@jbrowse/plugin-lollipop 2.6.1

package/esm/LollipopRenderer/LollipopRenderer.js

@@ -0,0 +1,23 @@
+import BoxRendererType, { LayoutSession, } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import MultiLayout from '@jbrowse/core/util/layouts/MultiLayout';
+import { FloatingLayout, PrecomputedFloatingLayout } from './Layout';
+class FloatingLayoutSession extends LayoutSession {
+    makeLayout() {
+        'sequenceAdapter';
+        const { end, start } = this.regions[0];
+        const widthPx = (end - start) / this.bpPerPx;
+        return new MultiLayout(FloatingLayout, { width: widthPx });
+    }
+    layoutIsValid( /* layout */) {
+        return false; // layout.left layout.width === this.width
+    }
+}
+export default class extends BoxRendererType {
+    createSession(args) {
+        return new FloatingLayoutSession(args);
+    }
+    deserializeLayoutInClient(json) {
+        return new PrecomputedFloatingLayout(json);
+    }
+}
+//# sourceMappingURL=LollipopRenderer.js.map

package/esm/LollipopRenderer/LollipopRenderer.js.map

@@ -0,0 +1 @@
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package/esm/LollipopRenderer/components/Lollipop.d.ts

@@ -0,0 +1,3 @@
+import React from 'react';
+declare const _default: (props: Record<string, any>) => React.JSX.Element;
+export default _default;

package/esm/LollipopRenderer/components/Lollipop.js

@@ -0,0 +1,58 @@
+import React from 'react';
+import { readConfObject } from '@jbrowse/core/configuration';
+import { observer } from 'mobx-react';
+import ScoreText from './ScoreText';
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+export default observer(function Lollipop(props) {
+    const { feature, config, layoutRecord, selectedFeatureId } = props;
+    const { anchorLocation, y, data: { radiusPx }, } = layoutRecord;
+    const onFeatureMouseDown = (event) => {
+        const { onFeatureMouseDown: handler, feature } = props;
+        return handler === null || handler === void 0 ? void 0 : handler(event, feature.id());
+    };
+    const onFeatureMouseEnter = (event) => {
+        const { onFeatureMouseEnter: handler, feature } = props;
+        return handler === null || handler === void 0 ? void 0 : handler(event, feature.id());
+    };
+    const onFeatureMouseOut = (event) => {
+        const { onFeatureMouseOut: handler, feature } = props;
+        return handler === null || handler === void 0 ? void 0 : handler(event, feature.id());
+    };
+    const onFeatureMouseOver = (event) => {
+        const { onFeatureMouseOver: handler, feature } = props;
+        return handler === null || handler === void 0 ? void 0 : handler(event, feature.id());
+    };
+    const onFeatureMouseUp = (event) => {
+        const { onFeatureMouseUp: handler, feature } = props;
+        return handler === null || handler === void 0 ? void 0 : handler(event, feature.id());
+    };
+    const onFeatureMouseLeave = (event) => {
+        const { onFeatureMouseLeave: handler, feature } = props;
+        return handler === null || handler === void 0 ? void 0 : handler(event, feature.id());
+    };
+    const onFeatureMouseMove = (event) => {
+        const { onFeatureMouseMove: handler, feature } = props;
+        return handler === null || handler === void 0 ? void 0 : handler(event, feature.id());
+    };
+    const onFeatureClick = (event) => {
+        const { onFeatureClick: handler, feature } = props;
+        event.stopPropagation();
+        return handler === null || handler === void 0 ? void 0 : handler(event, feature.id());
+    };
+    const styleOuter = {
+        fill: readConfObject(config, 'strokeColor', { feature }),
+    };
+    if (String(selectedFeatureId) === String(feature.id())) {
+        styleOuter.fill = 'red';
+    }
+    const styleInner = {
+        fill: readConfObject(config, 'innerColor', { feature }),
+    };
+    const strokeWidth = readConfObject(config, 'strokeWidth', { feature });
+    return (React.createElement("g", { "data-testid": feature.id() },
+        React.createElement("title", null, readConfObject(config, 'caption', { feature })),
+        React.createElement("circle", { cx: anchorLocation, cy: y + radiusPx, r: radiusPx, style: styleOuter, onMouseDown: onFeatureMouseDown, onMouseEnter: onFeatureMouseEnter, onMouseOut: onFeatureMouseOut, onMouseOver: onFeatureMouseOver, onMouseUp: onFeatureMouseUp, onMouseLeave: onFeatureMouseLeave, onMouseMove: onFeatureMouseMove, onClick: onFeatureClick, onFocus: onFeatureMouseOver, onBlur: onFeatureMouseOut }),
+        radiusPx - strokeWidth <= 2 ? null : (React.createElement("circle", { cx: anchorLocation, cy: y + radiusPx, r: radiusPx - strokeWidth, style: styleInner, onMouseDown: onFeatureMouseDown, onMouseEnter: onFeatureMouseEnter, onMouseOut: onFeatureMouseOut, onMouseOver: onFeatureMouseOver, onMouseUp: onFeatureMouseUp, onMouseLeave: onFeatureMouseLeave, onMouseMove: onFeatureMouseMove, onClick: onFeatureClick, onFocus: onFeatureMouseOver, onBlur: onFeatureMouseOut })),
+        React.createElement(ScoreText, { feature: feature, config: config, layoutRecord: layoutRecord })));
+});
+//# sourceMappingURL=Lollipop.js.map

