@rcsb/rcsb-saguaro-app 6.3.2 → 6.3.4

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvProteinSequence.js

@@ -1,50 +0,0 @@
-import { __awaiter } from "tslib";
-import { Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
-import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
-var assertDefined = Assertions.assertDefined;
-export class RcsbFvProteinSequence extends RcsbFvAbstractModule {
-    protectedBuild() {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e;
-            const buildConfig = this.buildConfig;
-            const queryId = buildConfig.queryId;
-            assertDefined(queryId);
-            const source = (_a = buildConfig.sources) !== null && _a !== void 0 ? _a : [Source.Uniprot];
-            const alignmentRequestContext = {
-                queryId: queryId,
-                from: buildConfig.from,
-                to: buildConfig.to,
-                dynamicDisplay: true,
-                externalTrackBuilder: (_b = buildConfig.additionalConfig) === null || _b === void 0 ? void 0 : _b.externalTrackBuilder
-            };
-            const alignmentResponse = yield this.alignmentCollector.collect(alignmentRequestContext, (_c = buildConfig.additionalConfig) === null || _c === void 0 ? void 0 : _c.alignmentFilter);
-            yield this.buildAlignmentTracks(alignmentRequestContext, alignmentResponse);
-            const annotationsRequestContext = {
-                queryId: queryId,
-                reference: buildConfig.from,
-                sources: source,
-                annotationProcessing: (_d = buildConfig.additionalConfig) === null || _d === void 0 ? void 0 : _d.annotationProcessing,
-                externalTrackBuilder: (_e = buildConfig.additionalConfig) === null || _e === void 0 ? void 0 : _e.externalTrackBuilder
-            };
-            const annotationsFeatures = yield this.annotationCollector.collect(annotationsRequestContext);
-            yield this.buildAnnotationsTrack(annotationsRequestContext, annotationsFeatures);
-            this.boardConfigData.length = yield this.alignmentCollector.getAlignmentLength();
-            this.boardConfigData.includeAxis = true;
-            return void 0;
-        });
-    }
-    concatAlignmentAndAnnotationTracks() {
-        var _a, _b;
-        const buildConfig = this.buildConfig;
-        if ((_a = buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.hideAlignments) {
-            this.rowConfigData = [this.referenceTrack].concat(this.annotationTracks);
-        }
-        else if ((_b = buildConfig.additionalConfig) === null || _b === void 0 ? void 0 : _b.bottomAlignments) {
-            this.rowConfigData = [this.referenceTrack].concat(this.annotationTracks).concat(this.alignmentTracks);
-        }
-        else {
-            this.rowConfigData = [this.referenceTrack].concat(this.alignmentTracks).concat(this.annotationTracks);
-        }
-    }
-}

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

@@ -1,5 +0,0 @@
-import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
-export declare class RcsbFvUniprot extends RcsbFvAbstractModule {
-    protected protectedBuild(): Promise<void>;
-    protected concatAlignmentAndAnnotationTracks(): void;
-}

