@jbrowse/plugin-alignments 3.6.5 → 3.7.0

package/esm/LinearReadCloudDisplay/drawPairChains.js

@@ -1,90 +0,0 @@
-import { getConf } from '@jbrowse/core/configuration';
-import { max, min } from '@jbrowse/core/util';
-import { fillRectCtx, strokeRectCtx } from './util';
-import { getPairedInsertSizeAndOrientationColor, getPairedInsertSizeColor, getPairedOrientationColor, } from '../shared/color';
-export function drawPairChains({ ctx, self, chainData, view, asm, }) {
-    var _a, _b, _c, _d, _e, _f, _g;
-    const coords = [];
-    const featureHeight = getConf(self, 'featureHeight');
-    const type = ((_a = self.colorBy) === null || _a === void 0 ? void 0 : _a.type) || 'insertSizeAndOrientation';
-    const { chains, stats } = chainData;
-    for (const chain of chains) {
-        if (chain.length > 1) {
-            const v0 = chain[0];
-            const v1 = chain[1];
-            const ra1 = asm.getCanonicalRefName(v0.refName) || v0.refName;
-            const ra2 = asm.getCanonicalRefName(v1.refName) || v1.refName;
-            const r1s = (_b = view.bpToPx({ refName: ra1, coord: v0.start })) === null || _b === void 0 ? void 0 : _b.offsetPx;
-            const r1e = (_c = view.bpToPx({ refName: ra1, coord: v0.end })) === null || _c === void 0 ? void 0 : _c.offsetPx;
-            const r2s = (_d = view.bpToPx({ refName: ra2, coord: v1.start })) === null || _d === void 0 ? void 0 : _d.offsetPx;
-            const r2e = (_e = view.bpToPx({ refName: ra2, coord: v1.end })) === null || _e === void 0 ? void 0 : _e.offsetPx;
-            let distance = 0;
-            if (r1s !== undefined &&
-                r1e !== undefined &&
-                r2s !== undefined &&
-                r2e !== undefined) {
-                if (v0.refName === v1.refName) {
-                    const s = Math.min(v0.start, v1.start);
-                    const e = Math.max(v0.end, v1.end);
-                    distance = Math.abs(e - s);
-                }
-                coords.push({
-                    r1s,
-                    r1e,
-                    r2s,
-                    r2e,
-                    v0,
-                    v1,
-                    distance,
-                });
-            }
-        }
-        else if (self.drawSingletons) {
-            const v0 = chain[0];
-            const ra1 = asm.getCanonicalRefName(v0.refName) || v0.refName;
-            const r1s = (_f = view.bpToPx({ refName: ra1, coord: v0.start })) === null || _f === void 0 ? void 0 : _f.offsetPx;
-            const r1e = (_g = view.bpToPx({ refName: ra1, coord: v0.end })) === null || _g === void 0 ? void 0 : _g.offsetPx;
-            if (r1s !== undefined && r1e !== undefined) {
-                const w1 = Math.max(r1e - r1s, 2);
-                fillRectCtx(r1s - view.offsetPx, 0, w1, featureHeight, ctx, '#f00');
-                strokeRectCtx(r1s - view.offsetPx, 0, w1, featureHeight, ctx, '#a00');
-            }
-        }
-    }
-    const maxD = Math.log(max(coords.map(c => c.distance)));
-    const minD = Math.max(Math.log(min(coords.map(c => c.distance))) - 1, 0);
-    const scaler = (self.height - 20) / (maxD - minD);
-    for (const { r1e, r1s, r2e, r2s, distance, v0, v1 } of coords) {
-        const w1 = Math.max(r1e - r1s, 2);
-        const w2 = Math.max(r2e - r2s, 2);
-        const [fill, stroke] = getPairedColor({ type, v0, v1, stats }) || [];
-        const top = (Math.log(distance) - minD) * scaler;
-        const halfHeight = featureHeight / 2 - 0.5;
-        const w = r2s - r1e;
-        fillRectCtx(r1e - view.offsetPx, top + halfHeight, w, 1, ctx, 'black');
-        strokeRectCtx(r1s - view.offsetPx, top, w1, featureHeight, ctx, stroke);
-        strokeRectCtx(r2s - view.offsetPx, top, w2, featureHeight, ctx, stroke);
-        fillRectCtx(r1s - view.offsetPx, top, w1, featureHeight, ctx, fill);
-        fillRectCtx(r2s - view.offsetPx, top, w2, featureHeight, ctx, fill);
-    }
-}
-export function getPairedColor({ type, v0, v1, stats, }) {
-    if (type === 'insertSizeAndOrientation') {
-        return getPairedInsertSizeAndOrientationColor(v0, v1, stats);
-    }
-    if (type === 'orientation') {
-        return getPairedOrientationColor(v0);
-    }
-    if (type === 'insertSize') {
-        return getPairedInsertSizeColor(v0, v1, stats);
-    }
-    if (type === 'gradient') {
-        const s = Math.min(v0.start, v1.start);
-        const e = Math.max(v0.end, v1.end);
-        return [
-            `hsl(${Math.log10(Math.abs(e - s)) * 10},50%,50%)`,
-            `hsl(${Math.log10(Math.abs(e - s)) * 10},50%,30%)`,
-        ];
-    }
-    return undefined;
-}

package/esm/PileupRenderer/renderModifications.js

@@ -1,41 +0,0 @@
-import { bpSpanPx, max, sum } from '@jbrowse/core/util';
-import { fillRect } from './util';
-import { getMaxProbModAtEachPosition } from '../shared/getMaximumModificationAtEachPosition';
-import { alphaColor } from '../shared/util';
-export function renderModifications({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, cigarOps, }) {
-    var _a, _b, _c;
-    const { feature, topPx, heightPx } = feat;
-    const { colorBy, visibleModifications = {} } = renderArgs;
-    const seq = feature.get('seq');
-    if (!seq) {
-        return;
-    }
-    const start = feature.get('start');
-    const isolatedModification = (_a = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _a === void 0 ? void 0 : _a.isolatedModification;
-    const twoColor = (_b = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _b === void 0 ? void 0 : _b.twoColor;
-    (_c = getMaxProbModAtEachPosition(feature, cigarOps)) === null || _c === void 0 ? void 0 : _c.forEach(({ allProbs, prob, type }, pos) => {
-        const r = start + pos;
-        const [leftPx, rightPx] = bpSpanPx(r, r + 1, region, bpPerPx);
-        const mod = visibleModifications[type];
-        if (!mod) {
-            console.warn(`${type} not known yet`);
-            return;
-        }
-        if (isolatedModification && mod.type !== isolatedModification) {
-            return;
-        }
-        const col = mod.color || 'black';
-        const s = 1 - sum(allProbs);
-        if (twoColor && s > max(allProbs)) {
-            const c = alphaColor('blue', s);
-            const w = rightPx - leftPx + 0.5;
-            fillRect(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
-        }
-        else {
-            const c = alphaColor(col, prob);
-            const w = rightPx - leftPx + 0.5;
-            fillRect(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
-        }
-        pos++;
-    });
-}