@rcsb/rcsb-saguaro-app 6.3.7-dev-js-seqcoord.14 → 6.3.7-react-downgrade.0

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvChromosome.js

@@ -28,14 +28,14 @@ function sequenceDisplayDynamicUpdate(reference, ranges, trackWidth) {
                     from: reference,
                     to: SequenceReference.NcbiGenome
                 });
-            })).then((alignments) => {
+            })).then(alignments => {
                 const out = new RcsbFvTrackData();
                 alignments.forEach((a, n) => {
                     var _c;
                     if (a.query_sequence == null)
                         return;
                     const sequence = a.query_sequence.split("");
-                    (_c = a.target_alignments) === null || _c === void 0 ? void 0 : _c.forEach(ta => {
+                    (_c = a.target_alignment) === null || _c === void 0 ? void 0 : _c.forEach(ta => {
                         var _c;
                         if (!ta)
                             return;
@@ -110,12 +110,12 @@ export class RcsbFvChromosome extends RcsbFvAbstractModule {
                 from: SequenceReference.PdbEntity,
                 to: to
             });
-        })).then((result) => {
+        })).then(result => {
             result.forEach(a => {
                 var _c;
                 if (!a)
                     return;
-                (_c = a.target_alignments) === null || _c === void 0 ? void 0 : _c.forEach(ta => {
+                (_c = a.target_alignment) === null || _c === void 0 ? void 0 : _c.forEach(ta => {
                     if ((ta === null || ta === void 0 ? void 0 : ta.target_id) && (ta === null || ta === void 0 ? void 0 : ta.coverage))
                         this.targetCoverages.set(ta.target_id, ta.coverage);
                 });
@@ -141,8 +141,8 @@ export class RcsbFvChromosome extends RcsbFvAbstractModule {
     collectPdbWorkerResults(ar, pdbEntityId, chrId) {
         return __awaiter(this, void 0, void 0, function* () {
             var _c, _d;
-            assertElementListDefined(ar.target_alignments);
-            const exonTracks = this.collectExons(ar.target_alignments, "target", RcsbAnnotationConstants.provenanceColorCode.rcsbPdb, RcsbAnnotationConstants.provenanceColorCode.rcsbPdb, SequenceReference.PdbEntity, chrId);
+            assertElementListDefined(ar.target_alignment);
+            const exonTracks = this.collectExons(ar.target_alignment, "target", RcsbAnnotationConstants.provenanceColorCode.rcsbPdb, RcsbAnnotationConstants.provenanceColorCode.rcsbPdb, SequenceReference.PdbEntity, chrId);
             this.pdbEntityTrack = this.mergeExonTracks(exonTracks, SequenceReference.PdbEntity)[0];
             (_d = (_c = this.pdbEntityTrack.displayConfig) === null || _c === void 0 ? void 0 : _c[0].displayData) === null || _d === void 0 ? void 0 : _d.forEach(d => {
                 d.description = [pdbEntityId];
@@ -316,8 +316,8 @@ export class RcsbFvChromosome extends RcsbFvAbstractModule {
             this.completeTasks++;
             const e = this.targetAlignmentList.get(reference);
             assertDefined(e);
-            assertElementListDefined(alignment.target_alignments);
-            e[index] = alignment.target_alignments;
+            assertElementListDefined(alignment.target_alignment);
+            e[index] = alignment.target_alignment;
             console.log("Completed " + Math.floor(this.completeTasks / this.nTasks * 100) + "%");
             if (forcePlot) {
                 yield this.plot();
@@ -736,4 +736,3 @@ export class RcsbFvChromosome extends RcsbFvAbstractModule {
     concatAlignmentAndAnnotationTracks() {
     }
 }
-//# sourceMappingURL=RcsbFvChromosome.js.map

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvDataProvider.js

@@ -23,4 +23,3 @@ export class RcsbFvDataProvider extends RcsbFvAbstractModule {
         this.rowConfigData = this.referenceTrack ? [this.referenceTrack].concat(this.alignmentTracks) : this.alignmentTracks;
     }
 }
-//# sourceMappingURL=RcsbFvDataProvider.js.map

