npm - @jbrowse/plugin-alignments - Versions diffs - 2.4.1 → 2.5.0 - Mend

@jbrowse/plugin-alignments 2.4.1 → 2.5.0

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Files changed (193) hide show

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.js ADDED Viewed

@@ -0,0 +1,31 @@
+import React from 'react';
+import { Typography, Link } from '@mui/material';
+import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
+import { getLengthOnRef } from '../MismatchParser';
+import { navToLoc } from './util';
+export default function SupplementaryAlignments(props) {
+    const { tag, model } = props;
+    return (React.createElement(BaseCard, { ...props, title: "Supplementary alignments" },
+        React.createElement(Typography, null, "List of supplementary alignment locations"),
+        React.createElement("ul", null, tag
+            .split(';')
+            .filter(SA => !!SA)
+            .map((SA, index) => {
+            const [saRef, saStart, saStrand, saCigar] = SA.split(',');
+            const saLength = getLengthOnRef(saCigar);
+            const extra = Math.floor(saLength / 5);
+            const start = +saStart;
+            const end = +saStart + saLength;
+            const locString = `${saRef}:${Math.max(1, start - extra)}-${end + extra}`;
+            const displayStart = start.toLocaleString('en-US');
+            const displayEnd = end.toLocaleString('en-US');
+            const displayString = `${saRef}:${displayStart}-${displayEnd} (${saStrand}) [${saLength}bp]`;
+            return (React.createElement("li", { key: `${locString}-${index}` },
+                React.createElement(Link, { onClick: async (event) => {
+                        event.preventDefault();
+                        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+                        navToLoc(locString, model);
+                    }, href: "#" }, displayString)));
+        }))));
+}
+//# sourceMappingURL=AlignmentsFeatureSuppAligns.js.map

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"AlignmentsFeatureSuppAligns.js","sourceRoot":"","sources":["../../src/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,UAAU,EAAE,IAAI,EAAE,MAAM,eAAe,CAAA;AAChD,OAAO,EAAE,QAAQ,EAAE,MAAM,mDAAmD,CAAA;AAC5E,OAAO,EAAE,cAAc,EAAE,MAAM,mBAAmB,CAAA;AAElD,OAAO,EAAE,QAAQ,EAAE,MAAM,QAAQ,CAAA;AAEjC,MAAM,CAAC,OAAO,UAAU,uBAAuB,CAAC,KAG/C;IACC,MAAM,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IAC5B,OAAO,CACL,oBAAC,QAAQ,OAAK,KAAK,EAAE,KAAK,EAAC,0BAA0B;QACnD,oBAAC,UAAU,oDAAuD;QAClE,gCACG,GAAG;aACD,KAAK,CAAC,GAAG,CAAC;aACV,MAAM,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;aAClB,GAAG,CAAC,CAAC,EAAE,EAAE,KAAK,EAAE,EAAE;YACjB,MAAM,CAAC,KAAK,EAAE,OAAO,EAAE,QAAQ,EAAE,OAAO,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;YACzD,MAAM,QAAQ,GAAG,cAAc,CAAC,OAAO,CAAC,CAAA;YACxC,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,QAAQ,GAAG,CAAC,CAAC,CAAA;YACtC,MAAM,KAAK,GAAG,CAAC,OAAO,CAAA;YACtB,MAAM,GAAG,GAAG,CAAC,OAAO,GAAG,QAAQ,CAAA;YAC/B,MAAM,SAAS,GAAG,GAAG,KAAK,IAAI,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,GAAG,KAAK,CAAC,IACtD,GAAG,GAAG,KACR,EAAE,CAAA;YACF,MAAM,YAAY,GAAG,KAAK,CAAC,cAAc,CAAC,OAAO,CAAC,CAAA;YAClD,MAAM,UAAU,GAAG,GAAG,CAAC,cAAc,CAAC,OAAO,CAAC,CAAA;YAC9C,MAAM,aAAa,GAAG,GAAG,KAAK,IAAI,YAAY,IAAI,UAAU,KAAK,QAAQ,MAAM,QAAQ,KAAK,CAAA;YAC5F,OAAO,CACL,4BAAI,GAAG,EAAE,GAAG,SAAS,IAAI,KAAK,EAAE;gBAC9B,oBAAC,IAAI,IACH,OAAO,EAAE,KAAK,EAAC,KAAK,EAAC,EAAE;wBACrB,KAAK,CAAC,cAAc,EAAE,CAAA;wBAEtB,mEAAmE;wBACnE,QAAQ,CAAC,SAAS,EAAE,KAAK,CAAC,CAAA;oBAC5B,CAAC,EACD,IAAI,EAAC,GAAG,IAEP,aAAa,CACT,CACJ,CACN,CAAA;QACH,CAAC,CAAC,CACD,CACI,CACZ,CAAA;AACH,CAAC"}

