@rcsb/rcsb-saguaro-app 4.4.0-models.29 → 4.4.0-models.31

package/build/dist/RcsbAnnotationConfig/AnnotationConfigInterface.d.ts

@@ -3,6 +3,7 @@ export interface AnnotationConfigInterface {
     provenance_color_code: {
         external: string;
         rcsb_pdb: string;
+        csm: string;
     };
     merge?: Array<{
         merged_types: Array<string>;

package/build/dist/RcsbAnnotationConfig/RcsbAnnotationConstants.d.ts

@@ -2,9 +2,11 @@ export declare const RcsbAnnotationConstants: {
     provenanceColorCode: {
         rcsbPdb: string;
         external: string;
+        csm: string;
     };
     provenanceName: {
         pdb: string;
+        csm: string;
         mmseqs: string;
         promotif: string;
         userInput: string;

package/build/dist/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/AlignmentTrackFactory.d.ts

@@ -1,4 +1,4 @@
-import { RcsbFvLink, RcsbFvRowConfigInterface, RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro";
+import { RcsbFvRowConfigInterface, RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro";
 import { AlignedRegion, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { PolymerEntityInstanceTranslate, AlignmentContextInterface } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { TrackFactoryInterface } from "../TrackFactoryInterface";
@@ -13,8 +13,6 @@ export declare class AlignmentTrackFactory implements TrackFactoryInterface<[Ali
     private readonly trackTitleFactory;
     constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate, trackTitleFactory?: TrackTitleFactoryInterface<[AlignmentRequestContextType, TargetAlignment]>);
     getTrack(alignmentRequestContext: AlignmentRequestContextType, targetAlignment: TargetAlignment, alignedRegionToTrackElementList?: (region: AlignedRegion, alignmentContext: AlignmentContextInterface) => Array<RcsbFvTrackDataElementInterface>): Promise<RcsbFvRowConfigInterface>;
-    buildAlignmentRowTitle(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string | RcsbFvLink>;
-    buildAlignmentRowTitlePrefix(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string>;
     private getAlignmentTrackConfiguration;
     alignedRegionToTrackElementList(region: AlignedRegion, alignmentContext: AlignmentContextInterface): Array<RcsbFvTrackDataElementInterface>;
     addAuthorResIds(e: RcsbFvTrackDataElementInterface, alignmentContext: AlignmentContextInterface): RcsbFvTrackDataElementInterface;

package/build/dist/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/Helper/TrackUtils.d.ts

@@ -0,0 +1,9 @@
+import { SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+export declare namespace TrackUtils {
+    function getProvenanceConfigFormTarget(targetId: string, targetSource: SequenceReference | Source): {
+        name: string;
+        color: string;
+    };
+    function transformSourceFromTarget(targetId: string, source: SequenceReference | Source): string;
+    function getProvenanceColorFromProvenance(provenance: string): string;
+}

package/build/dist/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/PlainAlignmentTrackFactory.d.ts

@@ -1,4 +1,4 @@
-import { RcsbFvColorGradient, RcsbFvLink, RcsbFvRowConfigInterface, RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro";
+import { RcsbFvColorGradient, RcsbFvRowConfigInterface, RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro";
 import { AlignedRegion, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { PolymerEntityInstanceTranslate, AlignmentContextInterface } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { TrackFactoryInterface } from "../TrackFactoryInterface";
@@ -12,7 +12,6 @@ export declare class PlainAlignmentTrackFactory implements TrackFactoryInterface
     private readonly trackTitleFactory;
     constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
     getTrack(alignmentRequestContext: AlignmentRequestContextType, targetAlignment: TargetAlignment, alignedRegionToTrackElementList?: (region: AlignedRegion, alignmentContext: AlignmentContextInterface) => Array<RcsbFvTrackDataElementInterface>, alignmentColor?: RcsbFvColorGradient): Promise<RcsbFvRowConfigInterface>;
-    buildAlignmentRowTitle(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string | RcsbFvLink>;
     getAlignmentTrackConfiguration(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment, alignedRegionToTrackElementList: (region: AlignedRegion, alignmentContext: AlignmentContextInterface) => Array<RcsbFvTrackDataElementInterface>): {
         alignedBlocks: Array<RcsbFvTrackDataElementInterface>;
         mismatchData: Array<RcsbFvTrackDataElementInterface>;

package/build/dist/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/AlignmentTrackTitleFactory.d.ts