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprot.js

@@ -1,69 +0,0 @@
-import { __awaiter } from "tslib";
-import { FieldName, OperationType, SequenceReference, Source, Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
-import { rcsbClient } from "../../RcsbGraphQL/RcsbClient";
-import { MsaAlignmentTrackFactory } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/MsaAlignmentTrackFactory";
-import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
-var assertDefined = Assertions.assertDefined;
-export class RcsbFvUniprot extends RcsbFvAbstractModule {
-    protectedBuild() {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d;
-            const buildConfig = this.buildConfig;
-            const upAcc = buildConfig.upAcc;
-            assertDefined(upAcc);
-            const source = [Source.Uniprot];
-            const alignmentRequestContext = {
-                queryId: upAcc,
-                from: SequenceReference.Uniprot,
-                to: SequenceReference.PdbEntity,
-                dynamicDisplay: false,
-                fitTitleWidth: true,
-                excludeFirstRowLink: true,
-                externalTrackBuilder: (_a = buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.externalTrackBuilder
-            };
-            const alignmentResponse = yield this.alignmentCollector.collect(alignmentRequestContext, (_b = buildConfig.additionalConfig) === null || _b === void 0 ? void 0 : _b.alignmentFilter);
-            const trackFactory = new MsaAlignmentTrackFactory(this.getPolymerEntityInstanceTranslator());
-            const alignmentFeatures = yield collectFeatures(upAcc);
-            yield trackFactory.prepareFeatures(alignmentFeatures.map(af => { var _a; return (Object.assign(Object.assign({}, af), { feature: (_a = af.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) == Type.UnobservedResidueXyz) })); }), alignmentFeatures.map(af => { var _a; return (Object.assign(Object.assign({}, af), { feature: (_a = af.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) == Type.MaQaMetricLocalTypePlddt) })); }));
-            yield this.buildAlignmentTracks(alignmentRequestContext, alignmentResponse, {
-                alignmentTrackFactory: trackFactory
-            });
-            const annotationsRequestContext = {
-                queryId: upAcc,
-                reference: SequenceReference.Uniprot,
-                sources: source,
-                annotationProcessing: (_c = buildConfig.additionalConfig) === null || _c === void 0 ? void 0 : _c.annotationProcessing,
-                externalTrackBuilder: (_d = buildConfig.additionalConfig) === null || _d === void 0 ? void 0 : _d.externalTrackBuilder
-            };
-            const annotationsFeatures = yield this.annotationCollector.collect(annotationsRequestContext);
-            yield this.buildAnnotationsTrack(annotationsRequestContext, annotationsFeatures);
-            this.boardConfigData.length = yield this.alignmentCollector.getAlignmentLength();
-            this.boardConfigData.includeAxis = true;
-            return void 0;
-        });
-    }
-    concatAlignmentAndAnnotationTracks() {
-        var _a;
-        const buildConfig = this.buildConfig;
-        this.rowConfigData = !((_a = buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.hideAlignments) ?
-            [this.referenceTrack].concat(this.annotationTracks).concat(this.alignmentTracks)
-            :
-                [this.referenceTrack].concat(this.annotationTracks);
-    }
-}
-function collectFeatures(upAcc) {
-    return __awaiter(this, void 0, void 0, function* () {
-        return yield rcsbClient.requestRcsbPdbAnnotations({
-            queryId: upAcc,
-            reference: SequenceReference.Uniprot,
-            sources: [Source.PdbInstance],
-            filters: [{
-                    source: Source.PdbInstance,
-                    operation: OperationType.Equals,
-                    field: FieldName.Type,
-                    values: [Type.UnobservedResidueXyz, Type.MaQaMetricLocalTypePlddt]
-                }]
-        });
-    });
-}

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

@@ -1,5 +0,0 @@
-import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
-export declare class RcsbFvUniprotAlignment extends RcsbFvAbstractModule {
-    protected protectedBuild(): Promise<void>;
-    protected concatAlignmentAndAnnotationTracks(): void;
-}

