@jbrowse/plugin-lollipop 2.6.1

package/dist/LollipopRenderer/Layout.js

@@ -0,0 +1,116 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.PrecomputedFloatingLayout = exports.FloatingLayout = void 0;
+const configuration_1 = require("@jbrowse/core/configuration");
+const range_1 = require("@jbrowse/core/util/range");
+class FloatingLayout {
+    constructor({ width }) {
+        this.totalHeight = 0;
+        this.items = [];
+        this.layout = new Map();
+        this.layoutDirty = false;
+        if (!width) {
+            throw new Error('width required to make a new FloatingLayout');
+        }
+        this.width = width;
+    }
+    add(uniqueId, anchorLocation, width, height, data) {
+        this.items.push({ uniqueId, anchorLocation, width, height, data });
+        this.layoutDirty = true;
+    }
+    /**
+     * @returns Map of `uniqueId => {x,y,anchorLocation,width,height,data}`
+     */
+    getLayout(configuration) {
+        if (!this.layoutDirty) {
+            return this.layout;
+        }
+        if (!configuration) {
+            throw new Error('configuration object required');
+        }
+        const minY = (0, configuration_1.readConfObject)(configuration, 'minStickLength');
+        // sort them by score ascending, so higher scores will always end up
+        // stacked last (toward the bottom)
+        const sorted = this.items.sort((a, b) => a.data.score - b.data.score);
+        // bump them
+        let maxBottom = 0;
+        const layoutEntries = new Array(sorted.length);
+        for (let i = 0; i < sorted.length; i += 1) {
+            const currentItem = sorted[i];
+            const { anchorLocation, width, height } = currentItem;
+            const start = anchorLocation - width / 2;
+            const end = start + width;
+            let top = minY;
+            let bottom = top + height;
+            // figure out how far down to put it
+            for (let j = 0; j < i; j += 1) {
+                const [, previouslyLaidOutItem] = layoutEntries[j];
+                const { x: prevStart, y: prevTop, width: prevWidth, height: prevHeight, } = previouslyLaidOutItem;
+                const prevEnd = prevStart + prevWidth;
+                const prevBottom = prevTop + prevHeight;
+                if ((0, range_1.doesIntersect2)(prevStart, prevEnd, start, end) &&
+                    (0, range_1.doesIntersect2)(prevTop, prevBottom, top, bottom)) {
+                    // bump this one to the bottom of the previous one
+                    top = prevBottom;
+                    bottom = top + height;
+                    j = -1; // we need to check all of them again after bumping
+                }
+            }
+            // record the entry and update the maxBottom
+            layoutEntries[i] = [
+                currentItem.uniqueId,
+                { ...currentItem, x: start, y: top },
+            ];
+            if (bottom > maxBottom) {
+                maxBottom = bottom;
+            }
+        }
+        // try to tile them left to right all at the same level
+        // if they don't fit, try to alternate them on 2 levels, then 3
+        this.totalHeight = maxBottom;
+        this.layout = new Map(layoutEntries);
+        this.layoutDirty = false;
+        return this.layout;
+    }
+    getTotalHeight() {
+        if (this.layoutDirty) {
+            throw new Error('getTotalHeight does not work when the layout is dirty.');
+        }
+        return this.totalHeight;
+    }
+    serializeRegion() {
+        return this.toJSON();
+    }
+    toJSON() {
+        if (this.layoutDirty) {
+            throw new Error('toJSON does not work when the layout is dirty.');
+        }
+        return { pairs: [...this.getLayout()], totalHeight: this.getTotalHeight() };
+    }
+    static fromJSON() {
+        throw new Error('not supported');
+    }
+}
+exports.FloatingLayout = FloatingLayout;
+class PrecomputedFloatingLayout {
+    constructor({ pairs, totalHeight, }) {
+        this.layout = new Map(pairs);
+        this.totalHeight = totalHeight;
+    }
+    add(uniqueId) {
+        if (!this.layout.has(uniqueId)) {
+            throw new Error(`layout error, precomputed layout is missing ${uniqueId}`);
+        }
+    }
+    getLayout() {
+        return this.layout;
+    }
+    getTotalHeight() {
+        return this.totalHeight;
+    }
+    static fromJSON(json) {
+        return new PrecomputedFloatingLayout(json);
+    }
+}
+exports.PrecomputedFloatingLayout = PrecomputedFloatingLayout;
+//# sourceMappingURL=Layout.js.map

package/dist/LollipopRenderer/Layout.js.map

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package/dist/LollipopRenderer/LollipopRenderer.d.ts

