jbrowse-plugin-graphgenomeviewer 7.1.0 → 7.1.2

package/dist/chunks/chunk-WX26KTZM.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+graph-walks@1.0.0/node_modules/@jbrowse/graph-walks/esm/walkChunk.js", "../../node_modules/.pnpm/@jbrowse+graph-walks@1.0.0/node_modules/@jbrowse/graph-walks/esm/util.js", "../../node_modules/.pnpm/@jbrowse+graph-walks@1.0.0/node_modules/@jbrowse/graph-walks/esm/walkRows.js", "../../node_modules/.pnpm/@jbrowse+graph-walks@1.0.0/node_modules/@jbrowse/graph-walks/esm/walkReader.js", "../../src/RgfaTabixAdapter/walkReader.ts"],
-  "sourcesContent": ["// A chunk of gfa-to-tabix's walk format 2, one file per reference (that\n// repo's docs/walks-format.md). A chunk lists its `ref` rows, which joined in\n// hapOffset order are the chunk's reference path R; a `nodes` row with the\n// lengths of the nodes its routes visit; `route` rows, each a way off R; and a\n// `walk` row per piece of every other path, naming the routes it takes in\n// order. A handle is 2 * id + 1 when reversed.\nconst NONE = -1;\nconst idOf = (handle) => (handle - (handle & 1)) / 2;\n// the other strand's handle; arithmetic, which holds past 2^31\nconst otherStrand = (handle) => (handle & 1 ? handle - 1 : handle + 1);\n// The handles a column of delta tokens names, each 2 * (id - previous id) +\n// reverse, from `previous.id`, which ends on the last id read\nfunction tokens(field, previous, out) {\n    if (field === '.') {\n        return out;\n    }\n    let v = 0;\n    let neg = false;\n    for (let p = 0; p <= field.length; p++) {\n        const ch = p < field.length ? field.charCodeAt(p) : 44;\n        if (ch === 44) {\n            const d = neg ? -v : v;\n            const r = d & 1;\n            previous.id += (d - r) / 2;\n            out.push(previous.id * 2 + r);\n            v = 0;\n            neg = false;\n        }\n        else if (ch === 45) {\n            neg = true;\n        }\n        else {\n            v = v * 10 + (ch - 48);\n        }\n    }\n    return out;\n}\nfunction numbers(field) {\n    return field === '.' ? [] : field.split(',').map(Number);\n}\n// A link the way round the converter writes it, so a link and its reverse\n// are one: the smaller of a and the flipped b first\nexport function canonicalLink(a, b) {\n    return a > otherStrand(b) ? [otherStrand(b), otherStrand(a)] : [a, b];\n}\nfunction tags(cols, from, anchor) {\n    let prev;\n    let next;\n    for (let k = from; k < cols.length; k++) {\n        const tag = cols[k];\n        if (tag.startsWith('pv:') || tag.startsWith('nx:')) {\n            const at = tag.lastIndexOf(':');\n            const chunk = {\n                refName: tag[3] === 'Z' ? tag.slice(5, at) : anchor,\n                start: +tag.slice(at + 1),\n            };\n            if (tag.startsWith('pv:')) {\n                prev = chunk;\n            }\n            else {\n                next = chunk;\n            }\n        }\n    }\n    return { prev, next };\n}\n// The chunk's reference path R: its handles, the bp of its steps before each\n// position, and each node's occurrences in R\nexport class RefPath {\n    constructor() {\n        this.handles = [];\n        this.before = [0];\n        this.occurrences = new Map();\n    }\n    add(handles, lengths) {\n        for (let k = 0; k < handles.length; k++) {\n            const h = handles[k];\n            const i = this.handles.length;\n            this.handles.push(h);\n            this.before.push(this.before[i] + lengths[k]);\n            const id = idOf(h);\n            const list = this.occurrences.get(id);\n            if (list) {\n                list.push(i);\n            }\n            else {\n                this.occurrences.set(id, [i]);\n            }\n        }\n    }\n    // bp of R's steps before position i\n    bp(i) {\n        return this.before[i];\n    }\n    first(handle) {\n        var _a;\n        return (_a = this.occurrences.get(idOf(handle))) === null || _a === void 0 ? void 0 : _a[0];\n    }\n    nearest(handle, i) {\n        var _a;\n        let best;\n        for (const j of (_a = this.occurrences.get(idOf(handle))) !== null && _a !== void 0 ? _a : []) {\n            if (best === undefined || Math.abs(j - i) <= Math.abs(best - i)) {\n                best = j;\n            }\n        }\n        return best;\n    }\n    // The position a stretch along R from position i, reading R the way `h`\n    // does there, first holds `target`, i itself included\n    reach(i, h, target) {\n        var _a;\n        const forward = this.handles[i] === h;\n        let found;\n        for (const j of (_a = this.occurrences.get(idOf(target))) !== null && _a !== void 0 ? _a : []) {\n            if (forward && j >= i && this.handles[j] === target) {\n                if (found === undefined || j < found) {\n                    found = j;\n                }\n            }\n            else if (!forward &&\n                j <= i &&\n                otherStrand(this.handles[j]) === target) {\n                if (found === undefined || j > found) {\n                    found = j;\n                }\n            }\n        }\n        return found;\n    }\n    handleAt(i, forward) {\n        return forward ? this.handles[i] : otherStrand(this.handles[i]);\n    }\n}\nexport class WalkRowError extends Error {\n}\nconst orientedEntry = (route, flip) => flip ? (route.exit === NONE ? NONE : otherStrand(route.exit)) : route.entry;\nconst orientedExit = (route, flip) => flip ? (route.entry === NONE ? NONE : otherStrand(route.entry)) : route.exit;\n// A route's interior handle k, taken the way round `flip` says\nconst interiorAt = (route, flip, k) => flip\n    ? otherStrand(route.interior[route.interior.length - 1 - k])\n    : route.interior[k];\n// A walk row's choices, three numbers each: route index, flip and step count,\n// from `tok` or `tok:count` tokens\nfunction parseChoices(field) {\n    const choices = [];\n    if (field !== '.') {\n        let previous = 0;\n        let v = 0;\n        let neg = false;\n        let tok = 0;\n        let colonSeen = false;\n        for (let p = 0; p <= field.length; p++) {\n            const ch = p < field.length ? field.charCodeAt(p) : 44;\n            if (ch === 44) {\n                const value = neg ? -v : v;\n                const d = colonSeen ? tok : value;\n                const r = d & 1;\n                previous += (d - r) / 2;\n                choices.push(previous, r, colonSeen ? value : 0);\n                v = 0;\n                neg = false;\n                colonSeen = false;\n            }\n            else if (ch === 58) {\n                tok = neg ? -v : v;\n                v = 0;\n                neg = false;\n                colonSeen = true;\n            }\n            else if (ch === 45) {\n                neg = true;\n            }\n            else {\n                v = v * 10 + (ch - 48);\n            }\n        }\n    }\n    return choices;\n}\n// Follows a walk row as docs/walks-format.md decodes it\nfunction traverse(path, routes, start, endField, choices, visit) {\n    const colon = endField.indexOf(':');\n    const end = start + +(colon < 0 ? endField : endField.slice(0, colon));\n    const counted = colon >= 0;\n    const tail = counted ? +endField.slice(colon + 1) : 0;\n    const routeOf = (index) => {\n        const route = routes[index];\n        if (!route) {\n            throw new WalkRowError(`route ${index} is not in the chunk`);\n        }\n        return route;\n    };\n    let k = 0;\n    if (choices.length > 0 &&\n        orientedEntry(routeOf(choices[0]), choices[1] === 1) === NONE) {\n        if (!visit.route(choices[0], choices[1] === 1)) {\n            return;\n        }\n        k = 3;\n    }\n    let h = start;\n    let i = path.first(h);\n    if (i === undefined) {\n        throw new WalkRowError('a walk row starts off its chunk');\n    }\n    visit.step(h);\n    const follow = (target, count) => {\n        const forward = path.handles[i] === h;\n        const j = counted\n            ? i + (forward ? count : -count)\n            : path.reach(i, h, target);\n        if (j === undefined || j < 0 || j >= path.handles.length) {\n            throw new WalkRowError('a walk row runs off its chunk');\n        }\n        if (j !== i) {\n            visit.stretch(i, j, forward);\n        }\n        i = j;\n        h = path.handleAt(j, forward);\n    };\n    for (; k < choices.length; k += 3) {\n        const index = choices[k];\n        const flip = choices[k + 1] === 1;\n        const route = routeOf(index);\n        const entry = orientedEntry(route, flip);\n        if (entry === NONE) {\n            throw new WalkRowError('an open route after the first choice');\n        }\n        follow(entry, choices[k + 2]);\n        if (!visit.route(index, flip)) {\n            return;\n        }\n        const exit = orientedExit(route, flip);\n        if (exit === NONE) {\n            return;\n        }\n        h = exit;\n        i = path.nearest(h, i);\n        if (i === undefined) {\n            throw new WalkRowError('a route lands off its chunk');\n        }\n        visit.step(h);\n    }\n    follow(end, tail);\n    if (h !== end) {\n        throw new WalkRowError('a walk row misses its last handle');\n    }\n}\n// A walk row's steps as node ids and reverse flags\nfunction decodeWalk(path, routes, cols, choices, n) {\n    const ids = new Int32Array(n);\n    const rev = new Uint8Array(n);\n    let at = 0;\n    const push = (h) => {\n        if (at >= n) {\n            throw new WalkRowError('a walk row decodes to more steps than it states');\n        }\n        ids[at] = idOf(h);\n        rev[at++] = h & 1;\n    };\n    traverse(path, routes, +cols[9], cols[10], choices, {\n        step: push,\n        stretch(from, to, forward) {\n            if (forward) {\n                for (let j = from + 1; j <= to; j++) {\n                    push(path.handles[j]);\n                }\n            }\n            else {\n                for (let j = from - 1; j >= to; j--) {\n                    push(otherStrand(path.handles[j]));\n                }\n            }\n        },\n        route(index, flip) {\n            const route = routes[index];\n            for (let k = 0; k < route.interior.length; k++) {\n                push(interiorAt(route, flip, k));\n            }\n            return true;\n        },\n    });\n    if (at !