jbrowse-plugin-graphgenomeviewer 4.0.0 → 4.0.2

package/dist/jbrowse-plugin-graphgenomeviewer.esm.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["global-externals:@jbrowse/core/Plugin", "global-externals:@jbrowse/core/pluggableElementTypes/AdapterType", "global-externals:@jbrowse/core/configuration", "global-externals:@jbrowse/core/data_adapters/dataAdapterCache", "global-externals:@jbrowse/core/pluggableElementTypes", "global-externals:@jbrowse/core/pluggableElementTypes/ViewType", "global-externals:@jbrowse/core/util/withLaunchInput", "global-externals:@jbrowse/core/pluggableElementTypes/models", "global-externals:@jbrowse/render-core/RenderLifecycleMixin", "global-externals:mobx", "global-externals:@jbrowse/core/pluggableElementTypes/DisplayType", "global-externals:@jbrowse/display-kit/trackHeightConfigSchemaFields", "global-externals:@jbrowse/display-kit/TrackHeightMixin", "../src/index.ts", "../node_modules/.pnpm/@mui+icons-material@9.4.0_@mui+material@9.4.0_@emotion+react@11.14.0_@types+react@19.3._3766ec55733e6b150ee672ad270cc236/node_modules/@mui/icons-material/BubbleChart.mjs", "../src/GbzBaseSyntenyAdapter/index.ts", "../src/GbzBaseSyntenyAdapter/configSchema.ts", "../src/GetSubgraph.ts", "../src/GraphAddTrackWorkflow/index.ts", "../src/GraphComputeLayout.ts", "../src/loadBandage.ts", "../src/GraphGenomeView/index.ts", "../src/GraphGenomeView/model.ts", "../src/GraphGenomeView/bubbles/bubbleHalos.ts", "../src/GraphGenomeView/bubbles/bubblesFromGraph.ts", "../src/GraphGenomeView/bubbles/popBubble.ts", "../src/GraphGenomeView/genes/geneFeatures.ts", "../src/GraphGenomeView/genes/genePins.ts", "../src/gfa-core/gfaParser.ts", "../src/GraphGenomeView/gfa/gfaConverter.ts", "../src/GraphGenomeView/host.ts", "../src/GraphGenomeView/laneRamp.ts", "../src/GraphGenomeView/layout/orientToReference.ts", "../src/GraphGenomeView/layout/referenceSeeds.ts", "../src/GraphGenomeView/repeats/repeatFeatures.ts", "../src/GraphGenomeView/walkHighlight.ts", "../src/hoverSync/lgvHover.ts", "../src/launchFromGraph/launchFromGraph.ts", "../src/launchFromGraph/linearViewTarget.ts", "../src/launchFromGraph/launchTracks.ts", "../src/launchFromGraph/syntenyTracks.ts", "../src/launchSubgraph/subgraphTracks.ts", "../src/LaunchGraphGenomeView.ts", "../src/LinearGraphDisplay/index.ts", "../src/LinearGraphDisplay/configSchema.ts", "../src/LinearGraphDisplay/model.ts", "../src/MinigraphBubbleAdapter/index.ts", "../src/MinigraphBubbleAdapter/configSchema.ts", "../src/RgfaTabixAdapter/index.ts", "../src/RgfaTabixAdapter/configSchema.ts", "../src/hoverSync/GraphNodeHighlight.tsx", "../src/hoverSync/graphViewHighlights.ts", "../src/hoverSync/index.tsx", "../src/pluginName.ts", "../src/version.ts"],
-  "sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/core/Plugin\"];", "module.exports = JBrowseExports[\"@jbrowse/core/pluggableElementTypes/AdapterType\"];", "module.exports = JBrowseExports[\"@jbrowse/core/configuration\"];", "module.exports = JBrowseExports[\"@jbrowse/core/data_adapters/dataAdapterCache\"];", "module.exports = JBrowseExports[\"@jbrowse/core/pluggableElementTypes\"];", "module.exports = JBrowseExports[\"@jbrowse/core/pluggableElementTypes/ViewType\"];", "module.exports = JBrowseExports[\"@jbrowse/core/util/withLaunchInput\"];", "module.exports = JBrowseExports[\"@jbrowse/core/pluggableElementTypes/models\"];", "module.exports = JBrowseExports[\"@jbrowse/render-core/RenderLifecycleMixin\"];", "module.exports = JBrowseExports[\"mobx\"];", "module.exports = JBrowseExports[\"@jbrowse/core/pluggableElementTypes/DisplayType\"];", "module.exports = JBrowseExports[\"@jbrowse/display-kit/trackHeightConfigSchemaFields\"];", "module.exports = JBrowseExports[\"@jbrowse/display-kit/TrackHeightMixin\"];", "import Plugin from '@jbrowse/core/Plugin'\nimport { isAbstractMenuManager } from '@jbrowse/core/util'\nimport BubbleChartIcon from '@mui/icons-material/BubbleChart'\n\nimport GbzBaseSyntenyAdapterF from './GbzBaseSyntenyAdapter/index'\nimport GetSubgraph from './GetSubgraph'\nimport GraphAddTrackWorkflowF from './GraphAddTrackWorkflow/index'\nimport GraphComputeLayout from './GraphComputeLayout'\nimport GraphGenomeViewF from './GraphGenomeView/index'\nimport LaunchGraphGenomeViewF from './LaunchGraphGenomeView'\nimport LinearGraphDisplayF from './LinearGraphDisplay/index'\nimport MinigraphBubbleAdapterF from './MinigraphBubbleAdapter/index'\nimport RgfaTabixAdapterF from './RgfaTabixAdapter/index'\nimport GraphHoverSyncF from './hoverSync/index'\nimport { PLUGIN_NAME } from './pluginName'\nimport { version } from './version'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { AbstractSessionModel } from '@jbrowse/core/util'\n\nexport default class GraphGenomeViewPlugin extends Plugin {\n  name = PLUGIN_NAME\n  version = version\n\n  install(pluginManager: PluginManager) {\n    GraphGenomeViewF(pluginManager)\n    LinearGraphDisplayF(pluginManager)\n    LaunchGraphGenomeViewF(pluginManager)\n    GraphHoverSyncF(pluginManager)\n    RgfaTabixAdapterF(pluginManager)\n    MinigraphBubbleAdapterF(pluginManager)\n    GbzBaseSyntenyAdapterF(pluginManager)\n    GraphAddTrackWorkflowF(pluginManager)\n    pluginManager.addRpcMethod(() => new GraphComputeLayout(pluginManager))\n    pluginManager.addRpcMethod(() => new GetSubgraph(pluginManager))\n  }\n\n  // A throw from configure() takes the whole session to its error page, and a\n  // menu entry is not worth that: hubs 1.0.9 did exactly this to every\n  // jbrowse.org/ucsc launch by appending to a menu a released host defines as\n  // a function. The view is still reachable without the entry.\n  configure(pluginManager: PluginManager) {\n    try {\n      if (isAbstractMenuManager(pluginManager.rootModel)) {\n        pluginManager.rootModel.appendToSubMenu(['Add'], {\n          label: 'Graph genome view',\n          icon: BubbleChartIcon,\n          onClick: (session: AbstractSessionModel) => {\n            session.addView('GraphGenomeView', {})\n          },\n        })\n      }\n    } catch (e) {\n      console.warn('[GraphGenomeView] could not add the Add menu entry', e)\n    }\n  }\n}\n", "\"use client\";\n\nimport createSvgIcon from \"./utils/createSvgIcon.mjs\";\nimport { jsx as _jsx } from \"react/jsx-runtime\";\nexport default createSvgIcon([/*#__PURE__*/_jsx(\"circle\", {\n  cx: \"7.2\",\n  cy: \"14.4\",\n  r: \"3.2\"\n}, \"0\"), /*#__PURE__*/_jsx(\"circle\", {\n  cx: \"14.8\",\n  cy: \"18\",\n  r: \"2\"\n}, \"1\"), /*#__PURE__*/_jsx(\"circle\", {\n  cx: \"15.2\",\n  cy: \"8.8\",\n  r: \"4.8\"\n}, \"2\")], 'BubbleChart');", "import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'\n\nimport configSchema from './configSchema.ts'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\n\nexport default function GbzBaseSyntenyAdapterF(pluginManager: PluginManager) {\n  pluginManager.addAdapterType(\n    () =>\n      new AdapterType({\n        name: 'GbzBaseSyntenyAdapter',\n        displayName: 'gbz-base pangenome adapter',\n        configSchema,\n        // The same opened database serves the graph view's subgraph, so the\n        // launch menu offers this track too (launchSubgraph/subgraphTracks).\n        // headerLanes: getHeader declares every haplotype as a lane, which is\n        // what makes MultiWaySyntenyDisplay read the header of an untiered\n        // adapter and offer its lane picker over the whole graph.\n        // lanePairsOnAnchor: a window of the anchor answers any two lanes'\n        // alignment to each other, so the display fetches each adjacent pair\n        // rather than composing it through the reference\n        adapterCapabilities: [\n          'getSubgraph',\n          'headerLanes',\n          'lanePairsOnAnchor',\n        ],\n        adapterMetadata: {\n          category: 'Synteny adapters',\n        },\n        getAdapterClass: () =>\n          import('./GbzBaseSyntenyAdapter.ts').then(r => r.default),\n      }),\n  )\n}\n", "import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { types } from '@jbrowse/mobx-state-tree'\n\nimport type { Instance } from '@jbrowse/mobx-state-tree'\n\n/**\n * #config GbzBaseSyntenyAdapter\n * #trackType SyntenyTrack\n * #fileFormat synteny | gbz-base pangenome database | Haplotype alignments read from the graph at query time, no PAF conversion\n * Serves a pangenome graph stored as a gbz-base SQLite database (`.gbz.db`) as\n * haplotype-versus-reference alignments, the shape `MultiWaySyntenyDisplay`\n * draws as one lane per haplotype. A window on the reference is located on the\n * graph's reference path, every haplotype's walk through the nodes it covers\n * is recovered and named, and each haplotype becomes one alignment record with\n * a CIGAR, so the graph is read through HTTP range requests with no offline\n * conversion. The database has to carry the `HaplotypeSamples` and\n * `HaplotypeLengths` side tables that `gbz-haplotype-index` (shipped with\n * `@gmod/gbz-base`) writes into an upstream-built database; without them the\n * graph cannot say which haplotype a walk belongs to.\n *\n * Only the fine tier exists: a whole-chromosome view stays on a PIF's coarse\n * tier. A query on a haplotype lane answers nothing, so the multi-way display\n * composes its lane-to-lane links through the reference.\n *\n * #example\n * ```js\n * {\n *   type: 'GbzBaseSyntenyAdapter',\n *   uri: 'hprc-v2.gbz.db',\n *   assemblyNames: ['hg38'],\n *   assemblyNameToPanSN: { hg38: 'GRCh38#0' },\n * }\n * ```\n */\nconst GbzBaseSyntenyAdapter = ConfigurationSchema(\n  'GbzBaseSyntenyAdapter',\n  {\n    /**\n     * #slot\n     * The first entry is the anchor: the JBrowse assembly the graph's reference\n     * sample is loaded as. Further entries are haplotypes loaded as JBrowse\n     * assemblies under their PanSN prefix (`HG002#1`); one loaded under another\n     * name only needs its `assemblyNameToPanSN` entry. A haplotype named in\n     * neither is still a lane, labelled by its PanSN prefix.\n     */\n    assemblyNames: {\n      type: 'stringArray',\n      defaultValue: [],\n    },\n    /**\n     * #slot\n     * The `.gbz.db` written by `gbz-base construct` and augmented by\n     * `gbz-haplotype-index`; read by HTTP range requests, so it can be large.\n     */\n    gbzDbLocation: {\n      type: 'fileLocation',\n      defaultValue: {\n        uri: '/path/to/graph.gbz.db',\n        locationType: 'UriLocation',\n      },\n    },\n    /**\n     * #slot\n     * A companion database written by `gbz-haplotype-index --output`, holding\n     * the `HaplotypeSamples` and `HaplotypeLengths` tables for a graph database\n     * that does not carry them itself, such as the one HPRC publishes. One\n     * built with anchor rows (the tool's default) lets a fetch for a chosen\n     * set of lanes walk only those haplotypes. Empty means the graph database\n     * carries the tables.\n     */\n    haplotypeIndexLocation: {\n      type: 'fileLocation',\n      defaultValue: {\n        uri: '',\n        locationType: 'UriLocation',\n      },\n    },\n    /**\n     * #slot\n     * How the graph view's subgraph is extended past the nodes the reference\n     * window touches. `contained` adds every top-level snarl with both\n     * boundary nodes in the window, which is what brings back the bubbles a\n     * reference-only walk leaves out; a haplotype still breaks into a new W\n     * line wherever it leaves the window's nodes (a 60 kb C4 window on the\n     * HPRC graph: 2,703 nodes, 8,083 walks for 464 haplotypes). `overlapping`\n     * also follows snarls that leave the window, so every haplotype is one\n     * walk (464), at the price of every node in those snarls (4,184 there,\n     * 24,547 across the KIV-2 repeat). `none` leaves only the bp `context`.\n     */\n    subgraphSnarls: {\n      type: 'stringEnum',\n      model: types.enumeration('SnarlOutput', [\n        'none',\n        'contained',\n        'overlapping',\n      ]),\n      defaultValue: 'contained',\n    },\n    /**\n     * #slot\n     * The graph sample the anchor window is located on. Empty means the sample\n     * the anchor's PanSN prefix names, or the database's one reference sample\n     * (`gbwt_reference_samples`) when the anchor names none; a database with\n     * several reference samples then needs this set.\n     */\n    referenceSample: {\n      type: 'string',\n      defaultValue: '',\n    },\n    /**\n     * #slot\n     * Maps a JBrowse assembly name to its PanSN prefix in the graph, sample or\n     * haplotype level (`{ hg38: 'GRCh38#0', 'HG002.1': 'HG002#1' }`). Defaults\n     * to identity.\n     */\n    assemblyNameToPanSN: {\n      type: 'frozen',\n      defaultValue: {},\n    },\n    /**\n     * #slot\n     * Graph context around the reference walk, in bp, on top of\n     * `subgraphSnarls`. Since `@gmod/gbz-base` joins the pieces of a walk that\n     * leaves the window's nodes and comes back (the private stretch becomes the\n     * record's insertion, the skipped reference its deletion), a lane's record\n     * count is one per haplotype at any context; what context trades is nodes\n     * read against pieces to identify and join. A window inside a snarl far\n     * larger than itself (MHC class II on the HPRC graph, 90 kb) is 1.1M pieces\n     * at 0 and 464 walks at 1000, three times faster; a window whose private\n     * stretches are short bubbles costs about the same either way. For the\n     * graph view's cut it is simply how far past the window the cut extends.\n     */\n    context: {\n      type: 'number',\n      defaultValue: 1000,\n      advanced: true,\n    },\n    /**\n     * #slot\n     * The most graph nodes one window may load before the query fails rather\n     * than reading a whole chromosome into the worker.\n     */\n    nodeLimit: {\n      type: 'number',\n      defaultValue: 100000,\n      advanced: true,\n    },\n  },\n  {\n    explicitlyTyped: true,\n\n    /**\n     * #preProcessSnapshot\n     *\n     *\n     * preprocessor to allow minimal config:\n     * ```json\n     * {\n     *   \"type\": \"GbzBaseSyntenyAdapter\",\n     *   \"uri\": \"graph.gbz.db\",\n     *   \"assemblyNames\": [\"hg38\"]\n     * }\n     * ```\n     */\n    preProcessSnapshot: snap => {\n      return snap.uri\n        ? {\n            ...snap,\n            gbzDbLocation: {\n              uri: snap.uri,\n              baseUri: snap.baseUri,\n            },\n          }\n        : snap\n    },\n  },\n)\n\nexport type GbzBaseSyntenyAdapterConfig = Instance<typeof GbzBaseSyntenyAdapter>\n\nexport default GbzBaseSyntenyAdapter\n", "import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'\nimport { RpcMethodTypeWithRenameRegion } from '@jbrowse/core/pluggableElementTypes'\n\nimport type { RpcExecuteArgs } from '@jbrowse/core/rpc/RpcRegistry'\nimport type { Region } from '@jbrowse/core/util'\n\n// No `sessionId`, `signal` or `statusCallback` here: those belong to the\n// CALL, not to this payload, and core's `EntriesDeclaringCallLevelFields` fails\n// the build for a registry entry that declares one. `execute` still receives\n// them, because `RpcExecuteArgs` intersects `RpcCallContext` in.\n// `hops` is how far past the window a cut follows links, which only the rGFA\n// cut reads; the GBZ cut has its own bp `context` slot. `haplotypes` is the\n// set the cut is for, lane assembly names or PanSN prefixes, which only the GBZ\n// cut reads: it keeps those walks and the nodes they visit. Undefined or empty\n// is every haplotype. `tier` picks which of an rGFA track's two index pairs the\n// cut reads, the adapter's own or its `coarse` one; fine when absent.\nexport type SubgraphTier = 'fine' | 'coarse'\n\nexport interface SubgraphCutOptions {\n  hops?: number\n  haplotypes?: string[]\n  tier?: SubgraphTier\n}\n\n// What an adapter's cut is handed: the payload, plus the call's own signal so\n// a cut the view has moved on from stops reading.\nexport interface SubgraphAdapterOptions extends SubgraphCutOptions {\n  signal?: AbortSignal\n}\n\nexport interface GetSubgraphArgs {\n  adapterConfig: Record<string, unknown>\n  region: Region\n  opts?: SubgraphCutOptions\n}\n\ndeclare module '@jbrowse/core/rpc/RpcRegistry' {\n  interface RpcRegistry {\n    GetSubgraph: {\n      args: GetSubgraphArgs\n      return: string\n    }\n  }\n}\n\n// Adapters that can cut a local subgraph out of a graph file implement this:\n// RgfaTabixAdapter and GbzBaseSyntenyAdapter today.\ninterface SubgraphAdapter {\n  getSubgraph(region: Region, opts?: SubgraphAdapterOptions): Promise<string>\n}\n\nfunction isSubgraphAdapter(adapter: object): adapter is SubgraphAdapter {\n  return (\n    'getSubgraph' in adapter &&\n    typeof (adapter as SubgraphAdapter).getSubgraph === 'function'\n  )\n}\n\n// RpcMethodTypeWithRenameRegion, not the plain RpcMethodType: the base class is\n// what maps `region.refName` from the assembly's spelling onto the adapter's own\n// before the call crosses to the worker. Without it a launch on an hg38 whose\n// contigs are bare (`6`, which is what every GRCh38 FASTA on jbrowse.org uses)\n// asked RgfaTabixAdapter for `GRCh38#0#6`, matched nothing, and opened a view\n// reading \"0 nodes, 0 edges\" with no error. The segments track drew the whole\n// time, because CoreGetFeatures renames and this did not, so the graph looked\n// broken while its own track looked fine. `assemblyNameToPanSN` covers the\n// sample half of a PanSN name only; the contig half is refName aliasing, which\n// the assembly already knows and this now consults.\nexport default class GetSubgraph extends RpcMethodTypeWithRenameRegion<'GetSubgraph'> {\n  name = 'GetSubgraph' as const\n\n  // Parameterized by the registry key, not left at the default `string`: a bare\n  // RpcMethodTypeWithRenameRegion resolves RpcExecuteArgs to `unknown`, so\n  // `execute` type-checks against nothing at all. `invoke` has already run\n  // `deserializeArguments` by the time this is called, so it does not.\n  async execute(args: RpcExecuteArgs<'GetSubgraph'>) {\n    // `signal` arrives on every call and has to be named to be forwarded:\n    // unnamed, a cut the view had replaced went on querying to the end, one\n    // tabix read per off-reference segment per hop.\n    const { adapterConfig, region, sessionId, opts, signal } = args\n\n    const { dataAdapter } = await getAdapter(\n      this.pluginManager,\n      sessionId,\n      adapterConfig,\n    )\n    if (isSubgraphAdapter(dataAdapter)) {\n      return dataAdapter.getSubgraph(region, { ...opts, signal })\n    }\n    // An empty result is how the view and the launch menu detect \"this track\n    // can't do subgraphs\" \u2014 see GraphGenomeView.loadFromTabixSubgraph.\n    console.warn(\n      `[GetSubgraph] ${dataAdapter.constructor.name} does not implement getSubgraph`,\n    )\n    return ''\n  }\n}\n", "import { lazy } from 'react'\n\nimport { AddTrackWorkflowType } from '@jbrowse/core/pluggableElementTypes'\nimport { types } from '@jbrowse/mobx-state-tree'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\n\nconst GraphAddTrackWidget = lazy(() => import('./AddTrackWorkflow'))\n\nexport default function GraphAddTrackWorkflowF(pluginManager: PluginManager) {\n  pluginManager.addAddTrackWorkflowType(\n    () =>\n      new AddTrackWorkflowType({\n        name: 'Pangenome graph track',\n        displayName: 'Add pangenome graph track',\n        ReactComponent: GraphAddTrackWidget,\n        stateModel: types.model({}),\n      }),\n  )\n}\n", "import { RpcMethodType } from '@jbrowse/core/pluggableElementTypes'\n\nimport loadBandage from './loadBandage'\n\nimport type { LayoutNode } from './GraphGenomeView/layout/referenceSeeds'\nimport type { Graph, LayoutResult } from './GraphGenomeView/types'\nimport type { RpcExecuteArgs } from '@jbrowse/core/rpc/RpcRegistry'\n\n// `sessionId` and `statusCallback` are the CALL's, not this payload's \u2014 core's\n// `EntriesDeclaringCallLevelFields` fails the build for a registry entry that\n// declares either, on the grounds that a field one method owns is a field the\n// other forty cannot be passed. `execute` still receives both, through\n// `RpcExecuteArgs`'s intersection with `RpcCallContext`.\nexport interface GraphComputeLayoutArgs {\n  // a node may carry an `x`/`y` seed, which the engine reads as where its\n  // chain starts (referenceSeeds.ts)\n  graph: { nodes: LayoutNode[]; edges: Graph['edges'] }\n  options: Record<string, unknown>\n}\n\ndeclare module '@jbrowse/core/rpc/RpcRegistry' {\n  interface RpcRegistry {\n    GraphComputeLayout: {\n      args: GraphComputeLayoutArgs\n      return: { result: LayoutResult; duration: number }\n    }\n  }\n}\n\nexport default class GraphComputeLayout extends RpcMethodType<'GraphComputeLayout'> {\n  name = 'GraphComputeLayout' as const\n\n  async execute(args: RpcExecuteArgs<'GraphComputeLayout'>) {\n    const { graph, options, statusCallback } = args\n\n    statusCallback?.('Loading layout engine')\n    const module = await loadBandage()\n\n    statusCallback?.('Computing layout')\n    const startTime = performance.now()\n    const result = module.computeLayout(graph, options)\n    const duration = performance.now() - startTime\n\n    return { result, duration }\n  }\n}\n", "export type { BandageModule } from './bandage/bandage-layout'\n\nimport type { BandageModule } from './bandage/bandage-layout'\n\n// The Bandage engine is a ~425kb self-contained ES module (Emscripten\n// -sSINGLE_FILE=1, wasm inlined as base64). A plain dynamic import lets the\n// bundler emit it as a sibling chunk that the browser resolves relative to this\n// module's own url via import.meta.url \u2014 so it downloads only when a\n// force-directed layout is requested, and works identically on the main thread\n// and in the RPC worker with no url plumbing.\nlet cached: Promise<BandageModule> | undefined\n\nexport default function loadBandage() {\n  cached ??= import('./bandage/bandage-layout')\n    .then(mod => mod.default())\n    .catch((e: unknown) => {\n      // let a later attempt retry rather than caching the failure forever\n      cached = undefined\n      throw e\n    })\n  return cached\n}\n", "import { lazy } from 'react'\n\nimport ViewType from '@jbrowse/core/pluggableElementTypes/ViewType'\nimport { defineLaunchKeys } from '@jbrowse/core/util/withLaunchInput'\n\nimport modelFactory from './model'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\n\n// This view has NO launch keys, and saying so is what turns the check on.\n//\n// A launch key is a spec field the launcher interprets rather than assigns \u2014 an\n// LGV's `assembly` and `loc`, resolved into `displayedRegions`. Every field of\n// a graph launch is a plain persisted prop instead (see\n// LaunchGraphGenomeView), so the registration is empty; what it buys is\n// `ViewType.acceptedKeys`, which is `undefined` until a view declares its\n// launch vocabulary, and which `loadSessionSpec` needs to report\n// `ignored unknown key(s)`.\n//\n// Without it a session spec's typo in a GraphGenomeView entry is silent: the\n// key lands in the snapshot, MST drops it, and the view opens on the import\n// form with nothing said. That surface is written by hand with no compiler\n// behind it \u2014 `sessionSpec()` takes a bare `object` \u2014 and the docs build two\n// dozen graph figures through it, `loadedRegion` and `loadedTrackId` among the\n// fields a misspelling would silently cost.\n//\n// Ignored by a host that predates `acceptedKeys`: its ViewType constructor\n// reads the options it knows and this is not one of them.