@rcsb/rcsb-saguaro-app 6.3.2 → 6.3.4

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvDataProvider.d.ts

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

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvDataProvider.js

@@ -1,29 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.RcsbFvDataProvider = void 0;
-const tslib_1 = require("tslib");
-const RcsbFvAbstractModule_1 = require("./RcsbFvAbstractModule");
-const PlainAlignmentTrackFactory_1 = require("../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PlainAlignmentTrackFactory");
-class RcsbFvDataProvider extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
-    protectedBuild() {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l, _m, _o;
-            if ((_b = (_a = this.buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.dataProvider) === null || _b === void 0 ? void 0 : _b.alignments) {
-                this.alignmentCollector = this.buildConfig.additionalConfig.dataProvider.alignments.collector;
-                const alignmentResponse = yield this.alignmentCollector.collect(Object.assign({}, (_d = (_c = this.buildConfig.additionalConfig) === null || _c === void 0 ? void 0 : _c.dataProvider) === null || _d === void 0 ? void 0 : _d.alignments.context), (_e = this.buildConfig.additionalConfig) === null || _e === void 0 ? void 0 : _e.alignmentFilter);
-                yield this.buildAlignmentTracks((_g = (_f = this.buildConfig.additionalConfig) === null || _f === void 0 ? void 0 : _f.dataProvider) === null || _g === void 0 ? void 0 : _g.alignments.context, alignmentResponse, Object.assign({ alignmentTrackFactory: new PlainAlignmentTrackFactory_1.PlainAlignmentTrackFactory(this.getPolymerEntityInstanceTranslator()) }, (_j = (_h = this.buildConfig.additionalConfig) === null || _h === void 0 ? void 0 : _h.dataProvider) === null || _j === void 0 ? void 0 : _j.alignments.trackFactories));
-                this.boardConfigData.length = yield ((_l = (_k = this.buildConfig.additionalConfig) === null || _k === void 0 ? void 0 : _k.dataProvider) === null || _l === void 0 ? void 0 : _l.alignments.collector.getAlignmentLength());
-            }
-            if ((_o = (_m = this.buildConfig.additionalConfig) === null || _m === void 0 ? void 0 : _m.dataProvider) === null || _o === void 0 ? void 0 : _o.annotations) {
-                this.annotationCollector = this.buildConfig.additionalConfig.dataProvider.annotations.collector;
-                const annotationsFeatures = yield this.annotationCollector.collect(Object.assign({}, this.buildConfig.additionalConfig.dataProvider.annotations.context));
-                yield this.buildAnnotationsTrack(this.buildConfig.additionalConfig.dataProvider.annotations.context, annotationsFeatures);
-            }
-            this.boardConfigData.includeAxis = true;
-        });
-    }
-    concatAlignmentAndAnnotationTracks() {
-        this.rowConfigData = this.referenceTrack ? [this.referenceTrack].concat(this.alignmentTracks) : this.alignmentTracks;
-    }
-}
-exports.RcsbFvDataProvider = RcsbFvDataProvider;