@@ -0,0 +1,13 @@
+export default class _default extends BoxRendererType {
+    createSession(args: any): FloatingLayoutSession;
+    deserializeLayoutInClient(json: any): PrecomputedFloatingLayout;
+}
+import BoxRendererType from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+declare class FloatingLayoutSession extends LayoutSession {
+    makeLayout(): MultiLayout<import("@jbrowse/core/util/layouts").BaseLayout<any>, any>;
+    layoutIsValid(): boolean;
+}
+import { PrecomputedFloatingLayout } from './Layout';
+import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import MultiLayout from '@jbrowse/core/util/layouts/MultiLayout';
+export {};

package/dist/LollipopRenderer/LollipopRenderer.js

@@ -0,0 +1,52 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const BoxRendererType_1 = __importStar(require("@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType"));
+const MultiLayout_1 = __importDefault(require("@jbrowse/core/util/layouts/MultiLayout"));
+const Layout_1 = require("./Layout");
+class FloatingLayoutSession extends BoxRendererType_1.LayoutSession {
+    makeLayout() {
+        'sequenceAdapter';
+        const { end, start } = this.regions[0];
+        const widthPx = (end - start) / this.bpPerPx;
+        return new MultiLayout_1.default(Layout_1.FloatingLayout, { width: widthPx });
+    }
+    layoutIsValid( /* layout */) {
+        return false; // layout.left layout.width === this.width
+    }
+}
+class default_1 extends BoxRendererType_1.default {
+    createSession(args) {
+        return new FloatingLayoutSession(args);
+    }
+    deserializeLayoutInClient(json) {
+        return new Layout_1.PrecomputedFloatingLayout(json);
+    }
+}
+exports.default = default_1;
+//# sourceMappingURL=LollipopRenderer.js.map

package/dist/LollipopRenderer/LollipopRenderer.js.map

@@ -0,0 +1 @@
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package/dist/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/dist/LollipopRenderer/components/Lollipop.js

@@ -0,0 +1,63 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const configuration_1 = require("@jbrowse/core/configuration");
+const mobx_react_1 = require("mobx-react");
+const ScoreText_1 = __importDefault(require("./ScoreText"));
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+exports.default = (0, mobx_react_1.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: (0, configuration_1.readConfObject)(config, 'strokeColor', { feature }),
+    };
+    if (String(selectedFeatureId) === String(feature.id())) {
+        styleOuter.fill = 'red';
+    }
+    const styleInner = {
+        fill: (0, configuration_1.readConfObject)(config, 'innerColor', { feature }),
+    };
+    const strokeWidth = (0, configuration_1.readConfObject)(config, 'strokeWidth', { feature });
+    return (react_1.default.createElement("g", { "data-testid": feature.id() },
+        react_1.default.createElement("title", null, (0, configuration_1.readConfObject)(config, 'caption', { feature })),
+        react_1.default.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_1.default.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_1.default.createElement(ScoreText_1.default, { feature: feature, config: config, layoutRecord: layoutRecord })));
+});
+//# sourceMappingURL=Lollipop.js.map

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

@@ -0,0 +1 @@
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package/dist/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/dist/LollipopRenderer/components/LollipopRendering.js

