Mercurial > repos > fubar > jbrowse2
view x/static/js/5727.f7a524b6.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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{ Feature, notEmpty } from '@jbrowse/core/util'\n\nimport { parseBreakend } from '@gmod/vcf'\n\n// this finds candidate alignment features, aimed at plotting split reads from\n// BAM/CRAM files\nexport function getBadlyPairedAlignments(features: Map<string, Feature>) {\n const candidates = new Map<string, Feature[]>()\n const alreadySeen = new Set<string>()\n\n // this finds candidate features that share the same name\n for (const feature of features.values()) {\n const flags = feature.get('flags')\n const id = feature.id()\n const unmapped = flags & 4\n const correctlyPaired = flags & 2\n\n if (!alreadySeen.has(id) && !correctlyPaired && !unmapped) {\n const n = feature.get('name')\n let val = candidates.get(n)\n if (!val) {\n val = []\n candidates.set(n, val)\n }\n val.push(feature)\n }\n alreadySeen.add(feature.id())\n }\n\n return [...candidates.values()].filter(v => v.length > 1)\n}\n\nfunction getTag(f: Feature, tag: string) {\n const tags = f.get('tags')\n return tags ? tags[tag] : f.get(tag)\n}\n\n// this finds candidate alignment features, aimed at plotting split reads from\n// BAM/CRAM files\nexport function getMatchedAlignmentFeatures(features: Map<string, Feature>) {\n const candidates = new Map<string, Feature[]>()\n const alreadySeen = new Set<string>()\n\n // this finds candidate features that share the same name\n for (const feature of features.values()) {\n const id = feature.id()\n const unmapped = feature.get('flags') & 4\n const hasSA = !!getTag(feature, 'SA')\n if (!alreadySeen.has(id) && !unmapped && hasSA) {\n const n = feature.get('name')\n let val = candidates.get(n)\n if (!val) {\n val = []\n candidates.set(n, val)\n }\n val.push(feature)\n }\n alreadySeen.add(feature.id())\n }\n\n return [...candidates.values()].filter(v => v.length > 1)\n}\n\nexport function hasPairedReads(features: Map<string, Feature>) {\n for (const f of features.values()) {\n if (f.get('flags') & 1) {\n return true\n }\n }\n return false\n}\n\nexport function findMatchingAlt(feat1: Feature, feat2: Feature) {\n const alts = feat1.get('ALT') as string[] | undefined\n if (alts) {\n return new Map(\n alts\n .map(alt => parseBreakend(alt))\n .filter(notEmpty)\n .map(bnd => [bnd.MatePosition, bnd]),\n ).get(`${feat2.get('refName')}:${feat2.get('start') + 1}`)\n }\n return undefined\n}\n\n// Returns paired BND features across multiple views by inspecting the ALT\n// field to get exact coordinate matches\nexport function getMatchedBreakendFeatures(feats: Map<string, Feature>) {\n const candidates = new Map<string, Feature[]>()\n const alreadySeen = new Set<string>()\n\n for (const f of feats.values()) {\n if (!alreadySeen.has(f.id()) && f.get('type') === 'breakend') {\n const alts = f.get('ALT') as string[] | undefined\n alts?.forEach(a => {\n const cur = `${f.get('refName')}:${f.get('start') + 1}`\n const bnd = parseBreakend(a)\n if (bnd) {\n const val = candidates.get(cur)\n if (!val) {\n candidates.set(bnd.MatePosition || 'none', [f])\n } else {\n val.push(f)\n }\n }\n })\n }\n alreadySeen.add(f.id())\n }\n\n return [...candidates.values()].filter(v => v.length > 1)\n}\n\n// Getting \"matched\" TRA means just return all TRA\nexport function getMatchedTranslocationFeatures(feats: Map<string, Feature>) {\n const ret: Feature[][] = []\n