@jbrowse/plugin-linear-genome-view 5.0.0-beta.1 → 5.0.0-beta.3

package/esm/LinearGenomeView/util.d.ts

@@ -1,6 +1,14 @@
 import type { AssemblyManager, ParsedLocString } from '@jbrowse/core/util';
+import type { PxToBpResult } from '@jbrowse/core/util/Base1DUtils';
 import type { BaseBlock, ContentBlock } from '@jbrowse/core/util/blockTypes';
 import type { Region } from '@jbrowse/core/util/types';
+interface CenterKeepingView {
+    width: number;
+    displayedRegions: Region[];
+    pxToBp: (px: number) => PxToBpResult;
+    setDisplayedRegions: (regions: Region[]) => void;
+    centerAt: (coord: number, refName: string, index?: number) => void;
+}
 /**
  * The stored viewport of a view showing `totalBp` of displayed regions fitted to
  * `width` — the regions filling it edge to edge, and centered in it only where
@@ -197,7 +205,29 @@ export declare function regionMoveActions(idx: number, numRegions: number): {
  * the new region set).
  */
 export declare function withRegionMoved(regions: Region[], from: number, to: number): Region[];
+/**
+ * Replace the region list and keep looking at whatever was under the middle of
+ * the viewport, when that region is in the new list.
+ *
+ * `setDisplayedRegions` carries `offsetPx` across and clamps it, which is a
+ * linear position in a coordinate space the write just redefined: dropping the
+ * regions to the left of the one on screen strands the view at the end of what
+ * remains, on blank space. Where the centred region is gone the clamp is still
+ * the only answer, so this falls back to it.
+ */
+export declare function setDisplayedRegionsKeepingCenter(model: CenterKeepingView, regions: Region[]): void;
 export declare function withRegionRemoved(regions: Region[], index: number): Region[];
+/**
+ * The full run of same-orientation regions on one refName that a scalebar
+ * label's `firstRegionIndex`..`lastRegionIndex` sits inside. Those come off the
+ * static blocks, which are clipped to the viewport and broken by an elided
+ * block, so a zoomed-in collapsed-introns view brackets only the exons on
+ * screen — which is the wrong answer for anything acting on the whole run.
+ */
+export declare function regionRunBounds(regions: Region[], firstIndex: number, lastIndex: number): {
+    first: number;
+    last: number;
+};
 export declare function withRegionReversed(regions: Region[], index: number): Region[];
 /**
  * Whether a label occupying [leftPx, leftPx + labelWidth] fits within a block
@@ -348,3 +378,4 @@ export declare function generateLocations({ regions, assemblyManager, assemblyNa
  */
 export declare function parseLocStrings(input: string, assemblyName: string, isValidRefName: (str: string, assemblyName: string) => boolean): ParsedLocString[];
 export declare function calculateVisibleLocStrings(contentBlocks: ContentBlock[]): string;
+export {};

package/esm/LinearGenomeView/util.js

@@ -415,9 +415,57 @@ export function withRegionMoved(regions, from, to) {
     out.splice(to, 0, moved);
     return out;
 }
+/**
+ * Replace the region list and keep looking at whatever was under the middle of
+ * the viewport, when that region is in the new list.
+ *
+ * `setDisplayedRegions` carries `offsetPx` across and clamps it, which is a
+ * linear position in a coordinate space the write just redefined: dropping the
+ * regions to the left of the one on screen strands the view at the end of what
+ * remains, on blank space. Where the centred region is gone the clamp is still
+ * the only answer, so this falls back to it.
+ */
+export function setDisplayedRegionsKeepingCenter(model, regions) {
+    const center = model.displayedRegions.length
+        ? model.pxToBp(model.width / 2)
+        : undefined;
+    model.setDisplayedRegions(regions);
+    const index = center
+        ? regions.findIndex(r => r.refName === center.refName &&
+            r.start === center.start &&
+            r.end === center.end)
+        : -1;
+    if (center && index !== -1) {
+        model.centerAt(center.coord0, center.refName, index);
+    }
+}
 export function withRegionRemoved(regions, index) {
     return regions.filter((_, i) => i !== index);
 }
+/**
+ * The full run of same-orientation regions on one refName that a scalebar
+ * label's `firstRegionIndex`..`lastRegionIndex` sits inside. Those come off the
+ * static blocks, which are clipped to the viewport and broken by an elided
+ * block, so a zoomed-in collapsed-introns view brackets only the exons on
+ * screen — which is the wrong answer for anything acting on the whole run.
