@rcsb/rcsb-saguaro-app 3.3.0-interfaces → 4.0.0-interfaces.2

package/CHANGELOG.md

@@ -2,7 +2,25 @@
 
 [Semantic Versioning](https://semver.org/)
 
-## [3.3.0] - 2021-11-29
+## [4.0.0-interfaces] - 2021-12-15
+###  Annotation collector improvements 
+- CollectAnnotationsInterface added method for generating new annotations internally (not exposed)
+    - `annotationGenerator?(annotations: Array<AnnotationFeatures>)` generates new annotations from the collected ones
+    - `annotationFilter?(annotations: Array<AnnotationFeatures>)` filter the collected annotations
+    - Both method are called before annotations processing and thus, they should be configured in `RcsbAnnotationConfig.ac.json` or equivalent config
+
+## [4.0.0-master] - 2021-12-07
+### Breaking change
+- `ExternalTrackBuilderInterface` methods return a promise and are executed asynchronous
+
+## [3.4.0] - 2021-12-07
+### UI improvements
+- Exposed methods for creating dropdown menus. Class `RcsbFvUI` static methods
+    - `createSelectButton` creates a select dropdown menu
+    - `addSelectButton` adds a second menu. Only an additional button can be created (replaced if a new one is created)
+    - `clearSelectButton` clear all menus
+
+## [3.3.0] - 2021-11-30
 ### Annotations configuration improvements
 - Removed interface `CollectAnnotationsInterface` attribute `addTargetInTitle`
 - Added `titleSuffix` and `trackTitle` attributes to `CollectAnnotationsInterface`
@@ -22,8 +40,8 @@
 
 ## [3.1.0] - 2021-10-27
 ### External track builder improvements
-- `ExternalTrackBuilderInterface` available through `RcsbFvAdditionalConfig` for all `RcsbFvBuilder` types.
-In addition, it includes the query context as additional parameter for processing and addition methods.
+- `ExternalTrackBuilderInterface` available through `RcsbFvAdditionalConfig` for all `RcsbFvBuilder` types
+In addition, it includes the query context as additional parameter for processing and addition methods
   - `processAlignmentAndFeatures` includes the query context as part of the input parameters
   - `addTo` includes the query context as part of the input parameters
   - `filterFeatures` new method for filtering positional features

package/README.md

@@ -8,7 +8,7 @@ Feature Summaries. The package allows access to RCSB Saguaro methods to add or c
 <!---
 <div id="pfvSelect" ></div>  
 <div id="pfv" ></div>
-<script type="text/javascript" src="https://cdn.jsdelivr.net/npm/@rcsb/rcsb-saguaro-app@3.2.1/build/dist/app.js"></script>
+<script type="text/javascript" src="https://cdn.jsdelivr.net/npm/@rcsb/rcsb-saguaro-app@3.4.0/build/dist/app.js"></script>
 <script type="text/javascript">
 RcsbFvWebApp.buildInstanceFv("pfv", "4Z35.A", {
     boardConfig:{
@@ -23,7 +23,7 @@ RcsbFvWebApp.buildInstanceFv("pfv", "4Z35.A", {
 `npm install @rcsb/rcsb-saguaro-app`
 
 ### CDN JavaScript
-`<script src="https://cdn.jsdelivr.net/npm/@rcsb/rcsb-saguaro-app@3.2.1/build/dist/app.js" type="text/javascript"></script>`
+`<script src="https://cdn.jsdelivr.net/npm/@rcsb/rcsb-saguaro-app@3.4.0/build/dist/app.js" type="text/javascript"></script>`
 
 ### JavaScript Examples
 * [PDB Instance Chain View](https://rcsb.github.io/rcsb-saguaro-app/examples/instance.html)

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

@@ -21,7 +21,7 @@ export declare class RcsbAnnotationConfig {
     uniprotOrder(): Array<string>;
     instanceOrder(): Array<string>;
     entityOrder(): Array<string>;
-    buildAndAddType(d: Feature, mainTitle?: string, titleSuffix?: string): string;
+    buildAndAddType(d: Feature, mainTitle?: string, titleSuffix?: string, typeSuffix?: string): string;
     private addNewType;
     sortAndIncludeNewTypes(): void;
     private checkAndIncludeNewType;

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

@@ -3,6 +3,7 @@ import { RcsbFvRowConfigInterface } from "@rcsb/rcsb-saguaro";
 import { AnnotationFeatures, Feature, QueryAnnotationsArgs } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
 import { AnnotationTrack, FeaturePositionGaps } from "./AnnotationTrack";
 import { ExternalTrackBuilderInterface } from "../FeatureTools/ExternalTrackBuilderInterface";
+import { PolymerEntityInstanceInterface } from "../Translators/PolymerEntityInstancesCollector";
 export declare type IncreaseAnnotationValueType = (feature: {
     type: string;
     targetId: string;
@@ -15,14 +16,16 @@ export interface AnnotationProcessingInterface {
     computeAnnotationValue?: (annotationTracks: Map<string, AnnotationTrack>) => void;
     addTrackElementCallback?: IncreaseAnnotationValueType;
 }
-interface CommonAnnotationInterface {
+export interface CollectAnnotationsInterface extends QueryAnnotationsArgs {
+    collectSwissModel?: boolean;
+    rcsbContext?: Partial<PolymerEntityInstanceInterface>;
     annotationProcessing?: AnnotationProcessingInterface;
     externalAnnotationTrackBuilder?: ExternalTrackBuilderInterface;
-}
-export interface CollectAnnotationsInterface extends QueryAnnotationsArgs, CommonAnnotationInterface {
-    collectSwissModel?: boolean;
+    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>;
 }
 export declare type AnnotationCollectConfig = Partial<CollectAnnotationsInterface>;
 export interface AnnotationCollectorInterface extends CoreCollectorInterface {
@@ -31,4 +34,3 @@ export interface AnnotationCollectorInterface extends CoreCollectorInterface {
     getAnnotationFeatures(): Promise<Array<AnnotationFeatures>>;
     getFeatures(): Promise<Array<Feature>>;
 }
-export {};

package/build/dist/RcsbCollectTools/FeatureTools/ExternalTrackBuilderInterface.d.ts

