jbrowse2: x/static/js/8856.4593419f.chunk.js.map annotate

annotate x/static/js/8856.4593419f.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

rev	line source
125 49f3d3878413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566 fubar parents: diff changeset	1 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{ addDisposer, getSnapshot } from 'mobx-state-tree'\n\nimport { Feature, getContainingView, getSession } from '@jbrowse/core/util'\nimport { bpToPx } from '@jbrowse/core/util/Base1DUtils'\nimport { MismatchParser } from '@jbrowse/plugin-alignments'\nimport { reaction, autorun } from 'mobx'\n\n// locals\nimport { LinearSyntenyViewModel } from '../LinearSyntenyView/model'\nimport { drawMouseoverSynteny, drawRef } from './drawSynteny'\nimport { LinearSyntenyDisplayModel } from './model'\n\ninterface Pos {\n offsetPx: number\n}\n\ninterface FeatPos {\n p11: Pos\n p12: Pos\n p21: Pos\n p22: Pos\n f: Feature\n cigar: string[]\n}\n\ntype LSV = LinearSyntenyViewModel\n\nexport function doAfterAttach(self: LinearSyntenyDisplayModel) {\n addDisposer(\n self,\n autorun(() => {\n const view = getContainingView(self) as LinearSyntenyViewModel\n if (!view.initialized) {\n return\n }\n const ctx1 = self.mainCanvas?.getContext('2d')\n const ctx3 = self.cigarClickMapCanvas?.getContext('2d')\n if (!ctx1 \|\| !ctx3) {\n return\n }\n\n const height = view.middleComparativeHeight\n const width = view.width\n ctx1.clearRect(0, 0, width, height)\n ctx3.clearRect(0, 0, width, height)\n drawRef(self, ctx1, ctx3)\n }),\n )\n\n addDisposer(\n self,\n autorun(() => {\n const view = getContainingView(self) as LinearSyntenyViewModel\n if (!view.initialized) {\n return\n }\n drawMouseoverSynteny(self)\n }),\n )\n\n // this attempts to reduce recalculation of feature positions drawn by\n // the synteny view\n //\n // uses a reaction to say \"we know the positions don't change in any\n // relevant way unless bpPerPx changes or displayedRegions changes\"\n addDisposer(\n self,\n reaction(\n () => {\n const view = getContainingView(self) as LSV\n return {\n bpPerPx: view.views.map(v => v.bpPerPx),\n\n // stringifying 'deeply' accesses the displayed regions, see\n // issue #3456\n displayedRegions: JSON.stringify(\n view.views.map(v => v.displayedRegions),\n ),\n features: self.features,\n initialized: view.initialized,\n }\n },\n ({ initialized }) => {\n if (!initialized) {\n return\n }\n const { assemblyManager } = getSession(self)\n const view = getContainingView(self) as LSV\n const viewSnaps = view.views.map(view => ({\n ...getSnapshot(view),\n width: view.width,\n staticBlocks: view.staticBlocks,\n interRegionPaddingWidth: view.interRegionPaddingWidth,\n minimumBlockWidth: view.minimumBlockWidth,\n }))\n\n const map = [] as FeatPos[]\n const feats = self.features \|\| []\n\n for (const f of feats) {\n const mate = f.get('mate')\n let f1s = f.get('start')\n let f1e = f.get('end')\n const f2s = mate.start\n const f2e = mate.end\n\n if (f.get('strand') === -1) {\n ;[f1e, f1s] = [f1s, f1e]\n }\n const a1 = assemblyManager.get(f.get('assemblyName'))\n const a2 = assemblyManager.get(mate.assemblyName)\n const r1 = f.get('refName')\n const r2 = mate.refName\n const ref1 = a1?.getCanonicalRefName(r1) \|\| r1\n const ref2 = a2?.getCanonicalRefName(r2) \|\| r2\n const v1 = viewSnaps[0]!\n const v2 = viewSnaps[1]!\n const p11 = bpToPx({ self: v1, refName: ref1, coord: f1s })\n const p12 = bpToPx({ self: v1, refName: ref1, coord: f1e })\n const p21 = bpToPx({ self: v2, refName: ref2, coord: f2s })\n const p22 = bpToPx({ self: v2, refName: ref2, coord: f2e })\n\n if (\n p11 === undefined \|\|\n p12 === undefined \|\|\n p21 === undefined \|\|\n p22 === undefined\n ) {\n continue\n }\n\n const cigar = f.get('CIGAR') as string \| undefined\n map.push({\n p11,\n p12,\n p21,\n p22,\n f,\n cigar: MismatchParser.parseCigar(cigar),\n })\n }\n\n self.setFeatPositions(map)\n },\n { fireImmediately: true },\n ),\n )\n}\n","import React from 'react'\nimport {\n assembleLocString,\n doesIntersect2,\n getSession,\n isSessionModelWithWidgets,\n Feature,\n getContainingTrack,\n getContainingView,\n} from '@jbrowse/core/util'\n\n// locals\nimport { getId, MAX_COLOR_RANGE } from '../drawSynteny'\nimport { LinearSyntenyDisplayModel } from '../model'\n\ninterface Pos {\n offsetPx: number\n}\n\nexport interface ClickCoord {\n clientX: number\n clientY: number\n feature: { f: Feature }\n}\n\ninterface FeatPos {\n p11: Pos\n p12: Pos\n p21: Pos\n p22: Pos\n f: Feature\n cigar: string[]\n}\n\nexport function drawMatchSimple({\n feature,\n ctx,\n offsets,\n cb,\n height,\n drawCurves,\n oobLimit,\n viewWidth,\n hideTiny,\n}: {\n feature: FeatPos\n ctx: CanvasRenderingContext2D\n offsets: number[]\n oobLimit: number\n viewWidth: number\n cb: (ctx: CanvasRenderingContext2D) => void\n height: number\n drawCurves?: boolean\n hideTiny?: boolean\n}) {\n const { p11, p12, p21, p22 } = feature\n\n const x11 = p11.offsetPx - offsets[0]!