jbrowse2: x/static/js/6946.dd09a891.chunk.js.map comparison

comparison x/static/js/6946.dd09a891.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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avoid drawing negative width features for SVG exports\nexport function fillRectCtx(\n x: number,\n y: number,\n width: number,\n height: number,\n ctx: CanvasRenderingContext2D,\n fillColor?: string,\n) {\n if (width < 0) {\n x += width\n width = -width\n }\n if (height < 0) {\n y += height\n height = -height\n }\n\n if (fillColor) {\n ctx.fillStyle = fillColor\n }\n\n ctx.fillRect(x, y, width, height)\n}\n\nexport function strokeRectCtx(\n x: number,\n y: number,\n width: number,\n height: number,\n ctx: CanvasRenderingContext2D,\n strokeColor?: string,\n) {\n if (width < 0) {\n x += width\n width = -width\n }\n if (height < 0) {\n y += height\n height = -height\n }\n\n if (strokeColor) {\n ctx.strokeStyle = strokeColor\n }\n ctx.strokeRect(x, y, width, height)\n}\n","import { getConf } from '@jbrowse/core/configuration'\nimport { max, min } from '@jbrowse/core/util'\nimport { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'\nimport { Assembly } from '@jbrowse/core/assemblyManager/assembly'\n\nimport { ChainData, ChainStats, ReducedFeature } from '../shared/fetchChains'\nimport { LinearReadCloudDisplayModel } from './model'\nimport { fillRectCtx, strokeRectCtx } from './util'\nimport {\n getPairedInsertSizeAndOrientationColor,\n getPairedInsertSizeColor,\n getPairedOrientationColor,\n} from '../shared/color'\n\ninterface ChainCoord {\n distance: number\n r1s: number\n r1e: number\n r2s: number\n r2e: number\n v0: ReducedFeature\n v1: ReducedFeature\n}\n\nexport function drawPairChains({\n ctx,\n self,\n chainData,\n view,\n asm,\n}: {\n ctx: CanvasRenderingContext2D\n self: LinearReadCloudDisplayModel\n chainData: ChainData\n view: LinearGenomeViewModel\n asm: Assembly\n}) {\n const coords: ChainCoord[] = []\n const featureHeight = getConf(self, 'featureHeight')\n const type = self.colorBy?.type \|\| 'insertSizeAndOrientation'\n const { chains, stats } = chainData\n\n for (const chain of chains) {\n // if we're looking at a paired read (flag 1) then assume it is just\n // two reads (some small cases may defy this assumption such as\n // secondary alignments but this may be uncommon)\n if (chain.length > 1) {\n const v0 = chain[0]!\n const v1 = chain[1]!\n const ra1 = asm.getCanonicalRefName(v0.refName) \|\| v0.refName\n const ra2 = asm.getCanonicalRefName(v1.refName) \|\| v1.refName\n const r1s = view.bpToPx({ refName: ra1, coord: v0.start })?.offsetPx\n const r1e = view.bpToPx({ refName: ra1, coord: v0.end })?.offsetPx\n const r2s = view.bpToPx({ refName: ra2, coord: v1.start })?.offsetPx\n const r2e = view.bpToPx({ refName: ra2, coord: v1.end })?.offsetPx\n\n let distance = 0\n\n if (\n r1s !== undefined &&\n r1e !== undefined &&\n r2s !== undefined &&\n r2e !== undefined\n ) {\n if (v0.refName === v1.refName) {\n const s = Math.min(v0.start, v1.start)\n const e = Math.max(v0.end, v1.end)\n distance = Math.abs(e - s)\n }\n coords.push({\n r1s,\n r1e,\n r2s,\n r2e,\n v0,\n v1,\n distance,\n })\n }\n } else if (self.drawSingletons) {\n const v0 = chain[0]!\n\n const ra1 = asm.getCanonicalRefName(v0.refName) \|\| v0.refName\n const r1s = view.bpToPx({ refName: ra1, coord: v0.start })?.offsetPx\n const r1e = view.bpToPx({ refName: ra1, coord: v0.end })?.offsetPx\n if (r1s !== undefined && r1e !