jbrowse2: x/static/js/3304.65e5d8dd.chunk.js.map comparison

comparison x/static/js/3304.65e5d8dd.chunk.js.map @ 125:49f3d3878413 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566

author	fubar
date	Sat, 05 Oct 2024 23:58:05 +0000
parents
children

comparison

equal deleted inserted replaced

124:137e08517410	125:49f3d3878413
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n\n}\n\ninterface CoreFeat {\n strand: number\n refName: string\n start: number\n end: number\n}\n\nfunction drawLineAtOffset(\n ctx: CanvasRenderingContext2D,\n offset: number,\n height: number,\n color: string,\n) {\n // draws a vertical line off to middle of nowhere if the second end not found\n ctx.strokeStyle = color\n ctx.beginPath()\n ctx.moveTo(offset, 0)\n ctx.lineTo(offset, height)\n ctx.stroke()\n}\n\nexport function drawFeats(\n self: LinearReadArcsDisplayModel,\n ctx: CanvasRenderingContext2D,\n width: number,\n height: number,\n) {\n const {\n chainData,\n colorBy,\n drawInter,\n drawLongRange,\n lineWidthSetting,\n jitterVal,\n } = self\n if (!chainData) {\n return\n }\n const view = getContainingView(self) as LGV\n const { assemblyManager } = getSession(self)\n const { chains, stats } = chainData\n const hasPaired = hasPairedReads(chainData)\n const asm = assemblyManager.get(view.assemblyNames[0]!)\n const type = colorBy?.type \|\| 'insertSizeAndOrientation'\n if (!asm) {\n return\n }\n ctx.lineWidth = lineWidthSetting\n\n function draw(\n k1: CoreFeat & { tlen?: number; pair_orientation?: string },\n k2: CoreFeat,\n assembly: Assembly,\n longRange?: boolean,\n ) {\n const s1 = k1.strand\n const s2 = k2.strand\n const f1 = s1 === -1\n const f2 = s2 === -1\n\n const p1 = f1 ? k1.start : k1.end\n const p2 = hasPaired ? (f2 ? k2.start : k2.end) : f2 ? k2.end : k2.start\n const ra1 = assembly.getCanonicalRefName(k1.refName) \|\| k1.refName\n const ra2 = assembly.getCanonicalRefName(k2.refName) \|\| k2.refName\n const r1 = view.bpToPx({ refName: ra1, coord: p1 })?.offsetPx\n const r2 = view.bpToPx({ refName: ra2, coord: p2 })?.offsetPx\n\n if (r1 !== undefined && r2 !== undefined) {\n const radius = (r2 - r1) / 2\n const absrad = Math.abs(radius)\n const p = r1 - view.offsetPx\n const p2 = r2 - view.offsetPx\n const drawArcInsteadOfBezier = absrad > 10_000\n\n // bezier (used for non-long-range arcs) requires moveTo before beginPath\n // arc (used for long-range) requires moveTo after beginPath (or else a\n // unwanted line at y=0 is rendered along with the arc)\n if (longRange && drawArcInsteadOfBezier) {\n ctx.moveTo(p, 0)\n ctx.beginPath()\n } else {\n ctx.beginPath()\n ctx.moveTo(p, 0)\n }\n\n if (longRange && drawArcInsteadOfBezier) {\n ctx.strokeStyle = 'red'\n } else {\n if (hasPaired) {\n if (type === 'insertSizeAndOrientation') {\n ctx.strokeStyle = getPairedInsertSizeAndOrientationColor(\n k1,\n k2,\n stats,\n )[0]\n } else if (type === 'orientation') {\n ctx.strokeStyle = getPairedOrientationColor(k1)[0]\n } else if (type === 'insertSize') {\n ctx.strokeStyle =\n getPairedInsertSizeColor(k1, k2, stats)?.