\nconst graphLaunchKeys = defineLaunchKeys<object>()({})\n\nexport default function GraphGenomeViewF(pluginManager: PluginManager) {\n  pluginManager.addViewType(() => {\n    return new ViewType({\n      name: 'GraphGenomeView',\n      displayName: 'Graph genome view',\n      stateModel: modelFactory(),\n      launchKeys: graphLaunchKeys,\n      ReactComponent: lazy(() => import('./components/GraphGenomeView')),\n    })\n  })\n}\n", "import { readConfObject } from '@jbrowse/core/configuration'\nimport { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models'\nimport { pushLaunchViewMenuItem } from '@jbrowse/core/ui'\nimport {\n  getContainingView,\n  getSession,\n  isSessionModelWithWidgets,\n  statusMessageText,\n} from '@jbrowse/core/util'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { addDisposer, flow, isAlive, types } from '@jbrowse/mobx-state-tree'\nimport { RenderLifecycleMixin } from '@jbrowse/render-core/RenderLifecycleMixin'\nimport { getDpr } from '@jbrowse/render-core/canvas2dUtils'\nimport { autorun, reaction, untracked } from 'mobx'\n\nimport { backboneNodes, backboneSpan, isBackbone } from './anchoredNodes'\nimport { BUBBLE_SPREAD_VALUES, spreadFor } from './bubbleSpreads'\nimport { bubbleHalos } from './bubbles/bubbleHalos'\nimport { bubblesFromGraph } from './bubbles/bubblesFromGraph'\nimport {\n  BUBBLE_KIND_NAMES,\n  bubbleSegmentIds,\n  classifyBubble,\n} from './bubbles/classifyBubble'\nimport { bubbleSubgraph } from './bubbles/popBubble'\nimport { COLOR_SCHEME_VALUES } from './colorSchemes'\nimport { deletionEdges } from './deletionEdges'\nimport {\n  GENE_ADAPTER_TYPES,\n  geneModelsFrom,\n  pickGeneTrack,\n} from './genes/geneFeatures'\nimport { genePins } from './genes/genePins'\nimport { convertGFAToGraph } from './gfa/gfaConverter'\nimport { cutHolds, hostCut, hostFrame, hostWindow, isLinearHost } from './host'\nimport {\n  paintSourceLane,\n  referencePositionColor,\n  sourceLaneDisplay,\n} from './laneRamp'\nimport { drawnNodeLength, layoutScaling } from './layout/drawnScale'\nimport { mergeRuns, splitRuns } from './layout/mergeRuns'\nimport { orientToReference } from './layout/orientToReference'\nimport { seededNodes } from './layout/referenceSeeds'\nimport { ROW_HEIGHT_PX } from './layout/rowSpacing'\nimport { walkRowsExtent } from './layout/walkRowLayout'\nimport { walkRows } from './layout/walkRows'\nimport {\n  LAYOUT_MODE_VALUES,\n  layoutModeByValue,\n  modeUsesLayoutEngine,\n} from './layoutModes'\nimport {\n  NODE_WIDTH_VALUES,\n  maxNodeWidthPx,\n  meanDepth,\n  nodeWidthPx,\n} from './nodeWidths'\nimport { anchorFromPaths, anchorGraph } from './pathAnchoring'\nimport { pathColorsLegible, pathLegend } from './pathColors'\nimport { buildNeighbors, nodeReferenceSpan } from './referenceSpan'\nimport { buildGeometry, computeReferenceRamp } from './renderer/GeometryBuilder'\nimport {\n  REPEAT_ADAPTER_TYPES,\n  pickRepeatTrack,\n  repeatArraysFrom,\n} from './repeats/repeatFeatures'\nimport { withCalls } from './repeats/walkCalls'\nimport { walkHighlight } from './walkHighlight'\nimport { parseGFA } from '../gfa-core/index'\nimport {\n  hoverInRegion,\n  nodeForLgvHover,\n  readLgvHover,\n} from '../hoverSync/lgvHover'\nimport {\n  contributingAssemblies,\n  locLabel,\n  nodeOwnLocation,\n  resolveContributors,\n  resolveLocationAssembly,\n} from '../launchFromGraph/contributors'\nimport { graphLaunchMenuItems } from '../launchFromGraph/graphMenuItems'\nimport {\n  highlightInLinearView,\n  launchSyntenyView,\n  paddedLocation,\n  showInLinearView,\n  withReferenceRegion,\n} from '../launchFromGraph/launchFromGraph'\nimport { launchTracks } from '../launchFromGraph/launchTracks'\nimport { linearViewTarget, withRows } from '../launchFromGraph/linearViewTarget'\nimport { launchableSyntenyTracks } from '../launchFromGraph/syntenyTracks'\nimport {\n  graphReferenceAssembly,\n  offReferenceProblem,\n} from '../launchSubgraph/subgraphTracks'\n\nimport type { BubbleSpread } from './bubbleSpreads'\nimport type { ColorScheme, ResolvedColorScheme } from './colorSchemes'\nimport type { GeneModel } from './genes/geneFeatures'\nimport type { HostWindow, LinearHost } from './host'\nimport type { LayoutScaling } from './layout/drawnScale'\nimport type { LayoutModeValue } from './layoutModes'\nimport type { NodeWidth } from './nodeWidths'\nimport type { Renderer } from './renderer/types'\nimport type { RepeatArray } from './repeats/repeatFeatures'\nimport type { Graph, GraphNode, LayoutResult } from './types'\nimport type { SubgraphCutOptions, SubgraphTier } from '../GetSubgraph'\nimport type { NodeInk } from './util/hitDetection'\nimport type { MinigraphBubble } from '../MinigraphBubbleAdapter/bubbleLine'\nimport type { AxisScale } from './util/geometry'\nimport type { GraphLocation } from '../launchFromGraph/contributors'\nimport type { SubgraphRegion } from '../launchSubgraph/launchSubgraphView'\nimport type { MenuItem } from '@jbrowse/core/ui'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { FileLocation } from '@jbrowse/core/util/types'\n\n// Ceiling on the pane, and what it falls back to before there is a layout to\n// size against. A roughly square drawing (FMMM) hits this and keeps the\n// scrollable pane it has always had.\nconst MAX_CANVAS_HEIGHT = 600\n// Floor, so a window holding only backbone \u2014 one row, no height at all \u2014 still\n// leaves room to hover a node and read its tooltip.\nconst MIN_CANVAS_HEIGHT = 160\nconst VARIANT_MAP_HEIGHT = 340\n\nconst SEGMENTS_SUFFIX = '.segs.bed.gz'\n\n// The rGFA index prefix an adapter config names, from either spelling the\n// config schema accepts: the `uri` shorthand or an explicit segments location.\nfunction bubblePrefix(adapterConfig: Record<string, unknown>) {\n  if (typeof adapterConfig.uri === 'string') {\n    return adapterConfig.uri\n  }\n  const segments = adapterConfig.segmentsLocation as\n    { uri?: string } | undefined\n  const uri = segments?.uri\n  return typeof uri === 'string' && uri.endsWith(SEGMENTS_SUFFIX)\n    ? uri.slice(0, -SEGMENTS_SUFFIX.length)\n    : undefined\n}\n// Gap between the drawing and the edge of the pane, on all four sides.\nconst FIT_PADDING = 40\nconst HOVER_BRIGHTEN = 1.4\nconst SELECT_BRIGHTEN = 1.6\nconst VIEWPORT_DEBOUNCE_MS = 150\nconst VIEWPORT_PANES_BUILT = 1\n\n// MobX tracks every observable read while a computed or autorun runs, so\n// passing values here registers them as dependencies without otherwise using\n// them.\nfunction dependOn(..._values: unknown[]) {}\n\n// Hard size cap for the single-mode graph view. Past it the view declines with a\n// \"zoom in\" message rather than switching to a degraded rendering mode \u2014 one mode\n// only, since the large-region case is a linear synteny view, not a graph.\n// (The `adr-027` citation this used to carry was stale: that number was reused\n// for wheel-input semantics after the large-mode ADR was removed in 9d8102f0b5.)\n//\n// This bounds the *fetch*, and it is the only cap that can be applied before one\n// happens. It is a poor proxy for cost, because cost tracks node count, so the\n// number is chosen against the density of the graphs it can actually guard: a\n// region is fetched through `getSubgraph`, and the rGFA cut is what this number\n// was chosen against (the GBZ cut is base-level and has its own `nodeLimit`,\n// which trips long before 5 Mb). Both measured rGFAs are sparse, and at 5 Mb\n// both land at or under the ~2k nodes that redraw in under 10 ms (see agent-docs/GRAPH_SCALE_AND_LOD.md):\n//\n//   HPRC MC GRCh38   ~7,000 bp/segment   whole 4.9 Mb MHC   1,173 nodes\n//   ecoli minigraph   3,078 bp/segment   whole 4.6 Mb genome 2,415 nodes\n//\n// Fetch cost does not scale with the window either: against the hosted HPRC\n// index a 4.9 Mb links query and a 100 kb one both cost ~1.3 s, being dominated\n// by HTTP setup. FMMM is the slowest consumer at this size and stays tolerable,\n// ~0.1-3 s for ~1k nodes depending on layout quality (bandage-layout-js), and it\n// runs off the main thread.\n//\n// A dense graph is what this cannot protect against, because bp per node varies\n// by orders of magnitude between graph types \u2014 a base-level pggb graph runs ~17\n// bp/node, where 5 Mb would be hundreds of thousands. Such a graph has no region\n// query to reach this check with today, and the node budget below is the cap that\n// catches it if one ever does.\nexport const MAX_GRAPH_REGION_BP = 5_000_000\n\n// The cap in a message, in the unit that reads: `5 Mb`, not `5000 kb`.\nexport function formatSpanBp(bp: number) {\n  return bp >= 1_000_000\n    ? `${+(bp / 1_000_000).toFixed(1)} Mb`\n    : `${Math.round(bp / 1000)} kb`\n}\n\n// What the view will actually draw, checked once the graph is parsed and so\n// applying to a whole-file import as much as to a subgraph fetch. Measured on\n// bubble-chain graphs: ~1-2k nodes redraws in under 10 ms, 10k takes ~43 ms of\n// geometry and ~125k canvas draw calls per frame (single-digit fps while\n// panning), and 100k needs 632 ms and 75 MB of vertex buffers. So this is set\n// where the tab stops being usable rather than where it stops being smooth, and\n// it is a view prop rather than a constant so a session can raise it \u2014 the same\n// escape hatch strangepg gives with `-T N`.\nexport const DEFAULT_MAX_GRAPH_NODES = 20_000\n\n// The floor exists to keep a scale positive and finite, not to express a useful\n// zoom level, so it has to clear the smallest scale a real layout asks for. In\n// the reference-anchored layouts world units are bp: fitting a chromosome-scale\n// rGFA (250 Mbp) into ~720 px needs ~3e-6, and the old 0.001 floor clamped that\n// to 7x too wide \u2014 zoomToFit could not fit a whole-file import at all.\nconst MIN_ZOOM = 1e-6\nconst MAX_ZOOM = 100\n\nfunction clampZoom(zoom: number) {\n  return Math.max(MIN_ZOOM, Math.min(MAX_ZOOM, zoom))\n}\n\n// The zoom as a pair of axis scales. One expression, read by all three getters\n// below: they sit in one `.views()` block and so cannot reach each other through\n// `self`, which had each of them restating the `pixelRows ? 1 : scale` rule that\n// AxisScale exists to keep in one place.\nfunction axisScaleOf(scale: number, pixelRows: boolean): AxisScale {\n  // pixelRows rides along rather than being derived downstream: the deletion\n  // bow is capped in a row layout and not in the isotropic one, and `scaleY !==\n  // scaleX` coincides at one zoom level. See AxisScale.\n  return { scaleX: scale, scaleY: pixelRows ? 1 : scale, pixelRows }\n}\n\ntype ViewportOwner = 'fit' | 'user' | 'host'\n\ninterface Bounds {\n  minX: number\n  minY: number\n  maxX: number\n  maxY: number\n}\n\n// What the pane shows, in layout units.\nfunction viewportOf(model: {\n  translateX: number\n  translateY: number\n  width: number\n  scaleX: number\n  scaleY: number\n  canvasHeight: number\n}): Bounds {\n  return {\n    minX: -model.translateX / model.scaleX,\n    minY: -model.translateY / model.scaleY,\n    maxX: (model.width - model.translateX) / model.scaleX,\n    maxY: (model.canvasHeight - model.translateY) / model.scaleY,\n  }\n}\n\n// The window a geometry build covers: the pane plus a whole pane on every\n// side, so a pan has that far to go before the drawing runs out and a rebuild\n// is due. Drawing three panes' worth is cheap now that a redraw is a few\n// batched strokes; what it buys is that an ordinary pan never blanks its\n// margins for the debounce and never rebuilds at all.\nfunction padded(v: Bounds, panes: number): Bounds {\n  const w = (v.maxX - v.minX) * panes\n  const h = (v.maxY - v.minY) * panes\n  return {\n    minX: v.minX - w,\n    minY: v.minY - h,\n    maxX: v.maxX + w,\n    maxY: v.maxY + h,\n  }\n}\n\n// Centre the leftover, but only when there IS leftover. A row layout fits on x\n// alone, so its drawing is routinely taller than the pane \u2014 that is the case\n// rowSpacing.ts means by \"reached by panning\" \u2014 and centring an overflow splits\n// the loss across both ends: at 41 rows the top row landed 100 px above the\n// pane. The top row is the reference backbone, i.e. the axis the whole layout\n// exists to put under the linear view, so it is the one row that must not be\n// the first thing to go. Pinned at the padding it opens where a fitting drawing\n// opens, and the rows past the ceiling are below, which is the direction a\n// reader already scrolls a track in.\nfunction fittedTranslateY(\n  bounds: { minY: number; h: number },\n  usableHeight: number,\n  yScale: number,\n) {\n  const leftoverY = usableHeight - bounds.h * yScale\n  return FIT_PADDING - bounds.minY * yScale + Math.max(0, leftoverY) / 2\n}\n\nfunction contains(outer: Bounds, inner: Bounds) {\n  return (\n    inner.minX >= outer.minX &&\n    inner.maxX <= outer.maxX &&\n    inner.minY >= outer.minY &&\n    inner.maxY <= outer.maxY\n  )\n}\n\n// Force layouts already computed for a graph, keyed by the view props the\n// engine reads. Every layout mode is local and costs a millisecond except this\n// one, which is seconds: measured on the committed engine, a 1,201-node bubble\n// chain is 0.6 s proportional, 4.3 s at 'Wide bubbles' and 3.4 s at the highest\n// quality.\n//\n// Worth keeping because a session revisits the same layout. The two drawings\n// answer different questions and the README's own figure is one subgraph in\n// both, so Anchored <-> Force is a round trip a reader makes repeatedly \u2014 and\n// every control in the settings dialog calls `recomputeLayout` on change\n// whether or not the current mode reads what it changed, which made picking a\n// reference path in force mode a multi-second re-run of an identical layout.\n// Both are hits.\n//\n// Entries are the live position objects rather than copies, which a node drag\n// mutates in place (see moveNode), so a layout comes back arranged the way it\n// was left rather than snapping back.\n//\n// Weak on the graph so nothing has to invalidate it: a graph is rebuilt by\n// every load and dropped by `clearGraph`, and its layouts go with it.\nconst forceLayouts = new WeakMap<Graph, Map<string, LayoutResult>>()\n\n// Enough to hold the settings a comparison moves between; past that the oldest\n// goes, since a big graph's positions are megabytes.\nconst FORCE_LAYOUT_CACHE_SIZE = 4\n\nfunction forceLayoutsOf(graph: Graph) {\n  let cache = forceLayouts.get(graph)\n  if (!cache) {\n    cache = new Map()\n    forceLayouts.set(graph, cache)\n  }\n  return cache\n}\n\n// Re-anchoring builds a new Graph, and the force layout of it is the same\n// drawing: `anchorFromPaths` rewrites each node's `stable` and `samples` and\n// touches neither the ids, the lengths, the depths nor the edges, which are all\n// the engine reads. So the layouts follow the graph they were computed for\n// rather than being thrown away with it.\nfunction inheritForceLayouts(from: Graph, to: Graph) {\n  const cache = forceLayouts.get(from)\n  if (cache && from !== to) {\n    forceLayouts.set(to, cache)\n  }\n}\n\nfunction remember(\n  cache: Map<string, LayoutResult>,\n  key: string,\n  result: LayoutResult,\n) {\n  if (cache.size >= FORCE_LAYOUT_CACHE_SIZE) {\n    cache.delete(cache.keys().next().value!)\n  }\n  cache.set(key, result)\n}\n\nexport default function stateModelFactory() {\n  return types\n    .compose(\n      'GraphGenomeView',\n      BaseViewModel,\n      RenderLifecycleMixin(),\n      types.model({\n        type: types.literal('GraphGenomeView'),\n        // FMMM's iteration budget, 0-4, the same scale Bandage's own settings\n        // dialog exposes: 3+1 iterations at 0, 15+10 at 1, 30+20 at 2, 60+40 at\n        // 3, 120+60 at 4 (BandageNG layout/graphlayoutworker.cpp).\n        //\n        // 2 because that is what the engine we vendor ships as its default\n        // (`graphLayoutQuality = IntSetting(2, 0, 4)`, program/settings.cpp).\n        // This was 1 for no recorded reason, i.e. one step BELOW upstream, and a\n        // first sight of any graph is the default: review kept asking whether\n        // the drawing could be iterated more (\"are you sure you can't iterate it\n        // more times for better layout?\") of figures that were simply on a lower\n        // setting than the tool they come from. Cost at the sizes this view\n        // draws is milliseconds, and the header states the layout time so the\n        // difference is visible rather than asserted.\n        layoutQuality: types.optional(types.number, 2),\n        linearLayout: types.optional(types.boolean, false),\n        // Which drawing to use; the modes and their fallbacks are described in\n        // LAYOUT_MODES. Default 'force' is the Bandage FMMM drawing, i.e. what\n        // someone who has seen a pangenome graph before expects to see.\n        //\n        // The default used to be 'auto', the reference-anchored layout, on the\n        // argument that lining the graph's x axis up with a linear view above it\n        // is what this view can do and Bandage cannot. Docs review disagreed\n        // twice, on figure after figure \u2014 \"the linear backbone is just\n        // confusing\", \"default to showing the bandage graphs over linear\n        // backbone in almost all cases\" \u2014 and the reason is that the anchored\n        // drawing looks like a track rather than a graph: a bubble collapses onto\n        // the reference axis, so the alternative alleles read as short bars\n        // hanging under a line rather than as two routes through the same locus.\n        // The anchored modes stay one dropdown click away, and are what the\n        // hover-sync and one-row-per-strain figures select deliberately.\n        layoutMode: types.optional(\n          types.enumeration(LAYOUT_MODE_VALUES),\n          'force',\n        ),\n        // 'auto' rather than a colour, resolved by `effectiveColorScheme`. See\n        // COLOR_SCHEMES for why the default is not 'uniform' any more. A session\n        // that names a scheme keeps it \u2014 this only decides what an unstated one\n        // opens as.\n        colorScheme: types.optional(\n          types.enumeration(COLOR_SCHEME_VALUES),\n          'auto',\n        ),\n        // How far the force layout opens a bubble, which on a variation graph is\n        // the difference between a legible drawing and a rope. See\n        // BUBBLE_SPREADS; no effect on the reference-anchored layouts, which\n        // place a node from its coordinates rather than from a force sim.\n        bubbleSpread: types.optional(\n          types.enumeration(BUBBLE_SPREAD_VALUES),\n          'auto',\n        ),\n        // Node thickness by depth, Bandage's own device; see NODE_WIDTHS.\n        nodeWidth: types.optional(\n          types.enumeration(NODE_WIDTH_VALUES),\n          'depth',\n        ),\n        // Whether the node layouts draw each bubble as a halo along its nodes\n        // with a label that opens it. The variant map draws glyphs instead.\n        showBubbles: types.optional(types.boolean, true),\n        showDeletionEdges: types.optional(types.boolean, false),\n        // The session's genes drawn onto the backbone: exons along the nodes\n        // that carry them, names pinned at their midpoints. See genes/.\n        showGenes: types.optional(types.boolean, true),\n        // Which track the genes come from; empty picks the assembly's\n        // annotation track (pickGeneTrack).\n        geneTrackId: types.optional(types.string, ''),\n        // Which track the walk rows read tandem repeat arrays from; empty\n        // picks a track whose name says repeats (pickRepeatTrack).\n        repeatTrackId: types.optional(types.string, ''),\n        // The array the walk rows measure between and tile by, as\n        // RepeatArray.key; empty measures the whole window untiled.\n        repeatKey: types.optional(types.string, ''),\n        // Samples whose walks the walk rows show, by the name before the\n        // haplotype number; undefined shows every walk the cut holds.\n        walkRowSamples: types.maybe(types.frozen<string[]>()),\n        // One walk, by its path name, lifted out of the drawing: its nodes and\n        // links keep their ink and the rest fades. Empty lifts none.\n        highlightedPath: types.optional(types.string, ''),\n        // Which of a general GFA's paths the anchored layouts put on x. A path\n        // GFA's names are arbitrary and none of them is marked as the\n        // reference, so this is a choice; empty means \"infer\", which is the\n        // assembly a subgraph was cut against, and the first path in the file\n        // for a whole-file import. No effect on an rGFA, whose segments carry\n        // their own coordinates. See pathAnchoring.ts.\n        referencePath: types.optional(types.string, ''),\n        // Whether the toolbar spells out `fetch 12371ms \u00B7 layout 4ms \u00B7 geom 9ms`.\n        // Off by default because it was in the toolbar of every published graph\n        // figure, where a machine's fetch time is noise a reader has to skip\n        // past. The numbers themselves are always on the element as `data-*`\n        // attributes, which is what browser tests assert against, so hiding the\n        // text costs no coverage.\n        showPerf: types.optional(types.boolean, false),\n        contigThickness: types.optional(types.number, 6),\n        connectorThickness: types.optional(types.number, 2),\n        darkMode: types.optional(types.boolean, false),\n        scale: types.optional(types.number, 1),\n        translateX: types.optional(types.number, 0),\n        translateY: types.optional(types.number, 0),\n        drawPaths: types.optional(types.boolean, false),\n        // Ceiling on the drawing pane, in css px, for a session or a figure that\n        // wants a shorter one than the drawing asks for. Unset means the built-in\n        // MAX_CANVAS_HEIGHT, which is what every existing session gets.\n        //\n        // Why this is a knob rather than a smaller default: the pane is as tall\n        // as the drawing's own aspect ratio (see canvasHeight), which is right \u2014\n        // a graph that is twice as tall as it is wide should not be squeezed\n        // into a strip. But one very long node in a cut of short ones makes that\n        // aspect ratio all arc: the HPRC CHM13 figure draws a 142 kb allele\n        // among sub-kb backbone segments, pins the 600 px ceiling and spends\n        // most of it on the loop, with the chain squashed along the bottom edge.\n        // Lowering the ceiling there scales the whole drawing down, which is\n        // exactly the trade that figure wants and the wrong default for a graph\n        // whose height is carrying information.\n        paneHeight: types.maybe(types.number),\n        // Raise to draw a bigger graph than the default budget allows; see\n        // DEFAULT_MAX_GRAPH_NODES for what the numbers cost.\n        maxGraphNodes: types.optional(types.number, DEFAULT_MAX_GRAPH_NODES),\n        // The bp ceiling on a cut, which is a PROXY for node count and only a\n        // good one at fine granularity: on a base-level index 5 Mb is already\n        // thousands of segments, so refusing by span is refusing by cost. A\n        // level-of-detail tier breaks the proxy \u2014 a whole 249 Mb human\n        // chromosome is 474 nodes off the hosted HPRC tier \u2014 so a session that\n        // knows which granularity it is pointed at can raise this. The real\n        // backstop stays `maxGraphNodes`, which counts what actually came back.\n        //\n        // The launch MENUS keep the constant deliberately (launchSubgraphView):\n        // a user rubber-banding 249 Mb over a fine index should still be told\n        // no, because nothing there has said the track is coarse.\n        maxRegionBp: types.optional(types.number, MAX_GRAPH_REGION_BP),\n        loadedTrackId: types.optional(types.string, ''),\n        loadedRegion: types.maybe(\n          types.frozen<{\n            refName: string\n            assemblyName: string\n            start: number\n            end: number\n          }>(),\n        ),\n        // The haplotypes the cut is for, lane assembly names or PanSN\n        // prefixes, beside the region so a re-cut asks for the same set;\n        // undefined is every haplotype. Only the GBZ cut reads it.\n        subgraphHaplotypes: types.maybe(types.frozen<string[]>()),\n        // How far the cut follows links past the segments the region's own\n        // links name, defaulting to one hop because at 0 the drawing is wrong\n        // rather than merely sparse. A detour that leaves the backbone before\n        // the window and rejoins after it has its interior indexed only under\n        // its own stable sequence, which no query on the reference reaches, so an\n        // arm that bypasses 21 kb of reference arrives as a 43 bp fragment: the\n        // one bubble draws as two unrelated small insertions, and nothing on\n        // screen says they are the same event. One hop closes those, and that is\n        // the whole of what a reader means by seeing the local graph.\n        //\n        // The cost is queries rather than nodes, and a hop only follows alleles\n        // (offReference in RgfaTabixAdapter, which is gfabase's stop-at-cutpoints\n        // rule read off the rank tag), so it is bounded by the off-reference\n        // segments the cut already reached and it does not walk the backbone out\n        // of the window. Measured: the E. coli paa locus goes 14 segments at 0 to\n        // 17 at 1 and stays at 17 at 2, so the cut closes and stays closed.\n        // HPRC's amylase window goes 63 to 78 to 92, because there the alleles\n        // have alleles; wall-clock is flat across all three, the remote index\n        // dominating. 0 stays available for a graph where even that is too much.\n        //\n        // Still not a graph-aware cut: a complete one needs the bubble\n        // decomposition (`gfatools view -R`, whose bubble rows state their own\n        // member segments) rather than a frontier, which is the follow-up noted\n        // in the adapter.\n        subgraphContext: types.optional(types.number, 1),\n        // Whole-GFA source loaded on attach \u2014 lets a GraphGenomeView be\n        // instantiated declaratively from a session/config snapshot.