Mercurial > repos > fubar > jbrowse2
view x/static/js/4753.834007ba.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 |
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React from 'react'\nimport { getContainingView, getSession, Feature } from '@jbrowse/core/util'\nimport { Menu } from '@jbrowse/core/ui'\n\n// locals\nimport { LinearSyntenyDisplayModel } from '../model'\nimport { LinearSyntenyViewModel } from '../../LinearSyntenyView/model'\n\ninterface ClickCoord {\n clientX: number\n clientY: number\n feature: { f: Feature }\n}\n\nexport default function SyntenyContextMenu({\n model,\n onClose,\n anchorEl,\n}: {\n onClose: () => void\n model: LinearSyntenyDisplayModel\n anchorEl: ClickCoord\n}) {\n const view = getContainingView(model) as LinearSyntenyViewModel\n const { clientX, clientY, feature } = anchorEl\n return (\n <Menu\n onMenuItemClick={(event, callback) => {\n callback(event)\n onClose()\n }}\n anchorEl={{\n nodeType: 1,\n getBoundingClientRect: () => {\n const x = clientX\n const y = clientY\n return {\n top: y,\n left: x,\n bottom: y,\n right: x,\n width: 0,\n height: 0,\n x,\n y,\n toJSON() {},\n }\n },\n }}\n onClose={onClose}\n open={Boolean(anchorEl)}\n menuItems={[\n {\n label: 'Center on feature',\n onClick: () => {\n const { f } = feature\n const start = f.get('start')\n const end = f.get('end')\n const refName = f.get('refName')\n const mate = f.get('mate')\n view.views[0]!.navToLocString(`${refName}:${start}-${end}`).catch(\n (e: unknown) => {\n console.error(e)\n getSession(model).notifyError(`${e}`, e)\n },\n )\n view.views[1]!.navToLocString(\n `${mate.refName}:${mate.start}-${mate.end}`,\n ).catch((e: unknown) => {\n console.error(e)\n getSession(model).notifyError(`${e}`, e)\n })\n },\n },\n ]}\n />\n )\n}\n","import React, { useState, useCallback, useRef, lazy } from 'react'\nimport { observer } from 'mobx-react'\nimport { getContainingView } from '@jbrowse/core/util'\nimport { transaction } from 'mobx'\nimport { makeStyles } from 'tss-react/mui'\n\n// locals\nimport { LinearSyntenyDisplayModel } from '../model'\nimport { getId, MAX_COLOR_RANGE } from '../drawSynteny'\nimport { LinearSyntenyViewModel } from '../../LinearSyntenyView/model'\nimport SyntenyContextMenu from './SyntenyContextMenu'\nimport { ClickCoord, getTooltip, onSynClick, onSynContextClick } from './util'\n\nconst SyntenyTooltip = lazy(() => import('./SyntenyTooltip'))\n\ntype Timer = ReturnType<typeof setTimeout>\n\nconst useStyles = makeStyles()({\n pix: {\n imageRendering: 'pixelated',\n pointerEvents: 'none',\n visibility: 'hidden',\n position: 'absolute',\n },\n rel: {\n position: 'relative',\n },\n abs: {\n position: 'absolute',\n },\n none: {\n pointEvents: 'none',\n },\n})\n\nconst LinearSyntenyRendering = observer(function ({\n model,\n}: {\n model: LinearSyntenyDisplayModel\n}) {\n const { classes, cx } = useStyles()\n const xOffset = useRef<number>(0)\n const currScrollFrame = useRef<number>()\n const view = getContainingView(model) as LinearSyntenyViewModel\n const height = view.middleComparativeHeight\n const width = view.width\n const delta = useRef(0)\n const timeout = useRef<Timer>()\n const [anchorEl, setAnchorEl] = useState<ClickCoord>()\n const [tooltip, setTooltip] = useState('')\n const [currX, setCurrX] = useState<number>()\n const [mouseCurrDownX, setMouseCurrDownX] = useState<number>()\n const [mouseInitialDownX, setMouseInitialDownX] = useState<number>()\n const [currY, setCurrY] = useState<number>()\n const { mouseoverId } = model\n\n // these useCallbacks avoid new refs from being created on any mouseover,\n // etc.