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvEntity.js

@@ -1,5 +1,5 @@
 import { __awaiter } from "tslib";
-import { SequenceReference, AnnotationReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { 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;
@@ -26,7 +26,7 @@ export class RcsbFvEntity extends RcsbFvAbstractModule {
             const annotationsRequestContext = {
                 queryId: buildConfig.entityId,
                 reference: SequenceReference.PdbEntity,
-                sources: (_d = (_c = buildConfig.additionalConfig) === null || _c === void 0 ? void 0 : _c.sources) !== null && _d !== void 0 ? _d : [AnnotationReference.PdbEntity, AnnotationReference.Uniprot],
+                sources: (_d = (_c = buildConfig.additionalConfig) === null || _c === void 0 ? void 0 : _c.sources) !== null && _d !== void 0 ? _d : [Source.PdbEntity, 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,
@@ -59,7 +59,7 @@ export class RcsbFvEntity extends RcsbFvAbstractModule {
         return __awaiter(this, void 0, void 0, function* () {
             if (!ann.target_id)
                 return;
-            if (this.polymerEntityInstance != null && ann.source === AnnotationReference.PdbInstance) {
+            if (this.polymerEntityInstance != null && ann.source === Source.PdbInstance) {
                 const labelAsymId = ann.target_id.split(TagDelimiter.instance)[1];
                 const authAsymId = this.polymerEntityInstance.translateAsymToAuth(labelAsymId);
                 return labelAsymId === authAsymId ? labelAsymId : labelAsymId + "[auth " + authAsymId + "]";
@@ -67,4 +67,3 @@ export class RcsbFvEntity extends RcsbFvAbstractModule {
         });
     }
 }
-//# sourceMappingURL=RcsbFvEntity.js.map

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvGroupAlignment.js

@@ -1,9 +1,10 @@
 import { __awaiter } from "tslib";
 import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
-import { FieldName, GroupReference, OperationType, AnnotationReference, FeaturesType } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { FieldName, GroupReference, OperationType, Source, Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { MsaAlignmentTrackFactory } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/MsaAlignmentTrackFactory";
 import { Assertions } from "../../RcsbUtils/Helpers/Assertions";
 var assertDefined = Assertions.assertDefined;
+import { TagDelimiter } from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter";
 import { Operator } from "../../RcsbUtils/Helpers/Operator";
 import { rcsbRequestCtxManager } from "../../RcsbRequest/RcsbRequestContextManager";
 export class RcsbFvGroupAlignment extends RcsbFvAbstractModule {
@@ -26,15 +27,16 @@ export class RcsbFvGroupAlignment extends RcsbFvAbstractModule {
                 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(this.getPolymerEntityInstanceTranslator());
-            const targetList = yield uniqueTargetList(alignmentResponse);
+            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) == FeaturesType.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) == FeaturesType.MaQaMetricLocalTypePlddt) })); }));
+            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
             });
@@ -50,38 +52,50 @@ export class RcsbFvGroupAlignment extends RcsbFvAbstractModule {
         });
     }
 }
-function uniqueTargetList(alignmentResponse) {
+function collectNextPage(alignmentRequestContext, alignmentCollector, annotationCollector) {
     return __awaiter(this, void 0, void 0, function* () {
-        var _a, _b;
-        const entityIds = Operator.uniqueValues((_b = (_a = alignmentResponse.target_alignments) === null || _a === void 0 ? void 0 : _a.map(ta => {
-            assertDefined(ta === null || ta === void 0 ? void 0 : ta.target_id);
-            return ta.target_id;
-        })) !== null && _b !== void 0 ? _b : []);
-        const instanceIds = (yield rcsbRequestCtxManager.getEntityProperties(entityIds)).map(e => e.rcsbId);
-        return Operator.uniqueValues(instanceIds !== null && instanceIds !== void 0 ? instanceIds : []);
+        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.uniqueValues(alignmentFeatures.map(af => { var _a; return TagDelimiter.parseInstance((_a = af.target_id) !== null && _a !== void 0 ? _a : "").entryId; }));
+            Operator.arrayChunk(featureTargetList, 100).forEach(ids => rcsbRequestCtxManager.getEntryProperties(ids));
+        }
     });
 }
+function uniqueTargetList(alignmentResponse) {
+    var _a, _b;
+    return 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.parseEntity(ta.target_id).entryId;
+    })) !== null && _b !== void 0 ? _b : []);
+}
 function collectFeatures(annotationsContext, annotationCollector) {
     return __awaiter(this, void 0, void 0, function* () {
-        return yield annotationCollector.collect(Object.assign(Object.assign({}, buildGroupAnnotationQuery(annotationsContext)), { isSummary: false, externalTrackBuilder: annotationsContext.externalTrackBuilder }));
+        const annotationsRequestContext = {
+            histogram: false,
+            groupId: annotationsContext.groupId,
+            group: GroupReference.SequenceIdentity,
+            sources: [Source.PdbInstance],
+            filters: [{
+                    source: Source.PdbInstance,
+                    operation: OperationType.Equals,
+                    field: FieldName.Type,
+                    values: [Type.UnobservedResidueXyz, Type.MaQaMetricLocalTypePlddt]
+                }, {
+                    source: Source.PdbInstance,
+                    operation: OperationType.Contains,
+                    field: FieldName.TargetId,
+                    values: annotationsContext.targetList
+                }],
+            externalTrackBuilder: annotationsContext.externalTrackBuilder
+        };
+        return yield annotationCollector.collect(annotationsRequestContext);
     });
 }
-function buildGroupAnnotationQuery(annotationsContext) {
-    return {
-        group: GroupReference.SequenceIdentity,
-        groupId: annotationsContext.groupId,
-        sources: [AnnotationReference.PdbInstance],
-        filters: [{
-                source: AnnotationReference.PdbInstance,
-                operation: OperationType.Equals,
-                field: FieldName.Type,
-                values: [FeaturesType.UnobservedResidueXyz, FeaturesType.MaQaMetricLocalTypePlddt]
-            }, {
-                source: AnnotationReference.PdbInstance,
-                operation: OperationType.Equals,
-                field: FieldName.TargetId,
-                values: annotationsContext.targetList
-            }]
-    };
-}
-//# sourceMappingURL=RcsbFvGroupAlignment.js.map

