@rcsb/rcsb-saguaro-app 4.0.0-interfaces.9 → 4.0.0

package/CHANGELOG.md

@@ -2,7 +2,7 @@
 
 [Semantic Versioning](https://semver.org/)
 
-## [4.0.0-interfaces] - 2022-01-24
+## [4.0.0] - 2022-02-08
 ###  Annotation collector improvements 
 -  Added interface `CollectAnnotationsInterface` for generating new annotations internally (not exposed)
     - `annotationGenerator?(annotations: Array<AnnotationFeatures>)` generates new annotations from the collected ones
@@ -13,9 +13,8 @@
     dropdown menu changes and before rendering the new 1D RcsbFv. 
     The callback may return a `RcsbContextType` object that will be included in the `additionalConfig`
 - Added two new classes (`AssemblyInterfacesCollector` and `AssemblyInterfacesTranslate`) to collect and handle assembly and interface id relationships
-
-## [4.0.0-master] - 2021-12-07
-### Breaking change
+- Exposing all feature types in a single object `FeatureType` (file: `src/RcsbExport/FeatureType.ts`)
+- New package `RcsbExport` to expose classes and methods outside the library
 - `ExternalTrackBuilderInterface` methods return a promise and are executed asynchronous
 
 ## [3.4.0] - 2021-12-07

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

@@ -1,7 +1,7 @@
 import { RcsbFvRowConfigInterface } from '@rcsb/rcsb-saguaro';
 import { AnnotationFeatures, Feature } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
-import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
+import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { AnnotationCollectConfig, AnnotationCollectorInterface } from "./AnnotationCollectorInterface";
 import { AnnotationConfigInterface } from "../../RcsbAnnotationConfig/AnnotationConfigInterface";
 import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";

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

@@ -1,6 +1,6 @@
 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/PolymerEntityInstanceTranslate";
+import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { RcsbAnnotationConfigInterface } from "../../RcsbAnnotationConfig/AnnotationConfigInterface";
 import { AnnotationProcessingInterface } from "./AnnotationCollectorInterface";
 export interface FeaturePositionGaps extends FeaturePosition {

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

@@ -1,7 +1,7 @@
 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/PolymerEntityInstanceTranslate";
+import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { AnnotationCollectConfig } from "./AnnotationCollectorInterface";
 export declare class AnnotationTrackManager {
     private readonly rcsbAnnotationConfig;

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

@@ -1,4 +1,4 @@
-import { PolymerEntityInstanceTranslate } from "../RcsbUtils/PolymerEntityInstanceTranslate";
+import { PolymerEntityInstanceTranslate } from "../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { RcsbClient } from "../RcsbGraphQL/RcsbClient";
 import { ExternalTrackBuilderInterface } from "./FeatureTools/ExternalTrackBuilderInterface";
 export interface CoreCollectorInterface {

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

@@ -1,7 +1,7 @@
 import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
 import { CollectAlignmentInterface, SequenceCollectorInterface } from "./SequenceCollectorInterface";
 import { SequenceCollectorDataInterface } from "./SequenceCollector";
-import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
+import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { AlignmentResponse } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";
 export declare class GenomeMapCollector implements SequenceCollectorInterface {

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

@@ -1,6 +1,6 @@
 import { AlignmentResponse } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { SequenceCollectorDataInterface } from "./SequenceCollector";
-import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
+import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
 import { AlignmentCollectConfig, SequenceCollectorInterface } from "./SequenceCollectorInterface";
 import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";

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

@@ -1,6 +1,6 @@
 import { RcsbFvRowConfigInterface } from '@rcsb/rcsb-saguaro';
 import { AlignedRegion, AlignmentResponse } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { PolymerEntityInstanceTranslate, TranslateContextInterface } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
+import { PolymerEntityInstanceTranslate, TranslateContextInterface } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { RcsbClient } from "../../RcsbGraphQL/RcsbClient";
 import { AlignmentCollectConfig, SequenceCollectorInterface } from "./SequenceCollectorInterface";
 import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";