@@ -0,0 +1,80 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
+const mobx_react_1 = require("mobx-react");
+// locals
+const Lollipop_1 = __importDefault(require("./Lollipop"));
+const Stick_1 = __importDefault(require("./Stick"));
+function layoutFeat(args) {
+    const { feature, bpPerPx, config, region, layout } = args;
+    const centerBp = Math.abs(feature.get('end') + feature.get('start')) / 2;
+    const centerPx = (0, util_1.bpToPx)(centerBp, region, bpPerPx);
+    const radiusPx = (0, configuration_1.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: (0, configuration_1.readConfObject)(args.config, 'score', { feature }),
+    });
+}
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+exports.default = (0, mobx_react_1.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_1.default.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_1.default.createElement(react_1.default.Fragment, { key: feature.id() },
+            react_1.default.createElement(Stick_1.default, { ...props, config: config, layoutRecord: layoutRecord, feature: feature, key: `stick-${feature.id()}` }),
+            react_1.default.createElement(Lollipop_1.default, { ...props, layoutRecord: layoutRecord, feature: feature, key: `body-${feature.id()}`, selectedFeatureId: selectedFeatureId })));
+    })));
+});
+//# sourceMappingURL=LollipopRendering.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"LollipopRendering.js","sourceRoot":"","sources":["../../../src/LollipopRenderer/components/LollipopRendering.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,+DAGoC;AACpC,6CAA4D;AAC5D,2CAAqC;AAErC,SAAS;AACT,0DAAiC;AACjC,oDAA2B;AAE3B,SAAS,UAAU,CAAC,IAMnB;IACC,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;IAEzD,MAAM,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,CAAA;IACxE,MAAM,QAAQ,GAAG,IAAA,aAAM,EAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,CAAC,CAAA;IAClD,MAAM,QAAQ,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,QAAQ,EAAE,EAAE,OAAO,EAAE,CAAC,CAAA;IAE9D,IAAI,CAAC,QAAQ,EAAE;QACb,OAAO,CAAC,KAAK,CACX,IAAI,KAAK,CACP,mBAAmB,QAAQ,2BAA2B,OAAO,CAAC,EAAE,EAAE,EAAE,CACrE,CACF,CAAA;KACF;IACD,MAAM,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,EAAE,EAAE,QAAQ,EAAE,QAAQ,GAAG,CAAC,EAAE,QAAQ,GAAG,CAAC,EAAE;QAC7D,SAAS,EAAE,OAAO,CAAC,EAAE,EAAE;QACvB,OAAO,EAAE,QAAQ;QACjB,QAAQ;QACR,KAAK,EAAE,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,OAAO,EAAE,EAAE,OAAO,EAAE,CAAC;KACzD,CAAC,CAAA;AACJ,CAAC;AAED,8DAA8D;AAC9D,kBAAe,IAAA,qBAAQ,EAAC,SAAS,iBAAiB,CAAC,KAA0B;IAC3E,MAAM,WAAW,GAAG,CAAC,KAAuB,EAAE,EAAE;QAC9C,MAAM,EAAE,WAAW,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;QACtC,OAAO,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAG,KAAK,CAAC,CAAA;IACzB,CAAC,CAAA;IAED,MAAM,SAAS,GAAG,CAAC,KAAuB,EAAE,EAAE;QAC5C,MAAM,EAAE,SAAS,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;QACpC,OAAO,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAG,KAAK,CAAC,CAAA;IACzB,CAAC,CAAA;IAED,MAAM,YAAY,GAAG,CAAC,KAA0C,EAAE,EAAE;QAClE,MAAM,EAAE,YAAY,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;QACvC,OAAO,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAG,KAAK,CAAC,CAAA;IACzB,CAAC,CAAA;IAED,MAAM,YAAY,GAAG,CAAC,KAA0C,EAAE,EAAE;QAClE,MAAM,EAAE,YAAY,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;QACvC,OAAO,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAG,KAAK,CAAC,CAAA;IACzB,CAAC,CAAA;IAED,MAAM,WAAW,GAAG,CAAC,KAAuB,EAAE,EAAE;QAC9C,MAAM,EAAE,WAAW,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;QACtC,OAAO,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAG,KAAK,CAAC,CAAA;IACzB,CAAC,CAAA;IAED,MAAM,UAAU,GAAG,CAAC,KAAuB,EAAE,EAAE;QAC7C,MAAM,EAAE,UAAU,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;QACrC,OAAO,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAG,KAAK,CAAC,CAAA;IACzB,CAAC,CAAA;IAED,MAAM,OAAO,GAAG,CAAC,KAAuB,EAAE,EAAE;QAC1C,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;QAClC,OAAO,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAG,KAAK,CAAC,CAAA;IACzB,CAAC,CAAA;IAED,MAAM,EACJ,OAAO,EACP,OAAO,EACP,MAAM,EACN,MAAM,EACN,QAAQ,GAAG,IAAI,GAAG,EAAE,EACpB,YAAY,GAAG,EAAE,GAClB,GAAG,KAAK,CAAA;IACT,MAAM,EAAE,iBAAiB,EAAE,GAAG,YAAY,CAAA;IAC1C,MAAM,CAAC,MAAM,CAAC,GAAG,OAAO,CAAA;IACxB,KAAK,MAAM,OAAO,IAAI,QAAQ,CAAC,MAAM,EAAE,EAAE;QACvC,UAAU,CAAC;YACT,OAAO;YACP,OAAO;YACP,MAAM;YACN,MAAM;YACN,MAAM;SACP,CAAC,CAAA;KACH;IAED,MAAM,KAAK,GAAG,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;IACnD,MAAM,OAAO,GAAG,CAAC,GAAG,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC,MAAM,EAAE,CAAC,CAAA;IACtD,MAAM,MAAM,GAAG,MAAM,CAAC,cAAc,EAAE,CAAA;IAEtC,OAAO,CACL,uCACE,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE,EAC/B,WAAW,EAAE,WAAW,EACxB,SAAS,EAAE,SAAS,EACpB,YAAY,EAAE,YAAY,EAC1B,YAAY,EAAE,YAAY,EAC1B,WAAW,EAAE,WAAW,EACxB,UAAU,EAAE,UAAU,EACtB,OAAO,EAAE,YAAY,EACrB,MAAM,EAAE,YAAY,EACpB,OAAO,EAAE,OAAO,IAEf,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE;QAC1B,MAAM,OAAO,GAAG,QAAQ,CAAC,GAAG,CAAC,YAAY,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;QACzD,OAAO,CACL,8BAAC,eAAK,CAAC,QAAQ,IAAC,GAAG,EAAE,OAAO,CAAC,EAAE,EAAE;YAC/B,8BAAC,eAAK,OACA,KAAK,EACT,MAAM,EAAE,MAAM,EACd,YAAY,EAAE,YAAY,EAC1B,OAAO,EAAE,OAAO,EAChB,GAAG,EAAE,SAAS,OAAO,CAAC,EAAE,EAAE,EAAE,GAC5B;YACF,8BAAC,kBAAQ,OACH,KAAK,EACT,YAAY,EAAE,YAAY,EAC1B,OAAO,EAAE,OAAO,EAChB,GAAG,EAAE,QAAQ,OAAO,CAAC,EAAE,EAAE,EAAE,EAC3B,iBAAiB,EAAE,iBAAiB,GACpC,CACa,CAClB,CAAA;IACH,CAAC,CAAC,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA"}

