npm - @jbrowse/plugin-wiggle - Versions diffs - 2.4.2 → 2.6.1 - Mend

@jbrowse/plugin-wiggle 2.4.2 → 2.6.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (220) hide show

package/esm/MultiLinearWiggleDisplay/models/model.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/esm/MultiLinearWiggleDisplay/models/renderSvg.d.ts ADDED Viewed

@@ -0,0 +1,4 @@
+import React from 'react';
+import { ExportSvgDisplayOptions } from '@jbrowse/plugin-linear-genome-view';
+import { WiggleDisplayModel } from './model';
+export declare function renderSvg(self: WiggleDisplayModel, opts: ExportSvgDisplayOptions, superRenderSvg: (opts: ExportSvgDisplayOptions) => Promise<React.ReactNode>): Promise<React.JSX.Element>;

package/esm/MultiLinearWiggleDisplay/models/renderSvg.js ADDED Viewed

@@ -0,0 +1,13 @@
+import React from 'react';
+import { getContainingView } from '@jbrowse/core/util';
+import { when } from 'mobx';
+import { StatBars } from '../components/WiggleDisplayComponent';
+export async function renderSvg(self, opts, superRenderSvg) {
+    await when(() => !!self.stats && !!self.regionCannotBeRenderedText);
+    const { offsetPx } = getContainingView(self);
+    return (React.createElement(React.Fragment, null,
+        React.createElement("g", { id: "snpcov" }, await superRenderSvg(opts)),
+        React.createElement("g", { transform: `translate(${Math.max(-offsetPx, 0)})` },
+            React.createElement(StatBars, { model: self, orientation: "left", exportSVG: true }))));
+}
+//# sourceMappingURL=renderSvg.js.map

package/esm/MultiLinearWiggleDisplay/models/renderSvg.js.map ADDED Viewed

@@ -0,0 +1 @@

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package/esm/MultiQuantitativeTrack/configSchema.d.ts CHANGED Viewed

@@ -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/esm/MultiRowLineRenderer/MultiRowLineRenderer.js CHANGED Viewed

@@ -1,4 +1,4 @@
-import { groupBy } from '../util';
+import { groupBy } from '@jbrowse/core/util';
 import { drawLine } from '../drawxy';
 import WiggleBaseRenderer from '../WiggleBaseRenderer';
 export default class MultiRowLineRenderer extends WiggleBaseRenderer {

package/esm/MultiRowLineRenderer/MultiRowLineRenderer.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/MultiRowLineRenderer/configSchema.d.ts CHANGED Viewed

@@ -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/esm/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.js CHANGED Viewed

@@ -1,4 +1,4 @@
-import { groupBy } from '../util';
+import { groupBy } from '@jbrowse/core/util';
 import { drawXY } from '../drawxy';
 import WiggleBaseRenderer from '../WiggleBaseRenderer';
 export default class MultiXYPlotRenderer extends WiggleBaseRenderer {

package/esm/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/MultiRowXYPlotRenderer/configSchema.d.ts CHANGED Viewed

@@ -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/esm/MultiWiggleAdapter/MultiWiggleAdapter.d.ts CHANGED Viewed

@@ -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/esm/MultiWiggleAdapter/MultiWiggleAdapter.js CHANGED Viewed

@@ -7,7 +7,7 @@ function getFilename(uri) {
     const filename = uri.slice(uri.lastIndexOf('/') + 1);
     return filename.slice(0, filename.lastIndexOf('.'));
 }
-export default class MultiWiggleAdapter extends BaseFeatureDataAdapter {
+class MultiWiggleAdapter extends BaseFeatureDataAdapter {
     async getAdapters() {
         const getSubAdapter = this.getSubAdapter;
         if (!getSubAdapter) {
@@ -66,7 +66,7 @@ export default class MultiWiggleAdapter extends 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
@@ -86,4 +86,5 @@ MultiWiggleAdapter.capabilities = [
     'hasLocalStats',
     'hasGlobalStats',
 ];
+export default MultiWiggleAdapter;
 //# sourceMappingURL=MultiWiggleAdapter.js.map

package/esm/MultiWiggleAdapter/MultiWiggleAdapter.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/MultiWiggleAdapter/configSchema.d.ts CHANGED Viewed