== undefined) {\n const w1 = Math.max(r1e - r1s, 2)\n fillRectCtx(r1s - view.offsetPx, 0, w1, featureHeight, ctx, '#f00')\n strokeRectCtx(r1s - view.offsetPx, 0, w1, featureHeight, ctx, '#a00')\n }\n }\n }\n\n const maxD = Math.log(max(coords.map(c => c.distance)))\n const minD = Math.max(Math.log(min(coords.map(c => c.distance))) - 1, 0)\n const scaler = (self.height - 20) / (maxD - minD)\n for (const { r1e, r1s, r2e, r2s, distance, v0, v1 } of coords) {\n const w1 = Math.max(r1e - r1s, 2)\n const w2 = Math.max(r2e - r2s, 2)\n const [fill, stroke] = getPairedColor({ type, v0, v1, stats }) \|\| []\n const top = (Math.log(distance) - minD) * scaler\n const halfHeight = featureHeight / 2 - 0.5\n const w = r2s - r1e\n fillRectCtx(r1e - view.offsetPx, top + halfHeight, w, 1, ctx, 'black')\n strokeRectCtx(r1s - view.offsetPx, top, w1, featureHeight, ctx, stroke)\n strokeRectCtx(r2s - view.offsetPx, top, w2, featureHeight, ctx, stroke)\n fillRectCtx(r1s - view.offsetPx, top, w1, featureHeight, ctx, fill)\n fillRectCtx(r2s - view.offsetPx, top, w2, featureHeight, ctx, fill)\n }\n}\n\nexport function getPairedColor({\n type,\n v0,\n v1,\n stats,\n}: {\n type: string\n v0: ReducedFeature\n v1: ReducedFeature\n stats?: ChainStats\n}): readonly [string, string] \| undefined {\n if (type === 'insertSizeAndOrientation') {\n return getPairedInsertSizeAndOrientationColor(v0, v1, stats)\n }\n if (type === 'orientation') {\n return getPairedOrientationColor(v0)\n }\n if (type === 'insertSize') {\n return getPairedInsertSizeColor(v0, v1, stats)\n }\n if (type === 'gradient') {\n const s = Math.min(v0.start, v1.start)\n const e = Math.max(v0.end, v1.end)\n return [\n `hsl(${Math.log10(Math.abs(e - s)) * 10},50%,50%)`,\n `hsl(${Math.log10(Math.abs(e - s)) * 10},50%,30%)`,\n ] as const\n }\n return undefined\n}\n","import { getContainingView, getSession } from '@jbrowse/core/util'\nimport { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'\n\n// locals\nimport { LinearReadCloudDisplayModel } from './model'\nimport { hasPairedReads } from '../shared/util'\nimport { drawPairChains } from './drawPairChains'\nimport { drawLongReadChains } from './drawLongReadChains'\n\ntype LGV = LinearGenomeViewModel\n\nexport function drawFeats(\n self: LinearReadCloudDisplayModel,\n ctx: CanvasRenderingContext2D,\n) {\n const { chainData } = self\n if (!chainData) {\n return\n }\n const { assemblyManager } = getSession(self)\n const view = getContainingView(self) as LGV\n const assemblyName = view.assemblyNames[0]!\n const asm = assemblyManager.get(assemblyName)\n if (!asm) {\n return\n }\n\n const hasPaired = hasPairedReads(chainData)\n\n if (hasPaired) {\n drawPairChains({ self, view, asm, ctx, chainData })\n } else {\n drawLongReadChains({ self, view, asm, ctx, chainData })\n }\n}\n","import { getConf } from '@jbrowse/core/configuration'\nimport { max, min } from '@jbrowse/core/util'\nimport { Assembly } from '@jbrowse/core/assemblyManager/assembly'\nimport { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'\n\n// locals\nimport { ChainData } from '../shared/fetchChains'\nimport { LinearReadCloudDisplayModel } from './model'\nimport { fillColor, strokeColor } from '../shared/color'\nimport { fillRectCtx, strokeRectCtx } from './util'\n\nexport function drawLongReadChains({\n ctx,\n self,\n chainData,\n view,\n asm,\n}: {\n ctx: CanvasRenderingContext2D\n self: LinearReadCloudDisplayModel\n chainData: ChainData\n view: LinearGenomeViewModel\n asm: Assembly\n}) {\n const distances: number[] = []\n const minXs: number[] = []\n const { chains } = chainData\n const { height } = self\n const featureHeight = getConf(self, 'featureHeight')\n\n // get bounds on the 'distances' (pixel span that a particular split long\n // read 'chain' would have in view)\n for (const chain of chains) {\n let minX = Number.MAX_VALUE\n let maxX = Number.MIN_VALUE\n for (const elt of chain) {\n const refName = asm.getCanonicalRefName(elt.refName) \|\| elt.refName\n const rs = view.bpToPx({ refName, coord: elt.start })?.offsetPx\n const re = view.bpToPx({ refName, coord: elt.end })?.offsetPx\n if (rs !== undefined && re !