@rcsb/rcsb-saguaro-app 6.0.0-development.1 → 6.0.0-development.3

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

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

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

@@ -0,0 +1,29 @@
+"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() {
+        var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l, _m, _o;
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            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

@@ -0,0 +1,6 @@
+import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
+export declare class RcsbFvEntity extends RcsbFvAbstractModule {
+    protected protectedBuild(): Promise<void>;
+    protected concatAlignmentAndAnnotationTracks(): void;
+    private titleSuffix;
+}

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

@@ -0,0 +1,60 @@
+"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");
+class RcsbFvEntity extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
+    protectedBuild() {
+        var _a, _b, _c, _d, _e, _f, _g;
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            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,
+                externalTrackBuilder: (_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;
+        });
+    }
+    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

@@ -0,0 +1,7 @@
+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

@@ -0,0 +1,105 @@
+"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() {
+        var _a, _b, _c, _d, _e, _f, _g, _h, _j;
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            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

@@ -0,0 +1,7 @@
+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

@@ -0,0 +1,56 @@
+"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() {
+        var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l;
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            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

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

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

@@ -0,0 +1,56 @@
+"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() {
+        var _a, _b, _c, _d;
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            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

@@ -0,0 +1,12 @@
+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

@@ -0,0 +1,129 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.filter = exports.interfaceAnnotations = exports.RcsbFvInterface = 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 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() {
+        var _a, _b, _c, _d, _e;
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            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) {
+        var _a;
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            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);
+    });
+}
+exports.interfaceAnnotations = interfaceAnnotations;
+function filter(ann) {
+    return new Promise(resolve => {
+        resolve((0, BurialFraction_1.burialFractionFilter)((0, BuriedResidues_1.buriedResiduesFilter)(ann)));
+    });
+}
+exports.filter = filter;

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

@@ -0,0 +1,95 @@
+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 {
+    getTargets(): Promise<Array<string>>;
+    getAlignmentResponse(): Promise<AlignmentResponse>;
+    getFeatures(): Promise<Array<Feature>>;
+    getAnnotationConfigData(): Promise<Array<RcsbFvRowConfigInterface>>;
+    getFv(): RcsbFv;
+    wait(): Promise<void>;
+}

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

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

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

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

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

@@ -0,0 +1,25 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.RcsbFvPairwiseAlignment = void 0;
+const tslib_1 = require("tslib");
+const RcsbFvAbstractModule_1 = require("./RcsbFvAbstractModule");
+const PairwiseAlignmentBuilder_1 = require("../../RcsbUtils/PairwiseAlignmentTools/PairwiseAlignmentBuilder");
+const Assertions_1 = require("../../RcsbUtils/Helpers/Assertions");
+var assertDefined = Assertions_1.Assertions.assertDefined;
+class RcsbFvPairwiseAlignment extends RcsbFvAbstractModule_1.RcsbFvAbstractModule {
+    protectedBuild() {
+        var _a;
+        return tslib_1.__awaiter(this, void 0, void 0, function* () {
+            const buildConfig = this.buildConfig;
+            assertDefined(buildConfig.psa);
+            const pab = new PairwiseAlignmentBuilder_1.PairwiseAlignmentBuilder(buildConfig.psa);
+            const config = Object.assign({ rowTitleWidth: 120, trackWidth: 800, length: pab.getLength(), includeAxis: !buildConfig.psa.pairwiseView }, (_a = buildConfig.additionalConfig) === null || _a === void 0 ? void 0 : _a.boardConfig);
+            this.boardConfigData = Object.assign(Object.assign({}, this.boardConfigData), config);
+            this.rowConfigData = buildConfig.psa.pairwiseView ? pab.buildPairwiseAlignment() : pab.buildReferenceAlignment();
+            return void 0;
+        });
+    }
+    concatAlignmentAndAnnotationTracks() {
+    }
+}
+exports.RcsbFvPairwiseAlignment = RcsbFvPairwiseAlignment;

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

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