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprotAlignment.js

@@ -1,71 +0,0 @@
-import { __awaiter } from "tslib";
-import { FieldName, GroupReference, OperationType, SequenceReference, Source, Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
-import { rcsbClient } from "../../RcsbGraphQL/RcsbClient";
-import { MsaAlignmentTrackFactory } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/MsaAlignmentTrackFactory";
-import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
-var assertDefined = Assertions.assertDefined;
-export class RcsbFvUniprotAlignment extends RcsbFvAbstractModule {
-    protectedBuild() {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e, _f, _g, _h, _j;
-            const buildConfig = this.buildConfig;
-            assertDefined((_a = buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.page), assertDefined(buildConfig.upAcc);
-            const alignmentRequestContext = {
-                group: GroupReference.MatchingUniprotAccession,
-                groupId: buildConfig.upAcc,
-                filter: (_b = buildConfig.additionalConfig) === null || _b === void 0 ? void 0 : _b.alignmentFilter,
-                page: (_c = buildConfig.additionalConfig) === null || _c === void 0 ? void 0 : _c.page,
-                from: SequenceReference.Uniprot,
-                to: SequenceReference.PdbEntity,
-                dynamicDisplay: false,
-                fitTitleWidth: true,
-                excludeFirstRowLink: true,
-                sequencePrefix: (_e = (_d = buildConfig.additionalConfig) === null || _d === void 0 ? void 0 : _d.sequencePrefix) !== null && _e !== void 0 ? _e : "",
-                externalTrackBuilder: (_f = buildConfig.additionalConfig) === null || _f === void 0 ? void 0 : _f.externalTrackBuilder
-            };
-            const alignmentResponse = yield this.alignmentCollector.collect(alignmentRequestContext, (_g = buildConfig.additionalConfig) === null || _g === void 0 ? void 0 : _g.alignmentFilter);
-            const trackFactory = new MsaAlignmentTrackFactory(this.getPolymerEntityInstanceTranslator());
-            const alignmentFeatures = yield collectFeatures(buildConfig.upAcc);
-            yield trackFactory.prepareFeatures(alignmentFeatures.map(af => { var _a; return (Object.assign(Object.assign({}, af), { feature: (_a = af.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) == Type.UnobservedResidueXyz) })); }), alignmentFeatures.map(af => { var _a; return (Object.assign(Object.assign({}, af), { feature: (_a = af.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) == Type.MaQaMetricLocalTypePlddt) })); }));
-            yield this.buildAlignmentTracks(alignmentRequestContext, alignmentResponse, {
-                alignmentTrackFactory: trackFactory
-            });
-            const annotationsRequestContext = {
-                queryId: buildConfig.upAcc,
-                reference: SequenceReference.Uniprot,
-                sources: [Source.Uniprot],
-                annotationProcessing: (_h = buildConfig.additionalConfig) === null || _h === void 0 ? void 0 : _h.annotationProcessing,
-                externalTrackBuilder: (_j = buildConfig.additionalConfig) === null || _j === void 0 ? void 0 : _j.externalTrackBuilder
-            };
-            const annotationsFeatures = yield this.annotationCollector.collect(annotationsRequestContext);
-            yield this.buildAnnotationsTrack(annotationsRequestContext, annotationsFeatures);
-            this.boardConfigData.length = yield this.alignmentCollector.getAlignmentLength();
-            this.boardConfigData.includeAxis = true;
-            return void 0;
-        });
-    }
-    concatAlignmentAndAnnotationTracks() {
-        var _a;
-        const buildConfig = this.buildConfig;
-        this.rowConfigData = !((_a = buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.hideAlignments) ?
-            [this.referenceTrack].concat(this.annotationTracks).concat(this.alignmentTracks)
-            :
-                [this.referenceTrack].concat(this.annotationTracks);
-    }
-}
-function collectFeatures(upAcc) {
-    return __awaiter(this, void 0, void 0, function* () {
-        return yield rcsbClient.requestRcsbPdbAnnotations({
-            queryId: upAcc,
-            reference: SequenceReference.Uniprot,
-            sources: [Source.PdbInstance],
-            filters: [{
-                    source: Source.PdbInstance,
-                    operation: OperationType.Equals,
-                    field: FieldName.Type,
-                    values: [Type.UnobservedResidueXyz, Type.MaQaMetricLocalTypePlddt]
-                }]
-        });
-    });
-}

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

@@ -1,9 +0,0 @@
-import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
-import { RcsbFvBoardConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-export declare class RcsbFvUniprotEntity extends RcsbFvAbstractModule {
-    private readonly unmodeledTrackBuilder;
-    protected protectedBuild(): Promise<void>;
-    protected getBoardConfig(): Promise<RcsbFvBoardConfigInterface>;
-    protected concatAlignmentAndAnnotationTracks(): void;
-    private titleSuffix;
-}