package/esm/LollipopRenderer/components/Lollipop.js.map

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package/esm/LollipopRenderer/components/LollipopRendering.d.ts

@@ -0,0 +1,3 @@
+import React from 'react';
+declare const _default: (props: Record<string, any>) => React.JSX.Element;
+export default _default;

package/esm/LollipopRenderer/components/LollipopRendering.js

@@ -0,0 +1,75 @@
+import React from 'react';
+import { readConfObject, } from '@jbrowse/core/configuration';
+import { bpToPx } from '@jbrowse/core/util';
+import { observer } from 'mobx-react';
+// locals
+import Lollipop from './Lollipop';
+import Stick from './Stick';
+function layoutFeat(args) {
+    const { feature, bpPerPx, config, region, layout } = args;
+    const centerBp = Math.abs(feature.get('end') + feature.get('start')) / 2;
+    const centerPx = bpToPx(centerBp, region, bpPerPx);
+    const radiusPx = readConfObject(config, 'radius', { feature });
+    if (!radiusPx) {
+        console.error(new Error(`lollipop radius ${radiusPx} configured for feature ${feature.id()}`));
+    }
+    layout.add(feature.id(), centerPx, radiusPx * 2, radiusPx * 2, {
+        featureId: feature.id(),
+        anchorX: centerPx,
+        radiusPx,
+        score: readConfObject(args.config, 'score', { feature }),
+    });
+}
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+export default observer(function LollipopRendering(props) {
+    const onMouseDown = (event) => {
+        const { onMouseDown: handler } = props;
+        return handler === null || handler === void 0 ? void 0 : handler(event);
+    };
+    const onMouseUp = (event) => {
+        const { onMouseUp: handler } = props;
+        return handler === null || handler === void 0 ? void 0 : handler(event);
+    };
+    const onMouseEnter = (event) => {
+        const { onMouseEnter: handler } = props;
+        return handler === null || handler === void 0 ? void 0 : handler(event);
+    };
+    const onMouseLeave = (event) => {
+        const { onMouseLeave: handler } = props;
+        return handler === null || handler === void 0 ? void 0 : handler(event);
+    };
+    const onMouseOver = (event) => {
+        const { onMouseOver: handler } = props;
+        return handler === null || handler === void 0 ? void 0 : handler(event);
+    };
+    const onMouseOut = (event) => {
+        const { onMouseOut: handler } = props;
+        return handler === null || handler === void 0 ? void 0 : handler(event);
+    };
+    const onClick = (event) => {
+        const { onClick: handler } = props;
+        return handler === null || handler === void 0 ? void 0 : handler(event);
+    };
+    const { regions, bpPerPx, layout, config, features = new Map(), displayModel = {}, } = props;
+    const { selectedFeatureId } = displayModel;
+    const [region] = regions;
+    for (const feature of features.values()) {
+        layoutFeat({
+            feature,
+            bpPerPx,
+            region,
+            config,
+            layout,
+        });
+    }
+    const width = (region.end - region.start) / bpPerPx;
+    const records = [...layout.getLayout(config).values()];
+    const height = layout.getTotalHeight();
+    return (React.createElement("svg", { width: width, height: height, style: { position: 'relative' }, onMouseDown: onMouseDown, onMouseUp: onMouseUp, onMouseEnter: onMouseEnter, onMouseLeave: onMouseLeave, onMouseOver: onMouseOver, onMouseOut: onMouseOut, onFocus: onMouseEnter, onBlur: onMouseLeave, onClick: onClick }, records.map(layoutRecord => {
+        const feature = features.get(layoutRecord.data.featureId);
+        return (React.createElement(React.Fragment, { key: feature.id() },
+            React.createElement(Stick, { ...props, config: config, layoutRecord: layoutRecord, feature: feature, key: `stick-${feature.id()}` }),
+            React.createElement(Lollipop, { ...props, layoutRecord: layoutRecord, feature: feature, key: `body-${feature.id()}`, selectedFeatureId: selectedFeatureId })));
+    })));
+});
+//# sourceMappingURL=LollipopRendering.js.map