== n) {\n        throw new WalkRowError(`a walk row decodes to ${at} steps, not ${n}`);\n    }\n    return { ids, rev };\n}\n// The bases an SQ:Z: tag at or after column `from` joins, one node's per\n// length, as `ids` names them\nfunction sliceBases(cols, from, ids, lengths, out) {\n    const tag = cols.slice(from).find(c => c.startsWith('SQ:Z:'));\n    if (tag === undefined) {\n        return;\n    }\n    let at = 5;\n    for (let k = 0; k < ids.length; k++) {\n        const length = lengths[k];\n        out.set(ids[k], tag.slice(at, at + length));\n        at += length;\n    }\n}\n/**\n * Decodes one chunk's rows, each split on tabs. `keep` names the walk rows\n * whose steps a cut wants, undefined for every one.\n */\nexport function decodeChunk(rows, keep, withSequences = false) {\n    var _a, _b, _c;\n    const path = new RefPath();\n    const lengths = new Map();\n    const routes = [];\n    const out = {\n        sequences: new Map(),\n        rows: [],\n        nodes: new Map(),\n        ends: [],\n        chunk: { path, routes, walks: [], lengths },\n    };\n    const previous = { id: 0 };\n    const refs = rows.filter(c => c[3] === 'ref').sort((a, b) => +a[6] - +b[6]);\n    for (const cols of refs) {\n        const anchor = cols[0];\n        const handles = tokens(cols[9], { id: 0 }, []);\n        const nodeLengths = numbers(cols[10]);\n        const hapOffset = +cols[6];\n        path.add(handles, nodeLengths);\n        if (withSequences) {\n            sliceBases(cols, 11, handles.map(idOf), nodeLengths, out.sequences);\n        }\n        let start = hapOffset;\n        for (let k = 0; k < handles.length; k++) {\n            const id = idOf(handles[k]);\n            const length = nodeLengths[k];\n            lengths.set(id, length);\n            if (!out.nodes.has(id)) {\n                out.nodes.set(id, {\n                    refName: cols[4],\n                    start,\n                    end: start + length,\n                    rank: 0,\n                });\n            }\n            start += length;\n        }\n        out.ends.push({\n            name: cols[4],\n            fragStart: +cols[5],\n            piece: +cols[7],\n            first: handles[0],\n            last: handles.at(-1),\n        });\n        if (keep === undefined || keep(cols[4])) {\n            out.rows.push({\n                chunkStart: +cols[1],\n                name: cols[4],\n                fragStart: +cols[5],\n                hapOffset,\n                piece: +cols[7],\n                n: handles.length,\n                steps: {\n                    ids: Int32Array.from(handles, idOf),\n                    rev: Uint8Array.from(handles, h => h & 1),\n                },\n                ...tags(cols, 11, anchor),\n            });\n        }\n    }\n    for (const cols of rows) {\n        if (cols[3] === 'nodes') {\n            const ids = numbers(cols[4]);\n            const nodeLengths = numbers(cols[5]);\n            let id = 0;\n            for (let k = 0; k < ids.length; k++) {\n                id += ids[k];\n                ids[k] = id;\n                lengths.set(id, nodeLengths[k]);\n            }\n            if (withSequences) {\n                sliceBases(cols, 6, ids, nodeLengths, out.sequences);\n            }\n        }\n        else if (cols[3] === 'route') {\n            const entry = tokens(cols[4], previous, []);\n            const interior = tokens(cols[5], previous, []);\n            const exit = tokens(cols[6], previous, []);\n            routes.push({ entry: (_a = entry[0]) !== null && _a !== void 0 ? _a : NONE, interior, exit: (_b = exit[0]) !== null && _b !== void 0 ? _b : NONE });\n        }\n    }\n    const routeOf = (index) => {\n        const route = routes[index];\n        if (!route) {\n            throw new WalkRowError(`route ${index} is not in the chunk`);\n        }\n        return route;\n    };\n    for (const cols of rows) {\n        if (cols[3] !== 'walk') {\n            continue;\n        }\n        const choices = parseChoices(cols[11]);\n        out.chunk.walks.push({ cols, choices });\n        const name = cols[4];\n        const start = +cols[9];\n        const endField = cols[10];\n        const colon = endField.indexOf(':');\n        let first = start;\n        let last = start + +(colon < 0 ? endField : endField.slice(0, colon));\n        if (choices.length > 0) {\n            const lead = routeOf(choices[0]);\n            const leadFlip = choices[1] === 1;\n            if (orientedEntry(lead, leadFlip) === NONE) {\n                first = interiorAt(lead, leadFlip, 0);\n            }\n            const at = choices.length - 3;\n            const tail = routeOf(choices[at]);\n            const tailFlip = choices[at + 1] === 1;\n            if (orientedExit(tail, tailFlip) === NONE) {\n                last = interiorAt(tail, tailFlip, tail.interior.length - 1);\n            }\n        }\n        out.ends.push({\n            name,\n            fragStart: +cols[5],\n            piece: +cols[7],\n            first,\n            last,\n        });\n        if (keep === undefined || keep(name)) {\n            const n = +cols[8];\n            // the walk's nodes off R, by length; placeAndLink gives their position\n            for (let k = 0; k < choices.length; k += 3) {\n                for (const h of routeOf(choices[k]).interior) {\n                    const id = idOf(h);\n                    if (!out.nodes.has(id)) {\n                        const length = (_c = lengths.get(id)) !== null && _c !== void 0 ? _c : 0;\n                        out.nodes.set(id, { refName: name, start: 0, end: length, rank: 1 });\n                    }\n                }\n            }\n            out.rows.push({\n                chunkStart: +cols[1],\n                name,\n                fragStart: +cols[5],\n                hapOffset: +cols[6],\n                piece: +cols[7],\n                n,\n                steps: decodeWalk(path, routes, cols, choices, n),\n                ...tags(cols, 12, cols[0]),\n            });\n        }\n    }\n    return out;\n}\n/**\n * The positions of the cut's nodes off R, and the links among the cut's\n * nodes, from the chunks a cut read: `kept` holds the node ids the cut draws.\n * A node off R takes its position from the path whose name sorts first among\n * those visiting it in the chunks read, at its earliest offset, as format 1's\n * node rows had it. Links are R's and the routes', both ends in the cut.\n */\nexport function placeAndLink(chunks, kept, place, link) {\n    const best = new Map();\n    for (const { path, routes, walks, lengths } of chunks) {\n        const handles = path.handles;\n        for (let k = 1; k < handles.length; k++) {\n            if (kept.has(idOf(handles[k - 1])) && kept.has(idOf(handles[k]))) {\n                link(...canonicalLink(handles[k - 1], handles[k]));\n            }\n        }\n        // routes holding a node of the cut off R\n        const wanted = new Uint8Array(routes.length);\n        for (let index = 0; index < routes.length; index++) {\n            const { entry, interior, exit } = routes[index];\n            let any = false;\n            let from = entry;\n            for (const h of interior) {\n                const inCut = kept.has(idOf(h));\n                any || (any = inCut);\n                if (inCut && from !== NONE && kept.has(idOf(from))) {\n                    link(...canonicalLink(from, h));\n                }\n                from = h;\n            }\n            if (from !== NONE &&\n                exit !== NONE &&\n                kept.has(idOf(from)) &&\n                kept.has(idOf(exit))) {\n                link(...canonicalLink(from, exit));\n            }\n            wanted[index] = any ? 1 : 0;\n        }\n        const lengthOf = (h) => { var _a; return (_a = lengths.get(idOf(h))) !== null && _a !== void 0 ? _a : 0; };\n        const bp = new Float64Array(routes.length).fill(-1);\n        const routeBp = (index) => {\n            if (bp[index] < 0) {\n                bp[index] = routes[index].interior.reduce((s, h) => s + lengthOf(h), 0);\n            }\n            return bp[index];\n        };\n        // Walk rows run in path-name order, so a route's first taker is the\n        // first-named path to reach its nodes here; each row is followed only as\n        // far as the last route it is first to take\n        const taken = new Uint8Array(routes.length);\n        for (const { cols, choices } of walks) {\n            let remaining = 0;\n            for (let k = 0; k < choices.length; k += 3) {\n                const index = choices[k];\n                if (wanted[index] && !taken[index]) {\n                    remaining++;\n                }\n            }\n            if (remaining === 0) {\n                continue;\n            }\n            const name = cols[4];\n            let offset = +cols[6];\n            traverse(path, routes, +cols[9], cols[10], choices, {\n                step(h) {\n                    offset += lengthOf(h);\n                },\n                stretch(from, to, forward) {\n                    offset += forward\n                        ? path.bp(to + 1) - path.bp(from + 1)\n                        : path.bp(from) - path.bp(to);\n                },\n                route(index, flip) {\n                    if (!wanted[index] || taken[index]) {\n                        offset += routeBp(index);\n                        return true;\n                    }\n                    taken[index] = 1;\n                    const route = routes[index];\n                    for (let k = 0; k < route.interior.length; k++) {\n                        const h = interiorAt(route, flip, k);\n                        const id = idOf(h);\n                        const length = lengthOf(h);\n                        if (kept.has(id)) {\n                            const held = best.get(id);\n                            if (!held ||\n                                name < held.refName ||\n                                (name === held.refName && offset < held.start)) {\n                                best.set(id, {\n                                    refName: name,\n                                    start: offset,\n                                    end: offset + length,\n                                    rank: 1,\n                                });\n                            }\n                        }\n                        offset += length;\n                    }\n                    remaining--;\n                    return remaining > 0;\n                },\n            });\n        }\n    }\n    for (const [id, node] of best) {\n        place(id, node);\n    }\n}\n// The reference's nodes in a chunk's ref rows, with their positions\nexport function referenceNodes(rows) {\n    const nodes = [];\n    for (const cols of rows) {\n        if (cols[3] !