jbrowse-plugin-gwas 2.1.1 → 2.2.0

package/README.md

@@ -53,7 +53,7 @@ in above section) to be the score that is plotted
 
 ```json
 {
-  "type": "FeatureTrack",
+  "type": "GWASTrack",
   "trackId": "gwas_track",
   "name": "GWAS",
   "category": ["Annotation"],

package/dist/GWASAdapter/index.d.ts

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

package/dist/GWASAdapter/index.js

@@ -0,0 +1,15 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default function GWASAdapterF(pluginManager) {
+    pluginManager.addAdapterType(() => {
+        const res = pluginManager.getAdapterType('BedTabixAdapter');
+        const configSchema = ConfigurationSchema('GWASAdapter', {}, { baseConfiguration: res.configSchema, explicitlyTyped: true });
+        return new AdapterType({
+            name: 'GWASAdapter',
+            displayName: 'GWAS adapter',
+            configSchema,
+            getAdapterClass: res.getAdapterClass,
+        });
+    });
+}
+//# sourceMappingURL=index.js.map

package/dist/GWASAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GWASAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAGzE,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,MAAM,CAAC,OAAO,UAAU,YAAY,CAAC,aAA4B;IAC/D,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,GAAG,GAAG,aAAa,CAAC,cAAc,CAAC,iBAAiB,CAAE,CAAA;QAC5D,MAAM,YAAY,GAAG,mBAAmB,CACtC,aAAa,EACb,EAAE,EACF,EAAE,iBAAiB,EAAE,GAAG,CAAC,YAAY,EAAE,eAAe,EAAE,IAAI,EAAE,CAC/D,CAAA;QACD,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,aAAa;YACnB,WAAW,EAAE,cAAc;YAC3B,YAAY;YACZ,eAAe,EAAE,GAAG,CAAC,eAAe;SACrC,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/dist/GWASAddTrackComponent/GWASAddTrackComponent.d.ts

@@ -0,0 +1,3 @@
+import React from 'react';
+declare const GWASAddTrackComponent: ({ model }: any) => React.JSX.Element;
+export default GWASAddTrackComponent;

package/dist/GWASAddTrackComponent/GWASAddTrackComponent.js

@@ -0,0 +1,18 @@
+import React, { useEffect, useState } from 'react';
+import { TextField } from '@mui/material';
+import { observer } from 'mobx-react';
+const GWASAddTrackComponent = observer(function ({ model }) {
+    const [scoreColumn, setScoreColumn] = useState('neg_log_pvalue');
+    useEffect(() => {
+        model.setMixinData({
+            adapter: {
+                scoreColumn,
+            },
+        });
+    }, [model, scoreColumn]);
+    return (React.createElement(TextField, { label: "Score column", helperText: "Name of the column to use as the score for the Manhattan plot (e.g., 'neg_log_pvalue', 'pvalue')", value: scoreColumn, onChange: event => {
+            setScoreColumn(event.target.value);
+        }, fullWidth: true }));
+});
+export default GWASAddTrackComponent;
+//# sourceMappingURL=GWASAddTrackComponent.js.map

package/dist/GWASAddTrackComponent/GWASAddTrackComponent.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"GWASAddTrackComponent.js","sourceRoot":"","sources":["../../src/GWASAddTrackComponent/GWASAddTrackComponent.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAElD,OAAO,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AACzC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,MAAM,qBAAqB,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAAO;IAC7D,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,QAAQ,CAAC,gBAAgB,CAAC,CAAA;IAEhE,SAAS,CAAC,GAAG,EAAE;QACb,KAAK,CAAC,YAAY,CAAC;YACjB,OAAO,EAAE;gBACP,WAAW;aACZ;SACF,CAAC,CAAA;IACJ,CAAC,EAAE,CAAC,KAAK,EAAE,WAAW,CAAC,CAAC,CAAA;IAExB,OAAO,CACL,oBAAC,SAAS,IACR,KAAK,EAAC,cAAc,EACpB,UAAU,EAAC,kGAAkG,EAC7G,KAAK,EAAE,WAAW,EAClB,QAAQ,EAAE,KAAK,CAAC,EAAE;YAChB,cAAc,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;QACpC,CAAC,EACD,SAAS,SACT,CACH,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,qBAAqB,CAAA"}