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvGroupAnnotation.js

@@ -8,7 +8,7 @@ const annotationConfigMap = acm;
 export class RcsbFvGroupAnnotation extends RcsbFvAbstractModule {
     protectedBuild() {
         return __awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l, _m, _o;
+            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 = {
@@ -31,11 +31,10 @@ export class RcsbFvGroupAnnotation extends RcsbFvAbstractModule {
             const annotationsRequestContext = {
                 group: buildConfig.group,
                 groupId: buildConfig.groupId,
-                isSummary: typeof ((_h = buildConfig.additionalConfig) === null || _h === void 0 ? void 0 : _h.isAnnotationsGroupSummary) === "boolean" ? buildConfig.additionalConfig.isAnnotationsGroupSummary : true,
-                sources: (_k = (_j = buildConfig.additionalConfig) === null || _j === void 0 ? void 0 : _j.sources) !== null && _k !== void 0 ? _k : [],
-                filters: (_l = buildConfig.additionalConfig) === null || _l === void 0 ? void 0 : _l.filters,
-                annotationProcessing: (_m = buildConfig.additionalConfig) === null || _m === void 0 ? void 0 : _m.annotationProcessing,
-                externalTrackBuilder: (_o = buildConfig.additionalConfig) === null || _o === void 0 ? void 0 : _o.externalTrackBuilder
+                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);
@@ -51,4 +50,3 @@ export class RcsbFvGroupAnnotation extends RcsbFvAbstractModule {
         this.rowConfigData = this.referenceTrack ? [this.referenceTrack].concat(this.alignmentTracks).concat(this.annotationTracks) : this.alignmentTracks.concat(this.annotationTracks);
     }
 }
-//# sourceMappingURL=RcsbFvGroupAnnotation.js.map

