@jbrowse/plugin-alignments 1.4.4 → 1.5.3

package/dist/AlignmentsFeatureDetail/index.d.ts

@@ -1,10 +1,13 @@
-export default function stateModelFactory(pluginManager: any): import("mobx-state-tree").IModelType<{
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").AnyConfigurationSchemaType;
+export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
     featureData: import("mobx-state-tree").IType<any, any, any>;
-    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<any>>;
+    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
 }, {
-    setFeatureData(data: any): void;
+    setFeatureData(data: unknown): void;
     clearFeatureData(): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export const configSchema: import("@jbrowse/core/configuration/configurationSchema").AnyConfigurationSchemaType;
+export default function register(pluginManager: PluginManager): void;
+export { configSchema };

package/dist/AlignmentsTrack/index.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function register(pluginManager: PluginManager): void;

package/dist/BamAdapter/index.d.ts

@@ -1,5 +1,3 @@
-declare const _default: () => {
-    configSchema: import("@jbrowse/core/configuration/configurationSchema").AnyConfigurationSchemaType;
-    getAdapterClass: () => Promise<typeof import("./BamAdapter").default>;
-};
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
 export default _default;

package/dist/CramAdapter/index.d.ts

@@ -1,6 +1,3 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => {
-    configSchema: import("@jbrowse/core/configuration/configurationSchema").AnyConfigurationSchemaType;
-    getAdapterClass: () => Promise<typeof import("./CramAdapter").default>;
-};
+declare const _default: (pluginManager: PluginManager) => void;
 export default _default;

package/dist/HtsgetBamAdapter/HtsgetBamAdapter.d.ts

@@ -1,8 +1,9 @@
+import { BamFile } from '@gmod/bam';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import BamAdapter from '../BamAdapter/BamAdapter';
 export default class HtsgetBamAdapter extends BamAdapter {
     protected configure(): Promise<{
-        bam: import("@gmod/bam").BamFile;
+        bam: BamFile;
         sequenceAdapter?: BaseFeatureDataAdapter | undefined;
     }>;
 }

package/dist/HtsgetBamAdapter/index.d.ts

@@ -1,5 +1,3 @@
-declare const _default: () => {
-    configSchema: import("@jbrowse/core/configuration/configurationSchema").AnyConfigurationSchemaType;
-    getAdapterClass: () => Promise<typeof import("./HtsgetBamAdapter").default>;
-};
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
 export default _default;

package/dist/LinearAlignmentsDisplay/index.d.ts

@@ -1,3 +1,2 @@
-export { default as configSchemaFactory } from './models/configSchema';
-export { default as modelFactory } from './models/model';
-export { default as ReactComponent } from './components/AlignmentsDisplay';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function (pluginManager: PluginManager): void;

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

@@ -19,7 +19,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: Al
     showPileup: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
 }, {
     rendererTypeName: string;
-    error: Error | undefined;
+    error: unknown;
 } & {
     readonly RenderingComponent: React.FC<{
         model: import("mobx-state-tree").ModelInstanceTypeProps<{
@@ -28,14 +28,14 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: Al
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }> & {
             rendererTypeName: string;
-            error: Error | undefined;
+            error: unknown;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
-            error: Error | undefined;
+            error: unknown;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
         onHorizontalScroll?: Function | undefined;
         blockState?: Record<string, any> | undefined;
@@ -47,14 +47,14 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: Al
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }> & {
             rendererTypeName: string;
-            error: Error | undefined;
+            error: unknown;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
-            error: Error | undefined;
+            error: unknown;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
@@ -66,7 +66,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: Al
     readonly viewMenuActions: MenuItem[];
     regionCannotBeRendered(): undefined;
 } & {
-    setError(error?: Error | undefined): void;
+    setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
 } & {

package/dist/LinearPileupDisplay/index.d.ts

@@ -1,2 +1,2 @@
-export { default as configSchemaFactory } from './configSchema';
-export { default as modelFactory } from './model';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function register(pluginManager: PluginManager): void;

package/dist/LinearPileupDisplay/model.d.ts

@@ -1,12 +1,11 @@
 /// <reference types="react" />
 import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
 import { Instance } from 'mobx-state-tree';
-import PluginManager from '@jbrowse/core/PluginManager';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
 import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
 import { LinearPileupDisplayConfigModel } from './configSchema';
-declare const stateModelFactory: (pluginManager: PluginManager, configSchema: LinearPileupDisplayConfigModel) => import("mobx-state-tree").IModelType<{
+declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel) => import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<string>;
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -34,7 +33,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: Li
         features: Map<string, Feature> | undefined;
         layout: any;
         status: string;
-        error: Error | undefined;
+        error: unknown;
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
@@ -54,7 +53,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: Li
             maxHeightReached: boolean;
             renderProps: any;
         } | undefined): void;
-        setError(error: Error): void;
+        setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -91,7 +90,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: Li
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }, {
     rendererTypeName: string;
-    error: Error | undefined;
+    error: unknown;
 } & {
     readonly RenderingComponent: import("react").FC<{
         model: import("mobx-state-tree").ModelInstanceTypeProps<{
@@ -100,14 +99,14 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: Li
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }> & {
             rendererTypeName: string;
-            error: Error | undefined;
+            error: unknown;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
-            error: Error | undefined;
+            error: unknown;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
         onHorizontalScroll?: Function | undefined;
         blockState?: Record<string, any> | undefined;
@@ -119,14 +118,14 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: Li
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }> & {
             rendererTypeName: string;
-            error: Error | undefined;
+            error: unknown;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
-            error: Error | undefined;
+            error: unknown;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
@@ -138,7 +137,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: Li
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): undefined;
 } & {
-    setError(error?: Error | undefined): void;
+    setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
 } & {

