@jbrowse/plugin-alignments 1.5.8 → 1.6.2

package/dist/BamAdapter/BamAdapter.d.ts

@@ -14,12 +14,17 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
         sequenceAdapter?: BaseFeatureDataAdapter | undefined;
     }>;
     getHeader(opts?: BaseOptions): Promise<any>;
+    private setupPre;
     private setup;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     private seqFetch;
     getFeatures(region: Region & {
         originalRefName?: string;
     }, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats | {
+        bytes: number;
+        fetchSizeLimit: any;
+    }>;
     freeResources(): void;
     refIdToName(refId: number): string | undefined;
 }

package/dist/BamAdapter/BamSlightlyLazyFeature.d.ts

@@ -13,10 +13,9 @@ export default class BamSlightlyLazyFeature implements Feature {
     _get_score(): number;
     _get_flags(): string;
     _get_strand(): number;
-    _get_read_group_id(): number;
     _get_pair_orientation(): string | null | undefined;
     _get_next_seq_id(): any;
-    _get_seq_id(): any;
+    _get_seq_id(): number;
     _get_next_refName(): string | undefined;
     _get_next_segment_position(): string | undefined;
     _get_seq(): string;

package/dist/CramAdapter/CramAdapter.d.ts

@@ -1,23 +1,24 @@
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { Region } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
+import CramSlightlyLazyFeature from './CramSlightlyLazyFeature';
 interface Header {
     idToName?: string[];
     nameToId?: Record<string, number>;
     readGroups?: number[];
 }
 export default class CramAdapter extends BaseFeatureDataAdapter {
-    private cram;
-    private setupP?;
-    private sequenceAdapter?;
     samHeader: Header;
+    private setupP?;
     private seqIdToRefName;
     private seqIdToOriginalRefName;
     configure(): Promise<{
-        sequenceAdapter: BaseFeatureDataAdapter;
+        cram: any;
+        sequenceAdapter: BaseFeatureDataAdapter | import("@jbrowse/core/data_adapters/BaseAdapter").BaseSequenceAdapter;
     }>;
     getHeader(opts?: BaseOptions): Promise<any>;
     private seqFetch;
+    private setupPre;
     private setup;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     refNameToId(refName: string): number | undefined;
@@ -27,6 +28,16 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         originalRefName?: string;
     }, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     freeResources(): void;
-    cramRecordToFeature(record: any): Feature;
+    cramRecordToFeature(record: unknown): CramSlightlyLazyFeature;
+    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<{
+        bytes: any;
+        fetchSizeLimit: any;
+    }>;
+    /**
+     * get the approximate number of bytes queried from the file for the given
+     * query regions
+     * @param regions - list of query regions
+     */
+    private bytesForRegions;
 }
 export {};

package/dist/LinearAlignmentsDisplay/models/model.d.ts

@@ -17,6 +17,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: Al
     height: import("mobx-state-tree").IType<number | undefined, number, number>;
     showCoverage: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     showPileup: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    userFeatureScreenDensity: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -89,7 +90,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: Al
     trackMenuItems(): MenuItem[];
 } & {
     setSNPCoverageDisplay(displayConfig: AnyConfigurationModel): void;
-    setUserBpPerPxLimit(limit: number): void;
+    setUserFeatureScreenDensity(limit: number): void;
     setPileupDisplay(displayConfig: AnyConfigurationModel): void;
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;

package/dist/LinearPileupDisplay/model.d.ts

@@ -58,6 +58,7 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
         beforeDestroy(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearPileupDisplay">;
     configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
@@ -141,15 +142,17 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
 } & {
+    currBpPerPx: number;
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: Feature | undefined;
     scrollTop: number;
+    estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
+    estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
     readonly blockType: "staticBlocks" | "dynamicBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
-    readonly maxViewBpPerPx: any;
     readonly renderDelay: number;
     readonly TooltipComponent: import("react").FC<any>;
     readonly selectedFeatureId: string | undefined;
@@ -160,14 +163,28 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
     getFeatureOverlapping(blockKey: string, x: number, y: number): any;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
+    readonly currentBytesRequested: number;
+    readonly currentFeatureScreenDensity: number;
+    readonly maxFeatureScreenDensity: any;
+    readonly estimatedStatsReady: boolean;
+    readonly maxAllowableBytes: number;
 } & {
+    setMessage(message: string): void;
     afterAttach(): void;
+    estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
+        headers?: Record<string, string> | undefined;
+        signal?: AbortSignal | undefined;
+        filters?: string[] | undefined;
+    }): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
+    setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
+    setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
+    clearRegionStats(): void;
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
     setScrollTop(scrollTop: number): void;
-    setUserBpPerPxLimit(limit: number): void;
-    setMessage(message: string): void;
+    updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
+    setCurrBpPerPx(n: number): void;
     deleteBlock(key: string): void;
     selectFeature(feature: Feature): void;
     clearFeatureSelection(): void;
@@ -175,7 +192,13 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
     reload(): void;
     setContextMenuFeature(feature?: Feature | undefined): void;
 } & {
-    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Zoom in to see features";
+    readonly regionTooLarge: boolean;
+    readonly regionTooLargeReason: string;
+} & {
+    reload(): Promise<void>;
+    afterAttach(): void;
+} & {
+    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | undefined;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     contextMenuItems(): {
@@ -192,10 +215,8 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
     colorTagMap: import("mobx").ObservableMap<string, string>;
     modificationTagMap: import("mobx").ObservableMap<string, string>;
     ready: boolean;
-    currBpPerPx: number;
 } & {
     setReady(flag: boolean): void;
-    setCurrBpPerPx(n: number): void;
     setMaxHeight(n: number): void;
     setFeatureHeight(n: number): void;
     setNoSpacing(flag: boolean): void;
@@ -293,6 +314,7 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
     rpcDriverName: string | undefined;
     height: number;
     userBpPerPxLimit: number | undefined;
+    userByteSizeLimit: number | undefined;
 } & import("mobx-state-tree")._NotCustomized>;
 export declare type LinearPileupDisplayStateModel = ReturnType<typeof stateModelFactory>;
 export declare type LinearPileupDisplayModel = Instance<LinearPileupDisplayStateModel>;

package/dist/LinearSNPCoverageDisplay/models/model.d.ts

@@ -54,6 +54,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
         beforeDestroy(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearWiggleDisplay">;
     configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
@@ -61,6 +62,8 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     fill: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     color: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    posColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    negColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     summaryScoreMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     rendererTypeNameState: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     scale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;

package/dist/SNPCoverageAdapter/SNPCoverageAdapter.d.ts

@@ -12,6 +12,7 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
         sequenceAdapter: BaseFeatureDataAdapter | undefined;
     }>;
     getFeatures(region: Region, opts?: SNPCoverageOptions): Observable<Feature>;
+    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     freeResources(): void;
     /**