@jbrowse/plugin-wiggle 2.4.1 → 2.5.0

package/dist/MultiLinearWiggleDisplay/models/model.js.map

@@ -1 +1 @@
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package/dist/MultiQuantitativeTrack/configSchema.d.ts

@@ -1,3 +1,75 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    name: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    assemblyNames: {
+        description: string;
+        type: string;
+        defaultValue: string[];
+    };
+    description: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    category: {
+        description: string;
+        type: string;
+        defaultValue: never[];
+    };
+    metadata: {
+        type: string;
+        description: string;
+        defaultValue: {};
+    };
+    adapter: import("mobx-state-tree").IAnyModelType;
+    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        indexingAttributes: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        indexingFeatureTypesToExclude: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        textSearchAdapter: import("mobx-state-tree").IAnyModelType;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        feature: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        subfeatures: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        depth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        config: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        hideUris: {
+            type: string;
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
 export default configSchema;

package/dist/MultiRowLineRenderer/configSchema.d.ts

@@ -1,2 +1,52 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    displayCrossHatches: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    summaryScoreMode: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    color: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    posColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    negColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    clipColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivot: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivotValue: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
 export default configSchema;

package/dist/MultiRowXYPlotRenderer/configSchema.d.ts

@@ -1,2 +1,69 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    filled: {
+        type: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    displayCrossHatches: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    summaryScoreMode: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */
+    minSize: {
+        type: string;
+        defaultValue: number;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    color: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    posColor: {
+        type: string;
+        description: string;
+        /**
+         * #slot
+         */
+        defaultValue: string;
+    };
+    negColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    clipColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivot: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivotValue: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
 export default configSchema;

package/dist/MultiWiggleAdapter/MultiWiggleAdapter.d.ts

@@ -18,7 +18,7 @@ export default class MultiWiggleAdapter extends BaseFeatureDataAdapter {
         scoreMax: number;
     }>;
     getFeatures(region: Region, opts?: WiggleOptions): import("rxjs").Observable<Feature>;
-    estimateRegionsStats(_regions: Region[]): Promise<{
+    getMultiRegionFeatureDensityStats(_regions: Region[]): Promise<{
         featureDensity: number;
     }>;
     getSources(): Promise<{

package/dist/MultiWiggleAdapter/MultiWiggleAdapter.js

@@ -68,7 +68,7 @@ class MultiWiggleAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         }, opts.signal);
     }
     // always render bigwig instead of calculating a feature density for it
-    async estimateRegionsStats(_regions) {
+    async getMultiRegionFeatureDensityStats(_regions) {
         return { featureDensity: 0 };
     }
     // in another adapter type, this could be dynamic depending on region or
@@ -83,10 +83,10 @@ class MultiWiggleAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     freeResources() { }
 }
-exports.default = MultiWiggleAdapter;
 MultiWiggleAdapter.capabilities = [
     'hasResolution',
     'hasLocalStats',
     'hasGlobalStats',
 ];
+exports.default = MultiWiggleAdapter;
 //# sourceMappingURL=MultiWiggleAdapter.js.map

package/dist/MultiWiggleAdapter/MultiWiggleAdapter.js.map

@@ -1 +1 @@
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package/dist/MultiWiggleAdapter/configSchema.d.ts

@@ -1,2 +1,19 @@
-declare const MultiWiggleAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const MultiWiggleAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    subadapters: {
+        type: string;
+        defaultValue: never[];
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    bigWigs: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default MultiWiggleAdapter;

package/dist/MultiWiggleAddTrackWidget/AddTrackWorkflow.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { AddTrackModel } from '@jbrowse/plugin-data-management';
 export default function MultiWiggleWidget({ model }: {
     model: AddTrackModel;

package/dist/MultiWiggleRendering.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { Region } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util';
 import { Source } from './util';

package/dist/MultiXYPlotRenderer/configSchema.d.ts

@@ -1,2 +1,66 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    filled: {
+        type: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    displayCrossHatches: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    summaryScoreMode: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */
+    minSize: {
+        type: string;
+        defaultValue: number;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    color: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    posColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    negColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    clipColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivot: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivotValue: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
 export default configSchema;

package/dist/QuantitativeTrack/configSchema.d.ts

@@ -1,3 +1,75 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare function configSchemaFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare function configSchemaFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    name: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    assemblyNames: {
+        description: string;
+        type: string;
+        defaultValue: string[];
+    };
+    description: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    category: {
+        description: string;
+        type: string;
+        defaultValue: never[];
+    };
+    metadata: {
+        type: string;
+        description: string;
+        defaultValue: {};
+    };
+    adapter: import("mobx-state-tree").IAnyModelType;
+    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        indexingAttributes: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        indexingFeatureTypesToExclude: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        textSearchAdapter: import("mobx-state-tree").IAnyModelType;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        feature: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        subfeatures: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        depth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        config: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        hideUris: {
+            type: string;
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
 export default configSchemaFactory;