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

@@ -1,4 +1,4 @@
-import { PolymerEntityInstanceTranslate, TranslateContextInterface } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
+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";

package/build/dist/RcsbExport/FeatureType.d.ts

@@ -0,0 +1,10 @@
+import { Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
+declare const ExtendedTypes: {
+    BurialFraction: Type;
+    BuriedResidues: Type;
+};
+declare type MergedType = typeof Type & typeof ExtendedTypes;
+declare const MergedType: MergedType;
+declare type FeatureType = typeof MergedType;
+export declare const FeatureType: FeatureType;
+export {};

package/build/dist/RcsbExport/RcsbFvContextManager.d.ts

@@ -0,0 +1,4 @@
+import { InterfaceInstanceTranslate } from "../RcsbUtils/Translators/InterfaceInstanceTranslate";
+export declare class RcsbFvContextManager {
+    static getInterfaceToInstance(interfaceId: string): Promise<InterfaceInstanceTranslate>;
+}

package/build/dist/RcsbExport/RcsbFvUI.d.ts

@@ -0,0 +1,7 @@
+import { GroupedOptionsInterface, SelectOptionInterface } from "../RcsbFvWeb/WebTools/SelectButton";
+import { SelectButtonConfigInterface } from "../RcsbFvWeb/WebTools/WebToolsManager";
+export declare class RcsbFvUI {
+    static clearSelectButton(elementFvId: string, selectButtonId: string): void;
+    static createSelectButton(elementFvId: string, selectButtonId: string, options: Array<SelectOptionInterface> | Array<GroupedOptionsInterface>, config?: SelectButtonConfigInterface): void;
+    static addSelectButton(elementFvId: string, selectButtonId: string, options: Array<SelectOptionInterface>, config?: SelectButtonConfigInterface): void;
+}

package/build/dist/RcsbFvWeb/RcsbFvBuilder/RcsbFvContextManager.d.ts

@@ -1,8 +1,8 @@
 import { RcsbFv, RcsbFvBoardConfigInterface } from "@rcsb/rcsb-saguaro";
-import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
-import { EntryAssemblyTranslate } from "../../RcsbUtils/EntryAssemblyTranslate";
-import { PolymerEntityChromosomeTranslate } from "../../RcsbUtils/PolymerEntityChromosomeTranslate";
-import { InterfaceInstanceTranslate } from "../../RcsbUtils/InterfaceInstanceTranslate";
+import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
+import { EntryAssemblyTranslate } from "../../RcsbUtils/Translators/EntryAssemblyTranslate";
+import { PolymerEntityChromosomeTranslate } from "../../RcsbUtils/Translators/PolymerEntityChromosomeTranslate";
+import { InterfaceInstanceTranslate } from "../../RcsbUtils/Translators/InterfaceInstanceTranslate";
 declare class RcsbFvContextManager {
     private rcsbFvManager;
     private rcsbButtonManager;

package/build/dist/RcsbFvWeb/RcsbFvBuilder/RcsbFvCoreBuilder.d.ts

@@ -1,4 +1,4 @@
-import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
+import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { RcsbFv } from "@rcsb/rcsb-saguaro";
 import { RcsbFvModuleBuildInterface, RcsbFvModuleInterface, RcsbFvModulePublicInterface } from "../RcsbFvModule/RcsbFvModuleInterface";
 import { SelectButtonConfigInterface } from "../WebTools/WebToolsManager";

package/build/dist/RcsbFvWeb/RcsbFvModule/RcsbFvAbstractModule.d.ts

@@ -1,6 +1,6 @@
 import { RcsbFv, RcsbFvBoardConfigInterface, RcsbFvRowConfigInterface } from '@rcsb/rcsb-saguaro';
 import { SequenceCollectorDataInterface } from "../../RcsbCollectTools/SequenceCollector/SequenceCollector";
-import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
+import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { SequenceCollectorInterface } from "../../RcsbCollectTools/SequenceCollector/SequenceCollectorInterface";
 import { AnnotationCollectorInterface } from "../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
 import { RcsbFvModuleBuildInterface, RcsbFvModuleInterface } from "./RcsbFvModuleInterface";

package/build/dist/RcsbFvWeb/RcsbFvModule/RcsbFvModuleInterface.d.ts

@@ -1,5 +1,5 @@
 import { Feature, FilterInput, SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/PolymerEntityInstanceTranslate";
+import { PolymerEntityInstanceTranslate } from "../../RcsbUtils/Translators/PolymerEntityInstanceTranslate";
 import { RcsbFv, RcsbFvBoardConfigInterface, RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro";
 import { PairwiseAlignmentInterface } from "../PairwiseAlignmentTools/PairwiseAlignmentBuilder";
 import { AnnotationProcessingInterface } from "../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";

package/build/dist/RcsbUtils/AnnotationGenerators/BurialFraction.d.ts

@@ -0,0 +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>;

package/build/dist/RcsbUtils/AnnotationGenerators/BuriedResidues.d.ts

@@ -0,0 +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>;

package/build/dist/RcsbUtils/{AssemblyInterfacesTranslate.d.ts → Translators/AssemblyInterfacesTranslate.d.ts}

