@jbrowse/plugin-wiggle 2.6.3 → 2.7.1

package/dist/drawxy.js

@@ -1,289 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.drawDensity = exports.drawLine = exports.drawXY = void 0;
-const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
-// locals
-const util_2 = require("./util");
-// avoid drawing negative width features for SVG exports
-function fillRectCtx(x, y, width, height, ctx, color) {
-    if (width < 0) {
-        x += width;
-        width = -width;
-    }
-    if (height < 0) {
-        y += height;
-        height = -height;
-    }
-    if (color) {
-        ctx.fillStyle = color;
-    }
-    ctx.fillRect(x, y, width, height);
-}
-const fudgeFactor = 0.4;
-const clipHeight = 2;
-function drawXY(ctx, props) {
-    const { features, bpPerPx, regions, scaleOpts, height: unadjustedHeight, config, ticks, displayCrossHatches, offset = 0, colorCallback, Color, } = props;
-    const [region] = regions;
-    const width = (region.end - region.start) / bpPerPx;
-    // 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 height = unadjustedHeight - offset * 2;
-    const filled = (0, configuration_1.readConfObject)(config, 'filled');
-    const clipColor = (0, configuration_1.readConfObject)(config, 'clipColor');
-    const summaryScoreMode = (0, configuration_1.readConfObject)(config, 'summaryScoreMode');
-    const pivotValue = (0, configuration_1.readConfObject)(config, 'bicolorPivotValue');
-    const minSize = (0, configuration_1.readConfObject)(config, 'minSize');
-    const scale = (0, util_2.getScale)({ ...scaleOpts, range: [0, height] });
-    const originY = (0, util_2.getOrigin)(scaleOpts.scaleType);
-    const [niceMin, niceMax] = scale.domain();
-    const toY = (n) => (0, util_1.clamp)(height - (scale(n) || 0), 0, height) + offset;
-    const toOrigin = (n) => toY(originY) - toY(n);
-    const getHeight = (n) => (filled ? toOrigin(n) : Math.max(minSize, 1));
-    let hasClipping = false;
-    let prevLeftPx = -Infinity;
-    const reducedFeatures = [];
-    const crossingOrigin = niceMin < pivotValue && niceMax > pivotValue;
-    // we handle whiskers separately to render max row, min row, and avg in three
-    // passes. this reduces subpixel rendering issues. note: for stylistic
-    // reasons, clipping indicator is only drawn for score, not min/max score
-    if (summaryScoreMode === 'whiskers') {
-        let lastCol;
-        let lastMix;
-        for (const feature of features.values()) {
-            const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
-            if (feature.get('summary')) {
-                const w = Math.max(rightPx - leftPx + fudgeFactor, minSize);
-                const max = feature.get('maxScore');
-                const c = colorCallback(feature, max);
-                const effectiveC = crossingOrigin
-                    ? c
-                    : c === lastCol
-                        ? lastMix
-                        : (lastMix = Color(c).lighten(0.4).toString());
-                fillRectCtx(leftPx, toY(max), w, getHeight(max), ctx, effectiveC);
-                lastCol = c;
-            }
-        }
-        lastMix = undefined;
-        lastCol = undefined;
-        for (const feature of features.values()) {
-            const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
-            const score = feature.get('score');
-            const max = feature.get('maxScore');
-            const min = feature.get('minScore');
-            const summary = feature.get('summary');
-            const c = colorCallback(feature, score);
-            const effectiveC = crossingOrigin && summary
-                ? c === lastCol
-                    ? lastMix
-                    : (lastMix = Color(colorCallback(feature, max))
-                        .mix(Color(colorCallback(feature, min)))
-                        .toString())
-                : c;
-            const w = Math.max(rightPx - leftPx + fudgeFactor, minSize);
-            // create reduced features, avoiding multiple features per px
-            if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
-                reducedFeatures.push(feature);
-                prevLeftPx = leftPx;
-            }
-            hasClipping = hasClipping || score < niceMin || score > niceMax;
-            fillRectCtx(leftPx, toY(score), w, getHeight(score), ctx, effectiveC);
-            lastCol = c;
-        }
-        lastMix = undefined;
-        lastCol = undefined;
-        for (const feature of features.values()) {
-            const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
-            if (feature.get('summary')) {
-                const min = feature.get('minScore');
-                const c = colorCallback(feature, min);
