@jbrowse/plugin-wiggle 1.7.11 → 2.0.0

package/esm/WiggleRPC/rpcMethods.js

@@ -0,0 +1,70 @@
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
+import { renameRegionsIfNeeded } from '@jbrowse/core/util';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
+export class WiggleGetGlobalStats extends RpcMethodType {
+    constructor() {
+        super(...arguments);
+        this.name = 'WiggleGetGlobalStats';
+    }
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    async deserializeArguments(args, rpcDriverClassName) {
+        const l = await super.deserializeArguments(args, rpcDriverClassName);
+        return {
+            ...l,
+            filters: args.filters
+                ? new SerializableFilterChain({
+                    filters: args.filters,
+                })
+                : undefined,
+        };
+    }
+    async execute(args, rpcDriverClassName) {
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const { adapterConfig, sessionId } = deserializedArgs;
+        const { dataAdapter } = await getAdapter(this.pluginManager, sessionId, adapterConfig);
+        // @ts-ignore
+        return dataAdapter.getGlobalStats(deserializedArgs);
+    }
+}
+export class WiggleGetMultiRegionStats extends RpcMethodType {
+    constructor() {
+        super(...arguments);
+        this.name = 'WiggleGetMultiRegionStats';
+    }
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    async deserializeArguments(args, rpcDriverClassName) {
+        const l = await super.deserializeArguments(args, rpcDriverClassName);
+        return {
+            ...l,
+            filters: args.filters
+                ? new SerializableFilterChain({
+                    filters: args.filters,
+                })
+                : undefined,
+        };
+    }
+    async serializeArguments(args, rpcDriverClassName) {
+        var _a, _b;
+        const assemblyManager = (_b = (_a = this.pluginManager.rootModel) === null || _a === void 0 ? void 0 : _a.session) === null || _b === void 0 ? void 0 : _b.assemblyManager;
+        if (!assemblyManager) {
+            return args;
+        }
+        const renamedArgs = await renameRegionsIfNeeded(assemblyManager, {
+            ...args,
+            filters: args.filters && args.filters.toJSON().filters,
+        });
+        return super.serializeArguments(renamedArgs, rpcDriverClassName);
+    }
+    async execute(args, rpcDriverClassName) {
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const { regions, adapterConfig, sessionId } = deserializedArgs;
+        const { dataAdapter } = await getAdapter(this.pluginManager, sessionId, adapterConfig);
+        if (dataAdapter instanceof BaseFeatureDataAdapter) {
+            return dataAdapter.getMultiRegionStats(regions, deserializedArgs);
+        }
+        throw new Error('Data adapter not found');
+    }
+}
+//# sourceMappingURL=rpcMethods.js.map

package/esm/WiggleRPC/rpcMethods.js.map

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package/esm/WiggleRendering.d.ts

@@ -0,0 +1,16 @@
+/// <reference types="react" />
+import { Region } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+declare function WiggleRendering(props: {
+    regions: Region[];
+    features: Map<string, Feature>;
+    bpPerPx: number;
+    width: number;
+    height: number;
+    onMouseLeave: Function;
+    onMouseMove: Function;
+    onFeatureClick: Function;
+    blockKey: string;
+}): JSX.Element;
+declare const _default: typeof WiggleRendering;
+export default _default;

package/esm/WiggleRendering.js

@@ -0,0 +1,40 @@
+import { observer } from 'mobx-react';
+import React, { useRef } from 'react';
+import { PrerenderedCanvas } from '@jbrowse/core/ui';
+function WiggleRendering(props) {
+    const { regions, features, bpPerPx, width, height, onMouseLeave = () => { }, onMouseMove = () => { }, onFeatureClick = () => { }, } = props;
+    const [region] = regions;
+    const ref = useRef(null);
+    function getFeatureUnderMouse(eventClientX) {
+        // calculates feature under mouse
+        let offset = 0;
+        if (ref.current) {
+            offset = ref.current.getBoundingClientRect().left;
+        }
+        const offsetX = eventClientX - offset;
+        const px = region.reversed ? width - offsetX : offsetX;
+        const clientBp = region.start + bpPerPx * px;
+        let featureUnderMouse;
+        for (const feature of features.values()) {
+            if (clientBp <= feature.get('end') && clientBp >= feature.get('start')) {
+                featureUnderMouse = feature;
+                break;
+            }
+        }
+        return featureUnderMouse;
+    }
+    return (React.createElement("div", { ref: ref, "data-testid": "wiggle-rendering-test", onMouseMove: event => {
+            const featureUnderMouse = getFeatureUnderMouse(event.clientX);
+            onMouseMove(event, featureUnderMouse ? featureUnderMouse.id() : undefined);
+        }, onClick: event => {
+            const featureUnderMouse = getFeatureUnderMouse(event.clientX);
+            onFeatureClick(event, featureUnderMouse ? featureUnderMouse.id() : undefined);
+        }, onMouseLeave: event => onMouseLeave(event), role: "presentation", className: "WiggleRendering", style: {
+            overflow: 'visible',
+            position: 'relative',
+            height,
+        } },
+        React.createElement(PrerenderedCanvas, { ...props })));
+}
+export default observer(WiggleRendering);
+//# sourceMappingURL=WiggleRendering.js.map