\n        gfaLocation: types.maybe(types.frozen<FileLocation>()),\n        // The reference span the reference-position ramp runs over. A graph cut\n        // from a track already states one as `loadedRegion`; a file-loaded graph\n        // has no region at all, and this is how its snapshot can still put a\n        // linear track beside it on the same ramp \u2014 both painted from one pair\n        // of numbers rather than from the file's own measured extent.\n        colorDomain: types.maybe(\n          types.frozen<{ start: number; end: number }>(),\n        ),\n        // The linear view this graph was launched from, so a hovered node can\n        // draw its reference span there and vice versa. Written by the launch\n        // menu; see hoverSync/.\n        connectedViewId: types.maybe(types.string),\n        // Whether the cut came from the source track's `coarse` pair\n        // (RgfaTabixAdapter), so a restored session re-makes the cut it saved.\n        // No bp cap applies to that pair; maxGraphNodes counts what came back.\n        coarseCut: types.optional(types.boolean, false),\n      }),\n    )\n    .volatile(() => ({\n      graph: undefined as Graph | undefined,\n      layoutResult: undefined as LayoutResult | undefined,\n      // The bubble index rows over the cut window, when the source track has\n      // one beside its segments. Undefined for a graph with no index, which the\n      // variant map draws from `derivedBubbles` instead.\n      indexBubbles: undefined as MinigraphBubble[] | undefined,\n      // the genes over the cut window, read once per cut from the gene track\n      geneFeatures: undefined as GeneModel[] | undefined,\n      // the tandem repeat arrays over the cut window, from the repeat track\n      repeatArrays: undefined as RepeatArray[] | undefined,\n      // The graphs the open bubble was popped out of, outermost first, each\n      // with what closing back to it restores without a refetch. A stack so a\n      // popped superbubble can be mapped and popped again.\n      popStack: [] as {\n        graph: Graph\n        layoutMode: LayoutModeValue\n        label: string\n        indexBubbles: MinigraphBubble[] | undefined\n      }[],\n\n      // eslint-disable-next-line @typescript-eslint/no-unnecessary-type-assertion\n      error: undefined as unknown,\n      isLoading: false,\n      loadCanceled: false,\n      statusMessage: '',\n      hoveredNode: null as string | null,\n      hoveredEdge: null as number | null,\n      selectedNode: null as string | null,\n      viewportDirty: 0,\n      // Bumped when the layout's positions are mutated IN PLACE, which only a\n      // node drag does. Separate from `viewportDirty` because that one also\n      // fires on pan and zoom, and the things keyed off this \u2014 the two hit\n      // indexes and the label placement's per-layout caches \u2014 do not depend on\n      // the transform at all. Rebuilding a 12k-edge hit index because the user\n      // panned cost ~14 ms of the first mousemove after every gesture.\n      positionsVersion: 0,\n      // Bumped per upload, so the hover autorun re-states its highlights\n      // against the batch the renderer now holds.\n      geometryVersion: 0,\n      // The zoom and the window the current batch was built for; a pan that\n      // stays inside it needs no rebuild.\n      builtViewport: undefined as { scale: number; bounds: Bounds } | undefined,\n      draggingNode: null as string | null,\n      // Dragging the background rather than a node. Lives here beside\n      // draggingNode instead of in a component ref+state pair, so the two\n      // mutually exclusive drag modes are one piece of state read from one place.\n      isPanning: false,\n      // Who places the view. 'fit' refits it to every new layout, 'user' leaves\n      // it where a gesture or a restored session put it, and 'host' takes x\n      // from the linear view the pane sits in. Not derived from\n      // `isDefaultViewport`, which zoomToFit itself invalidates on its first\n      // run \u2014 that made the fit fire once against not-yet-measured dimensions\n      // and then never re-fit.\n      // eslint-disable-next-line @typescript-eslint/no-unnecessary-type-assertion\n      viewportOwner: 'fit' as ViewportOwner,\n      // the pane height a host holds, so a re-cut with more rows does not\n      // move the pane while the linear view above it is being dragged\n      hostPaneHeight: undefined as number | undefined,\n      cutNote: undefined as string | undefined,\n      recuts: 0,\n      viewportDirtyTimer: undefined as\n        ReturnType<typeof setTimeout> | undefined,\n      // 0 is never a live rAF handle, so it doubles as \"nothing pending\"\n      positionsDirtyFrame: 0,\n      // Performance instrumentation, surfaced in GraphStats for browser tests\n      // to assert against budgets. `fetchMs` is the GetSubgraph RPC round-trip,\n      // `layoutMs` is the Bandage FMMM compute time reported by the\n      // GraphComputeLayout RPC, `geometryMs` is the main-thread buildGeometry\n      // pass and `geometryStrokeCount` the node strokes it produced.\n      lastFetchMs: undefined as number | undefined,\n      lastLayoutMs: undefined as number | undefined,\n      lastGeometryMs: undefined as number | undefined,\n      lastGeometryStrokeCount: undefined as number | undefined,\n    }))\n    .views(self => ({\n      get nodeById() {\n        if (self.graph) {\n          const m = new Map<string, GraphNode>()\n          for (const n of self.graph.nodes) {\n            m.set(n.id, n)\n          }\n          return m\n        }\n        return undefined\n      },\n      // bp per node id, which is all the label overlay needs of a GraphNode.\n      // Held here rather than rebuilt in the component: that render runs on\n      // every pan, and the map is a fact about the graph (measured 6.9 ms an\n      // allocation on a 30k-node cut).\n      get nodeLengths() {\n        const m = new Map<string, number>()\n        for (const n of self.graph?.nodes ?? []) {\n          m.set(n.id, n.length)\n        }\n        return m\n      },\n      get nodeCount() {\n        return self.graph?.nodes.length ?? 0\n      },\n      get edgeCount() {\n        return self.graph?.edges.length ?? 0\n      },\n      get pathCount() {\n        return self.graph?.paths?.length ?? 0\n      },\n      get hasGraph() {\n        return self.graph !== undefined\n      },\n      // The app-wide readiness contract (AppReadyMarker, @jbrowse/capture)\n      // reads this: a declared source still fetching, or a graph whose\n      // geometry has not been built yet.\n      get showLoading() {\n        return (\n          self.error === undefined &&\n          (self.isLoading ||\n            ((self.graph !== undefined ||\n              !!(self.loadedTrackId && self.loadedRegion) ||\n              !!self.gfaLocation) &&\n              self.lastGeometryStrokeCount === undefined))\n        )\n      },\n      get canRetryLoad() {\n        return !!(self.loadedTrackId && self.loadedRegion) || !!self.gfaLocation\n      },\n      // Only before anything is drawn: past that point a reload is superseded\n      // by the next setting change, and stopping one midway would leave a new\n      // graph under the previous graph's layout.\n      get canCancelLoad() {\n        return self.isLoading && !self.layoutResult\n      },\n      // Whether the drawing on screen is the FMMM engine's. False before there\n      // is a graph, since nothing is drawn by anything yet.\n      //\n      // Read by the settings that only the engine looks at: the layout quality\n      // and the bubble spread do nothing at all to an anchored drawing, which\n      // places a node from its coordinates, and the guide says so in prose\n      // precisely because the dialog did not. A control that silently does\n      // nothing is worse than one that says it cannot \u2014 the same rule the\n      // `drawPaths` switch already follows.\n      get usesLayoutEngine() {\n        return self.graph\n          ? modeUsesLayoutEngine(self.layoutMode, self.graph)\n          : false\n      },\n      // A rank-0 backbone to draw x against, whether the segments declared it\n      // (rGFA) or a path walk derived it. Only a GFA with neither tags nor\n      // paths has no backbone at all, and there force is the one honest layout.\n      get canAnchorLayout() {\n        return self.graph?.nodes.some(n => n.stable?.rank === 0) ?? false\n      },\n      // The paths this graph could be anchored on, for the picker. Empty for an\n      // rGFA, which has no P/W records and needs none.\n      get anchorPaths() {\n        return self.graph?.anchorPaths ?? []\n      },\n      // Which haplotype each ribbon colour belongs to, in the order the file\n      // states the paths \u2014 the same list and the same order the geometry keys\n      // its colours off, so the key cannot name a colour that is not drawn.\n      // Empty unless the ribbons are actually on: a colour key beside a drawing\n      // with no colours in it is a legend for nothing.\n      get pathLegend() {\n        const paths = self.graph?.paths\n        return self.drawPaths && paths && pathColorsLegible(paths.length)\n          ? pathLegend(paths)\n          : []\n      },\n      // Every walk the graph carries, named for a picker, whatever the count.\n      get walkChoices() {\n        const paths = self.graph?.paths\n        return paths?.length ? pathLegend(paths) : []\n      },\n      // The lifted walk, or undefined when none is named or the graph on\n      // screen does not carry the one that was.\n      get walkHighlight() {\n        return self.graph && self.highlightedPath\n          ? walkHighlight(self.graph, self.highlightedPath)\n          : undefined\n      },\n      // Whether the drawing is actually painted per path, which is not the same\n      // question as whether the user asked for it: past MAX_PATH_COLORS the\n      // colours say nothing and cost a stroke per path per edge. A bare getter\n      // returning a resolved value, the same shape and for the same reason as\n      // `effectiveColorScheme` \u2014 every consumer of a path colour reads this\n      // one, so the geometry, the hit index and the key cannot disagree about\n      // whether there are any. The switch in the settings dialog reads the raw\n      // `drawPaths`, so the user's choice stays visible as the choice it is.\n      get effectiveDrawPaths() {\n        return (\n          self.drawPaths && pathColorsLegible(self.graph?.paths?.length ?? 0)\n        )\n      },\n      // The path x is currently drawn on, which is not necessarily the one\n      // `referencePath` asked for: an unmatched name falls back rather than\n      // leaving the graph unanchored, and the picker has to show what happened.\n      get activeReferencePath() {\n        return self.graph?.referencePath\n      },\n      // What to anchor on. An explicit choice wins; otherwise a graph cut from\n      // a track is anchored on the assembly it was cut against, which is the\n      // one the linear view beside it is showing.\n      get preferredReferencePath() {\n        return self.referencePath === ''\n          ? self.loadedRegion?.assemblyName\n          : self.referencePath\n      },\n      // The span the reference-position ramp runs over: what the snapshot\n      // stated, else the region the graph was cut from. Undefined only for a\n      // file-loaded graph that states neither, where the ramp falls back to the\n      // drawn extent (computeReferenceRamp). A follow's re-cut moves\n      // loadedRegion, so the ramp re-spans every new cut, and the lane above\n      // with it.\n      get rampDomain() {\n        return self.colorDomain ?? self.loadedRegion\n      },\n      // The scheme the renderer actually paints with, which is the raw prop\n      // unless it is 'auto'. A bare getter returns a resolved value (root\n      // CLAUDE.md): every consumer of a colour reads this one, and the two\n      // dropdowns read `colorScheme` so \"Auto\" stays visible as the choice it\n      // is.\n      //\n      // 'auto' asks the GRAPH, not the layout. A hue along the reference is\n      // meaningful whenever the segments have reference coordinates \u2014\n      // `anchoredBy` is exactly that question \u2014 and a force-directed drawing of\n      // an rGFA is the case that proves it: the layout has no reference axis and\n      // the ramp still says where on the reference each node came from, which is\n      // the only quantity a linear track beside it can be painted with too.\n      get effectiveColorScheme(): ResolvedColorScheme {\n        return self.colorScheme !== 'auto'\n          ? self.colorScheme\n          : self.graph?.anchoredBy\n            ? 'reference-position'\n            : 'uniform'\n      },\n      get nodePositions() {\n        return self.layoutResult?.nodePositions\n      },\n      // Empty rather than undefined: every consumer maps over it, and a layout\n      // with no row structure (FMMM) is a normal state, not a missing one.\n      get rowLabels() {\n        return self.layoutResult?.rowLabels ?? []\n      },\n      // Deletions the layout found inside an allele, empty for the same reason\n      // rowLabels is: a layout drawn at sequence scale states none, because\n      // there a node's drawn extent already IS its length. `deletions` beside\n      // this one is the bare-edge kind, which every layout has.\n      get alleleDeletions() {\n        return self.layoutResult?.alleleDeletions ?? []\n      },\n      // Whether the current layout states y in screen px rather than in the same\n      // units as x (LayoutResult.pixelRows). Everything that has to put the two\n      // axes in one expression reads this through scaleX/scaleY.\n      get pixelRows() {\n        return self.layoutResult?.pixelRows ?? false\n      },\n      get zoomPercent() {\n        return `${(self.scale * 100).toFixed(1)}%`\n      },\n      // True while the persisted transform is still the schema default, i.e.\n      // neither a restored session nor the user has positioned this view yet,\n      // so an incoming layout is free to zoom-to-fit.\n      get isDefaultViewport() {\n        return (\n          self.scale === 1 && self.translateX === 0 && self.translateY === 0\n        )\n      },\n    }))\n    .views(self => ({\n      get poppedFrom() {\n        return self.popStack.at(-1)\n      },\n      // The bubbles the graph itself states, for a graph with no index: a GBZ\n      // cut, a pggb file, the inside of a popped bubble.\n      get derivedBubbles() {\n        return self.graph ? bubblesFromGraph(self.graph) : []\n      },\n    }))\n    .views(self => ({\n      // What the variant map draws. Index rows win where both exist: gfatools\n      // measured every allele, the layered order only bounds them.\n      get bubbles() {\n        return self.indexBubbles?.length\n          ? self.indexBubbles\n          : self.derivedBubbles\n      },\n    }))\n    .views(self => ({\n      // As written: a session track is a plain object until something\n      // hydrates it, so a slot left at its default reads undefined here.\n      get sourceAdapter() {\n        const track = getSession(self).tracks.find(\n          t => t.trackId === self.loadedTrackId,\n        )\n        return track\n          ? (readConfObject(track, 'adapter') as Record<string, unknown>)\n          : undefined\n      },\n      get assemblyTrackChoices() {\n        const region = self.loadedRegion\n        if (!region) {\n          return []\n        }\n        return getSession(self)\n          .tracks.filter(t =>\n            (readConfObject(t, 'assemblyNames') as string[]).includes(\n              region.assemblyName,\n            ),\n          )\n          .map(t => ({\n            trackId: t.trackId as string,\n            name: readConfObject(t, 'name') as string,\n            adapterType: (readConfObject(t, 'adapter') as { type: string })\n              .type,\n          }))\n      },\n    }))\n    .views(self => ({\n      get geneTrackChoices() {\n        return self.assemblyTrackChoices.filter(t =>\n          GENE_ADAPTER_TYPES.has(t.adapterType),\n        )\n      },\n      // The session's feature tracks a repeat annotation could be, for the\n      // picker; which one is read is pickRepeatTrack's choice.\n      get repeatTrackChoices() {\n        return self.assemblyTrackChoices.filter(t =>\n          REPEAT_ADAPTER_TYPES.has(t.adapterType),\n        )\n      },\n      // The arrays over the window that state a unit, for the Repeat picker.\n      get repeatChoices() {\n        return self.repeatArrays ?? []\n      },\n    }))\n    .views(self => ({\n      get repeatTrack() {\n        return pickRepeatTrack(self.repeatTrackChoices, self.repeatTrackId)\n      },\n      get selectedRepeat() {\n        return self.repeatChoices.find(r => r.key === self.repeatKey)\n      },\n    }))\n    .views(self => ({\n      get nodeNeighbors() {\n        return self.graph ? buildNeighbors(self.graph) : undefined\n      },\n      // How far each node's ink reaches from its centreline, for the hit test:\n      // the widths the geometry draws with, from the same function.\n      get nodeInk(): NodeInk {\n        const { contigThickness, nodeWidth, nodeById } = self\n        const mean = self.graph ? meanDepth(self.graph) : 0\n        return {\n          maxHalfWidthPx: maxNodeWidthPx(contigThickness, nodeWidth) / 2,\n          halfWidthPx: id => {\n            const node = nodeById?.get(id)\n            return node\n              ? nodeWidthPx(node, contigThickness, nodeWidth, mean) / 2\n              : contigThickness / 2\n          },\n        }\n      },\n      // Links that skip reference sequence, i.e. the deletions this graph\n      // holds. Computed once per graph rather than per geometry rebuild: it is\n      // a pass over the edges and the drawing rebuilds on every pan.\n      // Walk rows state what each walk skips as its own bar length, so the arcs\n      // over the backbone would only say it again, across the bars.\n      get deletions() {\n        return self.graph && self.layoutMode !== 'walkrows'\n          ? deletionEdges(self.graph)\n          : []\n      },\n      // One bar per haplotype walk on its own bp axis, for the walk-rows\n      // overlay. Empty under every other layout.\n      get walkRowBars() {\n        if (self.layoutMode !== 'walkrows' || !self.graph) {\n          return undefined\n        }\n        const repeat = self.selectedRepeat\n        const bars = repeat\n          ? walkRows(self.graph, repeat, repeat.unit)\n          : walkRows(self.graph, self.loadedRegion)\n        if (!bars) {\n          return undefined\n        }\n        const samples = self.walkRowSamples\n        const rows = samples\n          ? bars.rows\n              .filter(r => samples.includes(r.sample))\n              .sort(\n                (a, b) =>\n                  samples.indexOf(a.sample) - samples.indexOf(b.sample) ||\n                  a.label.localeCompare(b.label),\n              )\n          : bars.rows\n        return { ...bars, rows: withCalls(rows, repeat?.calls) }\n      },\n      // The labels drawn beside the rows. Walk rows label from the bars\n      // themselves, which follow the selected repeat and sample filter that\n      // the layout, run once per cut, cannot.\n      get drawnRowLabels() {\n        const bars = this.walkRowBars\n        return bars\n          ? [bars.reference, ...bars.rows].map((row, i) => ({\n              label: row.label,\n              y: i * ROW_HEIGHT_PX,\n            }))\n          : self.rowLabels\n      },\n      // Each bubble in the window with what it is, for the variant map's\n      // glyphs on the reference line.\n      get bubbleGlyphs() {\n        const bubbles = self.layoutMode === 'variants' ? self.bubbles : []\n        return bubbles.map(bubble => ({\n          bubble,\n          ...classifyBubble(bubble),\n        }))\n      },\n      // Exons and names on the backbone, in layout units. Reads\n      // positionsVersion so a dragged node takes its exons with it.\n      get genePins() {\n        dependOn(self.positionsVersion)\n        const positions = self.layoutResult?.nodePositions\n        return self.showGenes &&\n          self.layoutMode !== 'variants' &&\n          self.layoutMode !== 'walkrows' &&\n          self.graph &&\n          self.geneFeatures &&\n          positions\n          ? genePins(self.graph, self.geneFeatures, positions)\n          : []\n      },\n      // The same bubbles over every other layout, as halos along their nodes.\n      // Reads positionsVersion so a dragged node takes its halo with it.\n      get bubbleHalos() {\n        dependOn(self.positionsVersion)\n        const positions = self.layoutResult?.nodePositions\n        if (\n          !self.showBubbles ||\n          self.layoutMode === 'variants' ||\n          self.layoutMode === 'walkrows' ||\n          !self.graph ||\n          !positions\n        ) {\n          return []\n        }\n        const labels = new Map(self.walkChoices.map(c => [c.name, c.label]))\n        return bubbleHalos(\n          self.graph,\n          self.bubbles,\n          positions,\n          name => labels.get(name) ?? name,\n        )\n      },\n      // Every node's midpoint on the reference plus the interval the hue ramps\n      // over \u2014 what `reference-position` paints from, and undefined under every\n      // other scheme so the walk is never run for a colouring that ignores it.\n      //\n      // Here for the same reason `deletions` is, only more so: deriving it is a\n      // bounded neighbour walk PER NODE (referenceMidpoints), it depends on\n      // nothing the transform touches, and it was being redone inside every\n      // geometry rebuild \u2014 1.6 ms at 1.5k nodes, 45 ms at 30k, on a pass that\n      // reruns on each debounced pan and each drag frame. `reference-position`\n      // is also what `auto` resolves to on any anchored graph, so this was the\n      // default path rather than an opt-in one.\n      get referenceRamp() {\n        return self.effectiveColorScheme === 'reference-position' && self.graph\n          ? computeReferenceRamp(self.graph, self.rampDomain)\n          : undefined\n      },\n      // The assemblies this view is showing, which is the interface every\n      // assembly-aware piece of the app looks for \u2014 `viewTitle` first among\n      // them, which falls back through it and otherwise names the view\n      // \"Untitled view\". Every published HPRC figure showed that.\n      // `launchSubgraphView` only avoids it by writing `displayName`, so a\n      // declaratively-instantiated view (a session snapshot, a figure spec) got\n      // the fallback.\n      //\n      // A whole-file import has none: its stable names are a GFA's business and\n      // need not name anything the session has loaded. Empty rather than\n      // undefined, matching what an LGV with no displayed regions reports.\n      get assemblyNames() {\n        const region = self.loadedRegion\n        return region ? [region.assemblyName] : []\n      },\n      // Screen px per layout unit, per axis. `scale` is the x zoom and the whole\n      // of what a user's wheel moves; y is a second question the layout answers\n      // for itself.\n      //\n      // On a row layout the pitch is already in screen px (rowSpacing.ts), so\n      // scaleY is 1 and stays 1: rows are a track's row height, unchanged by\n      // zoom, and the backbone under them zooms the way the ruler above it does.\n      // On an isotropic layout (FMMM) x and y are one simulation space and one\n      // number scales both, exactly as before.\n      //\n      // Everything that mixes the two axes takes their ratio as `yToX`\n      // (scaleY / scaleX) \u2014 see computeEdgeCurves.\n      get scaleX() {\n        return axisScaleOf(self.scale, self.pixelRows).scaleX\n      },\n      get scaleY() {\n        return axisScaleOf(self.scale, self.pixelRows).scaleY\n      },\n      // The pair, for everything that draws or hit-tests. Handed over as one\n      // value on purpose: every consumer needs both, and passing them separately\n      // let a caller supply the x scale and default y, which compiles and draws\n      // a wrong picture. See AxisScale.\n      get axisScale() {\n        return axisScaleOf(self.scale, self.pixelRows)\n      },\n      // Extent of the drawing in layout units, shared by the pane height and\n      // zoomToFit. On a reference-bp layout x is the cut window rather than\n      // how far the drawing reaches: an allele anchored far outside it is a\n      // fact about the graph, not a reason to draw the window at 6% of the\n      // frame. A popped bubble fits to what it drew. Walk rows reach as far as\n      // the bars on screen, which a repeat pick or a sample filter narrows\n      // after the layout ran.