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvEntity.d.ts

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

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvEntity.js

@@ -1,73 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.RcsbFvEntity = void 0;
-const tslib_1 = require("tslib");
-const GqlTypes_1 = require("@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes");
-const RcsbFvAbstractModule_1 = require("./RcsbFvAbstractModule");
-const Assertions_1 = require("../../RcsbUtils/Helpers/Assertions");
-var assertDefined = Assertions_1.Assertions.assertDefined;
-const TagDelimiter_1 = require("@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter");
-const UnmodeledTrackBuilder_1 = require("../../RcsbUtils/TrackGenerators/UnmodeledTrackBuilder");
-class RcsbFvEntity extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
-    constructor() {
-        super(...arguments);
-        this.unmodeledTrackBuilder = new UnmodeledTrackBuilder_1.UnmodeledTrackBuilder();
-    }
-    protectedBuild() {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e, _f, _g;
-            const buildConfig = this.buildConfig;
-            assertDefined(buildConfig.entityId);
-            const alignmentRequestContext = {
-                queryId: buildConfig.entityId,
-                from: GqlTypes_1.SequenceReference.PdbEntity,
-                to: GqlTypes_1.SequenceReference.Uniprot,
-                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);
-            yield this.buildAlignmentTracks(alignmentRequestContext, alignmentResponse);
-            const annotationsRequestContext = {
-                queryId: buildConfig.entityId,
-                reference: GqlTypes_1.SequenceReference.PdbEntity,
-                sources: (_d = (_c = buildConfig.additionalConfig) === null || _c === void 0 ? void 0 : _c.sources) !== null && _d !== void 0 ? _d : [GqlTypes_1.Source.PdbEntity, GqlTypes_1.Source.Uniprot],
-                titleSuffix: this.titleSuffix.bind(this),
-                filters: (_e = buildConfig.additionalConfig) === null || _e === void 0 ? void 0 : _e.filters,
-                annotationProcessing: (_f = buildConfig.additionalConfig) === null || _f === void 0 ? void 0 : _f.annotationProcessing,
-                rcsbContext: {
-                    entityId: buildConfig.entityId
-                },
-                externalTrackBuilder: (0, UnmodeledTrackBuilder_1.addUnmodeledTrackBuilder)(this.unmodeledTrackBuilder, (_g = buildConfig.additionalConfig) === null || _g === void 0 ? void 0 : _g.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 tslib_1.__awaiter(this, void 0, void 0, function* () {
-            return Object.assign(Object.assign({}, this.boardConfigData), { tooltipGenerator: this.unmodeledTrackBuilder.getTooltip() });
-        });
-    }
-    concatAlignmentAndAnnotationTracks() {
-        var _a;
-        const buildConfig = this.buildConfig;
-        this.rowConfigData = !((_a = buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.hideAlignments) ?
-            [this.referenceTrack].concat(this.alignmentTracks).concat(this.annotationTracks)
-            :
-                [this.referenceTrack].concat(this.alignmentTracks).concat(this.annotationTracks);
-    }
-    titleSuffix(ann, d) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            if (!ann.target_id)
-                return;
-            if (this.polymerEntityInstance != null && ann.source === GqlTypes_1.Source.PdbInstance) {
-                const labelAsymId = ann.target_id.split(TagDelimiter_1.TagDelimiter.instance)[1];
-                const authAsymId = this.polymerEntityInstance.translateAsymToAuth(labelAsymId);
-                return labelAsymId === authAsymId ? labelAsymId : labelAsymId + "[auth " + authAsymId + "]";
-            }
-        });
-    }
-}
-exports.RcsbFvEntity = RcsbFvEntity;

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvGroupAlignment.d.ts

@@ -1,7 +0,0 @@
-import { RcsbFvBoardConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
-export declare class RcsbFvGroupAlignment extends RcsbFvAbstractModule {
-    protected protectedBuild(): Promise<void>;
-    protected concatAlignmentAndAnnotationTracks(): void;
-    protected getBoardConfig(): Promise<RcsbFvBoardConfigInterface>;
-}

