@rcsb/rcsb-saguaro-app 6.3.0 → 6.3.2-dev-js-seqcoord.13

package/lib/RcsbUtils/TrackGenerators/BurialFraction.d.ts

@@ -1,3 +1,3 @@
-import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-export declare function burialFraction(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures>;
-export declare function burialFractionFilter(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures>;
+import { SequenceAnnotations } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+export declare function burialFraction(annotations: Array<SequenceAnnotations>): Array<SequenceAnnotations>;
+export declare function burialFractionFilter(annotations: Array<SequenceAnnotations>): Array<SequenceAnnotations>;

package/lib/RcsbUtils/TrackGenerators/BurialFraction.js

@@ -1,16 +1,16 @@
-import { Source, Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AnnotationReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { cloneDeep } from "lodash";
 import { FeatureType } from "../../RcsbExport/FeatureType";
 export function burialFraction(annotations) {
     const burialFractionOut = new Array();
     const asaUnboundAnn = cloneDeep(annotations).map(ann => {
         var _a;
-        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) === Type.AsaUnbound));
+        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) === FeatureType.AsaUnbound));
         return ann;
     }).filter(ann => { var _a, _b; return (((_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0); });
     const asaBoundAnn = cloneDeep(annotations).map(ann => {
         var _a;
-        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) === Type.AsaBound));
+        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) === FeatureType.AsaBound));
         return ann;
     }).filter(ann => { var _a, _b; return (((_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0); });
     asaUnboundAnn.forEach((asaUnbound) => {
@@ -56,7 +56,8 @@ export function burialFraction(annotations) {
 export function burialFractionFilter(annotations) {
     return cloneDeep(annotations).map(ann => {
         var _a;
-        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => (ann.source !== Source.PdbInterface || (f === null || f === void 0 ? void 0 : f.type) === FeatureType.BurialFraction));
+        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => (ann.source !== AnnotationReference.PdbInterface || (f === null || f === void 0 ? void 0 : f.type) === FeatureType.BurialFraction));
         return ann;
     }).filter(ann => { var _a, _b; return (((_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0); });
 }
+//# sourceMappingURL=BurialFraction.js.map

package/lib/RcsbUtils/TrackGenerators/BurialFraction.js.map

@@ -0,0 +1 @@
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package/lib/RcsbUtils/TrackGenerators/BuriedResidues.d.ts

@@ -1,3 +1,3 @@
-import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-export declare function buriedResidues(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures>;
-export declare function buriedResiduesFilter(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures>;
+import { SequenceAnnotations } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+export declare function buriedResidues(annotations: Array<SequenceAnnotations>): Array<SequenceAnnotations>;
+export declare function buriedResiduesFilter(annotations: Array<SequenceAnnotations>): Array<SequenceAnnotations>;

package/lib/RcsbUtils/TrackGenerators/BuriedResidues.js

@@ -1,4 +1,4 @@
-import { Source, Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AnnotationReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { cloneDeep } from "lodash";
 import { FeatureType } from "../../RcsbExport/FeatureType";
 export function buriedResidues(annotations) {
@@ -7,11 +7,11 @@ export function buriedResidues(annotations) {
     let buriedResidues = {};
     let nBuried = 0;
     mainloop: for (const ann of annotations) {
-        if (ann.source === Source.PdbInstance) {
+        if (ann.source === AnnotationReference.PdbInstance) {
             for (const f of (_a = ann.features) !== null && _a !== void 0 ? _a : []) {
-                if ((f === null || f === void 0 ? void 0 : f.type) === Type.Asa) {
+                if ((f === null || f === void 0 ? void 0 : f.type) === FeatureType.Asa) {
                     buriedResidues = cloneDeep(ann);
-                    buriedResidues.source = Source.PdbInstance;
+                    buriedResidues.source = AnnotationReference.PdbInstance;
                     const feature = cloneDeep(f);
                     feature.type = FeatureType.BuriedResidues;
                     feature.name = "Unbound chain core residues";
@@ -41,7 +41,8 @@ export function buriedResidues(annotations) {
 export function buriedResiduesFilter(annotations) {
     return cloneDeep(annotations).map(ann => {
         var _a;
-        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) !== Type.Asa));
+        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) !== FeatureType.Asa));
         return ann;
     }).filter(ann => { var _a, _b; return (((_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0); });
 }
+//# sourceMappingURL=BuriedResidues.js.map

package/lib/RcsbUtils/TrackGenerators/BuriedResidues.js.map

@@ -0,0 +1 @@
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package/lib/RcsbUtils/TrackGenerators/GroupExternalTrackBuilder.js

@@ -94,3 +94,4 @@ export function groupExternalTrackBuilder() {
             }];
     }
 }
+//# sourceMappingURL=GroupExternalTrackBuilder.js.map

package/lib/RcsbUtils/TrackGenerators/GroupExternalTrackBuilder.js.map

@@ -0,0 +1 @@
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package/lib/RcsbUtils/TrackGenerators/Logo.js

@@ -43,3 +43,4 @@ export class Logo {
         return -this.aaTypes().map(aa => (this.get(aa) != 0 ? (this.get(aa) / this.n) * (Math.log(this.get(aa) / this.n) / Math.log(this.aaTypes().length)) : 0)).reduce((p, v) => (p + v));
     }
 }
+//# sourceMappingURL=Logo.js.map