[0] \|\| 'grey'\n } else if (type === 'gradient') {\n ctx.strokeStyle = `hsl(${Math.log10(absrad) * 10},50%,50%)`\n }\n } else {\n if (type === 'orientation' \|\| type === 'insertSizeAndOrientation') {\n if (s1 === -1 && s2 === 1) {\n ctx.strokeStyle = 'navy'\n } else if (s1 === 1 && s2 === -1) {\n ctx.strokeStyle = 'green'\n } else {\n ctx.strokeStyle = 'grey'\n }\n } else if (type === 'gradient') {\n ctx.strokeStyle = `hsl(${Math.log10(absrad) * 10},50%,50%)`\n }\n }\n }\n\n const destX = p + radius * 2\n const destY = Math.min(height + jitter(jitterVal), absrad)\n if (longRange) {\n // avoid drawing gigantic circles that glitch out the rendering,\n // instead draw vertical lines\n if (absrad > 100_000) {\n drawLineAtOffset(ctx, p + jitter(jitterVal), height, 'red')\n drawLineAtOffset(ctx, p2 + jitter(jitterVal), height, 'red')\n } else if (drawArcInsteadOfBezier) {\n ctx.arc(p + radius + jitter(jitterVal), 0, absrad, 0, Math.PI)\n ctx.stroke()\n } else {\n ctx.bezierCurveTo(\n p + jitter(jitterVal),\n destY,\n destX,\n destY,\n destX + jitter(jitterVal),\n 0,\n )\n ctx.stroke()\n }\n } else {\n ctx.bezierCurveTo(\n p + jitter(jitterVal),\n destY,\n destX,\n destY,\n destX + jitter(jitterVal),\n 0,\n )\n ctx.stroke()\n }\n } else if (r1 && drawInter) {\n drawLineAtOffset(ctx, r1 - view.offsetPx, height, 'purple')\n }\n }\n\n for (const chain of chains) {\n // chain.length === 1, singleton (other pairs/mates not in view)\n if (chain.length === 1 && drawLongRange) {\n const f = chain[0]!\n if (hasPaired && !(f.flags & 8)) {\n const mate = {\n refName: f.next_ref \|\| '',\n start: f.next_pos \|\| 0,\n end: f.next_pos \|\| 0,\n strand: f.strand,\n }\n draw(f, mate, asm, true)\n } else {\n const features = [f, ...featurizeSA(f.SA, f.id, f.strand, f.name)].sort(\n (a, b) => a.clipPos - b.clipPos,\n )\n for (let i = 0; i < features.length - 1; i++) {\n const f = features[i]!\n const v1 = features[i + 1]!\n draw(f, v1, asm, true)\n }\n }\n } else {\n const res = hasPaired\n ? chain.filter(f => !(f.flags & 2048) && !(f.flags & 8))\n : chain\n .sort((a, b) => a.clipPos - b.clipPos)\n .filter(f => !(f.flags & 256))\n for (let i = 0; i < res.length - 1; i++) {\n draw(res[i]!, res[i + 1]!, asm, false)\n }\n }\n }\n}\n","import { ChainData } from './fetchChains'\n\nexport function hasPairedReads(features: ChainData) {\n for (const f of features.chains.values()) {\n if (f[0]!.flags & 1) {\n return true\n }\n }\n return false\n}\n"],"names":["jitter","n","Math","random","drawLineAtOffset","ctx","offset","height","color","strokeStyle","beginPath","moveTo","lineTo","stroke","drawFeats","self","width","chainData","colorBy","drawInter","drawLongRange","lineWidthSetting","jitterVal","view","getContainingView","assemblyManager","getSession","chains","stats","hasPaired","hasPairedReads","asm","get","assemblyNames","type","lineWidth","chain","length","f","flags","features","featurizeSA","SA","id","strand","name","sort","a","b","clipPos","i","draw","refName","next_ref","start","next_pos","end","res","filter","k1","k2","assembly","longRange","s1","s2","f2","p1","p2","ra1","getCanonicalRefName","ra2","r1","bpToPx","coord","offsetPx","r2","undefined","radius","absrad","abs","p","drawArcInsteadOfBezier","getPairedInsertSizeAndOrientationColor","getPairedOrientationColor","getPairedInsertSizeColor","log10","destX","destY","min","arc","PI","bezierCurveTo","values"],"sourceRoot":""}