const alreadySeen = new Set<string>()\n\n for (const f of feats.values()) {\n if (!alreadySeen.has(f.id()) && f.get('ALT')[0] === '<TRA>') {\n ret.push([f])\n }\n alreadySeen.add(f.id())\n }\n\n return ret\n}\n\n// Getting \"matched\" TRA means just return all TRA\nexport function getMatchedPairedFeatures(feats: Map<string, Feature>) {\n const candidates = new Map<string, Feature[]>()\n const alreadySeen = new Set<string>()\n\n for (const f of feats.values()) {\n if (!alreadySeen.has(f.id()) && f.get('type') === 'paired_feature') {\n const r1 = f.id().replace('-r1', '')\n const r2 = f.id().replace('-r2', '')\n if (f.id().endsWith('-r1')) {\n if (!candidates.get(r1)) {\n candidates.set(r1, [])\n }\n candidates.get(r1)!.push(f)\n } else if (f.id().endsWith('-r2')) {\n if (!candidates.get(r2)) {\n candidates.set(r2, [])\n }\n candidates.get(r2)!.push(f)\n }\n }\n alreadySeen.add(f.id())\n }\n\n return [...candidates.values()].filter(v => v.length > 1)\n}\n","import { alpha } from '@mui/material'\n// orientation definitions from igv.js, see also\n// https://software.broadinstitute.org/software/igv/interpreting_pair_orientations\nexport const orientationTypes = {\n fr: {\n F1R2: 'LR',\n F2R1: 'LR',\n\n F1F2: 'LL',\n F2F1: 'LL',\n\n R1R2: 'RR',\n R2R1: 'RR',\n\n R1F2: 'RL',\n R2F1: 'RL',\n } as Record<string, string>,\n\n rf: {\n R1F2: 'LR',\n R2F1: 'LR',\n\n R1R2: 'LL',\n R2R1: 'LL',\n\n F1F2: 'RR',\n F2F1: 'RR',\n\n F1R2: 'RL',\n F2R1: 'RL',\n } as Record<string, string>,\n\n ff: {\n F2F1: 'LR',\n R1R2: 'LR',\n\n F2R1: 'LL',\n R1F2: 'LL',\n\n R2F1: 'RR',\n F1R2: 'RR',\n\n R2R1: 'RL',\n F1F2: 'RL',\n } as Record<string, string>,\n}\n\nexport const pairMap = {\n LR: 'color_pair_lr',\n LL: 'color_pair_ll',\n RR: 'color_pair_rr',\n RL: 'color_pair_rl',\n} as const\n\n// manually calculated by running\n// const color = require('color')\n// Object.fromEntries(Object.entries(fillColor).map(([key,val])=>{\n// return [key, color(val).darken('0.3').hex()]\n// }))\n// this avoids (expensive) use of Color module at runtime\nexport const strokeColor = {\n color_fwd_strand_not_proper: alpha('#CA6767', 0.8),\n color_rev_strand_not_proper: alpha('#7272AA', 0.8),\n color_fwd_strand: alpha('#DC2A2A', 0.8),\n color_rev_strand: alpha('#4141BA', 0.8),\n color_fwd_missing_mate: alpha('#921111', 0.8),\n color_rev_missing_mate: alpha('#111192', 0.8),\n color_fwd_diff_chr: alpha('#000000', 0.8),\n color_rev_diff_chr: alpha('#696969', 0.8),\n color_pair_lr: alpha('#8C8C8C', 0.8),\n color_pair_rr: alpha('#00005A', 0.8),\n color_pair_rl: alpha('#005A5A', 0.8),\n color_pair_ll: alpha('#005A00', 0.8),\n color_nostrand: alpha('#8C8C8C', 0.8),\n color_interchrom: alpha('#5A005A', 0.8),\n color_longinsert: alpha('#B30000', 0.8),\n color_shortinsert: alpha('#FF3A5C', 0.8),\n color_unknown: alpha('#555', 0.8),\n}\n\nconst defaultColor = strokeColor.color_unknown\n\nexport function getPairedOrientationColorOrDefault(f: {\n pair_orientation?: string\n}) {\n const type = orientationTypes.fr\n const r = type[f.pair_orientation || ''] as keyof typeof pairMap\n const type2 = pairMap[r] as keyof typeof strokeColor\n return r === 'LR' ? undefined : strokeColor[type2]\n}\n\nexport function getLongReadOrientationColorOrDefault(s1: number, s2: number) {\n if (s1 === -1 && s2 === 1) {\n return strokeColor.color_pair_rr\n } else if (s1 === 1 && s2 === -1) {\n return strokeColor.color_pair_ll\n } else {\n return strokeColor.color_unknown\n }\n}\n\nexport function getLongReadOrientationAbnormal(s1: number, s2: number) {\n if (s1 === -1 && s2 === 1) {\n return true\n } else if (s1 === 1 && s2 === -1) {\n return true\n } else {\n return false\n }\n}\n\nexport function isAbnormalOrientation(f: { pair_orientation?: string }) {\n const type = orientationTypes.fr\n const r = type[f.pair_orientation || ''] as keyof typeof pairMap\n return r !