+ */
+export function regionRunBounds(regions, firstIndex, lastIndex) {
+    const anchor = regions[firstIndex];
+    const inRun = (r) => r !== undefined &&
+        anchor !== undefined &&
+        r.refName === anchor.refName &&
+        r.assemblyName === anchor.assemblyName &&
+        !!r.reversed === !!anchor.reversed;
+    let first = firstIndex;
+    let last = lastIndex;
+    while (inRun(regions[first - 1])) {
+        first--;
+    }
+    while (inRun(regions[last + 1])) {
+        last++;
+    }
+    return { first, last };
+}
 export function withRegionReversed(regions, index) {
     return regions.map((region, i) => i === index ? { ...region, reversed: !region.reversed } : region);
 }

package/esm/displayKitTests/perRegionTestEnv.d.ts

@@ -33,6 +33,11 @@ export interface PerRegionTestControl {
     estimateCalls: number;
     /** the display's own density verdict, canvas's second too-large axis */
     densityTooLarge: boolean;
+    /**
+     * What the next fetch stores, so a test can tell the payload a refetch
+     * replaced from the one that replaced it.
+     */
+    payloadTag: string;
 }
 /**
  * The smallest possible display on `MultiRegionDisplayMixin`: it fetches, it
@@ -45,7 +50,6 @@ export interface PerRegionTestControl {
 /** Which of the gate's opt-in hooks this display overrides. */
 export interface GateOptIns {
     gateEnabled?: boolean;
-    densityGateEnabled?: boolean;
 }
 declare function makeStateModel(control: PerRegionTestControl, gate: GateOptIns, configSchema: AnyConfigurationSchemaType): import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -246,6 +250,16 @@ declare function makeStateModel(control: PerRegionTestControl, gate: GateOptIns,
     setError(error?: unknown): void;
     clearHoveredFeature(): void;
     reload(): void;
+    applyDisplaySettings(settings: Record<string, unknown>, options?: {
+        allowSetters?: boolean;
+    }): {
+        applied: string[];
+        unapplied: string[];
+        failed: {
+            key: string;
+            error: string;
+        }[];
+    };
 } & {
     scrollTop: number;
 } & {
@@ -265,7 +279,6 @@ declare function makeStateModel(control: PerRegionTestControl, gate: GateOptIns,
     gateMeasuredViewportKey: string | undefined;
 } & {
     readonly gateEnabled: boolean;
-    readonly densityGateEnabled: boolean;
     readonly byteGateAdapterConfig: Record<string, unknown>;
     readonly configuredFetchSizeLimit: number | undefined;
     readonly densityTooLarge: boolean;
@@ -295,15 +308,10 @@ declare function makeStateModel(control: PerRegionTestControl, gate: GateOptIns,
 } & {
     readonly gateSkipsMeasuredViewport: boolean;
 } & {
-    setByteEstimate(measurement: {
-        bytes: number;
-        viewport: import("@jbrowse/display-kit/regionTooLargeUtils").GateViewport;
-    }): void;
     clearByteEstimate(): void;
     setForceLoadTrack(flag: boolean): void;
-    reload(): void;
 } & {
-    commitFetchBytes(perRegionBytes: (number | undefined)[], issued: import("@jbrowse/display-kit/regionTooLargeUtils").GateFetchState): void;
+    commitFetchBytes(perRegionBytes: (number | undefined)[], issued: import("@jbrowse/display-kit/regionTooLargeUtils").GateFetchState, partial?: boolean): void;
 } & {
     forceLoad(): void;
 } & {
@@ -318,6 +326,7 @@ declare function makeStateModel(control: PerRegionTestControl, gate: GateOptIns,
     readonly canRender: boolean;
     readonly rendersCanvas: boolean;
     readonly paintInert: boolean;
+    readonly paintSuperseded: boolean;
 } & {
     readonly painted: boolean;
 } & {
@@ -349,7 +358,9 @@ declare function makeStateModel(control: PerRegionTestControl, gate: GateOptIns,
     readonly isLoadingOrCanceled: boolean;
     readonly fetchInert: boolean;