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvGroupAlignment.js

@@ -1,105 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.RcsbFvGroupAlignment = void 0;
-const tslib_1 = require("tslib");
-const RcsbFvAbstractModule_1 = require("./RcsbFvAbstractModule");
-const GqlTypes_1 = require("@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes");
-const MsaAlignmentTrackFactory_1 = require("../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/MsaAlignmentTrackFactory");
-const Assertions_1 = require("../../RcsbUtils/Helpers/Assertions");
-var assertDefined = Assertions_1.Assertions.assertDefined;
-const TagDelimiter_1 = require("@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter");
-const Operator_1 = require("../../RcsbUtils/Helpers/Operator");
-const RcsbRequestContextManager_1 = require("../../RcsbRequest/RcsbRequestContextManager");
-class RcsbFvGroupAlignment extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
-    protectedBuild() {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e, _f, _g, _h, _j;
-            const buildConfig = this.buildConfig;
-            assertDefined(buildConfig.groupId), assertDefined(buildConfig.group), assertDefined((_a = buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.page);
-            const alignmentRequestContext = {
-                group: buildConfig.group,
-                groupId: buildConfig.groupId,
-                filter: (_b = buildConfig.additionalConfig) === null || _b === void 0 ? void 0 : _b.alignmentFilter,
-                page: (_c = buildConfig.additionalConfig) === null || _c === void 0 ? void 0 : _c.page,
-                excludeLogo: (_d = buildConfig.additionalConfig) === null || _d === void 0 ? void 0 : _d.excludeLogo,
-                from: buildConfig.from,
-                to: buildConfig.to,
-                dynamicDisplay: false,
-                fitTitleWidth: true,
-                excludeFirstRowLink: true,
-                sequencePrefix: (_f = (_e = buildConfig.additionalConfig) === null || _e === void 0 ? void 0 : _e.sequencePrefix) !== null && _f !== void 0 ? _f : "",
-                externalTrackBuilder: (_g = buildConfig.additionalConfig) === null || _g === void 0 ? void 0 : _g.externalTrackBuilder
-            };
-            collectNextPage(alignmentRequestContext, this.alignmentCollector, this.annotationCollector).then(() => console.log("Next page ready"));
-            const alignmentResponse = yield this.alignmentCollector.collect(alignmentRequestContext, (_h = buildConfig.additionalConfig) === null || _h === void 0 ? void 0 : _h.alignmentFilter);
-            const trackFactory = new MsaAlignmentTrackFactory_1.MsaAlignmentTrackFactory(this.getPolymerEntityInstanceTranslator());
-            const targetList = uniqueTargetList(alignmentResponse);
-            const alignmentFeatures = yield collectFeatures({
-                groupId: buildConfig.groupId,
-                externalTrackBuilder: (_j = buildConfig.additionalConfig) === null || _j === void 0 ? void 0 : _j.externalTrackBuilder,
-                targetList
-            }, this.annotationCollector);
-            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) == GqlTypes_1.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) == GqlTypes_1.Type.MaQaMetricLocalTypePlddt) })); }));
-            yield this.buildAlignmentTracks(alignmentRequestContext, alignmentResponse, {
-                alignmentTrackFactory: trackFactory
-            });
-            return void 0;
-        });
-    }
-    concatAlignmentAndAnnotationTracks() {
-        this.rowConfigData = this.referenceTrack ? [this.referenceTrack].concat(this.alignmentTracks) : this.alignmentTracks;
-    }
-    getBoardConfig() {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            return Object.assign(Object.assign({}, this.boardConfigData), { length: yield this.alignmentCollector.getAlignmentLength(), includeAxis: true });
-        });
-    }
-}
-exports.RcsbFvGroupAlignment = RcsbFvGroupAlignment;
-function collectNextPage(alignmentRequestContext, alignmentCollector, annotationCollector) {
-    return tslib_1.__awaiter(this, void 0, void 0, function* () {
-        const alignmentResponse = yield alignmentCollector.collect(Object.assign(Object.assign({}, alignmentRequestContext), { excludeLogo: true, page: {
-                first: alignmentRequestContext.page.first,
-                after: (parseInt(alignmentRequestContext.page.after) + alignmentRequestContext.page.first).toString()
-            } }));
-        const targetList = uniqueTargetList(alignmentResponse);
-        if (alignmentRequestContext.groupId) {
-            const alignmentFeatures = yield collectFeatures({
-                groupId: alignmentRequestContext.groupId,
-                targetList
-            }, annotationCollector);
-            const featureTargetList = Operator_1.Operator.uniqueValues(alignmentFeatures.map(af => { var _a; return TagDelimiter_1.TagDelimiter.parseInstance((_a = af.target_id) !== null && _a !== void 0 ? _a : "").entryId; }));
-            Operator_1.Operator.arrayChunk(featureTargetList, 100).forEach(ids => RcsbRequestContextManager_1.rcsbRequestCtxManager.getEntryProperties(ids));
-        }
-    });
-}
-function uniqueTargetList(alignmentResponse) {
-    var _a, _b;
-    return Operator_1.Operator.uniqueValues((_b = (_a = alignmentResponse.target_alignment) === null || _a === void 0 ? void 0 : _a.map(ta => {
-        assertDefined(ta === null || ta === void 0 ? void 0 : ta.target_id);
-        return TagDelimiter_1.TagDelimiter.parseEntity(ta.target_id).entryId;
-    })) !== null && _b !== void 0 ? _b : []);
-}
-function collectFeatures(annotationsContext, annotationCollector) {
-    return tslib_1.__awaiter(this, void 0, void 0, function* () {
-        const annotationsRequestContext = {
-            histogram: false,
-            groupId: annotationsContext.groupId,
-            group: GqlTypes_1.GroupReference.SequenceIdentity,
-            sources: [GqlTypes_1.Source.PdbInstance],
-            filters: [{
-                    source: GqlTypes_1.Source.PdbInstance,
-                    operation: GqlTypes_1.OperationType.Equals,
-                    field: GqlTypes_1.FieldName.Type,
-                    values: [GqlTypes_1.Type.UnobservedResidueXyz, GqlTypes_1.Type.MaQaMetricLocalTypePlddt]
-                }, {
-                    source: GqlTypes_1.Source.PdbInstance,
-                    operation: GqlTypes_1.OperationType.Contains,
-                    field: GqlTypes_1.FieldName.TargetId,
-                    values: annotationsContext.targetList
-                }],
-            externalTrackBuilder: annotationsContext.externalTrackBuilder
-        };
-        return yield annotationCollector.collect(annotationsRequestContext);
-    });
-}