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprotEntity.js

@@ -1,76 +0,0 @@
-import { __awaiter } from "tslib";
-import { FieldName, OperationType, SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
-import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
-var assertDefined = Assertions.assertDefined;
-import { TagDelimiter } from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter";
-import { addUnmodeledTrackBuilder, UnmodeledTrackBuilder } from "../../RcsbUtils/TrackGenerators/UnmodeledTrackBuilder";
-export class RcsbFvUniprotEntity extends RcsbFvAbstractModule {
-    constructor() {
-        super(...arguments);
-        this.unmodeledTrackBuilder = new UnmodeledTrackBuilder();
-    }
-    protectedBuild() {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c;
-            const buildConfig = this.buildConfig;
-            const upAcc = buildConfig.upAcc;
-            const entityId = buildConfig.entityId;
-            const additionalConfig = buildConfig.additionalConfig;
-            assertDefined(upAcc), assertDefined(entityId);
-            const filters = [{
-                    field: FieldName.TargetId,
-                    operation: OperationType.Equals,
-                    source: Source.PdbEntity,
-                    values: [entityId]
-                }];
-            const alignmentRequestContext = {
-                queryId: upAcc,
-                from: SequenceReference.Uniprot,
-                to: SequenceReference.PdbEntity,
-                filterByTargetContains: entityId,
-                excludeAlignmentLinks: true,
-                externalTrackBuilder: (_a = buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.externalTrackBuilder
-            };
-            const alignmentResponse = yield this.alignmentCollector.collect(alignmentRequestContext, [entityId]);
-            yield this.buildAlignmentTracks(alignmentRequestContext, alignmentResponse);
-            const annotationsRequestContext = {
-                queryId: upAcc,
-                reference: SequenceReference.Uniprot,
-                sources: (additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.sources) ? additionalConfig.sources : [Source.PdbEntity, Source.Uniprot],
-                filters: (additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.filters) instanceof Array ? additionalConfig.filters.concat(filters) : filters,
-                titleSuffix: this.titleSuffix.bind(this),
-                annotationProcessing: (_b = buildConfig.additionalConfig) === null || _b === void 0 ? void 0 : _b.annotationProcessing,
-                rcsbContext: {
-                    entityId: buildConfig.entityId
-                },
-                externalTrackBuilder: addUnmodeledTrackBuilder(this.unmodeledTrackBuilder, (_c = buildConfig.additionalConfig) === null || _c === void 0 ? void 0 : _c.externalTrackBuilder)
-            };
-            const annotationsFeatures = yield this.annotationCollector.collect(annotationsRequestContext);
-            yield this.buildAnnotationsTrack(annotationsRequestContext, annotationsFeatures);
-            this.boardConfigData.length = yield this.alignmentCollector.getAlignmentLength();
-            this.boardConfigData.includeAxis = true;
-            return void 0;
-        });
-    }
-    getBoardConfig() {
-        return __awaiter(this, void 0, void 0, function* () {
-            return Object.assign(Object.assign({}, this.boardConfigData), { tooltipGenerator: this.unmodeledTrackBuilder.getTooltip() });
-        });
-    }
-    concatAlignmentAndAnnotationTracks() {
-        this.rowConfigData = [this.referenceTrack].concat(this.alignmentTracks).concat(this.annotationTracks);
-    }
-    titleSuffix(ann, d) {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a;
-            if (this.polymerEntityInstance != null && ann.source === Source.PdbInstance) {
-                const labelAsymId = (_a = ann.target_id) === null || _a === void 0 ? void 0 : _a.split(TagDelimiter.instance)[1];
-                if (!labelAsymId)
-                    return;
-                const authAsymId = this.polymerEntityInstance.translateAsymToAuth(labelAsymId);
-                return labelAsymId === authAsymId ? labelAsymId : labelAsymId + "[auth " + authAsymId + "]";
-            }
-        });
-    }
-}

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

@@ -1,5 +0,0 @@
-import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
-export declare class RcsbFvUniprotInstance extends RcsbFvAbstractModule {
-    protected protectedBuild(): Promise<void>;
-    protected concatAlignmentAndAnnotationTracks(): void;
-}