== 'ref') {\n            continue;\n        }\n        const handles = tokens(cols[9], { id: 0 }, []);\n        const nodeLengths = numbers(cols[10]);\n        let start = +cols[6];\n        for (let k = 0; k < handles.length; k++) {\n            const length = nodeLengths[k];\n            nodes.push({\n                id: idOf(handles[k]),\n                refName: cols[4],\n                start,\n                end: start + length,\n                rank: 0,\n            });\n            start += length;\n        }\n    }\n    return nodes;\n}\n// Links between consecutive pieces of a path, each piece's last step to the\n// next one's first, among the pieces read\nexport function pieceLinks(ends) {\n    const byPath = new Map();\n    for (const e of ends) {\n        const key = `${e.name}\\t${e.fragStart}`;\n        let pieces = byPath.get(key);\n        if (!pieces) {\n            pieces = new Map();\n            byPath.set(key, pieces);\n        }\n        pieces.set(e.piece, e);\n    }\n    const links = [];\n    for (const pieces of byPath.values()) {\n        for (const [piece, e] of pieces) {\n            const next = pieces.get(piece + 1);\n            if (next) {\n                links.push(canonicalLink(e.last, next.first));\n            }\n        }\n    }\n    return links;\n}\n", "/**\n * A window too large to cut. `regionTooLarge` and the name are what JBrowse\n * and @jbrowse/bandage-core read a zoom-in notice by; `fitsBp` is about how\n * wide a window would fit.\n */\nexport class RegionTooLargeError extends Error {\n    constructor(message, limit, windowBp, fitsBp) {\n        super(message);\n        this.regionTooLarge = true;\n        this.name = 'NodeLimitError';\n        this.limit = limit;\n        this.windowBp = windowBp;\n        this.fitsBp = fitsBp;\n    }\n}\nconst SEP = '#';\nexport function panSNHaplotype(refName) {\n    const parts = refName.split(SEP);\n    return parts.length >= 3 ? `${parts[0]}${SEP}${parts[1]}` : undefined;\n}\nexport function panSNMatchesPrefix(refName, prefix) {\n    return (prefix !== undefined &&\n        (refName === prefix || refName.startsWith(prefix + SEP)));\n}\nconst precise = (n) => Number.parseFloat(n.toPrecision(3));\n// `1.5Kbp`, `12Mbp`, `850bp`, as JBrowse writes a span\nexport function bpString(bp) {\n    const mb = precise(bp / 1000000);\n    return mb >= 1\n        ? `${mb.toLocaleString('en-US')}Mbp`\n        : bp >= 1000\n            ? `${precise(bp / 1000).toLocaleString('en-US')}Kbp`\n            : `${Math.floor(bp)}bp`;\n}\n", "import { RegionTooLargeError, bpString, panSNMatchesPrefix } from \"./util.js\";\nimport { placeAndLink } from \"./walkChunk.js\";\nfunction integerTag(line, tag) {\n    const match = new RegExp(`(?:^|\\\\t)${tag}:i:(\\\\d+)`).exec(line);\n    return match ? +match[1] : undefined;\n}\n/**\n * What a walk file's header states: a `#walks` line with the format, the\n * chunk size and the longest node in bp, `format:i:2\\tchunk:i:65536\\tmaxnode:i:1024`,\n * a `#reference\\tGRCh38` line naming the reference sample and a\n * `#haplotype\\tHG002#1` line per other haplotype with rows\n */\nexport function walkHeader(lines) {\n    var _a, _b, _c;\n    const header = { references: [], haplotypes: [] };\n    for (const line of lines) {\n        const [key, value = ''] = line.split('\\t');\n        if (key === '#reference') {\n            header.references.push(value);\n        }\n        else if (key === '#haplotype') {\n            header.haplotypes.push(value);\n        }\n        else {\n            (_a = header.format) !== null && _a !== void 0 ? _a : (header.format = integerTag(line, 'format'));\n            (_b = header.chunk) !== null && _b !== void 0 ? _b : (header.chunk = integerTag(line, 'chunk'));\n            (_c = header.maxNode) !== null && _c !== void 0 ? _c : (header.maxNode = integerTag(line, 'maxnode'));\n        }\n    }\n    return header;\n}\n/**\n * How many chunks before the window's own a cut reads. A node is filed under\n * the chunk holding its start, so a node `maxNode` bp long reaching into the\n * window starts at most ceil(maxNode / chunk) chunks back. At least one, since\n * the chunk before carries the detour a haplotype takes into the window's\n * first reference node; one when the header gives no `maxnode:i:`, which holds\n * for vg's graphs, chopped to nodes of at most 1,024 bp.\n */\nexport function lookbackChunks(maxNode, chunk) {\n    return maxNode === undefined ? 1 : Math.max(1, Math.ceil(maxNode / chunk));\n}\n// The first base a cut queries: the start of the chunk `lookback` chunks\n// before the one holding the window's start\nexport function chunkQueryStart(start, chunk, lookback = 1) {\n    return Math.max(0, (Math.floor(start / chunk) - lookback) * chunk);\n}\n// Which walks a cut decodes: the reference's, and those `wanted` names by\n// PanSN prefix at sample or haplotype depth; undefined decodes every one\nexport function walkNameFilter(wanted, referenceHaplotype) {\n    return wanted === undefined || wanted.length === 0\n        ? undefined\n        : (name) => panSNMatchesPrefix(name, referenceHaplotype) ||\n            wanted.some(prefix => panSNMatchesPrefix(name, prefix));\n}\nexport function joinPieces(rows) {\n    const byPath = new Map();\n    for (const row of rows) {\n        const key = `${row.name}\\t${row.fragStart}`;\n        const list = byPath.get(key);\n        if (list) {\n            list.push(row);\n        }\n        else {\n            byPath.set(key, [row]);\n        }\n    }\n    const runs = [];\n    for (const pieces of byPath.values()) {\n        pieces.sort((a, b) => a.piece - b.piece);\n        let from = 0;\n        for (let i = 1; i <= pieces.length; i++) {\n            if (i === pieces.length ||\n                pieces[i].piece !== pieces[i - 1].piece + 1) {\n                runs.push(decodeRun(pieces.slice(from, i)));\n                from = i;\n            }\n        }\n    }\n    return runs;\n}\nfunction decodeRun(pieces) {\n    const n = pieces.reduce((sum, p) => sum + p.n, 0);\n    const ids = new Int32Array(n);\n    const rev = new Uint8Array(n);\n    let at = 0;\n    for (const p of pieces) {\n        ids.set(p.steps.ids, at);\n        rev.set(p.steps.rev, at);\n        at += p.n;\n    }\n    const first = pieces[0];\n    return {\n        name: first.name,\n        hapOffset: first.hapOffset,\n        ids,\n        rev,\n        prev: first.prev,\n        next: pieces.at(-1).next,\n    };\n}\n/**\n * The cut a window draws from its walks: the reference inside the window plus\n * its context, and each run from its first to its last step on that stretch.\n * A run that leaves the reference there, through steps off it or across a\n * deletion, is followed to the reference step where it rejoins, when the read\n * holds it, and otherwise through the steps off the reference it holds: at\n * the ABCA7 VNTR four haplotypes leave inside the repeat and rejoin 1.8 kb\n * past the window, and cut at the context they measured as partial walks. The reference is cut out as far as those rejoins reach, and\n * a run then runs on outward while the next step's node is already in the\n * cut. Without the run-on a haplotype whose alternate allele straddles the\n * edge stopped short of a node other walks had brought into the cut, and that\n * node drew without it. The run-on adds no node, so one pass is enough, but\n * it reaches through nodes other walks brought in, so with a window edge inside\n * a collapsed array a row's length depends on which haplotypes are cut.\n */\nexport function walkCut(runs, nodes, refName) {\n    const onWindow = (id) => { var _a; return ((_a = nodes.get(id)) === null || _a === void 0 ? void 0 : _a.onWindow) === true; };\n    const reference = (id) => {\n        const node = nodes.get(id);\n        return (node === null || node === void 0 ? void 0 : node.rank) === 0 ? node : undefined;\n    };\n    // the chunks walks cut off at the end of a run go on in\n    const open = new Map();\n    const goesOn = (chunk) => {\n        if (chunk) {\n            open.set(`${chunk.refName}:${chunk.start}`, chunk);\n        }\n    };\n    // Where a walk stops being followed from step `at`, going by `dir`: the\n    // reference step it rejoins at past any steps off the reference, or across\n    // a deletion; else its last step off the reference before the run ends,\n    // noting the chunk the path goes on in, or reaches another reference\n    // sequence\n    const rejoin = (run, at, dir) => {\n        const { ids } = run;\n        let i = at + dir;\n        while (i >= 0 && i < ids.length && reference(ids[i]) === undefined) {\n            i += dir;\n        }\n        if (i < 0 || i >= ids.length) {\n            goesOn(dir < 0 ? run.prev : run.next);\n            return i - dir;\n        }\n        const from = reference(ids[at]);\n        const to = reference(ids[i]);\n        if (to.refName !== refName) {\n            return i - dir;\n        }\n        const adjacent = i === at + dir && (to.start === from.end || to.end === from.start);\n        return adjacent ? at : i;\n    };\n    let reachStart = Infinity;\n    let reachEnd = -Infinity;\n    const spans = [];\n    for (const run of runs) {\n        const { ids } = run;\n        let first = -1;\n        let last = -1;\n        for (let i = 0; i < ids.length; i++) {\n            if (onWindow(ids[i])) {\n                if (first < 0) {\n                    first = i;\n                }\n                last = i;\n            }\n        }\n        if (first >= 0) {\n            if (run.name !