\n const x12 = p12.offsetPx - offsets[0]!\n const x21 = p21.offsetPx - offsets[1]!\n const x22 = p22.offsetPx - offsets[1]!\n\n const l1 = Math.abs(x12 - x11)\n const l2 = Math.abs(x22 - x21)\n const y1 = 0\n const y2 = height\n const mid = (y2 - y1) / 2\n const minX = Math.min(x21, x22)\n const maxX = Math.max(x21, x22)\n\n if (!doesIntersect2(minX, maxX, -oobLimit, viewWidth + oobLimit)) {\n return\n }\n\n // drawing a line if the results are thin: drawing a line results in much\n // less pixellation than filling in a thin polygon\n if (l1 <= 1 && l2 <= 1) {\n // hideTiny can be used to avoid drawing mouseover for thin lines in this\n // case\n if (!hideTiny) {\n ctx.beginPath()\n ctx.moveTo(x11, y1)\n if (drawCurves) {\n ctx.bezierCurveTo(x11, mid, x21, mid, x21, y2)\n } else {\n ctx.lineTo(x21, y2)\n }\n ctx.stroke()\n }\n } else {\n draw(ctx, x11, x12, y1, x22, x21, y2, mid, drawCurves)\n cb(ctx)\n }\n}\n\nexport function draw(\n ctx: CanvasRenderingContext2D,\n x1: number,\n x2: number,\n y1: number,\n x3: number,\n x4: number,\n y2: number,\n mid: number,\n drawCurves?: boolean,\n) {\n if (drawCurves) {\n drawBezierBox(ctx, x1, x2, y1, x3, x4, y2, mid)\n } else {\n drawBox(ctx, x1, x2, y1, x3, x4, y2)\n }\n}\n\nexport function drawBox(\n ctx: CanvasRenderingContext2D,\n x1: number,\n x2: number,\n y1: number,\n x3: number,\n x4: number,\n y2: number,\n) {\n ctx.beginPath()\n ctx.moveTo(x1, y1)\n ctx.lineTo(x2, y1)\n ctx.lineTo(x3, y2)\n ctx.lineTo(x4, y2)\n ctx.closePath()\n ctx.fill()\n}\n\nexport function drawBezierBox(\n ctx: CanvasRenderingContext2D,\n x1: number,\n x2: number,\n y1: number,\n x3: number,\n x4: number,\n y2: number,\n mid: number,\n) {\n const len1 = Math.abs(x1 - x2)\n const len2 = Math.abs(x1 - x2)\n\n // heuristic to not draw hourglass inversions with bezier curves when they\n // are thin and far apart because it results in areas that are not drawn well\n // demo https://codesandbox.io/s/fast-glitter-q3b1or?file=/src/index.js\n if (len1 < 5 && len2 < 5 && x2 < x1 && Math.abs(x1 - x3) > 100) {\n const tmp = x1\n x1 = x2\n x2 = tmp\n }\n ctx.beginPath()\n ctx.moveTo(x1, y1)\n ctx.lineTo(x2, y1)\n ctx.bezierCurveTo(x2, mid, x3, mid, x3, y2)\n ctx.lineTo(x4, y2)\n ctx.bezierCurveTo(x4, mid, x1, mid, x1, y1)\n ctx.closePath()\n ctx.fill()\n}\n\nexport function onSynClick(\n event: React.MouseEvent,\n model: LinearSyntenyDisplayModel,\n) {\n const view = getContainingView(model)\n const track = getContainingTrack(model)\n const ref1 = model.clickMapCanvas\n const ref2 = model.cigarClickMapCanvas\n if (!ref1 \|\| !ref2) {\n return\n }\n const rect = ref1.getBoundingClientRect()\n const ctx1 = ref1.getContext('2d')\n const ctx2 = ref2.getContext('2d')\n if (!ctx1 \|\| !ctx2) {\n return\n }\n const x = event.clientX - rect.left\n const y = event.clientY - rect.top\n const [r1, g1, b1] = ctx1.getImageData(x, y, 1, 1).data\n const unitMultiplier = Math.floor(MAX_COLOR_RANGE / model.numFeats)\n const id = getId(r1!, g1!, b1!, unitMultiplier)\n const feat = model.featPositions[id]\n if (feat) {\n const { f } = feat\n model.setClickId(f.id())\n const session = getSession(model)\n if (isSessionModelWithWidgets(session)) {\n session.showWidget(\n session.addWidget('BaseFeatureWidget', 'baseFeature', {\n view,\n track,\n featureData: f.toJSON(),\n }),\n )\n }\n }\n return feat\n}\n\nexport function onSynContextClick(\n event: React.MouseEvent,\n model: LinearSyntenyDisplayModel,\n setAnchorEl: (arg: ClickCoord) => void,\n) {\n event.preventDefault()\n const ref1 = model.clickMapCanvas\n const ref2 = model.cigarClickMapCanvas\n if (!ref1 \|\| !ref2) {\n return\n }\n const rect = ref1.getBoundingClientRect()\n const ctx1 = ref1.getContext('2d')\n const ctx2 = ref2.getContext('2d')\n if (!ctx1 \|\| !ctx2) {\n return\n }\n const { clientX, clientY } = event\n const x = clientX - rect.left\n const y = clientY - rect.top\n const [r1, g1, b1] = ctx1.getImageData(x, y, 1, 1).data\n const unitMultiplier = Math.floor(MAX_COLOR_RANGE / model.numFeats)\n const id = getId(r1!, g1!, b1!, unitMultiplier)\n const f = model.featPositions[id]\n if (f) {\n model.setClickId(f.f.id())\n setAnchorEl({ clientX, clientY, feature: f })\n }\n}\n\nexport function getTooltip(f: Feature, cigarOp?: string, cigarOpLen?: string) {\n // @ts-expect-error\n const f1 = f.toJSON() as {\n refName: string\n start: number\n end: number\n strand?: number\n assemblyName: string\n identity?: number\n name?: string\n mate: {\n start: number\n end: number\n refName: string\n name: string\n }\n }\n const f2 = f1.mate\n const l1 = f1.end - f1.start\n const l2 = f2.end - f2.start\n const identity = f1.identity\n const n1 = f1.name\n const n2 = f2.name\n