\n      get layoutBounds() {\n        let bounds:\n          { minX: number; minY: number; w: number; h: number } | undefined\n        if (self.layoutResult) {\n          let minX = Infinity\n          let minY = Infinity\n          let maxX = -Infinity\n          let maxY = -Infinity\n          for (const segments of Object.values(\n            self.layoutResult.nodePositions,\n          )) {\n            for (const seg of segments) {\n              minX = Math.min(minX, seg.x)\n              minY = Math.min(minY, seg.y)\n              maxX = Math.max(maxX, seg.x)\n              maxY = Math.max(maxY, seg.y)\n            }\n          }\n          const region =\n            self.layoutResult.referenceAxis && self.popStack.length === 0\n              ? self.loadedRegion\n              : undefined\n          if (region && region.end > region.start) {\n            minX = region.start\n            maxX = region.end\n          }\n          const bars = this.walkRowBars\n          const extent =\n            bars && self.layoutResult.extent\n              ? walkRowsExtent(bars)\n              : self.layoutResult.extent\n          if (extent) {\n            maxX = Math.max(maxX, extent.maxX)\n            maxY = Math.max(maxY, extent.maxY)\n          }\n          bounds = { minX, minY, w: maxX - minX, h: maxY - minY }\n        }\n        return bounds\n      },\n      // The pane is as tall as the drawing, rather than a fixed box the drawing\n      // floats in the middle of.\n      //\n      // A row layout says how tall it is outright: rows are px, so the drawing's\n      // height is the row count times the pitch and this is a sum, not a\n      // derivation. It used to be derived from the drawing's ASPECT RATIO\n      // against the x-fit scale, because y was in bp and a height in px did not\n      // exist until a scale was chosen \u2014 which is also why a ceiling had to be\n      // put on the row pitch to stop tall graphs from binding the fit on the\n      // wrong axis. Both are gone with the unit.\n      //\n      // An isotropic layout still has no height of its own and keeps the aspect\n      // derivation. It reads neither `scale` nor the height it is replacing, so\n      // zoomToFit consumes this without feeding back into it.\n      get canvasHeight() {\n        if (\n          self.viewportOwner === 'host' &&\n          self.hostPaneHeight !== undefined\n        ) {\n          return self.hostPaneHeight\n        }\n        const bounds = this.layoutBounds\n        const usableWidth = self.width - FIT_PADDING * 2\n        // `paneHeight` replaces the built-in ceiling rather than adding a\n        // second clamp under it, and the floor still wins: a pane shorter than\n        // MIN_CANVAS_HEIGHT leaves no room to hover a node and read its\n        // tooltip, which is the reason that floor exists.\n        const ceiling = Math.max(\n          MIN_CANVAS_HEIGHT,\n          self.paneHeight ?? MAX_CANVAS_HEIGHT,\n        )\n        if (!bounds) {\n          return ceiling\n        }\n        if (self.pixelRows) {\n          // The variant map's drawing is one line; its glyphs and labels are\n          // painted above it by the overlay and need the room a row layout\n          // would give to rows.\n          const floor =\n            self.layoutMode === 'variants'\n              ? VARIANT_MAP_HEIGHT\n              : MIN_CANVAS_HEIGHT\n          return Math.min(ceiling, Math.max(floor, bounds.h + FIT_PADDING * 2))\n        }\n        return bounds.w > 0 && usableWidth > 0\n          ? Math.min(\n              ceiling,\n              Math.max(\n                MIN_CANVAS_HEIGHT,\n                (bounds.h * usableWidth) / bounds.w + FIT_PADDING * 2,\n              ),\n            )\n          : ceiling\n      },\n    }))\n    .views(self => ({\n      get geneTrack() {\n        return pickGeneTrack(self.geneTrackChoices, self.geneTrackId)\n      },\n      // Which of `graph.edges` are deletions, and what each one bypasses, keyed\n      // the way the geometry and the hit index address an edge. One map per\n      // graph rather than per rebuild, since both of those take it on every\n      // pan.\n      get deletionEdgeIndexes() {\n        return new Map(self.deletions.map(d => [d.edgeIndex, d.bypassed]))\n      },\n      get hiddenEdgeIndexes() {\n        return new Set(\n          self.showDeletionEdges ? [] : self.deletions.map(d => d.edgeIndex),\n        )\n      },\n      // The interval the reference-position ramp runs over, for the key beside\n      // the drawing, and undefined when no key should be drawn. Two tutorials\n      // carry \"red to magenta is left to right of the cut window\" as a sentence\n      // in prose because nothing on screen said it.\n      //\n      // Read off the ramp the drawing is actually painted with rather than\n      // re-derived from the domain, so the key cannot come to describe a\n      // different interval from the hues beside it \u2014 and so a graph that states\n      // no domain, whose interval has to be measured, does not pay for a second\n      // neighbour walk to say what the first one already worked out.\n      get referenceRampDomain() {\n        const ramp = self.referenceRamp\n        return ramp\n          ? { start: ramp.start, end: ramp.start + ramp.span }\n          : undefined\n      },\n      // The reference interval of the hovered node, for a connected linear view\n      // to highlight. Only a graph cut from a track has one: a whole-file import\n      // has no region, and its stable names need not name anything in a loaded\n      // assembly.\n      get hoverHighlight() {\n        let result:\n          | {\n              refName: string\n              assemblyName: string\n              start: number\n              end: number\n            }\n          | undefined\n        const region = self.loadedRegion\n        const nodeId = self.hoveredNode\n        const nodeById = self.nodeById\n        const neighbors = self.nodeNeighbors\n        if (region && nodeId !== null && nodeById && neighbors) {\n          const span = nodeReferenceSpan({ nodeId, nodeById, neighbors })\n          if (span) {\n            result = {\n              refName: region.refName,\n              assemblyName: region.assemblyName,\n              ...span,\n            }\n          }\n        }\n        return result\n      },\n    }))\n    .views(self => ({\n      // Every assembly this graph names a segment from, with the locus each one\n      // contributes here. rGFA's SN tag is what makes this knowable: the graph\n      // states its own contributors, so the view can offer a way out to each of\n      // them without consulting an alignment.\n      //\n      // Gaps larger than the backbone span split a contributor's segments into\n      // separate loci and the widest wins, so a sample that also contributes\n      // sequence from a distant duplication is launched at the locus on screen\n      // rather than at the union of the two.\n      get contributingAssemblies() {\n        const graph = self.graph\n        const backbone = graph ? backboneNodes(graph) : []\n        return graph\n          ? contributingAssemblies(graph, {\n              maxGap: backbone.length > 0 ? backboneSpan(backbone) : Infinity,\n            })\n          : []\n      },\n    }))\n    .views(self => ({\n      // A node's PanSN sample as an assembly this session can open, or\n      // undefined. The graph's spelling and the assembly's need not agree:\n      // HPRC writes `CHM13` where the assembly is UCSC's `hs1`. The track the\n      // graph was cut from states that pairing in its `assemblyNameToPanSN`,\n      // so its map is read first, then `assemblyManager`'s names and aliases.\n      //\n      // `has` before `get`, deliberately: `get` reports an unknown name to\n      // `Core-handleUnrecognizedAssembly`, which asks every installed plugin to\n      // go supply it, and this is a probe run for hundreds of haplotypes per\n      // graph.\n      get assemblyResolver() {\n        const { assemblyManager } = getSession(self)\n        const panSN = self.sourceAdapter?.assemblyNameToPanSN as\n          Record<string, string> | undefined\n        const byPrefix = new Map(\n          Object.entries(panSN ?? {}).map(([asm, prefix]) => [prefix, asm]),\n        )\n        const loaded = (name: string | undefined) =>\n          name !== undefined && assemblyManager.has(name)\n            ? (assemblyManager.get(name)?.name ?? name)\n            : undefined\n        return (sample: string) =>\n          loaded(byPrefix.get(sample)) ?? loaded(sample)\n      },\n    }))\n    .views(self => ({\n      // The contributors a view can actually be opened on: those naming an\n      // assembly this session has loaded. Every strain of an E. coli pangenome\n      // demo is its own assembly, so all of them resolve; an HPRC graph names\n      // hundreds of haplotypes that no session loads, so only the reference\n      // does.\n      get launchableAssemblies() {\n        return resolveContributors(\n          withReferenceRegion(self.contributingAssemblies, self.loadedRegion),\n          self.assemblyResolver,\n        )\n      },\n      // Whether there is a linear view this graph may draw a highlight into \u2014\n      // the paired one, or the session's only one on the reference assembly.\n      // Read by the node menu, which offers the item only when it would land\n      // somewhere.\n      get canHighlightInLinearView() {\n        const region = self.loadedRegion\n        return (\n          region !== undefined &&\n          linearViewTarget({\n            views: [...getSession(self).views],\n            connectedViewId: self.connectedViewId,\n            assemblyName: region.assemblyName,\n          }) !== undefined\n        )\n      },\n      // Where one node can be opened: on its own assembly, and on the reference\n      // the graph was cut against. Both are padded to a readable window \u2014 a\n      // base-level allele is a few bp, and a linear view framed on exactly that\n      // shows no context at all.\n      nodeLaunchTargets(nodeId: string) {\n        const node = self.nodeById?.get(nodeId)\n        const own = node ? nodeOwnLocation(node) : undefined\n        const ownAssembly = own\n          ? resolveLocationAssembly(self.assemblyResolver, own)\n          : undefined\n        const region = self.loadedRegion\n        const nodeById = self.nodeById\n        const neighbors = self.nodeNeighbors\n        const span =\n          region && nodeById && neighbors\n            ? nodeReferenceSpan({ nodeId, nodeById, neighbors })\n            : undefined\n        const onReference =\n          region && span\n            ? {\n                sample: region.assemblyName,\n                haplotype: undefined,\n                refName: region.refName,\n                ...span,\n              }\n            : undefined\n        return {\n          own:\n            own && ownAssembly\n              ? { location: paddedLocation(own), assembly: ownAssembly }\n              : undefined,\n          reference:\n            region && onReference\n              ? {\n                  location: paddedLocation(onReference),\n                  assembly: region.assemblyName,\n                }\n              : undefined,\n          // Unpadded: a mark is of the node, the same span its hover band\n          // draws. The padding above is room to read a view opened on it.\n          highlight:\n            region && onReference\n              ? { location: onReference, assembly: region.assemblyName }\n              : undefined,\n        }\n      },\n    }))\n    .views(self => ({\n      // The linear view's zoom past which a follow cuts the source track's\n      // coarse pair, or undefined for a track with none.\n      get coarseAboveBpPerPx() {\n        const coarse = self.sourceAdapter?.coarse as\n          { aboveBpPerPx?: unknown } | undefined\n        const above = coarse?.aboveBpPerPx\n        return typeof above === 'number' ? above : undefined\n      },\n    }))\n    .views(self => ({\n      get cutTier(): SubgraphTier {\n        return self.coarseCut && self.coarseAboveBpPerPx !== undefined\n          ? 'coarse'\n          : 'fine'\n      },\n    }))\n    .views(self => ({\n      get regionCapBp() {\n        return self.cutTier === 'coarse' ? Infinity : self.maxRegionBp\n      },\n    }))\n    .views(self => ({\n      // The linear view this pane draws inside, when a display hosts it: x is\n      // that view's window and the cut is re-made when the window leaves it.\n      // A pane that is a view of its own has none.\n      get host(): LinearHost | undefined {\n        let view: unknown\n        try {\n          view = getContainingView(self)\n        } catch {\n          return undefined\n        }\n        return view !== self && isLinearHost(view) ? view : undefined\n      },\n    }))\n    .views(self => ({\n      // Whether the host places x. Only a layout whose x is reference bp can\n      // take the window's transform; force, ordered and walk rows draw in\n      // their own coordinates inside the track, and a popped bubble is a\n      // picture of its own.\n      get hostPlacesX() {\n        const { host, loadedRegion: region, layoutResult: layout } = self\n        return (\n          host !== undefined &&\n          host.initialized &&\n          region !== undefined &&\n          layout?.referenceAxis === true &&\n          self.popStack.length === 0 &&\n          !host.dynamicBlocks.contentBlocks.some(\n            b => b.refName === region.refName && b.reversed,\n          )\n        )\n      },\n    }))\n    .views(self => ({\n      get hostFrame() {\n        const { host, loadedRegion } = self\n        return self.hostPlacesX && host && loadedRegion\n          ? hostFrame(host, loadedRegion)\n          : undefined\n      },\n    }))\n    .actions(self => ({\n      setError(error: unknown) {\n        self.error = error\n        self.isLoading = false\n      },\n      setStatusMessage(message: string) {\n        self.statusMessage = message\n      },\n      setFetchMs(ms: number) {\n        self.lastFetchMs = ms\n      },\n      setLayoutMs(ms: number) {\n        self.lastLayoutMs = ms\n      },\n      setGeometryMetrics(\n        ms: number,\n        strokeCount: number,\n        built: { scale: number; bounds: Bounds },\n      ) {\n        self.lastGeometryMs = ms\n        self.lastGeometryStrokeCount = strokeCount\n        self.builtViewport = built\n        self.geometryVersion++\n      },\n      setLayoutQuality(quality: number) {\n        self.layoutQuality = quality\n      },\n      setLinearLayout(linear: boolean) {\n        self.linearLayout = linear\n      },\n      setLayoutMode(mode: LayoutModeValue) {\n        self.layoutMode = mode\n      },\n      // Re-anchor in place rather than re-parsing: the coordinate walk is\n      // already recorded on the graph, and only which path counts as rank 0\n      // changes. The caller recomputes the layout, the same way it does after\n      // setLayoutMode. An rGFA is left alone \u2014 its coordinates are not derived.\n      setReferencePath(name: string) {\n        self.referencePath = name\n        const graph = self.graph\n        if (graph?.anchoredBy === 'paths') {\n          const reanchored = anchorFromPaths(graph, name)\n          inheritForceLayouts(graph, reanchored)\n          self.graph = reanchored\n        }\n      },\n      setDrawPaths(draw: boolean) {\n        self.drawPaths = draw\n      },\n      setShowPerf(show: boolean) {\n        self.showPerf = show\n      },\n      setColorScheme(scheme: ColorScheme) {\n        self.colorScheme = scheme\n      },\n      setBubbleSpread(spread: BubbleSpread) {\n        self.bubbleSpread = spread\n      },\n      setNodeWidth(width: NodeWidth) {\n        self.nodeWidth = width\n      },\n      setShowBubbles(show: boolean) {\n        self.showBubbles = show\n      },\n      setShowDeletionEdges(show: boolean) {\n        self.showDeletionEdges = show\n      },\n      setShowGenes(show: boolean) {\n        self.showGenes = show\n      },\n      setGeneTrackId(trackId: string) {\n        self.geneTrackId = trackId\n      },\n      setRepeatTrackId(trackId: string) {\n        self.repeatTrackId = trackId\n      },\n      setRepeatKey(key: string) {\n        self.repeatKey = key\n      },\n      setHighlightedPath(name: string) {\n        self.highlightedPath = name\n      },\n      // Undefined restores the built-in ceiling. Nothing recomputes: the pane\n      // reads canvasHeight and the drawing is placed by zoomToFit, which the\n      // caller runs if it wants the drawing refitted into the new pane.\n      setPaneHeight(px: number | undefined) {\n        self.paneHeight = px\n        if (self.viewportOwner === 'host') {\n          self.hostPaneHeight = px\n        }\n      },\n      // The track a hosted pane cuts from. The first settle makes the cut.\n      adoptTrack(trackId: string) {\n        if (self.loadedTrackId !== trackId) {\n          self.loadedTrackId = trackId\n          self.loadedRegion = undefined\n          self.coarseCut = false\n          self.graph = undefined\n          self.layoutResult = undefined\n        }\n      },\n      // The caller refetches \u2014 the number only describes how the next cut is\n      // made, and the graph on screen was cut with the old one.\n      setSubgraphContext(hops: number) {\n        self.subgraphContext = hops\n      },\n      // Same contract: the caller refetches, since the set describes the next\n      // cut and the graph on screen was cut for the old one.\n      setWalkRowSamples(samples: string[] | undefined) {\n        self.walkRowSamples = samples\n      },\n      setSubgraphHaplotypes(haplotypes: string[] | undefined) {\n        self.subgraphHaplotypes = haplotypes\n      },\n      // Same contract as setSubgraphContext: describes how the NEXT cut is\n      // gated, so the caller refetches. See the prop for why a session is\n      // allowed to move this and the launch menus are not.\n      setMaxRegionBp(bp: number) {\n        self.maxRegionBp = bp\n      },\n      // Pair with a linear view for the hover sync, without ever repointing an\n      // existing pairing: a graph launched *from* an LGV is already paired with\n      // it, and stealing that would break the sync the user came in on. So a\n      // launch out of the graph only claims the slot when it is empty.\n      //\n      // A slot naming a view that has been closed is empty too. Held, the view\n      // the graph opened next never got its hover, since a highlight is drawn\n      // only in the paired view.\n      pairWithLinearView(viewId: string) {\n        const paired = self.connectedViewId\n        const stillOpen =\n          paired !== undefined &&\n          withRows([...getSession(self).views]).some(\n            view => (view as { id?: unknown }).id === paired,\n          )\n        if (!stillOpen) {\n          self.connectedViewId = viewId\n        }\n      },\n      setHoveredNode(nodeId: string | null) {\n        self.hoveredNode = nodeId\n      },\n      setHoveredEdge(edgeIdx: number | null) {\n        self.hoveredEdge = edgeIdx\n      },\n      setSelectedNode(nodeId: string | null) {\n        self.selectedNode = nodeId\n      },\n      setDraggingNode(nodeId: string | null) {\n        self.draggingNode = nodeId\n      },\n      setPanning(panning: boolean) {\n        self.isPanning = panning\n      },\n      stopDragging() {\n        self.draggingNode = null\n        self.isPanning = false\n      },\n      // Everything that names a part of the current graph. Reset when the graph\n      // is replaced, and by clearGraph.\n      clearInteractionState() {\n        self.hoveredNode = null\n        self.hoveredEdge = null\n        self.selectedNode = null\n        self.draggingNode = null\n        self.isPanning = false\n      },\n      showNodeDetails(nodeId: string) {\n        const node = self.nodeById?.get(nodeId)\n        const nodeById = self.nodeById\n        const neighbors = self.nodeNeighbors\n        if (node && nodeById && neighbors) {\n          const session = getSession(self)\n          const region = self.loadedRegion\n          // refName/start/end are what makes the widget show a location rather\n          // than a bare id, and they are the same span the linear view\n          // highlights on hover.\n          const span = region\n            ? nodeReferenceSpan({ nodeId, nodeById, neighbors })\n            : undefined\n          if (isSessionModelWithWidgets(session)) {\n            session.showWidget(\n              session.addWidget('BaseFeatureWidget', 'baseFeature', {\n                featureData: {\n                  id: node.id,\n                  name: node.name,\n                  length: node.length,\n                  depth: node.depth,\n                  rank: node.stable?.rank,\n                  stableName: node.stable?.refName,\n                  // The assembly that contributed this segment, split off the\n                  // stable name. On an HPRC graph this is the only thing that\n                  // says which of 400-odd haplotypes an allele came from.\n                  contributingAssembly: nodeOwnLocation(node)?.sample,\n                  // and the haplotype, where the graph's names state one:\n                  // the assembly to load to open this node on its own\n                  // coordinates\n                  contributingHaplotype: nodeOwnLocation(node)?.haplotype,\n                  // Every assembly that traverses it, which is a different\n                  // question and one only a path GFA can answer. Absent on an\n                  // rGFA rather than approximated, so the two are never\n                  // confused: there `contributingAssembly` is first-seen, not\n                  // carriage.\n                  carriedBy: node.samples?.join(', '),\n                  ...(region && span\n                    ? {\n                        refName: region.refName,\n                        assemblyName: region.assemblyName,\n                        start: span.start,\n                        end: span.end,\n                      }\n                    : {}),\n                },\n              }),\n            )\n          }\n        }\n      },\n\n      // A gesture on a hosted graph moves the linear view, and the frame\n      // clock brings x back here; y stays the pane's own.\n      setTransform(s: number, tx: number, ty: number) {\n        const { host } = self\n        if (self.viewportOwner === 'host' && host) {\n          host.horizontalScroll(self.translateX - tx)\n        } else {\n          self.viewportOwner = 'user'\n          self.scale = clampZoom(s)\n          self.translateX = tx\n        }\n        self.translateY = ty\n      },\n      zoom(factor: number, centerX: number, centerY: number) {\n        const { host } = self\n        if (self.viewportOwner === 'host' && host) {\n          host.zoomTo(host.bpPerPx / factor, centerX)\n          return\n        }\n        self.viewportOwner = 'user'\n        const newScale = clampZoom(self.scale * factor)\n        const ratio = newScale / self.scale\n        self.scale = newScale\n        self.translateX = centerX - (centerX - self.translateX) * ratio\n        // y only follows when it is on the same scale. A row layout's y is\n        // screen px (scaleY === 1), so nothing about it changes as x zooms \u2014\n        // moving translateY by the ratio there would slide the rows off under\n        // the cursor while their pitch stayed put.\n        if (!self.pixelRows) {\n          self.translateY = centerY - (centerY - self.translateY) * ratio\n        }\n      },\n      setViewportDirty() {\n        self.viewportDirty++\n      },\n      // The positions themselves moved, as opposed to the window onto them.\n      setPositionsDirty() {\n        self.positionsVersion++\n      },\n      zoomToFit() {\n        // A layout is routinely degenerate on one axis: an anchored window\n        // holding only backbone segments puts every node on row 0. So each axis\n        // constrains the scale only when it has extent, and only a layout with\n        // no extent at all is unfittable. Requiring extent on both axes left\n        // that window at scale 1 with the graph off-screen entirely, since x\n        // there is reference bp.\n        const bounds = self.layoutBounds\n        const usableWidth = self.width - FIT_PADDING * 2\n        const usableHeight = self.canvasHeight - FIT_PADDING * 2\n        // A host owns x, so a fit while hosted places the rows only.\n        if (self.viewportOwner === 'host') {\n          if (bounds && usableHeight > 0) {\n            self.translateY = fittedTranslateY(\n              bounds,\n              usableHeight,\n              self.scaleY,\n            )\n          }\n          return\n        }\n        // Nothing to fit into before the canvas is measured. The autorun re-runs\n        // once width lands, so skipping here beats computing a negative scale\n        // and persisting that transform into the session snapshot.