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n\n}\n\ninterface CoreFeat {\n strand: number\n refName: string\n start: number\n end: number\n}\n\nfunction drawLineAtOffset(\n ctx: CanvasRenderingContext2D,\n offset: number,\n height: number,\n color: string,\n) {\n // draws a vertical line off to middle of nowhere if the second end not found\n ctx.strokeStyle = color\n ctx.beginPath()\n ctx.moveTo(offset, 0)\n ctx.lineTo(offset, height)\n ctx.stroke()\n}\n\nexport function drawFeats(\n self: LinearReadArcsDisplayModel,\n ctx: CanvasRenderingContext2D,\n width: number,\n height: number,\n) {\n const {\n chainData,\n colorBy,\n drawInter,\n drawLongRange,\n lineWidthSetting,\n jitterVal,\n } = self\n if (!chainData) {\n return\n }\n const view = getContainingView(self) as LGV\n const { assemblyManager } = getSession(self)\n const { chains, stats } = chainData\n const hasPaired = hasPairedReads(chainData)\n const asm = assemblyManager.get(view.assemblyNames[0]!)\n const type = colorBy?.type || 'insertSizeAndOrientation'\n if (!asm) {\n return\n }\n ctx.lineWidth = lineWidthSetting\n\n function draw(\n k1: CoreFeat & { tlen?: number; pair_orientation?: string },\n k2: CoreFeat,\n assembly: Assembly,\n longRange?: boolean,\n ) {\n const s1 = k1.strand\n const s2 = k2.strand\n const f1 = s1 === -1\n const f2 = s2 === -1\n\n const p1 = f1 ? k1.start : k1.end\n const p2 = hasPaired ? (f2 ? k2.start : k2.end) : f2 ? k2.end : k2.start\n const ra1 = assembly.getCanonicalRefName(k1.refName) || k1.refName\n const ra2 = assembly.getCanonicalRefName(k2.refName) || k2.refName\n const r1 = view.bpToPx({ refName: ra1, coord: p1 })?.offsetPx\n const r2 = view.bpToPx({ refName: ra2, coord: p2 })?.offsetPx\n\n if (r1 !== undefined && r2 !== undefined) {\n const radius = (r2 - r1) / 2\n const absrad = Math.abs(radius)\n const p = r1 - view.offsetPx\n const p2 = r2 - view.offsetPx\n const drawArcInsteadOfBezier = absrad > 10_000\n\n // bezier (used for non-long-range arcs) requires moveTo before beginPath\n // arc (used for long-range) requires moveTo after beginPath (or else a\n // unwanted line at y=0 is rendered along with the arc)\n if (longRange && drawArcInsteadOfBezier) {\n ctx.moveTo(p, 0)\n ctx.beginPath()\n } else {\n ctx.beginPath()\n ctx.moveTo(p, 0)\n }\n\n if (longRange && drawArcInsteadOfBezier) {\n ctx.strokeStyle = 'red'\n } else {\n if (hasPaired) {\n if (type === 'insertSizeAndOrientation') {\n ctx.strokeStyle = getPairedInsertSizeAndOrientationColor(\n k1,\n k2,\n stats,\n )[0]\n } else if (type === 'orientation') {\n ctx.strokeStyle = getPairedOrientationColor(k1)[0]\n } else if (type === 'insertSize') {\n ctx.strokeStyle =\n getPairedInsertSizeColor(k1, k2, stats)?.