== refName) {\n                first = rejoin(run, first, -1);\n                last = rejoin(run, last, 1);\n                for (const i of [first, last]) {\n                    const node = reference(ids[i]);\n                    if (node) {\n                        reachStart = Math.min(reachStart, node.start);\n                        reachEnd = Math.max(reachEnd, node.end);\n                    }\n                }\n            }\n            spans.push({ run, first, last });\n        }\n    }\n    const inReach = (id) => {\n        const node = reference(id);\n        return (onWindow(id) ||\n            ((node === null || node === void 0 ? void 0 : node.refName) === refName &&\n                node.end > reachStart &&\n                node.start < reachEnd));\n    };\n    const kept = new Set();\n    for (const [id, node] of nodes) {\n        if (node.onWindow) {\n            kept.add(id);\n        }\n    }\n    for (const span of spans) {\n        const { ids } = span.run;\n        if (span.run.name === refName) {\n            while (span.first > 0 && inReach(ids[span.first - 1])) {\n                span.first--;\n            }\n            while (span.last < ids.length - 1 && inReach(ids[span.last + 1])) {\n                span.last++;\n            }\n        }\n        for (let i = span.first; i <= span.last; i++) {\n            kept.add(ids[i]);\n        }\n    }\n    const length = (id) => {\n        const node = nodes.get(id);\n        return node === undefined ? 0 : node.end - node.start;\n    };\n    const fragments = [];\n    for (const { run, first: f, last: l } of spans) {\n        const { ids, rev } = run;\n        let first = f;\n        let last = l;\n        while (first > 0 && kept.has(ids[first - 1])) {\n            first--;\n        }\n        while (last < ids.length - 1 && kept.has(ids[last + 1])) {\n            last++;\n        }\n        let hapStart = run.hapOffset;\n        for (let i = 0; i < first; i++) {\n            hapStart += length(ids[i]);\n        }\n        let hapEnd = hapStart;\n        for (let i = first; i <= last; i++) {\n            hapEnd += length(ids[i]);\n        }\n        fragments.push({\n            name: run.name,\n            hapStart,\n            hapEnd,\n            ids: ids.subarray(first, last + 1),\n            rev: rev.subarray(first, last + 1),\n        });\n    }\n    return { kept, fragments, open: [...open.values()] };\n}\n/**\n * The nodes and links of the chunks a cut reads, and the tables of the cut\n * they make with its walks. A node in two chunks is placed once.\n */\nexport class WalkGraph {\n    constructor(window) {\n        this.nodes = new Map();\n        this.sequences = new Map();\n        this.links = [];\n        // the chunks read, whose nodes off R and links tables() fills in\n        this.chunks = [];\n        this.window = window;\n    }\n    // A node with its position, unless the cut already holds it\n    placeNode(id, node) {\n        if (this.nodes.has(id)) {\n            return;\n        }\n        const { window } = this;\n        this.nodes.set(id, {\n            ...node,\n            onWindow: node.rank === 0 &&\n                node.refName === window.refName &&\n                node.end > window.start - window.context &&\n                node.start < window.end + window.context,\n        });\n    }\n    // A link between two endpoints, each id * 2 + 1 when reversed\n    addLinkEnds(source, target) {\n        this.links.push(source, target);\n    }\n    addChunk(chunk) {\n        this.chunks.push(chunk);\n    }\n    // Bases of nodes a chunk's rows give, for a window that asks for them\n    addSequences(sequences) {\n        if (this.window.sequences) {\n            for (const [id, bases] of sequences) {\n                this.sequences.set(id, bases);\n            }\n        }\n    }\n    /**\n     * The cut as typed arrays, which the worker transfers rather than copies:\n     * nodes by reference position, each link once in the order its L line\n     * sorts, then a walk per fragment, the reference's first and the rest by\n     * name. graphTablesGFA writes them as the GFA they stand for, the same bytes\n     * for the same rows.\n     */\n    tables(kept, fragments) {\n        if (this.chunks.length > 0) {\n            placeAndLink(this.chunks, kept, (id, node) => {\n                const held = this.nodes.get(id);\n                if (held) {\n                    this.nodes.set(id, { ...held, ...node });\n                }\n            }, (a, b) => {\n                this.links.push(a, b);\n            });\n        }\n        const held = [];\n        for (const id of kept) {\n            const node = this.nodes.get(id);\n            if (node) {\n                held.push({ ...node, id });\n            }\n        }\n        held.sort((x, y) => x.refName < y.refName\n            ? -1\n            : x.refName > y.refName\n                ? 1\n                : x.start - y.start || x.id - y.id);\n        const index = new Map();\n        const names = [];\n        const refNames = [];\n        const refIndex = new Map();\n        const lengths = new Int32Array(held.length);\n        const refs = new Int32Array(held.length);\n        const starts = new Float64Array(held.length);\n        const ranks = new Int32Array(held.length);\n        held.forEach(({ id, refName, start, end, rank }, i) => {\n            index.set(id, i);\n            names.push(String(id));\n            let ref = refIndex.get(refName);\n            if (ref === undefined) {\n                ref = refNames.length;\n                refIndex.set(refName, ref);\n                refNames.push(refName);\n            }\n            lengths[i] = end - start;\n            refs[i] = ref;\n            starts[i] = start;\n            ranks[i] = rank;\n        });\n        // a kept node with no row of its own is named, and not drawn\n        const nodeIndex = (id) => {\n            let i = index.get(id);\n            if (i === undefined) {\n                i = names.length;\n                index.set(id, i);\n                names.push(String(id));\n            }\n            return i;\n        };\n        const byLine = new Map();\n        for (let i = 0; i < this.links.length; i += 2) {\n            const a = this.links[i];\n            const b = this.links[i + 1];\n            const source = Math.floor(a / 2);\n            const target = Math.floor(b / 2);\n            if (kept.has(source) && kept.has(target)) {\n                byLine.set(`${source}\\t${a % 2 ? '-' : '+'}\\t${target}\\t${b % 2 ? '-' : '+'}`, i);\n            }\n        }\n        const lines = [...byLine.keys()].sort();\n        const from = new Int32Array(lines.length);\n        const to = new Int32Array(lines.length);\n        const strands = new Uint8Array(lines.length);\n        lines.forEach((line, k) => {\n            const i = byLine.get(line);\n            const a = this.links[i];\n            const b = this.links[i + 1];\n            from[k] = nodeIndex(Math.floor(a / 2));\n            to[k] = nodeIndex(Math.floor(b / 2));\n            strands[k] = (a % 2) | ((b % 2) << 1);\n        });\n        const walks = this.referenceFirst(fragments);\n        const offsets = new Int32Array(walks.length + 1);\n        walks.forEach(({ ids }, p) => {\n            offsets[p + 1] = offsets[p] + ids.length;\n        });\n        const steps = new Int32Array(offsets[walks.length]);\n        const reversed = new Uint8Array(steps.length);\n        walks.forEach(({ ids, rev }, p) => {\n            const at = offsets[p];\n            for (let j = 0; j < ids.length; j++) {\n                steps[at + j] = nodeIndex(ids[j]);\n            }\n            reversed.set(rev, at);\n        });\n        return {\n            nodes: { names, lengths, refs, starts, ranks, refNames },\n            links: { from, to, strands },\n            walks: {\n                names: walks.map(f => f.name),\n                starts: Float64Array.from(walks, f => f.hapStart),\n                ends: Float64Array.from(walks, f => f.hapEnd),\n                offsets,\n                steps,\n                reversed,\n            },\n        };\n    }\n    // The view anchors on the first walk when no walk names the assembly, as\n    // gbz-base's cut has it; in file order that was whichever haplotype the\n    // chunk listed first, CHM13 on a GRCh38 window\n    referenceFirst(fragments) {\n        const { refName } = this.window;\n        return [...fragments].sort((a, b) => Number(b.name === refName) - Number(a.name === refName) ||\n            (a.name < b.name ? -1 : a.name > b.name ? 1 : a.hapStart - b.hapStart));\n    }\n}\nexport const BUDGET_NAMES = {\n    steps: 'the step budget',\n    bytes: 'a byte budget of',\n};\nexport function stepBudgetError(rows, stepBudget, readPerKept, window, chunk, filtered, names = BUDGET_NAMES) {\n    var _a;\n    let total = 0;\n    const perChunk = new Map();\n    const walks = new Set();\n    for (const row of rows) {\n        total += row.n;\n        perChunk.set(row.chunkStart, ((_a = perChunk.get(row.chunkStart)) !== null && _a !== void 0 ? _a : 0) + row.n);\n        walks.add(row.name);\n    }\n    const budget = stepBudget * readPerKept;\n    if (total <= budget) {\n        return undefined;\n    }\n    const windowBp = window.end - window.start;\n    let read = 0;\n    let fitsBp = 0;\n    for (const cs of [...perChunk.keys()].sort((a, b) => a - b)) {\n        read += perChunk.get(cs);\n        if (read > budget) {\n            break;\n        }\n        fitsBp = Math.max(fitsBp, cs + chunk - window.start);\n    }\n    const fewerFit = !filtered && walks.size > 2 && (2 * total) / walks.size <= budget;\n    return new RegionTooLargeError(fitsBp > 0\n        ? `Zoom in to about ${bpString(fitsBp)}${fewerFit ? ', or choose fewer haplotypes,' : ''} to see the graph`\n        : `Too many haplotype steps here to draw ${filtered ? 'these haplotypes' : 'every haplotype'} (${read.toLocaleString()} steps read, over ${readPerKept} \u00D7 ${names.steps} of ${stepBudget.toLocaleString()}); choose fewer haplotypes`, budget, windowBp, Math.max(fitsBp, 1));\n}\n/**\n * The zoom-in notice for a cut that keeps more steps than `budget`, or\n * undefined when it fits. The span that fits is the window scaled by how far\n * over the cut is.\n */\nexport function keptStepsError(fragments, budget, window, filtered) {\n    const total = fragments.reduce((sum, f) => sum + f.ids.length, 0);\n    if (total <= budget) {\n        return undefined;\n    }\n    const windowBp = window.end - window.start;\n    const fitsBp = Math.max(1, Math.floor((windowBp * budget) / total));\n    return new RegionTooLargeError(`Zoom in to about ${bpString(fitsBp)}${filtered ? '' : ', or choose fewer haplotypes,'} to see the graph`, budget, windowBp, fitsBp);\n}\n/**\n * The zoom-in notice for a cut whose three files would fetch more than\n * `budget` compressed bytes, or undefined when they fit. `bytesTo(end)` is the\n * indexes' estimate for a read from the window's first query base to `end`;\n * the span that fits grows a chunk at a time from the chunk holding the\n * window's start, and when that chunk and those before it are over on their\n * own, no zoom fits.