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvInstance.js

@@ -1,5 +1,5 @@
 import { __awaiter } from "tslib";
-import { SequenceReference, AnnotationReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
 import { buriedResidues, buriedResiduesFilter } from "../../RcsbUtils/TrackGenerators/BuriedResidues";
 import { SequenceTrackFactory } from "../RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/SequenceTrackFactory";
@@ -13,7 +13,7 @@ export class RcsbFvInstance extends RcsbFvAbstractModule {
             const buildConfig = this.buildConfig;
             const instanceId = buildConfig.instanceId;
             assertDefined(instanceId);
-            const source = [AnnotationReference.PdbEntity, AnnotationReference.PdbInstance, AnnotationReference.Uniprot];
+            const source = [Source.PdbEntity, Source.PdbInstance, Source.Uniprot];
             const alignmentRequestContext = {
                 queryId: instanceId,
                 from: SequenceReference.PdbInstance,
@@ -50,4 +50,3 @@ export class RcsbFvInstance extends RcsbFvAbstractModule {
                     this.alignmentTracks.concat(this.annotationTracks);
     }
 }
-//# sourceMappingURL=RcsbFvInstance.js.map

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

@@ -1,4 +1,4 @@
-import { SequenceAnnotations } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
 export declare class RcsbFvInterface extends RcsbFvAbstractModule {
     private instanceId;
@@ -8,5 +8,5 @@ export declare class RcsbFvInterface extends RcsbFvAbstractModule {
     private titleSuffix;
     private trackTitle;
 }
-export declare function interfaceAnnotations(annotations: Array<SequenceAnnotations>): Promise<Array<SequenceAnnotations>>;
-export declare function filter(ann: Array<SequenceAnnotations>): Promise<Array<SequenceAnnotations>>;
+export declare function interfaceAnnotations(annotations: Array<AnnotationFeatures>): Promise<Array<AnnotationFeatures>>;
+export declare function filter(ann: Array<AnnotationFeatures>): Promise<Array<AnnotationFeatures>>;

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvInterface.js

@@ -1,5 +1,5 @@
 import { __awaiter } from "tslib";
-import { SequenceReference, AnnotationReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbFvAbstractModule } from "./RcsbFvAbstractModule";
 import * as acm from "../../RcsbAnnotationConfig/RcsbAnnotationConfig.ac.json";
 import { buriedResidues, buriedResiduesFilter } from "../../RcsbUtils/TrackGenerators/BuriedResidues";
@@ -20,7 +20,7 @@ export class RcsbFvInterface extends RcsbFvAbstractModule {
             const instanceId = buildConfig.instanceId;
             assertDefined(instanceId);
             this.instanceId = instanceId;
-            const source = [AnnotationReference.PdbEntity, AnnotationReference.PdbInstance, AnnotationReference.Uniprot, AnnotationReference.PdbInterface];
+            const source = [Source.PdbEntity, Source.PdbInstance, Source.Uniprot, Source.PdbInterface];
             const alignmentRequestContext = {
                 queryId: instanceId,
                 from: SequenceReference.PdbInstance,
@@ -62,7 +62,7 @@ export class RcsbFvInterface extends RcsbFvAbstractModule {
     typeSuffix(ann, d) {
         return __awaiter(this, void 0, void 0, function* () {
             var _a;
-            if (ann.source === AnnotationReference.PdbInterface && ((_a = ann.target_identifiers) === null || _a === void 0 ? void 0 : _a.interface_id)) {
+            if (ann.source === 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;
             }
         });
@@ -70,28 +70,26 @@ export class RcsbFvInterface extends RcsbFvAbstractModule {
     titleSuffix(rcsbContext) {
         return ((ann, d) => __awaiter(this, void 0, void 0, function* () {
             var _a;
-            if (ann.source === AnnotationReference.PdbInterface) {
-                if (!ann.target_id || !ann.target_identifiers)
+            if (ann.source === Source.PdbInterface) {
+                if (!ann.target_id)
                     return "";
                 const interfaceTranslate = yield rcsbRequestCtxManager.getInterfaceToInstance(ann.target_id);
                 const chain = this.instanceId.split(TagDelimiter.instance)[1];
-                const interfaceId = TagDelimiter.getInterfaceId(ann.target_identifiers);
-                const chPair = interfaceTranslate.getInstances(interfaceId);
+                const chPair = interfaceTranslate.getInstances(ann.target_id);
                 if (!chPair)
                     return "";
                 const asym = chPair[0] == chain ? chPair[1] : chPair[0];
                 const auth = (yield rcsbRequestCtxManager.getEntityToInstance(this.instanceId.split(TagDelimiter.instance)[0])).translateAsymToAuth(asym);
-                const operators = interfaceTranslate.getOperatorIds(interfaceId);
+                const operators = interfaceTranslate.getOperatorIds(ann.target_id);
                 let partnerOperator = "";
-                const partner_idx = (_a = ann.target_identifiers) === null || _a === void 0 ? void 0 : _a.interface_partner_index;
-                if (operators && typeof partner_idx == "number" && rcsbContext && Array.isArray(rcsbContext.operatorIds)) {
-                    const opIndex = operators[partner_idx].map(o => o.join("-")).indexOf(rcsbContext.operatorIds.join("-"));
+                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]}],[${operators[1]}]]`);
                         console.error(ann.target_identifiers);
                     }
                     else {
-                        partnerOperator = TagDelimiter.operatorComposition + operators[1 - partner_idx][opIndex].join(TagDelimiter.operatorComposition);
+                        partnerOperator = TagDelimiter.operatorComposition + operators[1 - ann.target_identifiers.interface_partner_index][opIndex].join(TagDelimiter.operatorComposition);
                     }
                 }
                 return (asym == auth ? asym : `${asym}[auth ${auth}]`) + partnerOperator;
@@ -100,7 +98,7 @@ export class RcsbFvInterface extends RcsbFvAbstractModule {
     }
     trackTitle(ann, d) {
         return __awaiter(this, void 0, void 0, function* () {
-            if (ann.source === AnnotationReference.PdbInterface && d.type === FeatureType.BurialFraction) {
+            if (ann.source === Source.PdbInterface && d.type === FeatureType.BurialFraction) {
                 return "BINDING CHAIN ";
             }
         });
@@ -123,4 +121,3 @@ export function filter(ann) {
         resolve(burialFractionFilter(buriedResiduesFilter(ann)));
     });
 }
-//# sourceMappingURL=RcsbFvInterface.js.map

