jbrowse-plugin-gwas 2.0.5 → 2.0.6

package/dist/LinearManhattanDisplay/TooltipComponent.d.ts

@@ -1,11 +1,18 @@
 import React from 'react';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { Feature } from '@jbrowse/core/util';
 import type { TooltipContentsComponent } from '@jbrowse/plugin-wiggle';
+export interface Props {
+    feature: Feature;
+    model: Model;
+}
+export interface Model {
+    configuration: AnyConfigurationModel;
+    featureUnderMouse?: Feature;
+}
 type Coord = [number, number];
 declare const TooltipComponent: (props: {
-    model: {
-        featureUnderMouse?: Feature;
-    };
+    model: Model;
     height: number;
     offsetMouseCoord: Coord;
     clientMouseCoord: Coord;

package/dist/LinearManhattanDisplay/TooltipComponent.js

@@ -1,28 +1,11 @@
 import React from 'react';
+import { getConf } from '@jbrowse/core/configuration';
+import { SanitizedHTML } from '@jbrowse/core/ui';
 import { Tooltip } from '@jbrowse/plugin-wiggle';
 import { observer } from 'mobx-react';
-const en = (n) => n.toLocaleString('en-US');
-function toP(s = 0) {
-    return +(+s).toPrecision(6);
-}
-const TooltipContents = React.forwardRef(function TooltipContents2({ feature }, ref) {
-    const start = feature.get('start') + 1;
-    const end = feature.get('end');
-    const refName = feature.get('refName');
-    const name = feature.get('name');
-    const rsid = feature.get('rsid');
-    const loc = [
-        refName,
-        start === end ? en(start) : `${en(start)}..${en(end)}`,
-    ]
-        .filter(f => !!f)
-        .join(':');
+const TooltipContents = React.forwardRef(function TooltipContents2({ model, feature }, ref) {
     return (React.createElement("div", { ref: ref },
-        loc,
-        React.createElement("br", null),
-        `${toP(feature.get('score'))}`,
-        React.createElement("br", null),
-        name || rsid));
+        React.createElement(SanitizedHTML, { html: getConf(model, 'mouseover', { feature }) })));
 });
 const TooltipComponent = observer(function (props) {
     return React.createElement(Tooltip, { TooltipContents: TooltipContents, ...props });

package/dist/LinearManhattanDisplay/TooltipComponent.js.map

@@ -1 +1 @@
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+{"version":3,"file":"TooltipComponent.js","sourceRoot":"","sources":["../../src/LinearManhattanDisplay/TooltipComponent.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,OAAO,EAAE,MAAM,6BAA6B,CAAA;AACrD,OAAO,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAA;AAChD,OAAO,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAA;AAChD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAerC,MAAM,eAAe,GAAG,KAAK,CAAC,UAAU,CACtC,SAAS,gBAAgB,CAAC,EAAE,KAAK,EAAE,OAAO,EAAE,EAAE,GAAG;IAC/C,OAAO,CACL,6BAAK,GAAG,EAAE,GAAG;QACX,oBAAC,aAAa,IAAC,IAAI,EAAE,OAAO,CAAC,KAAK,EAAE,WAAW,EAAE,EAAE,OAAO,EAAE,CAAC,GAAI,CAC7D,CACP,CAAA;AACH,CAAC,CACF,CAAA;AAID,MAAM,gBAAgB,GAAG,QAAQ,CAAC,UAAU,KAO3C;IACC,OAAO,oBAAC,OAAO,IAAC,eAAe,EAAE,eAAe,KAAM,KAAK,GAAI,CAAA;AACjE,CAAC,CAAC,CAAA;AAEF,eAAe,gBAAgB,CAAA"}

package/dist/LinearManhattanDisplay/configSchemaFactory.d.ts

@@ -1,5 +1,10 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 export declare function configSchemaFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    mouseover: {
+        type: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
     autoscale: {
         type: string;
         defaultValue: string;

package/dist/LinearManhattanDisplay/configSchemaFactory.js

@@ -5,6 +5,11 @@ export function configSchemaFactory(pluginManager) {
     const { baseLinearDisplayConfigSchema } = LGVPlugin.exports;
     const LinearManhattanRendererConfigSchema = pluginManager.getRendererType('LinearManhattanRenderer').configSchema;
     return ConfigurationSchema('LinearManhattanDisplay', {
+        mouseover: {
+            type: 'string',
+            defaultValue: 'jexl:getTooltip(feature)',
+            contextVariable: ['feature'],
+        },
         autoscale: {
             type: 'stringEnum',
             defaultValue: 'local',