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvGroupAnnotation.d.ts

@@ -1,7 +0,0 @@
-import { RcsbFvBoardConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
-export declare class RcsbFvGroupAnnotation extends RcsbFvAbstractModule {
-    protectedBuild(): Promise<void>;
-    protected getBoardConfig(): Promise<RcsbFvBoardConfigInterface>;
-    protected concatAlignmentAndAnnotationTracks(): void;
-}

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvGroupAnnotation.js

@@ -1,56 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.RcsbFvGroupAnnotation = void 0;
-const tslib_1 = require("tslib");
-const RcsbFvAbstractModule_1 = require("./RcsbFvAbstractModule");
-const acm = tslib_1.__importStar(require("../../RcsbAnnotationConfig/GroupAnnotationConfig.ac.json"));
-const SequenceTrackFactory_1 = require("../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/SequenceTrackFactory");
-const Assertions_1 = require("../../RcsbUtils/Helpers/Assertions");
-var assertDefined = Assertions_1.Assertions.assertDefined;
-const annotationConfigMap = acm;
-class RcsbFvGroupAnnotation extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
-    protectedBuild() {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l;
-            const buildConfig = this.buildConfig;
-            assertDefined(buildConfig.group), assertDefined(buildConfig.groupId), assertDefined((_a = buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.page);
-            const alignmentRequestContext = {
-                group: buildConfig.group,
-                groupId: buildConfig.groupId,
-                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: buildConfig.from,
-                to: buildConfig.to,
-                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 sequenceTrackFactory = new SequenceTrackFactory_1.SequenceTrackFactory(this.getPolymerEntityInstanceTranslator());
-            if (alignmentResponse.query_sequence)
-                this.referenceTrack = yield sequenceTrackFactory.getTrack(alignmentRequestContext, alignmentResponse.query_sequence);
-            const annotationsRequestContext = {
-                group: buildConfig.group,
-                groupId: buildConfig.groupId,
-                sources: (_h = buildConfig.additionalConfig) === null || _h === void 0 ? void 0 : _h.sources,
-                filters: (_j = buildConfig.additionalConfig) === null || _j === void 0 ? void 0 : _j.filters,
-                annotationProcessing: (_k = buildConfig.additionalConfig) === null || _k === void 0 ? void 0 : _k.annotationProcessing,
-                externalTrackBuilder: (_l = buildConfig.additionalConfig) === null || _l === void 0 ? void 0 : _l.externalTrackBuilder
-            };
-            const annotationsFeatures = yield this.annotationCollector.collect(annotationsRequestContext);
-            yield this.buildAnnotationsTrack(annotationsRequestContext, annotationsFeatures, annotationConfigMap);
-            return void 0;
-        });
-    }
-    getBoardConfig() {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            return Object.assign(Object.assign({}, this.boardConfigData), { length: yield this.alignmentCollector.getAlignmentLength(), includeAxis: true });
-        });
-    }
-    concatAlignmentAndAnnotationTracks() {
-        this.rowConfigData = this.referenceTrack ? [this.referenceTrack].concat(this.alignmentTracks).concat(this.annotationTracks) : this.alignmentTracks.concat(this.annotationTracks);
-    }
-}
-exports.RcsbFvGroupAnnotation = RcsbFvGroupAnnotation;

