@jbrowse/plugin-alignments 3.7.0 → 4.0.1

package/esm/shared/drawLongReadChains.js

@@ -1,101 +0,0 @@
-import { fillRectCtx, strokeRectCtx } from './canvasUtils';
-import { drawChevron } from './chevron';
-import { fillColor, getSingletonColor, strokeColor } from './color';
-import { getPrimaryStrandFromFlags } from './primaryStrand';
-import { CHEVRON_WIDTH } from './util';
-export function drawLongReadChains({ ctx, chainData, view, asm, chainYOffsets, renderChevrons, featureHeight, featuresForFlatbush, computedChains, flipStrandLongReadChains, }) {
-    var _a, _b;
-    const getStrandColorKey = (strand) => strand === -1 ? 'color_rev_strand' : 'color_fwd_strand';
-    for (const computedChain of computedChains) {
-        const { id, chain, minX, maxX } = computedChain;
-        let isPairedEnd = false;
-        for (const element of chain) {
-            if (element.flags & 1) {
-                isPairedEnd = true;
-                break;
-            }
-        }
-        if (isPairedEnd) {
-            continue;
-        }
-        const chainY = chainYOffsets.get(id);
-        if (chainY === undefined) {
-            continue;
-        }
-        const nonSupplementary = [];
-        for (const element of chain) {
-            if (!(element.flags & 2048)) {
-                nonSupplementary.push(element);
-            }
-        }
-        const isSingleton = chain.length === 1;
-        const c1 = nonSupplementary[0] || chain[0];
-        const primaryStrand = getPrimaryStrandFromFlags(c1);
-        if (!isSingleton) {
-            const firstFeat = chain[0];
-            const lastFeat = chain[chain.length - 1];
-            const firstPx = (_a = view.bpToPx({
-                refName: asm.getCanonicalRefName2(firstFeat.refName),
-                coord: firstFeat.start,
-            })) === null || _a === void 0 ? void 0 : _a.offsetPx;
-            const lastPx = (_b = view.bpToPx({
-                refName: asm.getCanonicalRefName2(lastFeat.refName),
-                coord: lastFeat.end,
-            })) === null || _b === void 0 ? void 0 : _b.offsetPx;
-            if (firstPx !== undefined && lastPx !== undefined) {
-                const lineY = chainY + featureHeight / 2 - 0.5;
-                ctx.beginPath();
-                ctx.strokeStyle = '#666';
-                ctx.moveTo(firstPx - view.offsetPx, lineY);
-                ctx.lineTo(lastPx - view.offsetPx, lineY);
-                ctx.stroke();
-            }
-        }
-        const viewOffsetPx = view.offsetPx;
-        const chainMinXPx = minX - viewOffsetPx;
-        const chainMaxXPx = maxX - viewOffsetPx;
-        for (let i = 0, l = chain.length; i < l; i++) {
-            const feat = chain[i];
-            const s = view.bpToPx({
-                refName: asm.getCanonicalRefName2(feat.refName),
-                coord: feat.start,
-            });
-            const e = view.bpToPx({
-                refName: asm.getCanonicalRefName2(feat.refName),
-                coord: feat.end,
-            });
-            if (!s || !e) {
-                continue;
-            }
-            const effectiveStrand = isSingleton || !flipStrandLongReadChains
-                ? feat.strand
-                : feat.strand * primaryStrand;
-            const [featureFill, featureStroke] = isSingleton
-                ? getSingletonColor(feat, chainData.stats)
-                : [
-                    fillColor[getStrandColorKey(effectiveStrand)],
-                    strokeColor[getStrandColorKey(effectiveStrand)],
-                ];
-            const xPos = s.offsetPx - viewOffsetPx;
-            const width = Math.max(e.offsetPx - s.offsetPx, 3);
-            if (renderChevrons) {
-                drawChevron(ctx, xPos, chainY, width, featureHeight, effectiveStrand, featureFill, CHEVRON_WIDTH, featureStroke);
-            }
-            else {
-                fillRectCtx(xPos, chainY, width, featureHeight, ctx, featureFill);
-                strokeRectCtx(xPos, chainY, width, featureHeight, ctx, featureStroke);
-            }
-            featuresForFlatbush.push({
-                x1: xPos,
-                y1: chainY,
-                x2: xPos + width,
-                y2: chainY + featureHeight,
-                data: feat,
-                chainId: id,
-                chainMinX: chainMinXPx,
-                chainMaxX: chainMaxXPx,
-                chain,
-            });
-        }
-    }
-}

package/esm/shared/drawPairChains.d.ts

@@ -1,24 +0,0 @@
-import type { ChainData, ReducedFeature } from './fetchChains';
-import type { FlatbushEntry } from './flatbushType';
-import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-type LGV = LinearGenomeViewModel;
-export declare function drawPairChains({ ctx, type, chainData, view, asm, chainYOffsets, renderChevrons, featureHeight, featuresForFlatbush, computedChains, }: {
-    ctx: CanvasRenderingContext2D;
-    type: string;
-    chainData: ChainData;
-    view: LGV;
-    asm: Assembly;
-    chainYOffsets: Map<string, number>;
-    renderChevrons: boolean;
-    featureHeight: number;
-    featuresForFlatbush: FlatbushEntry[];
-    computedChains: {
-        distance: number;
-        minX: number;
-        maxX: number;
-        chain: ReducedFeature[];
-        id: string;
-    }[];
-}): void;
-export {};