package/esm/LollipopRenderer/components/LollipopRendering.js.map

@@ -0,0 +1 @@
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package/esm/LollipopRenderer/components/ScoreText.d.ts

@@ -0,0 +1,15 @@
+import React from 'react';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { Feature } from '@jbrowse/core/util';
+export default function ScoreText({ feature, config, layoutRecord: { y, data: { anchorX, radiusPx, score }, }, }: {
+    feature: Feature;
+    config: AnyConfigurationModel;
+    layoutRecord: {
+        y: number;
+        data: {
+            anchorX: number;
+            radiusPx: number;
+            score: number;
+        };
+    };
+}): React.JSX.Element | null;

package/esm/LollipopRenderer/components/ScoreText.js

@@ -0,0 +1,14 @@
+import React from 'react';
+import { readConfObject, } from '@jbrowse/core/configuration';
+import { contrastingTextColor } from '@jbrowse/core/util/color';
+export default function ScoreText({ feature, config, layoutRecord: { y, data: { anchorX, radiusPx, score }, }, }) {
+    const innerColor = readConfObject(config, 'innerColor', { feature });
+    const scoreString = String(score);
+    const fontWidth = (radiusPx * 2) / scoreString.length;
+    const fontHeight = fontWidth * 1.1;
+    if (fontHeight < 12) {
+        return null;
+    }
+    return (React.createElement("text", { style: { fontSize: fontHeight, fill: contrastingTextColor(innerColor) }, x: anchorX, y: y + radiusPx - fontHeight / 2.4, textAnchor: "middle", dominantBaseline: "hanging" }, scoreString));
+}
+//# sourceMappingURL=ScoreText.js.map

package/esm/LollipopRenderer/components/ScoreText.js.map

@@ -0,0 +1 @@
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package/esm/LollipopRenderer/components/Stick.d.ts

@@ -0,0 +1,15 @@
+import React from 'react';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { Feature } from '@jbrowse/core/util';
+declare const _default: ({ feature, config, layoutRecord: { anchorLocation, y, data: { radiusPx }, }, }: {
+    feature: Feature;
+    config: AnyConfigurationModel;
+    layoutRecord: {
+        anchorLocation: number;
+        y: number;
+        data: {
+            radiusPx: number;
+        };
+    };
+}) => React.JSX.Element;
+export default _default;

package/esm/LollipopRenderer/components/Stick.js

@@ -0,0 +1,7 @@
+import React from 'react';
+import { readConfObject, } from '@jbrowse/core/configuration';
+import { observer } from 'mobx-react';
+export default observer(function Stick({ feature, config, layoutRecord: { anchorLocation, y, data: { radiusPx }, }, }) {
+    return (React.createElement("line", { x1: anchorLocation, y1: 0, x2: anchorLocation, y2: y + 2 * radiusPx, stroke: readConfObject(config, 'stickColor', { feature }), strokeWidth: readConfObject(config, 'stickWidth', { feature }) }));
+});
+//# sourceMappingURL=Stick.js.map

package/esm/LollipopRenderer/components/Stick.js.map

@@ -0,0 +1 @@
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package/esm/LollipopRenderer/configSchema.d.ts