return [\n `Loc1: ${assembleLocString(f1)}`,\n `Loc2: ${assembleLocString(f2)}`,\n `Inverted: ${f1.strand === -1}`,\n `Query len: ${l1.toLocaleString('en-US')}`,\n `Target len: ${l2.toLocaleString('en-US')}`,\n identity ? `Identity: ${identity.toPrecision(2)}` : '',\n cigarOp ? `CIGAR operator: ${cigarOp}${cigarOpLen}` : '',\n n1 ? `Name 1: ${n1}` : '',\n n2 ? `Name 1: ${n2}` : '',\n ]\n .filter(f => !!f)\n .join('<br/>')\n}\n","import { doesIntersect2, getContainingView } from '@jbrowse/core/util'\n// locals\nimport { LinearSyntenyViewModel } from '../LinearSyntenyView/model'\nimport { LinearSyntenyDisplayModel } from './model'\nimport { draw, drawMatchSimple } from './components/util'\n\nexport const MAX_COLOR_RANGE = 255 * 255 * 255 // max color range\n\nfunction makeColor(idx: number) {\n const r = Math.floor(idx / (255 * 255)) % 255\n const g = Math.floor(idx / 255) % 255\n const b = idx % 255\n return `rgb(${r},${g},${b})`\n}\n\nconst colorMap = {\n I: '#ff03',\n N: '#0a03',\n D: '#00f3',\n X: 'brown',\n M: '#f003',\n '=': '#f003',\n}\n\nconst lineLimit = 3\n\nconst oobLimit = 1600\n\nexport function getId(r: number, g: number, b: number, unitMultiplier: number) {\n return Math.floor((r * 255 * 255 + g * 255 + b - 1) / unitMultiplier)\n}\n\nexport function drawRef(\n model: LinearSyntenyDisplayModel,\n ctx1: CanvasRenderingContext2D,\n ctx3?: CanvasRenderingContext2D,\n) {\n const view = getContainingView(model) as LinearSyntenyViewModel\n const drawCurves = view.drawCurves\n const drawCIGAR = view.drawCIGAR\n const height = view.middleComparativeHeight\n const width = view.width\n const bpPerPxs = view.views.map(v => v.bpPerPx)\n\n if (ctx3) {\n ctx3.imageSmoothingEnabled = false\n }\n\n ctx1.beginPath()\n const featPos = model.featPositions\n const offsets = view.views.map(v => v.offsetPx)\n\n const unitMultiplier = Math.floor(MAX_COLOR_RANGE / featPos.length)\n\n // this loop is optimized to draw many thin lines with a single ctx.stroke\n // call, a separate loop below draws larger boxes\n ctx1.fillStyle = colorMap.M\n ctx1.strokeStyle = colorMap.M\n for (const { p11, p12, p21, p22 } of featPos) {\n const x11 = p11.offsetPx - offsets[0]!\n const x12 = p12.offsetPx - offsets[0]!\n const x21 = p21.offsetPx - offsets[1]!\n const x22 = p22.offsetPx - offsets[1]!\n const l1 = Math.abs(x12 - x11)\n const l2 = Math.abs(x22 - x21)\n const y1 = 0\n const y2 = height\n const mid = (y2 - y1) / 2\n\n // drawing a line if the results are thin results in much less pixellation\n // than filling in a thin polygon\n if (\n l1 <= lineLimit &&\n l2 <= lineLimit &&\n x21 < width + oobLimit &&\n x21 > -oobLimit\n ) {\n ctx1.moveTo(x11, y1)\n if (drawCurves) {\n ctx1.bezierCurveTo(x11, mid, x21, mid, x21, y2)\n } else {\n ctx1.lineTo(x21, y2)\n }\n }\n }\n ctx1.stroke()\n\n // this loop only draws small lines as a polyline, the polyline calls\n // ctx.stroke once is much more efficient than calling stroke() many times\n ctx1.fillStyle = colorMap.M\n ctx1.strokeStyle = colorMap.M\n for (const { p11, p12, p21, p22, f, cigar } of featPos) {\n const x11 = p11.offsetPx - offsets[0]!\n const x12 = p12.offsetPx - offsets[0]!\n const x21 = p21.offsetPx - offsets[1]!\n const x22 = p22.offsetPx - offsets[1]!\n const l1 = Math.abs(x12 - x11)\n const l2 = Math.abs(x22 - x21)\n const minX = Math.min(x21, x22)\n const maxX = Math.max(x21, x22)\n const y1 = 0\n const y2 = height\n const mid = (y2 - y1) / 2\n\n if (\n !(l1 <= lineLimit && l2 <= lineLimit) &&\n doesIntersect2(minX, maxX, -oobLimit, view.width + oobLimit)\n ) {\n const s1 = f.get('strand')\n const k1 = s1 === -1 ? x12 : x11\n const k2 = s1 === -1 ? x11 : x12\n\n // rev1/rev2 flip the direction of the CIGAR drawing in horizontally flipped\n // modes. somewhat heuristically determined, but tested for\n const rev1 = k1 < k2 ? 1 : -1\n const rev2 = (x21 < x22 ? 1 : -1) * s1\n\n // cx1/cx2 are the current x positions on top and bottom rows\n let cx1 = k1\n let cx2 = s1 === -1 ? x22 : x21\n if (cigar.length && drawCIGAR) {\n // continuingFlag skips drawing commands on very small CIGAR features\n let continuingFlag = false\n\n // px1/px2 are the previous x positions on the top and bottom rows\n let px1 = 0\n let px2 = 0\n const unitMultiplier2 = Math.floor(MAX_COLOR_RANGE / cigar.length)\n for (let j = 0; j < cigar.length; j += 2) {\n const idx = j * unitMultiplier2 + 1\n\n const len = +cigar[j]!\n const op = cigar[j + 1] as keyof typeof colorMap\n\n if (!continuingFlag) {\n px1 = cx1\n px2 = cx2\n }\n\n const d1 = len / bpPerPxs[0]!\n const d2 = len / bpPerPxs[1]!\n\n if (op === 'M' \|\| op === '=' \|\| op === 'X') {\n cx1 += d1 * rev1\n cx2 += d2 * rev2\n } else if (op === 'D' \|\| op === 'N') {\n cx1 += d1 * rev1\n }\n // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition\n else if (op === 'I') {\n cx2 += d2 * rev2\n }\n\n // check that we are even drawing in view here, e.g. that all\n // points are not all less than 0 or greater than width\n if (\n !