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprotInstance.js

@@ -1,63 +0,0 @@
-import { __awaiter } from "tslib";
-import { FieldName, OperationType, SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
-import { buriedResidues, buriedResiduesFilter } from "../../RcsbUtils/TrackGenerators/BuriedResidues";
-import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
-var assertDefined = Assertions.assertDefined;
-export class RcsbFvUniprotInstance extends RcsbFvAbstractModule {
-    protectedBuild() {
-        return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c;
-            const buildConfig = this.buildConfig;
-            const upAcc = buildConfig.upAcc;
-            const entityId = buildConfig.entityId;
-            const instanceId = buildConfig.instanceId;
-            const additionalConfig = buildConfig.additionalConfig;
-            assertDefined(entityId), assertDefined(instanceId), assertDefined(upAcc);
-            let sources = [Source.Uniprot, Source.PdbEntity, Source.PdbInstance];
-            if (additionalConfig != null && additionalConfig.sources != null && additionalConfig.sources.length > 0)
-                sources = additionalConfig.sources;
-            let filters = [{
-                    field: FieldName.TargetId,
-                    operation: OperationType.Equals,
-                    source: Source.PdbEntity,
-                    values: [entityId]
-                }, {
-                    field: FieldName.TargetId,
-                    operation: OperationType.Contains,
-                    source: Source.PdbInstance,
-                    values: [instanceId]
-                }];
-            if (additionalConfig != null && additionalConfig.filters != null && additionalConfig.filters.length > 0)
-                filters = additionalConfig.filters;
-            const alignmentRequestContext = {
-                queryId: upAcc,
-                from: SequenceReference.Uniprot,
-                to: SequenceReference.PdbInstance,
-                filterByTargetContains: instanceId,
-                excludeFirstRowLink: true,
-                externalTrackBuilder: (_a = buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.externalTrackBuilder
-            };
-            const alignmentResponse = yield this.alignmentCollector.collect(alignmentRequestContext, [instanceId]);
-            yield this.buildAlignmentTracks(alignmentRequestContext, alignmentResponse);
-            const annotationsRequestContext = {
-                queryId: upAcc,
-                reference: SequenceReference.Uniprot,
-                sources: sources,
-                filters: filters,
-                annotationGenerator: (ann) => (new Promise((r) => (r(buriedResidues(ann))))),
-                annotationFilter: (ann) => (new Promise((r) => (r(buriedResiduesFilter(ann))))),
-                annotationProcessing: (_b = buildConfig.additionalConfig) === null || _b === void 0 ? void 0 : _b.annotationProcessing,
-                externalTrackBuilder: (_c = buildConfig.additionalConfig) === null || _c === void 0 ? void 0 : _c.externalTrackBuilder
-            };
-            const annotationsFeatures = yield this.annotationCollector.collect(annotationsRequestContext);
-            yield this.buildAnnotationsTrack(annotationsRequestContext, annotationsFeatures);
-            this.boardConfigData.length = yield this.alignmentCollector.getAlignmentLength();
-            this.boardConfigData.includeAxis = true;
-            return void 0;
-        });
-    }
-    concatAlignmentAndAnnotationTracks() {
-        this.rowConfigData = [this.referenceTrack].concat(this.alignmentTracks).concat(this.annotationTracks);
-    }
-}

package/lib/RcsbFvWeb/RcsbFvTooltip/RcsbFvTooltip.d.ts

@@ -1,8 +0,0 @@
-import { RcsbFvTooltipInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvTooltip/RcsbFvTooltipInterface";
-import { RcsbFvTrackDataAnnotationInterface } from "../RcsbFvFactories/RcsbFvTrackFactory/RcsbFvTrackDataAnnotationInterface";
-export declare class RcsbFvTooltip implements RcsbFvTooltipInterface {
-    showTooltip(d: RcsbFvTrackDataAnnotationInterface): HTMLElement;
-    showTooltipDescription(d: RcsbFvTrackDataAnnotationInterface): HTMLElement | undefined;
-    private static buildIndexNames;
-    private static bNode;
-}