\n        if (\n          bounds &&\n          usableWidth > 0 &&\n          usableHeight > 0 &&\n          // A row layout needs x extent specifically: y cannot stand in for it\n          // there, having no scale left to solve for.\n          (bounds.w > 0 || (!self.pixelRows && bounds.h > 0))\n        ) {\n          // A row layout fits on x ALONE, which is the point of it: the pane is\n          // as tall as the rows are and the rows are as tall as they need to be,\n          // so there is no height to fit into and nothing that can make the\n          // backbone narrower than the pane it is supposed to line up with. That\n          // is the bug this axis change is for \u2014 past ~12 rows the drawing was\n          // taller than it was wide, the vertical axis bound the fit, and the\n          // backbone stopped matching the linear view above it.\n          //\n          // An isotropic layout still fits on whichever axis binds, and the\n          // leftover on the other is split evenly.\n          const fitX = bounds.w > 0 ? usableWidth / bounds.w : Infinity\n          const fitY = bounds.h > 0 ? usableHeight / bounds.h : Infinity\n          const newScale = clampZoom(\n            self.pixelRows ? fitX : Math.min(fitX, fitY),\n          )\n          self.scale = newScale\n          self.translateX =\n            FIT_PADDING -\n            bounds.minX * newScale +\n            (usableWidth - bounds.w * newScale) / 2\n          // scaleY, which a row layout pins at 1\n          self.translateY = fittedTranslateY(\n            bounds,\n            usableHeight,\n            self.pixelRows ? 1 : newScale,\n          )\n        }\n      },\n      clearPerfMetrics() {\n        self.lastFetchMs = undefined\n        self.lastLayoutMs = undefined\n        self.lastGeometryMs = undefined\n        self.lastGeometryStrokeCount = undefined\n        self.builtViewport = undefined\n      },\n    }))\n    .actions(self => ({\n      // The frame clock. Unclamped, since clampZoom's floor is there to keep a\n      // scale finite and 1 / bpPerPx already is; clamped, a whole-chromosome\n      // window would stop lining up.\n      hostTransform(scale: number, translateX: number) {\n        const engaging = self.viewportOwner !== 'host'\n        if (engaging) {\n          self.hostPaneHeight = self.canvasHeight\n          self.viewportOwner = 'host'\n        }\n        self.scale = scale\n        self.translateX = translateX\n        if (engaging) {\n          self.zoomToFit()\n        }\n      },\n      // A drawing still on the reference stays where the host left it; one\n      // whose x no longer means bp is refit.\n      releaseHost() {\n        if (self.viewportOwner === 'host') {\n          self.hostPaneHeight = undefined\n          if (self.layoutResult?.referenceAxis) {\n            self.viewportOwner = 'user'\n          } else {\n            self.viewportOwner = 'fit'\n            self.zoomToFit()\n          }\n        }\n      },\n    }))\n    .actions(self => {\n      // Pan/zoom can wait: the geometry on screen is still correct while the\n      // gesture runs (the viewport bounds carry 20% overscan), so rebuilding is\n      // deferred until the user settles.\n      function scheduleViewportDirty() {\n        clearTimeout(self.viewportDirtyTimer)\n        self.viewportDirtyTimer = setTimeout(() => {\n          if (isAlive(self)) {\n            self.setViewportDirty()\n          }\n        }, VIEWPORT_DEBOUNCE_MS)\n      }\n\n      // A node drag cannot wait \u2014 the node only moves on screen when its\n      // geometry is rebuilt \u2014 but a bump costs a full geometry rebuild plus\n      // invalidation of both hit-detection indexes, and mousemove fires in\n      // bursts well above the frame rate. Coalescing to the next frame keeps the\n      // drag live while bounding that work to once per frame instead of once\n      // per event.\n      function requestPositionsDirtyFrame() {\n        cancelAnimationFrame(self.positionsDirtyFrame)\n        self.positionsDirtyFrame = requestAnimationFrame(() => {\n          if (isAlive(self)) {\n            self.setPositionsDirty()\n          }\n        })\n      }\n\n      return {\n        // Moves the position objects IN PLACE, which is the one thing\n        // jbrowse-components' upload invariant says not to do (\"per-region\n        // upload values must be freshly constructed, never mutated \u2014 backends\n        // diff by reference identity\"), so it is worth saying why this is not\n        // that case and what it costs instead.\n        //\n        // Nothing here diffs by identity: the geometry is rebuilt wholesale and\n        // handed over as one batch, so `nodePositions` identity is not a\n        // protocol between the model and the backend the way a per-region map\n        // is. What identity DOES drive is the fit: the zoom-to-fit autorun and\n        // `layoutBounds` \u2014 and so `canvasHeight` \u2014 key off `layoutResult`, and\n        // they mean \"a new LAYOUT arrived\", not \"a node moved\". Publishing a\n        // fresh positions record per frame of a drag would refit the drawing\n        // and resize the pane under the cursor, sixty times a second.\n        //\n        // So the change is announced by `positionsVersion` instead, and every\n        // cache that would otherwise trust identity takes it as a key. The cost\n        // of that trade is that the version is a thing to remember: a caller\n        // that mutates here and does not bump it gets stale curves, stale hit\n        // boxes and stale labels, silently. Everything downstream of it is\n        // reached from this one action.\n        moveNode(nodeId: string, dx: number, dy: number) {\n          const positions = self.layoutResult?.nodePositions\n          if (positions?.[nodeId]) {\n            for (const seg of positions[nodeId]) {\n              seg.x += dx\n              seg.y += dy\n            }\n            requestPositionsDirtyFrame()\n          }\n        },\n        scheduleViewportDirty,\n      }\n    })\n    .actions(self => {\n      let loadController: AbortController | undefined\n\n      // `scaling.nodes` rather than the graph's own: under a compressing\n      // drawn-length law a node's `length` crosses this boundary as a drawn\n      // length, which is all the engine ever reads it as.\n      //\n      // An anchored graph also carries a seed per node, the backbone along x,\n      // and asks the engine not to rotate components: FMMM then keeps the\n      // reference's coarse shape instead of curling it into a C\n      // (docs/layout-experiments.md, experiment 2).\n      function callLayout(graph: Graph, scaling: LayoutScaling) {\n        const session = getSession(self)\n        const { rpcManager } = session\n        // Stable grouping key for the layout RPC; a view has no display-level\n        // rpcSessionId. `rpcManager.call` injects sessionId into the args.\n        const sessionId = 'graph'\n        const anchored = graph.nodes.some(isBackbone)\n        return rpcManager.call(sessionId, 'GraphComputeLayout', {\n          graph: {\n            nodes: anchored ? seededNodes(graph, scaling) : scaling.nodes,\n            edges: graph.edges,\n          },\n          options: {\n            quality: self.layoutQuality,\n            linearLayout: self.linearLayout,\n            ...scaling.opts,\n            ...(anchored ? { rotateComponents: false } : {}),\n          },\n          signal: loadController?.signal,\n          // A StatusCallback takes an RpcStatus, not a string \u2014 it may be a\n          // bare label, a phase, or a phase that threw. `statusMessageText` is\n          // core's reader for the human-facing line.\n          statusCallback: status => {\n            self.setStatusMessage(statusMessageText(status) ?? '')\n          },\n        }) as Promise<{ result: LayoutResult; duration: number }>\n      }\n\n      // The engine's inputs, and only those: the graph, plus what `callLayout`\n      // puts in `options`. The reference path is there because the seeds are a\n      // function of it; the colour scheme and the anchored modes' own settings\n      // are absent because none of them reaches the engine.\n      function forceLayoutKey(graph: Graph) {\n        const anchored = graph.nodes.some(isBackbone)\n        return `${self.layoutQuality}|${self.linearLayout}|${self.bubbleSpread}|${anchored}|${graph.referencePath ?? ''}`\n      }\n\n      // Single dispatch point for every layout mode. A mode that returns a\n      // result computed it locally; one that returns undefined can't draw this\n      // graph and hands off to the remote FMMM engine, which is also how\n      // 'force' is expressed. See LAYOUT_MODES.\n      function* computeLayout(graph: Graph) {\n        const start = performance.now()\n        const local = layoutModeByValue(self.layoutMode).run(\n          graph,\n          self.loadedRegion,\n          self.host ? self.layoutResult?.sampleRows : undefined,\n        )\n        if (local) {\n          return { result: local, duration: performance.now() - start }\n        }\n        const cache = forceLayoutsOf(graph)\n        const key = forceLayoutKey(graph)\n        const hit = cache.get(key)\n        if (hit) {\n          return { result: hit, duration: performance.now() - start }\n        }\n        // The engine lays out the runs, not the nodes: a base-level cut is\n        // thousands of nodes in unbranching chains, and one chain per run is\n        // the same drawing at a third of the time. Members take their share of\n        // the run's polyline by drawn length, so the picture is per node again\n        // before anything else sees it.\n        const spread = spreadFor(self.bubbleSpread)\n        const merged = mergeRuns(graph)\n        const { result, duration } = (yield callLayout(\n          merged.graph,\n          layoutScaling(merged.graph, spread),\n        )) as { result: LayoutResult; duration: number }\n        const scaling = layoutScaling(graph, spread)\n        const drawn = new Map(\n          scaling.nodes.map(n => [\n            n.id,\n            drawnNodeLength(scaling.opts, n.length),\n          ]),\n        )\n        const positions = splitRuns(\n          result.nodePositions,\n          merged.runs,\n          id => drawn.get(id) ?? 0,\n        )\n        // Turned so the reference reads left to right, like the linear view\n        // above it. Before `remember`, so the cache hands back the drawing as\n        // it was shown.\n        const oriented = {\n          ...result,\n          nodePositions: graph.nodes.some(isBackbone)\n            ? orientToReference(graph, positions)\n            : positions,\n        }\n        // Under the key read BEFORE the call: the settings that produced this\n        // drawing are not necessarily the ones on screen now, and filing it\n        // under the current ones would serve it up as a layout it is not.\n        remember(cache, key, oriented)\n        return { result: oriented, duration }\n      }\n\n      // Which layout request is the live one. A layout is async and nothing in\n      // the UI waits for it, so several are routinely in flight: every control\n      // in the settings dialog fires `recomputeLayout` on change, and a force\n      // layout takes seconds where an anchored one is instant.\n      //\n      // The graph identity below is not enough to order them, because the\n      // competing requests are usually layouts of the SAME graph. Left to\n      // resolve order the last one to FINISH won rather than the last one\n      // asked for, so switching away from a slow force layout \u2014 to an anchored\n      // mode, a cheaper bubble spread, a lower quality \u2014 drew the abandoned\n      // one over the top of the chosen one seconds later, with the dropdown\n      // still naming the choice that was discarded.\n      let liveRequest = 0\n\n      // Applied under a guard because a layout is async and the user can load a\n      // different graph, or ask for a different layout of it, while one is in\n      // flight; the stale result must not land.\n      function* layoutInto(graph: Graph) {\n        const request = ++liveRequest\n        const isLive = () => self.graph === graph && request === liveRequest\n        const signal = loadController?.signal\n        let computed\n        try {\n          computed = yield* computeLayout(graph)\n        } catch (e) {\n          // A discarded layout's failure is not the user's problem: the drawing\n          // they asked for is on screen or on its way, and raising a banner\n          // over it reports a graph as broken because a setting they moved on\n          // from could not be drawn. An aborted one was discarded by the load\n          // that replaced it, even when the graph is still the same object.\n          if (!isLive() || signal?.aborted) {\n            return false\n          }\n          throw e\n        }\n        const live = isLive()\n        if (live) {\n          self.layoutResult = computed.result\n          self.setLayoutMs(computed.duration)\n        }\n        return live\n      }\n\n      // `keepSelection` for a re-cut of the same source: node ids survive one\n      // where edge indexes do not, so the selection is found again by id.\n      function* parseAndLayout(\n        text: string,\n        name: string,\n        keepSelection = false,\n      ) {\n        self.setStatusMessage('Parsing GFA')\n        const gfaGraph = parseGFA(text)\n        // A general GFA states its coordinates only in its P/W lines, so the\n        // walk that recovers them happens before anything reads `stable` \u2014\n        // otherwise the anchored layouts see an unanchored graph and hand off\n        // to force.\n        const graph = anchorGraph(\n          convertGFAToGraph(gfaGraph, name),\n          self.preferredReferencePath,\n        )\n        // Checked here, between parsing and laying out, because this is the one\n        // point both load paths pass through and it is upstream of everything\n        // expensive: the layout, the geometry and the per-frame draw calls all\n        // scale with this number. The whole-file import path had no cap at all,\n        // so a chromosome-scale GFA would parse and then freeze the tab.\n        if (graph.nodes.length === 0) {\n          throw new Error(`No graph segments in ${name}`)\n        }\n        if (graph.nodes.length > self.maxGraphNodes) {\n          throw new Error(\n            `Graph too large to draw: ${graph.nodes.length.toLocaleString()} nodes (limit ${self.maxGraphNodes.toLocaleString()}). Zoom in to a smaller region, or raise maxGraphNodes on this view.`,\n          )\n        }\n        const selected = keepSelection ? self.selectedNode : null\n        self.graph = graph\n        self.indexBubbles = undefined\n        self.geneFeatures = undefined\n        self.repeatArrays = undefined\n        self.popStack = []\n        // hoveredEdge is an index into graph.edges and hoveredNode/selectedNode\n        // are ids, so all three address the graph being replaced here. Carrying\n        // them over points the tooltip and the highlight at whatever now happens\n        // to sit at that index.\n        self.clearInteractionState()\n        if (selected !== null && self.nodeById?.has(selected)) {\n          self.selectedNode = selected\n        }\n        self.setStatusMessage('Computing layout')\n        yield* layoutInto(graph)\n      }\n\n      // Which load is the live one, for the reason liveRequest orders layouts:\n      // every change in the settings dialog re-cuts, a remote cut takes seconds,\n      // and the last one to finish is not the last one asked for.\n      let liveLoad = 0\n\n      function beginLoad() {\n        const load = ++liveLoad\n        loadController?.abort()\n        loadController = new AbortController()\n        self.loadCanceled = false\n        return {\n          isLive: () => load === liveLoad,\n          signal: loadController.signal,\n        }\n      }\n\n      function loadedTrack() {\n        return self.loadedTrackId\n          ? getSession(self).tracks.find(t => t.trackId === self.loadedTrackId)\n          : undefined\n      }\n\n      // The bubble index that the hosted HPRC build keeps beside its segments,\n      // `<prefix>.bubbles.bed.gz`, read through the bubble adapter over the same\n      // window. A graph whose source has no such file, the ordinary case for a\n      // graph of one's own, keeps its derived bubbles, so a failure here is not\n      // the graph's problem. A coarse cut reads none: its nodes are the\n      // bubbles, and the index over its window can run to a chromosome's rows.\n      function* loadBubbles(\n        adapterConfig: Record<string, unknown>,\n        region: SubgraphRegion,\n        isLive: () => boolean,\n      ) {\n        // The track config arrives as written, so the prefix is either the\n        // `uri` shorthand or the segments location it expands to.\n        const prefix = bubblePrefix(adapterConfig)\n        if (\n          adapterConfig.type !== 'RgfaTabixAdapter' ||\n          prefix === undefined ||\n          self.cutTier === 'coarse'\n        ) {\n          return\n        }\n        try {\n          const features = (yield getSession(self).rpcManager.call(\n            'graph',\n            'CoreGetFeatures',\n            {\n              adapterConfig: {\n                type: 'MinigraphBubbleAdapter',\n                uri: `${prefix}.bubbles.bed.gz`,\n                baseUri: adapterConfig.baseUri,\n                assemblyNameToPanSN: adapterConfig.assemblyNameToPanSN,\n              },\n              regions: [region],\n            },\n          )) as Feature[]\n          if (isLive()) {\n            self.indexBubbles = features.map(f => ({\n              refName: region.refName,\n              start: f.get('start'),\n              end: f.get('end'),\n              segmentCount: f.get('segmentCount') as number,\n              pathCount: (f.get('pathCount') as number | undefined) ?? 0,\n              inversion: f.get('inversion') as boolean,\n              shortestAlleleLength: f.get('shortestAlleleLength') as number,\n              longestAlleleLength: f.get('longestAlleleLength') as number,\n              segments: f.get('segments') as string,\n              shortestAllele: undefined,\n              longestAllele: undefined,\n            }))\n          }\n        } catch (e) {\n          console.warn('[GraphGenomeView] no bubble index for this graph', e)\n        }\n      }\n\n      // A session track's features over the cut. Undefined when the session\n      // has no such track or the read fails: an annotation is never the\n      // graph's problem.\n      function* trackFeatures(\n        trackId: string | undefined,\n        region: SubgraphRegion,\n        what: string,\n      ) {\n        const session = getSession(self)\n        const config = trackId\n          ? session.tracks.find(t => t.trackId === trackId)\n          : undefined\n        if (!config) {\n          return undefined\n        }\n        try {\n          return (yield session.rpcManager.call('graph', 'CoreGetFeatures', {\n            adapterConfig: readConfObject(config, 'adapter'),\n            regions: [region],\n          })) as Feature[]\n        } catch (e) {\n          console.warn(`[GraphGenomeView] no ${what} for this graph`, e)\n          return undefined\n        }\n      }\n\n      // The genes over the cut, from the session's annotation track for the\n      // assembly, so the backbone can carry its exons and names.\n      function* loadGenes(region: SubgraphRegion, isLive: () => boolean) {\n        const features = yield* trackFeatures(\n          self.geneTrack?.trackId,\n          region,\n          'genes',\n        )\n        if (features && isLive()) {\n          self.geneFeatures = geneModelsFrom(features)\n        }\n      }\n\n      // The tandem repeat arrays over the cut, from the session's repeat\n      // track, for the walk rows to measure between and tile by.\n      function* loadRepeats(region: SubgraphRegion, isLive: () => boolean) {\n        const features = yield* trackFeatures(\n          self.repeatTrack?.trackId,\n          region,\n          'repeats',\n        )\n        if (features && isLive()) {\n          self.repeatArrays = repeatArraysFrom(features)\n        }\n      }\n\n      // Inner loading logic shared by loadFromTabixSubgraph and refetchIfNeeded\n      function* doSubgraphLoad(\n        adapterConfig: Record<string, unknown>,\n        region: SubgraphRegion,\n        opts: SubgraphCutOptions = {},\n      ) {\n        const { isLive, signal } = beginLoad()\n        const track = loadedTrack()\n        const regionSize = region.end - region.start\n        // Past the size cap the graph view declines rather than degrading to a\n        // non-graph rectangle rendering; large-region and full-genome\n        // comparison is a linear synteny view instead.\n        const refusal =\n          (track &&\n            offReferenceProblem(\n              graphReferenceAssembly(track),\n              region.assemblyName,\n            )) ??\n          (regionSize > self.regionCapBp\n            ? `Region too large (${formatSpanBp(regionSize)}) \u2014 zoom in to view graph (max ${formatSpanBp(self.regionCapBp)})`\n            : undefined)\n        if (refusal !== undefined) {\n          self.graph = undefined\n          self.layoutResult = undefined\n          self.isLoading = false\n          self.error = new Error(refusal)\n          return\n        }\n        self.isLoading = true\n        self.error = undefined\n        self.setStatusMessage('Fetching subgraph')\n        try {\n          const session = getSession(self)\n          const { rpcManager } = session\n          const sessionId = 'graph' // getRpcSessionId(self) no rpcSessionId getter\n          const fetchStart = performance.now()\n          const gfaText = (yield rpcManager.call(sessionId, 'GetSubgraph', {\n            adapterConfig,\n            region,\n            opts,\n            signal,\n          })) as string\n          if (!isLive()) {\n            return\n          }\n          self.setFetchMs(performance.now() - fetchStart)\n          if (!gfaText) {\n            throw new Error(\n              'Adapter returned no GFA \u2014 region may be outside indexed data or the adapter does not implement getSubgraph',\n            )\n          }\n          const label = locLabel(region)\n          yield* parseAndLayout(gfaText, label, true)\n          if (!isLive()) {\n            return\n          }\n          // Three independent remote reads, each landing as it arrives: in\n          // turn they held the overlay over a drawn graph for the sum of their\n          // round trips.\n          self.setStatusMessage('Reading annotations')\n          yield Promise.all([\n            flow(loadBubbles)(adapterConfig, region, isLive),\n            flow(loadGenes)(region, isLive),\n            flow(loadRepeats)(region, isLive),\n          ])\n        } catch (e) {\n          if (isLive()) {\n            console.error('[GraphGenomeView.loadFromTabixSubgraph]', e)\n            self.error = e\n          }\n        } finally {\n          if (isLive()) {\n            self.isLoading = false\n          }\n        }\n      }\n\n      // The cut behind a graph whose source is a track in this session, which is\n      // what both a launch snapshot and a restored session carry. Silent when\n      // there is no such pair, which is the whole-file case. A pair naming a\n      // track the session lacks is reported, because otherwise the view sits on\n      // an empty import form with nothing saying why.\n      //\n      // Nothing here saves and restores the transform: `viewportOwner` is\n      // what protects a restored session's pan/zoom, and it gates the fit\n      // autorun \u2014 the only thing in this flow that would otherwise move the\n      // view. A save/restore pair around the load wrote back the values it had\n      // just read.\n      function* cutFromLoadedTrack() {\n        const region = self.loadedRegion\n        const track = loadedTrack()\n        if (region && self.loadedTrackId && !track) {\n          self.error = new Error(\n            `The track this graph was cut from, \"${self.loadedTrackId}\", is not in this session`,\n          )\n        } else if (track && region) {\n          // A hop past a coarse cut reaches nothing new: every bubble node's\n          // two links are indexed under the backbone either side of it.\n          const coarse = self.cutTier === 'coarse'\n          yield* doSubgraphLoad(readConfObject(track, 'adapter'), region, {\n            hops: coarse ? 