@jbrowse/plugin-wiggle 2.0.0 → 2.1.2

package/dist/MultiLinearWiggleDisplay/components/Tooltip.js

@@ -0,0 +1,49 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.Tooltip = void 0;
+const react_1 = __importDefault(require("react"));
+const mobx_react_1 = require("mobx-react");
+// locals
+const util_1 = require("../../util");
+const Tooltip_1 = __importDefault(require("../../Tooltip"));
+exports.Tooltip = Tooltip_1.default;
+const en = (n) => n.toLocaleString('en-US');
+const TooltipContents = react_1.default.forwardRef(({ model, feature }, ref) => {
+    const start = feature.get('start');
+    const end = feature.get('end');
+    const refName = feature.get('refName');
+    const coord = start === end ? en(start) : `${en(start)}..${en(end)}`;
+    const sources = feature.get('sources');
+    const source = feature.get('source');
+    const summary = feature.get('summary');
+    const obj = Object.fromEntries(model.sources.map(ent => [ent.name, ent]));
+    return (react_1.default.createElement("div", { ref: ref },
+        [refName, coord].filter(f => !!f).join(':'),
+        react_1.default.createElement("br", null),
+        sources ? (react_1.default.createElement("table", null,
+            react_1.default.createElement("thead", null,
+                react_1.default.createElement("tr", null,
+                    react_1.default.createElement("th", null, "color"),
+                    react_1.default.createElement("th", null, "source"),
+                    react_1.default.createElement("th", null, "score"))),
+            react_1.default.createElement("tbody", null, Object.entries(sources).map(([source, data]) => {
+                var _a;
+                return (react_1.default.createElement("tr", { key: source },
+                    react_1.default.createElement("td", { style: { background: (_a = obj[source]) === null || _a === void 0 ? void 0 : _a.color } }, " "),
+                    react_1.default.createElement("td", null, source),
+                    react_1.default.createElement("td", null, (0, util_1.toP)(data.score))));
+            })))) : (react_1.default.createElement("span", null,
+            source,
+            ' ',
+            summary
+                ? `min:${(0, util_1.toP)(feature.get('minScore'))} avg:${(0, util_1.toP)(feature.get('score'))} max:${(0, util_1.toP)(feature.get('maxScore'))}`
+                : (0, util_1.toP)(feature.get('score'))))));
+});
+const WiggleTooltip = (0, mobx_react_1.observer)((props) => {
+    return react_1.default.createElement(Tooltip_1.default, { useClientY: true, TooltipContents: TooltipContents, ...props });
+});
+exports.default = WiggleTooltip;
+//# sourceMappingURL=Tooltip.js.map

package/dist/MultiLinearWiggleDisplay/components/Tooltip.js.map

@@ -0,0 +1 @@
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package/dist/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.d.ts

@@ -0,0 +1,13 @@
+/// <reference types="react" />
+import { WiggleDisplayModel } from '../models/model';
+import YScaleBar from './YScaleBar';
+export declare const StatBars: (props: {
+    model: WiggleDisplayModel;
+    orientation?: string;
+    exportSVG?: boolean;
+}) => JSX.Element | null;
+declare const LinearWiggleDisplay: (props: {
+    model: WiggleDisplayModel;
+}) => JSX.Element;
+export default LinearWiggleDisplay;
+export { YScaleBar };