     readonly awaitingPrerequisite: boolean;
+    readonly awaitingDependentData: boolean;
     readonly rpcPropsCacheKey: string;
+    readonly adapterConfigKey: string;
 } & {
     setError(error?: unknown): void;
     setStatusMessage(status?: import("@jbrowse/core/util").RpcStatus): void;
@@ -359,8 +370,10 @@ declare function makeStateModel(control: PerRegionTestControl, gate: GateOptIns,
 } & {
     cancelFetch(): void;
     cancelFetchByUser(): void;
+    reload(): void;
     beforeDestroy(): void;
-    endFetch(current: boolean, stopToken: import("@jbrowse/core/util").StopToken): void;
+    beginFetch(stopToken: import("@jbrowse/core/util").StopToken): void;
+    endFetch(current: boolean): void;
 } & {
     runFetch: (work: (ctx: import("@jbrowse/display-kit/FetchMixin").FetchContext) => Promise<void>) => Promise<void>;
 } & {
@@ -368,29 +381,45 @@ declare function makeStateModel(control: PerRegionTestControl, gate: GateOptIns,
 } & {
     readonly host: import("@jbrowse/display-kit/regionHost").RegionHost;
     readonly canvasWidthPx: number;
+    readonly settledSubPixelBinBp: number;
     readonly canRender: boolean;
+    readonly rendersCanvas: boolean;
     readonly viewportWithinLoadedData: boolean;
     readonly viewportEmpty: boolean;
+    readonly fetchSuspended: boolean;
     readonly layoutReady: boolean;
-    readonly regionFetchKey: string;
-    regionHasData(_displayedRegionIndex: number): boolean;
+    readonly zoomFetchKey: string;
+    regionHasData(displayedRegionIndex: number): boolean;
     readonly dataSuperseded: boolean;
     readonly renderBlocks: import("@jbrowse/render-core/renderBlock").RenderBlock[];
+} & {
+    readonly fetchInputs: import("@jbrowse/display-kit/fetchInputs").FetchInputs;
+    readonly settingsFetchInputs: unknown;
+} & {
+    readonly regionPayloads: ReadonlyMap<number, unknown>;
+    readonly hasRegionData: boolean;
 } & {
     isCacheValid(displayedRegionIndex: number): boolean;
 } & {
+    readonly staleSettingsDrawn: boolean;
     readonly dataCurrent: boolean;
     readonly loadedAssembly: import("@jbrowse/core/assemblyManager/assembly").Assembly | undefined;
+} & {
+    readonly phaseViewportCurrent: boolean;
 } & {
     readonly svgReady: boolean;
     readonly paintInert: boolean;
+    readonly paintSuperseded: boolean;
     readonly displayPhase: import("@jbrowse/render-core/displayPhase").DisplayPhase;
 } & {
-    setLoadedRegion(displayedRegionIndex: number, region: import("@jbrowse/core/util").Region, fetchKey?: string): void;
+    setLoadedRegion(displayedRegionIndex: number, region: import("@jbrowse/core/util").Region, payload: import("@jbrowse/display-kit/regionCommit").RegionPayload | undefined, fetchInputs?: import("@jbrowse/display-kit/fetchInputs").FetchInputs): void;
+    evictRegionStore(keep: ReadonlySet<number>): void;
     dropLoadedRegion(displayedRegionIndex: number): void;
     clearDisplaySpecificData(): void;
+    clearSettingsBakedData(): void;
 } & {
     clearAllRpcData(): void;
+    invalidateSettings(): void;
     reload(): void;
 } & {
     fetchNeeded(_needed: IndexedRegion[]): void;
@@ -401,24 +430,23 @@ declare function makeStateModel(control: PerRegionTestControl, gate: GateOptIns,
 } & {
     /** every `fetchNeeded` call, as the region list it was handed */
     fetchLog: IndexedRegion[][];
-    loadedData: Map<number, string>;
     /**
-     * What `regionFetchKey` answers. A volatile, not a `control` knob, and
+     * What `zoomFetchKey` answers. A volatile, not a `control` knob, and
      * that is the point: a real display's key reads view state, so the
      * autorun re-runs when it moves. A plain closure value would be memoized
      * by the computed and never invalidate.