package/dist/GWASAddTrackComponent/index.d.ts

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

package/dist/GWASAddTrackComponent/index.js

@@ -0,0 +1,12 @@
+import { lazy } from 'react';
+const GWASAddTrackComponent = lazy(() => import('./GWASAddTrackComponent'));
+export default function GWASAddTrackComponentF(pluginManager) {
+    pluginManager.addToExtensionPoint('Core-addTrackComponent', 
+    // @ts-expect-error
+    (comp, { model }) => {
+        return model.trackAdapterType === 'GWASAdapter'
+            ? GWASAddTrackComponent
+            : comp;
+    });
+}
+//# sourceMappingURL=index.js.map

package/dist/GWASAddTrackComponent/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GWASAddTrackComponent/index.tsx"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAI5B,MAAM,qBAAqB,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,yBAAyB,CAAC,CAAC,CAAA;AAE3E,MAAM,CAAC,OAAO,UAAU,sBAAsB,CAC5C,aAA4B;IAE5B,aAAa,CAAC,mBAAmB,CAC/B,wBAAwB;IACxB,mBAAmB;IACnB,CAAC,IAAI,EAAE,EAAE,KAAK,EAAgC,EAAE,EAAE;QAChD,OAAO,KAAK,CAAC,gBAAgB,KAAK,aAAa;YAC7C,CAAC,CAAC,qBAAqB;YACvB,CAAC,CAAC,IAAI,CAAA;IACV,CAAC,CACF,CAAA;AACH,CAAC"}

package/dist/GWASTrack/configSchema.d.ts

@@ -0,0 +1,84 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+/**
+ * #config GWASTrack
+ * #category track
+ * used for GWAS (Genome-Wide Association Study) tracks with Manhattan plot display
+ */
+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;
+        };
+        maxDepth: {
+            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/dist/GWASTrack/configSchema.js

@@ -0,0 +1,16 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes';
+/**
+ * #config GWASTrack
+ * #category track
+ * used for GWAS (Genome-Wide Association Study) tracks with Manhattan plot display
+ */
+export default function configSchemaFactory(pluginManager) {
+    return ConfigurationSchema('GWASTrack', {}, {
+        /**
+         * #baseConfiguration
+         */
+        baseConfiguration: createBaseTrackConfig(pluginManager),
+    });
+}
+//# sourceMappingURL=configSchema.js.map

package/dist/GWASTrack/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/GWASTrack/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,qCAAqC,CAAA;AAI3E;;;;GAIG;AACH,MAAM,CAAC,OAAO,UAAU,mBAAmB,CAAC,aAA4B;IACtE,OAAO,mBAAmB,CACxB,WAAW,EACX,EAAE,EACF;QACE;;WAEG;QACH,iBAAiB,EAAE,qBAAqB,CAAC,aAAa,CAAC;KACxD,CACF,CAAA;AACH,CAAC"}

package/dist/GWASTrack/index.d.ts

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

package/dist/GWASTrack/index.js

@@ -0,0 +1,14 @@
+import { TrackType, createBaseTrackModel, } from '@jbrowse/core/pluggableElementTypes';
+import configSchemaF from './configSchema';
+export default function GWASTrackF(pm) {
+    pm.addTrackType(() => {
+        const configSchema = configSchemaF(pm);
+        return new TrackType({
+            name: 'GWASTrack',
+            displayName: 'GWAS track',
+            configSchema,
+            stateModel: createBaseTrackModel(pm, 'GWASTrack', configSchema),
+        });
+    });
+}
+//# sourceMappingURL=index.js.map