== 'LR'\n}\n\nexport function getPairedOrientationColor(f: { pair_orientation?: string }) {\n return getPairedOrientationColorOrDefault(f) || defaultColor\n}\n","import React, { useMemo, useState } from 'react'\nimport { observer } from 'mobx-react'\nimport { getSnapshot } from 'mobx-state-tree'\nimport { useTheme } from '@mui/material'\nimport { getSession, getStrokeProps } from '@jbrowse/core/util'\n\n// locals\nimport {\n getBadlyPairedAlignments,\n getMatchedAlignmentFeatures,\n hasPairedReads,\n} from './util'\nimport {\n yPos,\n useNextFrame,\n getPxFromCoordinate,\n heightFromSpecificLevel,\n} from '../util'\nimport { BreakpointViewModel } from '../model'\nimport {\n getLongReadOrientationAbnormal,\n getLongReadOrientationColorOrDefault,\n getPairedOrientationColor,\n isAbnormalOrientation,\n} from './getOrientationColor'\n\nconst [LEFT, , RIGHT] = [0, 1, 2, 3] as const\n\nconst AlignmentConnections = observer(function ({\n model,\n trackId,\n parentRef,\n getTrackYPosOverride,\n}: {\n model: BreakpointViewModel\n trackId: string\n parentRef: React.RefObject<SVGSVGElement>\n getTrackYPosOverride?: (trackId: string, level: number) => number\n}) {\n const { views, showIntraviewLinks } = model\n const theme = useTheme()\n const session = getSession(model)\n const snap = getSnapshot(model)\n const { assemblyManager } = session\n const v0 = views[0]\n const assembly = v0 ? assemblyManager.get(v0.assemblyNames[0]!) : undefined\n useNextFrame(snap)\n const allFeatures = model.getTrackFeatures(trackId)\n const hasPaired = useMemo(() => hasPairedReads(allFeatures), [allFeatures])\n const layoutMatches = useMemo(() => {\n const layoutMatches = model.getMatchedFeaturesInLayout(\n trackId,\n hasPaired\n ? getBadlyPairedAlignments(allFeatures)\n : getMatchedAlignmentFeatures(allFeatures),\n )\n if (!hasPaired) {\n layoutMatches.forEach(m => {\n m.sort((a, b) => a.feature.get('clipPos') - b.feature.get('clipPos'))\n })\n }\n return layoutMatches\n }, [allFeatures, trackId, hasPaired, model])\n\n const [mouseoverElt, setMouseoverElt] = useState<string>()\n\n let yOffset = 0\n if (parentRef.current) {\n const rect = parentRef.current.getBoundingClientRect()\n yOffset = rect.top\n }\n\n return assembly ? (\n <g\n fill=\"none\"\n data-testid={layoutMatches.length ? `${trackId}-loaded` : trackId}\n >\n {layoutMatches.map(chunk => {\n const ret = []\n // we follow a path in the list of chunks, not from top to bottom, just in series\n // following x1,y1 -> x2,y2\n for (let i = 0; i < chunk.length - 1; i++) {\n const { layout: c1, feature: f1, level: level1 } = chunk[i]!\n const { layout: c2, feature: f2, level: level2 } = chunk[i + 1]!