package/esm/WiggleRendering.js.map

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

@@ -0,0 +1,4 @@
+import WiggleBaseRenderer, { RenderArgsDeserializedWithFeatures } from '../WiggleBaseRenderer';
+export default class XYPlotRenderer extends WiggleBaseRenderer {
+    draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<void>;
+}

package/esm/XYPlotRenderer/XYPlotRenderer.js

@@ -0,0 +1,109 @@
+import { readConfObject } from '@jbrowse/core/configuration';
+import { featureSpanPx } from '@jbrowse/core/util';
+import { getOrigin, getScale } from '../util';
+import WiggleBaseRenderer from '../WiggleBaseRenderer';
+import { YSCALEBAR_LABEL_OFFSET } from '../LinearWiggleDisplay/models/model';
+function fillRect(ctx, x, y, width, height, color) {
+    if (color) {
+        ctx.fillStyle = String(color);
+    }
+    if (width < 0) {
+        x += width;
+        width = -width;
+    }
+    if (height < 0) {
+        y += height;
+        height = -height;
+    }
+    ctx.fillRect(x, y, width, height);
+}
+export default class XYPlotRenderer extends WiggleBaseRenderer {
+    async draw(ctx, props) {
+        const { features, bpPerPx, regions, scaleOpts, height: unadjustedHeight, config, ticks, displayCrossHatches, } = props;
+        const Color = await import('color').then(f => f.default);
+        const [region] = regions;
+        const width = (region.end - region.start) / bpPerPx;
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        const rc = (s, rest) => readConfObject(config, s, rest);
+        // the adjusted height takes into account YSCALEBAR_LABEL_OFFSET from the
+        // wiggle display, and makes the height of the actual drawn area add
+        // "padding" to the top and bottom of the display
+        const offset = YSCALEBAR_LABEL_OFFSET;
+        const height = unadjustedHeight - offset * 2;
+        const pivotValue = rc('bicolorPivotValue');
+        const negColor = rc('negColor');
+        const posColor = rc('posColor');
+        const filled = rc('filled');
+        const clipColor = rc('clipColor');
+        const highlightColor = rc('highlightColor');
+        const summaryScoreMode = rc('summaryScoreMode');
+        const scale = getScale({ ...scaleOpts, range: [0, height] });
+        const originY = getOrigin(scaleOpts.scaleType);
+        const [niceMin, niceMax] = scale.domain();
+        const toY = (n) => height - (scale(n) || 0) + offset;
+        const toHeight = (n) => toY(originY) - toY(n);
+        const colorCallback = rc('color') === '#f0f'
+            ? (_, score) => score < pivotValue ? negColor : posColor
+            : (feature, _score) => rc('color', { feature });
+        const crossingOrigin = niceMin < pivotValue && niceMax > pivotValue;
+        for (const feature of features.values()) {
+            const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
+            let score = feature.get('score');
+            const maxr = feature.get('maxScore');
+            const minr = feature.get('minScore');
+            const lowClipping = score < niceMin;
+            const highClipping = score > niceMax;
+            const w = rightPx - leftPx + 0.4; // fudge factor for subpixel rendering
+            const summary = feature.get('summary');
+            if (summaryScoreMode === 'max') {
+                score = summary ? maxr : score;
+                fillRect(ctx, leftPx, toY(score), w, filled ? toHeight(score) : 1, colorCallback(feature, score));
+            }
+            else if (summaryScoreMode === 'min') {
+                score = summary ? minr : score;
+                fillRect(ctx, leftPx, toY(score), w, filled ? toHeight(score) : 1, colorCallback(feature, score));
+            }
+            else if (summaryScoreMode === 'whiskers') {
+                const c = colorCallback(feature, score);
+                if (summary) {
+                    fillRect(ctx, leftPx, toY(maxr), w, filled ? toHeight(maxr) - toHeight(score) : 1, crossingOrigin
+                        ? colorCallback(feature, maxr)
+                        : Color(c).lighten(0.6));
+                }
+                // normal
+                fillRect(ctx, leftPx, toY(score), w, filled ? toHeight(score) - (summary ? toHeight(minr) : 0) : 1, crossingOrigin && summary
+                    ? Color(colorCallback(feature, maxr)).mix(Color(colorCallback(feature, minr)))
+                    : c);
+                // min
+                if (summary) {
+                    fillRect(ctx, leftPx, toY(minr), w, filled ? toHeight(minr) : 1, crossingOrigin
+                        ? colorCallback(feature, minr)
+                        : Color(c).darken(0.6));
+                }
+            }
+            else {
+                fillRect(ctx, leftPx, toY(score), w, filled ? toHeight(score) : 1, colorCallback(feature, score));
+            }
+            if (highClipping) {
+                fillRect(ctx, leftPx, 0, w, 4, clipColor);
+            }
+            else if (lowClipping && scaleOpts.scaleType !== 'log') {
+                fillRect(ctx, leftPx, unadjustedHeight - 4, w, 4, clipColor);
+            }
+            if (feature.get('highlighted')) {
+                fillRect(ctx, leftPx, 0, w, height, highlightColor);
+            }
+        }
+        if (displayCrossHatches) {
+            ctx.lineWidth = 1;
+            ctx.strokeStyle = 'rgba(200,200,200,0.8)';
+            ticks.values.forEach(tick => {
+                ctx.beginPath();
+                ctx.moveTo(0, Math.round(toY(tick)));
+                ctx.lineTo(width, Math.round(toY(tick)));
+                ctx.stroke();
+            });
+        }
+    }
+}
+//# sourceMappingURL=XYPlotRenderer.js.map