      */
     fetchKey: string;
 } & {
+    regionHasData(displayedRegionIndex: number): boolean;
+} & {
+    /** the fetched payloads, off the foundation's store */
+    readonly loadedData: ReadonlyMap<number, string>;
     readonly gateEnabled: boolean;
-    readonly densityGateEnabled: boolean;
     readonly densityTooLarge: boolean;
-    readonly regionFetchKey: string;
-    regionHasData(_displayedRegionIndex: number): boolean;
+    readonly zoomFetchKey: string;
 } & {
     setFetchKey(key: string): void;
-    setLoaded(displayedRegionIndex: number, value: string): void;
-    clearDisplaySpecificData(): void;
 } & {
     fetchNeeded(needed: IndexedRegion[]): Promise<void>;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
@@ -464,6 +492,8 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
                 level?: string;
                 actions: import("@jbrowse/core/util").SnackAction[];
             }[];
+            widgets: Map<string, unknown>;
+            openedWidgets: Record<string, unknown>[];
         } & {
             getTrackById: (id: string) => unknown;
             getDisplayTypeDefault(displayType: string, slot: string): unknown;
@@ -473,6 +503,11 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
             notifyError(message: string): void;
             queueDialog(cb: (handleClose: () => void) => import("@jbrowse/display-test-utils").QueuedDialog): void;
             setSelection(thing: unknown): void;
+            addWidget(type: string, id: string, initialState?: Record<string, unknown>): {
+                type: string;
+                id: string;
+            };
+            showWidget(_widget: unknown): void;
             setDisplayTypeDefault(displayType: string, slot: string, value: unknown): void;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
             name: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
@@ -491,6 +526,8 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
                 level?: string;
                 actions: import("@jbrowse/core/util").SnackAction[];
             }[];
+            widgets: Map<string, unknown>;
+            openedWidgets: Record<string, unknown>[];
         } & {
             getTrackById: (id: string) => unknown;
             getDisplayTypeDefault(displayType: string, slot: string): unknown;
@@ -500,6 +537,11 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
             notifyError(message: string): void;
             queueDialog(cb: (handleClose: () => void) => import("@jbrowse/display-test-utils").QueuedDialog): void;
             setSelection(thing: unknown): void;
+            addWidget(type: string, id: string, initialState?: Record<string, unknown>): {
+                type: string;
+                id: string;
+            };
+            showWidget(_widget: unknown): void;
             setDisplayTypeDefault(displayType: string, slot: string, value: unknown): void;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
         view: any;
@@ -703,6 +745,16 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
             setError(error?: unknown): void;
             clearHoveredFeature(): void;
             reload(): void;
+            applyDisplaySettings(settings: Record<string, unknown>, options?: {
+                allowSetters?: boolean;
+            }): {
+                applied: string[];
+                unapplied: string[];
+                failed: {
+                    key: string;
+                    error: string;
+                }[];
+            };
         } & {
             scrollTop: number;
         } & {
@@ -722,7 +774,6 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
             gateMeasuredViewportKey: string | undefined;
         } & {
             readonly gateEnabled: boolean;
-            readonly densityGateEnabled: boolean;
             readonly byteGateAdapterConfig: Record<string, unknown>;
             readonly configuredFetchSizeLimit: number | undefined;
             readonly densityTooLarge: boolean;
@@ -752,15 +803,10 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
         } & {
             readonly gateSkipsMeasuredViewport: boolean;
         } & {
-            setByteEstimate(measurement: {
-                bytes: number;
-                viewport: import("@jbrowse/display-kit/regionTooLargeUtils").GateViewport;
-            }): void;
             clearByteEstimate(): void;
             setForceLoadTrack(flag: boolean): void;
-            reload(): void;
         } & {
-            commitFetchBytes(perRegionBytes: (number | undefined)[], issued: import("@jbrowse/display-kit/regionTooLargeUtils").GateFetchState): void;
+            commitFetchBytes(perRegionBytes: (number | undefined)[], issued: import("@jbrowse/display-kit/regionTooLargeUtils").GateFetchState, partial?: boolean): void;