(\n Math.max(px1, px2, cx1, cx2) < 0 \|\|\n Math.min(px1, px2, cx1, cx2) > width\n )\n ) {\n // if it is a small feature and not the last element of the\n // CIGAR (which could skip rendering it entire if we did turn\n // it on), then turn on continuing flag\n const isNotLast = j < cigar.length - 2\n if (\n Math.abs(cx1 - px1) <= 1 &&\n Math.abs(cx2 - px2) <= 1 &&\n isNotLast\n ) {\n continuingFlag = true\n } else {\n // allow rendering the dominant color when using continuing flag\n // if the last element of continuing was a large feature, else\n // just use match\n ctx1.fillStyle =\n colorMap[(continuingFlag && d1 > 1) \|\| d2 > 1 ? op : 'M']\n continuingFlag = false\n\n draw(ctx1, px1, cx1, y1, cx2, px2, y2, mid, drawCurves)\n if (ctx3) {\n ctx3.fillStyle = makeColor(idx)\n draw(ctx3, px1, cx1, y1, cx2, px2, y2, mid, drawCurves)\n }\n }\n }\n }\n } else {\n draw(ctx1, x11, x12, y1, x22, x21, y2, mid, drawCurves)\n }\n }\n }\n\n // draw click map\n const ctx2 = model.clickMapCanvas?.getContext('2d')\n if (!ctx2) {\n return\n }\n ctx2.imageSmoothingEnabled = false\n ctx2.clearRect(0, 0, width, height)\n for (let i = 0; i < featPos.length; i++) {\n const feature = featPos[i]!\n const idx = i * unitMultiplier + 1\n ctx2.fillStyle = makeColor(idx)\n\n // too many click map false positives with colored stroked lines\n drawMatchSimple({\n cb: ctx => {\n ctx.fill()\n },\n feature,\n ctx: ctx2,\n drawCurves,\n offsets,\n oobLimit,\n viewWidth: view.width,\n hideTiny: true,\n height,\n })\n }\n return undefined\n}\n\nexport function drawMouseoverSynteny(model: LinearSyntenyDisplayModel) {\n const { clickId, mouseoverId } = model\n const highResolutionScaling = 1\n const view = getContainingView(model) as LinearSyntenyViewModel\n const drawCurves = view.drawCurves\n const height = view.middleComparativeHeight\n const width = view.width\n const ctx = model.mouseoverCanvas?.getContext('2d')\n const offsets = view.views.map(v => v.offsetPx)\n\n if (!ctx) {\n return\n }\n ctx.resetTransform()\n ctx.scale(highResolutionScaling, highResolutionScaling)\n ctx.clearRect(0, 0, width, height)\n const feature1 = model.featMap[mouseoverId \|\| '']\n if (feature1) {\n ctx.fillStyle = 'rgb(0,0,0,0.1)'\n drawMatchSimple({\n cb: ctx => {\n ctx.fill()\n },\n feature: feature1,\n ctx,\n oobLimit,\n viewWidth: view.width,\n drawCurves,\n offsets,\n height,\n })\n }\n const feature2 = model.featMap[clickId \|\| '']\n if (feature2) {\n ctx.strokeStyle = 'rgb(0, 0, 0, 0.9)'\n\n drawMatchSimple({\n cb: ctx => {\n ctx.stroke()\n },\n feature: feature2,\n ctx,\n oobLimit,\n viewWidth: view.width,\n drawCurves,\n offsets,\n height,\n })\n }\n}\n"],"names":["doAfterAttach","self","addDisposer","autorun","view","getContainingView","initialized","ctx1","mainCanvas","getContext","ctx3","cigarClickMapCanvas","height","middleComparativeHeight","width","clearRect","drawRef","drawMouseoverSynteny","reaction","bpPerPx","views","map","v","displayedRegions","JSON","stringify","features","assemblyManager","getSession","viewSnaps","getSnapshot","staticBlocks","interRegionPaddingWidth","minimumBlockWidth","feats","f","mate","get","f1s","f1e","f2s","start","f2e","end","a1","a2","assemblyName","r1","r2","refName","ref1","getCanonicalRefName","ref2","v1","v2","p11","bpToPx","coord","p12","p21","p22","undefined","cigar","push","MismatchParser","setFeatPositions","fireImmediately","drawMatchSimple","feature","ctx","offsets","cb","drawCurves","oobLimit","viewWidth","hideTiny","x11","offsetPx","x12","x21","x22","l1","Math","abs","l2","y2","mid","minX","min","maxX","max","doesIntersect2","beginPath","moveTo","bezierCurveTo","lineTo","stroke","draw","x1","x2","y1","x3","x4","len1","len2","tmp","closePath","fill","drawBezierBox","drawBox","onSynClick","event","model","track","getContainingTrack","clickMapCanvas","rect","getBoundingClientRect","ctx2","x","clientX","left","y","clientY","top","g1","b1","getImageData","data","unitMultiplier","floor","MAX_COLOR_RANGE","numFeats","id","getId","feat","featPositions","setClickId","session","isSessionModelWithWidgets","showWidget","addWidget","featureData","toJSON","onSynContextClick","setAnchorEl","preventDefault","getTooltip","cigarOp","cigarOpLen","f1","f2","identity","n1","name","n2","assembleLocString","strand","toLocaleString","toPrecision","filter","join","makeColor","idx","colorMap","I","N","D","X","M","lineLimit","r","g","b","drawCIGAR","bpPerPxs","imageSmoothingEnabled","featPos","length","fillStyle","strokeStyle","s1","k1","rev1","rev2","cx1","cx2","continuingFlag","px1","px2","unitMultiplier2","j","len","op","d1","d2","isNotLast","i","clickId","mouseoverId","mouseoverCanvas","resetTransform","scale","feature1","featMap","feature2"],"sourceRoot":""}