\n */\nexport async function byteBudgetError(bytesTo, budget, window, chunk, names = BUDGET_NAMES) {\n    const bytes = await bytesTo(window.end);\n    if (bytes <= budget) {\n        return undefined;\n    }\n    let fitsBp = 0;\n    let least;\n    for (let cs = Math.floor(window.start / chunk) * chunk; cs < window.end; cs += chunk) {\n        const read = await bytesTo(cs + 1);\n        least !== null && least !== void 0 ? least : (least = read);\n        if (read > budget) {\n            break;\n        }\n        fitsBp = cs + chunk - window.start;\n    }\n    const windowBp = window.end - window.start;\n    return new RegionTooLargeError(fitsBp > 0\n        ? `Zoom in to about ${bpString(fitsBp)} to see the graph`\n        : `Too much graph here to fetch (${megabytes(least !== null && least !== void 0 ? least : bytes)} against ${names.bytes} ${megabytes(budget)})`, budget, windowBp, Math.max(fitsBp, 1));\n}\nconst megabytes = (bytes) => `${(bytes / 1e6).toFixed(1)} MB`;\n", "import { decodeChunk, pieceLinks } from \"./walkChunk.js\";\nimport { WalkGraph, byteBudgetError, chunkQueryStart, joinPieces, keptStepsError, lookbackChunks, stepBudgetError, walkCut, walkHeader, } from \"./walkRows.js\";\n// A window reads whole chunks and keeps the steps on it, so a narrow window\n// reads several times what it keeps: 464 haplotypes across the 1.5 kb ABCA7\n// repeat read 5.0 M steps and keep 1.16 M, and the cut takes 0.4 s from warm\n// files. The step budget bounds what the cut keeps, and rows are read to this\n// multiple of it.\nconst READ_STEPS_PER_KEPT = 8;\n// A walk the read cuts off goes on in the chunk its row names, out to which a\n// cut reads on, in at most this many rounds and this many chunks from the read\nconst FOLLOW_ROUNDS = 3;\nconst FOLLOW_CHUNKS = 4;\n// bp of reference a cut keeps past each end of the window\nconst WALK_CONTEXT = 1000;\n// A walk file gfa-to-tabix 0.12 or earlier wrote, which the reader refuses\nexport class WalkFormatError extends Error {\n    constructor() {\n        super(...arguments);\n        this.name = 'WalkFormatError';\n    }\n}\n// @gmod/tabix loops forever on a NaN end and reads nothing for a NaN start\n// (GMOD/tabix-js#157), so every query refuses a range that is not finite first\nfunction checkRange(refName, start, end) {\n    if (!Number.isFinite(start) || !Number.isFinite(end)) {\n        throw new Error(`${refName}:${start}-${end} is not a finite range to query the graph's index for`);\n    }\n}\n// Settles like `promise` unless `signal` aborts first\nfunction raceAbort(promise, signal) {\n    if (!signal) {\n        return promise;\n    }\n    signal.throwIfAborted();\n    return new Promise((resolve, reject) => {\n        const onAbort = () => {\n            reject(signal.reason instanceof Error\n                ? signal.reason\n                : new Error(String(signal.reason)));\n        };\n        signal.addEventListener('abort', onAbort, { once: true });\n        promise.then(resolve, reject).finally(() => {\n            signal.removeEventListener('abort', onAbort);\n        });\n    });\n}\n/**\n * A `gfa-to-tabix --walks` file, `<prefix>.<sample>.walks.bed.gz`, read a\n * window at a time: one read over whole chunks, from the lookback chunks\n * before the window to its end, each chunk decoded once. The index first\n * estimates the bytes the read fetches, and a window past the byte budget\n * reads no row. Only the walks `keep` accepts are decoded. The step budget\n * bounds the steps the cut keeps, and rows holding READ_STEPS_PER_KEPT times\n * as many stop the read.\n */\nexport class WalkReader {\n    constructor(walks) {\n        this.walks = walks;\n    }\n    // The header, read once for every caller: one caller giving up stops only\n    // its own wait, and a read that fails is tried again by the next caller\n    header(opts = {}) {\n        if (!this.headerRead) {\n            const read = this.walks.getHeaderLines().then(lines => {\n                var _a;\n                const header = walkHeader(lines);\n                if (header.format !== 2) {\n                    throw new WalkFormatError('This walk file is format 1, from gfa-to-tabix 0.12 or earlier; rebuild it with gfa-to-tabix 1.0 or later');\n                }\n                const chunk = (_a = header.chunk) !== null && _a !== void 0 ? _a : 65536;\n                return {\n                    ...header,\n                    chunk,\n                    lookback: lookbackChunks(header.maxNode, chunk),\n                };\n            });\n            read.catch(() => {\n                if (this.headerRead === read) {\n                    this.headerRead = undefined;\n                }\n            });\n            this.headerRead = read;\n        }\n        return raceAbort(this.headerRead, opts.signal);\n    }\n    // The reference sequences the walk file holds windows on\n    referenceSequences(opts = {}) {\n        return this.walks.getReferenceSequenceNames(opts);\n    }\n    async queryStart(start, opts = {}) {\n        const { chunk, lookback } = await this.header(opts);\n        return chunkQueryStart(start, chunk, lookback);\n    }\n    async cut(refName, region, opts = {}) {\n        var _a;\n        const { signal, keep, context = WALK_CONTEXT, stepBudget = Infinity, byteBudget = Infinity, links = true, } = opts;\n        const { chunk, lookback } = await this.header({ signal });\n        const from = chunkQueryStart(region.start, chunk, lookback);\n        const bytesForRegions = (_a = this.walks.bytesForRegions) === null || _a === void 0 ? void 0 : _a.bind(this.walks);\n        const budgeted = Number.isFinite(byteBudget) && bytesForRegions !== undefined;\n        const bytesFor = async (spans) => budgeted\n            ? bytesForRegions(spans.map(span => ({ refName, ...span })), { signal })\n            : 0;\n        const tooLarge = budgeted\n            ? await byteBudgetError(async (end) => {\n                checkRange(refName, from, end);\n                return bytesFor([{ start: from, end }]);\n            }, byteBudget, region, chunk, opts.budgetNames)\n            : undefined;\n        if (tooLarge) {\n            throw tooLarge;\n        }\n        const reads = new AbortController();\n        const stop = () => {\n            reads.abort(signal === null || signal === void 0 ? void 0 : signal.reason);\n        };\n        signal === null || signal === void 0 ? void 0 : signal.throwIfAborted();\n        signal === null || signal === void 0 ? void 0 : signal.addEventListener('abort', stop, { once: true });\n        const rows = [];\n        let cut;\n        const graph = new WalkGraph({\n            refName,\n            start: region.start,\n            end: region.end,\n            context,\n            sequences: opts.sequences,\n        });\n        const decoded = new Set();\n        const ends = [];\n        // each chunk read is decoded once, into its rows, nodes and the links\n        // between pieces\n        const readChunks = async (start, end) => {\n            checkRange(refName, start, end);\n            const byChunk = new Map();\n            await this.walks.getLines(refName, start, end, {\n                signal: reads.signal,\n                lineCallback: line => {\n                    const cols = line.split('\\t');\n                    const cs = +cols[1];\n                    const held = byChunk.get(cs);\n                    if (held) {\n                        held.push(cols);\n                    }\n                    else {\n                        byChunk.set(cs, [cols]);\n                    }\n                },\n            });\n            for (const [cs, chunkRows] of byChunk) {\n                if (decoded.has(cs)) {\n                    continue;\n                }\n                decoded.add(cs);\n                const chunkCut = decodeChunk(chunkRows, keep, opts.sequences);\n                rows.push(...chunkCut.rows);\n                for (const [id, node] of chunkCut.nodes) {\n                    graph.placeNode(id, node);\n                }\n                graph.addSequences(chunkCut.sequences);\n                graph.addChunk(chunkCut.chunk);\n                ends.push(...chunkCut.ends);\n            }\n            if (links) {\n                for (const [a, b] of pieceLinks(ends)) {\n                    graph.addLinkEnds(a, b);\n                }\n            }\n        };\n        try {\n            await readChunks(from, region.end);\n            const tooManyRead = stepBudgetError(rows, stepBudget, READ_STEPS_PER_KEPT, region, chunk, keep !== undefined, opts.budgetNames);\n            if (tooManyRead) {\n                throw tooManyRead;\n            }\n            // the chunks read, first to last, which a follow widens to the\n            // farthest chunk a cut-off walk goes on in, so the reference between\n            // is read too\n            let first = from;\n            let last = Math.floor((region.end - 1) / chunk) * chunk;\n            const reach = FOLLOW_CHUNKS * chunk;\n            const [lo, hi] = [first - reach, last + reach];\n            cut = walkCut(joinPieces(rows), graph.nodes, refName);\n            let spent = await bytesFor([{ start: from, end: region.end }]);\n            for (let round = 0; round < FOLLOW_ROUNDS; round++) {\n                const starts = cut.open\n                    .filter(c => c.refName === refName && c.start >= lo && c.start <= hi)\n                    .map(c => c.start);\n                const spans = [\n                    { start: Math.min(first, ...starts), end: first },\n                    { start: last + chunk, end: Math.max(last, ...starts) + 1 },\n                ].filter(span => span.end > span.start);\n                if (spans.length === 0) {\n                    break;\n                }\n                spent += await bytesFor(spans);\n                if (spent > byteBudget) {\n                    break;\n                }\n                first = Math.min(first, ...starts);\n                last = Math.max(last, ...starts);\n                await Promise.all(spans.map(({ start, end }) => readChunks(start, end)));\n                cut = walkCut(joinPieces(rows), graph.nodes, refName);\n            }\n        }\n        catch (error) {\n            reads.abort();\n            throw error;\n        }\n        finally {\n            signal === null || signal === void 0 ? void 0 : signal.removeEventListener('abort', stop);\n        }\n        const tooMany = keptStepsError(cut.fragments, stepBudget, region, keep !