package/lib/RcsbUtils/TrackGenerators/Logo.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"Logo.js","sourceRoot":"","sources":["../../../src/RcsbUtils/TrackGenerators/Logo.ts"],"names":[],"mappings":"AACA,OAAO,EAAC,UAAU,EAAC,MAAM,uBAAuB,CAAC;AACjD,IAAO,wBAAwB,GAAG,UAAU,CAAC,wBAAwB,CAAC;AACtE,IAAO,aAAa,GAAG,UAAU,CAAC,aAAa,CAAC;AAEhD,MAAM,OAAO,IAAI;IAKb,YAAY,IAAqB;QAHhB,YAAO,GAAwB,MAAM,EAAE,CAAC;QACjD,MAAC,GAAW,CAAC,CAAC;QAGlB,wBAAwB,CAAC,IAAI,CAAC,CAAC;QAC/B,IAAI,CAAC,OAAO,CAAC,CAAC,CAAA,EAAE;YACZ,aAAa,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC;YACxB,aAAa,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC;YACvB,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,MAAW,CAAC,GAAG,CAAC,CAAC,KAAK,CAAC;YACtC,IAAI,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC;QACtB,CAAC,CAAC,CAAC;IACP,CAAC;IAEO,OAAO;QACX,OAAO,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAQ,CAAC;IAC5C,CAAC;IAED;;;OAGG;IAEH,GAAG,CAAC,EAAK;QACL,MAAM,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;QAC3B,aAAa,CAAC,CAAC,CAAC,CAAA;QAChB,OAAO,CAAC,CAAC;IACb,CAAC;IAED,KAAK;QACD,OAAO,IAAI,CAAC,CAAC,CAAC;IAClB,CAAC;IAED,OAAO,CAAC,QAAiC;QACrC,IAAI,CAAC,OAAO,EAAE,CAAC,OAAO,CAAE,CAAC,EAAE,EAAE,CAAC,EAAC,EAAE;YAC7B,QAAQ,CAAC,EAAE,EAAC,CAAC,CAAC,CAAC;QACnB,CAAC,CAAC,CAAC;IACP,CAAC;IAED,IAAI;QACA,OAAO,IAAI,CAAC,OAAO,EAAE,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAC,EAAE,CAAA,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,GAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IAC7E,CAAC;IAED,SAAS;QACL,OAAO,IAAI,CAAC,OAAO,EAAE,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAC,EAAE,CAAA,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,GAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA,EAAE,CAAA,CAAC,EAAC,MAAM,EAAC,CAAC,EAAE,KAAK,EAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,GAAC,IAAI,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzH,CAAC;IAED,OAAO;QACH,OAAO,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,GAAG,CAAS,EAAE,CAAA,EAAE,CAAA,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAE,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAC,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAC,IAAI,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAC,CAAC,EAAC,EAAE,CAAA,CAAC,CAAC,GAAC,CAAC,CAAC,CAAC,CAAC;IACnL,CAAC;CAEJ"}

package/lib/RcsbUtils/TrackGenerators/UnmodeledTrackBuilder.d.ts

@@ -1,4 +1,4 @@
-import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceAnnotations } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { PolymerEntityInstanceInterface } from "../../RcsbCollectTools/DataCollectors/PolymerEntityInstancesCollector";
 import { RcsbFvTooltipInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvTooltip/RcsbFvTooltipInterface";
 import { ExternalTrackBuilderInterface } from "../../RcsbCollectTools/FeatureTools/ExternalTrackBuilderInterface";
@@ -6,9 +6,9 @@ export declare function addUnmodeledTrackBuilder(unmodeledTrackBuilder: Unmodele
 export declare class UnmodeledTrackBuilder {
     private readonly unmodeledDescription;
     filterFeatures(data: {
-        annotations: Array<AnnotationFeatures>;
+        annotations: Array<SequenceAnnotations>;
         rcsbContext?: Partial<PolymerEntityInstanceInterface>;
-    }): Promise<Array<AnnotationFeatures>>;
+    }): Promise<Array<SequenceAnnotations>>;
     getTooltip(): RcsbFvTooltipInterface;
     private buildUnobserved;
 }

package/lib/RcsbUtils/TrackGenerators/UnmodeledTrackBuilder.js

@@ -1,5 +1,5 @@
 import { __awaiter } from "tslib";
-import { Source, Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AnnotationReference, FeaturesType } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { range } from "lodash";
 import { rcsbRequestCtxManager } from "../../RcsbRequest/RcsbRequestContextManager";
 import { RcsbFvTooltip } from "../../RcsbFvWeb/RcsbFvTooltip/RcsbFvTooltip";
@@ -43,10 +43,10 @@ export class UnmodeledTrackBuilder {
             const nInstances = (yield rcsbRequestCtxManager.getEntityProperties((_a = rcsbContext.entityId) !== null && _a !== void 0 ? _a : "none"))[0].instances.length;
             const featurePositions = Array.from(annotations.filter(ann => {
                 var _a, _b, _c;
-                return (_c = (_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) == Type.UnobservedResidueXyz)) === null || _b === void 0 ? void 0 : _b.length) !== null && _c !== void 0 ? _c : 0 > 0;
+                return (_c = (_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) == FeaturesType.UnobservedResidueXyz)) === null || _b === void 0 ? void 0 : _b.length) !== null && _c !== void 0 ? _c : 0 > 0;
             }).map(ann => {
                 var _a, _b;
-                return (_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter((f) => (f === null || f === void 0 ? void 0 : f.type) == Type.UnobservedResidueXyz)) !== null && _b !== void 0 ? _b : [];
+                return (_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter((f) => (f === null || f === void 0 ? void 0 : f.type) == FeaturesType.UnobservedResidueXyz)) !== null && _b !== void 0 ? _b : [];
             }).flat().map(feature => {
                 var _a, _b;
                 return (_b = (_a = feature.feature_positions) === null || _a === void 0 ? void 0 : _a.filter((p) => typeof p != "undefined")) !== null && _b !== void 0 ? _b : [];
@@ -58,7 +58,7 @@ export class UnmodeledTrackBuilder {
                 };
             });
             return [{
-                    source: Source.PdbEntity,
+                    source: AnnotationReference.PdbEntity,
                     target_id: rcsbContext.entityId,
                     features: [{
                             type: UNMODELED,
@@ -94,7 +94,8 @@ class UnobservedToolTip {
 function filterUnobserved(annotations) {
     return annotations.map(ann => {
         var _a;
-        return Object.assign(Object.assign({}, ann), { features: (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) != Type.UnobservedResidueXyz && (f === null || f === void 0 ? void 0 : f.type) != Type.UnobservedAtomXyz) });
+        return Object.assign(Object.assign({}, ann), { features: (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => (f === null || f === void 0 ? void 0 : f.type) != FeaturesType.UnobservedResidueXyz && (f === null || f === void 0 ? void 0 : f.type) != FeaturesType.UnobservedAtomXyz) });
     });
 }
 const UNMODELED = "UNMODELED";
+//# sourceMappingURL=UnmodeledTrackBuilder.js.map