-                const w = Math.max(rightPx - leftPx + fudgeFactor, minSize);
-                const effectiveC = crossingOrigin
-                    ? c
-                    : c === lastCol
-                        ? lastMix
-                        : (lastMix = Color(c).darken(0.4).toString());
-                fillRectCtx(leftPx, toY(min), w, getHeight(min), ctx, effectiveC);
-                lastCol = c;
-            }
-        }
-    }
-    else {
-        for (const feature of features.values()) {
-            const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
-            // create reduced features, avoiding multiple features per px
-            if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
-                reducedFeatures.push(feature);
-                prevLeftPx = leftPx;
-            }
-            const score = feature.get('score');
-            const c = colorCallback(feature, score);
-            hasClipping = hasClipping || score < niceMin || score > niceMax;
-            const w = Math.max(rightPx - leftPx + fudgeFactor, minSize);
-            if (summaryScoreMode === 'max') {
-                const s = feature.get('summary') ? feature.get('maxScore') : score;
-                fillRectCtx(leftPx, toY(s), w, getHeight(s), ctx, c);
-            }
-            else if (summaryScoreMode === 'min') {
-                const s = feature.get('summary') ? feature.get('minScore') : score;
-                fillRectCtx(leftPx, toY(s), w, getHeight(s), ctx, c);
-            }
-            else {
-                fillRectCtx(leftPx, toY(score), w, getHeight(score), ctx, c);
-            }
-        }
-    }
-    // second pass: draw clipping
-    // avoid persisting the red fillstyle with save/restore
-    ctx.save();
-    if (hasClipping) {
-        ctx.fillStyle = clipColor;
-        for (const feature of features.values()) {
-            const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
-            const w = rightPx - leftPx + fudgeFactor;
-            const score = feature.get('score');
-            if (score > niceMax) {
-                fillRectCtx(leftPx, offset, w, clipHeight, ctx);
-            }
-            else if (score < niceMin && scaleOpts.scaleType !== 'log') {
-                fillRectCtx(leftPx, unadjustedHeight, w, clipHeight, ctx);
-            }
-        }
-    }
-    ctx.restore();
-    if (displayCrossHatches) {
-        ctx.lineWidth = 1;
-        ctx.strokeStyle = 'rgba(200,200,200,0.5)';
-        ticks.values.forEach(tick => {
-            ctx.beginPath();
-            ctx.moveTo(0, Math.round(toY(tick)));
-            ctx.lineTo(width, Math.round(toY(tick)));
-            ctx.stroke();
-        });
-    }
-    return { reducedFeatures };
-}
-exports.drawXY = drawXY;
-function drawLine(ctx, props) {
-    const { features, regions, bpPerPx, scaleOpts, height: unadjustedHeight, ticks: { values }, displayCrossHatches, colorCallback, config, offset = 0, } = props;
-    const [region] = regions;
-    const width = (region.end - region.start) / bpPerPx;
-    // 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 height = unadjustedHeight - offset * 2;
-    const clipColor = (0, configuration_1.readConfObject)(config, 'clipColor');
-    const scale = (0, util_2.getScale)({ ...scaleOpts, range: [0, height] });
-    const [niceMin, niceMax] = scale.domain();
-    const toY = (n) => (0, util_1.clamp)(height - (scale(n) || 0), 0, height) + offset;
-    let lastVal;
-    let prevLeftPx = -Infinity;
-    const reducedFeatures = [];
-    for (const feature of features.values()) {
-        const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
-        // create reduced features, avoiding multiple features per px
-        if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
-            reducedFeatures.push(feature);
-            prevLeftPx = leftPx;
-        }
-        const score = feature.get('score');
-        const lowClipping = score < niceMin;
-        const highClipping = score > niceMax;
-        const w = rightPx - leftPx + fudgeFactor;
-        const c = colorCallback(feature, score);
-        ctx.beginPath();
-        ctx.strokeStyle = c;
-        const startPos = lastVal !== undefined ? lastVal : score;
-        if (!region.reversed) {
-            ctx.moveTo(leftPx, toY(startPos));
-            ctx.lineTo(leftPx, toY(score));
-            ctx.lineTo(rightPx, toY(score));
-        }
-        else {
-            ctx.moveTo(rightPx, toY(startPos));
-            ctx.lineTo(rightPx, toY(score));
-            ctx.lineTo(leftPx, toY(score));
-        }
-        ctx.stroke();
-        lastVal = score;
-        if (highClipping) {
-            ctx.fillStyle = clipColor;
-            ctx.fillRect(leftPx, offset, w, clipHeight);
-        }