== undefined);\n        if (tooMany) {\n            throw tooMany;\n        }\n        return { graph, ...cut };\n    }\n}\n", "import { panSNHaplotype } from '@jbrowse/bandage-core/pansn'\nimport { walkNameFilter } from '@jbrowse/graph-walks'\n\nimport { walkCutFor } from './walkRowRuns.ts'\n\nimport type { WalkReader } from '@jbrowse/graph-walks'\n\n// The zoom-in notices name the config slots that set the budgets\nexport const BUDGET_SLOTS = {\n  steps: 'walkStepBudget',\n  bytes: 'walkByteBudget',\n}\n\n/**\n * The graph display's cut of a walk-indexed window: the reference walk, the\n * walks of `prefixes` (every walk when undefined), and the nodes and links\n * they visit. Walk rows draw runs, so the step budget spares them.\n * @jbrowse/graph-walks reads and cuts the window.\n */\nexport async function walkSubgraph(\n  reader: WalkReader,\n  refName: string,\n  region: { start: number; end: number },\n  opts: {\n    signal?: AbortSignal\n    prefixes?: string[]\n    walkRows?: boolean\n    stepBudget: number\n    byteBudget: number\n  },\n) {\n  const { graph, kept, fragments } = await reader.cut(refName, region, {\n    signal: opts.signal,\n    keep: walkNameFilter(opts.prefixes, panSNHaplotype(refName)),\n    stepBudget: opts.walkRows ? Infinity : opts.stepBudget,\n    byteBudget: opts.byteBudget,\n    budgetNames: BUDGET_SLOTS,\n  })\n  return walkCutFor(graph.tables(kept, fragments), region, opts.walkRows)\n}\n"],
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-}

package/dist/chunks/renderSvg-ST2GBBOC.js

@@ -1,2 +0,0 @@
-import{a as W,b as y,c as D,e as H,f as O,g as B,i as j,k as z,l as A,n as F,p as J}from"./chunk-GOFS7BXK.js";import{K as L,L as M,V as G,X as R,da as $,ma as E}from"./chunk-5SFGHDQA.js";import"./chunk-DZ4OUKQV.js";import"./chunk-MHPJB22Z.js";import"./chunk-XT766CZ5.js";import"./chunk-3Q4RBDCL.js";import"./chunk-AU73K7LX.js";import"./chunk-446RWIA3.js";import"./chunk-NDRLCGPC.js";import"./chunk-6OPB7FOJ.js";import{a as m,b as t,c as g}from"./chunk-JMBDTNUR.js";var b=JBrowseExports["@jbrowse/display-kit/renderDisplaySvg"],Q=e=>b!=null&&e in Object(b)?b[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/display-kit/renderDisplaySvg' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e});var N=Q("renderDisplaySvg");var se=b&&b.__esModule?b.default:b;var x=JBrowseExports["@jbrowse/core/util/paintLayer"],ee=e=>x!=null&&e in Object(x)?x[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/core/util/paintLayer' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),T=ee("PaintLayer"),pe=x&&x.__esModule?x.default:x;var P={fontFamily:"sans-serif",fontSize:11},C=6.2,S=16,k=2,K=e=>e;function q({model:e,lift:o,drawPaths:a,width:r,height:n,rasterize:s}){let i=e.buildDrawing(o,a);if(!i)return null;let c={scaleX:e.scaleX,scaleY:e.scaleY,translateX:e.translateX,translateY:e.translateY};if(s){let l=document.createElement("canvas");l.width=Math.round(r*k),l.height=Math.round(n*k);let d=new R(l);return d.uploadGeometry(i.batch),d.updateTransform({scaleX:c.scaleX*k,scaleY:c.scaleY*k,translateX:c.translateX*k,translateY:c.translateY*k,dpr:k}),d.render([0,0,0,0]),t("image",{width:r,height:n,href:l.toDataURL("image/png")})}let{canvas:p,markup:f}=G(r,n),u=p.getContext("2d");u.clearRect??=()=>{};let h=new R(p);return h.uploadGeometry(i.batch),h.updateTransform({...c,dpr:1}),h.render([0,0,0,0]),t("svg",{width:r,height:n,overflow:"hidden",children:t("g",{dangerouslySetInnerHTML:{__html:f()}})})}function V({id:e,x:o,y:a,stops:r,width:n,height:s,square:i}){let c=p=>t("rect",{x:o,y:a,width:n,height:s,rx:i?0:2,fill:p});return r.length>1?g(m,{children:[t("defs",{children:t("linearGradient",{id:e,children:r.map((p,f)=>t("stop",{offset:p.offset,stopColor:p.color},f))})}),c(`url(#${e})`)]}):c(r[0].color)}function te({swatch:e,x:o,id:a}){switch(e.kind){case"fill":{let n=e.height??8;return t(V,{id:a,x:o,y:-5-n/2,stops:e.stops,width:D(e),height:n,square:e.square})}case"bands":{let n=e.bands.length>1?3:4,s=-5-n*e.bands.length/2;return t(m,{children:e.bands.map((i,c)=>t(V,{id:`${a}-${c}`,x:o,y:s+c*n,stops:i,width:y,height:n,square:!0},c))})}case"line":return t("rect",{x:o,y:-5-1.5,width:y,height:3,rx:2,fill:e.color});case"halo":return t("line",{x1:o+5,x2:o+13,y1:-5,y2:-5,stroke:e.color,strokeOpacity:.35,strokeWidth:8,strokeLinecap:"round"});case"outline":{let n=e.stroke/2;return t("rect",{x:o+n,y:-5-e.height/2+n,width:y-e.stroke,height:e.height-e.stroke,rx:Math.max(0,e.radius-n),fill:"none",stroke:e.color,strokeWidth:e.stroke})}case"overhang":return t("path",{transform:`translate(${o} -10)`,d:"M0,5 L8,0 L8,10 Z M18,5 L10,0 L10,10 Z",fill:"#18181c"});case"glyph":return t("text",{x:o+y/2,y:0,textAnchor:"middle",fontFamily:"monospace",fontSize:12,children:e.char});case"tick":{let n=-5-e.height/2;return g(m,{children:[e.backing?t("rect",{x:o,y:n,width:y,height:e.height,fill:e.backing}):null,t("rect",{x:o+y/2-1,y:n,width:2,height:e.height,fill:e.color})]})}case"bracket":return t("path",{transform:`translate(${o} -9)`,d:`M0.5,6 V1.5 H5.5 V6 M8.5,6 V1.5 H${y-.5} V6`,fill:"none",stroke:E()});case"blank":return null}}function X(e,o){if(!e.swatch)return{key:e.key,width:e.label.length*C,height:S,draw:s=>t("text",{...P,x:s,y:0,fill:"#666",children:e.label},e.key)};let a=e.swatch,r=D(a),n=(e.strong??"")+e.label;return{key:e.key,width:Math.max(r+5+n.length*C,(e.under?.length??0)*C),height:e.under?S*2:S,draw:s=>g("g",{...P,children:[t(te,{swatch:a,x:s,id:o}),g("text",{x:s+r+5,y:0,children:[e.strong?t("tspan",{fontWeight:"bold",children:e.strong}):null,e.label]}),e.under?t("text",{x:s,y:S,children:e.under}):null]},e.key)}}function re({model:e,idPrefix:o}){let a=B(e).map(({testid:l,rows:d})=>d.map((w,v)=>X(w,`${o}-${l}-${v}`)));if(a.length===0)return null;let r=6,n=a.flat(),s=Math.max(...n.map(l=>l.width))+r*2,i=n.reduce((l,d)=>l+d.height,0)+a.length*r,p=e.paneWidth-$-s+r,f=$+e.referenceStripZonePx,u=[],h=f+12-r/2;for(let l of a){h+=r;for(let d of l)u.push({row:d,y:h}),h+=d.height}return g("g",{"data-testid":"graph-svg-keys",children:[t("rect",{x:p-r,y:f,width:s,height:i,rx:3,fill:"#fff",fillOpacity:.82}),u.map(({row:l,y:d})=>t("g",{transform:`translate(0 ${d})`,children:l.draw(p)},l.key))]})}function I({x:e,y:o,text:a,fontSize:r,anchor:n,bold:s}){let i=a.length*r*.56+6,c=n==="middle"?e-i/2:e-3;return g(m,{children:[t("rect",{x:c,y:o-r*.65,width:i,height:r*1.3,rx:3,fill:"#fff",fillOpacity:.8}),t("text",{x:e,y:o+r*.35,textAnchor:n,fontSize:r,fontWeight:s?600:void 0,fill:"#18181c",children:a})]})}function ne({model:e}){return t("g",{fontFamily:P.fontFamily,children:e.overlayLabels.sizes.map(({key:o,text:a,x:r,y:n,kind:s,leader:i})=>g("g",{children:[i?t("line",{x1:i.arcX,y1:i.arcY,x2:i.labelX,y2:i.labelY,stroke:"#18181c"}):null,t(I,{x:r,y:n,text:a,fontSize:10,anchor:"middle",bold:s==="deletion"})]},o))})}function oe({model:e}){return t("g",{fontFamily:P.fontFamily,children:e.drawnRowLabels.map(({label:o,y:a})=>{let r=a*e.scaleY+e.translateY;return r>=0&&r<=e.canvasHeight?t(I,{x:10,y:r,text:o,fontSize:11,anchor:"start"},a):null})})}function ae({model:e,rasterize:o,idPrefix:a}){let r=e.facetPanels,n=e.facetGrid,s=e.facetPlacement;if(!r||!n||!s)return null;let{columns:i,width:c,height:p}=n,f=n.total+L+14,u=O(e).map((l,d)=>X(l,`${a}-facet-key-${d}`)),h=u.map((l,d)=>u.slice(0,d).reduce((w,v)=>w+v.width+14,6));return g(m,{children:[t("g",{transform:`translate(0 ${f})`,children:u.map((l,d)=>l.draw(h[d]))}),r.map((l,d)=>{let w=s.cells[d],v=w%i*(c+L),Z=Math.floor(w/i)*(M+p+L),Y=l.walks[0],U=X(H(e,Y),`${a}-facet-${d}`);return g("g",{transform:`translate(${v} ${Z})`,children:[t("g",{transform:`translate(0 ${S-2})`,children:U.draw(6)}),t("g",{transform:`translate(0 ${M})`,children:t(q,{model:e,lift:l,drawPaths:!1,width:c,height:p,rasterize:o})})]},Y.name)})]})}function _({model:e,rasterize:o=!1,idPrefix:a}){let r=e.paneWidth,n=e.canvasHeight,s=!!e.layoutResult?.tubeMap,i={rasterizeLayers:o};return g("g",{"data-testid":"graph-pane-svg",children:[e.facetPanels?t(ae,{model:e,rasterize:o,idPrefix:a}):s?t(T,{width:r,height:n,opts:i,paint:c=>{F(K(c),e,{highlightNode:null})}}):t(q,{model:e,lift:e.walkLift,drawPaths:e.effectiveDrawPaths,width:r,height:n,rasterize:o}),e.facetPanels?null:g(m,{children:[t(W,{model:e}),t(j,{model:e}),t(ne,{model:e}),t(z,{model:e}),t(J,{model:e,vector:!0}),t(oe,{model:e})]}),e.referenceStripShown?t(T,{width:r,height:n,opts:i,paint:c=>{A(K(c),e,{lit:void 0,dpr:1})}}):null,e.facetPanels?null:t(re,{model:e,idPrefix:a})]})}function ie({model:e,opts:o}){return t(_,{model:e,rasterize:!!o?.rasterizeLayers,idPrefix:`graph-${e.id}`})}function De(e,o){return N(e,o,ie)}export{De as renderGraphTrackSvg};
-//# sourceMappingURL=renderSvg-ST2GBBOC.js.map

package/dist/chunks/renderSvg-ST2GBBOC.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["host:@jbrowse/display-kit/renderDisplaySvg", "host:@jbrowse/core/util/paintLayer", "../../src/GraphGenomeView/components/PaneSvg.tsx", "../../src/LinearGraphDisplay/renderSvg.tsx"],