package/dist/LinearManhattanDisplay/configSchemaFactory.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchemaFactory.js","sourceRoot":"","sources":["../../src/LinearManhattanDisplay/configSchemaFactory.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAKvC,MAAM,UAAU,mBAAmB,CAAC,aAA4B;IAC9D,MAAM,SAAS,GAAG,aAAa,CAAC,SAAS,CACvC,wBAAwB,CACZ,CAAA;IACd,MAAM,EAAE,6BAA6B,EAAE,GAAG,SAAS,CAAC,OAAO,CAAA;IAE3D,MAAM,mCAAmC,GAAG,aAAa,CAAC,eAAe,CACvE,yBAAyB,CACzB,CAAC,YAAY,CAAA;IAEf,OAAO,mBAAmB,CACxB,wBAAwB,EACxB;QACE,SAAS,EAAE;YACT,IAAI,EAAE,QAAQ;YACd,YAAY,EAAE,0BAA0B;YACxC,eAAe,EAAE,CAAC,SAAS,CAAC;SAC7B;QACD,SAAS,EAAE;YACT,IAAI,EAAE,YAAY;YAClB,YAAY,EAAE,OAAO;YACrB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,gBAAgB,EAAE;gBACzC,QAAQ;gBACR,OAAO;gBACP,UAAU;gBACV,SAAS;gBACT,QAAQ;aACT,CAAC;YACF,WAAW,EACT,sFAAsF;SACzF;QACD,QAAQ,EAAE;YACR,IAAI,EAAE,QAAQ;YACd,YAAY,EAAE,MAAM,CAAC,SAAS;YAC9B,WAAW,EAAE,+BAA+B;SAC7C;QACD,QAAQ,EAAE;YACR,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,+BAA+B;YAC5C,YAAY,EAAE,MAAM,CAAC,SAAS;SAC/B;QACD,SAAS,EAAE;YACT,IAAI,EAAE,QAAQ;YACd,WAAW,EACT,8EAA8E;YAChF,YAAY,EAAE,CAAC;SAChB;QACD,SAAS,EAAE;YACT,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,YAAY,EAAE,CAAC,QAAQ,EAAE,KAAK,CAAC,CAAC,EAAE,cAAc;YACzE,WAAW,EAAE,0BAA0B;YACvC,YAAY,EAAE,QAAQ;SACvB;QACD,QAAQ,EAAE;YACR,IAAI,EAAE,SAAS;YACf,WAAW,EAAE,kBAAkB;YAC/B,YAAY,EAAE,KAAK;SACpB;QAED,gBAAgB,EAAE;YAChB,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,SAAS,EAAE,QAAQ,EAAE,MAAM,CAAC,CAAC;YACpE,YAAY,EAAE,QAAQ;SACvB;QACD,SAAS,EAAE,mBAAmB,CAAC,wBAAwB,EAAE;YACvD,uBAAuB,EAAE,mCAAmC;SAC7D,CAAC;KACH,EACD;QACE,iBAAiB,EAAE,6BAA6B;QAChD,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC"}

package/dist/LinearManhattanDisplay/jexlMouseover.d.ts

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

package/dist/LinearManhattanDisplay/jexlMouseover.js

@@ -0,0 +1,19 @@
+function toP(s = 0) {
+    return +(+s).toPrecision(6);
+}
+const en = (n) => n.toLocaleString('en-US');
+function getTooltip(feature) {
+    const start = feature.get('start') + 1;
+    const end = feature.get('end');
+    const refName = feature.get('refName');
+    const name = feature.get('name');
+    const rsid = feature.get('rsid');
+    const loc = [refName, start === end ? en(start) : `${en(start)}..${en(end)}`]
+        .filter(f => !!f)
+        .join(':');
+    return `${loc}<br/>${toP(feature.get('score'))}<br/>${name || rsid}`;
+}
+export default function JexlMouseoverF(pluginManager) {
+    pluginManager.jexl.addFunction('getTooltip', (feature) => getTooltip(feature));
+}
+//# sourceMappingURL=jexlMouseover.js.map

package/dist/LinearManhattanDisplay/jexlMouseover.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"jexlMouseover.js","sourceRoot":"","sources":["../../src/LinearManhattanDisplay/jexlMouseover.ts"],"names":[],"mappings":"AAGA,SAAS,GAAG,CAAC,CAAC,GAAG,CAAC;IAChB,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;AAC7B,CAAC;AAED,MAAM,EAAE,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,CAAC,cAAc,CAAC,OAAO,CAAC,CAAA;AAEnD,SAAS,UAAU,CAAC,OAAgB;IAClC,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;IACtC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IAC9B,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;IACtC,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,MAAM,GAAG,GAAG,CAAC,OAAO,EAAE,KAAK,KAAK,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,KAAK,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;SAC1E,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,IAAI,CAAC,GAAG,CAAC,CAAA;IAEZ,OAAO,GAAG,GAAG,QAAQ,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,QAAQ,IAAI,IAAI,IAAI,EAAE,CAAA;AACtE,CAAC;AAED,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,aAA4B;IACjE,aAAa,CAAC,IAAI,CAAC,WAAW,CAAC,YAAY,EAAE,CAAC,OAAgB,EAAE,EAAE,CAChE,UAAU,CAAC,OAAO,CAAC,CACpB,CAAA;AACH,CAAC"}