package/lib/RcsbUtils/TrackGenerators/UnmodeledTrackBuilder.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"UnmodeledTrackBuilder.js","sourceRoot":"","sources":["../../../src/RcsbUtils/TrackGenerators/UnmodeledTrackBuilder.ts"],"names":[],"mappings":";AAAA,OAAO,EAIH,mBAAmB,EACnB,YAAY,EACf,MAAM,+DAA+D,CAAC;AAEvE,OAAO,EAAC,KAAK,EAAC,MAAM,QAAQ,CAAC;AAC7B,OAAO,EAAC,qBAAqB,EAAC,MAAM,6CAA6C,CAAC;AAElF,OAAO,EAAC,aAAa,EAAC,MAAM,6CAA6C,CAAC;AAM1E,MAAM,UAAU,wBAAwB,CACpC,qBAA4C,EAC5C,oBAAoD;IAEpD,MAAM,YAAY,GAAG,CAAO,IAG3B,EAAuC,EAAE;;QACtC,OAAO;YACH,GAAI,MAAA,MAAM,CAAA,MAAA,oBAAoB,aAApB,oBAAoB,uBAApB,oBAAoB,CAAE,cAAc,qEAAG,IAAI,CAAC,CAAA,mCAAI,EAAE;YAC5D,GAAI,MAAM,qBAAqB,CAAC,cAAc,CAAC,IAAI,CAAC;SACvD,CAAC;IACN,CAAC,CAAA,CAAA;IACD,uCACQ,oBAAoB,KACxB,cAAc,EAAE,CAAO,IAAI,EAAE,EAAE;;YAC3B,MAAA,oBAAoB,aAApB,oBAAoB,uBAApB,oBAAoB,CAAE,cAAc,qEAAG,IAAI,CAAC,CAAC;YAC7C,OAAO,YAAY,CAAC;gBAChB,WAAW,EAAE,MAAA,MAAM,CAAA,MAAA,oBAAoB,aAApB,oBAAoB,uBAApB,oBAAoB,CAAE,cAAc,qEAAG,IAAI,CAAC,CAAA,mCAAI,IAAI,CAAC,WAAW;gBACnF,WAAW,EAAE,IAAI,CAAC,WAAW;aAChC,CAAC,CAAC;QACP,CAAC,CAAA,IACJ;AACL,CAAC;AAED,MAAM,OAAO,qBAAqB;IAAlC;QAEqB,yBAAoB,GAAgC,IAAI,GAAG,EAAE,CAAC;IAqDnF,CAAC;IApDgB,cAAc,CAAC,IAG3B;;YACG,IAAI,CAAC,IAAI,CAAC,WAAW;gBACjB,OAAO,IAAI,CAAC,WAAW,CAAC;YAC5B,OAAO;gBACH,GAAG,MAAM,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,WAAW,EAAE,IAAI,CAAC,WAAW,CAAC;gBACjE,GAAG,gBAAgB,CAAC,IAAI,CAAC,WAAW,CAAC;aACxC,CAAC;QACN,CAAC;KAAA;IAEM,UAAU;QACb,OAAO,IAAI,iBAAiB,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC;IAC5D,CAAC;IAEa,eAAe,CAAC,WAAuC,EAAE,WAAoD;;;YACvH,MAAM,UAAU,GAAG,CAAC,MAAM,qBAAqB,CAAC,mBAAmB,CAAC,MAAA,WAAW,CAAC,QAAQ,mCAAI,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,MAAM,CAAC;YACzH,MAAM,gBAAgB,GAAG,KAAK,CAAC,IAAI,CAAC,WAAW,CAAC,MAAM,CAClD,GAAG,CAAC,EAAE;;gBAAC,OAAA,MAAA,MAAA,MAAA,GAAG,CAAC,QAAQ,0CAAE,MAAM,CACvB,CAAC,CAAC,EAAE,CAAC,CAAA,CAAC,aAAD,CAAC,uBAAD,CAAC,CAAE,IAAI,KAAI,YAAY,CAAC,oBAAoB,CACpD,0CAAE,MAAM,mCAAI,CAAC,GAAG,CAAC,CAAA;aAAA,CACrB,CAAC,GAAG,CACD,GAAG,CAAC,EAAE;;gBAAC,OAAA,MAAA,MAAA,GAAG,CAAC,QAAQ,0CAAE,MAAM,CACvB,CAAC,CAAC,EAAiB,EAAE,CAAC,CAAA,CAAC,aAAD,CAAC,uBAAD,CAAC,CAAE,IAAI,KAAI,YAAY,CAAC,oBAAoB,CACrE,mCAAI,EAAE,CAAA;aAAA,CACV,CAAC,IAAI,EAAE,CAAC,GAAG,CACR,OAAO,CAAC,EAAE;;gBAAC,OAAA,MAAA,MAAA,OAAO,CAAC,iBAAiB,0CAAE,MAAM,CACxC,CAAC,CAAC,EAAiC,EAAE,CAAC,OAAO,CAAC,IAAI,WAAW,CAChE,mCAAI,EAAE,CAAA;aAAA,CACV,CAAC,IAAI,EAAE,CAAC,GAAG,CACR,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,UAAU,IAAI,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,UAAU,EAAC,CAAC,CAAC,UAAU,GAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAC9E,CAAC,IAAI,EAAE,CAAC,MAAM,CACX,CAAC,GAAG,EAAC,GAAG,EAAE,EAAE,WAAC,OAAA,GAAG,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,MAAA,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,mCAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA,EAAA,EAClD,IAAI,GAAkB,CACzB,CAAC,OAAO,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAC,UAAU,CAAC,EAAC,EAAE;gBACjC,IAAI,CAAC,oBAAoB,CAAC,GAAG,CAAC,GAAG,WAAW,CAAC,QAAQ,IAAI,GAAG,EAAE,EAAE,CAAC,UAAU,EAAE,UAAU,CAAC,CAAC,CAAC;gBAC1F,OAAO;oBACH,UAAU,EAAE,GAAG;oBACf,MAAM,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,UAAU,GAAG,UAAU,GAAG,GAAG,CAAC,GAAC,GAAG,CAAC;iBAC1D,CAAA;YACL,CAAC,CAAC,CAAC;YACH,OAAO,CAAC;oBACJ,MAAM,EAAE,mBAAmB,CAAC,SAAS;oBACrC,SAAS,EAAE,WAAW,CAAC,QAAQ;oBAC/B,QAAQ,EAAE,CAAC;4BACP,IAAI,EAAE,SAAyB;4BAC/B,iBAAiB,EAAE,gBAAgB;yBACtC,CAAC;iBACL,CAAC,CAAA;QACN,CAAC;KAAA;CAEJ;AAED,MAAM,iBAAiB;IAKnB,YAAY,gBAA6C;QAHxC,mBAAc,GAAkB,IAAI,aAAa,EAAE,CAAC;QAIjE,IAAI,CAAC,gBAAgB,GAAG,gBAAgB,CAAC;IAC7C,CAAC;IAED,WAAW,CAAC,CAAqC;QAC7C,OAAO,IAAI,CAAC,cAAc,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC;IAC9C,CAAC;IAED,sBAAsB,CAAC,CAAqC;QACxD,IAAG,CAAC,CAAC,KAAK,IAAI,SAAyB;YACnC,OAAO,IAAI,CAAC,0BAA0B,CAAC,CAAC,CAAC,CAAC;QAC9C,OAAO,IAAI,CAAC,cAAc,CAAC,sBAAsB,CAAC,CAAC,CAAC,CAAC;IACzD,CAAC;IAED,0BAA0B,CAAC,CAAqC;;QAC5D,IAAG,CAAC,IAAI,CAAC,gBAAgB,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,QAAQ,IAAI,CAAC,CAAC,KAAK,EAAE,CAAC;YACrD,OAAO,SAAS,CAAC;QACrB,MAAM,qBAAqB,GAAG,QAAQ,CAAC,aAAa,CAAQ,KAAK,CAAC,CAAC;QACnE,MAAM,CAAC,UAAU,EAAE,KAAK,CAAC,GAAG,MAAA,IAAI,CAAC,gBAAgB,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,QAAQ,IAAI,CAAC,CAAC,KAAK,EAAE,CAAC,mCAAI,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;QAC3F,qBAAqB,CAAC,MAAM,CAAC,gBAAgB,UAAU,OAAO,KAAK,SAAS,CAAC,CAAC;QAC9E,OAAO,qBAAqB,CAAC;IACjC,CAAC;CAEJ;AAED,SAAS,gBAAgB,CAAC,WAAuC;IAC7D,OAAO,WAAW,CAAC,GAAG,CAAC,GAAG,CAAA,EAAE;;QACxB,uCACO,GAAG,KACN,QAAQ,EAAE,MAAA,GAAG,CAAC,QAAQ,0CAAE,MAAM,CAC1B,CAAC,CAAA,EAAE,CAAC,CAAA,CAAC,aAAD,CAAC,uBAAD,CAAC,CAAE,IAAI,KAAI,YAAY,CAAC,oBAAoB,IAAI,CAAA,CAAC,aAAD,CAAC,uBAAD,CAAC,CAAE,IAAI,KAAI,YAAY,CAAC,iBAAiB,CAChG,IACJ;IACL,CAAC,CAAC,CAAC;AACP,CAAC;AAED,MAAM,SAAS,GAAG,WAAW,CAAC"}

