@rcsb/rcsb-saguaro-app 4.3.6 → 4.4.0-models.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@rcsb/rcsb-saguaro-app",
-  "version": "4.3.6",
+  "version": "4.4.0-models.2",
   "description": "RCSB 1D Saguaro Web App",
   "main": "build/dist/app.js",
   "files": [
@@ -10,7 +10,9 @@
     "buildAll": "npm run buildApp && npm run buildAllDoc",
     "buildOnlyApp": "npm run tsc && npm run copyQueries && npm run copyCss && npm run build && npm run copyConfig",
     "buildApp": "npm run cleanAll && npm run checkQueries && npm run buildOnlyApp && npm run clean",
+    "buildAppDev": "npm run cleanAll && npm run checkQueries && npm run buildDev",
     "build": "webpack --config ./webpack.config.js",
+    "buildDev": "webpack --config ./webpack.dev.js",
     "checkQueries": "ts-node src/RcsbGraphQL/Queries/QueryCheck.ts",
     "copyQueries": "ncp src/RcsbGraphQL/Queries build/src/RcsbGraphQL/Queries",
     "copyConfig": "ncp build/src/RcsbServerConfig/ServerConfig.js build/dist/config.js",
@@ -57,6 +59,7 @@
     "bootstrap-icons": "^1.8.1",
     "css-loader": "^6.5.1",
     "del-cli": "^4.0.1",
+    "html-webpack-plugin": "^5.5.0",
     "lodash": "^4.17.21",
     "ncp": "^2.0.0",
     "object-hash": "^3.0.0",
@@ -78,11 +81,12 @@
     "victory": "^36.3.1",
     "webpack": "^5.64.4",
     "webpack-cli": "^4.9.1",
+    "webpack-dev-server": "^4.9.2",
     "worker-loader": "^3.0.8"
   },
   "dependencies": {
-    "@rcsb/rcsb-api-tools": "^4.0.5",
-    "@rcsb/rcsb-saguaro": "^2.0.6",
+    "@rcsb/rcsb-api-tools": "^4.1.0-models",
+    "@rcsb/rcsb-saguaro": "^2.1.0",
     "ideogram": "^1.33.0",
     "react-select": "^5.2.2",
     "rxjs": "^6.6.0"

package/build/dist/RcsbCollectTools/AnnotationCollector/AnnotationCollectorHelper.d.ts

@@ -1,11 +0,0 @@
-import { AnnotationTrack } from "./AnnotationTrack";
-import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro";
-import { RcsbAnnotationConfigInterface } from "../../RcsbAnnotationConfig/AnnotationConfigInterface";
-export declare class AnnotationCollectorHelper {
-    static buildAnnotationTrack(annotationHandler: AnnotationTrack, type: string, rcsbAnnotationConfig: RcsbAnnotationConfigInterface, provenanceList: Array<string>): RcsbFvRowConfigInterface;
-    private static buildRcsbFvRowConfigTrack;
-    private static buildRcsbFvRowConfigArea;
-    private static buildRcsbFvRowConfigBlockArea;
-    private static buildRcsbFvRowConfigComposite;
-    private static buildRowTitle;
-}

package/build/dist/RcsbCollectTools/AnnotationCollector/AnnotationTrack.d.ts

@@ -1,40 +0,0 @@
-import { RcsbFvTrackDataElementGapInterface, RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro";
-import { Feature, FeaturePosition, SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-import { RcsbAnnotationConfigInterface } from "../../RcsbAnnotationConfig/AnnotationConfigInterface";
-import { AnnotationProcessingInterface } from "./AnnotationCollectorInterface";
-export interface FeaturePositionGaps extends FeaturePosition {
-    gaps?: Array<RcsbFvTrackDataElementGapInterface>;
-}
-export declare class AnnotationTrack {
-    private valueRange;
-    private readonly entityInstanceTranslator;
-    private readonly type;
-    private readonly annotationConfig;
-    private readonly trackElementMap;
-    constructor(type: string, annotationConfig: RcsbAnnotationConfigInterface, entityInstanceTranslator: PolymerEntityInstanceTranslate);
-    getRange(): {
-        min: number;
-        max: number;
-    };
-    addFeature(ann: {
-        reference: SequenceReference | undefined;
-        queryId: string;
-        source: Source;
-        targetId: string;
-        feature: Feature;
-    }, annotationProcessing?: AnnotationProcessingInterface): void;
-    size(): number;
-    forEach(f: (ann: RcsbFvTrackDataElementInterface, loc: string) => void): void;
-    addAll(trackElementsMap: AnnotationTrack, color?: string): void;
-    getTrackProvenance(): Set<string>;
-    set(loc: string, ann: RcsbFvTrackDataElementInterface): void;
-    values(): Array<RcsbFvTrackDataElementInterface>;
-    private buildRcsbFvTrackDataElement;
-    private addRange;
-    private transformToNumerical;
-    private expandValues;
-    private addAuthorResIds;
-    private isNumericalDisplay;
-    private annotationRangeKeys;
-}

package/build/dist/RcsbCollectTools/AnnotationCollector/AnnotationTrackManager.d.ts