package/dist/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.js

@@ -0,0 +1,105 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.YScaleBar = exports.StatBars = void 0;
+const react_1 = __importDefault(require("react"));
+const util_1 = require("@jbrowse/core/util");
+const configuration_1 = require("@jbrowse/core/configuration");
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+const mobx_react_1 = require("mobx-react");
+const YScaleBar_1 = __importDefault(require("./YScaleBar"));
+exports.YScaleBar = YScaleBar_1.default;
+const trackLabelFontSize = 12.8;
+function getOffset(model) {
+    const { prefersOffset } = model;
+    const { trackLabels } = (0, util_1.getContainingView)(model);
+    const track = (0, util_1.getContainingTrack)(model);
+    const trackName = (0, configuration_1.getConf)(track, 'name');
+    return trackLabels === 'overlapping' && !prefersOffset
+        ? (0, util_1.measureText)(trackName, trackLabelFontSize) + 100
+        : 10;
+}
+const Wrapper = (0, mobx_react_1.observer)(({ children, model, exportSVG, }) => {
+    if (exportSVG) {
+        return react_1.default.createElement(react_1.default.Fragment, null, children);
+    }
+    else {
+        const { height } = model;
+        return (react_1.default.createElement("svg", { style: {
+                position: 'absolute',
+                top: 0,
+                left: 0,
+                pointerEvents: 'none',
+                height,
+                width: 1800,
+            } }, children));
+    }
+});
+const RectBg = (props) => {
+    const { color = 'rgb(255,255,255,0.8)' } = props;
+    return react_1.default.createElement("rect", { ...props, fill: color });
+};
+const ScoreLegend = (0, mobx_react_1.observer)(({ model }) => {
+    const { ticks, scaleType } = model;
+    const { width } = (0, util_1.getContainingView)(model);
+    const legend = `[${ticks.values[0]}-${ticks.values[1]}]` +
+        (scaleType === 'log' ? ' (log scale)' : '');
+    const len = (0, util_1.measureText)(legend, 14);
+    const padding = 25;
+    const xpos = width - len - padding;
+    return (react_1.default.createElement(react_1.default.Fragment, null,
+        react_1.default.createElement(RectBg, { y: 0, x: xpos, width: len + 6, height: 16 }),
+        react_1.default.createElement("text", { y: 13, x: xpos }, legend)));
+});
+const ColorLegend = (0, mobx_react_1.observer)(({ model, rowHeight, labelWidth, exportSVG, }) => {
+    const { needsCustomLegend, needsScalebar, needsFullHeightScalebar, rowHeightTooSmallForScalebar, renderColorBoxes, sources, } = model;
+    const svgFontSize = Math.min(rowHeight, 12);
+    const canDisplayLabel = rowHeight > 11;
+    const colorBoxWidth = renderColorBoxes ? 15 : 0;
+    const legendWidth = labelWidth + colorBoxWidth + 5;
+    const svgOffset = exportSVG ? 10 : 0;
+    const extraOffset = svgOffset || (needsScalebar && !rowHeightTooSmallForScalebar ? 50 : 0);
+    return sources ? (react_1.default.createElement(react_1.default.Fragment, null,
+        /* 0.25 for hanging letters like g */
+        needsFullHeightScalebar ? (react_1.default.createElement(RectBg, { y: 0, x: extraOffset, width: legendWidth, height: (sources.length + 0.25) * rowHeight })) : null,