== undefined) {\n minX = Math.min(minX, rs)\n maxX = Math.max(maxX, re)\n }\n }\n const distance = Math.abs(maxX - minX)\n distances.push(distance)\n minXs.push(minX)\n }\n\n const maxD = Math.log(max(distances))\n const minD = Math.max(Math.log(min(distances)) - 1, 0)\n const scaler = (height - 20) / (maxD - minD)\n const halfHeight = featureHeight / 2 - 0.5\n\n // draw split long read 'chains' as connected entities\n for (let i = 0; i < chains.length; i++) {\n const chain = chains[i]!\n const w = distances[i]!\n const top = (Math.log(w) - minD) * scaler\n const min = minXs[i]!\n fillRectCtx(min - view.offsetPx, top + halfHeight, w, 1, ctx, 'black')\n const c1 = chain[0]!\n let primaryStrand: undefined \| number\n if (!(c1.flags & 2048)) {\n primaryStrand = c1.strand\n } else {\n const res = c1.SA?.split(';')[0]!.split(',')[2]\n primaryStrand = res === '-' ? -1 : 1\n }\n for (const v0 of chain) {\n const ra = asm.getCanonicalRefName(v0.refName) \|\| v0.refName\n const rs = view.bpToPx({ refName: ra, coord: v0.start })?.offsetPx\n const re = view.bpToPx({ refName: ra, coord: v0.end })?.offsetPx\n if (rs !== undefined && re !== undefined) {\n const w = Math.max(re - rs, 2)\n const l = rs - view.offsetPx\n const effectiveStrand = v0.strand * primaryStrand\n const c =\n effectiveStrand === -1 ? 'color_rev_strand' : 'color_fwd_strand'\n strokeRectCtx(l, top, w, featureHeight, ctx, strokeColor[c])\n fillRectCtx(l, top, w, featureHeight, ctx, fillColor[c])\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":["fillRectCtx","x","y","width","height","ctx","fillColor","fillStyle","fillRect","strokeRectCtx","strokeColor","strokeStyle","strokeRect","getPairedColor","type","v0","v1","stats","getPairedInsertSizeAndOrientationColor","getPairedOrientationColor","getPairedInsertSizeColor","s","Math","min","start","e","max","end","log10","abs","drawFeats","self","chainData","assemblyManager","getSession","view","getContainingView","assemblyName","assemblyNames","asm","get","hasPairedReads","coords","featureHeight","getConf","colorBy","chains","chain","length","ra1","getCanonicalRefName","refName","ra2","r1s","bpToPx","coord","offsetPx","r1e","r2s","r2e","distance","undefined","push","drawSingletons","w1","maxD","log","map","c","minD","scaler","w2","fill","stroke","top","halfHeight","w","drawPairChains","distances","minXs","minX","Number","MAX_VALUE","maxX","MIN_VALUE","elt","rs","re","i","c1","primaryStrand","flags","res","SA","split","strand","ra","l","drawLongReadChains","features","f","values"],"sourceRoot":""}

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avoid drawing negative width features for SVG exports\nexport function fillRectCtx(\n x: number,\n y: number,\n width: number,\n height: number,\n ctx: CanvasRenderingContext2D,\n fillColor?: string,\n) {\n if (width < 0) {\n x += width\n width = -width\n }\n if (height < 0) {\n y += height\n height = -height\n }\n\n if (fillColor) {\n ctx.fillStyle = fillColor\n }\n\n ctx.fillRect(x, y, width, height)\n}\n\nexport function strokeRectCtx(\n x: number,\n y: number,\n width: number,\n height: number,\n ctx: CanvasRenderingContext2D,\n strokeColor?: string,\n) {\n if (width < 0) {\n x += width\n width = -width\n }\n if (height < 0) {\n y += height\n height = -height\n }\n\n if (strokeColor) {\n ctx.strokeStyle = strokeColor\n }\n ctx.strokeRect(x, y, width, height)\n}\n","import { getConf } from '@jbrowse/core/configuration'\nimport { max, min } from '@jbrowse/core/util'\nimport { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'\nimport { Assembly } from '@jbrowse/core/assemblyManager/assembly'\n\nimport { ChainData, ChainStats, ReducedFeature } from '../shared/fetchChains'\nimport { LinearReadCloudDisplayModel } from './model'\nimport { fillRectCtx, strokeRectCtx } from './util'\nimport {\n getPairedInsertSizeAndOrientationColor,\n