package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts

@@ -6,5 +6,5 @@ declare const SNPCoverageTooltip: (props: {
     offsetMouseCoord: Coord;
     clientMouseCoord: Coord;
     clientRect?: ClientRect;
-}) => JSX.Element;
+}) => JSX.Element | null;
 export default SNPCoverageTooltip;

package/dist/LinearSNPCoverageDisplay/index.d.ts

@@ -1,2 +1,2 @@
-export { default as configSchemaFactory } from './models/configSchema';
-export { default as modelFactory } from './models/model';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function register(pluginManager: PluginManager): void;

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

@@ -29,7 +29,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
         features: Map<string, import("@jbrowse/core/util/simpleFeature").Feature> | undefined;
         layout: any;
         status: string;
-        error: Error | undefined;
+        error: unknown;
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
@@ -49,7 +49,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
             maxHeightReached: boolean;
             renderProps: any;
         } | undefined): void;
-        setError(error: Error): void;
+        setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -74,6 +74,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     type: import("mobx-state-tree").ISimpleType<"LinearSNPCoverageDisplay">;
     drawInterbaseCounts: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     drawIndicators: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    drawArcs: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
         flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
         flagExclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;

package/dist/PileupRPC/rpcMethods.d.ts

@@ -7,14 +7,7 @@ export declare class PileupGetGlobalValueForTag extends RpcMethodType {
     serializeArguments(args: RenderArgs & {
         signal?: AbortSignal;
         statusCallback?: Function;
-    }): Promise<RenderArgs & {
-        signal?: AbortSignal | undefined;
-        statusCallback?: Function | undefined;
-    } & {
-        regions: (Region & {
-            originalRefName?: string | undefined;
-        })[];
-    }>;
+    }, rpcDriverClassName: string): Promise<{}>;
     execute(args: {
         adapterConfig: {};
         signal?: RemoteAbortSignal;
@@ -29,14 +22,7 @@ export declare class PileupGetVisibleModifications extends RpcMethodType {
     serializeArguments(args: RenderArgs & {
         signal?: AbortSignal;
         statusCallback?: Function;
-    }): Promise<RenderArgs & {
-        signal?: AbortSignal | undefined;
-        statusCallback?: Function | undefined;
-    } & {
-        regions: (Region & {
-            originalRefName?: string | undefined;
-        })[];
-    }>;
+    }, rpcDriverClassName: string): Promise<{}>;
     execute(args: {
         adapterConfig: {};
         signal?: RemoteAbortSignal;