package/esm/AlignmentsFeatureDetail/index.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 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<"BaseFeatureWidget">;
@@ -13,10 +13,13 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
 } & {
     type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
 }, {
+    error: unknown;
+} & {
     setFeatureData(featureData: Record<string, unknown>): void;
     clearFeatureData(): void;
     setFormattedData(feat: Record<string, unknown>): void;
     setExtra(type?: string | undefined, trackId?: string | undefined): void;
+    setError(e: unknown): void;
 } & {
     afterCreate(): void;
 }, {
@@ -32,8 +35,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
-    id: string;
     type: "BaseFeatureWidget";
+    id: string;
     track: import("mobx-state-tree").ReferenceIdentifier | undefined;
     view: import("mobx-state-tree").ReferenceIdentifier | undefined;
     trackId: string | undefined;

package/esm/AlignmentsFeatureDetail/util.d.ts ADDED Viewed

@@ -0,0 +1,8 @@
+import { IAnyStateTreeNode } from 'mobx-state-tree';
+export declare function getTag(tag: string, feat: {
+    tags?: {
+        [key: string]: unknown;
+    };
+    [key: string]: unknown;
+}): unknown;
+export declare function navToLoc(locString: string, model: IAnyStateTreeNode): Promise<void>;

package/esm/AlignmentsFeatureDetail/util.js ADDED Viewed

@@ -0,0 +1,22 @@
+import { getSession } from '@jbrowse/core/util';
+export function getTag(tag, feat) {
+    var _a;
+    return ((_a = feat.tags) === null || _a === void 0 ? void 0 : _a[tag]) || feat[tag];
+}
+export async function navToLoc(locString, model) {
+    const session = getSession(model);
+    const { view } = model;
+    try {
+        if (view) {
+            await view.navToLocString(locString);
+        }
+        else {
+            throw new Error('No view associated with this view anymore');
+        }
+    }
+    catch (e) {
+        console.error(e);
+        session.notify(`${e}`);
+    }
+}
+//# sourceMappingURL=util.js.map

package/esm/AlignmentsFeatureDetail/util.js.map ADDED Viewed

@@ -0,0 +1 @@

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package/esm/AlignmentsTrack/configSchemaF.d.ts ADDED Viewed

@@ -0,0 +1,74 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default 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>>;

package/esm/AlignmentsTrack/configSchemaF.js ADDED Viewed

@@ -0,0 +1,16 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes';
+/**
+ * #config AlignmentsTrack
+ * has very little config; most config and state logic is on the display
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+export default function configSchemaFactory(pluginManager) {
+    return ConfigurationSchema('AlignmentsTrack', {}, {
+        /**
+         * #baseConfiguration
+         */
+        baseConfiguration: createBaseTrackConfig(pluginManager),
+    });
+}
+//# sourceMappingURL=configSchemaF.js.map

package/esm/AlignmentsTrack/configSchemaF.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"configSchemaF.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/configSchemaF.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,qCAAqC,CAAA;AAG3E;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,CAAC,OAAO,UAAU,mBAAmB,CAAC,aAA4B;IACtE,OAAO,mBAAmB,CACxB,iBAAiB,EACjB,EAAE,EACF;QACE;;WAEG;QACH,iBAAiB,EAAE,qBAAqB,CAAC,aAAa,CAAC;KACxD,CACF,CAAA;AACH,CAAC"}