package/lib/RcsbUtils/Translators/AssemblyInterfacesTranslate.js

@@ -13,3 +13,4 @@ export class AssemblyInterfacesTranslate {
         return this.rawData;
     }
 }
+//# sourceMappingURL=AssemblyInterfacesTranslate.js.map

package/lib/RcsbUtils/Translators/AssemblyInterfacesTranslate.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"AssemblyInterfacesTranslate.js","sourceRoot":"","sources":["../../../src/RcsbUtils/Translators/AssemblyInterfacesTranslate.ts"],"names":[],"mappings":"AAEA,MAAM,OAAO,2BAA2B;IAKpC,YAAY,IAAwC;QAF5C,iBAAY,GAA8B,IAAI,GAAG,EAAyB,CAAC;QAG/E,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC;QACpB,IAAI,CAAC,OAAO,CAAC,CAAC,CAAA,EAAE;YACZ,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,YAAY,CAAC,CAAC;QACpD,CAAC,CAAC,CAAA;IACN,CAAC;IAED,aAAa,CAAC,UAAkB;QAC5B,OAAO,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,UAAU,CAAC,CAAC;IAC7C,CAAC;IAED,UAAU;QACN,OAAO,IAAI,CAAC,OAAO,CAAC;IACxB,CAAC;CAEJ"}

package/lib/RcsbUtils/Translators/EntryAssemblyTranslate.js

@@ -6,3 +6,4 @@ export class EntryAssemblyTranslate {
         return this.rawData;
     }
 }
+//# sourceMappingURL=EntryAssemblyTranslate.js.map

package/lib/RcsbUtils/Translators/EntryAssemblyTranslate.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"EntryAssemblyTranslate.js","sourceRoot":"","sources":["../../../src/RcsbUtils/Translators/EntryAssemblyTranslate.ts"],"names":[],"mappings":"AAEA,MAAM,OAAO,sBAAsB;IAG/B,YAAY,IAAuD;QAC/D,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC;IACxB,CAAC;IAED,OAAO;QACH,OAAO,IAAI,CAAC,OAAO,CAAC;IACxB,CAAC;CACJ"}

package/lib/RcsbUtils/Translators/InterfaceInstanceTranslate.js

@@ -18,3 +18,4 @@ export class InterfaceInstanceTranslate {
         return this.rawData;
     }
 }
+//# sourceMappingURL=InterfaceInstanceTranslate.js.map

package/lib/RcsbUtils/Translators/InterfaceInstanceTranslate.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"InterfaceInstanceTranslate.js","sourceRoot":"","sources":["../../../src/RcsbUtils/Translators/InterfaceInstanceTranslate.ts"],"names":[],"mappings":"AAEA,MAAM,OAAO,0BAA0B;IAMnC,YAAY,IAAuC;QAHlC,cAAS,GAAiC,IAAI,GAAG,EAA4B,CAAC;QAC9E,iBAAY,GAA6D,IAAI,GAAG,EAAwD,CAAC;QAGtJ,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC;QACpB,IAAI,CAAC,OAAO,CAAC,CAAC,CAAA,EAAE;YACZ,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC;YACxC,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,WAAW,CAAC,CAAC;QACnD,CAAC,CAAC,CAAA;IACN,CAAC;IAED,YAAY,CAAC,MAAc;QACvB,OAAO,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;IACtC,CAAC;IAED,cAAc,CAAC,MAAc;QACzB,OAAO,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;IACzC,CAAC;IAED,UAAU;QACN,OAAO,IAAI,CAAC,OAAO,CAAC;IACxB,CAAC;CAEJ"}