\n // biome-ignore lint/correctness/useExhaustiveDependencies:\n const k1 = useCallback(\n (ref: HTMLCanvasElement | null) => {\n model.setMouseoverCanvasRef(ref)\n },\n // eslint-disable-next-line react-hooks/exhaustive-deps\n [model, height, width],\n )\n // biome-ignore lint/correctness/useExhaustiveDependencies:\n const k2 = useCallback(\n (ref: HTMLCanvasElement | null) => {\n model.setMainCanvasRef(ref)\n function onWheel(event: WheelEvent) {\n event.preventDefault()\n if (event.ctrlKey) {\n delta.current += event.deltaY / 500\n for (const v of view.views) {\n v.setScaleFactor(\n delta.current < 0 ? 1 - delta.current : 1 / (1 + delta.current),\n )\n }\n if (timeout.current) {\n clearTimeout(timeout.current)\n }\n timeout.current = setTimeout(() => {\n for (const v of view.views) {\n v.setScaleFactor(1)\n v.zoomTo(\n delta.current > 0\n ? v.bpPerPx * (1 + delta.current)\n : v.bpPerPx / (1 - delta.current),\n event.clientX - (ref?.getBoundingClientRect().left || 0),\n )\n }\n delta.current = 0\n }, 300)\n } else {\n if (Math.abs(event.deltaY) < Math.abs(event.deltaX)) {\n xOffset.current += event.deltaX / 2\n }\n if (currScrollFrame.current === undefined) {\n currScrollFrame.current = requestAnimationFrame(() => {\n transaction(() => {\n for (const v of view.views) {\n v.horizontalScroll(xOffset.current)\n }\n xOffset.current = 0\n currScrollFrame.current = undefined\n })\n })\n }\n }\n }\n ref?.addEventListener('wheel', onWheel)\n\n // this is a react 19-ism to have a cleanup in the ref callback\n // https://react.dev/blog/2024/04/25/react-19#cleanup-functions-for-refs\n // note: it warns in earlier versions of react\n return () => {\n ref?.removeEventListener('wheel', onWheel)\n }\n },\n // eslint-disable-next-line react-hooks/exhaustive-deps\n [model, height, width],\n )\n // biome-ignore lint/correctness/useExhaustiveDependencies:\n const k3 = useCallback(\n (ref: HTMLCanvasElement | null) => {\n model.setClickMapCanvasRef(ref)\n },\n // eslint-disable-next-line react-hooks/exhaustive-deps\n [model, height, width],\n )\n // biome-ignore lint/correctness/useExhaustiveDependencies:\n const k4 = useCallback(\n (ref: HTMLCanvasElement | null) => {\n model.setCigarClickMapCanvasRef(ref)\n },\n // eslint-disable-next-line react-hooks/exhaustive-deps\n [model, height, width],\n )\n\n return (\n <div className={classes.rel}>\n <canvas\n ref={k1}\n width={width}\n height={height}\n className={cx(classes.abs, classes.none)}\n />\n <canvas\n ref={k2}\n onMouseMove={event => {\n if (mouseCurrDownX !== undefined) {\n xOffset.current += mouseCurrDownX - event.clientX\n setMouseCurrDownX(event.clientX)\n if (currScrollFrame.current === undefined) {\n currScrollFrame.current = requestAnimationFrame(() => {\n transaction(() => {\n for (const v of view.views) {\n v.horizontalScroll(xOffset.current)\n }\n xOffset.current = 0\n currScrollFrame.current = undefined\n })\n })\n }\n } else {\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 setCurrX(clientX)\n setCurrY(clientY)\n const [r1, g1, b1] = ctx1.getImageData(x, y, 1, 1).data\n const [r2, g2, b2] = ctx2.