package/dist/GWASTrack/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GWASTrack/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,SAAS,EACT,oBAAoB,GACrB,MAAM,qCAAqC,CAAA;AAE5C,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAI1C,MAAM,CAAC,OAAO,UAAU,UAAU,CAAC,EAAiB;IAClD,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE;QACnB,MAAM,YAAY,GAAG,aAAa,CAAC,EAAE,CAAC,CAAA;QACtC,OAAO,IAAI,SAAS,CAAC;YACnB,IAAI,EAAE,WAAW;YACjB,WAAW,EAAE,YAAY;YACzB,YAAY;YACZ,UAAU,EAAE,oBAAoB,CAAC,EAAE,EAAE,WAAW,EAAE,YAAY,CAAC;SAChE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/dist/GuessAdapter/index.d.ts

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

package/dist/GuessAdapter/index.js

@@ -0,0 +1,31 @@
+import { testAdapter } from '@jbrowse/core/util';
+import { getFileName, makeIndex, makeIndexType, } from '@jbrowse/core/util/tracks';
+export default function GuessAdapterF(pluginManager) {
+    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+        return (file, index, adapterHint) => {
+            const fileName = getFileName(file);
+            const indexName = index && getFileName(index);
+            if (testAdapter(fileName, /\.txt\.gz$/i, adapterHint, 'GWASAdapter')) {
+                return {
+                    type: 'GWASAdapter',
+                    bedGzLocation: file,
+                    index: {
+                        location: index || makeIndex(file, '.tbi'),
+                        indexType: makeIndexType(indexName, 'CSI', 'TBI'),
+                    },
+                };
+            }
+            else {
+                return adapterGuesser(file, index, adapterHint);
+            }
+        };
+    });
+    pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+        return (adapterName) => {
+            return adapterName === 'GWASAdapter'
+                ? 'GWASTrack'
+                : trackTypeGuesser(adapterName);
+        };
+    });
+}
+//# sourceMappingURL=index.js.map

package/dist/GuessAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GuessAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAA;AAChD,OAAO,EACL,WAAW,EACX,SAAS,EACT,aAAa,GACd,MAAM,2BAA2B,CAAA;AASlC,MAAM,CAAC,OAAO,UAAU,aAAa,CAAC,aAA4B;IAChE,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;QACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;YACF,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;YAClC,MAAM,SAAS,GAAG,KAAK,IAAI,WAAW,CAAC,KAAK,CAAC,CAAA;YAC7C,IACE,WAAW,CAAC,QAAQ,EAAE,aAAa,EAAE,WAAW,EAAE,aAAa,CAAC,EAChE,CAAC;gBACD,OAAO;oBACL,IAAI,EAAE,aAAa;oBACnB,aAAa,EAAE,IAAI;oBACnB,KAAK,EAAE;wBACL,QAAQ,EAAE,KAAK,IAAI,SAAS,CAAC,IAAI,EAAE,MAAM,CAAC;wBAC1C,SAAS,EAAE,aAAa,CAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC;qBAClD;iBACF,CAAA;YACH,CAAC;iBAAM,CAAC;gBACN,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;YACjD,CAAC;QACH,CAAC,CAAA;IACH,CAAC,CACF,CAAA;IAED,aAAa,CAAC,mBAAmB,CAC/B,gCAAgC,EAChC,CAAC,gBAAkC,EAAE,EAAE;QACrC,OAAO,CAAC,WAAmB,EAAE,EAAE;YAC7B,OAAO,WAAW,KAAK,aAAa;gBAClC,CAAC,CAAC,WAAW;gBACb,CAAC,CAAC,gBAAgB,CAAC,WAAW,CAAC,CAAA;QACnC,CAAC,CAAA;IACH,CAAC,CACF,CAAA;AACH,CAAC"}

package/dist/LinearManhattanDisplay/index.js

@@ -10,7 +10,7 @@ export default function LinearManhattanDisplayF(pluginManager) {
             name: 'LinearManhattanDisplay',
             configSchema,
             stateModel: stateModelFactory(pluginManager, configSchema),
-            trackType: 'FeatureTrack',
+            trackType: 'GWASTrack',
             viewType: 'LinearGenomeView',
             ReactComponent: LinearWiggleDisplayReactComponent,
         });