package/lib/RcsbUtils/Translators/MultipleEntityInstanceTranslate.js

@@ -31,3 +31,4 @@ export class MultipleEntityInstanceTranslate {
         return Operator.uniqueValues(Array.from(this.entityInstanceTranslateMap.values()).map(peit => peit.getData()).flat().map(e => e.asymId));
     }
 }
+//# sourceMappingURL=MultipleEntityInstanceTranslate.js.map

package/lib/RcsbUtils/Translators/MultipleEntityInstanceTranslate.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"MultipleEntityInstanceTranslate.js","sourceRoot":"","sources":["../../../src/RcsbUtils/Translators/MultipleEntityInstanceTranslate.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,8BAA8B,EAAC,MAAM,kCAAkC,CAAC;AAEhF,OAAO,EAAC,QAAQ,EAAC,MAAM,qBAAqB,CAAC;AAC7C,OAAO,EAAC,YAAY,EAAC,MAAM,mDAAmD,CAAC;AAE/E,MAAM,OAAO,+BAA+B;IAA5C;QAEqB,+BAA0B,GAAgD,IAAI,GAAG,EAA0C,CAAC;IAqCjJ,CAAC;IAnCU,GAAG,CAAC,IAA2C;QAClD,MAAM,0BAA0B,GAAuD,IAAI,GAAG,EAAiD,CAAC;QAChJ,IAAI,CAAC,OAAO,CAAC,CAAC,CAAA,EAAE;;YACZ,MAAM,QAAQ,GAAW,CAAC,CAAC,OAAO,GAAC,YAAY,CAAC,MAAM,GAAC,CAAC,CAAC,QAAQ,CAAC;YAClE,IAAG,CAAC,0BAA0B,CAAC,GAAG,CAAC,QAAQ,CAAC;gBACxC,0BAA0B,CAAC,GAAG,CAAC,QAAQ,EAAE,IAAI,KAAK,EAAkC,CAAC,CAAA;YACzF,MAAA,0BAA0B,CAAC,GAAG,CAAC,QAAQ,CAAC,0CAAE,IAAI,CAAC,CAAC,CAAC,CAAC;QACtD,CAAC,CAAC,CAAC;QACH,0BAA0B,CAAC,OAAO,CAAC,CAAC,CAAC,EAAC,QAAQ,EAAC,EAAE;YAC7C,IAAI,CAAC,0BAA0B,CAAC,GAAG,CAAC,QAAQ,EAAE,IAAI,8BAA8B,CAAC,CAAC,CAAC,CAAC,CAAC;QACzF,CAAC,CAAC,CAAC;IACP,CAAC;IAEM,SAAS,CAAC,QAAgB;QAC7B,OAAO,IAAI,CAAC,0BAA0B,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC;IACzD,CAAC;IAEM,WAAW;QACd,OAAO,KAAK,CAAC,IAAI,CAAS,IAAI,CAAC,0BAA0B,CAAC,IAAI,EAAE,CAAC,CAAC;IACtE,CAAC;IAEM,UAAU;QACb,OAAO,QAAQ,CAAC,YAAY,CACxB,KAAK,CAAC,IAAI,CAAS,IAAI,CAAC,0BAA0B,CAAC,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAA,EAAE,CAAA,YAAY,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAC,OAAO,CAAC,CACvH,CAAC;IACN,CAAC;IAEM,YAAY;QACf,OAAO,QAAQ,CAAC,YAAY,CACxB,KAAK,CAAC,IAAI,CAAiC,IAAI,CAAC,0BAA0B,CAAC,MAAM,EAAE,CAAC,CAAC,GAAG,CAAC,IAAI,CAAA,EAAE,CAAA,IAAI,CAAC,OAAO,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,CAC3I,CAAC;IACN,CAAC;CAIJ"}

package/lib/RcsbUtils/Translators/PolymerEntityChromosomeTranslate.js

@@ -6,3 +6,4 @@ export class PolymerEntityChromosomeTranslate {
         return this.rawData;
     }
 }
+//# sourceMappingURL=PolymerEntityChromosomeTranslate.js.map

package/lib/RcsbUtils/Translators/PolymerEntityChromosomeTranslate.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"PolymerEntityChromosomeTranslate.js","sourceRoot":"","sources":["../../../src/RcsbUtils/Translators/PolymerEntityChromosomeTranslate.ts"],"names":[],"mappings":"AACA,MAAM,OAAO,gCAAgC;IAIzC,YAAa,SAAqC;QAC9C,IAAI,CAAC,OAAO,GAAG,SAAS,CAAC;IAC7B,CAAC;IAED,OAAO;QACH,OAAO,IAAI,CAAC,OAAO,CAAC;IACxB,CAAC;CAEJ"}

package/lib/RcsbUtils/Translators/PolymerEntityInstanceTranslate.d.ts

@@ -1,11 +1,11 @@
 import { PolymerEntityInstanceInterface } from "../../RcsbCollectTools/DataCollectors/PolymerEntityInstancesCollector";
 import { RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro/lib/RcsbDataManager/RcsbDataManager";
-import { SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceReference, AnnotationReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 export interface AlignmentContextInterface {
     queryId: string;
     targetId: string;
     from: SequenceReference | undefined;
-    to: SequenceReference | Source | undefined;
+    to: SequenceReference | AnnotationReference | undefined;
     targetSequenceLength?: number;
     querySequenceLength?: number;
 }

package/lib/RcsbUtils/Translators/PolymerEntityInstanceTranslate.js

@@ -1,4 +1,4 @@
-import { SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceReference, AnnotationReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { TagDelimiter } from "@rcsb/rcsb-api-tools/build/RcsbUtils/TagDelimiter";
 export class PolymerEntityInstanceTranslate {
     constructor(data) {
@@ -67,7 +67,7 @@ export class PolymerEntityInstanceTranslate {
         const authResIds = this.instanceAuthResIds.get(asymId);
         if (!authResIds)
             return out;
-        if (reference === SequenceReference.PdbInstance || (reference === SequenceReference.PdbEntity && source === Source.PdbInstance)) {
+        if (reference === SequenceReference.PdbInstance || (reference === SequenceReference.PdbEntity && source === AnnotationReference.PdbInstance)) {
             const x = authResIds[e.begin - 1];
             if (typeof e.end === "number" && authResIds[e.end - 1] != x) {
                 out.beginName = x;
@@ -77,7 +77,7 @@ export class PolymerEntityInstanceTranslate {
                 out.beginName = x;
             }
         }
-        else if (source === Source.PdbInstance && e.oriBegin) {
+        else if (source === AnnotationReference.PdbInstance && e.oriBegin) {
             const x = authResIds[e.oriBegin - 1];
             if (typeof e.oriEnd === "number" && authResIds[e.oriEnd - 1] != x) {
                 out.oriBeginName = x;
@@ -90,3 +90,4 @@ export class PolymerEntityInstanceTranslate {
         return out;
     }
 }
+//# sourceMappingURL=PolymerEntityInstanceTranslate.js.map

package/lib/RcsbUtils/Translators/PolymerEntityInstanceTranslate.js.map

@@ -0,0 +1 @@
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package/lib/app.js