+        sources.map((source, idx) => {
+            const boxHeight = Math.min(20, rowHeight);
+            return (react_1.default.createElement(react_1.default.Fragment, { key: source.name + '-' + idx },
+                !needsFullHeightScalebar ? (react_1.default.createElement(RectBg, { y: idx * rowHeight + 1, x: extraOffset, width: legendWidth, height: boxHeight })) : null,
+                source.color ? (react_1.default.createElement(RectBg, { y: idx * rowHeight + 1, x: extraOffset, width: colorBoxWidth, height: needsCustomLegend ? rowHeight : boxHeight, color: source.color })) : null,
+                canDisplayLabel ? (react_1.default.createElement("text", { y: idx * rowHeight + 13, x: extraOffset + colorBoxWidth + 2, fontSize: svgFontSize }, source.name)) : null));
+        }))) : null;
+});
+exports.StatBars = (0, mobx_react_1.observer)((props) => {
+    const { model, orientation, exportSVG } = props;
+    const { stats, needsCustomLegend, needsFullHeightScalebar, rowHeightTooSmallForScalebar, rowHeight, sources, ticks, } = model;
+    const svgFontSize = Math.min(rowHeight, 12);
+    const canDisplayLabel = rowHeight > 11;
+    const { width: viewWidth } = (0, util_1.getContainingView)(model);
+    const minWidth = 20;
+    const ready = stats && sources;
+    if (!ready) {
+        return null;
+    }
+    const labelWidth = Math.max(...(sources
+        .map(s => (0, util_1.measureText)(s.name, svgFontSize))
+        .map(width => (canDisplayLabel ? width : minWidth)) || [0]));
+    return (react_1.default.createElement(Wrapper, { ...props }, needsFullHeightScalebar ? (react_1.default.createElement(react_1.default.Fragment, null,
+        react_1.default.createElement("g", { transform: `translate(${!exportSVG ? getOffset(model) : 0},0)` },
+            react_1.default.createElement(YScaleBar_1.default, { model: model, orientation: orientation })),
+        react_1.default.createElement("g", { transform: `translate(${viewWidth - labelWidth - 100},0)` },
+            react_1.default.createElement(ColorLegend, { exportSVG: exportSVG, model: model, rowHeight: 12, labelWidth: labelWidth })))) : (react_1.default.createElement(react_1.default.Fragment, null,
+        react_1.default.createElement(ColorLegend, { exportSVG: exportSVG, model: model, rowHeight: model.rowHeight, labelWidth: labelWidth }),
+        rowHeightTooSmallForScalebar || needsCustomLegend ? (react_1.default.createElement(ScoreLegend, { ...props })) : (sources.map((_source, idx) => (react_1.default.createElement("g", { transform: `translate(0 ${rowHeight * idx})`, key: JSON.stringify(ticks) + '-' + idx },
+            react_1.default.createElement(YScaleBar_1.default, { model: model, orientation: orientation })))))))));
+});
+const LinearWiggleDisplay = (0, mobx_react_1.observer)((props) => {
+    const { model } = props;
+    return (react_1.default.createElement("div", null,
+        react_1.default.createElement(plugin_linear_genome_view_1.BaseLinearDisplayComponent, { ...props }),
+        react_1.default.createElement(exports.StatBars, { model: model })));
+});
+exports.default = LinearWiggleDisplay;
+//# sourceMappingURL=WiggleDisplayComponent.js.map