@@ -0,0 +1,56 @@
+declare const _default: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    strokeColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+    innerColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+    strokeWidth: {
+        type: string;
+        description: string;
+        defaultValue: number;
+        contextVariable: string[];
+    };
+    radius: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+    caption: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+    minStickLength: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    stickColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+    stickWidth: {
+        type: string;
+        description: string;
+        defaultValue: number;
+        contextVariable: string[];
+    };
+    score: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default _default;

package/esm/LollipopRenderer/configSchema.js

@@ -0,0 +1,57 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default ConfigurationSchema('LollipopRenderer', {
+    strokeColor: {
+        type: 'color',
+        description: 'the outer color of each lollipop',
+        defaultValue: 'green',
+        contextVariable: ['feature'],
+    },
+    innerColor: {
+        type: 'color',
+        description: 'the inner color of each lollipop',
+        defaultValue: '#7fc75f',
+        contextVariable: ['feature'],
+    },
+    strokeWidth: {
+        type: 'number',
+        description: 'width of the stroked border',
+        defaultValue: 4,
+        contextVariable: ['feature'],
+    },
+    radius: {
+        type: 'number',
+        description: 'radius in pixels of each lollipop body',
+        defaultValue: `jexl:sqrt(max(3, (get(feature,'score')*10)/3.14))`,
+        contextVariable: ['feature'],
+    },
+    caption: {
+        type: 'string',
+        description: 'the tooltip caption displayed when the mouse hovers over a lollipop',
+        defaultValue: `jexl:get(feature,'name')`,
+        contextVariable: ['feature'],
+    },
+    minStickLength: {
+        type: 'number',
+        description: 'minimum lollipop "stick" length, in pixels',
+        defaultValue: 5,
+    },
+    stickColor: {
+        type: 'color',
+        description: 'color of the lollipop stick',
+        defaultValue: 'black',
+        contextVariable: ['feature'],
+    },
+    stickWidth: {
+        type: 'number',
+        description: 'width in pixels of the lollipop stick',
+        defaultValue: 2,
+        contextVariable: ['feature'],
+    },
+    score: {
+        type: 'number',
+        description: 'the "score" of each lollipop, displayed as a number in the center of the circle',
+        defaultValue: `jexl:get(feature,'score')`,
+        contextVariable: ['feature'],
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/esm/LollipopRenderer/configSchema.js.map

@@ -0,0 +1 @@
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package/esm/LollipopRenderer/index.d.ts

@@ -0,0 +1,3 @@
+export { default as ReactComponent } from './components/LollipopRendering';
+export { default as configSchema } from './configSchema';
+export { default } from './LollipopRenderer';

package/esm/LollipopRenderer/index.js

@@ -0,0 +1,4 @@
+export { default as ReactComponent } from './components/LollipopRendering';
+export { default as configSchema } from './configSchema';
+export { default } from './LollipopRenderer';
+//# sourceMappingURL=index.js.map

package/esm/LollipopRenderer/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LollipopRenderer/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,cAAc,EAAE,MAAM,gCAAgC,CAAA;AAC1E,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA;AACxD,OAAO,EAAE,OAAO,EAAE,MAAM,oBAAoB,CAAA"}

package/esm/index.d.ts

@@ -0,0 +1,6 @@
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default class extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+}