\n\n if (!c1 || !c2) {\n console.warn('received null layout for a overlay feature')\n return null\n }\n\n // disable rendering connections in a single row\n if (!showIntraviewLinks && level1 === level2) {\n return null\n }\n const f1ref = assembly.getCanonicalRefName(f1.get('refName'))\n const f2ref = assembly.getCanonicalRefName(f2.get('refName'))\n\n if (!f1ref || !f2ref) {\n throw new Error(`unable to find ref for ${f1ref || f2ref}`)\n }\n const r = {\n pair_orientation: f1.get('pair_orientation'),\n }\n\n const s1 = f1.get('strand')\n const s2 = f2.get('strand')\n const sameRef = f1ref === f2ref\n const checkOrientation = sameRef\n let orientationColor = ''\n let isAbnormal = false\n if (checkOrientation) {\n if (hasPaired) {\n orientationColor = getPairedOrientationColor(r)\n isAbnormal = isAbnormalOrientation(r)\n } else {\n orientationColor = getLongReadOrientationColorOrDefault(s1, s2)\n isAbnormal = getLongReadOrientationAbnormal(s1, s2)\n }\n }\n const p1 = c1[s1 === -1 ? LEFT : RIGHT]\n const sn1 = s2 === -1\n const p2 = hasPaired ? c2[sn1 ? LEFT : RIGHT] : c2[sn1 ? RIGHT : LEFT]\n const x1 = getPxFromCoordinate(views[level1]!, f1ref, p1)\n const x2 = getPxFromCoordinate(views[level2]!, f2ref, p2)\n const reversed1 = views[level1]!.pxToBp(x1).reversed\n const reversed2 = views[level2]!.pxToBp(x2).reversed\n const rf1 = reversed1 ? -1 : 1\n const rf2 = reversed2 ? -1 : 1\n const tracks = views.map(v => v.getTrack(trackId))\n const y1 =\n yPos(trackId, level1, views, tracks, c1, getTrackYPosOverride) -\n yOffset\n const y2 =\n yPos(trackId, level2, views, tracks, c2, getTrackYPosOverride) -\n yOffset\n const sameLevel = level1 === level2\n const abnormalSpecialRenderFlag = sameLevel && isAbnormal\n const trackHeight = abnormalSpecialRenderFlag\n ? tracks[level1].displays[0].height\n : 0\n const pf1 = hasPaired ? -1 : 1\n const y0 = heightFromSpecificLevel(\n views,\n trackId,\n level1,\n getTrackYPosOverride,\n )\n\n // possible todo: use totalCurveHeight to possibly make alternative\n // squiggle if the S is too small\n const path = [\n 'M',\n x1,\n y1,\n 'C',\n\n // first bezier x,y\n x1 + 200 * f1.get('strand') * rf1,\n abnormalSpecialRenderFlag\n ? Math.min(y0 - yOffset + trackHeight, y1 + trackHeight)\n : y1,\n\n // second bezier x,y\n x2 - 200 * f2.get('strand') * rf2 * pf1,\n abnormalSpecialRenderFlag\n ? Math.min(y0 - yOffset + trackHeight, y2 + trackHeight)\n : y2,\n\n // third bezier x,y\n x2,\n y2,\n ].join(' ')\n const id = `${f1.id()}-${f2.id()}`\n ret.push(\n <path\n d={path}\n key={id}\n data-testid=\"r1\"\n strokeWidth={mouseoverElt === id ? 5 : 1}\n {...getStrokeProps(\n orientationColor || theme.palette.text.disabled,\n )}\n onClick={() => {\n const featureWidget = session.addWidget?.(\n 'BreakpointAlignmentsWidget',\n 'breakpointAlignments',\n {\n featureData: {\n feature1: (\n allFeatures.get(f1.id()) || { toJSON: () => {} }\n ).toJSON(),\n feature2: (\n allFeatures.get(f2.id()) || { toJSON: () => {} }\n ).toJSON(),\n },\n },\n )\n session.showWidget?.(featureWidget)\n }}\n onMouseOver={() => {\n setMouseoverElt(id)\n }}\n onMouseOut={() => {\n setMouseoverElt(undefined)\n }}\n />,\n )\n }\n return ret\n })}\n </g>\n ) : null\n})\n\nexport default AlignmentConnections\n","import React, { useState, useMemo } from 'react'\nimport { getSession } from '@jbrowse/core/util'\nimport { observer } from 'mobx-react'\nimport { getSnapshot } from 'mobx-state-tree'\n\n// locals\nimport { findMatchingAlt, getMatchedBreakendFeatures } from './util'\nimport { yPos, getPxFromCoordinate, useNextFrame } from '../util'\nimport { BreakpointViewModel } from '../model'\n\nconst [LEFT] = [0, 1, 2, 3] as const\n\nconst Breakends = observer(function ({\n model,\n trackId,\n parentRef: ref,\n getTrackYPosOverride,\n}: {\n model: BreakpointViewModel\n trackId: string\n