@@ -1,19 +0,0 @@
-import { AnnotationTrack } from "./AnnotationTrack";
-import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { RcsbAnnotationConfig } from "../../RcsbAnnotationConfig/RcsbAnnotationConfig";
-import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-import { AnnotationCollectConfig } from "./AnnotationCollectorInterface";
-export declare class AnnotationTrackManager {
-    private readonly rcsbAnnotationConfig;
-    private readonly annotationTracks;
-    private polymerEntityInstanceTranslator;
-    constructor(rcsbAnnotationConfig: RcsbAnnotationConfig);
-    processRcsbPdbAnnotations(data: Array<AnnotationFeatures>, requestConfig: AnnotationCollectConfig): Promise<void>;
-    getAnnotationTracks(): Map<string, AnnotationTrack>;
-    private getPolymerEntityInstanceTranslator;
-    setPolymerEntityInstanceTranslator(p: PolymerEntityInstanceTranslate): void;
-    private addAnnotationToTracks;
-    private addFeature;
-    private buildType;
-    private mergeTracks;
-}

package/build/dist/RcsbCollectTools/CoreCollectorInterface.d.ts

@@ -1,8 +0,0 @@
-import { PolymerEntityInstanceTranslate } from "../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-import { RcsbClient } from "../RcsbGraphQL/RcsbClient";
-import { ExternalTrackBuilderInterface } from "./FeatureTools/ExternalTrackBuilderInterface";
-export interface CoreCollectorInterface {
-    readonly rcsbFvQuery: RcsbClient;
-    setPolymerEntityInstanceTranslator(p: PolymerEntityInstanceTranslate): void;
-    setExternalTrackBuilder(externalTrackBuilder: ExternalTrackBuilderInterface): void;
-}

package/build/dist/RcsbCollectTools/SequenceCollector/GenomeMapCollector.d.ts

@@ -1,16 +0,0 @@
-import { CollectAlignmentInterface, SequenceCollectorInterface } from "./SequenceCollectorInterface";
-import { SequenceCollectorDataInterface } from "./SequenceCollector";
-import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-import { AlignmentResponse } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";
-import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
-export declare class GenomeMapCollector implements SequenceCollectorInterface {
-    readonly rcsbFvQuery: RcsbClient;
-    collect(requestConfig: CollectAlignmentInterface, filter?: Array<string>, entityInstanceMapCollector?: (instanceIds: Array<string>) => Promise<null>): Promise<SequenceCollectorDataInterface>;
-    getPolymerEntityInstanceTranslator(): PolymerEntityInstanceTranslate;
-    getSequenceLength(): number;
-    getTargets(): Promise<Array<string>>;
-    setPolymerEntityInstanceTranslator(p: PolymerEntityInstanceTranslate): void;
-    getAlignmentResponse(): Promise<AlignmentResponse>;
-    setExternalTrackBuilder(externalTrackBuilder: ExternalTrackBuilderInterface): void;
-}

package/build/dist/RcsbCollectTools/SequenceCollector/ObservedSequenceCollector.d.ts

@@ -1,26 +0,0 @@
-import { AlignmentResponse } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { SequenceCollectorDataInterface } from "./SequenceCollector";
-import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
-import { AlignmentCollectConfig, SequenceCollectorInterface } from "./SequenceCollectorInterface";
-import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";
-export declare class ObservedSequenceCollector implements SequenceCollectorInterface {
-    private entityInstanceMap;
-    private unObservedMap;
-    private sequenceCollector;
-    readonly rcsbFvQuery: RcsbClient;
-    private polymerEntityInstanceTranslator;
-    private externalTrackBuilder;
-    collect(requestConfig: AlignmentCollectConfig, filter?: Array<string>): Promise<SequenceCollectorDataInterface>;
-    getTargets(): Promise<Array<string>>;
-    getAlignmentResponse(): Promise<AlignmentResponse>;
-    getSequenceLength(): number;
-    getPolymerEntityInstanceTranslator(): PolymerEntityInstanceTranslate;
-    setPolymerEntityInstanceTranslator(p: PolymerEntityInstanceTranslate): void;
-    setExternalTrackBuilder(externalTrackBuilder: ExternalTrackBuilderInterface): void;
-    private loadObservedRegions;
-    private addUnmodelled;
-    private collectUnmodeledRegions;
-    private tagObservedRegions;
-    private collectEntityInstanceMap;
-}