-        else if (lowClipping && scaleOpts.scaleType !== 'log') {
-            ctx.fillStyle = clipColor;
-            ctx.fillRect(leftPx, height - clipHeight, w, height);
-        }
-    }
-    if (displayCrossHatches) {
-        ctx.lineWidth = 1;
-        ctx.strokeStyle = 'rgba(200,200,200,0.5)';
-        values.forEach(tick => {
-            ctx.beginPath();
-            ctx.moveTo(0, Math.round(toY(tick)));
-            ctx.lineTo(width, Math.round(toY(tick)));
-            ctx.stroke();
-        });
-    }
-    return { reducedFeatures };
-}
-exports.drawLine = drawLine;
-function drawDensity(ctx, props) {
-    const { features, regions, bpPerPx, scaleOpts, height, config } = props;
-    const [region] = regions;
-    const pivot = (0, configuration_1.readConfObject)(config, 'bicolorPivot');
-    const pivotValue = (0, configuration_1.readConfObject)(config, 'bicolorPivotValue');
-    const negColor = (0, configuration_1.readConfObject)(config, 'negColor');
-    const posColor = (0, configuration_1.readConfObject)(config, 'posColor');
-    const color = (0, configuration_1.readConfObject)(config, 'color');
-    const clipColor = (0, configuration_1.readConfObject)(config, 'clipColor');
-    const crossing = pivot !== 'none' && scaleOpts.scaleType !== 'log';
-    const scale = (0, util_2.getScale)({
-        ...scaleOpts,
-        pivotValue: crossing ? pivotValue : undefined,
-        range: crossing ? [negColor, 'white', posColor] : ['white', posColor],
-    });
-    const scale2 = (0, util_2.getScale)({ ...scaleOpts, range: [0, height] });
-    const cb = color === '#f0f'
-        ? (_, score) => scale(score)
-        : (feature, score) => (0, configuration_1.readConfObject)(config, 'color', { feature, score });
-    const [niceMin, niceMax] = scale2.domain();
-    let prevLeftPx = -Infinity;
-    let hasClipping = false;
-    const reducedFeatures = [];
-    for (const feature of features.values()) {
-        const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
-        // create reduced features, avoiding multiple features per px
-        if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
-            reducedFeatures.push(feature);
-            prevLeftPx = leftPx;
-        }
-        const score = feature.get('score');
-        hasClipping = hasClipping || score > niceMax || score < niceMin;
-        const w = rightPx - leftPx + fudgeFactor;
-        ctx.fillStyle = cb(feature, score);
-        ctx.fillRect(leftPx, 0, w, height);
-    }
-    // second pass: draw clipping
-    // avoid persisting the red fillstyle with save/restore
-    ctx.save();
-    if (hasClipping) {
-        ctx.fillStyle = clipColor;
-        for (const feature of features.values()) {
-            const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
-            const w = rightPx - leftPx + fudgeFactor;
-            const score = feature.get('score');
-            if (score > niceMax) {
-                fillRectCtx(leftPx, 0, w, clipHeight, ctx);
-            }
-            else if (score < niceMin && scaleOpts.scaleType !== 'log') {
-                fillRectCtx(leftPx, 0, w, clipHeight, ctx);
-            }
-        }
-    }
-    ctx.restore();
-    return { reducedFeatures };
-}
-exports.drawDensity = drawDensity;

package/esm/drawxy.d.ts

@@ -1,50 +0,0 @@
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { Feature, Region } from '@jbrowse/core/util';
-import { ScaleOpts } from './util';
-export declare function drawXY(ctx: CanvasRenderingContext2D, props: {
-    features: Map<string, Feature> | Feature[];
-    bpPerPx: number;
-    regions: Region[];
-    scaleOpts: ScaleOpts;
-    height: number;
-    ticks: {
-        values: number[];
-    };
-    config: AnyConfigurationModel;
-    displayCrossHatches: boolean;
-    offset?: number;
-    colorCallback: (f: Feature, score: number) => string;
-    Color: typeof import('color');
-}): {
-    reducedFeatures: Feature[];
-};
-export declare function drawLine(ctx: CanvasRenderingContext2D, props: {
-    features: Map<string, Feature> | Feature[];
-    regions: Region[];
-    bpPerPx: number;
-    scaleOpts: ScaleOpts;
-    height: number;
-    ticks: {
-        values: number[];
-    };
-    displayCrossHatches: boolean;
-    colorCallback: (f: Feature, score: number) => string;
-    config: AnyConfigurationModel;
-    offset?: number;
-}): {
-    reducedFeatures: Feature[];
-};
-export declare function drawDensity(ctx: CanvasRenderingContext2D, props: {
-    features: Map<string, Feature> | Feature[];
-    regions: Region[];
-    bpPerPx: number;
-    scaleOpts: ScaleOpts;
-    height: number;
-    ticks: {
-        values: number[];
-    };
-    displayCrossHatches: boolean;
-    config: AnyConfigurationModel;
-}): {
-    reducedFeatures: Feature[];
-};