package/esm/shared/drawPairChains.js

@@ -1,91 +0,0 @@
-import { fillRectCtx, strokeRectCtx } from './canvasUtils';
-import { drawChevron } from './chevron';
-import { getPairedColor, getSingletonColor } from './color';
-import { CHEVRON_WIDTH } from './util';
-export function drawPairChains({ ctx, type, chainData, view, asm, chainYOffsets, renderChevrons, featureHeight, featuresForFlatbush, computedChains, }) {
-    var _a, _b;
-    for (const computedChain of computedChains) {
-        const { id, chain, minX, maxX } = computedChain;
-        let isPairedEnd = false;
-        for (const element of chain) {
-            if (element.flags & 1) {
-                isPairedEnd = true;
-                break;
-            }
-        }
-        if (!isPairedEnd) {
-            continue;
-        }
-        const chainY = chainYOffsets.get(id);
-        if (chainY === undefined) {
-            continue;
-        }
-        const nonSupplementary = [];
-        for (const element of chain) {
-            if (!(element.flags & 2048)) {
-                nonSupplementary.push(element);
-            }
-        }
-        const hasBothMates = nonSupplementary.length === 2;
-        const [pairedFill, pairedStroke] = hasBothMates
-            ? getPairedColor({
-                type,
-                v0: nonSupplementary[0],
-                v1: nonSupplementary[1],
-                stats: chainData.stats,
-            }) || ['#888', '#888']
-            : getSingletonColor(nonSupplementary[0] || chain[0], chainData.stats);
-        if (hasBothMates) {
-            const v0 = nonSupplementary[0];
-            const v1 = nonSupplementary[1];
-            const r1s = (_a = view.bpToPx({
-                refName: asm.getCanonicalRefName2(v0.refName),
-                coord: v0.start,
-            })) === null || _a === void 0 ? void 0 : _a.offsetPx;
-            const r2s = (_b = view.bpToPx({
-                refName: asm.getCanonicalRefName2(v1.refName),
-                coord: v1.start,
-            })) === null || _b === void 0 ? void 0 : _b.offsetPx;
-            if (r1s !== undefined && r2s !== undefined) {
-                fillRectCtx(r1s - view.offsetPx, chainY + featureHeight / 2 - 0.5, r2s - r1s, 1, ctx, '#666');
-            }
-        }
-        const viewOffsetPx = view.offsetPx;
-        const chainMinXPx = minX - viewOffsetPx;
-        const chainMaxXPx = maxX - viewOffsetPx;
-        for (let i = 0, l = chain.length; i < l; i++) {
-            const feat = chain[i];
-            const s = view.bpToPx({
-                refName: asm.getCanonicalRefName2(feat.refName),
-                coord: feat.start,
-            });
-            const e = view.bpToPx({
-                refName: asm.getCanonicalRefName2(feat.refName),
-                coord: feat.end,
-            });
-            if (!s || !e) {
-                continue;
-            }
-            const xPos = s.offsetPx - viewOffsetPx;
-            const width = Math.max(e.offsetPx - s.offsetPx, 3);
-            if (renderChevrons) {
-                drawChevron(ctx, xPos, chainY, width, featureHeight, feat.strand, pairedFill, CHEVRON_WIDTH, pairedStroke);
-            }
-            else {
-                fillRectCtx(xPos, chainY, width, featureHeight, ctx, pairedFill);
-                strokeRectCtx(xPos, chainY, width, featureHeight, ctx, pairedStroke);
-            }
-            featuresForFlatbush.push({
-                x1: xPos,
-                y1: chainY,
-                x2: xPos + width,
-                y2: chainY + featureHeight,
-                data: feat,
-                chainId: id,
-                chainMinX: chainMinXPx,
-                chainMaxX: chainMaxXPx,
-                chain,
-            });
-        }
-    }
-}

package/esm/shared/fetchChains.d.ts

@@ -1,28 +0,0 @@
-import type { LinearReadArcsDisplayModel } from '../LinearReadArcsDisplay/model';
-import type { LinearReadCloudDisplayModel } from '../LinearReadCloudDisplay/model';
-export interface ReducedFeature {
-    name: string;
-    strand: number;
-    refName: string;
-    start: number;
-    end: number;
-    id: string;
-    flags: number;
-    tlen: number;
-    pair_orientation: string;
-    next_ref?: string;
-    next_pos?: number;
-    clipPos: number;
-    SA?: string;
-}
-export interface ChainStats {
-    max: number;
-    min: number;
-    upper: number;
-    lower: number;
-}
-export interface ChainData {
-    chains: ReducedFeature[][];
-    stats?: ChainStats;
-}
-export declare function fetchChains(self: LinearReadArcsDisplayModel | LinearReadCloudDisplayModel): Promise<void>;

package/esm/shared/fetchChains.js

@@ -1,19 +0,0 @@
-import { getContainingView, getSession } from '@jbrowse/core/util';
-import { getRpcSessionId } from '@jbrowse/core/util/tracks';
-export async function fetchChains(self) {
-    const sessionId = getRpcSessionId(self);
-    const { rpcManager } = getSession(self);
-    const view = getContainingView(self);
-    if (!view.initialized || self.error || !self.statsReadyAndRegionNotTooLarge) {
-        return;
-    }
-    self.setLoading(true);
-    const ret = (await rpcManager.call(sessionId, 'PileupGetReducedFeatures', {
-        sessionId,
-        regions: view.staticBlocks.contentBlocks,
-        filterBy: self.filterBy,
-        adapterConfig: self.adapterConfig,
-    }));
-    self.setChainData(ret);
-    self.setLoading(false);
-}