package/build/dist/RcsbCollectTools/SequenceCollector/SequenceCollector.d.ts

@@ -1,40 +0,0 @@
-import { RcsbFvRowConfigInterface } from '@rcsb/rcsb-saguaro';
-import { AlignedRegion, AlignmentResponse } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { PolymerEntityInstanceTranslate, TranslateContextInterface } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
-import { AlignmentCollectConfig, SequenceCollectorInterface } from "./SequenceCollectorInterface";
-import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";
-export interface AlignedObservedRegion extends AlignedRegion {
-    unModelled?: boolean;
-    openBegin?: boolean;
-    openEnd?: boolean;
-}
-export interface SequenceCollectorDataInterface {
-    sequence: Array<RcsbFvRowConfigInterface>;
-    alignment: Array<RcsbFvRowConfigInterface>;
-}
-export declare class SequenceCollector implements SequenceCollectorInterface {
-    private sequenceLength;
-    private targets;
-    private requestStatus;
-    private dynamicDisplay;
-    private readonly helper;
-    readonly rcsbFvQuery: RcsbClient;
-    private polymerEntityInstanceTranslator;
-    private readonly targetsSubject;
-    private alignmentResponse;
-    private readonly alignmentResponseSubject;
-    private externalTrackBuilder;
-    private tagObservedRegions;
-    collect(requestConfig: AlignmentCollectConfig, filter?: Array<string>, entityInstanceMapCollector?: (instanceIds: Array<string>) => Promise<void>, tagObservedRegions?: (region: AlignedRegion, commonContext: TranslateContextInterface) => Array<AlignedObservedRegion>): Promise<SequenceCollectorDataInterface>;
-    getTargets(): Promise<Array<string>>;
-    getAlignmentResponse(): Promise<AlignmentResponse>;
-    getSequenceLength(): number;
-    setPolymerEntityInstanceTranslator(p: PolymerEntityInstanceTranslate): void;
-    setExternalTrackBuilder(externalTrackBuilder: ExternalTrackBuilderInterface): void;
-    private complete;
-    private buildAlignments;
-    private buildSequenceTrack;
-    private collectGenomeRegions;
-    private requestAlignment;
-}

package/build/dist/RcsbCollectTools/SequenceCollector/SequenceCollectorHelper.d.ts

@@ -1,36 +0,0 @@
-import { PolymerEntityInstanceTranslate, TranslateContextInterface } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
-import { AlignedRegion, SequenceReference, TargetAlignment } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { RcsbFvLink, RcsbFvRowConfigInterface, RcsbFvTrackDataElementInterface } from "@rcsb/rcsb-saguaro";
-import { AlignedObservedRegion } from "./SequenceCollector";
-import { AlignmentCollectConfig } from "./SequenceCollectorInterface";
-export interface BuildAlignmentsInterface {
-    targetAlignmentList: Array<TargetAlignment>;
-    queryId: string;
-    querySequence: string;
-    filterByTargetContains?: string;
-    to: SequenceReference;
-    from: SequenceReference;
-    sortAlignments?: (a: TargetAlignment, b: TargetAlignment) => number;
-    excludeAlignmentLinks?: boolean;
-    fitTitleWidth?: boolean;
-}
-interface BuildSequenceDataInterface extends TranslateContextInterface {
-    sequenceData: Array<RcsbFvTrackDataElementInterface>;
-    sequence: string;
-    begin: number;
-    oriBegin: number;
-}
-export declare class SequenceCollectorHelper {
-    private entityInstanceTranslator;
-    buildAlignments(alignmentData: BuildAlignmentsInterface, dynamicDisplayFlag: boolean, tagObservedRegions: (region: AlignedRegion, commonContext: TranslateContextInterface, noQuerySequenceFlag?: boolean) => Array<AlignedObservedRegion>): {
-        alignments: Array<RcsbFvRowConfigInterface>;
-        targets: Array<string>;
-    };
-    buildSequenceData(config: BuildSequenceDataInterface, isQuerySequence?: boolean): Array<RcsbFvTrackDataElementInterface>;
-    buildSequenceRowTitle(requestConfig: AlignmentCollectConfig): string | RcsbFvLink;
-    buildAlignmentRowTitle(targetAlignment: TargetAlignment, alignmentData: BuildAlignmentsInterface): string | RcsbFvLink;
-    addAuthorResIds(e: RcsbFvTrackDataElementInterface, alignmentContext: TranslateContextInterface): RcsbFvTrackDataElementInterface;
-    buildInstanceId(targetId: string): string;
-    setPolymerEntityInstanceTranslator(p: PolymerEntityInstanceTranslate): void;
-}
-export {};