package/dist/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/dist/LollipopRenderer/components/ScoreText.js

@@ -0,0 +1,20 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const configuration_1 = require("@jbrowse/core/configuration");
+const color_1 = require("@jbrowse/core/util/color");
+function ScoreText({ feature, config, layoutRecord: { y, data: { anchorX, radiusPx, score }, }, }) {
+    const innerColor = (0, configuration_1.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_1.default.createElement("text", { style: { fontSize: fontHeight, fill: (0, color_1.contrastingTextColor)(innerColor) }, x: anchorX, y: y + radiusPx - fontHeight / 2.4, textAnchor: "middle", dominantBaseline: "hanging" }, scoreString));
+}
+exports.default = ScoreText;
+//# sourceMappingURL=ScoreText.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"ScoreText.js","sourceRoot":"","sources":["../../../src/LollipopRenderer/components/ScoreText.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,+DAGoC;AACpC,oDAA+D;AAG/D,SAAwB,SAAS,CAAC,EAChC,OAAO,EACP,MAAM,EACN,YAAY,EAAE,EACZ,CAAC,EACD,IAAI,EAAE,EAAE,OAAO,EAAE,QAAQ,EAAE,KAAK,EAAE,GACnC,GAQF;IACC,MAAM,UAAU,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,YAAY,EAAE,EAAE,OAAO,EAAE,CAAC,CAAA;IAEpE,MAAM,WAAW,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,SAAS,GAAG,CAAC,QAAQ,GAAG,CAAC,CAAC,GAAG,WAAW,CAAC,MAAM,CAAA;IACrD,MAAM,UAAU,GAAG,SAAS,GAAG,GAAG,CAAA;IAClC,IAAI,UAAU,GAAG,EAAE,EAAE;QACnB,OAAO,IAAI,CAAA;KACZ;IACD,OAAO,CACL,wCACE,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE,IAAI,EAAE,IAAA,4BAAoB,EAAC,UAAU,CAAC,EAAE,EACvE,CAAC,EAAE,OAAO,EACV,CAAC,EAAE,CAAC,GAAG,QAAQ,GAAG,UAAU,GAAG,GAAG,EAClC,UAAU,EAAC,QAAQ,EACnB,gBAAgB,EAAC,SAAS,IAEzB,WAAW,CACP,CACR,CAAA;AACH,CAAC;AAlCD,4BAkCC"}

package/dist/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/dist/LollipopRenderer/components/Stick.js