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvInstance.d.ts

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

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvInstance.js

@@ -1,56 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.RcsbFvInstance = void 0;
-const tslib_1 = require("tslib");
-const GqlTypes_1 = require("@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes");
-const RcsbFvAbstractModule_1 = require("./RcsbFvAbstractModule");
-const BuriedResidues_1 = require("../../RcsbUtils/TrackGenerators/BuriedResidues");
-const SequenceTrackFactory_1 = require("../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/SequenceTrackFactory");
-const InstanceSequenceTrackTitleFactory_1 = require("../RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/InstanceSequenceTrackTitleFactory");
-const Assertions_1 = require("../../RcsbUtils/Helpers/Assertions");
-var assertDefined = Assertions_1.Assertions.assertDefined;
-class RcsbFvInstance extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
-    protectedBuild() {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d;
-            const buildConfig = this.buildConfig;
-            const instanceId = buildConfig.instanceId;
-            assertDefined(instanceId);
-            const source = [GqlTypes_1.Source.PdbEntity, GqlTypes_1.Source.PdbInstance, GqlTypes_1.Source.Uniprot];
-            const alignmentRequestContext = {
-                queryId: instanceId,
-                from: GqlTypes_1.SequenceReference.PdbInstance,
-                to: GqlTypes_1.SequenceReference.Uniprot,
-                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);
-            yield this.buildAlignmentTracks(alignmentRequestContext, alignmentResponse, {
-                sequenceTrackFactory: new SequenceTrackFactory_1.SequenceTrackFactory(this.getPolymerEntityInstanceTranslator(), new InstanceSequenceTrackTitleFactory_1.InstanceSequenceTrackTitleFactory(this.getPolymerEntityInstanceTranslator()))
-            });
-            const annotationsRequestContext = {
-                queryId: instanceId,
-                reference: GqlTypes_1.SequenceReference.PdbInstance,
-                annotationGenerator: (ann) => (new Promise((r) => (r((0, BuriedResidues_1.buriedResidues)(ann))))),
-                annotationFilter: (ann) => (new Promise((r) => (r((0, BuriedResidues_1.buriedResiduesFilter)(ann))))),
-                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.alignmentTracks).concat(this.annotationTracks)
-                :
-                    this.alignmentTracks.concat(this.annotationTracks);
-    }
-}
-exports.RcsbFvInstance = RcsbFvInstance;

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvInterface.d.ts

@@ -1,12 +0,0 @@
-import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
-export declare class RcsbFvInterface extends RcsbFvAbstractModule {
-    private instanceId;
-    protected protectedBuild(): Promise<void>;
-    protected concatAlignmentAndAnnotationTracks(): void;
-    private typeSuffix;
-    private titleSuffix;
-    private trackTitle;
-}
-export declare function interfaceAnnotations(annotations: Array<AnnotationFeatures>): Promise<Array<AnnotationFeatures>>;
-export declare function filter(ann: Array<AnnotationFeatures>): Promise<Array<AnnotationFeatures>>;