-  "sourcesContent": ["const host = JBrowseExports[\"@jbrowse/display-kit/renderDisplaySvg\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/display-kit/renderDisplaySvg\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const SvgLegend = /* @__PURE__ */ read(\"SvgLegend\")\nexport const SvgPinnedHighlight = /* @__PURE__ */ read(\"SvgPinnedHighlight\")\nexport const SvgYAxis = /* @__PURE__ */ read(\"SvgYAxis\")\nexport const exportsTooLargeNote = /* @__PURE__ */ read(\"exportsTooLargeNote\")\nexport const renderDisplaySvg = /* @__PURE__ */ read(\"renderDisplaySvg\")\nexport const svgSidebarWidthOf = /* @__PURE__ */ read(\"svgSidebarWidthOf\")\nexport default host && host.__esModule ? host.default : host", "const host = JBrowseExports[\"@jbrowse/core/util/paintLayer\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/core/util/paintLayer\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const PaintLayer = /* @__PURE__ */ read(\"PaintLayer\")\nexport default host && host.__esModule ? host.default : host", "import { FACET_GAP_PX, FACET_TITLE_PX } from '@jbrowse/bandage-core/facetGrid'\nimport { LEGEND_INSET_PX } from '@jbrowse/bandage-core/labelLayout'\nimport { Canvas2DRenderer } from '@jbrowse/bandage-core/renderer/Canvas2DRenderer'\nimport { svgCanvas } from '@jbrowse/bandage-core/renderer/svgCanvas'\nimport { rulerInk } from '@jbrowse/bandage-core/tubeMap/axis'\nimport { PaintLayer } from '@jbrowse/core/util/paintLayer'\n\nimport BubbleHalos from './BubbleHalos'\nimport GenePins from './GenePins'\nimport LabelLayer from './LabelLayer'\nimport { paintReferenceStrip } from './ReferenceStripOverlay'\nimport { paintTubeMap } from './TubeMapOverlay'\nimport WalkRowsOverlay from './WalkRowsOverlay'\nimport {\n  SWATCH_PX,\n  facetKeyRows,\n  legendSections,\n  swatchWidth,\n  walkKeyRow,\n} from '../legendSections'\n\nimport type { LegendRow, LegendSwatch, Stop } from '../legendSections'\nimport type { GraphPaneModel } from '../model'\nimport type { WalkLift } from '@jbrowse/bandage-core/walkHighlight'\nimport type { Ctx2D } from '@jbrowse/core/util/paintLayer'\n\nconst FONT = { fontFamily: 'sans-serif', fontSize: 11 }\nconst CHAR_PX = 6.2\nconst ROW_PX = 16\nconst RASTER_SCALE = 2\n\nconst asCanvasCtx = (ctx: Ctx2D) => ctx as CanvasRenderingContext2D\n\n// The drawing's nodes and edges through the pane's own transform, so the\n// export lines up with the linear view's ruler wherever the screen does\nfunction Body({\n  model,\n  lift,\n  drawPaths,\n  width,\n  height,\n  rasterize,\n}: {\n  model: GraphPaneModel\n  lift: WalkLift | undefined\n  drawPaths: boolean\n  width: number\n  height: number\n  rasterize: boolean\n}) {\n  const built = model.buildDrawing(lift, drawPaths)\n  if (!built) {\n    return null\n  }\n  const transform = {\n    scaleX: model.scaleX,\n    scaleY: model.scaleY,\n    translateX: model.translateX,\n    translateY: model.translateY,\n  }\n  if (rasterize) {\n    const canvas = document.createElement('canvas')\n    canvas.width = Math.round(width * RASTER_SCALE)\n    canvas.height = Math.round(height * RASTER_SCALE)\n    const renderer = new Canvas2DRenderer(canvas)\n    renderer.uploadGeometry(built.batch)\n    renderer.updateTransform({\n      scaleX: transform.scaleX * RASTER_SCALE,\n      scaleY: transform.scaleY * RASTER_SCALE,\n      translateX: transform.translateX * RASTER_SCALE,\n      translateY: transform.translateY * RASTER_SCALE,\n      dpr: RASTER_SCALE,\n    })\n    renderer.render([0, 0, 0, 0])\n    return (\n      <image\n        width={width}\n        height={height}\n        href={canvas.toDataURL('image/png')}\n      />\n    )\n  }\n  const { canvas, markup } = svgCanvas(width, height)\n  const ctx = canvas.getContext('2d') as unknown as { clearRect?: () => void }\n  ctx.clearRect ??= () => {}\n  const renderer = new Canvas2DRenderer(canvas)\n  renderer.uploadGeometry(built.batch)\n  renderer.updateTransform({ ...transform, dpr: 1 })\n  renderer.render([0, 0, 0, 0])\n  return (\n    <svg width={width} height={height} overflow=\"hidden\">\n      <g dangerouslySetInnerHTML={{ __html: markup() }} />\n    </svg>\n  )\n}\n\nfunction Gradient({\n  id,\n  x,\n  y,\n  stops,\n  width,\n  height,\n  square,\n}: {\n  id: string\n  x: number\n  y: number\n  stops: readonly Stop[]\n  width: number\n  height: number\n  square?: boolean\n}) {\n  const rect = (fill: string) => (\n    <rect\n      x={x}\n      y={y}\n      width={width}\n      height={height}\n      rx={square ? 0 : 2}\n      fill={fill}\n    />\n  )\n  return stops.length > 1 ? (\n    <>\n      <defs>\n        <linearGradient id={id}>\n          {stops.map((s, i) => (\n            <stop key={i} offset={s.offset} stopColor={s.color} />\n          ))}\n        </linearGradient>\n      </defs>\n      {rect(`url(#${id})`)}\n    </>\n  ) : (\n    rect(stops[0]!.color)\n  )\n}\n\n// A row's swatch with its left edge at x, centred on the row's text 5 px\n// above the baseline, as the screen centres it\nfunction SvgSwatch({\n  swatch,\n  x,\n  id,\n}: {\n  swatch: LegendSwatch\n  x: number\n  id: string\n}) {\n  const mid = -5\n  switch (swatch.kind) {\n    case 'fill': {\n      const height = swatch.height ?? 8\n      return (\n        <Gradient\n          id={id}\n          x={x}\n          y={mid - height / 2}\n          stops={swatch.stops}\n          width={swatchWidth(swatch)}\n          height={height}\n          square={swatch.square}\n        />\n      )\n    }\n    case 'bands': {\n      const band = swatch.bands.length > 1 ? 3 : 4\n      const top = mid - (band * swatch.bands.length) / 2\n      return (\n        <>\n          {swatch.bands.map((stops, i) => (\n            <Gradient\n              key={i}\n              id={`${id}-${i}`}\n              x={x}\n              y={top + i * band}\n              stops={stops}\n              width={SWATCH_PX}\n              height={band}\n              square\n            />\n          ))}\n        </>\n      )\n    }\n    case 'line':\n      return (\n        <rect\n          x={x}\n          y={mid - 1.5}\n          width={SWATCH_PX}\n          height={3}\n          rx={2}\n          fill={swatch.color}\n        />\n      )\n    case 'halo':\n      return (\n        <line\n          x1={x + 5}\n          x2={x + 13}\n          y1={mid}\n          y2={mid}\n          stroke={swatch.color}\n          strokeOpacity={0.35}\n          strokeWidth={8}\n          strokeLinecap=\"round\"\n        />\n      )\n    case 'outline': {\n      const inset = swatch.stroke / 2\n      return (\n        <rect\n          x={x + inset}\n          y={mid - swatch.height / 2 + inset}\n          width={SWATCH_PX - swatch.stroke}\n          height={swatch.height - swatch.stroke}\n          rx={Math.max(0, swatch.radius - inset)}\n          fill=\"none\"\n          stroke={swatch.color}\n          strokeWidth={swatch.stroke}\n        />\n      )\n    }\n    case 'overhang':\n      return (\n        <path\n          transform={`translate(${x} ${mid - 5})`}\n          d=\"M0,5 L8,0 L8,10 Z M18,5 L10,0 L10,10 Z\"\n          fill=\"#18181c\"\n        />\n      )\n    case 'glyph':\n      return (\n        <text\n          x={x + SWATCH_PX / 2}\n          y={0}\n          textAnchor=\"middle\"\n          fontFamily=\"monospace\"\n          fontSize={12}\n        >\n          {swatch.char}\n        </text>\n      )\n    case 'tick': {\n      const y = mid - swatch.height / 2\n      return (\n        <>\n          {swatch.backing ? (\n            <rect\n              x={x}\n              y={y}\n              width={SWATCH_PX}\n              height={swatch.height}\n              fill={swatch.backing}\n            />\n          ) : null}\n          <rect\n            x={x + SWATCH_PX / 2 - 1}\n            y={y}\n            width={2}\n            height={swatch.height}\n            fill={swatch.color}\n          />\n        </>\n      )\n    }\n    case 'bracket':\n      return (\n        <path\n          transform={`translate(${x} ${mid - 4})`}\n          d={`M0.5,6 V1.5 H5.5 V6 M8.5,6 V1.5 H${SWATCH_PX - 0.5} V6`}\n          fill=\"none\"\n          stroke={rulerInk()}\n        />\n      )\n    case 'blank':\n      return null\n  }\n}\n\ninterface KeyRow {\n  key: string\n  width: number\n  height: number\n  draw: (left: number) => React.ReactNode\n}\n\n// A legend row as the screen lays it out: its swatch, then its words, the\n// line under it if any; a note is grey words alone\nfunction svgRow(row: LegendRow, id: string): KeyRow {\n  if (!row.swatch) {\n    return {\n      key: row.key,\n      width: row.label.length * CHAR_PX,\n      height: ROW_PX,\n      draw: left => (\n        <text key={row.key} {...FONT} x={left} y={0} fill=\"#666\">\n          {row.label}\n        </text>\n      ),\n    }\n  }\n  const swatch = row.swatch\n  const sw = swatchWidth(swatch)\n  const words = (row.strong ?? '') + row.label\n  return {\n    key: row.key,\n    width: Math.max(\n      sw + 5 + words.length * CHAR_PX,\n      (row.under?.length ?? 0) * CHAR_PX,\n    ),\n    height: row.under ? ROW_PX * 2 : ROW_PX,\n    draw: left => (\n      <g key={row.key} {...FONT}>\n        <SvgSwatch swatch={swatch} x={left} id={id} />\n        <text x={left + sw + 5} y={0}>\n          {row.strong ? <tspan fontWeight=\"bold\">{row.strong}</tspan> : null}\n          {row.label}\n        </text>\n        {row.under ? (\n          <text x={left} y={ROW_PX}>\n            {row.under}\n          </text>\n        ) : null}\n      </g>\n    ),\n  }\n}\n\n// The screen's legend panel, section by section\nfunction Keys({\n  model,\n  idPrefix,\n}: {\n  model: GraphPaneModel\n  idPrefix: string\n}) {\n  const sections = legendSections(model).map(({ testid, rows }) =>\n    rows.map((row, i) => svgRow(row, `${idPrefix}-${testid}-${i}`)),\n  )\n  if (sections.length === 0) {\n    return null\n  }\n  const pad = 6\n  const rows = sections.flat()\n  const boxWidth = Math.max(...rows.map(r => r.width)) + pad * 2\n  const boxHeight =\n    rows.reduce((sum, r) => sum + r.height, 0) + sections.length * pad\n  const right = model.paneWidth - LEGEND_INSET_PX\n  const left = right - boxWidth + pad\n  const top = LEGEND_INSET_PX + model.referenceStripZonePx\n  const placed: { row: KeyRow; y: number }[] = []\n  let y = top + 12 - pad / 2\n  for (const section of sections) {\n    y += pad\n    for (const row of section) {\n      placed.push({ row, y })\n      y += row.height\n    }\n  }\n  return (\n    <g data-testid=\"graph-svg-keys\">\n      <rect\n        x={left - pad}\n        y={top}\n        width={boxWidth}\n        height={boxHeight}\n        rx={3}\n        fill=\"#fff\"\n        fillOpacity={0.82}\n      />\n      {placed.map(({ row, y }) => (\n        <g key={row.key} transform={`translate(0 ${y})`}>\n          {row.draw(left)}\n        </g>\n      ))}\n    </g>\n  )\n}\n\n// Words on a pale rounded backing, as the screen's labels sit\nfunction Chip({\n  x,\n  y,\n  text,\n  fontSize,\n  anchor,\n  bold,\n}: {\n  x: number\n  y: number\n  text: string\n  fontSize: number\n  anchor: 'start' | 'middle'\n  bold?: boolean\n}) {\n  const w = text.length * fontSize * 0.56 + 6\n  const left = anchor === 'middle' ? x - w / 2 : x - 3\n  return (\n    <>\n      <rect\n        x={left}\n        y={y - fontSize * 0.65}\n        width={w}\n        height={fontSize * 1.3}\n        rx={3}\n        fill=\"#fff\"\n        fillOpacity={0.8}\n      />\n      <text\n        x={x}\n        y={y + fontSize * 0.35}\n        textAnchor={anchor}\n        fontSize={fontSize}\n        fontWeight={bold ? 