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 model.setMouseoverId(model.featPositions[id]?.f.id())\n if (id === -1) {\n setTooltip('')\n } else if (model.featPositions[id]) {\n const { f, cigar } = model.featPositions[id]\n const unitMultiplier2 = Math.floor(MAX_COLOR_RANGE / cigar.length)\n const cigarIdx = getId(r2!, g2!, b2!, unitMultiplier2)\n setTooltip(getTooltip(f, cigar[cigarIdx], cigar[cigarIdx + 1]))\n }\n }\n }}\n onMouseLeave={() => {\n model.setMouseoverId(undefined)\n setMouseInitialDownX(undefined)\n setMouseCurrDownX(undefined)\n }}\n onMouseDown={evt => {\n setMouseCurrDownX(evt.clientX)\n setMouseInitialDownX(evt.clientX)\n }}\n onMouseUp={evt => {\n setMouseCurrDownX(undefined)\n if (\n mouseInitialDownX !== undefined &&\n Math.abs(evt.clientX - mouseInitialDownX) < 5\n ) {\n onSynClick(evt, model)\n }\n }}\n onContextMenu={evt => {\n onSynContextClick(evt, model, setAnchorEl)\n }}\n data-testid=\"synteny_canvas\"\n className={classes.abs}\n width={width}\n height={height}\n />\n <canvas ref={k3} className={classes.pix} width={width} height={height} />\n <canvas ref={k4} className={classes.pix} width={width} height={height} />\n {mouseoverId && tooltip && currX && currY ? (\n <SyntenyTooltip title={tooltip} />\n ) : null}\n {anchorEl ? (\n <SyntenyContextMenu\n model={model}\n anchorEl={anchorEl}\n onClose={() => {\n setAnchorEl(undefined)\n }}\n />\n ) : null}\n </div>\n )\n})\n\nexport default LinearSyntenyRendering\n","import React, { useEffect, useState } from 'react'\nimport { makeStyles } from 'tss-react/mui'\nimport { observer } from 'mobx-react'\nimport { LoadingEllipses } from '@jbrowse/core/ui'\n\n// locals\nimport LinearSyntenyRendering from './LinearSyntenyRendering'\nimport { LinearSyntenyDisplayModel } from '../model'\n\nconst useStyles = makeStyles()(theme => {\n const bg = theme.palette.action.disabledBackground\n return {\n loading: {\n paddingLeft: '0.6em',\n backgroundColor: theme.palette.background.default,\n backgroundImage: `repeating-linear-gradient(45deg, transparent, transparent 5px, ${bg} 5px, ${bg} 10px)`,\n textAlign: 'center',\n },\n blockMessage: {\n background: '#f1f1f1',\n padding: 10,\n },\n blockError: {\n background: '#f1f1f1',\n padding: 10,\n color: 'red',\n },\n }\n})\n\nfunction LoadingMessage() {\n // only show the loading message after 300ms to prevent excessive flickering\n const [shown, setShown] = useState(false)\n const { classes } = useStyles()\n useEffect(() => {\n const timeout = setTimeout(() => {\n setShown(true)\n }, 300)\n return () => {\n clearTimeout(timeout)\n }\n })\n\n return shown ? (\n <div className={classes.loading}>\n <LoadingEllipses />\n </div>\n ) : null\n}\n\nfunction BlockMessage({ messageText }: { messageText: string }) {\n const { classes } = useStyles()\n return <div className={classes.blockMessage}>{messageText}</div>\n}\n\nfunction BlockError({ error }: { error: unknown }) {\n const { classes } = useStyles()\n return <div className={classes.blockError}>{`${error}`}</div>\n}\n\nconst ServerSideRenderedBlockContent = observer(function ({\n model,\n}: {\n model: LinearSyntenyDisplayModel\n}) {\n if (model.error) {\n return <BlockError error={model.error} />\n }\n if (model.message) {\n return <BlockMessage messageText={model.message} />\n }\n if (!model.features) {\n return <LoadingMessage />\n }\n\n return <LinearSyntenyRendering model={model} />\n})\n\nexport default ServerSideRenderedBlockContent\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 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