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvInterface.js

@@ -1,129 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.RcsbFvInterface = void 0;
-exports.interfaceAnnotations = interfaceAnnotations;
-exports.filter = filter;
-const tslib_1 = require("tslib");
-const GqlTypes_1 = require("@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes");
-const RcsbFvAbstractModule_1 = require("./RcsbFvAbstractModule");
-const acm = tslib_1.__importStar(require("../../RcsbAnnotationConfig/RcsbAnnotationConfig.ac.json"));
-const BuriedResidues_1 = require("../../RcsbUtils/TrackGenerators/BuriedResidues");
-const BurialFraction_1 = require("../../RcsbUtils/TrackGenerators/BurialFraction");
-const FeatureType_1 = require("../../RcsbExport/FeatureType");
-const RcsbRequestContextManager_1 = require("../../RcsbRequest/RcsbRequestContextManager");
-const SequenceTrackFactory_1 = require("../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/SequenceTrackFactory");
-const InstanceSequenceTrackTitleFactory_1 = require("../RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/InstanceSequenceTrackTitleFactory");
-const Assertions_1 = require("../../RcsbUtils/Helpers/Assertions");
-var assertDefined = Assertions_1.Assertions.assertDefined;
-const TagDelimiter_1 = require("@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter");
-const annotationConfigMap = acm;
-class RcsbFvInterface extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
-    protectedBuild() {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e;
-            const buildConfig = this.buildConfig;
-            const instanceId = buildConfig.instanceId;
-            assertDefined(instanceId);
-            this.instanceId = instanceId;
-            const source = [GqlTypes_1.Source.PdbEntity, GqlTypes_1.Source.PdbInstance, GqlTypes_1.Source.Uniprot, GqlTypes_1.Source.PdbInterface];
-            const alignmentRequestContext = {
-                queryId: instanceId,
-                from: GqlTypes_1.SequenceReference.PdbInstance,
-                to: GqlTypes_1.SequenceReference.Uniprot,
-                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);
-            yield this.buildAlignmentTracks(alignmentRequestContext, alignmentResponse, {
-                sequenceTrackFactory: new SequenceTrackFactory_1.SequenceTrackFactory(this.getPolymerEntityInstanceTranslator(), new InstanceSequenceTrackTitleFactory_1.InstanceSequenceTrackTitleFactory(this.getPolymerEntityInstanceTranslator()))
-            });
-            const annotationsRequestContext = {
-                queryId: instanceId,
-                reference: GqlTypes_1.SequenceReference.PdbInstance,
-                titleSuffix: this.titleSuffix((_c = buildConfig === null || buildConfig === void 0 ? void 0 : buildConfig.additionalConfig) === null || _c === void 0 ? void 0 : _c.rcsbContext).bind(this),
-                trackTitle: this.trackTitle.bind(this),
-                typeSuffix: this.typeSuffix.bind(this),
-                sources: source,
-                annotationGenerator: interfaceAnnotations,
-                annotationFilter: filter,
-                rcsbContext: (_d = buildConfig.additionalConfig) === null || _d === void 0 ? void 0 : _d.rcsbContext,
-                externalTrackBuilder: (_e = buildConfig.additionalConfig) === null || _e === void 0 ? void 0 : _e.externalTrackBuilder
-            };
-            const annotationsFeatures = yield this.annotationCollector.collect(annotationsRequestContext);
-            yield this.buildAnnotationsTrack(annotationsRequestContext, annotationsFeatures, annotationConfigMap);