@@ -7,12 +7,18 @@ export interface ExternalTrackBuilderInterface {
         annotations?: Array<AnnotationFeatures>;
         alignments?: AlignmentResponse;
         rcsbContext?: Partial<PolymerEntityInstanceInterface>;
-    }): void;
-    filterAlignments?(alignments: AlignmentResponse): AlignmentResponse;
-    filterFeatures?(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures>;
+    }): Promise<void>;
+    filterAlignments?(data: {
+        alignments: AlignmentResponse;
+        rcsbContext?: Partial<PolymerEntityInstanceInterface>;
+    }): Promise<AlignmentResponse>;
+    filterFeatures?(data: {
+        annotations: Array<AnnotationFeatures>;
+        rcsbContext?: Partial<PolymerEntityInstanceInterface>;
+    }): Promise<Array<AnnotationFeatures>>;
     addTo?(tracks: {
         alignmentTracks?: SequenceCollectorDataInterface;
         annotationTracks?: Array<RcsbFvRowConfigInterface>;
         rcsbContext?: Partial<PolymerEntityInstanceInterface>;
-    }): void;
+    }): Promise<void>;
 }

package/build/dist/RcsbCollectTools/Translators/InterfaceInstanceCollector.d.ts

@@ -4,6 +4,7 @@ export interface InterfaceInstanceInterface {
     assemblyId: string;
     interfaceId: string;
     asymIds: [string, string];
+    operatorIds: [Array<Array<string>>, Array<Array<string>>];
 }
 export declare class InterfaceInstanceCollector {
     private readonly rcsbFvQuery;

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

@@ -13,6 +13,7 @@ declare type instanceModule = "interface" | "instance";
 export interface InstanceSequenceConfig {
     dropdownTitle?: string;
     defaultValue?: string | undefined | null;
+    beforeRenderCallback?: (x: InstanceSequenceOnchangeInterface) => void;
     onChangeCallback?: (x: InstanceSequenceOnchangeInterface) => void;
     filterInstances?: Set<string>;
     displayAuthId?: boolean;

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

@@ -3,8 +3,10 @@ import { RcsbFvModuleBuildInterface } from "./RcsbFvModuleInterface";
 import { AnnotationCollectorInterface } from "../../RcsbCollectTools/AnnotationCollector/AnnotationCollectorInterface";
 export declare class RcsbFvInterface extends RcsbFvAbstractModule {
     protected readonly annotationCollector: AnnotationCollectorInterface;
+    private instanceId;
     protected protectedBuild(buildConfig: RcsbFvModuleBuildInterface): Promise<void>;
     protected concatAlignmentAndAnnotationTracks(buildConfig: RcsbFvModuleBuildInterface): void;
+    private typeSuffix;
     private titleSuffix;
     private trackTitle;
 }

package/build/dist/RcsbFvWeb/WebTools/SelectButton.d.ts

@@ -13,6 +13,7 @@ export interface SelectOptionInterface {
     onChange: () => void;
 }
 interface SelectButtonInterface {
+    elementId: string;
     options?: Array<SelectOptionInterface> | Array<GroupedOptionsInterface>;
     additionalOptions?: Array<SelectOptionInterface>;
     addTitle: boolean;
@@ -20,6 +21,7 @@ interface SelectButtonInterface {
     width?: number;
     dropdownTitle?: string;
     optionProps?: (props: OptionProps<OptionPropsInterface>) => JSX.Element;
+    isAdditionalButton?: boolean;
 }
 export interface OptionPropsInterface extends SelectOptionInterface {
     value: number;
@@ -28,6 +30,7 @@ interface SelectButtonState {
     selectedOption: OptionPropsInterface;
 }
 export declare class SelectButton extends React.Component<SelectButtonInterface, SelectButtonState> {
+    static readonly BUTTON_CONTAINER_DIV_SUFFIX = "_buttonContainerDiv";
     private defaultValue;
     readonly state: SelectButtonState;
     constructor(props: SelectButtonInterface);
@@ -38,6 +41,7 @@ export declare class SelectButton extends React.Component<SelectButtonInterface,
     private selectRender;
     private titleRender;
     private selectButtonRender;
+    private innerSelectButtonRender;
     private configStyle;
     private getSelectOpt;
 }

package/build/dist/RcsbFvWeb/WebTools/WebToolsManager.d.ts

@@ -7,6 +7,7 @@ export interface SelectButtonConfigInterface {
     width?: number;
     dropdownTitle?: string;
     optionProps?: (props: OptionProps<OptionPropsInterface>) => JSX.Element;
+    isAdditionalButton?: boolean;
 }
 export declare class WebToolsManager {
     private static suffix;

package/build/dist/RcsbUtils/InterfaceInstanceTranslate.d.ts

@@ -2,6 +2,8 @@ import { InterfaceInstanceInterface } from "../RcsbCollectTools/Translators/Inte
 export declare class InterfaceInstanceTranslate {
     private readonly rawData;
     private readonly instances;
+    private readonly operatorsIds;
     constructor(data: Array<InterfaceInstanceInterface>);
     getInstances(rcsbId: string): [string, string];
+    getOperatorIds(rcsbId: string): [Array<Array<string>>, Array<Array<string>>];
 }

package/build/dist/app.d.ts

@@ -1 +1,12 @@
+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>;
+}