package/esm/index.js

@@ -0,0 +1,31 @@
+import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
+import Plugin from '@jbrowse/core/Plugin';
+import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
+import { configSchemaFactory as linearLollipopDisplayConfigSchemaFactory, stateModelFactory as LinearLollipopDisplayStateModelFactory, } from './LinearLollipopDisplay';
+import LollipopRenderer, { configSchema as lollipopRendererConfigSchema, ReactComponent as LollipopRendererReactComponent, } from './LollipopRenderer';
+export default class extends Plugin {
+    constructor() {
+        super(...arguments);
+        this.name = 'LollipopPlugin';
+    }
+    install(pluginManager) {
+        pluginManager.addRendererType(() => new LollipopRenderer({
+            name: 'LollipopRenderer',
+            ReactComponent: LollipopRendererReactComponent,
+            configSchema: lollipopRendererConfigSchema,
+            pluginManager,
+        }));
+        pluginManager.addDisplayType(() => {
+            const configSchema = linearLollipopDisplayConfigSchemaFactory(pluginManager);
+            return new DisplayType({
+                name: 'LinearLollipopDisplay',
+                configSchema,
+                stateModel: LinearLollipopDisplayStateModelFactory(configSchema),
+                trackType: 'LollipopTrack',
+                viewType: 'LinearGenomeView',
+                ReactComponent: BaseLinearDisplayComponent,
+            });
+        });
+    }
+}
+//# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -0,0 +1,56 @@
+{
+  "name": "@jbrowse/plugin-lollipop",
+  "version": "2.6.1",
+  "description": "JBrowse 2 plugin for lollipops",
+  "keywords": [
+    "jbrowse",
+    "jbrowse2"
+  ],
+  "license": "Apache-2.0",
+  "homepage": "https://jbrowse.org",
+  "bugs": "https://github.com/GMOD/jbrowse-components/issues",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/GMOD/jbrowse-components.git",
+    "directory": "plugins/lollipop"
+  },
+  "author": "JBrowse Team",
+  "distMain": "dist/index.js",
+  "srcMain": "src/index.ts",
+  "main": "dist/index.js",
+  "files": [
+    "dist",
+    "src",
+    "esm"
+  ],
+  "scripts": {
+    "build": "npm-run-all build:*",
+    "test": "cd ../..; jest plugins/lollipop",
+    "prepublishOnly": "yarn test",
+    "prepack": "yarn build && yarn useDist",
+    "postpack": "yarn useSrc",
+    "useDist": "node ../../scripts/useDist.js",
+    "useSrc": "node ../../scripts/useSrc.js",
+    "prebuild": "npm run clean",
+    "build:esm": "tsc --build tsconfig.build.esm.json",
+    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "clean": "rimraf dist esm *.tsbuildinfo"
+  },
+  "peerDependencies": {
+    "@jbrowse/core": "^2.0.0",
+    "@jbrowse/plugin-linear-genome-view": "^2.0.0",
+    "@mui/material": "^5.0.0",
+    "mobx": "^6.0.0",
+    "mobx-react": "^7.0.0",
+    "mobx-state-tree": "^5.0.0",
+    "prop-types": "^15.0.0",
+    "react": ">=16.8.0"
+  },
+  "distModule": "esm/index.js",
+  "srcModule": "src/index.ts",
+  "module": "esm/index.js",
+  "publishConfig": {
+    "access": "public"
+  },
+  "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
+}

package/src/LinearLollipopDisplay/configSchema.ts

@@ -0,0 +1,14 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view'
+
+export function configSchemaFactory(pluginManager: PluginManager) {
+  return ConfigurationSchema(
+    'LinearLollipopDisplay',
+    { renderer: pluginManager.pluggableConfigSchemaType('renderer') },
+    {
+      baseConfiguration: baseLinearDisplayConfigSchema,
+      explicitlyTyped: true,
+    },
+  )
+}

package/src/LinearLollipopDisplay/index.ts

@@ -0,0 +1,2 @@
+export { configSchemaFactory } from './configSchema'
+export { stateModelFactory } from './model'

package/src/LinearLollipopDisplay/model.ts

@@ -0,0 +1,40 @@
+import {
+  AnyConfigurationSchemaType,
+  ConfigurationReference,
+} from '@jbrowse/core/configuration'
+import { types } from 'mobx-state-tree'
+import { BaseLinearDisplay } from '@jbrowse/plugin-linear-genome-view'
+
+export function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
+  return types
+    .compose(
+      'LinearLollipopDisplay',
+      BaseLinearDisplay,
+      types.model({
+        type: types.literal('LinearLollipopDisplay'),
+        configuration: ConfigurationReference(configSchema),
+      }),
+    )
+
+    .views(self => {
+      const { renderProps: superRenderProps } = self
+      return {
+        get blockType() {
+          return 'dynamicBlocks'
+        },
+        get renderDelay() {
+          return 500
+        },
+        renderProps() {
+          return {
+            ...superRenderProps(),
+            rpcDriverName: self.rpcDriverName,
+            config: self.configuration.renderer,
+          }
+        },
+        get rendererTypeName() {
+          return self.configuration.renderer.type
+        },
+      }
+    })
+}