package/dist/LinearManhattanDisplay/stateModelFactory.d.ts

@@ -12,21 +12,12 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
 } & {
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
-        region: import("mobx-state-tree").IModelType<{
-            refName: import("mobx-state-tree").ISimpleType<string>;
-            start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree").ISimpleType<number>;
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>;
-        }, {
-            setRefName(newRefName: string): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
         reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        renderInProgress: AbortController | undefined;
+        stopToken: string | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -50,15 +41,9 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
+        setLoading(newStopToken: string): void;
         setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: React.ReactElement;
-            features: Map<string, import("@jbrowse/core/util").Feature>;
-            layout: any;
-            maxHeightReached: boolean;
-            renderProps: any;
-        } | undefined): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
@@ -202,6 +187,7 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
+    readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
 } & {
@@ -245,7 +231,7 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
         scoreMin: number;
         scoreMax: number;
     } | undefined;
-    statsFetchInProgress: undefined | AbortController;
+    statsFetchInProgress: undefined | string;
 } & {
     updateQuantitativeStats(stats: {
         currStatsBpPerPx: number;
@@ -255,7 +241,7 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
     setColor(color?: string): void;
     setPosColor(color?: string): void;
     setNegColor(color?: string): void;
-    setStatsLoading(aborter: AbortController): void;
+    setStatsLoading(arg?: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     setResolution(res: number): void;
     setFill(fill: number): void;
@@ -400,9 +386,7 @@ export declare function stateModelFactory(pluginManager: PluginManager, configSc
     renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
 } & {
     readonly TooltipComponent: (props: {
-        model: {
-            featureUnderMouse?: Feature;
-        };
+        model: import("./TooltipComponent").Model;
         height: number;
         offsetMouseCoord: [number, number];
         clientMouseCoord: [number, number];

package/dist/LinearManhattanRenderer/LinearManhattanRenderer.js

@@ -23,18 +23,20 @@ export default function rendererFactory(pluginManager) {
             const [region] = regions;
             const YSCALEBAR_LABEL_OFFSET = 5;
             const height = unadjustedHeight - YSCALEBAR_LABEL_OFFSET * 2;
-            const opts = { ...scaleOpts, range: [0, height] };
             const width = (region.end - region.start) / bpPerPx;
             const rbush = new RBush();
-            const defaultColor = readConfObject(config, 'color');
-            const scale = getScale(opts);
+            const scale = getScale({
+                ...scaleOpts,
+                range: [0, height],
+            });
             const toY = (n) => height - scale(n) + YSCALEBAR_LABEL_OFFSET;
             let start = performance.now();
             checkStopToken(stopToken);
             let lastRenderedBlobX = 0;
             let lastRenderedBlobY = 0;
-            if (!config.color.isCallback) {
-                ctx.fillStyle = defaultColor;
+            const { isCallback } = config.color;
+            if (!isCallback) {
+                ctx.fillStyle = config.color.value;
             }
             for (const feature of features.values()) {
                 if (performance.now() - start > 200) {
@@ -46,7 +48,7 @@ export default function rendererFactory(pluginManager) {
                 const y = toY(score);
                 if (Math.abs(leftPx - lastRenderedBlobX) > 1 ||
                     Math.abs(y - lastRenderedBlobY) > 1) {
-                    if (config.color.isCallback) {
+                    if (isCallback) {
                         ctx.fillStyle = readConfObject(config, 'color', { feature });
                     }
                     ctx.beginPath();

package/dist/LinearManhattanRenderer/LinearManhattanRenderer.js.map

@@ -1 +1 @@
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package/dist/index.js

@@ -1,5 +1,6 @@
 import Plugin from '@jbrowse/core/Plugin';
 import LinearManhattanDisplayF from './LinearManhattanDisplay';
+import JexlMouseoverF from './LinearManhattanDisplay/jexlMouseover';
 import LinearManhattanRendererF from './LinearManhattanRenderer';
 import { version } from '../package.json';
 export default class GWASPlugin extends Plugin {
@@ -11,6 +12,7 @@ export default class GWASPlugin extends Plugin {
     install(pluginManager) {
         LinearManhattanDisplayF(pluginManager);
         LinearManhattanRendererF(pluginManager);
+        JexlMouseoverF(pluginManager);
     }
 }
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
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