-            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.alignmentTracks).concat(this.annotationTracks)
-                :
-                    this.alignmentTracks.concat(this.annotationTracks);
-    }
-    typeSuffix(ann, d) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            var _a;
-            if (ann.source === GqlTypes_1.Source.PdbInterface && ((_a = ann.target_identifiers) === null || _a === void 0 ? void 0 : _a.interface_id)) {
-                return ann.target_identifiers.interface_id + "|" + ann.target_identifiers.interface_partner_index;
-            }
-        });
-    }
-    titleSuffix(rcsbContext) {
-        return ((ann, d) => tslib_1.__awaiter(this, void 0, void 0, function* () {
-            var _a;
-            if (ann.source === GqlTypes_1.Source.PdbInterface) {
-                if (!ann.target_id)
-                    return "";
-                const interfaceTranslate = yield RcsbRequestContextManager_1.rcsbRequestCtxManager.getInterfaceToInstance(ann.target_id);
-                const chain = this.instanceId.split(TagDelimiter_1.TagDelimiter.instance)[1];
-                const chPair = interfaceTranslate.getInstances(ann.target_id);
-                if (!chPair)
-                    return "";
-                const asym = chPair[0] == chain ? chPair[1] : chPair[0];
-                const auth = (yield RcsbRequestContextManager_1.rcsbRequestCtxManager.getEntityToInstance(this.instanceId.split(TagDelimiter_1.TagDelimiter.instance)[0])).translateAsymToAuth(asym);
-                const operators = interfaceTranslate.getOperatorIds(ann.target_id);
-                let partnerOperator = "";
-                if (operators && ((_a = ann.target_identifiers) === null || _a === void 0 ? void 0 : _a.interface_partner_index) && rcsbContext && Array.isArray(rcsbContext.operatorIds)) {
-                    const opIndex = operators[ann.target_identifiers.interface_partner_index].map(o => o.join("-")).indexOf(rcsbContext.operatorIds.join("-"));
-                    if (opIndex < 0) {
-                        console.error(`Operator Id ${rcsbContext.operatorIds.join("-")} not found in [[${operators[0]}],[${operators[1]}]]`);
-                        console.error(ann.target_identifiers);
-                    }
-                    else {
-                        partnerOperator = TagDelimiter_1.TagDelimiter.operatorComposition + operators[1 - ann.target_identifiers.interface_partner_index][opIndex].join(TagDelimiter_1.TagDelimiter.operatorComposition);
-                    }
-                }
-                return (asym == auth ? asym : `${asym}[auth ${auth}]`) + partnerOperator;
-            }
-        }));
-    }
-    trackTitle(ann, d) {
-        return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            if (ann.source === GqlTypes_1.Source.PdbInterface && d.type === FeatureType_1.FeatureType.BurialFraction) {
-                return "BINDING CHAIN ";
-            }
-        });
-    }
-}
-exports.RcsbFvInterface = RcsbFvInterface;
-function interfaceAnnotations(annotations) {
-    const buried = (0, BuriedResidues_1.buriedResidues)(annotations);
-    const burial = (0, BurialFraction_1.burialFraction)(annotations);
-    return new Promise(resolve => {
-        const out = new Array();
-        if (buried && buried.length > 0)
-            out.push(...buried);
-        if (burial && burial.length > 0)
-            out.push(...burial);
-        resolve(out);
-    });
-}
-function filter(ann) {
-    return new Promise(resolve => {
-        resolve((0, BurialFraction_1.burialFractionFilter)((0, BuriedResidues_1.buriedResiduesFilter)(ann)));
-    });
-}