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49f3d3878413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566

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{ addDisposer, getSnapshot } from 'mobx-state-tree'\n\nimport { Feature, getContainingView, getSession } from '@jbrowse/core/util'\nimport { bpToPx } from '@jbrowse/core/util/Base1DUtils'\nimport { MismatchParser } from '@jbrowse/plugin-alignments'\nimport { reaction, autorun } from 'mobx'\n\n// locals\nimport { LinearSyntenyViewModel } from '../LinearSyntenyView/model'\nimport { drawMouseoverSynteny, drawRef } from './drawSynteny'\nimport { LinearSyntenyDisplayModel } from './model'\n\ninterface Pos {\n offsetPx: number\n}\n\ninterface FeatPos {\n p11: Pos\n p12: Pos\n p21: Pos\n p22: Pos\n f: Feature\n cigar: string[]\n}\n\ntype LSV = LinearSyntenyViewModel\n\nexport function doAfterAttach(self: LinearSyntenyDisplayModel) {\n addDisposer(\n self,\n autorun(() => {\n const view = getContainingView(self) as LinearSyntenyViewModel\n if (!view.initialized) {\n return\n }\n const ctx1 = self.mainCanvas?.getContext('2d')\n const ctx3 = self.cigarClickMapCanvas?.getContext('2d')\n if (!ctx1 || !ctx3) {\n return\n }\n\n const height = view.middleComparativeHeight\n const width = view.width\n ctx1.clearRect(0, 0, width, height)\n ctx3.clearRect(0, 0, width, height)\n drawRef(self, ctx1, ctx3)\n }),\n )\n\n addDisposer(\n self,\n autorun(() => {\n const view = getContainingView(self) as LinearSyntenyViewModel\n if (!view.initialized) {\n return\n }\n drawMouseoverSynteny(self)\n }),\n )\n\n // this attempts to reduce recalculation of feature positions drawn by\n // the synteny view\n //\n // uses a reaction to say \"we know the positions don't change in any\n // relevant way unless bpPerPx changes or displayedRegions changes\"\n addDisposer(\n self,\n reaction(\n () => {\n const view = getContainingView(self) as LSV\n return {\n bpPerPx: view.views.map(v => v.bpPerPx),\n\n // stringifying 'deeply' accesses the displayed regions, see\n // issue #3456\n displayedRegions: JSON.stringify(\n view.views.map(v => v.displayedRegions),\n ),\n features: self.features,\n initialized: view.initialized,\n }\n },\n ({ initialized }) => {\n if (!initialized) {\n return\n }\n const { assemblyManager } = getSession(self)\n const view = getContainingView(self) as LSV\n const viewSnaps = view.views.map(view => ({\n ...getSnapshot(view),\n width: view.width,\n staticBlocks: view.staticBlocks,\n interRegionPaddingWidth: view.interRegionPaddingWidth,\n minimumBlockWidth: view.minimumBlockWidth,\n }))\n\n const map = [] as FeatPos[]\n const feats = self.features || []\n\n for (const f of feats) {\n const mate = f.get('mate')\n let f1s = f.get('start')\n let f1e = f.get('end')\n const f2s = mate.start\n const f2e = mate.end\n\n if (f.get('strand') === -1) {\n ;[f1e, f1s] = [f1s, f1e]\n }\n const a1 = assemblyManager.get(f.get('assemblyName'))\n const a2 = assemblyManager.get(mate.assemblyName)\n const r1 = f.get('refName')\n const r2 = mate.refName\n const ref1 = a1?.getCanonicalRefName(r1) || r1\n const ref2 = a2?.getCanonicalRefName(r2) || r2\n const v1 = viewSnaps[0]!\n const v2 = viewSnaps[1]!\n const p11 = bpToPx({ self: v1, refName: ref1, coord: f1s })\n const p12 = bpToPx({ self: v1, refName: ref1, coord: f1e })\n const p21 = bpToPx({ self: v2, refName: ref2, coord: f2s })\n const p22 = bpToPx({ self: v2, refName: ref2, coord: f2e })\n\n if (\n p11 === undefined ||\n p12 === undefined ||\n p21 === undefined ||\n p22 === undefined\n ) {\n continue\n }\n\n const cigar = f.get('CIGAR') as string | undefined\n map.push({\n p11,\n p12,\n p21,\n p22,\n f,\n cigar: MismatchParser.parseCigar(cigar),\n })\n }\n\n self.setFeatPositions(map)\n },\n { fireImmediately: true },\n ),\n )\n}\n","import React from 'react'\nimport {\n assembleLocString,\n doesIntersect2,\n getSession,\n isSessionModelWithWidgets,\n Feature,\n getContainingTrack,\n getContainingView,\n} from '@jbrowse/core/util'\n\n// locals\nimport { getId, MAX_COLOR_RANGE } from '../drawSynteny'\nimport { LinearSyntenyDisplayModel } from '../model'\n\ninterface Pos {\n offsetPx: number\n}\n\nexport interface ClickCoord {\n clientX: number\n clientY: number\n feature: { f: Feature }\n}\n\ninterface FeatPos {\n p11: Pos\n p12: Pos\n p21: Pos\n p22: Pos\n f: Feature\n cigar: string[]\n}\n\nexport function drawMatchSimple({\n feature,\n ctx,\n offsets,\n cb,\n height,\n drawCurves,\n oobLimit,\n viewWidth,\n hideTiny,\n}: {\n feature: FeatPos\n ctx: CanvasRenderingContext2D\n offsets: number[]\n oobLimit: number\n viewWidth: number\n cb: (ctx: CanvasRenderingContext2D) => void\n height: number\n drawCurves?: boolean\n hideTiny?: boolean\n}) {\n const { p11, p12, p21, p22 } = feature\n\n const x11 = p11.offsetPx - offsets[0]!