         } & {
             forceLoad(): void;
         } & {
@@ -775,6 +821,7 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
             readonly canRender: boolean;
             readonly rendersCanvas: boolean;
             readonly paintInert: boolean;
+            readonly paintSuperseded: boolean;
         } & {
             readonly painted: boolean;
         } & {
@@ -806,7 +853,9 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
             readonly isLoadingOrCanceled: boolean;
             readonly fetchInert: boolean;
             readonly awaitingPrerequisite: boolean;
+            readonly awaitingDependentData: boolean;
             readonly rpcPropsCacheKey: string;
+            readonly adapterConfigKey: string;
         } & {
             setError(error?: unknown): void;
             setStatusMessage(status?: import("@jbrowse/core/util").RpcStatus): void;
@@ -816,8 +865,10 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
         } & {
             cancelFetch(): void;
             cancelFetchByUser(): void;
+            reload(): void;
             beforeDestroy(): void;
-            endFetch(current: boolean, stopToken: import("@jbrowse/core/util").StopToken): void;
+            beginFetch(stopToken: import("@jbrowse/core/util").StopToken): void;
+            endFetch(current: boolean): void;
         } & {
             runFetch: (work: (ctx: import("@jbrowse/display-kit/FetchMixin").FetchContext) => Promise<void>) => Promise<void>;
         } & {
@@ -825,29 +876,45 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
         } & {
             readonly host: import("@jbrowse/display-kit/regionHost").RegionHost;
             readonly canvasWidthPx: number;
+            readonly settledSubPixelBinBp: number;
             readonly canRender: boolean;
+            readonly rendersCanvas: boolean;
             readonly viewportWithinLoadedData: boolean;
             readonly viewportEmpty: boolean;
+            readonly fetchSuspended: boolean;
             readonly layoutReady: boolean;
-            readonly regionFetchKey: string;
-            regionHasData(_displayedRegionIndex: number): boolean;
+            readonly zoomFetchKey: string;
+            regionHasData(displayedRegionIndex: number): boolean;
             readonly dataSuperseded: boolean;
             readonly renderBlocks: import("@jbrowse/render-core/renderBlock").RenderBlock[];
+        } & {
+            readonly fetchInputs: import("@jbrowse/display-kit/fetchInputs").FetchInputs;
+            readonly settingsFetchInputs: unknown;
+        } & {
+            readonly regionPayloads: ReadonlyMap<number, unknown>;
+            readonly hasRegionData: boolean;
         } & {
             isCacheValid(displayedRegionIndex: number): boolean;
         } & {
+            readonly staleSettingsDrawn: boolean;
             readonly dataCurrent: boolean;
             readonly loadedAssembly: import("@jbrowse/core/assemblyManager/assembly").Assembly | undefined;
+        } & {
+            readonly phaseViewportCurrent: boolean;
         } & {
             readonly svgReady: boolean;
             readonly paintInert: boolean;
+            readonly paintSuperseded: boolean;
             readonly displayPhase: import("@jbrowse/render-core/displayPhase").DisplayPhase;
         } & {
-            setLoadedRegion(displayedRegionIndex: number, region: import("@jbrowse/core/util").Region, fetchKey?: string): void;
+            setLoadedRegion(displayedRegionIndex: number, region: import("@jbrowse/core/util").Region, payload: import("@jbrowse/display-kit/regionCommit").RegionPayload | undefined, fetchInputs?: import("@jbrowse/display-kit/fetchInputs").FetchInputs): void;
+            evictRegionStore(keep: ReadonlySet<number>): void;
             dropLoadedRegion(displayedRegionIndex: number): void;
             clearDisplaySpecificData(): void;
+            clearSettingsBakedData(): void;
         } & {
             clearAllRpcData(): void;
+            invalidateSettings(): void;
             reload(): void;
         } & {
             fetchNeeded(_needed: IndexedRegion[]): void;
@@ -858,24 +925,23 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
         } & {
             /** every `fetchNeeded` call, as the region list it was handed */
             fetchLog: IndexedRegion[][];
-            loadedData: Map<number, string>;
             /**
-             * What `regionFetchKey` answers. A volatile, not a `control` knob, and
+             * What `zoomFetchKey` answers. A volatile, not a `control` knob, and
              * that is the point: a real display's key reads view state, so the
              * autorun re-runs when it moves. A plain closure value would be memoized
              * by the computed and never invalidate.