@@ -1,4 +1,4 @@
-import { AssemblyInterfacesInterface } from "../RcsbCollectTools/Translators/AssemblyInterfacesCollector";
+import { AssemblyInterfacesInterface } from "../../RcsbCollectTools/Translators/AssemblyInterfacesCollector";
 export declare class AssemblyInterfacesTranslate {
     private readonly rawData;
     private interfaceMap;

package/build/dist/RcsbUtils/{EntryAssemblyTranslate.d.ts → Translators/EntryAssemblyTranslate.d.ts}

@@ -1,4 +1,4 @@
-import { PolymerEntityInstanceInterface } from "../RcsbCollectTools/Translators/PolymerEntityInstancesCollector";
+import { PolymerEntityInstanceInterface } from "../../RcsbCollectTools/Translators/PolymerEntityInstancesCollector";
 export declare class EntryAssemblyTranslate {
     private readonly rawData;
     constructor(data: Map<string, Array<PolymerEntityInstanceInterface>>);

package/build/dist/RcsbUtils/{InterfaceInstanceTranslate.d.ts → Translators/InterfaceInstanceTranslate.d.ts}

@@ -1,4 +1,4 @@
-import { InterfaceInstanceInterface } from "../RcsbCollectTools/Translators/InterfaceInstanceCollector";
+import { InterfaceInstanceInterface } from "../../RcsbCollectTools/Translators/InterfaceInstanceCollector";
 export declare class InterfaceInstanceTranslate {
     private readonly rawData;
     private readonly instances;

package/build/dist/RcsbUtils/{MultipleEntityInstanceTranslate.d.ts → Translators/MultipleEntityInstanceTranslate.d.ts}

@@ -1,5 +1,5 @@
 import { PolymerEntityInstanceTranslate } from "./PolymerEntityInstanceTranslate";
-import { PolymerEntityInstanceInterface } from "../RcsbCollectTools/Translators/PolymerEntityInstancesCollector";
+import { PolymerEntityInstanceInterface } from "../../RcsbCollectTools/Translators/PolymerEntityInstancesCollector";
 export declare class MultipleEntityInstanceTranslate {
     private readonly entityInstanceTranslateMap;
     add(data: Array<PolymerEntityInstanceInterface>): void;

package/build/dist/RcsbUtils/{PolymerEntityInstanceTranslate.d.ts → Translators/PolymerEntityInstanceTranslate.d.ts}

@@ -1,4 +1,4 @@
-import { PolymerEntityInstanceInterface } from "../RcsbCollectTools/Translators/PolymerEntityInstancesCollector";
+import { PolymerEntityInstanceInterface } from "../../RcsbCollectTools/Translators/PolymerEntityInstancesCollector";
 import { RcsbFvTrackDataElementInterface } from '@rcsb/rcsb-saguaro';
 import { SequenceReference, Source } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 export interface TranslateContextInterface {

package/build/dist/app.d.ts

@@ -1,12 +1,4 @@
-import { GroupedOptionsInterface, SelectOptionInterface } from "./RcsbFvWeb/WebTools/SelectButton";
 export { buildEntryChromosome, buildFullChromosome, buildEntityChromosome, buildChromosome, buildEntityFv, buildEntitySummaryFv, buildSingleEntitySummaryFv, buildInstanceFv, buildInstanceSequenceFv, buildMultipleInstanceSequenceFv, buildAssemblySequenceFv, buildPairwiseAlignment, buildPfv, buildMultipleAlignmentSequenceFv, buildUniprotEntityFv, buildUniprotEntityInstanceFv, buildUniprotFv, unmount } from "./RcsbFvWeb/RcsbFvBuilder";
-import { SelectButtonConfigInterface } from "./RcsbFvWeb/WebTools/WebToolsManager";
-import { InterfaceInstanceTranslate } from "./RcsbUtils/InterfaceInstanceTranslate";
-export declare class RcsbFvUI {
-    static clearSelectButton(elementFvId: string, selectButtonId: string): void;
-    static createSelectButton(elementFvId: string, selectButtonId: string, options: Array<SelectOptionInterface> | Array<GroupedOptionsInterface>, config?: SelectButtonConfigInterface): void;
-    static addSelectButton(elementFvId: string, selectButtonId: string, options: Array<SelectOptionInterface>, config?: SelectButtonConfigInterface): void;
-}
-export declare class RcsbFvContextManager {
-    static getInterfaceToInstance(interfaceId: string): Promise<InterfaceInstanceTranslate>;
-}
+export { RcsbFvContextManager } from "./RcsbExport/RcsbFvContextManager";
+export { RcsbFvUI } from "./RcsbExport/RcsbFvUI";
+export { FeatureType } from "./RcsbExport/FeatureType";