package/dist/LinearManhattanDisplay/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearManhattanDisplay/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,qCAAqC,CAAA;AAEjE,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAA;AAC3D,OAAO,EAAE,iBAAiB,EAAE,MAAM,qBAAqB,CAAA;AAKvD,MAAM,CAAC,OAAO,UAAU,uBAAuB,CAAC,aAA4B;IAC1E,MAAM,YAAY,GAAG,aAAa,CAAC,SAAS,CAAC,cAAc,CAAiB,CAAA;IAE5E,MAAM,EAAE,iCAAiC,EAAE,GAAG,YAAY,CAAC,OAAO,CAAA;IAElE,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,mBAAmB,CAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,wBAAwB;YAC9B,YAAY;YACZ,UAAU,EAAE,iBAAiB,CAAC,aAAa,EAAE,YAAY,CAAC;YAC1D,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,iCAAiC;SAClD,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearManhattanDisplay/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,qCAAqC,CAAA;AAEjE,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAA;AAC3D,OAAO,EAAE,iBAAiB,EAAE,MAAM,qBAAqB,CAAA;AAKvD,MAAM,CAAC,OAAO,UAAU,uBAAuB,CAAC,aAA4B;IAC1E,MAAM,YAAY,GAAG,aAAa,CAAC,SAAS,CAAC,cAAc,CAAiB,CAAA;IAE5E,MAAM,EAAE,iCAAiC,EAAE,GAAG,YAAY,CAAC,OAAO,CAAA;IAElE,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,mBAAmB,CAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,wBAAwB;YAC9B,YAAY;YACZ,UAAU,EAAE,iBAAiB,CAAC,aAAa,EAAE,YAAY,CAAC;YAC1D,SAAS,EAAE,WAAW;YACtB,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,iCAAiC;SAClD,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/dist/LinearManhattanDisplay/stateModelFactory.d.ts

@@ -202,6 +202,7 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
+    mouseoverExtraInformation: string | undefined;
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
 } & {
@@ -212,20 +213,35 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
     readonly renderDelay: number;
     readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
     readonly selectedFeatureId: string | undefined;
+    copyInfoToClipboard(feature: import("@jbrowse/core/util").Feature): void;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
+    readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, [number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]>;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
-    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
-    searchFeatureByID(id: string): [number, number, number, number] | undefined;
+    getFeatureByID(blockKey: string, id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
+    searchFeatureByID(id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
+    setMouseoverExtraInformation(extra?: string): void;
 } & {
     reload(): Promise<void>;
 } & {

package/dist/LinearManhattanRenderer/LinearManhattanRenderer.d.ts

@@ -24,7 +24,16 @@ export default function rendererFactory(pluginManager: PluginManager): {
         pluginManager: PluginManager;
     }): {
         draw(ctx: CanvasRenderingContext2D, props: ManhattanProps): Promise<{
-            clickMap: any;
+            clickMap: {
+                index: ArrayBufferLike;
+                items: {
+                    minX: number;
+                    minY: number;
+                    maxX: number;
+                    maxY: number;
+                    feature: any;
+                }[];
+            };
         }>;
         supportsSVG: boolean;
         render(renderProps: import("@jbrowse/plugin-wiggle/dist/WiggleBaseRenderer").RenderArgsDeserialized): Promise<{
@@ -67,7 +76,7 @@ export default function rendererFactory(pluginManager: PluginManager): {
         freeResources(_args: any): void;
         name: string;
         maybeDisplayName?: string;
-        readonly displayName: string;
+        get displayName(): string;
     };
 };
 export {};