0 : self.subgraphContext,\n            haplotypes: self.subgraphHaplotypes,\n            tier: coarse ? 'coarse' : undefined,\n          })\n        }\n      }\n\n      // Raises `isLoading` before any fetch, so a view waiting on a remote file\n      // shows its loading state instead of the import form. Text already in\n      // hand is parsed without yielding first.\n      // `region` is the window a declared file was stated beside. Held through\n      // the load rather than restored after it, so the parse anchors on that\n      // assembly's path and a failed or canceled load can still be retried\n      // with it.\n      function* loadWholeGFA(\n        name: string,\n        source: string | ((signal: AbortSignal) => Promise<string>),\n        region?: SubgraphRegion,\n      ) {\n        const { isLive, signal } = beginLoad()\n        self.loadedTrackId = ''\n        self.loadedRegion = region\n        self.coarseCut = false\n        self.isLoading = true\n        self.error = undefined\n        try {\n          const text =\n            typeof source === 'string'\n              ? source\n              : ((yield source(signal)) as string)\n          if (isLive()) {\n            yield* parseAndLayout(text, name)\n          }\n        } catch (e) {\n          if (isLive()) {\n            console.error('[GraphGenomeView.loadWholeGFA]', e)\n            self.error = e\n          }\n        } finally {\n          if (isLive()) {\n            self.isLoading = false\n          }\n        }\n        return isLive()\n      }\n\n      return {\n        // Back to the import form: drop the graph, everything derived from it,\n        // and the source it came from. Leaving the source declared kept\n        // `showLoading` true over the import form and had a reloaded session\n        // cut the dismissed graph again. Any load in flight ends here too,\n        // or it would land its graph afterwards.\n        clearGraph() {\n          loadController?.abort()\n          loadController = undefined\n          liveLoad++\n          liveRequest++\n          self.graph = undefined\n          self.layoutResult = undefined\n          self.loadedTrackId = ''\n          self.loadedRegion = undefined\n          self.coarseCut = false\n          self.cutNote = undefined\n          self.gfaLocation = undefined\n          self.indexBubbles = undefined\n          self.geneFeatures = undefined\n          self.repeatArrays = undefined\n          self.popStack = []\n          self.error = undefined\n          self.isLoading = false\n          self.loadCanceled = false\n          self.statusMessage = ''\n          self.clearInteractionState()\n          self.clearPerfMetrics()\n        },\n        cancelLoad() {\n          if (self.canCancelLoad) {\n            loadController?.abort()\n            loadController = undefined\n            liveLoad++\n            liveRequest++\n            self.graph = undefined\n            self.isLoading = false\n            self.statusMessage = ''\n            self.loadCanceled = true\n          }\n        },\n        loadGFA: flow(function* (text: string, name = 'Imported GFA') {\n          yield* loadWholeGFA(name, text)\n        }),\n        loadGFAFromLocation: flow(function* (location: FileLocation) {\n          self.setStatusMessage('Fetching GFA')\n          const stated = self.loadedRegion\n          const live = yield* loadWholeGFA(\n            'uri' in location\n              ? (location.uri.split('/').pop() ?? 'GFA')\n              : 'GFA',\n            signal =>\n              openLocation(location).readFile({ encoding: 'utf8', signal }),\n            stated,\n          )\n          if (stated && live && self.graph) {\n            yield* loadRepeats(stated, () => self.loadedRegion === stated)\n          }\n        }),\n        loadFromTabixSubgraph: flow(function* (\n          adapterConfig: Record<string, unknown>,\n          region: SubgraphRegion,\n          opts: {\n            trackId?: string\n          } = {},\n        ) {\n          self.loadedTrackId = opts.trackId ?? ''\n          self.loadedRegion = opts.trackId ? region : undefined\n          self.coarseCut = false\n          yield* doSubgraphLoad(adapterConfig, region, {\n            hops: self.subgraphContext,\n            haplotypes: self.subgraphHaplotypes,\n          })\n        }),\n        // Cut on attach only \u2014 a graph already on screen is either the user's\n        // own or one this just drew.\n        refetchIfNeeded: flow(function* () {\n          if (!self.graph) {\n            yield* cutFromLoadedTrack()\n          }\n        }),\n        // Cut the same region again, for a change to what the cut returns\n        // rather than to how it is drawn (subgraphContext).\n        reloadSubgraph: flow(function* () {\n          yield* cutFromLoadedTrack()\n        }),\n        // Re-read one annotation track alone, for a track change or a graph\n        // that came from a whole file beside a stated region. The graph, its\n        // layout and any open bubble stay as they are. Live only while the\n        // track it read is still the one chosen, so a slow read cannot land\n        // over the pick that followed it.\n        reloadRepeats: flow(function* () {\n          const region = self.loadedRegion\n          const trackId = self.repeatTrack?.trackId\n          if (region) {\n            yield* loadRepeats(\n              region,\n              () =>\n                self.loadedRegion === region &&\n                self.repeatTrack?.trackId === trackId,\n            )\n          }\n        }),\n        reloadGenes: flow(function* () {\n          const region = self.loadedRegion\n          const trackId = self.geneTrack?.trackId\n          if (region) {\n            yield* loadGenes(\n              region,\n              () =>\n                self.loadedRegion === region &&\n                self.geneTrack?.trackId === trackId,\n            )\n          }\n        }),\n        // Open one bubble: the graph becomes the segments the bubble row names,\n        // drawn in the layout the reader is in, or force-directed from the\n        // variant map. The graph it came from stays behind it, one click away,\n        // and the popped graph gets its own derived bubbles, so a superbubble\n        // opens progressively.\n        popBubble: flow(function* (bubble: MinigraphBubble) {\n          const graph = self.graph\n          if (!graph) {\n            return\n          }\n          const sub = bubbleSubgraph(graph, bubbleSegmentIds(bubble))\n          if (sub.nodes.length === 0) {\n            getSession(self).notify(\n              'None of the segments of this bubble are in the cut; widen the graph context to open it',\n              'info',\n            )\n            return\n          }\n          const { isLive } = beginLoad()\n          self.popStack = [\n            ...self.popStack,\n            {\n              graph,\n              layoutMode: self.layoutMode,\n              label: graph.name,\n              indexBubbles: self.indexBubbles,\n            },\n          ]\n          self.indexBubbles = undefined\n          const label = `${BUBBLE_KIND_NAMES[classifyBubble(bubble).kind]} at ${bubble.refName}:${bubble.start.toLocaleString()}`\n          self.graph = { ...sub, name: label }\n          if (self.layoutMode === 'variants') {\n            self.layoutMode = 'force'\n          }\n          self.clearInteractionState()\n          self.viewportOwner = 'fit'\n          self.isLoading = true\n          try {\n            if (yield* layoutInto(self.graph)) {\n              self.isLoading = false\n            }\n          } catch (e) {\n            if (isLive()) {\n              self.error = e\n              self.isLoading = false\n            }\n          }\n        }),\n        unpopBubble: flow(function* () {\n          const from = self.poppedFrom\n          if (!from) {\n            return\n          }\n          self.popStack = self.popStack.slice(0, -1)\n          self.graph = from.graph\n          self.layoutMode = from.layoutMode\n          self.indexBubbles = from.indexBubbles\n          self.clearInteractionState()\n          self.viewportOwner = 'fit'\n          self.isLoading = true\n          try {\n            if (yield* layoutInto(from.graph)) {\n              self.isLoading = false\n            }\n          } catch (e) {\n            self.error = e\n            self.isLoading = false\n          }\n        }),\n        recomputeLayout: flow(function* () {\n          const graph = self.graph\n          if (!graph) {\n            return\n          }\n          self.isLoading = true\n          self.setStatusMessage('Computing layout')\n\n          try {\n            // A superseded request leaves the spinner to the request that\n            // replaced it: clearing it here reports \"done\" while the layout the\n            // user actually asked for is still being computed, which is the\n            // common case when a cheap choice follows an expensive one.\n            if (yield* layoutInto(graph)) {\n              self.isLoading = false\n            }\n          } catch (e) {\n            console.error('[GraphGenomeView.recomputeLayout]', e)\n            self.error = e\n            self.isLoading = false\n          }\n        }),\n      }\n    })\n    .actions(self => ({\n      // The settle clock. A pan the cut still holds fetches nothing; one past\n      // its edge re-cuts the window plus a window-width each side, on the tier\n      // the zoom asks for. Overlapping re-cuts are ordered by doSubgraphLoad's\n      // liveLoad, so the latest window wins.\n      settleOn(seen: HostWindow) {\n        const above = self.coarseAboveBpPerPx\n        const tier =\n          above !== undefined && seen.bpPerPx > above ? 'coarse' : 'fine'\n        const cap = tier === 'coarse' ? Infinity : self.maxRegionBp\n        const visible = seen.end - seen.start\n        self.cutNote =\n          visible > cap\n            ? `Holding the last cut: ${formatSpanBp(visible)} is past the ${formatSpanBp(cap)} a cut may span`\n            : undefined\n        if (\n          self.cutNote !== undefined ||\n          (tier === self.cutTier && cutHolds(self.loadedRegion, seen))\n        ) {\n          return\n        }\n        self.coarseCut = tier === 'coarse'\n        self.loadedRegion = hostCut(seen, cap)\n        self.recuts++\n        void self.reloadSubgraph()\n      },\n    }))\n    .actions(self => ({\n      // The host's two clocks, started by the display that hosts the pane.\n      // The frame clock moves x with every frame of the linear view and\n      // fetches nothing; the settle clock wakes on its debounced blocks and\n      // re-cuts only when the window has left the cut, whatever the layout.\n      startHosting() {\n        addDisposer(\n          self,\n          reaction(\n            () => self.hostPlacesX,\n            places => {\n              if (!places) {\n                self.releaseHost()\n              }\n            },\n            { name: 'GraphHostPlacesX' },\n          ),\n        )\n        addDisposer(\n          self,\n          reaction(\n            () => self.hostFrame,\n            frame => {\n              if (frame) {\n                self.hostTransform(frame.scale, frame.translateX)\n              }\n            },\n            {\n              equals: (a, b) =>\n                a?.scale === b?.scale && a?.translateX === b?.translateX,\n              fireImmediately: true,\n              name: 'GraphHostFrame',\n            },\n          ),\n        )\n        addDisposer(\n          self,\n          reaction(\n            () => self.host?.coarseDynamicBlocks,\n            blocks => {\n              const { host } = self\n              const seen = blocks && host ? hostWindow(host) : undefined\n              if (seen) {\n                self.settleOn(seen)\n              }\n            },\n            { fireImmediately: true, name: 'GraphHostSettle' },\n          ),\n        )\n      },\n    }))\n    .actions(self => ({\n      startRenderingBackend(backend: Renderer) {\n        if (!self.autorunsInstalled) {\n          // Autorun: paint the lane this graph was cut from in the graph's own\n          // reference-position ramp, so a block above and its node below share\n          // a hue with nothing configured. Follows the domain, so a re-cut or\n          // an opened bubble moves the lane's ramp with the drawing.\n          addDisposer(\n            self,\n            autorun(() => {\n              const domain = self.rampDomain\n              const trackId = self.loadedTrackId\n              if (\n                domain &&\n                trackId &&\n                self.effectiveColorScheme === 'reference-position'\n              ) {\n                const display = untracked(() =>\n                  sourceLaneDisplay(\n                    getSession(self).views,\n                    self.connectedViewId,\n                    trackId,\n                  ),\n                )\n                if (display) {\n                  paintSourceLane(display, referencePositionColor(domain))\n                }\n              }\n            }),\n          )\n\n          // Autorun: keep the view fitted to the graph until the user moves it.\n          // Reads layoutResult plus (via zoomToFit) width/canvasHeight, so it\n          // re-fires \u2014 and re-fits \u2014 as the layout arrives and the canvas is\n          // measured, rather than firing once against not-yet-known dimensions.\n          // A manual pan/zoom (or a restored-session transform) makes the\n          // viewport the user's, and a host makes it the linear view's.\n          addDisposer(\n            self,\n            autorun(() => {\n              if (\n                self.layoutResult &&\n                untracked(() => self.viewportOwner === 'fit')\n              ) {\n                self.zoomToFit()\n              }\n            }),\n          )\n\n          // Autorun: mirror a connected linear view's hover onto the graph. An\n          // LGV writes `{hoverPosition, hoverFeature}` to session.hovered on\n          // every mousemove; neither field names the source view, so the guard\n          // is that the position lies in the region this graph was cut from.\n          //\n          // Only `hovered` is tracked \u2014 the graph reads are untracked, so a\n          // geometry rebuild can't re-fire this and clobber a hover the canvas\n          // itself set. Assigning an unchanged id doesn't notify, so a hover\n          // that travels within one segment costs nothing downstream.\n          addDisposer(\n            self,\n            autorun(() => {\n              const hover = readLgvHover(getSession(self).hovered)\n              untracked(() => {\n                const region = self.loadedRegion\n                const graph = self.graph\n                if (region && graph) {\n                  self.setHoveredNode(\n                    hover && hoverInRegion(hover, region)\n                      ? nodeForLgvHover({ hover, nodes: graph.nodes })\n                      : null,\n                  )\n                }\n              })\n            }),\n          )\n\n          // Reaction: drop a hover the pointer cannot still be over.\n          //\n          // A hover is set by a mousemove on the canvas, and here the drawing\n          // moves under a STATIONARY cursor on three axes \u2014 the wheel zoom, the\n          // toolbar's zoom and fit buttons, and a pan \u2014 none of which fire a\n          // pointer event. Left alone the tooltip goes on naming the node that\n          // used to be under the cursor, `hoverHighlight` goes on publishing its\n          // span, and the paired linear view paints a band over the wrong\n          // sequence until the mouse happens to move.\n          //\n          // This is jbrowse-components' `installClearHoverOnViewportChange`\n          // (BaseLinearDisplay), whose three axes are bpPerPx / offsetPx /\n          // scrollTop; a graph view's are its own transform. Its rule is worth\n          // restating rather than just citing: a sticky canvas gets no\n          // mousemove and no mouseleave for any of them. Not imported because\n          // it lives in the LGV plugin and reads a containing LGV, and this\n          // plugin deliberately takes no runtime dependency on that plugin\n          // (see hoverSync/index.tsx).\n          //\n          // A `reaction`, not an autorun, for the reason stated there: the\n          // effect touches hover state, and an autorun would re-enter itself.\n          // Selection is untouched \u2014 a click is a choice, and the content\n          // moving does not unmake it.\n          addDisposer(\n            self,\n            reaction(\n              () => `${self.scale}-${self.translateX}-${self.translateY}`,\n              () => {\n                self.setHoveredNode(null)\n                self.setHoveredEdge(null)\n              },\n              { name: 'GraphClearHoverOnViewportChange' },\n            ),\n          )\n\n          // Autorun: a zoom, or a pan that leaves the window the last build\n          // covered, schedules a debounced rebuild. A pan inside it costs a\n          // repaint and nothing else. Skips the first run.\n          let firstViewport = true\n          addDisposer(\n            self,\n            autorun(() => {\n              const { scale } = self\n              const viewport = viewportOf(self)\n              if (firstViewport) {\n                firstViewport = false\n                return\n              }\n              const built = untracked(() => self.builtViewport)\n              if (built?.scale === scale && contains(built.bounds, viewport)) {\n                return\n              }\n              self.scheduleViewportDirty()\n            }),\n          )\n\n          // Autorun: hover/select are draw-time colour overrides, stated whole\n          // on every change, so there is nothing to restore and nothing to go\n          // stale when a rebuild renumbers the batch. Tracks `geometryVersion`\n          // because an upload drops the renderer's edge highlight.\n          addDisposer(\n            self,\n            autorun(() => {\n              const b = self.currentRenderingBackend as Renderer | undefined\n              const hoveredNode = self.hoveredNode\n              const hoveredEdge = self.hoveredEdge\n              const selectedNode = self.selectedNode\n              dependOn(self.geometryVersion)\n              if (b) {\n                const nodes = new Map<string, number>()\n                if (selectedNode !== null) {\n                  nodes.set(selectedNode, SELECT_BRIGHTEN)\n                }\n                if (hoveredNode !== null && hoveredNode !== selectedNode) {\n                  nodes.set(hoveredNode, HOVER_BRIGHTEN)\n                }\n                b.setNodeHighlights(nodes)\n                b.setEdgeHighlight(hoveredEdge, HOVER_BRIGHTEN)\n                self.renderNow()\n              }\n            }),\n          )\n        }\n\n        // The second argument is a SETUP THUNK, not the callbacks themselves:\n        // anything it closes over lives exactly as long as the callbacks that\n        // read it, which is what lets a per-backend memo work.\n        self.attachRenderingBackend<Renderer>(backend, () => ({\n          // Autorun: rebuild geometry when graph data or display options\n          // change. scale/translate are untracked so they don't trigger a full\n          // rebuild \u2014 only the debounced viewportDirty flag does.\n          upload: (b: Renderer) => {\n            b.resize(self.width, self.canvasHeight)\n            const nodeById = self.nodeById\n            if (self.nodePositions && self.graph && nodeById) {\n              // The window moved (debounced pan/zoom), or the positions did (a\n              // node drag, coalesced to a frame). Both change the drawing;\n              // everything below reads them untracked or not at all.\n              dependOn(self.viewportDirty, self.positionsVersion)\n              const geometryStart = performance.now()\n              const viewportBounds = untracked(() =>\n                padded(viewportOf(self), VIEWPORT_PANES_BUILT),\n              )\n              const batch = buildGeometry({\n                nodePositions: self.nodePositions,\n                graph: self.graph,\n                nodeById,\n                colorScheme: self.effectiveColorScheme,\n                contigThickness: self.contigThickness,\n                connectorThickness: self.connectorThickness,\n                drawPaths: self.effectiveDrawPaths,\n                nodeWidth: self.nodeWidth,\n                highlight: self.walkHighlight,\n                // Untracked, so a zoom does not eagerly rebuild geometry \u2014 the\n                // debounced viewportDirty bump drives the scale-dependent\n                // rebuild (flatness, arrow visibility, viewport culling), same\n                // as pan.\n                axis: untracked(() => self.axisScale),\n                linearLayout: self.linearLayout,\n                viewportBounds,\n                // Where each node sits on the reference and what interval the\n                // hue spans. Held against the graph rather than derived here,\n                // the same way `deletions` is and for the same reason \u2014 see\n                // the `referenceRamp` view.\n                referenceRamp: self.referenceRamp,\n                deletions: self.deletionEdgeIndexes,\n                hiddenEdges: self.hiddenEdgeIndexes,\n                // Read tracked above; passed here so the shared edge-curve\n                // cache can tell a drag from a pan.\n                version: self.positionsVersion,\n              })\n              b.uploadGeometry(batch)\n              self.setGeometryMetrics(\n                performance.now() - geometryStart,\n                batch.nodeStrokes.length,\n                { scale: untracked(() => self.scale), bounds: viewportBounds },\n              )\n              return true\n            }\n            // Nothing reached the backend, so the autorun may skip the redraw\n            // it would otherwise force. Safe despite the resize above: with no\n            // positions there is nothing to draw, which is the same case\n            // `render` below returns false for.\n            return false\n          },\n          // Autorun: re-render on pan/zoom/darkMode without rebuilding geometry\n          render: (b: Renderer) => {\n            if (!self.nodePositions) {\n              return false\n            }\n            // getDpr(), never a bare `devicePixelRatio`: it is capped at\n            // MAX_DPR so this canvas costs what every other canvas in the app\n            // costs on a 3x display (the square of the ratio, i.e. 9x the\n            // pixels of 1x against the 4x everything else pays), and it is the\n            // same read `syncCanvasSize` sizes the backing store with \u2014 two\n            // call sites reading the global separately can disagree, and then\n            // the geometry lands at a different scale from the canvas under it.\n            const dpr = getDpr()\n            b.updateTransform({\n              scaleX: self.scaleX * dpr,\n              scaleY: self.scaleY * dpr,\n              translateX: self.translateX * dpr,\n              translateY: self.translateY * dpr,\n              // Handed over rather than read again by the backend: the\n              // thicknesses in the vertex buffer are css px and are expanded\n              // after this transform, so they need the same ratio the fields\n              // above were already multiplied by. See TransformUniform.dpr.\n              dpr,\n            })\n            b.render(self.darkMode ? [0.12, 0.12, 0.12, 1] : [1, 1, 1, 1])\n            return true\n          },\n        }))\n      },\n    }))\n    .actions(self => ({\n      // A layout picked from a menu: the mode, then the drawing it makes.\n      switchLayout(mode: LayoutModeValue) {\n        self.setLayoutMode(mode)\n        return self.recomputeLayout()\n      },\n      retryLoad() {\n        if (self.loadedTrackId && self.loadedRegion) {\n          void self.reloadSubgraph()\n        } else if (self.gfaLocation) {\n          void self.loadGFAFromLocation(self.gfaLocation)\n        }\n      },\n      // A declaratively-instantiated view loads itself on attach, from either\n      // declarative source: a whole-GFA `gfaLocation`, or the\n      // `loadedTrackId`/`loadedRegion` pair the launch menu writes and a\n      // reloaded session restores.\n      //\n      // This has to happen here rather than when the rendering backend starts:\n      // the canvas only mounts once `hasGraph` is true, so a view whose graph\n      // must be fetched would never fetch it.