              */
             fetchKey: string;
         } & {
+            regionHasData(displayedRegionIndex: number): boolean;
+        } & {
+            /** the fetched payloads, off the foundation's store */
+            readonly loadedData: ReadonlyMap<number, string>;
             readonly gateEnabled: boolean;
-            readonly densityGateEnabled: boolean;
             readonly densityTooLarge: boolean;
-            readonly regionFetchKey: string;
-            regionHasData(_displayedRegionIndex: number): boolean;
+            readonly zoomFetchKey: string;
         } & {
             setFetchKey(key: string): void;
-            setLoaded(displayedRegionIndex: number, value: string): void;
-            clearDisplaySpecificData(): void;
         } & {
             fetchNeeded(needed: IndexedRegion[]): Promise<void>;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{
@@ -1077,6 +1143,16 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
             setError(error?: unknown): void;
             clearHoveredFeature(): void;
             reload(): void;
+            applyDisplaySettings(settings: Record<string, unknown>, options?: {
+                allowSetters?: boolean;
+            }): {
+                applied: string[];
+                unapplied: string[];
+                failed: {
+                    key: string;
+                    error: string;
+                }[];
+            };
         } & {
             scrollTop: number;
         } & {
@@ -1096,7 +1172,6 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
             gateMeasuredViewportKey: string | undefined;
         } & {
             readonly gateEnabled: boolean;
-            readonly densityGateEnabled: boolean;
             readonly byteGateAdapterConfig: Record<string, unknown>;
             readonly configuredFetchSizeLimit: number | undefined;
             readonly densityTooLarge: boolean;
@@ -1126,15 +1201,10 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
         } & {
             readonly gateSkipsMeasuredViewport: boolean;
         } & {
-            setByteEstimate(measurement: {
-                bytes: number;
-                viewport: import("@jbrowse/display-kit/regionTooLargeUtils").GateViewport;
-            }): void;
             clearByteEstimate(): void;
             setForceLoadTrack(flag: boolean): void;
-            reload(): void;
         } & {
-            commitFetchBytes(perRegionBytes: (number | undefined)[], issued: import("@jbrowse/display-kit/regionTooLargeUtils").GateFetchState): void;
+            commitFetchBytes(perRegionBytes: (number | undefined)[], issued: import("@jbrowse/display-kit/regionTooLargeUtils").GateFetchState, partial?: boolean): void;
         } & {
             forceLoad(): void;
         } & {
@@ -1149,6 +1219,7 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
             readonly canRender: boolean;
             readonly rendersCanvas: boolean;
             readonly paintInert: boolean;
+            readonly paintSuperseded: boolean;
         } & {
             readonly painted: boolean;
         } & {
@@ -1180,7 +1251,9 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
             readonly isLoadingOrCanceled: boolean;
             readonly fetchInert: boolean;
             readonly awaitingPrerequisite: boolean;
+            readonly awaitingDependentData: boolean;
             readonly rpcPropsCacheKey: string;
+            readonly adapterConfigKey: string;
         } & {
             setError(error?: unknown): void;
             setStatusMessage(status?: import("@jbrowse/core/util").RpcStatus): void;
@@ -1190,8 +1263,10 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
         } & {
             cancelFetch(): void;
             cancelFetchByUser(): void;
+            reload(): void;
             beforeDestroy(): void;
-            endFetch(current: boolean, stopToken: import("@jbrowse/core/util").StopToken): void;
+            beginFetch(stopToken: import("@jbrowse/core/util").StopToken): void;
+            endFetch(current: boolean): void;
         } & {
             runFetch: (work: (ctx: import("@jbrowse/display-kit/FetchMixin").FetchContext) => Promise<void>) => Promise<void>;