\n const x12 = p12.offsetPx - offsets[0]!\n const x21 = p21.offsetPx - offsets[1]!\n const x22 = p22.offsetPx - offsets[1]!\n\n const l1 = Math.abs(x12 - x11)\n const l2 = Math.abs(x22 - x21)\n const y1 = 0\n const y2 = height\n const mid = (y2 - y1) / 2\n const minX = Math.min(x21, x22)\n const maxX = Math.max(x21, x22)\n\n if (!doesIntersect2(minX, maxX, -oobLimit, viewWidth + oobLimit)) {\n return\n }\n\n // drawing a line if the results are thin: drawing a line results in much\n // less pixellation than filling in a thin polygon\n if (l1 <= 1 && l2 <= 1) {\n // hideTiny can be used to avoid drawing mouseover for thin lines in this\n // case\n if (!hideTiny) {\n ctx.beginPath()\n ctx.moveTo(x11, y1)\n if (drawCurves) {\n ctx.bezierCurveTo(x11, mid, x21, mid, x21, y2)\n } else {\n ctx.lineTo(x21, y2)\n }\n ctx.stroke()\n }\n } else {\n draw(ctx, x11, x12, y1, x22, x21, y2, mid, drawCurves)\n cb(ctx)\n }\n}\n\nexport function draw(\n ctx: CanvasRenderingContext2D,\n x1: number,\n x2: number,\n y1: number,\n x3: number,\n x4: number,\n y2: number,\n mid: number,\n drawCurves?: boolean,\n) {\n if (drawCurves) {\n drawBezierBox(ctx, x1, x2, y1, x3, x4, y2, mid)\n } else {\n drawBox(ctx, x1, x2, y1, x3, x4, y2)\n }\n}\n\nexport function drawBox(\n ctx: CanvasRenderingContext2D,\n x1: number,\n x2: number,\n y1: number,\n x3: number,\n x4: number,\n y2: number,\n) {\n ctx.beginPath()\n ctx.moveTo(x1, y1)\n ctx.lineTo(x2, y1)\n ctx.lineTo(x3, y2)\n ctx.lineTo(x4, y2)\n ctx.closePath()\n ctx.fill()\n}\n\nexport function drawBezierBox(\n ctx: CanvasRenderingContext2D,\n x1: number,\n x2: number,\n y1: number,\n x3: number,\n x4: number,\n y2: number,\n mid: number,\n) {\n const len1 = Math.abs(x1 - x2)\n const len2 = Math.abs(x1 - x2)\n\n // heuristic to not draw hourglass inversions with bezier curves when they\n // are thin and far apart because it results in areas that are not drawn well\n // demo https://codesandbox.io/s/fast-glitter-q3b1or?file=/src/index.js\n if (len1 < 5 && len2 < 5 && x2 < x1 && Math.abs(x1 - x3) > 100) {\n const tmp = x1\n x1 = x2\n x2 = tmp\n }\n ctx.beginPath()\n ctx.moveTo(x1, y1)\n ctx.lineTo(x2, y1)\n ctx.bezierCurveTo(x2, mid, x3, mid, x3, y2)\n ctx.lineTo(x4, y2)\n ctx.bezierCurveTo(x4, mid, x1, mid, x1, y1)\n ctx.closePath()\n ctx.fill()\n}\n\nexport function onSynClick(\n event: React.MouseEvent,\n model: LinearSyntenyDisplayModel,\n) {\n const view = getContainingView(model)\n const track = getContainingTrack(model)\n const ref1 = model.clickMapCanvas\n const ref2 = model.cigarClickMapCanvas\n if (!ref1 || !ref2) {\n return\n }\n const rect = ref1.getBoundingClientRect()\n const ctx1 = ref1.getContext('2d')\n const ctx2 = ref2.getContext('2d')\n if (!ctx1 || !ctx2) {\n return\n }\n const x = event.clientX - rect.left\n const y = event.clientY - rect.top\n const [r1, g1, b1] = ctx1.getImageData(x, y, 1, 1).data\n const unitMultiplier = Math.floor(MAX_COLOR_RANGE / model.numFeats)\n const id = getId(r1!, g1!, b1!, unitMultiplier)\n const feat = model.featPositions[id]\n if (feat) {\n const { f } = feat\n model.setClickId(f.id())\n const session = getSession(model)\n if (isSessionModelWithWidgets(session)) {\n session.showWidget(\n session.addWidget('BaseFeatureWidget', 'baseFeature', {\n view,\n track,\n featureData: f.toJSON(),\n }),\n )\n }\n }\n return feat\n}\n\nexport function onSynContextClick(\n event: React.MouseEvent,\n model: LinearSyntenyDisplayModel,\n setAnchorEl: (arg: ClickCoord) => void,\n) {\n event.preventDefault()\n const ref1 = model.clickMapCanvas\n const ref2 = model.cigarClickMapCanvas\n if (!ref1 || !ref2) {\n return\n }\n const rect = ref1.getBoundingClientRect()\n const ctx1 = ref1.getContext('2d')\n const ctx2 = ref2.getContext('2d')\n if (!ctx1 || !ctx2) {\n return\n }\n const { clientX, clientY } = event\n const x = clientX - rect.left\n const y = clientY - rect.top\n const [r1, g1, b1] = ctx1.getImageData(x, y, 1, 1).data\n const unitMultiplier = Math.floor(MAX_COLOR_RANGE / model.numFeats)\n const id = getId(r1!, g1!, b1!, unitMultiplier)\n const f = model.featPositions[id]\n if (f) {\n model.setClickId(f.f.id())\n setAnchorEl({ clientX, clientY, feature: f })\n }\n}\n\nexport function getTooltip(f: Feature, cigarOp?: string, cigarOpLen?: string) {\n // @ts-expect-error\n const f1 = f.toJSON() as {\n refName: string\n start: number\n end: number\n strand?: number\n assemblyName: string\n identity?: number\n name?: string\n mate: {\n start: number\n end: number\n refName: string\n name: string\n }\n }\n const f2 = f1.mate\n const l1 = f1.end - f1.start\n const l2 = f2.end - f2.start\n const identity = f1.identity\n const n1 = f1.name\n const n2 = f2.name\n return [\n `Loc1: ${assembleLocString(f1)}`,\n `Loc2: ${assembleLocString(f2)}`,\n `Inverted: ${f1.strand === -1}`,\n `Query len: ${l1.toLocaleString('en-US')}`,\n `Target len: ${l2.toLocaleString('en-US')}`,\n identity ? `Identity: ${identity.toPrecision(2)}` : '',\n cigarOp ? `CIGAR operator: ${cigarOp}${cigarOpLen}` : '',\n n1 ? `Name 1: ${n1}` : '',\n n2 ? `Name 1: ${n2}` : '',\n ]\n .filter(f => !!f)\n .join('<br/>')\n}\n","import { doesIntersect2, getContainingView } from '@jbrowse/core/util'\n// locals\nimport { LinearSyntenyViewModel } from '../LinearSyntenyView/model'\nimport { LinearSyntenyDisplayModel } from './model'\nimport { draw, drawMatchSimple } from './components/util'\n\nexport const MAX_COLOR_RANGE = 255 * 255 * 255 // max color range\n\nfunction makeColor(idx: number) {\n const r = Math.floor(idx / (255 * 255)) % 255\n const g = Math.floor(idx / 255) % 255\n const b = idx % 255\n return `rgb(${r},${g},${b})`\n}\n\nconst colorMap = {\n I: '#ff03',\n N: '#0a03',\n D: '#00f3',\n X: 'brown',\n M: '#f003',\n '=': '#f003',\n}\n\nconst lineLimit = 3\n\nconst oobLimit = 1600\n\nexport function getId(r: number, g: number, b: number, unitMultiplier: number) {\n return Math.floor((r * 255 * 255 + g * 255 + b - 1) / unitMultiplier)\n}\n\nexport function drawRef(\n model: LinearSyntenyDisplayModel,\n ctx1: CanvasRenderingContext2D,\n ctx3?: CanvasRenderingContext2D,\n) {\n const view = getContainingView(model) as LinearSyntenyViewModel\n const drawCurves = view.drawCurves\n const drawCIGAR = view.drawCIGAR\n const height = view.middleComparativeHeight\n const width = view.width\n const bpPerPxs = view.views.map(v => v.bpPerPx)\n\n if (ctx3) {\n ctx3.imageSmoothingEnabled = false\n }\n\n ctx1.beginPath()\n const featPos = model.featPositions\n const offsets = view.views.map(v => v.offsetPx)\n\n const unitMultiplier = Math.floor(MAX_COLOR_RANGE / featPos.length)\n\n // this loop is optimized to draw many thin lines with a single ctx.stroke\n // call, a separate loop below draws larger boxes\n ctx1.fillStyle = colorMap.M\n ctx1.strokeStyle = colorMap.M\n for (const { p11, p12, p21, p22 } of featPos) {\n const x11 = p11.offsetPx - offsets[0]!\n const x12 = p12.offsetPx - offsets[0]!\n const x21 = p21.offsetPx - offsets[1]!\n const x22 = p22.offsetPx - offsets[1]!\n const l1 = Math.abs(x12 - x11)\n const l2 = Math.abs(x22 - x21)\n const y1 = 0\n const y2 = height\n const mid = (y2 - y1) / 2\n\n // drawing a line if the results are thin results in much less pixellation\n // than filling in a thin polygon\n if (\n l1 <= lineLimit &&\n l2 <= lineLimit &&\n x21 < width + oobLimit &&\n x21 > -oobLimit\n ) {\n ctx1.moveTo(x11, y1)\n if (drawCurves) {\n ctx1.bezierCurveTo(x11, mid, x21, mid, x21, y2)\n } else {\n ctx1.lineTo(x21, y2)\n }\n }\n }\n ctx1.stroke()\n\n // this loop only draws small lines as a polyline, the polyline calls\n // ctx.stroke once is much more efficient than calling stroke() many times\n ctx1.fillStyle = colorMap.M\n ctx1.strokeStyle = colorMap.M\n for (const { p11, p12, p21, p22, f, cigar } of featPos) {\n const x11 = p11.offsetPx - offsets[0]!\n const x12 = p12.offsetPx - offsets[0]!\n const x21 = p21.offsetPx - offsets[1]!\n const x22 = p22.offsetPx - offsets[1]!\n const l1 = Math.abs(x12 - x11)\n const l2 = Math.abs(x22 - x21)\n const minX = Math.min(x21, x22)\n const maxX = Math.max(x21, x22)\n const y1 = 0\n const y2 = height\n const mid = (y2 - y1) / 2\n\n if (\n !(l1 <= lineLimit && l2 <= lineLimit) &&\n doesIntersect2(minX, maxX, -oobLimit, view.width + oobLimit)\n ) {\n const s1 = f.get('strand')\n const k1 = s1 === -1 ? x12 : x11\n const k2 = s1 === -1 ? x11 : x12\n\n // rev1/rev2 flip the direction of the CIGAR drawing in horizontally flipped\n // modes. somewhat heuristically determined, but tested for\n const rev1 = k1 < k2 ? 1 : -1\n const rev2 = (x21 < x22 ? 1 : -1) * s1\n\n // cx1/cx2 are the current x positions on top and bottom rows\n let cx1 = k1\n let cx2 = s1 === -1 ? x22 : x21\n if (cigar.length && drawCIGAR) {\n // continuingFlag skips drawing commands on very small CIGAR features\n let continuingFlag = false\n\n // px1/px2 are the previous x positions on the top and bottom rows\n let px1 = 0\n let px2 = 0\n const unitMultiplier2 = Math.floor(MAX_COLOR_RANGE / cigar.length)\n for (let j = 0; j < cigar.length; j += 2) {\n const idx = j * unitMultiplier2 + 1\n\n const len = +cigar[j]!\n const op = cigar[j + 1] as keyof typeof colorMap\n\n if (!continuingFlag) {\n px1 = cx1\n px2 = cx2\n }\n\n const d1 = len / bpPerPxs[0]!\n const d2 = len / bpPerPxs[1]!\n\n if (op === 'M' || op === '=' || op === 'X') {\n cx1 += d1 * rev1\n cx2 += d2 * rev2\n } else if (op === 'D' || op === 'N') {\n cx1 += d1 * rev1\n }\n // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition\n else if (op === 'I') {\n cx2 += d2 * rev2\n }\n\n // check that we are even drawing in view here, e.g. that all\n // points are not all less than 0 or greater than width\n if (\n !