package/esm/AlignmentsTrack/index.js CHANGED Viewed

@@ -1,22 +1,9 @@
 import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import { createBaseTrackConfig, createBaseTrackModel, } from '@jbrowse/core/pluggableElementTypes/models';
-/**
- * #config AlignmentsTrack
- * has very little config; most config and state logic is on the display
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
-function configSchemaFactory(pluginManager) {
-    return ConfigurationSchema('AlignmentsTrack', {}, {
-        /**
-         * #baseConfiguration
-         */
-        baseConfiguration: createBaseTrackConfig(pluginManager),
-    });
-}
+import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
+import configSchemaF from './configSchemaF';
 export default function register(pm) {
     pm.addTrackType(() => {
-        const configSchema = configSchemaFactory(pm);
+        const configSchema = configSchemaF(pm);
         const track = new TrackType({
             name: 'AlignmentsTrack',
             displayName: 'Alignments track',

package/esm/AlignmentsTrack/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/index.ts"],"names":[],"mappings":"AACA,OAAO,SAAS,MAAM,+CAA+C,CAAA;AACrE,OAAO,EAAE,oBAAoB,EAAE,MAAM,4CAA4C,CAAA;AACjF,OAAO,aAAa,MAAM,iBAAiB,CAAA;AAE3C,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,EAAiB;IAChD,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE;QACnB,MAAM,YAAY,GAAG,aAAa,CAAC,EAAE,CAAC,CAAA;QACtC,MAAM,KAAK,GAAG,IAAI,SAAS,CAAC;YAC1B,IAAI,EAAE,iBAAiB;YACvB,WAAW,EAAE,kBAAkB;YAC/B,YAAY;YACZ,UAAU,EAAE,oBAAoB,CAAC,EAAE,EAAE,iBAAiB,EAAE,YAAY,CAAC;SACtE,CAAC,CAAA;QACF,MAAM,uBAAuB,GAAG,EAAE,CAAC,cAAc,CAAC,yBAAyB,CAAC,CAAA;QAC5E,0EAA0E;QAC1E,yEAAyE;QACzE,qDAAqD;QACrD,KAAK,CAAC,cAAc,CAAC,uBAAuB,CAAC,CAAA;QAC7C,OAAO,KAAK,CAAA;IACd,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/esm/BamAdapter/BamAdapter.d.ts CHANGED Viewed

@@ -39,7 +39,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
             readName: string;
         };
     }): import("rxjs").Observable<Feature>;
-    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats | {
+    getMultiRegionFeatureDensityStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | {
         bytes: number;
         fetchSizeLimit: any;
     }>;

package/esm/BamAdapter/BamAdapter.js CHANGED Viewed

@@ -156,7 +156,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         }, signal);
     }
-    async estimateRegionsStats(regions, opts) {
+    async getMultiRegionFeatureDensityStats(regions, opts) {
         const { bam } = await this.configure();
         // this is a method to avoid calling on htsget adapters
         // @ts-expect-error
@@ -166,7 +166,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
             return { bytes, fetchSizeLimit };
         }
         else {
-            return super.estimateRegionsStats(regions, opts);
+            return super.getMultiRegionFeatureDensityStats(regions, opts);
         }
     }
     freeResources( /* { region } */) { }