package/lib/RcsbFvWeb/RcsbFvTooltip/RcsbFvTooltip.js

@@ -1,82 +0,0 @@
-export class RcsbFvTooltip {
-    showTooltip(d) {
-        const tooltipDiv = document.createElement("div");
-        let region = "Position: " + d.begin.toString();
-        if (typeof d.end === "number" && d.end != d.begin)
-            region += " - " + d.end.toString();
-        const spanRegion = document.createElement("span");
-        spanRegion.append(region);
-        if (typeof d.beginName === "string" && d.indexName != undefined) {
-            spanRegion.append(RcsbFvTooltip.buildIndexNames(d.beginName, d.endName, d.indexName));
-        }
-        if (typeof d.oriBegin === "number") {
-            let ori_region = d.oriBegin.toString();
-            if (typeof d.oriEnd === "number")
-                ori_region += " - " + d.oriEnd.toString();
-            const spanOriRegion = document.createElement("span");
-            if (d.source != undefined)
-                spanOriRegion.append(" | [" + d.source.replace("_", " ") + "] " + d.sourceId + ": " + ori_region);
-            spanOriRegion.style.color = "#888888";
-            if (typeof d.oriBeginName === "string" && d.indexName != undefined)
-                spanOriRegion.append(RcsbFvTooltip.buildIndexNames(d.oriBeginName, d.oriEndName, d.indexName));
-            spanRegion.append(spanOriRegion);
-        }
-        let title = d.title;
-        if (typeof d.name === "string")
-            title = d.name;
-        else if (typeof d.featureId === "string")
-            title = d.featureId;
-        if (title != undefined)
-            tooltipDiv.append(title);
-        if (typeof d.provenanceName === "string") {
-            const spanProvenance = document.createElement("span");
-            const spanProvenanceString = document.createElement("span");
-            spanProvenanceString.append(d.provenanceName);
-            if (typeof d.provenanceColor === "string")
-                spanProvenanceString.style.color = d.provenanceColor;
-            else
-                spanProvenanceString.style.color = "#888888";
-            spanProvenance.append(" [", spanProvenanceString, "]");
-            spanProvenance.style.color = "#888888";
-            tooltipDiv.append(spanProvenance);
-            tooltipDiv.append(RcsbFvTooltip.bNode());
-        }
-        else if (title != undefined) {
-            tooltipDiv.append(RcsbFvTooltip.bNode());
-        }
-        if (typeof d.value === "number") {
-            const valueRegion = document.createElement("span");
-            valueRegion.append(" value: " + d.value);
-            tooltipDiv.append(valueRegion);
-            tooltipDiv.append(RcsbFvTooltip.bNode());
-        }
-        tooltipDiv.append(spanRegion);
-        return tooltipDiv;
-    }
-    showTooltipDescription(d) {
-        if (d.description == null || d.description.length == 0)
-            return undefined;
-        const tooltipDescriptionDiv = document.createElement("div");
-        d.description.forEach(des => {
-            const desDiv = document.createElement("div");
-            desDiv.append(des);
-            tooltipDescriptionDiv.append(desDiv);
-        });
-        return tooltipDescriptionDiv;
-    }
-    static buildIndexNames(beginName, endName, name) {
-        const spanAuthRegion = document.createElement("span");
-        let authRegion = beginName;
-        if (typeof endName === "string")
-            authRegion += " - " + endName;
-        spanAuthRegion.append(" [" + name + ": " + authRegion + "]");
-        spanAuthRegion.style.color = "#888888";
-        return spanAuthRegion;
-    }
-    static bNode() {
-        const b = document.createElement("span");
-        b.append(" | ");
-        b.style.fontWeight = "bold";
-        return b;
-    }
-}

package/lib/RcsbFvWeb/RcsbFvWorkers/RcsbFvAlignmentCollectorQueue.d.ts

@@ -1,12 +0,0 @@
-import { QueryAlignmentArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-export declare class RcsbFvAlignmentCollectorQueue {
-    private readonly nWorkers;
-    private readonly workerList;
-    private readonly taskQueue;
-    private isQueueActive;
-    constructor(nWorkers?: number);
-    sendTask(request: QueryAlignmentArgs, callback: (data: any) => void): void;
-    private activateQueue;
-    private recursiveExec;
-    terminateWorkers(): void;
-}

package/lib/RcsbFvWeb/RcsbFvWorkers/RcsbFvAlignmentCollectorQueue.js

@@ -1,67 +0,0 @@
-import { asyncScheduler } from "rxjs";
-export class RcsbFvAlignmentCollectorQueue {
-    constructor(nWorkers) {
-        this.workerList = new Array();
-        this.taskQueue = new Array();
-        this.isQueueActive = false;
-        if (nWorkers != null)
-            this.nWorkers = nWorkers;
-        else
-            this.nWorkers = self.navigator.hardwareConcurrency;
-        for (let i = 0; i < this.nWorkers; i++) {
-            this.workerList.push({
-                available: true,
-                worker: new Worker("/saguaro/worker.js")
-            });
-        }
-    }
-    sendTask(request, callback) {
-        const available = this.workerList.filter(d => d.available);
-        if (available.length > 0) {
-            available[0].available = false;
-            available[0].worker.postMessage(request);
-            available[0].worker.onmessage = (e) => {
-                callback(e.data);
-                available[0].available = true;
-            };
-        }
-        else {
-            this.taskQueue.push({ request: request, callback: callback });
-            if (!this.isQueueActive)
-                this.activateQueue();
-        }
-    }
-    activateQueue() {
-        this.isQueueActive = true;
-        this.recursiveExec();
-    }
-    recursiveExec() {
-        if (this.taskQueue.length == 0) {
-            this.isQueueActive = false;
-        }
-        else {
-            this.isQueueActive = true;
-            this.workerList.filter(d => d.available).forEach(aW => {
-                if (this.taskQueue.length > 0) {
-                    aW.available = false;
-                    const task = this.taskQueue.shift();
-                    if (!task)
-                        return;
-                    aW.worker.postMessage(task.request);
-                    aW.worker.onmessage = (e) => {
-                        task.callback(e.data);
-                        aW.available = true;
-                    };
-                }
-            });
-            asyncScheduler.schedule(() => {
-                this.recursiveExec();
-            }, 1000);
-        }
-    }
-    terminateWorkers() {
-        this.workerList.forEach(w => {
-            w.worker.terminate();
-        });
-    }
-}