package/dist/PileupRenderer/PileupRenderer.d.ts

@@ -6,7 +6,6 @@ import { Feature } from '@jbrowse/core/util/simpleFeature';
 import { Region } from '@jbrowse/core/util/types';
 import { BaseLayout } from '@jbrowse/core/util/layouts/BaseLayout';
 import { PileupLayoutSession, PileupLayoutSessionProps } from './PileupLayoutSession';
-export type { RenderArgs, RenderArgsSerialized, RenderResults, ResultsSerialized, ResultsDeserialized, };
 export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
     colorBy?: {
         type: string;
@@ -47,7 +46,15 @@ export default class PileupRenderer extends BoxRendererType {
         charWidth: number;
         charHeight: number;
     };
-    layoutFeature(feature: Feature, layout: BaseLayout<Feature>, config: AnyConfigurationModel, bpPerPx: number, region: Region, showSoftClip?: boolean): LayoutRecord | null;
+    layoutFeature({ feature, layout, bpPerPx, region, showSoftClip, heightPx, displayMode, }: {
+        feature: Feature;
+        layout: BaseLayout<Feature>;
+        bpPerPx: number;
+        region: Region;
+        showSoftClip?: boolean;
+        heightPx: number;
+        displayMode: string;
+    }): LayoutRecord | null;
     getExpandedRegion(region: Region, renderArgs: RenderArgsDeserialized): {
         start: number;
         end: number;
@@ -63,21 +70,26 @@ export default class PileupRenderer extends BoxRendererType {
     colorByModifications(ctx: CanvasRenderingContext2D, layoutFeature: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number, props: RenderArgsDeserializedWithFeaturesAndLayout): void;
     colorByMethylation(ctx: CanvasRenderingContext2D, layoutFeature: LayoutFeature, _config: AnyConfigurationModel, region: Region, bpPerPx: number, props: RenderArgsDeserializedWithFeaturesAndLayout): void;
     drawRect(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserialized): void;
-    drawAlignmentRect(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout): void;
+    drawAlignmentRect(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout & {
+        defaultColor: boolean;
+    }): void;
     drawMismatches(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout, theme: Theme, colorForBase: {
         [key: string]: string;
     }, opts: {
         mismatchAlpha?: boolean;
         drawSNPs?: boolean;
         drawIndels?: boolean;
+        minSubfeatureWidth: number;
+        largeInsertionIndicatorScale: number;
+        charWidth: number;
+        charHeight: number;
     }): void;
     drawSoftClipping(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserializedWithFeaturesAndLayout, config: AnyConfigurationModel, theme: Theme): void;
-    makeImageData(ctx: CanvasRenderingContext2D, layoutRecords: any, // eslint-disable-line @typescript-eslint/no-explicit-any
-    props: RenderArgsDeserializedWithFeaturesAndLayout): Promise<void>;
+    makeImageData(ctx: CanvasRenderingContext2D, layoutRecords: (LayoutFeature | null)[], props: RenderArgsDeserializedWithFeaturesAndLayout): Promise<void>;
     layoutFeats(props: RenderArgsDeserializedWithFeaturesAndLayout): (LayoutRecord | null)[];
     render(renderProps: RenderArgsDeserialized): Promise<{
         features: Map<string, Feature>;
-        layout: import("@jbrowse/core/util/layouts/GranularRectLayout").default<unknown>;
+        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
         height: number;
         width: number;
         maxHeightReached: boolean;
@@ -86,7 +98,7 @@ export default class PileupRenderer extends BoxRendererType {
         html?: string | undefined;
     } | {
         features: Map<string, Feature>;
-        layout: import("@jbrowse/core/util/layouts/GranularRectLayout").default<unknown>;
+        layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
         height: number;
         width: number;
         maxHeightReached: boolean;
@@ -96,3 +108,4 @@ export default class PileupRenderer extends BoxRendererType {
     }>;
     createSession(args: PileupLayoutSessionProps): PileupLayoutSession;
 }
+export type { RenderArgs, RenderArgsSerialized, RenderResults, ResultsSerialized, ResultsDeserialized, };

package/dist/PileupRenderer/index.d.ts

@@ -1,3 +1,2 @@
-export { default as ReactComponent } from './components/PileupRendering';
-export { default as configSchema } from './configSchema';
-export { default } from './PileupRenderer';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function register(pluginManager: PluginManager): void;

package/dist/SNPCoverageAdapter/SNPCoverageAdapter.d.ts

@@ -1,5 +1,5 @@
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
+import { AugmentedRegion as Region } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
 import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
 import { Observable } from 'rxjs';
@@ -29,38 +29,50 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
             tag?: string;
         };
     }): Promise<{
-        total: number;
-        lowqual: {
+        bins: {
             total: number;
-            strands: {
-                [key: string]: number;
+            lowqual: {
+                total: number;
+                strands: {
+                    [key: string]: number;
+                };
             };
-        };
-        cov: {
-            total: number;
-            strands: {
-                [key: string]: number;
+            cov: {
+                total: number;
+                strands: {
+                    [key: string]: number;
+                };
             };
-        };
-        delskips: {
-            total: number;
-            strands: {
-                [key: string]: number;
+            delskips: {
+                total: number;
+                strands: {
+                    [key: string]: number;
+                };
             };
-        };
-        noncov: {
-            total: number;
-            strands: {
-                [key: string]: number;
+            noncov: {
+                total: number;
+                strands: {
+                    [key: string]: number;
+                };
             };
-        };
-        ref: {
-            total: number;
-            strands: {
-                [key: string]: number;
+            ref: {
+                total: number;
+                strands: {
+                    [key: string]: number;
+                };
+            };
+        }[];
+        skipmap: {
+            [key: string]: {
+                score: number;
+                feature: unknown;
+                start: number;
+                end: number;
+                strand: number;
+                xs: string;
             };
         };
-    }[]>;
+    }>;
 }
 declare const capabilities: string[];
 export { capabilities };

package/dist/SNPCoverageAdapter/index.d.ts

@@ -1,7 +1,3 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => {
-    getAdapterClass: () => Promise<typeof import("./SNPCoverageAdapter").default>;
-    configSchema: import("@jbrowse/core/configuration/configurationSchema").AnyConfigurationSchemaType;
-    adapterCapabilities: string[];
-};
+declare const _default: (pluginManager: PluginManager) => void;
 export default _default;

package/dist/SNPCoverageRenderer/index.d.ts

@@ -1,3 +1,3 @@
-export { WiggleRendering as ReactComponent } from "@jbrowse/plugin-wiggle";
-export { default } from "./SNPCoverageRenderer";
-export const configSchema: import("@jbrowse/core/configuration/configurationSchema").AnyConfigurationSchemaType;
+import PluginManager from '@jbrowse/core/PluginManager';
+export declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").AnyConfigurationSchemaType;
+export default function register(pluginManager: PluginManager): void;