@@ -0,0 +1,12 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const configuration_1 = require("@jbrowse/core/configuration");
+const mobx_react_1 = require("mobx-react");
+exports.default = (0, mobx_react_1.observer)(function Stick({ feature, config, layoutRecord: { anchorLocation, y, data: { radiusPx }, }, }) {
+    return (react_1.default.createElement("line", { x1: anchorLocation, y1: 0, x2: anchorLocation, y2: y + 2 * radiusPx, stroke: (0, configuration_1.readConfObject)(config, 'stickColor', { feature }), strokeWidth: (0, configuration_1.readConfObject)(config, 'stickWidth', { feature }) }));
+});
+//# sourceMappingURL=Stick.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"Stick.js","sourceRoot":"","sources":["../../../src/LollipopRenderer/components/Stick.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,+DAGoC;AACpC,2CAAqC;AAGrC,kBAAe,IAAA,qBAAQ,EAAC,SAAS,KAAK,CAAC,EACrC,OAAO,EACP,MAAM,EACN,YAAY,EAAE,EACZ,cAAc,EACd,CAAC,EACD,IAAI,EAAE,EAAE,QAAQ,EAAE,GACnB,GASF;IACC,OAAO,CACL,wCACE,EAAE,EAAE,cAAc,EAClB,EAAE,EAAE,CAAC,EACL,EAAE,EAAE,cAAc,EAClB,EAAE,EAAE,CAAC,GAAG,CAAC,GAAG,QAAQ,EACpB,MAAM,EAAE,IAAA,8BAAc,EAAC,MAAM,EAAE,YAAY,EAAE,EAAE,OAAO,EAAE,CAAC,EACzD,WAAW,EAAE,IAAA,8BAAc,EAAC,MAAM,EAAE,YAAY,EAAE,EAAE,OAAO,EAAE,CAAC,GAC9D,CACH,CAAA;AACH,CAAC,CAAC,CAAA"}

package/dist/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/dist/LollipopRenderer/configSchema.js

@@ -0,0 +1,59 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+exports.default = (0, configuration_1.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/dist/LollipopRenderer/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LollipopRenderer/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,kBAAkB,EAClB;IACE,WAAW,EAAE;QACX,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,kCAAkC;QAC/C,YAAY,EAAE,OAAO;QACrB,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IACD,UAAU,EAAE;QACV,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,kCAAkC;QAC/C,YAAY,EAAE,SAAS;QACvB,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IACD,WAAW,EAAE;QACX,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,6BAA6B;QAC1C,YAAY,EAAE,CAAC;QACf,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IACD,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,wCAAwC;QACrD,YAAY,EAAE,mDAAmD;QACjE,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IACD,OAAO,EAAE;QACP,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,qEAAqE;QACvE,YAAY,EAAE,0BAA0B;QACxC,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IACD,cAAc,EAAE;QACd,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,4CAA4C;QACzD,YAAY,EAAE,CAAC;KAChB;IACD,UAAU,EAAE;QACV,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,6BAA6B;QAC1C,YAAY,EAAE,OAAO;QACrB,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IACD,UAAU,EAAE;QACV,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,uCAAuC;QACpD,YAAY,EAAE,CAAC;QACf,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IACD,KAAK,EAAE;QACL,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,iFAAiF;QACnF,YAAY,EAAE,2BAA2B;QACzC,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/dist/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/dist/LollipopRenderer/index.js

@@ -0,0 +1,13 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = exports.configSchema = exports.ReactComponent = void 0;
+var LollipopRendering_1 = require("./components/LollipopRendering");
+Object.defineProperty(exports, "ReactComponent", { enumerable: true, get: function () { return __importDefault(LollipopRendering_1).default; } });
+var configSchema_1 = require("./configSchema");
+Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_1).default; } });
+var LollipopRenderer_1 = require("./LollipopRenderer");
+Object.defineProperty(exports, "default", { enumerable: true, get: function () { return __importDefault(LollipopRenderer_1).default; } });
+//# sourceMappingURL=index.js.map

package/dist/LollipopRenderer/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LollipopRenderer/index.ts"],"names":[],"mappings":";;;;;;AAAA,oEAA0E;AAAjE,oIAAA,OAAO,OAAkB;AAClC,+CAAwD;AAA/C,6HAAA,OAAO,OAAgB;AAChC,uDAA4C;AAAnC,4HAAA,OAAO,OAAA"}

package/dist/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;
+}