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

@@ -1,6 +1,6 @@
 import { RcsbFvBoardConfigInterface, RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
 import { RcsbFv } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFv";
-import { SequenceAlignments, Features, AnnotationFilterInput, GroupReference, SequenceReference, AnnotationReference, TargetAlignments } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+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";
@@ -22,8 +22,8 @@ export type RcsbContextType = Partial<{
     operatorIds: Array<string>;
 }>;
 export interface RcsbFvAdditionalConfig {
-    sources?: Array<AnnotationReference>;
-    filters?: Array<AnnotationFilterInput>;
+    sources?: Array<Source>;
+    filters?: Array<FilterInput>;
     alignmentFilter?: Array<string>;
     hideAlignments?: boolean;
     bottomAlignments?: boolean;
@@ -33,12 +33,12 @@ export interface RcsbFvAdditionalConfig {
     externalTrackBuilder?: ExternalTrackBuilderInterface;
     page?: {
         first: number;
-        after: number;
+        after: string;
     };
     excludeLogo?: boolean;
     rcsbContext?: RcsbContextType;
     trackConfigModifier?: {
-        alignment?: (alignmentContext: AlignmentRequestContextType, targetAlignment: TargetAlignments, alignmentResponse: SequenceAlignments, alignmentIndex: number) => Promise<Partial<RcsbFvRowConfigInterface>>;
+        alignment?: (alignmentContext: AlignmentRequestContextType, targetAlignment: TargetAlignment, alignmentResponse: AlignmentResponse, alignmentIndex: number) => Promise<Partial<RcsbFvRowConfigInterface>>;
         annotations?: (trackManager: TrackManagerInterface) => Promise<Partial<RcsbFvRowConfigInterface>>;
     };
     externalUiComponents?: {
@@ -46,14 +46,13 @@ export interface RcsbFvAdditionalConfig {
         replace?: UiComponentType<any>[];
     };
     dataProvider?: RcsbModuleDataProviderInterface;
-    isAnnotationsGroupSummary?: boolean;
 }
 export interface RcsbModuleDataProviderInterface {
     alignments?: {
         collector: AlignmentCollectorInterface;
         context: AlignmentCollectConfig;
         trackFactories?: {
-            alignmentTrackFactory?: TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignments]>;
+            alignmentTrackFactory?: TrackFactoryInterface<[AlignmentRequestContextType, TargetAlignment]>;
             sequenceTrackFactory?: TrackFactoryInterface<[AlignmentRequestContextType, string]>;
         };
     };
@@ -68,7 +67,7 @@ export interface RcsbFvModuleBuildInterface {
     queryId?: string;
     from?: SequenceReference;
     to?: SequenceReference;
-    sources?: Array<AnnotationReference>;
+    sources?: Array<Source>;
     entityId?: string;
     instanceId?: string;
     upAcc?: string;
@@ -96,8 +95,8 @@ export interface RcsbFvModulePublicInterface<P extends {
     [k: string]: any;
 } = {}> {
     getTargets(): Promise<Array<string>>;
-    getAlignmentResponse(): Promise<SequenceAlignments>;
-    getFeatures(): Promise<Array<Features>>;
+    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/RcsbFvWeb/RcsbFvModule/RcsbFvModuleInterface.js