parentRef: React.RefObject<SVGSVGElement>\n getTrackYPosOverride?: (trackId: string, level: number) => number\n}) {\n const { views } = model\n const session = getSession(model)\n const { assemblyManager } = session\n const totalFeatures = model.getTrackFeatures(trackId)\n const layoutMatches = useMemo(\n () =>\n model.getMatchedFeaturesInLayout(\n trackId,\n getMatchedBreakendFeatures(totalFeatures),\n ),\n [totalFeatures, trackId, model],\n )\n\n const [mouseoverElt, setMouseoverElt] = useState<string>()\n const snap = getSnapshot(model)\n useNextFrame(snap)\n const assembly = assemblyManager.get(views[0]!.assemblyNames[0]!)\n\n if (!assembly) {\n return null\n }\n\n let yoff = 0\n if (ref.current) {\n const rect = ref.current.getBoundingClientRect()\n yoff = rect.top\n }\n\n return (\n <g\n stroke=\"green\"\n strokeWidth={5}\n fill=\"none\"\n data-testid={layoutMatches.length ? `${trackId}-loaded` : trackId}\n >\n {layoutMatches.map(chunk => {\n const ret = []\n // we follow a path in the list of chunks, not from top to bottom, just\n // in series following x1,y1 -> x2,y2\n for (let i = 0; i < chunk.length - 1; i += 1) {\n const { layout: c1, feature: f1, level: level1 } = chunk[i]!\n const { layout: c2, feature: f2, level: level2 } = chunk[i + 1]!\n const id = f1.id()\n\n const relevantAlt = findMatchingAlt(f1, f2)\n if (!c1 || !c2) {\n return null\n }\n const f1origref = f1.get('refName')\n const f2origref = f2.get('refName')\n const f1ref = assembly.getCanonicalRefName(f1origref)\n const f2ref = assembly.getCanonicalRefName(f2origref)\n if (!f1ref || !f2ref) {\n throw new Error(`unable to find ref for ${f1ref || f2ref}`)\n }\n const x1 = getPxFromCoordinate(views[level1]!, f1ref, c1[LEFT])\n const x2 = getPxFromCoordinate(views[level2]!, f2ref, c2[LEFT])\n const reversed1 = views[level1]!.pxToBp(x1).reversed\n const reversed2 = views[level2]!.pxToBp(x2).reversed\n\n const tracks = views.map(v => v.getTrack(trackId))\n const y1 =\n yPos(trackId, level1, views, tracks, c1, getTrackYPosOverride) -\n yoff\n const y2 =\n yPos(trackId, level2, views, tracks, c2, getTrackYPosOverride) -\n yoff\n if (!relevantAlt) {\n console.warn('the relevant ALT allele was not found, cannot render')\n } else {\n const path = [\n 'M', // move to\n x1 -\n 20 *\n (relevantAlt.Join === 'left' ? -1 : 1) *\n (reversed1 ? -1 : 1),\n y1,\n 'L', // line to\n x1,\n y1,\n 'L', // line to\n x2,\n y2,\n 'L', // line to\n x2 -\n 20 *\n (relevantAlt.MateDirection === 'left' ? 1 : -1) *\n (reversed2 ? -1 : 1),\n y2,\n ].join(' ')\n ret.push(\n <path\n d={path}\n data-testid=\"r2\"\n key={JSON.stringify(path)}\n strokeWidth={id === mouseoverElt ? 10 : 5}\n onClick={() => {\n const featureWidget = session.addWidget?.(\n 'VariantFeatureWidget',\n 'variantFeature',\n {\n featureData: totalFeatures.get(id)?.toJSON(),\n },\n )\n session.showWidget?.(featureWidget)\n }}\n onMouseOver={() => {\n setMouseoverElt(id)\n }}\n onMouseOut={() => {\n setMouseoverElt(undefined)\n }}\n />,\n )\n }\n }\n return ret\n })}\n </g>\n )\n})\n\nexport default Breakends\n","import React, { useState, useMemo } from 'react'\nimport { getSession } from '@jbrowse/core/util'\nimport { observer } from 'mobx-react'\nimport { getSnapshot } from 'mobx-state-tree'\n\n// locals\nimport { getMatchedTranslocationFeatures } from './util'\nimport { yPos, getPxFromCoordinate, useNextFrame } from '../util'\nimport { BreakpointViewModel, LayoutRecord } from '../model'\n\nconst [LEFT] = [0, 1, 2, 3] as const\n\nfunction str(s: string) {\n if (s === '+') {\n return 1\n } else if (s === '-') {\n return -1\n } else {\n return 0\n }\n}\n\nconst Translocations = observer(function ({\n model,\n trackId,\n parentRef: ref,\n getTrackYPosOverride,\n}: {\n model: BreakpointViewModel\n trackId: string\n parentRef: React.RefObject<SVGSVGElement>\n getTrackYPosOverride?: (trackId: string, level: number) => number\n}) {\n const { views } = model\n const session = getSession(model)\n const { assemblyManager } = session\n const totalFeatures = model.getTrackFeatures(trackId)\n const layoutMatches = useMemo(\n () =>\n model.getMatchedFeaturesInLayout(\n trackId,\n getMatchedTranslocationFeatures(totalFeatures),\n ),\n\n [totalFeatures, trackId, model],\n )\n\n const [mouseoverElt, setMouseoverElt] = useState<string>()\n const snap = getSnapshot(model)\n useNextFrame(snap)\n\n const assembly = assemblyManager.get(views[0]!.assemblyNames[0]!)\n if (!assembly) {\n return null\n }\n\n let yOffset = 0\n if (ref.current) {\n const rect = ref.current.getBoundingClientRect()\n yOffset = rect.top\n }\n\n // we hardcode the TRA to go to the \"other view\" and if there is none, we\n // just return null here note: would need to do processing of the INFO\n // CHR2/END and see which view could contain those coordinates to really do\n // it properly\n if (views.length < 2) {\n return null\n }\n return (\n <g\n fill=\"none\"\n stroke=\"green\"\n strokeWidth={5}\n data-testid={layoutMatches.length ? `${trackId}-loaded` : trackId}\n >\n {layoutMatches.map(chunk => {\n // we follow a path in the list of chunks, not from top to bottom,\n // just in series following x1,y1 -> x2,y2\n const ret = []\n for (const { layout: c1, feature: f1, level: level1 } of chunk) {\n const level2 = level1 === 0 ? 1 : 0\n const id = f1.id()\n if (!c1) {\n return null\n }\n\n const info = f1.get('INFO')\n const chr2 = info.CHR2[0]\n const end2 = info.END[0]\n const res = info.STRANDS?.[0]?.split('') // not all files have STRANDS\n const [myDirection, mateDirection] = res ?? ['.', '.']\n\n const r = getPxFromCoordinate(views[level2]!, chr2, end2)\n if (r) {\n const c2: LayoutRecord = [r, 0, r + 1, 0]\n const x1 = getPxFromCoordinate(\n views[level1]!,\n f1.get('refName'),\n c1[LEFT],\n )\n const x2 = r\n const reversed1 = views[level1]!.pxToBp(x1).reversed\n const reversed2 = views[level2]!.pxToBp(x2).reversed\n\n const tracks = views.map(v => v.getTrack(trackId))\n const y1 =\n yPos(trackId, level1, views, tracks, c1, getTrackYPosOverride) -\n yOffset\n const y2 =\n yPos(trackId, level2, views, tracks, c2, getTrackYPosOverride) -\n yOffset\n\n const path = [\n 'M', // move to\n x1 - 20 * str(myDirection) * (reversed1 ? -1 : 1),\n y1,\n 'L', // line to\n x1,\n y1,\n 'L', // line to as const\n x2,\n y2,\n 'L', // line to\n x2 - 20 * str(mateDirection) * (reversed2 ? -1 : 1),\n y2,\n ].join(' ')\n ret.push(\n <path\n d={path}\n key={JSON.stringify(path)}\n strokeWidth={id === mouseoverElt ? 10 : 5}\n onClick={() => {\n const featureWidget = session.addWidget?.(\n 'VariantFeatureWidget',\n 'variantFeature',\n {\n featureData: (\n totalFeatures.get(id) || { toJSON: () => {} }\n ).toJSON(),\n },\n )\n session.showWidget?.