package/dist/LinearManhattanRenderer/LinearManhattanRenderer.js

@@ -1,6 +1,6 @@
 import { readConfObject, } from '@jbrowse/core/configuration';
 import { featureSpanPx, updateStatus, } from '@jbrowse/core/util';
-import RBush from 'rbush';
+import Flatbush from 'flatbush';
 import { checkStopToken } from './util';
 export default function rendererFactory(pluginManager) {
     const WigglePlugin = pluginManager.getPlugin('WigglePlugin');
@@ -12,7 +12,6 @@ export default function rendererFactory(pluginManager) {
             const YSCALEBAR_LABEL_OFFSET = 5;
             const height = unadjustedHeight - YSCALEBAR_LABEL_OFFSET * 2;
             const width = (region.end - region.start) / bpPerPx;
-            const rbush = new RBush();
             const scale = getScale({
                 ...scaleOpts,
                 range: [0, height],
@@ -26,6 +25,7 @@ export default function rendererFactory(pluginManager) {
             if (!isCallback) {
                 ctx.fillStyle = config.color.value;
             }
+            const items = [];
             await updateStatus('Rendering plot', statusCallback, () => {
                 for (const feature of features.values()) {
                     if (performance.now() - start > 200) {
@@ -45,7 +45,7 @@ export default function rendererFactory(pluginManager) {
                         ctx.fill();
                         lastRenderedBlobY = y;
                         lastRenderedBlobX = leftPx;
-                        rbush.insert({
+                        items.push({
                             minX: leftPx - 2,
                             minY: y - 2,
                             maxX: leftPx + 2,
@@ -65,8 +65,21 @@ export default function rendererFactory(pluginManager) {
                     ctx.stroke();
                 });
             }
+            const index = new Flatbush(Math.max(items.length, 1));
+            if (items.length === 0) {
+                index.add(0, 0, 0, 0);
+            }
+            else {
+                for (const item of items) {
+                    index.add(item.minX, item.minY, item.maxX, item.maxY);
+                }
+            }
+            index.finish();
             return {
-                clickMap: rbush.toJSON(),
+                clickMap: {
+                    index: index.data,
+                    items,
+                },
             };
         }
     };

package/dist/LinearManhattanRenderer/LinearManhattanRenderer.js.map

@@ -1 +1 @@
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package/dist/LinearManhattanRenderer/LinearManhattanRendering.js

@@ -2,15 +2,16 @@ import React, { useMemo, useRef } from 'react';
 import { PrerenderedCanvas } from '@jbrowse/core/ui';
 import { SimpleFeature } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
-import RBush from 'rbush';
+import Flatbush from 'flatbush';
 const LinearManhattanRendering = observer(function (props) {
     const { height, onMouseLeave, onMouseMove, onFeatureClick, clickMap } = props;
-    const clickMap2 = useMemo(() => {
-        return new RBush().fromJSON(clickMap);
+    const clickMapData = useMemo(() => {
+        const index = Flatbush.from(clickMap.index);
+        return { index, items: clickMap.items };
     }, [clickMap]);
     const ref = useRef(null);
     function getFeatureUnderMouse(eventClientX, eventClientY) {
-        // calculates feature under mouse
+        var _a;
         let offsetX = 0;
         let offsetY = 0;
         if (ref.current) {