@@ -5,8 +5,10 @@ import { RcsbFvLink } from "@rcsb/rcsb-saguaro";
 import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 export declare class AlignmentTrackTitleFactory implements TrackTitleFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
     private readonly entityInstanceTranslator;
+    private readonly experimentalTrackTitleFactory;
+    private readonly modelTrackTitleFactory;
     constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
     getTrackTitle(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string | RcsbFvLink>;
     getTrackTitlePrefix(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string>;
-    private buildInstanceId;
+    getTrackTitleFlagColor(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string>;
 }

package/build/dist/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/ExperimentalAlignmentTrackTitleFactory.d.ts

@@ -0,0 +1,13 @@
+import { TrackTitleFactoryInterface } from "../TrackTitleFactoryInterface";
+import { TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { AlignmentRequestContextType } from "../TrackFactoryImpl/AlignmentTrackFactory";
+import { RcsbFvLink } from "@rcsb/rcsb-saguaro";
+import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
+export declare class ExperimentalAlignmentTrackTitleFactory implements TrackTitleFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
+    private readonly entityInstanceTranslator;
+    constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
+    getTrackTitle(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string | RcsbFvLink>;
+    getTrackTitlePrefix(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string>;
+    getTrackTitleFlagColor(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string>;
+    private buildInstanceId;
+}

package/build/dist/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/InstanceSequenceTrackTitleFactory.d.ts

@@ -7,4 +7,5 @@ export declare class InstanceSequenceTrackTitleFactory implements TrackTitleFact
     constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
     getTrackTitle(alignmentQueryContext: AlignmentRequestContextType): Promise<string | RcsbFvLink>;
     getTrackTitlePrefix(alignmentQueryContext: AlignmentRequestContextType): Promise<string>;
+    getTrackTitleFlagColor(alignmentQueryContext: AlignmentRequestContextType): Promise<string>;
 }

package/build/dist/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/ModelAlignmentTrackTitleFactory.d.ts

@@ -0,0 +1,13 @@
+import { TrackTitleFactoryInterface } from "../TrackTitleFactoryInterface";
+import { AlignmentRequestContextType } from "../TrackFactoryImpl/AlignmentTrackFactory";
+import { TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+import { RcsbFvLink } from "@rcsb/rcsb-saguaro";
+import { PolymerEntityInstanceTranslate } from "../../../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
+export declare class ModelAlignmentTrackTitleFactory implements TrackTitleFactoryInterface<[AlignmentRequestContextType, TargetAlignment]> {
+    private readonly entityInstanceTranslator;
+    private readonly alignmentTrackTitleFactory;
+    constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
+    getTrackTitle(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string | RcsbFvLink>;
+    getTrackTitlePrefix(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string>;
+    getTrackTitleFlagColor(alignmentQueryContext: AlignmentRequestContextType, targetAlignment: TargetAlignment): Promise<string>;
+}

package/build/dist/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryImpl/SequenceTrackTitleFactory.d.ts

@@ -7,5 +7,6 @@ export declare class SequenceTrackTitleFactory implements TrackTitleFactoryInter
     constructor(entityInstanceTranslator?: PolymerEntityInstanceTranslate);
     getTrackTitle(alignmentQueryContext: AlignmentRequestContextType): Promise<string | RcsbFvLink>;
     getTrackTitlePrefix(alignmentQueryContext: AlignmentRequestContextType): Promise<string>;
+    getTrackTitleFlagColor(alignmentQueryContext: AlignmentRequestContextType): Promise<string>;
     private buildInstanceId;
 }

package/build/dist/RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackTitleFactoryInterface.d.ts

@@ -2,4 +2,5 @@ import { RcsbFvLink } from "@rcsb/rcsb-saguaro";
 export interface TrackTitleFactoryInterface<T extends any[]> {
     getTrackTitle(...args: T): Promise<string | RcsbFvLink>;
     getTrackTitlePrefix(...args: T): Promise<string>;
+    getTrackTitleFlagColor(...args: T): Promise<string>;
 }

package/build/dist/RcsbUtils/Helpers/TagDelimiter.d.ts

@@ -8,6 +8,8 @@ export declare class TagDelimiter {
     private static rcsbEntryRegExp;
     private static rcsbEntityRegExp;
     private static rcsbInstanceRegExp;
+    private static alphaFoldRegExp;
+    private static modelArchiveRegExp;
     static parseEntity(rcsbId: string): {
         entryId: string;
         entityId: string;
@@ -18,4 +20,5 @@ export declare class TagDelimiter {
     };
     static isEntityOrInstanceId(rcsb: string): boolean;
     static isRcsbId(rcsb: string): boolean;
+    static isModel(rcsb: string): boolean;
 }