600 : undefined}\n        fill=\"#18181c\"\n      >\n        {text}\n      </text>\n    </>\n  )\n}\n\n// The node and deletion lengths written on the drawing, with their leaders\nfunction SizeLabels({ model }: { model: GraphPaneModel }) {\n  return (\n    <g fontFamily={FONT.fontFamily}>\n      {model.overlayLabels.sizes.map(({ key, text, x, y, kind, leader }) => (\n        <g key={key}>\n          {leader ? (\n            <line\n              x1={leader.arcX}\n              y1={leader.arcY}\n              x2={leader.labelX}\n              y2={leader.labelY}\n              stroke=\"#18181c\"\n            />\n          ) : null}\n          <Chip\n            x={x}\n            y={y}\n            text={text}\n            fontSize={10}\n            anchor=\"middle\"\n            bold={kind === 'deletion'}\n          />\n        </g>\n      ))}\n    </g>\n  )\n}\n\nfunction RowLabels({ model }: { model: GraphPaneModel }) {\n  return (\n    <g fontFamily={FONT.fontFamily}>\n      {model.drawnRowLabels.map(({ label, y }) => {\n        const screenY = y * model.scaleY + model.translateY\n        return screenY >= 0 && screenY <= model.canvasHeight ? (\n          <Chip\n            key={y}\n            x={10}\n            y={screenY}\n            text={label}\n            fontSize={11}\n            anchor=\"start\"\n          />\n        ) : null\n      })}\n    </g>\n  )\n}\n\n// Each lifted walk in a panel of its own, its key as the panel's title\nfunction Facets({\n  model,\n  rasterize,\n  idPrefix,\n}: {\n  model: GraphPaneModel\n  rasterize: boolean\n  idPrefix: string\n}) {\n  const panels = model.facetPanels\n  const grid = model.facetGrid\n  const place = model.facetPlacement\n  if (!panels || !grid || !place) {\n    return null\n  }\n  const { columns, width, height } = grid\n  const keyY = grid.total + FACET_GAP_PX + 14\n  const key = facetKeyRows(model).map((row, i) =>\n    svgRow(row, `${idPrefix}-facet-key-${i}`),\n  )\n  const keyX = key.map((_, i) =>\n    key.slice(0, i).reduce((x, row) => x + row.width + 14, 6),\n  )\n  return (\n    <>\n      <g transform={`translate(0 ${keyY})`}>\n        {key.map((row, i) => row.draw(keyX[i]!))}\n      </g>\n      {panels.map((lift, i) => {\n        const cell = place.cells[i]!\n        const x = (cell % columns) * (width + FACET_GAP_PX)\n        const y =\n          Math.floor(cell / columns) * (FACET_TITLE_PX + height + FACET_GAP_PX)\n        const walk = lift.walks[0]!\n        const title = svgRow(walkKeyRow(model, walk), `${idPrefix}-facet-${i}`)\n        return (\n          <g key={walk.name} transform={`translate(${x} ${y})`}>\n            <g transform={`translate(0 ${ROW_PX - 2})`}>{title.draw(6)}</g>\n            <g transform={`translate(0 ${FACET_TITLE_PX})`}>\n              <Body\n                model={model}\n                lift={lift}\n                drawPaths={false}\n                width={width}\n                height={height}\n                rasterize={rasterize}\n              />\n            </g>\n          </g>\n        )\n      })}\n    </>\n  )\n}\n\n// The pane as the screen draws it, for the linear view's SVG export: the\n// canvas's ink, the tube map and reference strip painters, and the SVG\n// overlays the screen mounts over them. Hover and selection are left out.\nexport default function PaneSvg({\n  model,\n  rasterize = false,\n  idPrefix,\n}: {\n  model: GraphPaneModel\n  rasterize?: boolean\n  idPrefix: string\n}) {\n  const width = model.paneWidth\n  const height = model.canvasHeight\n  const tubeMap = !!model.layoutResult?.tubeMap\n  const opts = { rasterizeLayers: rasterize }\n  return (\n    <g data-testid=\"graph-pane-svg\">\n      {model.facetPanels ? (\n        <Facets model={model} rasterize={rasterize} idPrefix={idPrefix} />\n      ) : tubeMap ? (\n        <PaintLayer\n          width={width}\n          height={height}\n          opts={opts}\n          paint={ctx => {\n            paintTubeMap(asCanvasCtx(ctx), model, { highlightNode: null })\n          }}\n        />\n      ) : (\n        <Body\n          model={model}\n          lift={model.walkLift}\n          drawPaths={model.effectiveDrawPaths}\n          width={width}\n          height={height}\n          rasterize={rasterize}\n        />\n      )}\n      {/* in the screen's stacking order, bottom first */}\n      {model.facetPanels ? null : (\n        <>\n          <BubbleHalos model={model} />\n          <GenePins model={model} />\n          <SizeLabels model={model} />\n          <LabelLayer model={model} />\n          <WalkRowsOverlay model={model} vector />\n          <RowLabels model={model} />\n        </>\n      )}\n      {model.referenceStripShown ? (\n        <PaintLayer\n          width={width}\n          height={height}\n          opts={opts}\n          paint={ctx => {\n            paintReferenceStrip(asCanvasCtx(ctx), model, {\n              lit: undefined,\n              dpr: 1,\n            })\n          }}\n        />\n      ) : null}\n      {model.facetPanels ? null : <Keys model={model} idPrefix={idPrefix} />}\n    </g>\n  )\n}\n", "import { renderDisplaySvg } from '@jbrowse/display-kit/renderDisplaySvg'\n\nimport PaneSvg from '../GraphGenomeView/components/PaneSvg'\n\nimport type { LinearGraphDisplayModel } from './model'\nimport type { LgvSvgBodyProps } from '@jbrowse/display-kit/renderDisplaySvg'\nimport type { ExportSvgDisplayOptions } from '@jbrowse/display-kit/types'\n\nfunction GraphTrackSvgBody({\n  model,\n  opts,\n}: LgvSvgBodyProps<LinearGraphDisplayModel>) {\n  return (\n    <PaneSvg\n      model={model}\n      rasterize={!!opts?.rasterizeLayers}\n      idPrefix={`graph-${model.id}`}\n    />\n  )\n}\n\nexport function renderGraphTrackSvg(\n  model: LinearGraphDisplayModel,\n  opts?: ExportSvgDisplayOptions,\n) {\n  return renderDisplaySvg(model, opts, GraphTrackSvgBody)\n}\n"],
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-  "names": ["host", "read", "name", "renderDisplaySvg", "read", "renderDisplaySvg_default", "host", "host", "read", "name", "PaintLayer", "paintLayer_default", "FONT", "CHAR_PX", "ROW_PX", "RASTER_SCALE", "asCanvasCtx", "ctx", "Body", "model", "lift", "drawPaths", "width", "height", "rasterize", "built", "transform", "canvas", "renderer", "Canvas2DRenderer", "jsx", "markup", "svgCanvas", "Gradient", "id", "x", "y", "stops", "square", "rect", "fill", "jsxs", "Fragment", "s", "i", "SvgSwatch", "swatch", "swatchWidth", "band", "top", "SWATCH_PX", "inset", "rulerInk", "svgRow", "row", "left", "sw", "words", "Keys", "idPrefix", "sections", "legendSections", "testid", "rows", "pad", "boxWidth", "r", "boxHeight", "sum", "LEGEND_INSET_PX", "placed", "section", "Chip", "text", "fontSize", "anchor", "bold", "w", "SizeLabels", "key", "kind", "leader", "RowLabels", "label", "screenY", "Facets", "panels", "grid", "place", "columns", "keyY", "FACET_GAP_PX", "facetKeyRows", "keyX", "_", "cell", "FACET_TITLE_PX", "walk", "title", "walkKeyRow", "PaneSvg", "tubeMap", "opts", "PaintLayer", "paintTubeMap", "BubbleHalos_default", "GenePins_default", "LabelLayer_default", "WalkRowsOverlay_default", "paintReferenceStrip", "GraphTrackSvgBody", "model", "opts", "jsx", "PaneSvg", "renderGraphTrackSvg", "renderDisplaySvg"]
-}

package/src/GraphGenomeView/components/WalkRowContextMenu.tsx

@@ -1,105 +0,0 @@
-import { Menu } from '@jbrowse/core/ui'
-import FilterListIcon from '@mui/icons-material/FilterList'
-import FilterListOffIcon from '@mui/icons-material/FilterListOff'
-import LineStyleIcon from '@mui/icons-material/LineStyle'
-import { observer } from 'mobx-react'
-
-import { locLabel } from '../../launchFromGraph/contributors'
-
-import type { GraphPaneModel } from '../model'
-import type { WalkRows } from '@jbrowse/bandage-core/layout/walkRows'
-
-// A walk row's bar stands for a span of its haplotype's own contig, so the
-// question a right-click asks is answered by a linear view on that assembly,
-// with its genes
-export const WalkRowContextMenu = observer(function WalkRowContextMenu({
-  model,
-  row,
-  bars,
-  top,
-  left,
-  onClose,
-}: {
-  model: GraphPaneModel
-  row: number
-  // the rows `row` indexes, walk rows' own unless a strip's
-  bars?: WalkRows
-  top: number
-  left: number
-  onClose: () => void
-}) {
-  const rows = bars ?? model.walkRowBars
-  const target = model.walkRowLaunchTarget(row, rows)
-  const assembly = target?.assembly
-  const walk = row > 0 ? rows?.rows[row - 1] : undefined
-  const sample = walk?.sample
-  // the strip's rows are not walk rows', and take no sample filter
-  const filters = !bars && model.walkRowBars
-  const shown = model.walkRowSamples
-  return (
-    <Menu
-      open
-      anchorReference="anchorPosition"
-      anchorPosition={{ top, left }}
-      onClose={() => {
-        onClose()
-      }}
-      onMenuItemClick={callback => {
-        callback()
-      }}
-      menuItems={[
-        target && assembly
-          ? {
-              label: `Linear genome view — ${assembly} ${locLabel(target.location)}`,
-              icon: LineStyleIcon,
-              onClick: () => {
-                model.showInLinearView({ location: target.location, assembly })
-              },
-            }
-          : {
-              label: 'Linear genome view',
-              icon: LineStyleIcon,
-              disabled: true,
-              disabledHelpText: target
-                ? `No assembly in this session is ${target.location.haplotype ?? target.label}`
-                : 'This walk states no contig coordinates',
-              onClick: () => {},
-            },
-        ...(walk && model.liftsWalks && model.modeDrawsNodes
-          ? [
-              {
-                type: 'checkbox' as const,
-                label: `Highlight ${walk.label}`,
-                checked: model.walkLayers.some(l => l.walk === walk.name),
-                onClick: () => {
-                  model.toggleWalk(walk.name)
-                },
-              },
-            ]
-          : []),
-        ...(filters && sample && !(shown?.length === 1 && shown[0] === sample)
-          ? [
-              {
-                label: `Show only ${sample}`,
-                icon: FilterListIcon,
-                onClick: () => {
-                  model.setWalkRowSamples([sample])
-                },
-              },
-            ]
-          : []),
-        ...(filters && shown
-          ? [
-              {
-                label: 'Show every sample',
-                icon: FilterListOffIcon,
-                onClick: () => {
-                  model.setWalkRowSamples(undefined)
-                },
-              },
-            ]
-          : []),
-      ]}
-    />
-  )
-})