@@ -18,13 +19,11 @@ const LinearManhattanRendering = observer(function (props) {
             offsetX = eventClientX - r.left;
             offsetY = eventClientY - r.top;
         }
-        const ret = clickMap2.search({
-            minX: offsetX,
-            minY: offsetY,
-            maxX: offsetX + 3,
-            maxY: offsetY + 3,
-        });
-        return ret[0] ? new SimpleFeature(ret[0].feature) : undefined;
+        const indices = clickMapData.index.search(offsetX, offsetY, offsetX + 3, offsetY + 3);
+        const firstIndex = indices[0];
+        return firstIndex !== undefined
+            ? new SimpleFeature((_a = clickMapData.items[firstIndex]) === null || _a === void 0 ? void 0 : _a.feature)
+            : undefined;
     }
     return (React.createElement("div", { ref: ref, "data-testid": "wiggle-rendering-test", onMouseMove: e => { var _a; return onMouseMove === null || onMouseMove === void 0 ? void 0 : onMouseMove(e, (_a = getFeatureUnderMouse(e.clientX, e.clientY)) === null || _a === void 0 ? void 0 : _a.id()); }, onClick: e => { var _a; return onFeatureClick === null || onFeatureClick === void 0 ? void 0 : onFeatureClick(e, (_a = getFeatureUnderMouse(e.clientX, e.clientY)) === null || _a === void 0 ? void 0 : _a.id()); }, onMouseLeave: e => onMouseLeave === null || onMouseLeave === void 0 ? void 0 : onMouseLeave(e), style: {
             overflow: 'visible',

package/dist/LinearManhattanRenderer/LinearManhattanRendering.js.map

@@ -1 +1 @@
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package/dist/config.json

@@ -37,7 +37,7 @@
   ],
   "tracks": [
     {
-      "type": "FeatureTrack",
+      "type": "GWASTrack",
       "trackId": "gwas_track",
       "name": "GWAS",
       "category": ["Annotation"],

package/dist/index.js

@@ -1,4 +1,8 @@
 import Plugin from '@jbrowse/core/Plugin';
+import GWASAdapterF from './GWASAdapter';
+import GWASAddTrackComponentF from './GWASAddTrackComponent';
+import GWASTrackF from './GWASTrack';
+import GuessAdapterF from './GuessAdapter';
 import LinearManhattanDisplayF from './LinearManhattanDisplay';
 import JexlMouseoverF from './LinearManhattanDisplay/jexlMouseover';
 import LinearManhattanRendererF from './LinearManhattanRenderer';
@@ -10,6 +14,10 @@ export default class GWASPlugin extends Plugin {
         this.version = version;
     }
     install(pluginManager) {
+        GWASAdapterF(pluginManager);
+        GWASAddTrackComponentF(pluginManager);
+        GWASTrackF(pluginManager);
+        GuessAdapterF(pluginManager);
         LinearManhattanDisplayF(pluginManager);
         LinearManhattanRendererF(pluginManager);
         JexlMouseoverF(pluginManager);

package/dist/index.js.map

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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAEzC,OAAO,YAAY,MAAM,eAAe,CAAA;AACxC,OAAO,sBAAsB,MAAM,yBAAyB,CAAA;AAC5D,OAAO,UAAU,MAAM,aAAa,CAAA;AACpC,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAC1C,OAAO,uBAAuB,MAAM,0BAA0B,CAAA;AAC9D,OAAO,cAAc,MAAM,wCAAwC,CAAA;AACnE,OAAO,wBAAwB,MAAM,2BAA2B,CAAA;AAChE,OAAO,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAA;AAIzC,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,MAAM;IAA9C;;QACE,SAAI,GAAG,YAAY,CAAA;QACnB,YAAO,GAAG,OAAO,CAAA;IAWnB,CAAC;IATC,OAAO,CAAC,aAA4B;QAClC,YAAY,CAAC,aAAa,CAAC,CAAA;QAC3B,sBAAsB,CAAC,aAAa,CAAC,CAAA;QACrC,UAAU,CAAC,aAAa,CAAC,CAAA;QACzB,aAAa,CAAC,aAAa,CAAC,CAAA;QAC5B,uBAAuB,CAAC,aAAa,CAAC,CAAA;QACtC,wBAAwB,CAAC,aAAa,CAAC,CAAA;QACvC,cAAc,CAAC,aAAa,CAAC,CAAA;IAC/B,CAAC;CACF"}