package/dist/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.js.map

@@ -0,0 +1 @@
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package/dist/MultiLinearWiggleDisplay/components/YScaleBar.d.ts

@@ -0,0 +1,7 @@
+/// <reference types="react" />
+import { WiggleDisplayModel } from '../models/model';
+declare const YScaleBar: ({ model, orientation, }: {
+    model: WiggleDisplayModel;
+    orientation?: string | undefined;
+}) => JSX.Element | null;
+export default YScaleBar;

package/dist/MultiLinearWiggleDisplay/components/YScaleBar.js

@@ -0,0 +1,14 @@
+"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 mobx_react_1 = require("mobx-react");
+const react_d3_axis_mod_1 = require("react-d3-axis-mod");
+const YScaleBar = (0, mobx_react_1.observer)(({ model, orientation, }) => {
+    const { ticks } = model;
+    return ticks ? (react_1.default.createElement(react_d3_axis_mod_1.Axis, { ...ticks, shadow: 2, format: (n) => n, style: { orient: orientation === 'left' ? react_d3_axis_mod_1.LEFT : react_d3_axis_mod_1.RIGHT } })) : null;
+});
+exports.default = YScaleBar;
+//# sourceMappingURL=YScaleBar.js.map

package/dist/MultiLinearWiggleDisplay/components/YScaleBar.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"YScaleBar.js","sourceRoot":"","sources":["../../../src/MultiLinearWiggleDisplay/components/YScaleBar.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AACrC,yDAAqD;AAGrD,MAAM,SAAS,GAAG,IAAA,qBAAQ,EACxB,CAAC,EACC,KAAK,EACL,WAAW,GAIZ,EAAE,EAAE;IACH,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,OAAO,KAAK,CAAC,CAAC,CAAC,CACb,8BAAC,wBAAI,OACC,KAAK,EACT,MAAM,EAAE,CAAC,EACT,MAAM,EAAE,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,EACxB,KAAK,EAAE,EAAE,MAAM,EAAE,WAAW,KAAK,MAAM,CAAC,CAAC,CAAC,wBAAI,CAAC,CAAC,CAAC,yBAAK,EAAE,GACxD,CACH,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CACF,CAAA;AACD,kBAAe,SAAS,CAAA"}

package/dist/MultiLinearWiggleDisplay/components/util.d.ts

@@ -0,0 +1,10 @@
+export declare function moveUp(arr: {
+    name: string;
+}[], sel: string[], by?: number): {
+    name: string;
+}[];
+export declare function moveDown(arr: {
+    name: string;
+}[], sel: string[], by?: number): {
+    name: string;
+}[];

package/dist/MultiLinearWiggleDisplay/components/util.js

@@ -0,0 +1,36 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.moveDown = exports.moveUp = void 0;
+function moveUp(arr, sel, by = 1) {
+    const idxs = sel
+        .map(l => arr.findIndex(v => v.name === l))
+        .sort((a, b) => a - b);
+    let lastIdx = 0;
+    for (let i = 0; i < idxs.length; i++) {
+        const old = idxs[i];
+        const idx = Math.max(lastIdx, old - by);
+        if (idx >= lastIdx) {
+            arr.splice(idx, 0, arr.splice(old, 1)[0]);
+        }
+        lastIdx = lastIdx + 1;
+    }
+    return arr;
+}
+exports.moveUp = moveUp;
+function moveDown(arr, sel, by = 1) {
+    const idxs = sel
+        .map(l => arr.findIndex(v => v.name === l))
+        .sort((a, b) => b - a);
+    let lastIdx = arr.length - 1;
+    for (let i = 0; i < idxs.length; i++) {
+        const old = idxs[i];
+        const idx = Math.min(lastIdx, old + by);
+        if (idx <= lastIdx) {
+            arr.splice(idx, 0, arr.splice(old, 1)[0]);
+        }
+        lastIdx = lastIdx - 1;
+    }
+    return arr;
+}
+exports.moveDown = moveDown;
+//# sourceMappingURL=util.js.map

package/dist/MultiLinearWiggleDisplay/components/util.js.map

@@ -0,0 +1 @@
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package/dist/MultiLinearWiggleDisplay/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/dist/MultiLinearWiggleDisplay/index.js

@@ -0,0 +1,23 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
+const configSchema_1 = __importDefault(require("./models/configSchema"));
+const model_1 = __importDefault(require("./models/model"));
+const WiggleDisplayComponent_1 = __importDefault(require("./components/WiggleDisplayComponent"));
+exports.default = (pluginManager) => {
+    pluginManager.addDisplayType(() => {
+        const configSchema = (0, configSchema_1.default)(pluginManager);
+        return new DisplayType_1.default({
+            name: 'MultiLinearWiggleDisplay',
+            configSchema,
+            stateModel: (0, model_1.default)(pluginManager, configSchema),
+            trackType: 'MultiQuantitativeTrack',
+            viewType: 'LinearGenomeView',
+            ReactComponent: WiggleDisplayComponent_1.default,
+        });
+    });
+};
+//# sourceMappingURL=index.js.map

package/dist/MultiLinearWiggleDisplay/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/MultiLinearWiggleDisplay/index.ts"],"names":[],"mappings":";;;;;AACA,kGAAyE;AAEzE,yEAAuD;AACvD,2DAAyC;AACzC,iGAAgE;AAEhE,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,sBAAmB,EAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,0BAA0B;YAChC,YAAY;YACZ,UAAU,EAAE,IAAA,eAAY,EAAC,aAAa,EAAE,YAAY,CAAC;YACrD,SAAS,EAAE,wBAAwB;YACnC,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAd,gCAAc;SACf,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/dist/MultiLinearWiggleDisplay/models/configSchema.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function WiggleConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/dist/MultiLinearWiggleDisplay/models/configSchema.js