         } & {
@@ -1199,29 +1274,45 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
         } & {
             readonly host: import("@jbrowse/display-kit/regionHost").RegionHost;
             readonly canvasWidthPx: number;
+            readonly settledSubPixelBinBp: number;
             readonly canRender: boolean;
+            readonly rendersCanvas: boolean;
             readonly viewportWithinLoadedData: boolean;
             readonly viewportEmpty: boolean;
+            readonly fetchSuspended: boolean;
             readonly layoutReady: boolean;
-            readonly regionFetchKey: string;
-            regionHasData(_displayedRegionIndex: number): boolean;
+            readonly zoomFetchKey: string;
+            regionHasData(displayedRegionIndex: number): boolean;
             readonly dataSuperseded: boolean;
             readonly renderBlocks: import("@jbrowse/render-core/renderBlock").RenderBlock[];
+        } & {
+            readonly fetchInputs: import("@jbrowse/display-kit/fetchInputs").FetchInputs;
+            readonly settingsFetchInputs: unknown;
+        } & {
+            readonly regionPayloads: ReadonlyMap<number, unknown>;
+            readonly hasRegionData: boolean;
         } & {
             isCacheValid(displayedRegionIndex: number): boolean;
         } & {
+            readonly staleSettingsDrawn: boolean;
             readonly dataCurrent: boolean;
             readonly loadedAssembly: import("@jbrowse/core/assemblyManager/assembly").Assembly | undefined;
+        } & {
+            readonly phaseViewportCurrent: boolean;
         } & {
             readonly svgReady: boolean;
             readonly paintInert: boolean;
+            readonly paintSuperseded: boolean;
             readonly displayPhase: import("@jbrowse/render-core/displayPhase").DisplayPhase;
         } & {
-            setLoadedRegion(displayedRegionIndex: number, region: import("@jbrowse/core/util").Region, fetchKey?: string): void;
+            setLoadedRegion(displayedRegionIndex: number, region: import("@jbrowse/core/util").Region, payload: import("@jbrowse/display-kit/regionCommit").RegionPayload | undefined, fetchInputs?: import("@jbrowse/display-kit/fetchInputs").FetchInputs): void;
+            evictRegionStore(keep: ReadonlySet<number>): void;
             dropLoadedRegion(displayedRegionIndex: number): void;
             clearDisplaySpecificData(): void;
+            clearSettingsBakedData(): void;
         } & {
             clearAllRpcData(): void;
+            invalidateSettings(): void;
             reload(): void;
         } & {
             fetchNeeded(_needed: IndexedRegion[]): void;
@@ -1232,24 +1323,23 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
         } & {
             /** every `fetchNeeded` call, as the region list it was handed */
             fetchLog: IndexedRegion[][];
-            loadedData: Map<number, string>;
             /**
-             * What `regionFetchKey` answers. A volatile, not a `control` knob, and
+             * What `zoomFetchKey` answers. A volatile, not a `control` knob, and
              * that is the point: a real display's key reads view state, so the
              * autorun re-runs when it moves. A plain closure value would be memoized
              * by the computed and never invalidate.
              */
             fetchKey: string;
         } & {
+            regionHasData(displayedRegionIndex: number): boolean;
+        } & {
+            /** the fetched payloads, off the foundation's store */
+            readonly loadedData: ReadonlyMap<number, string>;
             readonly gateEnabled: boolean;
-            readonly densityGateEnabled: boolean;
             readonly densityTooLarge: boolean;
-            readonly regionFetchKey: string;
-            regionHasData(_displayedRegionIndex: number): boolean;
+            readonly zoomFetchKey: string;
         } & {
             setFetchKey(key: string): void;
-            setLoaded(displayedRegionIndex: number, value: string): void;
-            clearDisplaySpecificData(): void;
         } & {
             fetchNeeded(needed: IndexedRegion[]): Promise<void>;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;