@jbrowse/plugin-lollipop 3.6.5 → 4.0.0

package/dist/LollipopRenderer/components/LollipopRendering.js

@@ -1,81 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
-const mobx_react_1 = require("mobx-react");
-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 }),
-    });
-}
-const LollipopRendering = (0, mobx_react_1.observer)(function (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 [client, setClient] = (0, react_1.useState)(false);
-    (0, react_1.useEffect)(() => {
-        setClient(true);
-    }, []);
-    const { regions, bpPerPx, layout, config, features = new Map(), displayModel = {}, } = props;
-    const { selectedFeatureId } = displayModel;
-    const region = regions[0];
-    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 ((0, jsx_runtime_1.jsx)("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, children: client ? ((0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: records.map(layoutRecord => {
-                const feature = features.get(layoutRecord.data.featureId);
-                return ((0, jsx_runtime_1.jsxs)(react_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(Stick_1.default, { ...props, config: config, layoutRecord: layoutRecord, feature: feature }, `stick-${feature.id()}`), (0, jsx_runtime_1.jsx)(Lollipop_1.default, { ...props, layoutRecord: layoutRecord, feature: feature, selectedFeatureId: selectedFeatureId }, `body-${feature.id()}`)] }, feature.id()));
-            }) })) : null }));
-});
-exports.default = LollipopRendering;

package/dist/LollipopRenderer/components/ScoreText.d.ts

@@ -1,14 +0,0 @@
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { 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;
-        };
-    };
-}): import("react/jsx-runtime").JSX.Element | null;

package/dist/LollipopRenderer/components/ScoreText.js

@@ -1,20 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = ScoreText;
-const jsx_runtime_1 = require("react/jsx-runtime");
-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 ((0, jsx_runtime_1.jsx)("text", { style: {
-            pointerEvents: 'none',
-            fontSize: fontHeight,
-            fill: (0, color_1.contrastingTextColor)(innerColor),
-        }, x: anchorX, y: y + radiusPx - fontHeight / 2.4, textAnchor: "middle", dominantBaseline: "hanging", children: scoreString }));
-}

package/dist/LollipopRenderer/components/Stick.d.ts

@@ -1,14 +0,0 @@
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { Feature } from '@jbrowse/core/util';
-declare const Stick: ({ feature, config, layoutRecord: { anchorLocation, y, data: { radiusPx }, }, }: {
-    feature: Feature;
-    config: AnyConfigurationModel;
-    layoutRecord: {
-        anchorLocation: number;
-        y: number;
-        data: {
-            radiusPx: number;
-        };
-    };
-}) => import("react/jsx-runtime").JSX.Element;
-export default Stick;

package/dist/LollipopRenderer/components/Stick.js

@@ -1,9 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const configuration_1 = require("@jbrowse/core/configuration");
-const mobx_react_1 = require("mobx-react");
-const Stick = (0, mobx_react_1.observer)(function Stick({ feature, config, layoutRecord: { anchorLocation, y, data: { radiusPx }, }, }) {
-    return ((0, jsx_runtime_1.jsx)("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 }) }));
-});
-exports.default = Stick;

package/dist/LollipopRenderer/configSchema.d.ts

@@ -1,56 +0,0 @@
-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

@@ -1,58 +0,0 @@
-"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 });

package/dist/LollipopRenderer/index.d.ts

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

package/dist/LollipopRenderer/index.js

@@ -1,17 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = LollipopRendererF;
-const LollipopRenderer_1 = __importDefault(require("./LollipopRenderer"));
-const LollipopRendering_1 = __importDefault(require("./components/LollipopRendering"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-function LollipopRendererF(pluginManager) {
-    pluginManager.addRendererType(() => new LollipopRenderer_1.default({
-        name: 'LollipopRenderer',
-        ReactComponent: LollipopRendering_1.default,
-        configSchema: configSchema_1.default,
-        pluginManager,
-    }));
-}

package/dist/index.d.ts

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

package/dist/index.js

@@ -1,19 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const LinearLollipopDisplay_1 = __importDefault(require("./LinearLollipopDisplay"));
-const LollipopRenderer_1 = __importDefault(require("./LollipopRenderer"));
-class LollipopPlugin extends Plugin_1.default {
-    constructor() {
-        super(...arguments);
-        this.name = 'LollipopPlugin';
-    }
-    install(pluginManager) {
-        (0, LollipopRenderer_1.default)(pluginManager);
-        (0, LinearLollipopDisplay_1.default)(pluginManager);
-    }
-}
-exports.default = LollipopPlugin;

package/esm/LollipopRenderer/FloatingLayoutSession.d.ts

@@ -1,6 +0,0 @@
-import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/LayoutSession';
-import { MultiLayout } from '@jbrowse/core/util/layouts';
-export declare class FloatingLayoutSession extends LayoutSession {
-    makeLayout(): MultiLayout<import("@jbrowse/core/util/layouts").BaseLayout<unknown>, unknown>;
-    layoutIsValid(): boolean;
-}

package/esm/LollipopRenderer/FloatingLayoutSession.js

@@ -1,13 +0,0 @@
-import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/LayoutSession';
-import { MultiLayout } from '@jbrowse/core/util/layouts';
-import { FloatingLayout } from './Layout';
-export class FloatingLayoutSession extends LayoutSession {
-    makeLayout() {
-        const { end, start } = this.props.regions[0];
-        const widthPx = (end - start) / this.props.bpPerPx;
-        return new MultiLayout(FloatingLayout, { width: widthPx });
-    }
-    layoutIsValid() {
-        return false;
-    }
-}