\n      afterAttach() {\n        // A restored session that already carries a non-default transform is\n        // the user's own view \u2014 mark it so the fit autorun leaves it alone.\n        if (!self.isDefaultViewport) {\n          self.viewportOwner = 'user'\n        }\n        // loadGFAFromLocation leaves `gfaLocation` intact, so the source\n        // round-trips through a session snapshot.\n        if (self.gfaLocation && !self.graph) {\n          void self.loadGFAFromLocation(self.gfaLocation)\n        }\n        void self.refetchIfNeeded()\n      },\n    }))\n    .actions(self => ({\n      // Move the linear view already on screen, or open one if there is none,\n      // and pair with whichever it was. A view being created gets the session's\n      // annotation for the assembly it opens on (see launchTracks), led by the\n      // graph's own segments track when the launch is on the reference \u2014 the one\n      // assembly that track is configured for.\n      //\n      // Only a view on the reference is paired with. A node's hover band is on\n      // that assembly, so paired with a view on another the band fails that\n      // view's assembly check and the reference view's id check, and is drawn\n      // nowhere.\n      showInLinearView(target: { location: GraphLocation; assembly: string }) {\n        const session = getSession(self)\n        const onReference = target.assembly === self.loadedRegion?.assemblyName\n        const viewId = showInLinearView({\n          session,\n          location: target.location,\n          assembly: target.assembly,\n          connectedViewId: self.connectedViewId,\n          tracks: launchTracks({\n            session,\n            assemblyName: target.assembly,\n            first:\n              self.loadedTrackId && onReference\n                ? self.loadedTrackId\n                : undefined,\n          }),\n        })\n        if (onReference) {\n          self.pairWithLinearView(viewId)\n        }\n      },\n      // Mark the node's reference interval in the linear view beside the graph.\n      // Not an action that opens anything: with no view to mark, the menu does\n      // not offer it (see nodeLaunchMenuItems).\n      highlightInLinearView(target: {\n        location: GraphLocation\n        assembly: string\n      }) {\n        highlightInLinearView({\n          session: getSession(self),\n          location: target.location,\n          assembly: target.assembly,\n          connectedViewId: self.connectedViewId,\n        })\n      },\n      showSyntenyView(trackId: string) {\n        launchSyntenyView({\n          session: getSession(self),\n          contributors: self.launchableAssemblies,\n          trackId,\n          graphTrackId: self.loadedTrackId || undefined,\n        })\n      },\n    }))\n    .views(self => ({\n      // Synteny datasets that could fill the panels of a multi-genome launch.\n      // Below two openable contributors there is nothing to compare, so the scan\n      // is skipped rather than run and discarded.\n      get syntenyLaunchTracks() {\n        const samples = self.launchableAssemblies.map(c => c.sample)\n        return samples.length >= 2\n          ? launchableSyntenyTracks(getSession(self), samples)\n          : []\n      },\n    }))\n    .views(self => ({\n      // The graph's way out, in the same shared \"Launch view\" submenu every\n      // other view contributes to. Until this existed the triangle had two edges:\n      // a linear view could open a graph or a synteny view of a locus, and the\n      // graph could open nothing at all.\n      menuItems(): MenuItem[] {\n        const items: MenuItem[] = []\n        for (const item of graphLaunchMenuItems({\n          contributors: self.launchableAssemblies,\n          syntenyTracks: self.syntenyLaunchTracks,\n          onShowLinear: target => {\n            self.showInLinearView(target)\n          },\n          onShowSynteny: trackId => {\n            self.showSyntenyView(trackId)\n          },\n        })) {\n          pushLaunchViewMenuItem(items, item)\n        }\n        return items\n      },\n    }))\n}\n\nexport type GraphGenomeViewModel = ReturnType<\n  ReturnType<typeof stateModelFactory>['create']\n>\n", "import { bubbleSegmentIds, classifyBubble, formatBp } from './classifyBubble'\nimport { isBackbone } from '../anchoredNodes'\nimport { svgPath } from '../util/geometry'\n\nimport type { BubbleKind } from './classifyBubble'\nimport type {\n  BubbleRoute,\n  MinigraphBubble,\n} from '../../MinigraphBubbleAdapter/bubbleLine'\nimport type { Graph, NodeSegment } from '../types'\n\n// A bubble drawn over the graph itself: a wide translucent stroke along the\n// nodes inside it, in layout coordinates, so the same halo follows the nodes\n// through the force layout's loops as through the ordered layout's lenses. The\n// two backbone nodes a bubble hangs between are not inside it, and are left\n// out so neighbouring halos do not touch.\nexport interface BubbleHalo {\n  bubble: MinigraphBubble\n  kind: BubbleKind\n  label: string\n  // an SVG path in layout units; a drawing transform puts it on screen\n  path: string\n  // where the label goes: the highest point of the halo, in layout units\n  top: NodeSegment\n  members: number\n  // the ids of those nodes, so a lifted walk can say which bubbles it enters\n  nodeIds: string[]\n  // the bubble is the whole drawing, as a popped bubble's own row is: its\n  // label still names it, but a halo around everything marks nothing\n  whole: boolean\n  // each route the walks take through the bubble, the reference's own\n  // included, named for the haplotypes that take it; a route with no steps, a\n  // deletion, has nowhere to carry a chip\n  routes: RouteLabel[]\n}\n\nexport interface RouteLabel {\n  route: BubbleRoute\n  at: NodeSegment\n  text: string\n}\n\nconst WHOLE_FRACTION = 0.9\nconst NAMED_WALKS = 2\n// a SNP's routes are a dot each; chips are for loops a reader can see\nconst MIN_CHIPPED_BP = 1000\n\nexport function bubbleHalos(\n  graph: Graph,\n  bubbles: MinigraphBubble[],\n  positions: Record<string, NodeSegment[]>,\n  walkLabel: (name: string) => string = name => name,\n): BubbleHalo[] {\n  const byName = new Map(graph.nodes.map(n => [n.name, n]))\n  const halos: BubbleHalo[] = []\n  for (const bubble of bubbles) {\n    const parts: string[] = []\n    let top: NodeSegment | undefined\n    const nodeIds: string[] = []\n    const ends: NodeSegment[] = []\n    for (const name of bubbleSegmentIds(bubble)) {\n      const node = byName.get(name)\n      const line = node && positions[node.id]\n      if (!node || !line?.length) {\n        continue\n      }\n      if (\n        isBackbone(node) &&\n        (node.stable.start < bubble.start || node.stable.start >= bubble.end)\n      ) {\n        ends.push(line[Math.floor(line.length / 2)]!)\n        continue\n      }\n      nodeIds.push(node.id)\n      // a one-point line still needs a segment to stroke as a dot\n      parts.push(svgPath(line.length === 1 ? [line[0]!, line[0]!] : line))\n      for (const p of line) {\n        if (!top || p.y < top.y) {\n          top = p\n        }\n      }\n    }\n    if (!top) {\n      continue\n    }\n    const anchor = ends.length\n      ? {\n          x: ends.reduce((s, p) => s + p.x, 0) / ends.length,\n          y: ends.reduce((s, p) => s + p.y, 0) / ends.length,\n        }\n      : top\n    // A chip goes on the stretch that is the route's own: among the nodes the\n    // fewest other routes share, the point farthest from the bubble's ends.\n    // Routes through a repeat array share most of their copies, and the far\n    // point of a shared copy would put every chip on one loop.\n    const sharing = new Map<string, number>()\n    for (const route of bubble.routes ?? []) {\n      for (const id of new Set(route.steps)) {\n        sharing.set(id, (sharing.get(id) ?? 0) + 1)\n      }\n    }\n    const routes: RouteLabel[] = []\n    for (const route of bubble.routes ?? []) {\n      if (bubble.longestAlleleLength < MIN_CHIPPED_BP) {\n        break\n      }\n      if (route.steps.length === 0) {\n        continue\n      }\n      const rarest = Math.min(...route.steps.map(id => sharing.get(id)!))\n      let at: NodeSegment | undefined\n      let far = -1\n      for (const id of route.steps) {\n        if (sharing.get(id) !== rarest) {\n          continue\n        }\n        for (const p of positions[id] ?? []) {\n          const d = Math.hypot(p.x - anchor.x, p.y - anchor.y)\n          if (d > far) {\n            far = d\n            at = p\n          }\n        }\n      }\n      if (at) {\n        routes.push({ route, at, text: routeText(route, walkLabel) })\n      }\n    }\n    halos.push({\n      bubble,\n      ...classifyBubble(bubble),\n      path: parts.join(''),\n      top,\n      members: nodeIds.length,\n      nodeIds,\n      whole: nodeIds.length >= WHOLE_FRACTION * graph.nodes.length,\n      routes,\n    })\n  }\n  return halos\n}\n\nfunction routeText(route: BubbleRoute, walkLabel: (name: string) => string) {\n  const names = [...new Set(route.walks.map(walkLabel))].sort()\n  const shown = names.slice(0, NAMED_WALKS).join(', ')\n  const more =\n    names.length > NAMED_WALKS ? ` +${names.length - NAMED_WALKS}` : ''\n  return `${shown}${more} \u00B7 ${formatBp(route.bp)}`\n}\n", "import { SATURATED_PATH_COUNT } from '../../MinigraphBubbleAdapter/bubbleLine'\nimport { isBackbone } from '../anchoredNodes'\nimport { referenceOrder } from '../layout/orderedLayout'\n\nimport type {\n  BubbleRoute,\n  MinigraphBubble,\n} from '../../MinigraphBubbleAdapter/bubbleLine'\nimport type { Graph, GraphNode } from '../types'\n\n// Bubbles from the graph alone, off the reference order the ordered layout is\n// also drawn from (referenceOrder): a backbone node no link reaches across is a\n// bubble boundary, and whatever sorts between two consecutive boundaries is a\n// bubble. Needs a reference, not an index, so it works on a GBZ cut, a pggb\n// file and the inside of a popped superbubble alike.\n//\n// Read off the order itself, not off the layers the drawing puts it in. A\n// layer is where a node is drawn, and one nothing leads into is drawn in the\n// first layer wherever it sorts. That is every node a walk enters the cut at,\n// the ordinary shape of a GBZ cut whose context stops short of a haplotype's\n// walk: its link into the backbone then crossed every layer between, and the\n// bubbles on either side of those boundaries fused into one.\n//\n// Route statistics come from the walks when the graph has paths (exact, and\n// immune to a repeat array whose copies the order cannot direct), and from a\n// DP over the ordered DAG otherwise. A reversed stretch comes out as one\n// bubble whose interior runs against the reference, not as an inversion flag.\n\ninterface Routes {\n  min: number\n  max: number\n  n: number\n}\n\nexport function bubblesFromGraph(graph: Graph): MinigraphBubble[] {\n  if (!graph.nodes.some(isBackbone)) {\n    return []\n  }\n  const byId = new Map(graph.nodes.map(n => [n.id, n]))\n  const order = referenceOrder(graph)\n  const indexOf = new Map(order.map((id, i) => [id, i]))\n  // how many links reach across each place in the order, as a running sum of\n  // where each one starts and stops\n  const reach = new Int32Array(order.length + 1)\n  // successors as a set: a repeat's back edge is the same DAG edge as its\n  // forward one, and counting it twice doubles every route through the copy\n  const succ = new Map<string, Set<string>>()\n  const linked = new Set<string>()\n  for (const e of graph.edges) {\n    const a = indexOf.get(e.from)\n    const b = indexOf.get(e.to)\n    if (a === undefined || b === undefined || a === b) {\n      continue\n    }\n    linked.add(`${e.from}>${e.to}`).add(`${e.to}>${e.from}`)\n    const [lo, hi] = a < b ? [a, b] : [b, a]\n    reach[lo + 1]!++\n    reach[hi]!--\n    const [from, to] = a < b ? [e.from, e.to] : [e.to, e.from]\n    ;(succ.get(from) ?? succ.set(from, new Set()).get(from)!).add(to)\n  }\n  for (let i = 1; i < reach.length; i++) {\n    reach[i]! += reach[i - 1]!\n  }\n  // Boundaries are nodes: every backbone node no link reaches across, plus the\n  // window's first and last backbone node whatever reaches across them, since a\n  // repeat array whose copies reach the last backbone node would otherwise\n  // never close.\n  const backbone = graph.nodes\n    .filter(isBackbone)\n    .sort((a, b) => a.stable.start - b.stable.start)\n  const ends = new Set([backbone[0]!.id, backbone.at(-1)!.id])\n  const boundaries = backbone\n    .map(node => [node, indexOf.get(node.id)!] as const)\n    .filter(([node, i]) => ends.has(node.id) || reach[i] === 0)\n    .sort(([a, ia], [b, ib]) => ia - ib || a.stable.start - b.stable.start)\n  const walkIndex = graph.paths?.map(p => {\n    const at = new Map<string, number>()\n    p.nodeIds.forEach((id, i) => {\n      if (!at.has(id)) {\n        at.set(id, i)\n      }\n    })\n    return at\n  })\n\n  const bubbles: MinigraphBubble[] = []\n  for (let i = 0; i + 1 < boundaries.length; i++) {\n    const [start, i0] = boundaries[i]!\n    const [end, i1] = boundaries[i + 1]!\n    const interior = order.slice(i0 + 1, i1)\n    if (interior.length === 0) {\n      continue\n    }\n\n    const best = new Map<string, Routes>([[start.id, { min: 0, max: 0, n: 1 }]])\n    for (const id of [start.id, ...interior]) {\n      const cur = best.get(id)\n      if (!cur) {\n        continue\n      }\n      for (const t of succ.get(id) ?? []) {\n        const ti = indexOf.get(t)!\n        if (ti > i1) {\n          continue\n        }\n        const add = t === end.id ? 0 : byId.get(t)!.length\n        const prev = best.get(t)\n        best.set(t, {\n          min: Math.min(prev?.min ?? Infinity, cur.min + add),\n          max: Math.max(prev?.max ?? -Infinity, cur.max + add),\n          n: Math.min(SATURATED_PATH_COUNT, cur.n + (prev?.n ?? 0)),\n        })\n      }\n    }\n    const walked =\n      walkIndex && walkRoutes(graph, byId, walkIndex, start.id, end.id)\n    const crossed = walked?.n ? walked : undefined\n    const routes = crossed ?? best.get(end.id) ?? { min: 0, max: 0, n: 0 }\n    // A walk that enters the bubble and never reaches its other end left the\n    // cut: a GBZ cut of a repeat array at 1 kb of context splits each\n    // haplotype's walk into pieces, and the routes seen are then a floor.\n    const walksLeave = walked !== undefined && walked.left > 0\n\n    const refStart = start.stable.start + start.length\n    const refEnd = end.stable.start\n    // The reference route exists in the cut only if every backbone pair inside\n    // is linked; a flank the hop reached from an allele is not.\n    const chain = [\n      start.id,\n      ...interior.filter(id => isBackbone(byId.get(id)!)),\n      end.id,\n    ]\n    const chainBroken = chain.some(\n      (id, k) => k > 0 && !linked.has(`${chain[k - 1]}>${id}`),\n    )\n    const partial = chainBroken || walksLeave\n    const fallback = chainBroken && !crossed\n    bubbles.push({\n      refName: start.stable.refName,\n      start: refStart,\n      end: refEnd,\n      segmentCount: interior.length + 2,\n      pathCount: routes.n,\n      // a real inversion test needs each walk's direction relative to the\n      // reference; the first visit's strand is just whichever path anchored the\n      // node\n      inversion: false,\n      shortestAlleleLength: fallback ? refEnd - refStart : routes.min,\n      longestAlleleLength: fallback ? refEnd - refStart : routes.max,\n      segments: [start, ...interior.map(id => byId.get(id)!), end]\n        .map(n => n.name)\n        .join(','),\n      shortestAllele: undefined,\n      longestAllele: undefined,\n      partial,\n      routes: crossed?.routes,\n    })\n  }\n  return bubbles\n}\n\n// For every walk that passes both boundary nodes, the bp between them and the\n// step sequence, so routes are distinct sequences and lengths are the true\n// haplotype lengths. `left` counts the walks that pass one boundary and end\n// before the other.\n//\n// `byId` is the caller's: this runs once per bubble, and a map of every node\n// built here made the whole pass quadratic, seven seconds at 15k nodes.\nfunction walkRoutes(\n  graph: Graph,\n  byId: Map<string, GraphNode>,\n  walkIndex: Map<string, number>[],\n  startId: string,\n  endId: string,\n): (Routes & { left: number; routes: BubbleRoute[] }) | undefined {\n  const seen = new Map<string, BubbleRoute>()\n  let min = Infinity\n  let max = -Infinity\n  let left = 0\n  graph.paths!.forEach((p, k) => {\n    const i0 = walkIndex[k]!.get(startId)\n    const i1 = walkIndex[k]!.get(endId)\n    if (i0 === undefined || i1 === undefined) {\n      if (i0 !== undefined || i1 !== undefined) {\n        left++\n      }\n      return\n    }\n    // Start to end, whichever way the walk crosses: a contig on the reverse\n    // strand takes the same route, and read end-first it keyed as a second one.\n    const steps = p.nodeIds.slice(Math.min(i0, i1) + 1, Math.max(i0, i1))\n    if (i1 < i0) {\n      steps.reverse()\n    }\n    let bp = 0\n    for (const id of steps) {\n      bp += byId.get(id)?.length ?? 0\n    }\n    const key = steps.join(',')\n    const route = seen.get(key) ?? { steps, bp, walks: [] }\n    route.walks.push(p.name)\n    seen.set(key, route)\n    min = Math.min(min, bp)\n    max = Math.max(max, bp)\n  })\n  return seen.size || left\n    ? { min, max, n: seen.size, left, routes: [...seen.values()] }\n    : undefined\n}\n", "import type { Graph } from '../types'\n\n// The graph inside one bubble: the segments the bubble row names, with the\n// links among them. The row's list includes the two backbone segments the\n// bubble hangs between, so the cut keeps its anchors and every layout that\n// needs a backbone still has one. A walk keeps the steps it takes inside the\n// bubble, so the bubbles derived inside it still read their routes and\n// lengths off the haplotypes, and carriage still sets node width.\nexport function bubbleSubgraph(graph: Graph, segmentIds: string[]): Graph {\n  const keep = new Set(segmentIds)\n  const nodes = graph.nodes.filter(n => keep.has(n.name))\n  const ids = new Set(nodes.map(n => n.id))\n  const paths = graph.paths\n    ?.map(p => ({ ...p, nodeIds: p.nodeIds.filter(id => ids.has(id)) }))\n    .filter(p => p.nodeIds.length > 0)\n  return {\n    name: graph.name,\n    nodes,\n    edges: graph.edges.filter(e => ids.has(e.from) && ids.has(e.to)),\n    ...(paths?.length ? { paths } : {}),\n    anchorPaths: graph.anchorPaths,\n    pathVisits: graph.pathVisits,\n    anchoredBy: graph.anchoredBy,\n    referencePath: graph.referencePath,\n  }\n}\n", "import type { Feature } from '@jbrowse/core/util'\n\n// A gene as the pins need it: its name, its span on the reference, and the\n// exons of all its transcripts merged into one set of intervals.\nexport interface GeneModel {\n  name: string\n  refName: string\n  start: number\n  end: number\n  strand: number\n  exons: { start: number; end: number }[]\n}\n\n// The adapters whose tracks hold gene models, in the order the session's\n// tracks are searched when no track is named.\nexport const GENE_ADAPTER_TYPES = new Set([\n  'Gff3TabixAdapter',\n  'Gff3Adapter',\n  'GtfTabixAdapter',\n  'GtfAdapter',\n  'BigBedAdapter',\n  'NCListAdapter',\n])\n\nconst GENE_TRACK_HINT = /gene|refseq|gencode|ensembl|annotation/i\n\n// Which of the session's tracks to read genes from: the named one, else the\n// first gene-bearing track on the assembly whose name says it is annotation,\n// else the first gene-bearing track at all.\nexport function pickGeneTrack<\n  T extends { trackId: string; name?: string; adapterType: string },\n>(tracks: T[], named: string) {\n  if (named) {\n    return tracks.find(t => t.trackId === named)\n  }\n  const candidates = tracks.filter(t => GENE_ADAPTER_TYPES.has(t.adapterType))\n  return (\n    candidates.find(t =>\n      GENE_TRACK_HINT.test(`${t.trackId} ${t.name ?? ''}`),\n    ) ?? candidates[0]\n  )\n}\n\ntype FeatureLike = Feature | Record<string, unknown>\n\nfunction field(f: FeatureLike, name: string): unknown {\n  return typeof (f as Feature).get === 'function'\n    ? (f as Feature).get(name)\n    : (f as Record<string, unknown>)[name]\n}\n\nfunction exonsOf(f: FeatureLike, into: { start: number; end: number }[]) {\n  const type = field(f, 'type')\n  if (type === 'exon') {\n    into.push({\n      start: field(f, 'start') as number,\n      end: field(f, 'end') as number,\n    })\n  }\n  const children = field(f, 'subfeatures') as FeatureLike[] | undefined\n  for (const child of children ?? []) {\n    exonsOf(child, into)\n  }\n}\n\nfunction merged(intervals: { start: number; end: number }[]) {\n  const sorted = [...intervals].sort((a, b) => a.start - b.start)\n  const out: { start: number; end: number }[] = []\n  for (const iv of sorted) {\n    const last = out.at(-1)\n    if (last && iv.start <= last.end) {\n      last.end = Math.max(last.end, iv.end)\n    } else {\n      out.push({ ...iv })\n    }\n  }\n  return out\n}\n\n// Genes from a track's features: every top-level feature, named by the first\n// of gene_name, name and id it carries, with the exons found anywhere under it\n// merged. A feature with no exons is one exon, its whole span.\nexport function geneModelsFrom(features: FeatureLike[]): GeneModel[] {\n  const genes: GeneModel[] = []\n  for (const f of features) {\n    const name =\n      (field(f, 'gene_name') as string | undefined) ??\n      (field(f, 'name') as string | undefined) ??\n      (field(f, 'id') as string | undefined)\n    const start = field(f, 'start') as number\n    const end = field(f, 'end') as number\n    if (!name || !(end > start)) {\n      continue\n    }\n    const exons: { start: number; end: number }[] = []\n    exonsOf(f, exons)\n    genes.push({\n      name,\n      refName: field(f, 'refName') as string,\n      start,\n      end,\n      strand: (field(f, 'strand') as number | undefined) ?? 0,\n      exons: exons.length ? merged(exons) : [{ start, end }],\n    })\n  }\n  return genes\n}\n", "import { firstNodeAtOrAfter, isBackbone } from '../anchoredNodes'\nimport { polylineSlice } from '../layout/mergeRuns'\nimport { svgPath } from '../util/geometry'\n\nimport type { GeneModel } from './geneFeatures'\nimport type { AnchoredNode } from '../anchoredNodes'\nimport type { Graph, NodeSegment } from '../types'\n\n// A gene drawn onto the graph: its exons as stretches of the backbone nodes\n// that carry them, in layout units, and one point on the backbone to pin its\n// name to. Only the backbone has coordinates, so an allele shows no exon even\n// where a haplotype's own annotation would put one.\nexport interface GenePin {\n  gene: GeneModel\n  // an SVG path of the exon stretches, in layout units\n  exons: string\n  // where the name goes: the backbone point at the gene's midpoint, or the\n  // nearest backbone point inside the gene where the midpoint is not in the cut\n  at: NodeSegment\n  // how much of the gene's span the cut's backbone covers, so a label can say\n  // when a gene runs off the cut\n  covered: number\n}\n\n// A backbone node names its sequence the way the graph does, `GRCh38#0#chr6`,\n// and a gene the way the assembly does, `chr6`; the contig is the part they\n// share.\nfunction contig(name: string) {\n  return name.split('#').at(-1)!\n}\n\n// The backbone of one contig in offset order, for finding the nodes a gene\n// lies over without reading the rest. `reach` is the longest node: a node over\n// a gene's start begins no further before it than that.\ninterface ContigBackbone {\n  nodes: AnchoredNode[]\n  reach: number\n}\n\nexport function genePins(\n  graph: Graph,\n  genes: GeneModel[],\n  positions: Record<string, NodeSegment[]>,\n): GenePin[] {\n  // Per contig and sorted once, so a gene reads the few nodes it lies over.\n  // Every gene used to read every backbone node, splitting both names each\n  // time, on each frame of a node drag: 199 ms for 100 genes over 15k nodes,\n  // now 12.\n  const byContig = new Map<string, ContigBackbone>()\n  const contigOf = new Map<string, string>()\n  for (const node of graph.nodes) {\n    if (isBackbone(node) && positions[node.id]?.length) {\n      const { refName } = node.stable\n      const name =\n        contigOf.get(refName) ??\n        contigOf.set(refName, contig(refName)).get(refName)!\n      const entry =\n        byContig.get(name) ??\n        byContig.set(name, { nodes: [], reach: 0 }).get(name)!\n      entry.nodes.push(node)\n      entry.reach = Math.max(entry.reach, node.length)\n    }\n  }\n  for (const { nodes } of byContig.values()) {\n    nodes.sort((a, b) => a.stable.start - b.stable.start)\n  }\n  const pins: GenePin[] = []\n  for (const gene of genes) {\n    const backbone = byContig.get(contig(gene.refName))\n    if (!backbone) {\n      continue\n    }\n    const parts: string[] = []\n    let at: NodeSegment | undefined\n    let atDistance = Infinity\n    let covered = 0\n    const mid = (gene.start + gene.end) / 2\n    const { nodes, reach } = backbone\n    for (\n      let i = firstNodeAtOrAfter(nodes, gene.start - reach);\n      i < nodes.length && nodes[i]!.stable.start < gene.end;\n      i++\n    ) {\n      const node = nodes[i]!