(featureWidget)\n }}\n onMouseOver={() => {\n setMouseoverElt(id)\n }}\n onMouseOut={() => {\n setMouseoverElt(undefined)\n }}\n />,\n )\n }\n }\n return ret\n })}\n </g>\n )\n})\n\nexport default Translocations\n","import React, { useState, useMemo } from 'react'\nimport { getSession } from '@jbrowse/core/util'\nimport { observer } from 'mobx-react'\nimport { getSnapshot } from 'mobx-state-tree'\n\n// locals\nimport { getMatchedPairedFeatures } from './util'\nimport { yPos, getPxFromCoordinate, useNextFrame } from '../util'\nimport { BreakpointViewModel } from '../model'\n\nconst [LEFT] = [0, 1, 2, 3] as const\n\nconst PairedFeatures = observer(function ({\n model,\n trackId,\n parentRef: ref,\n getTrackYPosOverride,\n}: {\n model: BreakpointViewModel\n trackId: string\n parentRef: React.RefObject<SVGSVGElement>\n getTrackYPosOverride?: (trackId: string, level: number) => number\n}) {\n const { views } = model\n const session = getSession(model)\n const { assemblyManager } = session\n const totalFeatures = model.getTrackFeatures(trackId)\n const layoutMatches = useMemo(\n () =>\n model.getMatchedFeaturesInLayout(\n trackId,\n getMatchedPairedFeatures(totalFeatures),\n ),\n [totalFeatures, trackId, model],\n )\n\n const [mouseoverElt, setMouseoverElt] = useState<string>()\n const snap = getSnapshot(model)\n useNextFrame(snap)\n const assembly = assemblyManager.get(views[0]!.assemblyNames[0]!)\n\n if (!assembly) {\n return null\n }\n\n let yoff = 0\n if (ref.current) {\n const rect = ref.current.getBoundingClientRect()\n yoff = rect.top\n }\n\n return (\n <g\n stroke=\"green\"\n strokeWidth={5}\n fill=\"none\"\n data-testid={layoutMatches.length ? `${trackId}-loaded` : trackId}\n >\n {layoutMatches.map(chunk => {\n const ret = []\n // we follow a path in the list of chunks, not from top to bottom, just\n // in series following x1,y1 -> x2,y2\n for (let i = 0; i < chunk.length - 1; i += 1) {\n const { layout: c1, feature: f1, level: level1 } = chunk[i]!\n const { layout: c2, feature: f2, level: level2 } = chunk[i + 1]!\n const id = f1.id()\n\n if (!c1 || !c2) {\n return null\n }\n const f1origref = f1.get('refName')\n const f2origref = f2.get('refName')\n const f1ref = assembly.getCanonicalRefName(f1origref)\n const f2ref = assembly.getCanonicalRefName(f2origref)\n if (!f1ref || !f2ref) {\n throw new Error(`unable to find ref for ${f1ref || f2ref}`)\n }\n const x1 = getPxFromCoordinate(views[level1]!, f1ref, c1[LEFT])\n const x2 = getPxFromCoordinate(views[level2]!, f2ref, c2[LEFT])\n\n const tracks = views.map(v => v.getTrack(trackId))\n const y1 =\n yPos(trackId, level1, views, tracks, c1, getTrackYPosOverride) -\n yoff\n const y2 =\n yPos(trackId, level2, views, tracks, c2, getTrackYPosOverride) -\n yoff\n const path = [\n 'M', // move to\n x1,\n y1,\n 'L', // line to\n x2,\n y2,\n ].join(' ')\n ret.push(\n <path\n d={path}\n data-testid=\"r2\"\n key={JSON.stringify(path)}\n strokeWidth={id === mouseoverElt ? 10 : 5}\n onClick={() => {\n const featureWidget = session.addWidget?.(\n 'VariantFeatureWidget',\n 'variantFeature',\n {\n featureData: totalFeatures.get(id)?.toJSON(),\n },\n )\n session.showWidget?.