molstar 3.26.0 → 3.28.0

package/lib/extensions/volumes-and-segmentations/entry-root.d.ts

@@ -0,0 +1,122 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+import { BehaviorSubject } from 'rxjs';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
+import { PluginBehavior } from '../../mol-plugin/behavior';
+import { PluginContext } from '../../mol-plugin/context';
+import { StateObjectCell, StateSelection, StateTransform } from '../../mol-state';
+import { ParamDefinition } from '../../mol-util/param-definition';
+import { VolumeApiV2 } from './volseg-api/api';
+import { Segment } from './volseg-api/data';
+import { MetadataWrapper } from './volseg-api/utils';
+import { VolsegVolumeData, SimpleVolumeParamValues } from './entry-volume';
+import { Choice } from './helpers';
+export declare const MAX_VOXELS: number;
+export declare const BOX: [[number, number, number], [number, number, number]] | null;
+declare const SourceChoice: Choice<"emdb" | "empiar" | "idr", "emdb">;
+export type Source = Choice.Values<typeof SourceChoice>;
+export declare function createLoadVolsegParams(plugin?: PluginContext, entrylists?: {
+    [source: string]: string[];
+}): {
+    serverUrl: ParamDefinition.Text<string>;
+    source: ParamDefinition.Mapped<ParamDefinition.NamedParams<unknown, string>>;
+};
+type LoadVolsegParamValues = ParamDefinition.Values<ReturnType<typeof createLoadVolsegParams>>;
+export declare function createVolsegEntryParams(plugin?: PluginContext): {
+    serverUrl: ParamDefinition.Text<string>;
+    source: ParamDefinition.Select<"emdb" | "empiar" | "idr">;
+    entryId: ParamDefinition.Text<string>;
+};
+type VolsegEntryParamValues = ParamDefinition.Values<ReturnType<typeof createVolsegEntryParams>>;
+export declare namespace VolsegEntryParamValues {
+    function fromLoadVolsegParamValues(params: LoadVolsegParamValues): VolsegEntryParamValues;
+}
+declare const VolsegEntry_base: {
+    new (data: VolsegEntryData, props?: {
+        label: string;
+        description?: string | undefined;
+    } | undefined): {
+        id: import("../../mol-util/uuid").UUID;
+        type: PluginStateObject.TypeInfo;
+        label: string;
+        description?: string | undefined;
+        data: VolsegEntryData;
+    };
+    type: PluginStateObject.TypeInfo;
+    is(obj?: import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>> | undefined): obj is {
+        id: import("../../mol-util/uuid").UUID;
+        type: PluginStateObject.TypeInfo;
+        label: string;
+        description?: string | undefined;
+        data: VolsegEntryData;
+    };
+};
+export declare class VolsegEntry extends VolsegEntry_base {
+}
+export declare class VolsegEntryData extends PluginBehavior.WithSubscribers<VolsegEntryParamValues> {
+    plugin: PluginContext;
+    ref: string;
+    api: VolumeApiV2;
+    source: Source;
+    /** Number part of entry ID; e.g. '1832' */
+    entryNumber: string;
+    /** Full entry ID; e.g. 'emd-1832' */
+    entryId: string;
+    metadata: MetadataWrapper;
+    pdbs: string[];
+    readonly volumeData: VolsegVolumeData;
+    private readonly latticeSegmentationData;
+    private readonly meshSegmentationData;
+    private readonly modelData;
+    private highlightRequest;
+    private getStateNode;
+    currentState: BehaviorSubject<ParamDefinition.Values<{
+        volumeType: ParamDefinition.Select<"off" | "direct-volume" | "isosurface">;
+        volumeIsovalueKind: ParamDefinition.Select<string>;
+        volumeIsovalueValue: ParamDefinition.Numeric;
+        volumeOpacity: ParamDefinition.Numeric;
+        segmentOpacity: ParamDefinition.Numeric;
+        selectedSegment: ParamDefinition.Numeric;
+        visibleSegments: ParamDefinition.ObjectList<ParamDefinition.Normalize<{
+            segmentId: number;
+        }>>;
+        visibleModels: ParamDefinition.ObjectList<ParamDefinition.Normalize<{
+            pdbId: string;
+        }>>;
+    }>>;
+    currentVolume: BehaviorSubject<StateTransform<import("../../mol-state/transformer").StateTransformer<PluginStateObject.Volume.Data, PluginStateObject.Volume.Representation3D, ParamDefinition.Normalize<{
+        type: ParamDefinition.NamedParams<any, string>;
+        colorTheme: ParamDefinition.NamedParams<any, string>;
+        sizeTheme: ParamDefinition.NamedParams<any, string>;
+    }>>> | undefined>;
+    private constructor();
+    private initialize;
+    static create(plugin: PluginContext, params: VolsegEntryParamValues): Promise<VolsegEntryData>;
+    register(ref: string): Promise<void>;
+    unregister(): Promise<void>;
+    loadVolume(): Promise<void>;
+    loadSegmentations(): Promise<void>;
+    actionHighlightSegment(segment?: Segment): void;
+    actionToggleSegment(segment: number): Promise<void>;
+    actionToggleAllSegments(): Promise<void>;
+    actionSelectSegment(segment?: number): Promise<void>;
+    actionSetOpacity(opacity: number): Promise<void>;
+    actionShowFittedModel(pdbIds: string[]): Promise<void>;
+    actionSetVolumeVisual(type: 'isosurface' | 'direct-volume' | 'off'): Promise<void>;
+    actionUpdateVolumeVisual(params: SimpleVolumeParamValues): Promise<void>;
+    private actionShowSegments;
+    private highlightSegment;
+    private selectSegment;
+    private updateStateNode;
+    /** Find the nodes under this entry root which have all of the given tags. */
+    findNodesByTags(...tags: string[]): StateSelection.CellSeq<StateObjectCell<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, StateTransform<import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>>>;
+    newUpdate(): import("../../mol-state/state/builder").StateBuilder.To<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
+    private readonly labelProvider;
+    private getSegmentIdFromLoci;
+    setTryUseGpu(tryUseGpu: boolean): Promise<void>;
+    setSelectionMode(selectSegments: boolean): Promise<void>;
+}
+export {};