getPairedInsertSizeColor,\n getPairedOrientationColor,\n} from '../shared/color'\n\ninterface ChainCoord {\n distance: number\n r1s: number\n r1e: number\n r2s: number\n r2e: number\n v0: ReducedFeature\n v1: ReducedFeature\n}\n\nexport function drawPairChains({\n ctx,\n self,\n chainData,\n view,\n asm,\n}: {\n ctx: CanvasRenderingContext2D\n self: LinearReadCloudDisplayModel\n chainData: ChainData\n view: LinearGenomeViewModel\n asm: Assembly\n}) {\n const coords: ChainCoord[] = []\n const featureHeight = getConf(self, 'featureHeight')\n const type = self.colorBy?.type || 'insertSizeAndOrientation'\n const { chains, stats } = chainData\n\n for (const chain of chains) {\n // if we're looking at a paired read (flag 1) then assume it is just\n // two reads (some small cases may defy this assumption such as\n // secondary alignments but this may be uncommon)\n if (chain.length > 1) {\n const v0 = chain[0]!\n const v1 = chain[1]!\n const ra1 = asm.getCanonicalRefName(v0.refName) || v0.refName\n const ra2 = asm.getCanonicalRefName(v1.refName) || v1.refName\n const r1s = view.bpToPx({ refName: ra1, coord: v0.start })?.offsetPx\n const r1e = view.bpToPx({ refName: ra1, coord: v0.end })?.offsetPx\n const r2s = view.bpToPx({ refName: ra2, coord: v1.start })?.offsetPx\n const r2e = view.bpToPx({ refName: ra2, coord: v1.end })?.offsetPx\n\n let distance = 0\n\n if (\n r1s !== undefined &&\n r1e !== undefined &&\n r2s !== undefined &&\n r2e !== undefined\n ) {\n if (v0.refName === v1.refName) {\n const s = Math.min(v0.start, v1.start)\n const e = Math.max(v0.end, v1.end)\n distance = Math.abs(e - s)\n }\n coords.push({\n r1s,\n r1e,\n r2s,\n r2e,\n v0,\n v1,\n distance,\n })\n }\n } else if (self.drawSingletons) {\n const v0 = chain[0]!\n\n const ra1 = asm.getCanonicalRefName(v0.refName) || v0.refName\n const r1s = view.bpToPx({ refName: ra1, coord: v0.start })?.offsetPx\n const r1e = view.bpToPx({ refName: ra1, coord: v0.end })?.offsetPx\n if (r1s !== undefined && r1e !== undefined) {\n const w1 = Math.max(r1e - r1s, 2)\n fillRectCtx(r1s - view.offsetPx, 0, w1, featureHeight, ctx, '#f00')\n strokeRectCtx(r1s - view.offsetPx, 0, w1, featureHeight, ctx, '#a00')\n }\n }\n }\n\n const maxD = Math.log(max(coords.map(c => c.distance)))\n const minD = Math.max(Math.log(min(coords.map(c => c.distance))) - 1, 0)\n const scaler = (self.height - 20) / (maxD - minD)\n for (const { r1e, r1s, r2e, r2s, distance, v0, v1 } of coords) {\n const w1 = Math.max(r1e - r1s, 2)\n const w2 = Math.max(r2e - r2s, 2)\n const [fill, stroke] = getPairedColor({ type, v0, v1, stats }) || []\n const top = (Math.log(distance) - minD) * scaler\n const halfHeight = featureHeight / 2 - 0.5\n const w = r2s - r1e\n fillRectCtx(r1e - view.offsetPx, top + halfHeight, w, 1, ctx, 'black')\n strokeRectCtx(r1s - view.offsetPx, top, w1, featureHeight, ctx, stroke)\n strokeRectCtx(r2s - view.offsetPx, top, w2, featureHeight, ctx, stroke)\n fillRectCtx(r1s - view.offsetPx, top, w1, featureHeight, ctx, fill)\n fillRectCtx(r2s - view.offsetPx, top, w2, featureHeight, ctx, fill)\n }\n}\n\nexport function getPairedColor({\n type,\n v0,\n v1,\n stats,\n}: {\n type: string\n v0: ReducedFeature\n v1: ReducedFeature\n stats?: ChainStats\n}): readonly [string, string] | undefined {\n if (type === 'insertSizeAndOrientation') {\n return getPairedInsertSizeAndOrientationColor(v0, v1, stats)\n }\n if (type === 'orientation') {\n return getPairedOrientationColor(v0)\n }\n if (type === 'insertSize') {\n return getPairedInsertSizeColor(v0, v1, stats)\n }\n if (type === 'gradient') {\n const s = Math.min(v0.start, v1.start)\n const e = Math.max(v0.end, v1.end)\n return [\n `hsl(${Math.log10(Math.abs(e - s)) * 10},50%,50%)`,\n `hsl(${Math.log10(Math.abs(e - s)) * 10},50%,30%)`,\n ] as const\n }\n