package/dist/WiggleRPC/MultiWiggleGetSources.d.ts

@@ -0,0 +1,21 @@
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
+import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods';
+import { Region } from '@jbrowse/core/util';
+import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export declare class MultiWiggleGetSources extends RpcMethodType {
+    name: string;
+    deserializeArguments(args: any, rpcDriverClassName: string): Promise<any>;
+    serializeArguments(args: RenderArgs & {
+        signal?: AbortSignal;
+        statusCallback?: (arg: string) => void;
+    }, rpcDriverClassName: string): Promise<{}>;
+    execute(args: {
+        adapterConfig: AnyConfigurationModel;
+        signal?: RemoteAbortSignal;
+        sessionId: string;
+        headers?: Record<string, string>;
+        regions: Region[];
+        bpPerPx: number;
+    }, rpcDriverClassName: string): Promise<any>;
+}

package/dist/WiggleRPC/MultiWiggleGetSources.js

@@ -0,0 +1,51 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.MultiWiggleGetSources = void 0;
+const RpcMethodType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodType"));
+const serializableFilterChain_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain"));
+const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
+const util_1 = require("@jbrowse/core/util");
+class MultiWiggleGetSources extends RpcMethodType_1.default {
+    constructor() {
+        super(...arguments);
+        this.name = 'MultiWiggleGetSources';
+    }
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    async deserializeArguments(args, rpcDriverClassName) {
+        const l = await super.deserializeArguments(args, rpcDriverClassName);
+        return {
+            ...l,
+            filters: args.filters
+                ? new serializableFilterChain_1.default({
+                    filters: args.filters,
+                })
+                : undefined,
+        };
+    }
+    async serializeArguments(args, rpcDriverClassName) {
+        var _a, _b, _c;
+        const pm = this.pluginManager;
+        const assemblyManager = (_b = (_a = pm.rootModel) === null || _a === void 0 ? void 0 : _a.session) === null || _b === void 0 ? void 0 : _b.assemblyManager;
+        if (!assemblyManager) {
+            return args;
+        }
+        const renamedArgs = await (0, util_1.renameRegionsIfNeeded)(assemblyManager, {
+            ...args,
+            filters: (_c = args.filters) === null || _c === void 0 ? void 0 : _c.toJSON().filters,
+        });
+        return super.serializeArguments(renamedArgs, rpcDriverClassName);
+    }
+    async execute(args, rpcDriverClassName) {
+        const pm = this.pluginManager;
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const { regions, adapterConfig, sessionId } = deserializedArgs;
+        const { dataAdapter } = await (0, dataAdapterCache_1.getAdapter)(pm, sessionId, adapterConfig);
+        // @ts-expect-error
+        return dataAdapter.getSources(regions, deserializedArgs);
+    }
+}
+exports.MultiWiggleGetSources = MultiWiggleGetSources;
+//# sourceMappingURL=MultiWiggleGetSources.js.map

package/dist/WiggleRPC/MultiWiggleGetSources.js.map

@@ -0,0 +1 @@
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package/dist/WiggleRPC/WiggleGetGlobalQuantitativeStats.d.ts

@@ -0,0 +1,14 @@
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
+import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
+import { QuantitativeStats } from '@jbrowse/core/util/stats';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export declare class WiggleGetGlobalQuantitativeStats extends RpcMethodType {
+    name: string;
+    deserializeArguments(args: any, rpcDriverClassName: string): Promise<any>;
+    execute(args: {
+        adapterConfig: AnyConfigurationModel;
+        signal?: RemoteAbortSignal;
+        headers?: Record<string, string>;
+        sessionId: string;
+    }, rpcDriverClassName: string): Promise<QuantitativeStats>;
+}

package/dist/WiggleRPC/WiggleGetGlobalQuantitativeStats.js

@@ -0,0 +1,37 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.WiggleGetGlobalQuantitativeStats = void 0;
+const RpcMethodType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodType"));
+const serializableFilterChain_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain"));
+const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
+class WiggleGetGlobalQuantitativeStats extends RpcMethodType_1.default {
+    constructor() {
+        super(...arguments);
+        this.name = 'WiggleGetGlobalQuantitativeStats';
+    }
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    async deserializeArguments(args, rpcDriverClassName) {
+        const l = await super.deserializeArguments(args, rpcDriverClassName);
+        return {
+            ...l,
+            filters: args.filters
+                ? new serializableFilterChain_1.default({
+                    filters: args.filters,
+                })
+                : undefined,
+        };
+    }
+    async execute(args, rpcDriverClassName) {
+        const pm = this.pluginManager;
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const { adapterConfig, sessionId } = deserializedArgs;
+        const { dataAdapter } = await (0, dataAdapterCache_1.getAdapter)(pm, sessionId, adapterConfig);
+        // @ts-expect-error
+        return dataAdapter.getGlobalStats(deserializedArgs);
+    }
+}
+exports.WiggleGetGlobalQuantitativeStats = WiggleGetGlobalQuantitativeStats;
+//# sourceMappingURL=WiggleGetGlobalQuantitativeStats.js.map

package/dist/WiggleRPC/WiggleGetGlobalQuantitativeStats.js.map

@@ -0,0 +1 @@
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