@@ -1,2 +1 @@
 export {};
-//# sourceMappingURL=RcsbFvModuleInterface.js.map

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvPairwiseAlignment.js

@@ -19,4 +19,3 @@ export class RcsbFvPairwiseAlignment extends RcsbFvAbstractModule {
     concatAlignmentAndAnnotationTracks() {
     }
 }
-//# sourceMappingURL=RcsbFvPairwiseAlignment.js.map

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvProteinSequence.js

@@ -1,5 +1,5 @@
 import { __awaiter } from "tslib";
-import { AnnotationReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+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;
@@ -8,11 +8,9 @@ export class RcsbFvProteinSequence extends RcsbFvAbstractModule {
         return __awaiter(this, void 0, void 0, function* () {
             var _a, _b, _c, _d, _e;
             const buildConfig = this.buildConfig;
-            if (!buildConfig.from || !buildConfig.to)
-                return;
             const queryId = buildConfig.queryId;
             assertDefined(queryId);
-            const source = (_a = buildConfig.sources) !== null && _a !== void 0 ? _a : [AnnotationReference.Uniprot];
+            const source = (_a = buildConfig.sources) !== null && _a !== void 0 ? _a : [Source.Uniprot];
             const alignmentRequestContext = {
                 queryId: queryId,
                 from: buildConfig.from,
@@ -50,4 +48,3 @@ export class RcsbFvProteinSequence extends RcsbFvAbstractModule {
         }
     }
 }
-//# sourceMappingURL=RcsbFvProteinSequence.js.map

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprot.js

@@ -1,5 +1,5 @@
 import { __awaiter } from "tslib";
-import { FieldName, OperationType, SequenceReference, AnnotationReference, FeaturesType } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+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";
@@ -12,7 +12,7 @@ export class RcsbFvUniprot extends RcsbFvAbstractModule {
             const buildConfig = this.buildConfig;
             const upAcc = buildConfig.upAcc;
             assertDefined(upAcc);
-            const source = [AnnotationReference.Uniprot];
+            const source = [Source.Uniprot];
             const alignmentRequestContext = {
                 queryId: upAcc,
                 from: SequenceReference.Uniprot,
@@ -25,7 +25,7 @@ export class RcsbFvUniprot extends RcsbFvAbstractModule {
             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) == FeaturesType.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) == FeaturesType.MaQaMetricLocalTypePlddt) })); }));
+            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
             });
@@ -57,14 +57,13 @@ function collectFeatures(upAcc) {
         return yield rcsbClient.requestRcsbPdbAnnotations({
             queryId: upAcc,
             reference: SequenceReference.Uniprot,
-            sources: [AnnotationReference.PdbInstance],
+            sources: [Source.PdbInstance],
             filters: [{
-                    source: AnnotationReference.PdbInstance,
+                    source: Source.PdbInstance,
                     operation: OperationType.Equals,
                     field: FieldName.Type,
-                    values: [FeaturesType.UnobservedResidueXyz, FeaturesType.MaQaMetricLocalTypePlddt]
+                    values: [Type.UnobservedResidueXyz, Type.MaQaMetricLocalTypePlddt]
                 }]
         });
     });
 }
-//# sourceMappingURL=RcsbFvUniprot.js.map