@@ -0,0 +1,77 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+const mobx_state_tree_1 = require("mobx-state-tree");
+function WiggleConfigFactory(pluginManager) {
+    const MultiXYPlotRendererConfigSchema = pluginManager.getRendererType('MultiXYPlotRenderer').configSchema;
+    const MultiDensityRendererConfigSchema = pluginManager.getRendererType('MultiDensityRenderer').configSchema;
+    const MultiRowXYPlotRendererConfigSchema = pluginManager.getRendererType('MultiRowXYPlotRenderer').configSchema;
+    const MultiLineRendererConfigSchema = pluginManager.getRendererType('MultiLineRenderer').configSchema;
+    const MultiRowLineRendererConfigSchema = pluginManager.getRendererType('MultiRowLineRenderer').configSchema;
+    return (0, configuration_1.ConfigurationSchema)('MultiLinearWiggleDisplay', {
+        autoscale: {
+            type: 'stringEnum',
+            defaultValue: 'local',
+            model: mobx_state_tree_1.types.enumeration('Autoscale type', [
+                'global',
+                'local',
+                'globalsd',
+                'localsd',
+                'zscore',
+            ]),
+            description: 'global/local using their min/max values or w/ standard deviations (globalsd/localsd)',
+        },
+        minimalTicks: {
+            type: 'boolean',
+            defaultValue: false,
+            description: 'use the minimal amount of ticks',
+        },
+        minScore: {
+            type: 'number',
+            defaultValue: Number.MIN_VALUE,
+            description: 'minimum value for the y-scale',
+        },
+        maxScore: {
+            type: 'number',
+            description: 'maximum value for the y-scale',
+            defaultValue: Number.MAX_VALUE,
+        },
+        numStdDev: {
+            type: 'number',
+            description: 'number of standard deviations to use for autoscale types globalsd or localsd',
+            defaultValue: 3,
+        },
+        scaleType: {
+            type: 'stringEnum',
+            model: mobx_state_tree_1.types.enumeration('Scale type', ['linear', 'log']),
+            description: 'The type of scale to use',
+            defaultValue: 'linear',
+        },
+        inverted: {
+            type: 'boolean',
+            description: 'draw upside down',
+            defaultValue: false,
+        },
+        defaultRendering: {
+            type: 'stringEnum',
+            model: mobx_state_tree_1.types.enumeration('Rendering', [
+                'multirowxy',
+                'xyplot',
+                'multirowdensity',
+                'multiline',
+                'multirowline',
+            ]),
+            defaultValue: 'multirowxy',
+        },
+        renderers: (0, configuration_1.ConfigurationSchema)('RenderersConfiguration', {
+            MultiXYPlotRenderer: MultiXYPlotRendererConfigSchema,
+            MultiDensityRenderer: MultiDensityRendererConfigSchema,
+            MultiRowXYPlotRenderer: MultiRowXYPlotRendererConfigSchema,
+            MultiLineRenderer: MultiLineRendererConfigSchema,
+            MultiRowLineRenderer: MultiRowLineRendererConfigSchema,
+        }),
+    }, { baseConfiguration: plugin_linear_genome_view_1.baseLinearDisplayConfigSchema, explicitlyTyped: true });
+}
+exports.default = WiggleConfigFactory;
+//# sourceMappingURL=configSchema.js.map

package/dist/MultiLinearWiggleDisplay/models/configSchema.js.map

@@ -0,0 +1 @@
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