package/lib/RcsbFvWeb/RcsbFvWorkers/RcsbFvAlignmentCollectorWorker.worker.d.ts

@@ -1 +0,0 @@
-export {};

package/lib/RcsbFvWeb/RcsbFvWorkers/RcsbFvAlignmentCollectorWorker.worker.js

@@ -1,10 +0,0 @@
-import { rcsbClient } from "../../RcsbGraphQL/RcsbClient";
-const worker = self;
-worker.onmessage = function (message) {
-    const request = message.data;
-    const rcsbFvQuery = rcsbClient;
-    rcsbFvQuery.requestAlignment(request).then((result) => {
-        // @ts-ignore
-        postMessage(result);
-    });
-};

package/lib/RcsbGraphQL/RcsbClient.d.ts

@@ -1,35 +0,0 @@
-import { RcsbQueryGroupAlignmentArguments } from "./RcsbQueryAlignment";
-import { AlignmentResponse, AnnotationFeatures, QueryAlignmentArgs, QueryAnnotationsArgs, QueryGroup_AnnotationsArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { CoreAssembly, CoreEntry, CoreInterface, CorePolymerEntity, QueryAssembliesArgs, GroupPolymerEntity, QueryEntriesArgs, QueryEntryArgs, QueryInterfacesArgs, QueryPolymer_EntitiesArgs, QueryPolymer_Entity_GroupArgs, QueryPolymer_Entity_InstancesArgs, CorePolymerEntityInstance } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Yosemite/GqlTypes";
-import { GraphQLRequest } from "@rcsb/rcsb-api-tools";
-declare class RcsbClientClass {
-    private readonly rcsbQueryAnnotations;
-    private readonly rcsbQueryGroupAnnotations;
-    private readonly rcsbQueryAlignment;
-    private readonly rcsbQueryGroupAlignment;
-    private readonly rcsbQueryEntityInstances;
-    private readonly rcsbQueryMutipleEntityInstances;
-    private readonly rcsbQueryEntryProperties;
-    private readonly rcsbQueryInterfaceInstances;
-    private readonly rcsbQueryAssemblyInterfaces;
-    private readonly rcsbQueryGroup;
-    private readonly rcsbQueryMultipleInstanceSequences;
-    constructor(get: {
-        borrego: () => GraphQLRequest;
-        yosemite: () => GraphQLRequest;
-    });
-    requestRcsbPdbAnnotations(requestConfig: QueryAnnotationsArgs): Promise<Array<AnnotationFeatures>>;
-    requestRcsbPdbGroupAnnotations(requestConfig: QueryGroup_AnnotationsArgs): Promise<Array<AnnotationFeatures>>;
-    requestAlignment(requestConfig: QueryAlignmentArgs): Promise<AlignmentResponse>;
-    requestGroupAlignment(requestConfig: RcsbQueryGroupAlignmentArguments): Promise<AlignmentResponse>;
-    requestEntityInstances(requestConfig: QueryEntryArgs): Promise<CoreEntry>;
-    requestMultipleEntityInstances(requestConfig: QueryPolymer_EntitiesArgs): Promise<Array<CorePolymerEntity>>;
-    requestGroupInfo(requestConfig: QueryPolymer_Entity_GroupArgs): Promise<GroupPolymerEntity>;
-    requestMultipleEntriesProperties(requestConfig: QueryEntriesArgs): Promise<Array<CoreEntry>>;
-    requestInterfaceInstances(requestConfig: QueryInterfacesArgs): Promise<Array<CoreInterface>>;
-    requestAssemblyInterfaces(requestConfig: QueryAssembliesArgs): Promise<Array<CoreAssembly>>;
-    requestMultipleInstanceSequences(requestConfig: QueryPolymer_Entity_InstancesArgs): Promise<CorePolymerEntityInstance[]>;
-}
-export declare const rcsbClient: RcsbClientClass;
-export type RcsbClient = typeof rcsbClient;
-export {};