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprotAlignment.js

@@ -1,5 +1,5 @@
 import { __awaiter } from "tslib";
-import { FieldName, GroupReference, OperationType, SequenceReference, AnnotationReference, FeaturesType } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+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";
@@ -27,14 +27,14 @@ export class RcsbFvUniprotAlignment extends RcsbFvAbstractModule {
             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) == FeaturesType.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) == FeaturesType.MaQaMetricLocalTypePlddt) })); }));
+            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: [AnnotationReference.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
             };
@@ -59,14 +59,13 @@ function collectFeatures(upAcc) {
         return yield rcsbClient.requestRcsbPdbAnnotations({
             queryId: upAcc,
             reference: SequenceReference.Uniprot,
-            sources: [AnnotationReference.PdbInstance],
+            sources: [Source.PdbInstance],
             filters: [{
-                    source: AnnotationReference.PdbInstance,
+                    source: Source.PdbInstance,
                     operation: OperationType.Equals,
                     field: FieldName.Type,
-                    values: [FeaturesType.UnobservedResidueXyz, FeaturesType.MaQaMetricLocalTypePlddt]
+                    values: [Type.UnobservedResidueXyz, Type.MaQaMetricLocalTypePlddt]
                 }]
         });
     });
 }
-//# sourceMappingURL=RcsbFvUniprotAlignment.js.map

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprotEntity.js

@@ -1,5 +1,5 @@
 import { __awaiter } from "tslib";
-import { FieldName, OperationType, SequenceReference, AnnotationReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+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;
@@ -21,7 +21,7 @@ export class RcsbFvUniprotEntity extends RcsbFvAbstractModule {
             const filters = [{
                     field: FieldName.TargetId,
                     operation: OperationType.Equals,
-                    source: AnnotationReference.PdbEntity,
+                    source: Source.PdbEntity,
                     values: [entityId]
                 }];
             const alignmentRequestContext = {
@@ -37,7 +37,7 @@ export class RcsbFvUniprotEntity extends RcsbFvAbstractModule {
             const annotationsRequestContext = {
                 queryId: upAcc,
                 reference: SequenceReference.Uniprot,
-                sources: (additionalConfig === null || additionalConfig === void 0 ? void 0 : additionalConfig.sources) ? additionalConfig.sources : [AnnotationReference.PdbEntity, AnnotationReference.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,
@@ -64,7 +64,7 @@ export class RcsbFvUniprotEntity extends RcsbFvAbstractModule {
     titleSuffix(ann, d) {
         return __awaiter(this, void 0, void 0, function* () {
             var _a;
-            if (this.polymerEntityInstance != null && ann.source === AnnotationReference.PdbInstance) {
+            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;
@@ -74,4 +74,3 @@ export class RcsbFvUniprotEntity extends RcsbFvAbstractModule {
         });
     }
 }
-//# sourceMappingURL=RcsbFvUniprotEntity.js.map

package/lib/RcsbFvWeb/RcsbFvModule/RcsbFvUniprotInstance.js

@@ -1,5 +1,5 @@
 import { __awaiter } from "tslib";
-import { FieldName, OperationType, SequenceReference, AnnotationReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+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";
@@ -14,18 +14,18 @@ export class RcsbFvUniprotInstance extends RcsbFvAbstractModule {
             const instanceId = buildConfig.instanceId;
             const additionalConfig = buildConfig.additionalConfig;
             assertDefined(entityId), assertDefined(instanceId), assertDefined(upAcc);
-            let sources = [AnnotationReference.Uniprot, AnnotationReference.PdbEntity, AnnotationReference.PdbInstance];
+            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: AnnotationReference.PdbEntity,
+                    source: Source.PdbEntity,
                     values: [entityId]
                 }, {
                     field: FieldName.TargetId,
                     operation: OperationType.Contains,
-                    source: AnnotationReference.PdbInstance,
+                    source: Source.PdbInstance,
                     values: [instanceId]
                 }];
             if (additionalConfig != null && additionalConfig.filters != null && additionalConfig.filters.length > 0)
@@ -61,4 +61,3 @@ export class RcsbFvUniprotInstance extends RcsbFvAbstractModule {
         this.rowConfigData = [this.referenceTrack].concat(this.alignmentTracks).concat(this.annotationTracks);
     }
 }
-//# sourceMappingURL=RcsbFvUniprotInstance.js.map