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvModuleInterface.d.ts

@@ -1,103 +0,0 @@
-import { RcsbFvBoardConfigInterface, RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-import { RcsbFv } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFv";
-import { AlignmentResponse, Feature, FilterInput, GroupReference, SequenceReference, Source, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-import { AnnotationCollectorInterface, AnnotationProcessingInterface, AnnotationsCollectConfig } from "../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
-import { ExternalTrackBuilderInterface } from "../../RcsbCollectTools/FeatureTools/ExternalTrackBuilderInterface";
-import { PairwiseAlignmentInterface } from "../../RcsbUtils/PairwiseAlignmentTools/PairwiseAlignmentBuilder";
-import { AlignmentRequestContextType } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AlignmentTrackFactory";
-import { TrackManagerInterface } from "../RcsbFvFactories/RcsbFvBlockFactory/BlockManager/TrackManagerInterface";
-import { UiComponentType } from "../../RcsbFvUI/GroupPfvUI";
-import { TrackFactoryInterface } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryInterface";
-import { AlignmentCollectConfig, AlignmentCollectorInterface } from "../../RcsbCollectTools/AlignmentCollector/AlignmentCollectorInterface";
-export type RcsbContextType = Partial<{
-    entryId: string;
-    entityId: string;
-    asymId: string;
-    authId: string;
-    upAcc: string;
-    chrId: string;
-    targetId: string;
-    queryId: string;
-    operatorIds: Array<string>;
-}>;
-export interface RcsbFvAdditionalConfig {
-    sources?: Array<Source>;
-    filters?: Array<FilterInput>;
-    alignmentFilter?: Array<string>;
-    hideAlignments?: boolean;
-    bottomAlignments?: boolean;
-    boardConfig?: Partial<RcsbFvBoardConfigInterface>;
-    sequencePrefix?: string;
-    annotationProcessing?: AnnotationProcessingInterface;
-    externalTrackBuilder?: ExternalTrackBuilderInterface;
-    page?: {
-        first: number;
-        after: string;
-    };
-    excludeLogo?: boolean;
-    rcsbContext?: RcsbContextType;
-    trackConfigModifier?: {
-        alignment?: (alignmentContext: AlignmentRequestContextType, targetAlignment: TargetAlignment, alignmentResponse: AlignmentResponse, alignmentIndex: number) => Promise<Partial<RcsbFvRowConfigInterface>>;
-        annotations?: (trackManager: TrackManagerInterface) => Promise<Partial<RcsbFvRowConfigInterface>>;
-    };
-    externalUiComponents?: {
-        add?: UiComponentType<any>[];
-        replace?: UiComponentType<any>[];
-    };
-    dataProvider?: RcsbModuleDataProviderInterface;
-}
-export interface RcsbModuleDataProviderInterface {
-    alignments?: {
-        collector: AlignmentCollectorInterface;
-        context: AlignmentCollectConfig;
-        trackFactories?: {
-            alignmentTrackFactory?: TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]>;
-            sequenceTrackFactory?: TrackFactoryInterface<[AlignmentRequestContextType, string]>;
-        };
-    };
-    annotations?: {
-        collector: AnnotationCollectorInterface;
-        context: AnnotationsCollectConfig;
-    };
-}
-export interface RcsbFvModuleBuildInterface {
-    group?: GroupReference;
-    groupId?: string;
-    queryId?: string;
-    from?: SequenceReference;
-    to?: SequenceReference;
-    sources?: Array<Source>;
-    entityId?: string;
-    instanceId?: string;
-    upAcc?: string;
-    refSeqId?: string;
-    chrId?: string;
-    psa?: PairwiseAlignmentInterface;
-    additionalConfig?: RcsbFvAdditionalConfig;
-    elementSelectId?: string;
-    resolve(module: RcsbFvModulePublicInterface): void;
-}
-export interface RcsbFvModuleInterface extends RcsbFvModulePublicInterface {
-    activeDisplay(): boolean;
-    display(): void;
-    build(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
-    setPolymerEntityInstanceTranslator(polymerEntityInstance: PolymerEntityInstanceTranslate): void;
-    getPolymerEntityInstanceTranslator(): PolymerEntityInstanceTranslate;
-}
-export interface RcsbFvModulePublicInterface<P extends {
-    [k: string]: any;
-} = {}, S extends {
-    [k: string]: any;
-} = {}, R extends {
-    [k: string]: any;
-} = {}, M extends {
-    [k: string]: any;
-} = {}> {
-    getTargets(): Promise<Array<string>>;
-    getAlignmentResponse(): Promise<AlignmentResponse>;
-    getFeatures(): Promise<Array<Feature>>;
-    getAnnotationConfigData(): Promise<Array<RcsbFvRowConfigInterface<P, S, R, M>>>;
-    getFv(): RcsbFv<P, S, R, M>;
-    wait(): Promise<void>;
-}

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvModuleInterface.js

@@ -1,2 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });

package/lib/commonjs/RcsbFvWeb/RcsbFvModule/RcsbFvPairwiseAlignment.d.ts

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