package/esm/XYPlotRenderer/XYPlotRenderer.js.map

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

@@ -0,0 +1,3 @@
+export { default as ReactComponent } from '../WiggleRendering';
+export { default } from './XYPlotRenderer';
+export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/esm/XYPlotRenderer/index.js

@@ -0,0 +1,23 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import ConfigSchema from '../configSchema';
+import { types } from 'mobx-state-tree';
+export { default as ReactComponent } from '../WiggleRendering';
+export { default } from './XYPlotRenderer';
+export const configSchema = ConfigurationSchema('XYPlotRenderer', {
+    filled: {
+        type: 'boolean',
+        defaultValue: true,
+    },
+    displayCrossHatches: {
+        type: 'boolean',
+        description: 'choose to draw cross hatches (sideways lines)',
+        defaultValue: false,
+    },
+    summaryScoreMode: {
+        type: 'stringEnum',
+        model: types.enumeration('Score type', ['max', 'min', 'avg', 'whiskers']),
+        description: 'choose whether to use max/min/average or whiskers which combines all three into the same rendering',
+        defaultValue: 'whiskers',
+    },
+}, { baseConfiguration: ConfigSchema, explicitlyTyped: true });
+//# sourceMappingURL=index.js.map

package/esm/XYPlotRenderer/index.js.map

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

@@ -0,0 +1,2 @@
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/esm/configSchema.js

@@ -0,0 +1,46 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { types } from 'mobx-state-tree';
+export default ConfigurationSchema('WiggleRenderer', {
+    color: {
+        type: 'color',
+        description: 'the color of track, overrides posColor and negColor',
+        defaultValue: '#f0f',
+    },
+    posColor: {
+        type: 'color',
+        description: 'the color to use when the score is positive',
+        defaultValue: 'blue',
+    },
+    negColor: {
+        type: 'color',
+        description: 'the color to use when the score is negative',
+        defaultValue: 'red',
+    },
+    highlightColor: {
+        type: 'color',
+        description: 'the color of highlights over the wiggle track',
+        defaultValue: 'rgba(255,255,0,0.5)',
+    },
+    clipColor: {
+        type: 'color',
+        description: 'the color of the clipping marker',
+        defaultValue: 'red',
+    },
+    bicolorPivot: {
+        type: 'stringEnum',
+        model: types.enumeration('Scale type', [
+            'numeric',
+            'mean',
+            'z_score',
+            'none',
+        ]),
+        description: 'type of bicolor pivot',
+        defaultValue: 'numeric',
+    },
+    bicolorPivotValue: {
+        type: 'number',
+        defaultValue: 0,
+        description: 'value to use for bicolor pivot',
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/esm/configSchema.js.map

@@ -0,0 +1 @@
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