return undefined\n}\n","import { getContainingView, getSession } from '@jbrowse/core/util'\nimport { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'\n\n// locals\nimport { LinearReadCloudDisplayModel } from './model'\nimport { hasPairedReads } from '../shared/util'\nimport { drawPairChains } from './drawPairChains'\nimport { drawLongReadChains } from './drawLongReadChains'\n\ntype LGV = LinearGenomeViewModel\n\nexport function drawFeats(\n self: LinearReadCloudDisplayModel,\n ctx: CanvasRenderingContext2D,\n) {\n const { chainData } = self\n if (!chainData) {\n return\n }\n const { assemblyManager } = getSession(self)\n const view = getContainingView(self) as LGV\n const assemblyName = view.assemblyNames[0]!\n const asm = assemblyManager.get(assemblyName)\n if (!asm) {\n return\n }\n\n const hasPaired = hasPairedReads(chainData)\n\n if (hasPaired) {\n drawPairChains({ self, view, asm, ctx, chainData })\n } else {\n drawLongReadChains({ self, view, asm, ctx, chainData })\n }\n}\n","import { getConf } from '@jbrowse/core/configuration'\nimport { max, min } from '@jbrowse/core/util'\nimport { Assembly } from '@jbrowse/core/assemblyManager/assembly'\nimport { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'\n\n// locals\nimport { ChainData } from '../shared/fetchChains'\nimport { LinearReadCloudDisplayModel } from './model'\nimport { fillColor, strokeColor } from '../shared/color'\nimport { fillRectCtx, strokeRectCtx } from './util'\n\nexport function drawLongReadChains({\n ctx,\n self,\n chainData,\n view,\n asm,\n}: {\n ctx: CanvasRenderingContext2D\n self: LinearReadCloudDisplayModel\n chainData: ChainData\n view: LinearGenomeViewModel\n asm: Assembly\n}) {\n const distances: number[] = []\n const minXs: number[] = []\n const { chains } = chainData\n const { height } = self\n const featureHeight = getConf(self, 'featureHeight')\n\n // get bounds on the 'distances' (pixel span that a particular split long\n // read 'chain' would have in view)\n for (const chain of chains) {\n let minX = Number.MAX_VALUE\n let maxX = Number.MIN_VALUE\n for (const elt of chain) {\n const refName = asm.getCanonicalRefName(elt.refName) || elt.refName\n const rs = view.bpToPx({ refName, coord: elt.start })?.offsetPx\n const re = view.bpToPx({ refName, coord: elt.end })?.offsetPx\n if (rs !== undefined && re !== undefined) {\n minX = Math.min(minX, rs)\n maxX = Math.max(maxX, re)\n }\n }\n const distance = Math.abs(maxX - minX)\n distances.push(distance)\n minXs.push(minX)\n }\n\n const maxD = Math.log(max(distances))\n const minD = Math.max(Math.log(min(distances)) - 1, 0)\n const scaler = (height - 20) / (maxD - minD)\n const halfHeight = featureHeight / 2 - 0.5\n\n // draw split long read 'chains' as connected entities\n for (let i = 0; i < chains.length; i++) {\n const chain = chains[i]!\n const w = distances[i]!\n const top = (Math.log(w) - minD) * scaler\n const min = minXs[i]!\n fillRectCtx(min - view.offsetPx, top + halfHeight, w, 1, ctx, 'black')\n const c1 = chain[0]!\n let primaryStrand: undefined | number\n if (!(c1.flags & 2048)) {\n primaryStrand = c1.strand\n } else {\n const res = c1.SA?.split(';')[0]!.split(',')[2]\n primaryStrand = res === '-' ? -1 : 1\n }\n for (const v0 of chain) {\n const ra = asm.getCanonicalRefName(v0.refName) || v0.refName\n const rs = view.bpToPx({ refName: ra, coord: v0.start })?.offsetPx\n const re = view.bpToPx({ refName: ra, coord: v0.end })?.offsetPx\n if (rs !== undefined && re !== undefined) {\n const w = Math.max(re - rs, 2)\n const l = rs - view.offsetPx\n const effectiveStrand = v0.strand * primaryStrand\n const c =\n effectiveStrand === -1 ? 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Mercurial > repos > fubar > jbrowse2

comparison x/static/js/6946.dd09a891.chunk.js.map @ 125:49f3d3878413 draft