@@ -9,3 +9,4 @@ export { PlainAlignmentTrackFactory } from "./RcsbFvWeb/RcsbFvFactories/RcsbFvTr
 export { MsaAlignmentTrackFactory } from "./RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/MsaAlignmentTrackFactory";
 export { AnnotationsTrackFactory } from "./RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AnnotationsTrackFactory";
 export { AlignmentTrackFactory } from "./RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AlignmentTrackFactory";
+//# sourceMappingURL=app.js.map

package/lib/app.js.map

@@ -0,0 +1 @@
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package/lib/commonjs/RcsbAnnotationConfig/RcsbAnnotationConfig.d.ts

@@ -1,4 +1,4 @@
-import { AnnotationFeatures, Feature } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceAnnotations, Features } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbFvDisplayTypes } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvDefaultConfigValues";
 import { AnnotationConfigInterface, RcsbAnnotationConfigInterface } from "./AnnotationConfigInterface";
 import { AnnotationRequestContext } from "../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
@@ -19,7 +19,7 @@ export declare class RcsbAnnotationConfig {
     uniprotOrder(): Array<string>;
     instanceOrder(): Array<string>;
     entityOrder(): Array<string>;
-    getAnnotationType(requestConfig: AnnotationRequestContext, ann: AnnotationFeatures, feature: Feature): Promise<string>;
+    getAnnotationType(requestConfig: AnnotationRequestContext, ann: SequenceAnnotations, feature: Features): Promise<string>;
     isMergedType(type: string): boolean;
     getMergeConfig(type: string): RcsbMergedTypesInterface | undefined;
     private addNewType;

package/lib/commonjs/RcsbCollectTools/AlignmentCollector/AlignmentCollector.d.ts

@@ -1,6 +1,6 @@
 import { AlignmentCollectConfig, AlignmentCollectorInterface } from "./AlignmentCollectorInterface";
 import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
-import { AlignmentResponse } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceAlignments } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 export declare class AlignmentCollector implements AlignmentCollectorInterface {
     private requestStatus;
     readonly rcsbFvQuery: RcsbClient;
@@ -8,10 +8,10 @@ export declare class AlignmentCollector implements AlignmentCollectorInterface {
     private alignmentResponse;
     private readonly alignmentResponseSubject;
     private readonly alignmentLengthSubject;
-    collect(requestConfig: AlignmentCollectConfig, filter?: Array<string>): Promise<AlignmentResponse>;
+    collect(requestConfig: AlignmentCollectConfig, filter?: Array<string>): Promise<SequenceAlignments>;
     getTargets(): Promise<Array<string>>;
-    getAlignment(): Promise<AlignmentResponse>;
+    getAlignment(): Promise<SequenceAlignments>;
     getAlignmentLength(): Promise<number>;
-    requestAlignment(requestConfig: AlignmentCollectConfig): Promise<AlignmentResponse>;
+    requestAlignment(requestConfig: AlignmentCollectConfig): Promise<SequenceAlignments>;
     private complete;
 }

package/lib/commonjs/RcsbCollectTools/AlignmentCollector/AlignmentCollector.js

@@ -17,15 +17,15 @@ class AlignmentCollector {
     }
     collect(requestConfig, filter) {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            var _a, _b, _c, _d, _e, _f;
+            var _a, _b;
             this.requestStatus = "pending";
             this.alignmentResponse = yield this.requestAlignment(requestConfig);
-            const targetAlignment = (_b = (_a = this.alignmentResponse) === null || _a === void 0 ? void 0 : _a.target_alignment) !== null && _b !== void 0 ? _b : (_e = (_d = (_c = this.alignmentResponse) === null || _c === void 0 ? void 0 : _c.target_alignment_subset) === null || _d === void 0 ? void 0 : _d.edges) === null || _e === void 0 ? void 0 : _e.map(e => e === null || e === void 0 ? void 0 : e.node);
+            const targetAlignment = (_a = this.alignmentResponse) === null || _a === void 0 ? void 0 : _a.target_alignments;
             if (targetAlignment) {
                 assertElementListDefined(targetAlignment);
-                this.alignmentResponse.target_alignment = !filter ? targetAlignment : targetAlignment === null || targetAlignment === void 0 ? void 0 : targetAlignment.filter(ta => { var _a; return filter.includes((_a = ta === null || ta === void 0 ? void 0 : ta.target_id) !== null && _a !== void 0 ? _a : "not-included"); });
+                this.alignmentResponse.target_alignments = !filter ? targetAlignment : targetAlignment === null || targetAlignment === void 0 ? void 0 : targetAlignment.filter(ta => { var _a; return filter.includes((_a = ta === null || ta === void 0 ? void 0 : ta.target_id) !== null && _a !== void 0 ? _a : "not-included"); });
             }
-            this.alignmentResponse = typeof ((_f = requestConfig.externalTrackBuilder) === null || _f === void 0 ? void 0 : _f.filterAlignments) === "function" ? yield requestConfig.externalTrackBuilder.filterAlignments({ alignments: this.alignmentResponse }) : this.alignmentResponse;
+            this.alignmentResponse = typeof ((_b = requestConfig.externalTrackBuilder) === null || _b === void 0 ? void 0 : _b.filterAlignments) === "function" ? yield requestConfig.externalTrackBuilder.filterAlignments({ alignments: this.alignmentResponse }) : this.alignmentResponse;
             this.complete();
             return this.alignmentResponse;
         });
@@ -35,7 +35,7 @@ class AlignmentCollector {
             return new Promise((resolve, reject) => {
                 var _a, _b;
                 if (this.requestStatus === "complete") {
-                    const targetIds = (_b = (_a = this.alignmentResponse) === null || _a === void 0 ? void 0 : _a.target_alignment) === null || _b === void 0 ? void 0 : _b.map(ta => ta === null || ta === void 0 ? void 0 : ta.target_id);
+                    const targetIds = (_b = (_a = this.alignmentResponse) === null || _a === void 0 ? void 0 : _a.target_alignments) === null || _b === void 0 ? void 0 : _b.map(ta => ta === null || ta === void 0 ? void 0 : ta.target_id);
                     assertElementListDefined(targetIds);
                     resolve(targetIds);
                 }
@@ -71,7 +71,7 @@ class AlignmentCollector {
     requestAlignment(requestConfig) {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
             this.requestStatus = "pending";
-            if (requestConfig.queryId) {
+            if (requestConfig.queryId && requestConfig.from && requestConfig.to) {
                 return yield this.rcsbFvQuery.requestAlignment({
                     queryId: requestConfig.queryId,
                     from: requestConfig.from,
@@ -79,7 +79,7 @@ class AlignmentCollector {
                 });
             }
             else {
-                if (requestConfig.group && requestConfig.page) {
+                if (requestConfig.group && requestConfig.groupId && requestConfig.page) {
                     return yield this.rcsbFvQuery.requestGroupAlignment({
                         group: requestConfig.group,
                         groupId: requestConfig.groupId,
@@ -97,7 +97,7 @@ class AlignmentCollector {
     complete() {
         var _a, _b, _c, _d, _e;
         this.requestStatus = "complete";
-        const targetIds = (_b = (_a = this.alignmentResponse.target_alignment) === null || _a === void 0 ? void 0 : _a.map(ta => ta === null || ta === void 0 ? void 0 : ta.target_id)) !== null && _b !== void 0 ? _b : [];
+        const targetIds = (_b = (_a = this.alignmentResponse.target_alignments) === null || _a === void 0 ? void 0 : _a.map(ta => ta === null || ta === void 0 ? void 0 : ta.target_id)) !== null && _b !== void 0 ? _b : [];
         assertElementListDefined(targetIds);
         this.targetsSubject.next(targetIds);
         this.alignmentResponseSubject.next(this.alignmentResponse);

