    getFeatures() {
-        return __awaiter(this, void 0, void 0, function* () {
-            //return (await this.annotationCollector.getAnnotationFeatures()).map(af=>af.features).flat();
-            return yield this.annotationCollector.getFeatures();
-        });
-    }
-    getAnnotationConfigData() {
-        return __awaiter(this, void 0, void 0, function* () {
-            return this.annotationTracks;
-        });
-    }
-    build(buildConfig) {
-        return __awaiter(this, void 0, void 0, function* () {
-            SingletonMap.update(this.elementId, this);
-            this.buildConfig = buildConfig;
-            yield this.protectedBuild();
-            yield this.buildExternalTracks();
-            this.concatAlignmentAndAnnotationTracks();
-            yield this.display();
-            return void 0;
-        });
-    }
-    wait() {
-        return this.rcsbFvRowUpdatePromise;
-    }
-    buildAlignmentTracks(alignmentRequestContext, alignmentResponse, trackFactories) {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d;
-            const sequenceTrackFactory = (_a = trackFactories === null || trackFactories === void 0 ? void 0 : trackFactories.sequenceTrackFactory) !== null && _a !== void 0 ? _a : new SequenceTrackFactory(this.getPolymerEntityInstanceTranslator());
-            if (alignmentResponse.query_sequence)
-                this.referenceTrack = yield sequenceTrackFactory.getTrack(alignmentRequestContext, alignmentResponse.query_sequence);
-            const alignmentBlockFactory = new AlignmentBlockFactory((_b = trackFactories === null || trackFactories === void 0 ? void 0 : trackFactories.alignmentTrackFactory) !== null && _b !== void 0 ? _b : new AlignmentTrackFactory(this.getPolymerEntityInstanceTranslator()), (_d = (_c = this.buildConfig.additionalConfig) === null || _c === void 0 ? void 0 : _c.trackConfigModifier) === null || _d === void 0 ? void 0 : _d.alignment);
-            this.alignmentTracks = yield alignmentBlockFactory.getBlock(alignmentRequestContext, alignmentResponse);
-        });
-    }
-    buildAnnotationsTrack(annotationsRequestContext, annotationsFeatures, annotationConfigMap) {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b;
-            const defaultAnnotationConfigMap = annotationConfigMap !== null && annotationConfigMap !== void 0 ? annotationConfigMap : acm;
-            const annotationsBlockFactory = new AnnotationsBlockFactory(new AnnotationBlockManager(new AnnotationTrackManagerFactory(), new RcsbAnnotationConfig(defaultAnnotationConfigMap), this.getPolymerEntityInstanceTranslator()), new AnnotationsTrackFactory(), (_b = (_a = this.buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.trackConfigModifier) === null || _b === void 0 ? void 0 : _b.annotations);
-            this.annotationTracks = yield annotationsBlockFactory.getBlock(annotationsRequestContext, annotationsFeatures);
-        });
-    }
-    getBoardConfig() {
-        return __awaiter(this, void 0, void 0, function* () {
-            return this.boardConfigData;
-        });
-    }
-    getRowsConfig() {
-        return __awaiter(this, void 0, void 0, function* () {
-            return this.rowConfigData;
-        });
-    }
-    buildExternalTracks() {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b;
-            const externalTrackBuilder = (_a = this.buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.externalTrackBuilder;
-            const rcsbContext = (_b = this.buildConfig.additionalConfig) === null || _b === void 0 ? void 0 : _b.rcsbContext;
-            if (!externalTrackBuilder)
-                return;
-            if (typeof externalTrackBuilder.processAlignmentAndFeatures === "function")
-                yield externalTrackBuilder.processAlignmentAndFeatures({
-                    annotations: yield this.annotationCollector.getAnnotationFeatures(),
-                    alignments: yield this.alignmentCollector.getAlignment(),
-                    rcsbContext: rcsbContext
-                });
-            if (typeof externalTrackBuilder.addTo === "function")
-                yield externalTrackBuilder.addTo({
-                    alignmentTracks: this.alignmentTracks,
-                    annotationTracks: this.annotationTracks,
-                    rcsbContext: rcsbContext
-                });
-            return void 0;
-        });
-    }
-}

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvChromosome.d.ts

@@ -1,49 +0,0 @@
-import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
-export declare class RcsbFvChromosome extends RcsbFvAbstractModule {
-    private readonly targetAlignmentList;
-    private maxRange;
-    private minRange;
-    private alignmentCollectorQueue;
-    private nTasks;
-    private completeTasks;
-    private pdbEntityTrack;
-    private batchSize;
-    private beginView;
-    private endView;
-    private entityBegin;
-    private entityEnd;
-    private nonExonConfigData;
-    private featuresConfigData;
-    private targetCoverages;
-    private chrSet;
-    private targetFilterFlag;
-    private entityId;
-    private IDEOGRAM_DIV_ID;
-    private TITLE_CHR_DIV_ID;
-    private TITLE_CHR_REGION_ID;
-    private currentDisplayedChrId;
-    private elementSelectId;
-    private readonly buildSubject;
-    private readonly targetsSubject;
-    private buildPdbGenomeFv;
-    private buildFullGenomeRangeFv;
-    private collectPdbWorkerResults;
-    private buildChromosomeFv;
-    private plotChromosomeTitle;
-    private updateChromosomeTitleRegion;
-    private plotIdeogram;
-    private genomeSequenceTracks;
-    private collectChromosomeEntityRegion;
-    private collectChromosomeAlignments;
-    private collectChromosomeWorkerResults;
-    private collectExons;
-    private normalizeTargetAlignment;
-    private simplifyExonTracks;
-    private mergeExonTracks;
-    private addSequences;
-    private setDisplayView;
-    private plot;
-    protected protectedBuild(): Promise<void>;
-    getTargets(): Promise<Array<string>>;
-    protected concatAlignmentAndAnnotationTracks(): void;
-}