@@ -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/esm/MultiWiggleAddTrackWidget/AddTrackWorkflow.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
-/// <reference types="react" />
+import React from 'react';
 import { AddTrackModel } from '@jbrowse/plugin-data-management';
 export default function MultiWiggleWidget({ model }: {
     model: AddTrackModel;
-}): JSX.Element;
+}): React.JSX.Element;

package/esm/MultiWiggleAddTrackWidget/AddTrackWorkflow.js CHANGED Viewed

@@ -46,7 +46,7 @@ export default function MultiWiggleWidget({ model }) {
                 var _a;
                 const session = getSession(model);
                 const trackId = [
-                    `${trackName.toLowerCase().replace(/ /g, '_')}-${Date.now()}`,
+                    `${trackName.toLowerCase().replaceAll(' ', '_')}-${Date.now()}`,
                     `${session.adminMode ? '' : '-sessionTrack'}`,
                 ].join('');
                 // allow list of bigwigs in JSON format or line-by-line

package/esm/MultiWiggleAddTrackWidget/AddTrackWorkflow.js.map CHANGED Viewed

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package/esm/MultiWiggleRendering.d.ts CHANGED Viewed

@@ -1,4 +1,4 @@
-/// <reference types="react" />
+import React from 'react';
 import { Region } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util';
 import { Source } from './util';
@@ -16,6 +16,6 @@ declare function WiggleRendering(props: {
     displayModel: {
         isMultiRow: boolean;
     };
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof WiggleRendering;
 export default _default;

package/esm/MultiXYPlotRenderer/MultiXYPlotRenderer.js CHANGED Viewed

@@ -1,5 +1,6 @@
+import { groupBy } from '@jbrowse/core/util';
 import { drawXY } from '../drawxy';
-import { groupBy, YSCALEBAR_LABEL_OFFSET } from '../util';
+import { YSCALEBAR_LABEL_OFFSET } from '../util';
 import WiggleBaseRenderer from '../WiggleBaseRenderer';
 export default class MultiXYPlotRenderer extends WiggleBaseRenderer {
     // @ts-expect-error

package/esm/MultiXYPlotRenderer/MultiXYPlotRenderer.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"MultiXYPlotRenderer.js","sourceRoot":"","sources":["../../src/MultiXYPlotRenderer/MultiXYPlotRenderer.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAW,MAAM,oBAAoB,CAAA;AACrD,OAAO,EAAE,MAAM,EAAE,MAAM,WAAW,CAAA;AAClC,OAAO,EAAE,sBAAsB,EAAE,MAAM,SAAS,CAAA;AAEhD,OAAO,kBAEN,MAAM,uBAAuB,CAAA;AAE9B,MAAM,CAAC,OAAO,OAAO,mBAAoB,SAAQ,kBAAkB;IACjE,mBAAmB;IACnB,KAAK,CAAC,IAAI,CAAC,GAA6B,EAAE,KAAgB;QACxD,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;QACnC,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAA;QACpE,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAA;QACxD,IAAI,KAAK,GAAG,EAAe,CAAA;QAC3B,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE;YAC5B,MAAM,QAAQ,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;YACpC,IAAI,CAAC,QAAQ,EAAE;gBACb,SAAQ;aACT;YACD,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,CAAC,GAAG,EAAE;gBACtC,GAAG,KAAK;gBACR,QAAQ;gBACR,MAAM,EAAE,sBAAsB;gBAC9B,aAAa,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,KAAK,IAAI,MAAM;gBAC3C,KAAK;aACN,CAAC,CAAA;YACF,KAAK,GAAG,CAAC,GAAG,KAAK,EAAE,GAAG,eAAe,CAAC,CAAA;SACvC;QACD,OAAO,EAAE,eAAe,EAAE,KAAK,EAAE,CAAA;IACnC,CAAC;CACF"}

package/esm/MultiXYPlotRenderer/configSchema.d.ts CHANGED Viewed

@@ -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/esm/QuantitativeTrack/configSchema.d.ts CHANGED Viewed

@@ -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/esm/Tooltip.d.ts CHANGED Viewed

@@ -15,6 +15,6 @@ declare function Tooltip({ model, height, clientMouseCoord, offsetMouseCoord, cl
     offsetMouseCoord: Coord;
     clientRect?: DOMRect;
     TooltipContents: TooltipContentsComponent;
-}): JSX.Element | null;
+}): React.JSX.Element | null;
 declare const _default: typeof Tooltip;
 export default _default;

package/esm/WiggleBaseRenderer.d.ts CHANGED Viewed

@@ -38,7 +38,7 @@ export default abstract class WiggleBaseRenderer extends FeatureRendererType {
         height: number;
         width: number;
         containsNoTransferables: boolean;
-        reactElement: JSX.Element;
+        reactElement: import("react").JSX.Element;
         html?: string | undefined;
     } | {
         features: Map<string, Feature>;