package/lib/commonjs/RcsbCollectTools/AlignmentCollector/AlignmentCollectorInterface.d.ts

@@ -1,4 +1,4 @@
-import { AlignmentResponse, QueryAlignmentArgs, SequenceReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceAlignments, QueryAlignmentsArgs, SequenceReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbQueryGroupAlignmentArguments } from "../../RcsbGraphQL/RcsbQueryAlignment";
 import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";
 interface CommonAlignmentInterface {
@@ -10,7 +10,7 @@ interface CommonAlignmentInterface {
     excludeFirstRowLink?: boolean;
 }
 type QueryAlignmentArgsTypes = {
-    [K in keyof QueryAlignmentArgs]: NonNullable<QueryAlignmentArgs[K]>;
+    [K in keyof QueryAlignmentsArgs]: NonNullable<QueryAlignmentsArgs[K]>;
 };
 export interface CollectAlignmentInterface extends QueryAlignmentArgsTypes, CommonAlignmentInterface {
 }
@@ -22,8 +22,8 @@ export interface CollectGroupAlignmentInterface extends RcsbQueryGroupAlignmentA
 export type AlignmentCollectConfig = Partial<CollectAlignmentInterface & CollectGroupAlignmentInterface>;
 export interface AlignmentCollectorInterface {
     getTargets(): Promise<Array<string>>;
-    getAlignment(): Promise<AlignmentResponse>;
+    getAlignment(): Promise<SequenceAlignments>;
     getAlignmentLength(): Promise<number>;
-    collect(requestConfig: AlignmentCollectConfig, filter?: Array<string>): Promise<AlignmentResponse>;
+    collect(requestConfig: AlignmentCollectConfig, filter?: Array<string>): Promise<SequenceAlignments>;
 }
 export {};

package/lib/commonjs/RcsbCollectTools/AnnotationCollector/AnnotationCollector.d.ts

@@ -1,4 +1,4 @@
-import { AnnotationFeatures, Feature } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceAnnotations, Features } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
 import { AnnotationRequestContext, AnnotationCollectorInterface } from "./AnnotationCollectorInterface";
 export declare class AnnotationCollector implements AnnotationCollectorInterface {
@@ -8,9 +8,9 @@ export declare class AnnotationCollector implements AnnotationCollectorInterface
     private annotationFeatures;
     private readonly rawFeaturesSubject;
     private readonly annotationFeaturesSubject;
-    collect(requestConfig: AnnotationRequestContext): Promise<Array<AnnotationFeatures>>;
-    getFeatures(): Promise<Array<Feature>>;
-    getAnnotationFeatures(): Promise<Array<AnnotationFeatures>>;
+    collect(requestConfig: AnnotationRequestContext): Promise<Array<SequenceAnnotations>>;
+    getFeatures(): Promise<Array<Features>>;
+    getAnnotationFeatures(): Promise<Array<SequenceAnnotations>>;
     private requestAnnotations;
     private complete;
 }

package/lib/commonjs/RcsbCollectTools/AnnotationCollector/AnnotationCollector.js

@@ -58,7 +58,22 @@ class AnnotationCollector {
     }
     requestAnnotations(requestConfig) {
         return tslib_1.__awaiter(this, void 0, void 0, function* () {
-            if (requestConfig.queryId)
+            if (requestConfig.group && requestConfig.groupId && requestConfig.sources)
+                if (requestConfig.isSummary)
+                    return yield this.rcsbFvQuery.requestRcsbPdbGroupAnnotationsSummary({
+                        group: requestConfig.group,
+                        groupId: requestConfig.groupId,
+                        sources: requestConfig.sources,
+                        filters: requestConfig.filters
+                    });
+                else
+                    return yield this.rcsbFvQuery.requestRcsbPdbGroupAnnotations({
+                        group: requestConfig.group,
+                        groupId: requestConfig.groupId,
+                        sources: requestConfig.sources,
+                        filters: requestConfig.filters
+                    });
+            else if (requestConfig.queryId && requestConfig.reference && requestConfig.sources)
                 return yield this.rcsbFvQuery.requestRcsbPdbAnnotations({
                     queryId: requestConfig.queryId,
                     reference: requestConfig.reference,
@@ -66,14 +81,6 @@ class AnnotationCollector {
                     filters: requestConfig.filters,
                     range: requestConfig.range
                 });
-            else if (requestConfig.group && requestConfig.groupId)
-                return yield this.rcsbFvQuery.requestRcsbPdbGroupAnnotations({
-                    group: requestConfig.group,
-                    groupId: requestConfig.groupId,
-                    sources: requestConfig.sources,
-                    filters: requestConfig.filters,
-                    histogram: requestConfig.histogram
-                });
             throw new Error(`Annotation query error`);
         });
     }

package/lib/commonjs/RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface.d.ts