(\n Math.max(px1, px2, cx1, cx2) < 0 ||\n Math.min(px1, px2, cx1, cx2) > width\n )\n ) {\n // if it is a small feature and not the last element of the\n // CIGAR (which could skip rendering it entire if we did turn\n // it on), then turn on continuing flag\n const isNotLast = j < cigar.length - 2\n if (\n Math.abs(cx1 - px1) <= 1 &&\n Math.abs(cx2 - px2) <= 1 &&\n isNotLast\n ) {\n continuingFlag = true\n } else {\n // allow rendering the dominant color when using continuing flag\n // if the last element of continuing was a large feature, else\n // just use match\n ctx1.fillStyle =\n colorMap[(continuingFlag && d1 > 1) || d2 > 1 ? op : 'M']\n continuingFlag = false\n\n draw(ctx1, px1, cx1, y1, cx2, px2, y2, mid, drawCurves)\n if (ctx3) {\n ctx3.fillStyle = makeColor(idx)\n draw(ctx3, px1, cx1, y1, cx2, px2, y2, mid, drawCurves)\n }\n }\n }\n }\n } else {\n draw(ctx1, x11, x12, y1, x22, x21, y2, mid, drawCurves)\n }\n }\n }\n\n // draw click map\n const ctx2 = model.clickMapCanvas?.getContext('2d')\n if (!ctx2) {\n return\n }\n ctx2.imageSmoothingEnabled = false\n ctx2.clearRect(0, 0, width, height)\n for (let i = 0; i < featPos.length; i++) {\n const feature = featPos[i]!\n const idx = i * unitMultiplier + 1\n ctx2.fillStyle = makeColor(idx)\n\n // too many click map false positives with colored stroked lines\n drawMatchSimple({\n cb: ctx => {\n ctx.fill()\n },\n feature,\n ctx: ctx2,\n drawCurves,\n offsets,\n oobLimit,\n viewWidth: view.width,\n hideTiny: true,\n height,\n })\n }\n return undefined\n}\n\nexport function drawMouseoverSynteny(model: LinearSyntenyDisplayModel) {\n const { clickId, mouseoverId } = model\n const highResolutionScaling = 1\n const view = getContainingView(model) as LinearSyntenyViewModel\n const drawCurves = view.drawCurves\n const height = view.middleComparativeHeight\n const width = view.width\n const ctx = model.mouseoverCanvas?.getContext('2d')\n const offsets = view.views.map(v => v.offsetPx)\n\n if (!ctx) {\n return\n }\n ctx.resetTransform()\n ctx.scale(highResolutionScaling, highResolutionScaling)\n ctx.clearRect(0, 0, width, height)\n const feature1 = model.featMap[mouseoverId || '']\n if (feature1) {\n ctx.fillStyle = 'rgb(0,0,0,0.1)'\n drawMatchSimple({\n cb: ctx => {\n ctx.fill()\n },\n feature: feature1,\n ctx,\n oobLimit,\n viewWidth: view.width,\n drawCurves,\n offsets,\n height,\n })\n }\n const feature2 = model.featMap[clickId || '']\n if (feature2) {\n ctx.strokeStyle = 'rgb(0, 0, 0, 0.9)'\n\n drawMatchSimple({\n cb: ctx => {\n ctx.stroke()\n },\n feature: feature2,\n ctx,\n oobLimit,\n viewWidth: view.width,\n drawCurves,\n offsets,\n height,\n })\n }\n}\n"],"names":["doAfterAttach","self","addDisposer","autorun","view","getContainingView","initialized","ctx1","mainCanvas","getContext","ctx3","cigarClickMapCanvas","height","middleComparativeHeight","width","clearRect","drawRef","drawMouseoverSynteny","reaction","bpPerPx","views","map","v","displayedRegions","JSON","stringify","features","assemblyManager","getSession","viewSnaps","getSnapshot","staticBlocks","interRegionPaddingWidth","minimumBlockWidth","feats","f","mate","get","f1s","f1e","f2s","start","f2e","end","a1","a2","assemblyName","r1","r2","refName","ref1","getCanonicalRefName","ref2","v1","v2","p11","bpToPx","coord","p12","p21","p22","undefined","cigar","push","MismatchParser","setFeatPositions","fireImmediately","drawMatchSimple","feature","ctx","offsets","cb","drawCurves","oobLimit","viewWidth","hideTiny","x11","offsetPx","x12","x21","x22","l1","Math","abs","l2","y2","mid","minX","min","maxX","max","doesIntersect2","beginPath","moveTo","bezierCurveTo","lineTo","stroke","draw","x1","x2","y1","x3","x4","len1","len2","tmp","closePath","fill","drawBezierBox","drawBox","onSynClick","event","model","track","getContainingTrack","clickMapCanvas","rect","getBoundingClientRect","ctx2","x","clientX","left","y","clientY","top","g1","b1","getImageData","data","unitMultiplier","floor","MAX_COLOR_RANGE","numFeats","id","getId","feat","featPositions","setClickId","session","isSessionModelWithWidgets","showWidget","addWidget","featureData","toJSON","onSynContextClick","setAnchorEl","preventDefault","getTooltip","cigarOp","cigarOpLen","f1","f2","identity","n1","name","n2","assembleLocString","strand","toLocaleString","toPrecision","filter","join","makeColor","idx","colorMap","I","N","D","X","M","lineLimit","r","g","b","drawCIGAR","bpPerPxs","imageSmoothingEnabled","featPos","length","fillStyle","strokeStyle","s1","k1","rev1","rev2","cx1","cx2","continuingFlag","px1","px2","unitMultiplier2","j","len","op","d1","d2","isNotLast","i","clickId","mouseoverId","mouseoverCanvas","resetTransform","scale","feature1","featMap","feature2"],"sourceRoot":""}

Mercurial > repos > fubar > jbrowse2

annotate x/static/js/8856.4593419f.chunk.js.map @ 125:49f3d3878413 draft