@jbrowse/plugin-variants 1.4.3 → 1.5.2

package/dist/ChordVariantDisplay/index.d.ts

@@ -1,3 +1,3 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => import("@jbrowse/core/pluggableElementTypes/DisplayType").default;
+declare const _default: (pluginManager: PluginManager) => import("@jbrowse/core/pluggableElementTypes").DisplayType;
 export default _default;

package/dist/LinearVariantDisplay/model.d.ts

@@ -29,7 +29,7 @@ export default function (configSchema: LinearVariantDisplayConfigModel): import(
         features: Map<string, Feature> | undefined;
         layout: any;
         status: string;
-        error: Error | undefined;
+        error: unknown;
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
@@ -49,7 +49,7 @@ export default function (configSchema: LinearVariantDisplayConfigModel): import(
             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>>;
@@ -57,6 +57,7 @@ export default function (configSchema: LinearVariantDisplayConfigModel): import(
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">;
     trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    trackShowDescriptions: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     trackDisplayMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
@@ -65,7 +66,7 @@ export default function (configSchema: LinearVariantDisplayConfigModel): import(
     configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
 }, {
     rendererTypeName: string;
-    error: Error | undefined;
+    error: unknown;
 } & {
     readonly RenderingComponent: import("react").FC<{
         model: import("mobx-state-tree").ModelInstanceTypeProps<{
@@ -74,14 +75,14 @@ export default function (configSchema: LinearVariantDisplayConfigModel): import(
             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;
@@ -93,14 +94,14 @@ export default function (configSchema: LinearVariantDisplayConfigModel): import(
             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;
@@ -112,7 +113,7 @@ export default function (configSchema: LinearVariantDisplayConfigModel): import(
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): undefined;
 } & {
-    setError(error?: Error | undefined): void;
+    setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
 } & {
@@ -166,11 +167,13 @@ export default function (configSchema: LinearVariantDisplayConfigModel): import(
 } & {
     readonly rendererTypeName: any;
     readonly showLabels: any;
+    readonly showDescriptions: any;
     readonly maxHeight: any;
     readonly displayMode: any;
     readonly rendererConfig: any;
 } & {
     toggleShowLabels(): void;
+    toggleShowDescriptions(): void;
     setDisplayMode(val: string): void;
     setMaxHeight(val: number): void;
 } & {

package/dist/VcfAdapter/VcfAdapter.d.ts

@@ -1,17 +1,23 @@
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { Region } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
-import VcfFeature from '../VcfTabixAdapter/VcfFeature';
+import IntervalTree from '@flatten-js/interval-tree';
 export default class VcfAdapter extends BaseFeatureDataAdapter {
     static capabilities: string[];
-    private setupP?;
-    constructor(config: AnyConfigurationModel);
-    private decodeFileContents;
+    protected vcfFeatures?: Promise<{
+        header: string;
+        intervalTree: Record<string, IntervalTree>;
+    }>;
     getHeader(): Promise<string>;
     getMetadata(): Promise<any>;
-    getLines(): Promise<VcfFeature[]>;
-    setup(): Promise<Feature[]>;
+    setupP(): Promise<{
+        header: string;
+        intervalTree: Record<string, IntervalTree<any>>;
+    }>;
+    setup(): Promise<{
+        header: string;
+        intervalTree: Record<string, IntervalTree<any>>;
+    }>;
     getRefNames(_?: BaseOptions): Promise<string[]>;
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     freeResources(): void;