@@ -1,4 +1,4 @@
-import { AnnotationFeatures, Feature, QueryAnnotationsArgs, QueryGroup_AnnotationsArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceAnnotations, Features, QueryAnnotationsArgs, QueryGroup_AnnotationsArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { FeaturePositionGaps } from "../../RcsbFvWeb/RcsbFvFactories/RcsbFvBlockFactory/BlockManager/AnnotationTrackManager";
 import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";
 import { PolymerEntityInstanceInterface } from "../DataCollectors/PolymerEntityInstancesCollector";
@@ -7,7 +7,7 @@ export type IncreaseAnnotationValueType = (feature: {
     type: string;
     targetId: string;
     positionKey: string;
-    d: Feature;
+    d: Features;
     p: FeaturePositionGaps;
 }) => number;
 export interface AnnotationProcessingInterface {
@@ -19,19 +19,20 @@ export interface CommonAnnotationInterface {
     rcsbContext?: Partial<PolymerEntityInstanceInterface>;
     annotationProcessing?: AnnotationProcessingInterface;
     externalTrackBuilder?: ExternalTrackBuilderInterface;
-    annotationGenerator?(annotations: Array<AnnotationFeatures>): Promise<Array<AnnotationFeatures>>;
-    annotationFilter?(annotations: Array<AnnotationFeatures>): Promise<Array<AnnotationFeatures>>;
-    titleSuffix?(ann: AnnotationFeatures, d: Feature): Promise<string | undefined>;
-    trackTitle?(ann: AnnotationFeatures, d: Feature): Promise<string | undefined>;
-    typeSuffix?(ann: AnnotationFeatures, d: Feature): Promise<string | undefined>;
+    annotationGenerator?(annotations: Array<SequenceAnnotations>): Promise<Array<SequenceAnnotations>>;
+    annotationFilter?(annotations: Array<SequenceAnnotations>): Promise<Array<SequenceAnnotations>>;
+    titleSuffix?(ann: SequenceAnnotations, d: Features): Promise<string | undefined>;
+    trackTitle?(ann: SequenceAnnotations, d: Features): Promise<string | undefined>;
+    typeSuffix?(ann: SequenceAnnotations, d: Features): Promise<string | undefined>;
 }
 export interface AnnotationsCollectConfig extends QueryAnnotationsArgs, CommonAnnotationInterface {
 }
 export interface CollectGroupAnnotationsInterface extends QueryGroup_AnnotationsArgs, CommonAnnotationInterface {
+    isSummary: boolean;
 }
 export type AnnotationRequestContext = Partial<AnnotationsCollectConfig & CollectGroupAnnotationsInterface>;
 export interface AnnotationCollectorInterface {
-    collect(requestConfig: AnnotationsCollectConfig | CollectGroupAnnotationsInterface): Promise<Array<AnnotationFeatures>>;
-    getAnnotationFeatures(): Promise<Array<AnnotationFeatures>>;
-    getFeatures(): Promise<Array<Feature>>;
+    collect(requestConfig: AnnotationsCollectConfig | CollectGroupAnnotationsInterface): Promise<Array<SequenceAnnotations>>;
+    getAnnotationFeatures(): Promise<Array<SequenceAnnotations>>;
+    getFeatures(): Promise<Array<Features>>;
 }

package/lib/commonjs/RcsbCollectTools/DataCollectors/PolymerEntityChromosomeCollector.js

@@ -16,7 +16,7 @@ class PolymerEntityChromosomeCollector {
             }));
             result.forEach((alignment, n) => {
                 var _a;
-                (_a = alignment.target_alignment) === null || _a === void 0 ? void 0 : _a.forEach(ta => {
+                (_a = alignment.target_alignments) === null || _a === void 0 ? void 0 : _a.forEach(ta => {
                     var _a, _b, _c;
                     if (((_b = (_a = ta === null || ta === void 0 ? void 0 : ta.aligned_regions) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0) {
                         if (!entityMap.has(entityIds[n]))

package/lib/commonjs/RcsbCollectTools/FeatureTools/ExternalTrackBuilderInterface.d.ts

@@ -1,20 +1,20 @@
 import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro/lib/RcsbFv/RcsbFvConfig/RcsbFvConfigInterface";
-import { AlignmentResponse, AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { SequenceAlignments, SequenceAnnotations } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { PolymerEntityInstanceInterface } from "../DataCollectors/PolymerEntityInstancesCollector";
 export interface ExternalTrackBuilderInterface {
     processAlignmentAndFeatures?(data: {
-        annotations?: Array<AnnotationFeatures>;
-        alignments?: AlignmentResponse;
+        annotations?: Array<SequenceAnnotations>;
+        alignments?: SequenceAlignments;
         rcsbContext?: Partial<PolymerEntityInstanceInterface>;
     }): Promise<void>;
     filterAlignments?(data: {
-        alignments: AlignmentResponse;
+        alignments: SequenceAlignments;
         rcsbContext?: Partial<PolymerEntityInstanceInterface>;
-    }): Promise<AlignmentResponse>;
+    }): Promise<SequenceAlignments>;
     filterFeatures?(data: {
-        annotations: Array<AnnotationFeatures>;
+        annotations: Array<SequenceAnnotations>;
         rcsbContext?: Partial<PolymerEntityInstanceInterface>;
-    }): Promise<Array<AnnotationFeatures>>;
+    }): Promise<Array<SequenceAnnotations>>;
     addTo?(tracks: {
         alignmentTracks?: Array<RcsbFvRowConfigInterface>;
         annotationTracks?: Array<RcsbFvRowConfigInterface>;