[0] || 'grey'\n } else if (type === 'gradient') {\n ctx.strokeStyle = `hsl(${Math.log10(absrad) * 10},50%,50%)`\n }\n } else {\n if (type === 'orientation' || type === 'insertSizeAndOrientation') {\n if (s1 === -1 && s2 === 1) {\n ctx.strokeStyle = 'navy'\n } else if (s1 === 1 && s2 === -1) {\n ctx.strokeStyle = 'green'\n } else {\n ctx.strokeStyle = 'grey'\n }\n } else if (type === 'gradient') {\n ctx.strokeStyle = `hsl(${Math.log10(absrad) * 10},50%,50%)`\n }\n }\n }\n\n const destX = p + radius * 2\n const destY = Math.min(height + jitter(jitterVal), absrad)\n if (longRange) {\n // avoid drawing gigantic circles that glitch out the rendering,\n // instead draw vertical lines\n if (absrad > 100_000) {\n drawLineAtOffset(ctx, p + jitter(jitterVal), height, 'red')\n drawLineAtOffset(ctx, p2 + jitter(jitterVal), height, 'red')\n } else if (drawArcInsteadOfBezier) {\n ctx.arc(p + radius + jitter(jitterVal), 0, absrad, 0, Math.PI)\n ctx.stroke()\n } else {\n ctx.bezierCurveTo(\n p + jitter(jitterVal),\n destY,\n destX,\n destY,\n destX + jitter(jitterVal),\n 0,\n )\n ctx.stroke()\n }\n } else {\n ctx.bezierCurveTo(\n p + jitter(jitterVal),\n destY,\n destX,\n destY,\n destX + jitter(jitterVal),\n 0,\n )\n ctx.stroke()\n }\n } else if (r1 && drawInter) {\n drawLineAtOffset(ctx, r1 - view.offsetPx, height, 'purple')\n }\n }\n\n for (const chain of chains) {\n // chain.length === 1, singleton (other pairs/mates not in view)\n if (chain.length === 1 && drawLongRange) {\n const f = chain[0]!\n if (hasPaired && !(f.flags & 8)) {\n const mate = {\n refName: f.next_ref || '',\n start: f.next_pos || 0,\n end: f.next_pos || 0,\n strand: f.strand,\n }\n draw(f, mate, asm, true)\n } else {\n const features = [f, ...featurizeSA(f.SA, f.id, f.strand, f.name)].sort(\n (a, b) => a.clipPos - b.clipPos,\n )\n for (let i = 0; i < features.length - 1; i++) {\n const f = features[i]!\n const v1 = features[i + 1]!\n draw(f, v1, asm, true)\n }\n }\n } else {\n const res = hasPaired\n ? chain.filter(f => !(f.flags & 2048) && !(f.flags & 8))\n : chain\n .sort((a, b) => a.clipPos - b.clipPos)\n .filter(f => !(f.flags & 256))\n for (let i = 0; i < res.length - 1; i++) {\n draw(res[i]!, res[i + 1]!, asm, false)\n }\n }\n }\n}\n","import { ChainData } from './fetchChains'\n\nexport function hasPairedReads(features: ChainData) {\n for (const f of features.chains.values()) {\n if (f[0]!.flags & 1) {\n return true\n }\n }\n return false\n}\n"],"names":["jitter","n","Math","random","drawLineAtOffset","ctx","offset","height","color","strokeStyle","beginPath","moveTo","lineTo","stroke","drawFeats","self","width","chainData","colorBy","drawInter","drawLongRange","lineWidthSetting","jitterVal","view","getContainingView","assemblyManager","getSession","chains","stats","hasPaired","hasPairedReads","asm","get","assemblyNames","type","lineWidth","chain","length","f","flags","features","featurizeSA","SA","id","strand","name","sort","a","b","clipPos","i","draw","refName","next_ref","start","next_pos","end","res","filter","k1","k2","assembly","longRange","s1","s2","f2","p1","p2","ra1","getCanonicalRefName","ra2","r1","bpToPx","coord","offsetPx","r2","undefined","radius","absrad","abs","p","drawArcInsteadOfBezier","getPairedInsertSizeAndOrientationColor","getPairedOrientationColor","getPairedInsertSizeColor","log10","destX","destY","min","arc","PI","bezierCurveTo","values"],"sourceRoot":""}

Mercurial > repos > fubar > jbrowse2

comparison x/static/js/3304.65e5d8dd.chunk.js.map @ 125:49f3d3878413 draft