(featureWidget)\n }}\n onMouseOver={() => {\n setMouseoverElt(id)\n }}\n onMouseOut={() => {\n setMouseoverElt(undefined)\n }}\n />,\n )\n }\n return ret\n })}\n </g>\n )\n})\n\nexport default PairedFeatures\n","import React from 'react'\nimport { observer } from 'mobx-react'\n\n// locals\nimport { BreakpointViewModel } from '../model'\nimport AlignmentConnections from './AlignmentConnections'\nimport Breakends from './Breakends'\nimport Translocations from './Translocations'\nimport PairedFeatures from './PairedFeatures'\n\nconst Overlay = observer(function (props: {\n parentRef: React.RefObject<SVGSVGElement>\n model: BreakpointViewModel\n trackId: string\n getTrackYPosOverride?: (trackId: string, level: number) => number\n}) {\n const { model, trackId } = props\n const tracks = model.getMatchedTracks(trackId)\n\n // curvy line type arcs\n if (tracks[0]?.type === 'AlignmentsTrack') {\n return <AlignmentConnections {...props} />\n }\n\n // translocation type arcs\n else if (tracks[0]?.type === 'VariantTrack') {\n return model.hasTranslocations(trackId) ? (\n <Translocations {...props} />\n ) : model.hasPairedFeatures(trackId) ? (\n <PairedFeatures {...props} />\n ) : (\n <Breakends {...props} />\n )\n } else {\n return null\n }\n})\n\nexport default Overlay\n"],"names":["getTag","f","tag","tags","get","findMatchingAlt","feat1","feat2","alts","Map","map","alt","parseBreakend","filter","notEmpty","bnd","MatePosition","orientationTypes","F1R2","F2R1","F1F2","F2F1","R1R2","R2R1","R1F2","R2F1","pairMap","LR","LL","RR","RL","strokeColor","color_fwd_strand_not_proper","alpha","color_rev_strand_not_proper","color_fwd_strand","color_rev_strand","color_fwd_missing_mate","color_rev_missing_mate","color_fwd_diff_chr","color_rev_diff_chr","color_pair_lr","color_pair_rr","color_pair_rl","color_pair_ll","color_nostrand","color_interchrom","color_longinsert","color_shortinsert","color_unknown","defaultColor","getLongReadOrientationColorOrDefault","s1","s2","getLongReadOrientationAbnormal","LEFT","RIGHT","observer","model","trackId","parentRef","getTrackYPosOverride","views","showIntraviewLinks","theme","useTheme","session","getSession","snap","getSnapshot","assemblyManager","v0","assembly","assemblyNames","undefined","useNextFrame","allFeatures","getTrackFeatures","hasPaired","useMemo","features","values","hasPairedReads","layoutMatches","getMatchedFeaturesInLayout","candidates","alreadySeen","Set","feature","flags","id","unmapped","correctlyPaired","has","n","val","set","push","add","v","length","getBadlyPairedAlignments","hasSA","getMatchedAlignmentFeatures","forEach","m","sort","a","b","mouseoverElt","setMouseoverElt","useState","yOffset","current","rect","getBoundingClientRect","top","React","fill","chunk","ret","i","layout","c1","f1","level","level1","c2","f2","level2","console","warn","f1ref","getCanonicalRefName","f2ref","Error","r","pair_orientation","orientationColor","isAbnormal","getPairedOrientationColorOrDefault","p1","sn1","p2","x1","getPxFromCoordinate","x2","rf1","pxToBp","reversed","rf2","tracks","getTrack","y1","yPos","y2","abnormalSpecialRenderFlag","trackHeight","displays","height","pf1","y0","heightFromSpecificLevel","path","Math","min","join","_extends","d","key","strokeWidth","getStrokeProps","palette","text","disabled","onClick","featureWidget","addWidget","featureData","feature1","toJSON","feature2","showWidget","onMouseOver","onMouseOut","ref","totalFeatures","feats","cur","getMatchedBreakendFeatures","yoff","stroke","relevantAlt","f1origref","f2origref","reversed1","reversed2","Join","MateDirection","JSON","stringify","str","s","getMatchedTranslocationFeatures","info","chr2","CHR2","end2","END","res","STRANDS","split","myDirection","mateDirection","r1","replace","r2","endsWith","getMatchedPairedFeatures","props","getMatchedTracks","type","AlignmentConnections","hasTranslocations","Translocations","hasPairedFeatures","PairedFeatures","Breakends"],"sourceRoot":""}