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

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

@@ -1,2 +1,51 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    bamLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        /**
+         * #slot index.indexType
+         */
+        indexType: {
+            model: import("mobx-state-tree").ISimpleType<string>;
+            type: string;
+            defaultValue: string;
+        };
+        /**
+         * #slot index.location
+         */
+        location: {
+            type: string;
+            defaultValue: {
+                uri: string;
+                locationType: string;
+            };
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    /**
+     * #slot
+     */
+    fetchSizeLimit: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     * generally refers to the reference genome assembly's sequence adapter
+     * currently needs to be manually added
+     */
+    sequenceAdapter: {
+        type: string;
+        description: string;
+        defaultValue: null;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;

package/esm/CramAdapter/CramAdapter.d.ts CHANGED Viewed

@@ -45,7 +45,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     }): import("rxjs").Observable<Feature>;
     freeResources(): void;
     cramRecordToFeature(record: CramRecord): CramSlightlyLazyFeature;
-    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<{
+    getMultiRegionFeatureDensityStats(regions: Region[], opts?: BaseOptions): Promise<{
         bytes: number;
         fetchSizeLimit: any;
     }>;

package/esm/CramAdapter/CramAdapter.js CHANGED Viewed

@@ -195,7 +195,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         return new CramSlightlyLazyFeature(record, this);
     }
     // we return the configured fetchSizeLimit, and the bytes for the region
-    async estimateRegionsStats(regions, opts) {
+    async getMultiRegionFeatureDensityStats(regions, opts) {
         const bytes = await this.bytesForRegions(regions, opts);
         const fetchSizeLimit = this.getConf('fetchSizeLimit');
         return {

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

	@@ -1 +1 @@
1	- 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package/esm/CramAdapter/CramTestAdapters.js CHANGED Viewed

@@ -1,7 +1,7 @@
 import { Observable } from 'rxjs';
 import SimpleFeature from '@jbrowse/core/util/simpleFeature';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { ConfigurationSchema } from '@jbrowse/core/configuration/configurationSchema';
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
 // setup for Cram Adapter Testing
 export function parseSmallFasta(text) {
     return text

package/esm/CramAdapter/CramTestAdapters.js.map CHANGED Viewed

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

@@ -1,2 +1,41 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot fetchSizeLimit
+     */
+    fetchSizeLimit: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot cramLocation
+     */
+    cramLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot craiLocation
+     */
+    craiLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot sequenceAdapter
+     * generally refers to the reference genome assembly's sequence adapter
+     * currently needs to be manually added
+     */
+    sequenceAdapter: {
+        type: string;
+        description: string;
+        defaultValue: null;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;

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

@@ -1,2 +1,27 @@
-declare const HtsgetBamAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const HtsgetBamAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    htsgetBase: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */
+    htsgetTrackId: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */
+    sequenceAdapter: {
+        type: string;
+        description: string;
+        defaultValue: null;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default HtsgetBamAdapter;

package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { AlignmentsDisplayModel } from '../models/model';
 declare function AlignmentsDisplay({ model }: {
     model: AlignmentsDisplayModel;

package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js CHANGED Viewed

@@ -5,7 +5,7 @@ import { getConf } from '@jbrowse/core/configuration';
 import { ResizeHandle } from '@jbrowse/core/ui';
 const useStyles = makeStyles()({
     resizeHandle: {
-        height: 2,
+        height: 5,
         position: 'absolute',
         zIndex: 2,
     },
@@ -20,7 +20,7 @@ function AlignmentsDisplay({ model }) {
         React.createElement(ResizeHandle, { onDrag: delta => {
                 SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta);
                 return delta;
-            }, className: classes.resizeHandle, style: { top } }),
+            }, className: classes.resizeHandle, style: { top: top - 4 } }),
         React.createElement("div", { "data-testid": "Blockset-pileup", style: {
                 position: 'absolute',
                 top,

package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map CHANGED Viewed

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

@@ -4,4 +4,42 @@ import PluginManager from '@jbrowse/core/PluginManager';
  * has a "pileup" sub-display, where you can see individual reads and a
  * quantitative "snpcoverage" sub-display track showing SNP frequencies
  */
-export default function configModelFactory(pm: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default function configModelFactory(pm: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    pileupDisplay: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+    /**
+     * #slot
+     */
+    snpCoverageDisplay: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+    /**
+     * #slot
+     */
+    height: {
+        type: string;
+        defaultValue: number;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    maxFeatureScreenDensity: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    fetchSizeLimit: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    height: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    mouseover: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;