\n      const nodeStart = node.stable.start\n      const nodeEnd = nodeStart + node.length\n      if (nodeEnd <= gene.start) {\n        continue\n      }\n      const line = positions[node.id]!\n      covered += Math.min(nodeEnd, gene.end) - Math.max(nodeStart, gene.start)\n      for (const exon of gene.exons) {\n        const a = Math.max(exon.start, nodeStart)\n        const b = Math.min(exon.end, nodeEnd)\n        if (b <= a) {\n          continue\n        }\n        const stretch = polylineSlice(\n          line,\n          (a - nodeStart) / node.length,\n          (b - nodeStart) / node.length,\n        )\n        if (stretch.length === 1) {\n          stretch.push({ ...stretch[0]! })\n        }\n        parts.push(svgPath(stretch))\n      }\n      const pinBp = Math.min(Math.max(mid, nodeStart), nodeEnd)\n      const distance = Math.abs(pinBp - mid)\n      if (distance < atDistance) {\n        atDistance = distance\n        const [p] = polylineSlice(\n          line,\n          (pinBp - nodeStart) / node.length,\n          (pinBp - nodeStart) / node.length,\n        )\n        at = p\n      }\n    }\n    if (at) {\n      pins.push({\n        gene,\n        exons: parts.join(''),\n        at,\n        covered: covered / (gene.end - gene.start),\n      })\n    }\n  }\n  return pins\n}\n", "// Minimal GFA (Graphical Fragment Assembly) text parser shared by the graph\n// pangenome plugins (GraphGenomeView, TubeMapView). Handles GFA1/GFA2 segment,\n// link, edge, path and walk records plus header tags.\n\n// Only the first two colons delimit a tag; everything after them is the value.\n// A Z value may contain colons of its own, and rGFA stable names routinely do\n// (`SN:Z:chr1:1-1000` from a sliced reference), where splitting on every colon\n// silently truncates the name to `chr1` and mis-anchors the whole layout.\nfunction parseTag(tag: string, tags: Record<string, string | number>) {\n  const nameEnd = tag.indexOf(':')\n  const typeEnd = tag.indexOf(':', nameEnd + 1)\n  if (nameEnd !== -1 && typeEnd !== -1) {\n    const name = tag.slice(0, nameEnd)\n    const type = tag.slice(nameEnd + 1, typeEnd)\n    const val = tag.slice(typeEnd + 1)\n    if (type === 'i' || type === 'f') {\n      tags[name] = +val\n    } else if (type === 'Z') {\n      tags[name] = val\n    }\n  }\n}\n\nfunction parseTags(fields: string[]) {\n  const tags: Record<string, string | number> = {}\n  for (const field of fields) {\n    parseTag(field, tags)\n  }\n  return tags\n}\n\nexport interface GFANode {\n  id: string\n  length: number\n  sequence: string\n  tags: Record<string, string | number>\n}\n\n// rGFA (minigraph) anchors every segment to a reference coordinate: SN is the\n// stable sequence name, SO the offset on it, and SR the stable rank, where 0 is\n// the reference backbone and higher ranks are the sequence that diverges from\n// it. Plain GFA (pggb, odgi, Minigraph-Cactus) carries none of these, which is\n// why coordinates there exist only inside the P/W lines.\nexport interface StableCoordinate {\n  refName: string\n  start: number\n  rank: number\n  // How the anchoring path reads this segment. Only path-derived coordinates\n  // set it: an rGFA segment is by construction forward on the sequence SN\n  // names, so there is nothing there for it to say.\n  strand?: '+' | '-'\n}\n\nexport function stableCoordinate(node: GFANode): StableCoordinate | undefined {\n  const { SN, SO, SR } = node.tags\n  return typeof SN === 'string' &&\n    typeof SO === 'number' &&\n    typeof SR === 'number'\n    ? { refName: SN, start: SO, rank: SR }\n    : undefined\n}\n\nexport interface GFALink {\n  source: string\n  target: string\n  strand1?: string\n  strand2?: string\n  cigar: string\n  tags: Record<string, string | number>\n}\n\nexport interface GFAPath {\n  name: string\n  path: string\n  rest: string[]\n}\n\nexport interface GFAWalkSegment {\n  id: string\n  strand: string\n}\n\nexport interface GFAWalk {\n  sample: string\n  haplotype: number\n  contig: string\n  start: number\n  end: number\n  segments: GFAWalkSegment[]\n  tags: Record<string, string | number>\n}\n\nconst GT = 62 // '>'\nconst LT = 60 // '<'\n\n// A W record's body is `>s1<s2>s3\u2026`, and on a Minigraph-Cactus graph one record\n// is the whole walk of one haplotype across a chromosome \u2014 hundreds of\n// thousands of steps in a single field.\n//\n// So the ids are cut out by index rather than accumulated a character at a\n// time. `current += ch` builds and discards one string per character of every\n// id, and it dominated the parse: a file whose single W record walks 200k steps\n// went from ~55 ms to ~24 ms by slicing instead. `pnpm bench` keeps the number.\nfunction parseWalkBody(body: string) {\n  const segments: GFAWalkSegment[] = []\n  let strand = '+'\n  let start = 0\n  // An empty run \u2014 a leading delimiter, or two in a row \u2014 names no segment.\n  function push(end: number) {\n    if (end > start) {\n      segments.push({ id: body.slice(start, end), strand })\n    }\n  }\n  for (let i = 0; i < body.length; i++) {\n    const ch = body.charCodeAt(i)\n    if (ch === GT || ch === LT) {\n      push(i)\n      strand = ch === GT ? '+' : '-'\n      start = i + 1\n    }\n  }\n  push(body.length)\n  return segments\n}\n\nexport interface GFAGraph {\n  nodes: GFANode[]\n  links: GFALink[]\n  paths: GFAPath[]\n  walks: GFAWalk[]\n  header: Record<string, string | number>[]\n  id: string\n}\n\nexport function parseGFA(file: string) {\n  const graph: GFAGraph = {\n    nodes: [],\n    links: [],\n    paths: [],\n    walks: [],\n    header: [],\n    id: '',\n  }\n\n  // \\r is stripped rather than split on, so a CRLF file does not leave it on\n  // whichever field happens to be last: a trailing Z tag would carry it into a\n  // stable name and a trailing cigar into the CIGAR string.\n  //\n  // Stripped per line inside the loop rather than with a .map() over the split,\n  // which would hold a second copy of every line in the file at once.\n  for (const rawLine of file.split('\\n')) {\n    const line = rawLine.endsWith('\\r') ? rawLine.slice(0, -1) : rawLine\n    if (line.startsWith('H')) {\n      const [, ...rest] = line.split('\\t')\n      graph.header.push(parseTags(rest))\n    } else if (line.startsWith('S')) {\n      const [, name, ...rest] = line.split('\\t')\n      let len: number\n      let seq: string\n      let tagfields: string[]\n      let gfa1 = false\n      // A truncated record has no field to read; `*` is what the spec writes for\n      // a segment whose sequence is absent, so treating a missing one the same\n      // way yields a 0 bp segment instead of throwing partway through the file.\n      const first = rest[0] ?? '*'\n      // GFA2 puts an integer length in this field, GFA1 the sequence. Testing\n      // the digits rather than the coerced number keeps a GFA2 `S sid 0 *` from\n      // being read as a GFA1 sequence of \"0\".\n      if (/^\\d+$/.test(first)) {\n        len = +first\n        seq = rest[1] ?? '*'\n        tagfields = rest.slice(2)\n      } else {\n        gfa1 = true\n        seq = first\n        // `*` is GFA1's \"no sequence here\"; its length is whatever LN says\n        // below, and 0 if the file states none. Counting the placeholder's own\n        // character instead reports every such segment as 1 bp.\n        len = seq === '*' ? 0 : seq.length\n        tagfields = rest.slice(1)\n      }\n      const tags = parseTags(tagfields)\n      if (gfa1 && 'LN' in tags) {\n        len = +tags.LN\n      }\n      graph.nodes.push({ id: name!, length: len, sequence: seq, tags })\n    } else if (line.startsWith('E')) {\n      // From here down, a record cut off before the fields that make it a\n      // link, walk or path states nothing drawable and is dropped; the file\n      // around it still reads. A link missing only its overlap is kept.\n      const [, , source, target, , , , , cigar, ...rest] = line.split('\\t')\n      if (source && target) {\n        graph.links.push({\n          source: source.slice(0, -1),\n          target: target.slice(0, -1),\n          strand1: source.at(-1),\n          strand2: target.at(-1),\n          cigar: cigar ?? '*',\n          tags: parseTags(rest),\n        })\n      }\n    } else if (line.startsWith('L')) {\n      const [, source, strand1, target, strand2, cigar, ...rest] =\n        line.split('\\t')\n      if (source && target && strand2) {\n        graph.links.push({\n          source,\n          target,\n          strand1,\n          strand2,\n          cigar: cigar ?? '*',\n          tags: parseTags(rest),\n        })\n      }\n    } else if (line.startsWith('W')) {\n      const [, sample, hap, contig, start, end, body, ...rest] =\n        line.split('\\t')\n      if (sample && hap && contig && start && end && body) {\n        graph.walks.push({\n          sample,\n          haplotype: +hap,\n          contig,\n          start: start === '*' ? -1 : +start,\n          end: end === '*' ? -1 : +end,\n          segments: parseWalkBody(body),\n          tags: parseTags(rest),\n        })\n      }\n    } else if (line.startsWith('P')) {\n      const [, name, path, ...rest] = line.split('\\t')\n      if (name && path) {\n        graph.paths.push({ name, path, rest })\n      }\n    }\n  }\n  return graph\n}\n", "import { stableCoordinate } from '../../gfa-core/index'\nimport { pathOrigin, surveyPaths } from '../pathAnchoring'\n\nimport type { GFAGraph, GFANode } from '../../gfa-core/index'\nimport type { PathSteps } from '../pathAnchoring'\nimport type { Graph, GraphEdge, GraphNode, GraphPath } from '../types'\n\n// Single pass over every reference a GFA makes to a segment, collecting the two\n// things the drawn graph needs from them.\n//\n// `canonical` is the one orientation each segment is drawn in, which is what\n// Bandage calls single-node mode. A segment is the same sequence read either\n// way (`L 1 + 2 +` is the same edge as `L 2 - 1 -`), so `1+` and `1-` are one\n// node, not two: drawing both doubles every segment, and since the L lines only\n// wire one of the pair, the other copy has no edges at all and scatters loose\n// across the layout. Links carry the topology, so their orientation wins; a\n// segment only paths mention takes the orientation they walk it in.\n//\n// `traversals` is how many paths cross each segment. Assembly GFAs carry read\n// depth in a dp/RC/FC/KC tag, but a pangenome GFA (odgi, vg) carries none \u2014\n// there the meaningful depth is how many samples go through the segment, i.e.\n// core versus accessory sequence.\nfunction surveySegments(gfaGraph: GFAGraph) {\n  const canonical = new Map<string, '+' | '-'>()\n  const traversals = new Map<string, number>()\n  function claim(id: string, strand: '+' | '-') {\n    if (!canonical.has(id)) {\n      canonical.set(id, strand)\n    }\n  }\n  function traverse(id: string, strand: '+' | '-') {\n    claim(id, strand)\n    traversals.set(id, (traversals.get(id) ?? 0) + 1)\n  }\n  for (const link of gfaGraph.links) {\n    claim(link.source, link.strand1 === '-' ? '-' : '+')\n    claim(link.target, link.strand2 === '-' ? '-' : '+')\n  }\n  for (const gfaPath of gfaGraph.paths) {\n    for (const segment of gfaPath.path.split(',')) {\n      traverse(segment.slice(0, -1), segment.endsWith('-') ? '-' : '+')\n    }\n  }\n  for (const walk of gfaGraph.walks) {\n    for (const seg of walk.segments) {\n      traverse(seg.id, seg.strand === '-' ? '-' : '+')\n    }\n  }\n  return { canonical, traversals }\n}\n\n// P and W state the same thing in different shapes: a P body is a comma-joined\n// `<id><strand>` list whose start offset lives in the record's *name*, a W\n// record arrives already split into steps and states its start as a field.\n// Normalized here so the coordinate walk sees one kind of path.\nfunction anchorablePaths(gfaGraph: GFAGraph): PathSteps[] {\n  return [\n    ...gfaGraph.paths.map(p => ({\n      ...pathOrigin(p.name),\n      steps: p.path.split(',').map(segment => ({\n        id: segment.slice(0, -1),\n        strand: segment.endsWith('-') ? ('-' as const) : ('+' as const),\n      })),\n    })),\n    ...gfaGraph.walks.map(w => ({\n      name: `${w.sample}#${w.haplotype}#${w.contig}`,\n      // `*` parses to -1, meaning the record declines to say; 0 is then the\n      // only offset that can be assumed, and it makes the walk self-relative\n      // rather than wrong\n      start: w.start === -1 ? 0 : w.start,\n      steps: w.segments.map(s => ({\n        id: s.id,\n        strand: s.strand === '-' ? ('-' as const) : ('+' as const),\n      })),\n    })),\n  ]\n}\n\n// Carriage stated as a tag rather than derived from a walk. `RgfaTabixAdapter`\n// synthesizes its S-lines from a segs.bed whose sixth column is a list of GFA\n// tags, and `scripts/pggb_gfa_to_bed.py` in jbrowse-components puts every\n// haplotype that visits a segment there as `SM:Z:K12.1,Sakai.1`. That is the\n// only way carriage reaches an INDEXED graph: the cut has no P or W lines to\n// walk, so `pathAnchoring` has no visits to derive it from.\n//\n// It does not compete with that walk. `pathAnchoring.anchorNode` rebuilds\n// `samples` from the visits whenever there are any, so a graph loaded as a file\n// keeps the authoritative path-derived set and this is what a tabix cut falls\n// back to.\nfunction carriedSamples(gfaNode: GFANode) {\n  const sm = gfaNode.tags.SM\n  if (typeof sm !== 'string') {\n    return undefined\n  }\n  const samples = sm\n    .split(',')\n    .map(s => s.trim())\n    .filter(Boolean)\n  return samples.length > 0 ? samples : undefined\n}\n\nconst positive = (v: unknown) =>\n  typeof v === 'number' && v > 0 ? v : undefined\n\n// The depth a segment states, or undefined. DP is a depth in either case it is\n// written. RC, FC and KC are read, fragment and k-mer counts, so depth is the\n// count over the length: taken raw, a 100 kb node at 5x outweighed a 1 kb node\n// at 50x tenfold in every width drawn from it.\nfunction statedDepth({ tags, length }: GFANode) {\n  const count = positive(tags.RC) ?? positive(tags.FC) ?? positive(tags.KC)\n  return (\n    positive(tags.dp) ??\n    positive(tags.DP) ??\n    (count !== undefined && length > 0 ? count / length : undefined)\n  )\n}\n\nfunction makeNode(\n  gfaNode: GFANode,\n  strand: '+' | '-',\n  depth: number,\n): GraphNode {\n  return {\n    id: `${gfaNode.id}${strand}`,\n    name: gfaNode.id,\n    length: gfaNode.length,\n    depth,\n    stable: stableCoordinate(gfaNode),\n    samples: carriedSamples(gfaNode),\n  }\n}\n\nexport function convertGFAToGraph(gfaGraph: GFAGraph, name = 'Imported GFA') {\n  const nodes: GraphNode[] = []\n  const edges: GraphEdge[] = []\n\n  const { canonical, traversals } = surveySegments(gfaGraph)\n  // segments no link, path, or walk mentions are drawn forward-strand\n  const nodeId = (segmentId: string) =>\n    `${segmentId}${canonical.get(segmentId) ?? '+'}`\n\n  for (const gfaNode of gfaGraph.nodes) {\n    const depth =\n      statedDepth(gfaNode) ?? Math.max(traversals.get(gfaNode.id) ?? 1, 1)\n    nodes.push(makeNode(gfaNode, canonical.get(gfaNode.id) ?? '+', depth))\n  }\n\n  for (const link of gfaGraph.links) {\n    edges.push({\n      from: nodeId(link.source),\n      to: nodeId(link.target),\n      fromStrand: link.strand1 === '-' ? '-' : '+',\n      toStrand: link.strand2 === '-' ? '-' : '+',\n    })\n  }\n\n  const paths: GraphPath[] = []\n  const edgeToPathsMap = new Map<string, Set<string>>()\n\n  // A path that walks the graph on the reverse strand visits an edge's nodes in\n  // the opposite order to the L line that declared it, so the key is unordered.\n  const edgeKey = (a: string, b: string) => [a, b].sort().join('--')\n\n  function recordPathEdges(nodeIds: string[], name: string) {\n    for (let i = 0; i < nodeIds.length - 1; i++) {\n      const key = edgeKey(nodeIds[i]!, nodeIds[i + 1]!)\n      if (!edgeToPathsMap.has(key)) {\n        edgeToPathsMap.set(key, new Set())\n      }\n      edgeToPathsMap.get(key)!.add(name)\n    }\n  }\n\n  for (const gfaPath of gfaGraph.paths) {\n    // path segments arrive as `<id><strand>`; the node they land on is the\n    // segment's canonical orientation, whichever way this path reads it\n    const nodeIds = gfaPath.path\n      .split(',')\n      .map(segment => nodeId(segment.slice(0, -1)))\n    paths.push({ name: gfaPath.name, nodeIds } satisfies GraphPath)\n    recordPathEdges(nodeIds, gfaPath.name)\n  }\n\n  for (const walk of gfaGraph.walks) {\n    const nodeIds = walk.segments.map(seg => nodeId(seg.id))\n    // The full PanSN name, contig included, which is also what `anchorablePaths`\n    // above calls the same record. Dropping the contig made a path's name an\n    // ASSEMBLY's name, and one assembly walks one W record per contig: two walks\n    // of `HG00438#1` then shared an identity, so `edgeToPathsMap` merged them,\n    // `pathColors` (keyed by name) kept only the last colour written while the\n    // node stripes kept the first, and the key drew one haplotype twice in two\n    // colours. That is the ordinary Minigraph-Cactus shape, not a corner case.\n    //\n    // The legend narrows it back: `labelTiers` tries sample, then sample and\n    // haplotype, then the whole name, so a graph with one contig per haplotype\n    // is labelled exactly as before and only a colliding one widens.\n    const name = `${walk.sample}#${walk.haplotype}#${walk.contig}`\n    paths.push({\n      name,\n      nodeIds,\n      sample: walk.sample,\n      haplotype: walk.haplotype,\n      contig: walk.contig,\n    } satisfies GraphPath)\n    recordPathEdges(nodeIds, name)\n  }\n\n  for (const edge of edges) {\n    const pathIds = edgeToPathsMap.get(edgeKey(edge.from, edge.to))\n    if (pathIds && pathIds.size > 0) {\n      edge.pathIds = [...pathIds]\n    }\n  }\n\n  // Only walked when the file has paths to walk, so an rGFA \u2014 which has none at\n  // all \u2014 pays nothing for it. `lengthOf` reads the segment table rather than\n  // the nodes just built, because a path may name a segment no S line declared.\n  const lengths = new Map(gfaGraph.nodes.map(n => [n.id, n.length]))\n  const anchoring =\n    gfaGraph.paths.length > 0 || gfaGraph.walks.length > 0\n      ? surveyPaths(anchorablePaths(gfaGraph), id => lengths.get(id) ?? 0)\n      : undefined\n\n  return {\n    name,\n    nodes,\n    edges,\n    paths: paths.length > 0 ? paths : undefined,\n    anchorPaths: anchoring?.anchorPaths,\n    pathVisits: anchoring?.pathVisits,\n    // rGFA's own tags win wherever they are present; pathAnchoring only ever\n    // fills in for a graph that carries none.\n    anchoredBy: nodes.some(n => n.stable) ? 'tags' : undefined,\n  } satisfies Graph\n}\n", "import type { SubgraphRegion } from '../launchSubgraph/launchSubgraphView'\n\n// The members of a LinearGenomeView a hosted pane reads and drives.\n// Structural, because this plugin takes no runtime dependency on the LGV\n// plugin (see hoverSync/index.tsx).\nexport interface HostBlock {\n  refName: string\n  assemblyName: string\n  start: number\n  end: number\n  offsetPx: number\n  reversed?: boolean\n  displayedRegionIndex?: number\n}\n\nexport interface LinearHost {\n  id: string\n  initialized: boolean\n  bpPerPx: number\n  offsetPx: number\n  width: number\n  displayedRegions: readonly { start: number; end: number }[]\n  dynamicBlocks: { contentBlocks: readonly HostBlock[] }\n  coarseDynamicBlocks: readonly HostBlock[]\n  horizontalScroll: (distance: number) => number\n  zoomTo: (bpPerPx: number, offset?: number) => number\n}\n\nexport function isLinearHost(view: unknown): view is LinearHost {\n  if (typeof view !== 'object' || view === null) {\n    return false\n  }\n  const v = view as Record<string, unknown>\n  return (\n    typeof v.horizontalScroll === 'function' &&\n    typeof v.zoomTo === 'function' &&\n    'coarseDynamicBlocks' in v &&\n    'dynamicBlocks' in v\n  )\n}\n\n// launchSubgraphView's widestBlock, restated rather than imported: that module\n// imports the model, which imports this.\nfunction widest(blocks: readonly HostBlock[]) {\n  return blocks.reduce<HostBlock | undefined>(\n    (best, b) => (best && best.end - best.start >= b.end - b.start ? best : b),\n    undefined,\n  )\n}\n\nexport interface HostWindow {\n  refName: string\n  assemblyName: string\n  start: number\n  end: number\n  bpPerPx: number\n  // the view's width in bp, which the margin is sized by: a block at a contig\n  // end is clipped, the zoom is not\n  span: number\n  regionStart: number\n  regionEnd: number\n}\n\n// x is reference bp on an anchored layout, so the graph shows what the linear\n// view shows when one bp is as many px in both and the cut's refName sits at\n// the same screen x. Undefined when the linear view shows no block of that\n// refName, which is a re-cut's job rather than the frame's.\nexport function hostFrame(view: LinearHost, region: SubgraphRegion) {\n  const block = widest(\n    view.dynamicBlocks.contentBlocks.filter(\n      b =>\n        b.refName === region.refName && b.assemblyName === region.assemblyName,\n    ),\n  )\n  const { bpPerPx } = view\n  return block && bpPerPx > 0\n    ? {\n        scale: 1 / bpPerPx,\n        translateX: block.offsetPx - view.offsetPx - block.start / bpPerPx,\n      }\n    : undefined\n}\n\n// Read off the LIVE blocks even when the coarse ones woke the caller: those\n// name where the window was half a second ago (SyntenyFollow/CLAUDE.md).\nexport function hostWindow(view: LinearHost): HostWindow | undefined {\n  const block = widest(view.dynamicBlocks.contentBlocks)\n  const displayed =\n    block?.displayedRegionIndex === undefined\n      ? undefined\n      : view.displayedRegions[block.displayedRegionIndex]\n  return block && view.bpPerPx > 0\n    ? {\n        refName: block.refName,\n        assemblyName: block.assemblyName,\n        start: block.start,\n        end: block.end,\n        bpPerPx: view.bpPerPx,\n        span: view.bpPerPx * view.width,\n        regionStart: displayed?.start ?? block.start,\n        regionEnd: displayed?.end ?? block.end,\n      }\n    : undefined\n}\n\n// The window plus one window-width each side, clamped to the displayed\n// region, with the margins narrowed until the whole cut fits under `capBp`.\nexport function hostCut(window: HostWindow, capBp: number): SubgraphRegion {\n  const visible = window.end - window.start\n  const margin = Math.max(0, Math.min(window.span, (capBp - visible) / 2))\n  return {\n    refName: window.refName,\n    assemblyName: window.assemblyName,\n    start: Math.max(window.regionStart, Math.floor(window.start - margin)),\n    end: Math.min(window.regionEnd, Math.ceil(window.end + margin)),\n  }\n}\n\nexport function cutHolds(cut: SubgraphRegion | undefined, window: HostWindow) {\n  return (\n    cut?.refName === window.refName &&\n    cut.assemblyName === window.assemblyName &&\n    cut.start <= window.start &&\n    window.end <= cut.end\n  )\n}\n", "import { setConf } from '@jbrowse/core/configuration'\nimport { getSnapshot } from '@jbrowse/mobx-state-tree'\n\nimport type { AnyConfigurationModel } from '@jbrowse/core/configuration'\n\n// The graph's own off-ramp charcoal, for a segment with no reference\n// coordinate (GeometryBuilder's REFERENCE_RAMP_ALT_COLOR).\nexport const OFF_REFERENCE_COLOR = 'rgb(60,65,72)'\n\n// The reference-position ramp as a `color` expression a linear track can run:\n// hue 0 to 300 over the domain by the feature's reference midpoint, the same\n// function of the same two numbers the graph paints its nodes with. `rank` is\n// what RgfaTabixAdapter puts on a feature; a track carrying none reads\n// `undefined > 0` as false and stays on the ramp.\nexport function referencePositionColor({\n  start,\n  end,\n}: {\n  start: number\n  end: number\n}) {\n  const mid = \"(get(feature,'start')+get(feature,'end'))/2\"\n  const hue = `min(300, max(0, (${mid} - ${start}) / ${end - start} * 300))`\n  return `jexl:get(feature,'rank')>0 ? '${OFF_REFERENCE_COLOR}' : 'hsl(' + ${hue} + ',70%,50%)'`\n}\n\nexport interface LaneDisplay {\n  type: string\n  configuration: AnyConfigurationModel\n}\n\ninterface LaneTrack {\n  configuration: { trackId: string }\n  displays: LaneDisplay[]\n}\n\ninterface LaneView {\n  id: string\n  tracks?: LaneTrack[]\n}\n\nfunction isLaneView(view: unknown): view is LaneView {\n  return (\n    typeof view === 'object' &&\n    view !== null &&\n    'id' in view &&\n    Array.isArray((view as { tracks?: unknown }).tracks)\n  )\n}\n\n// The display a graph was cut from: the track by id in the linear view it is\n// paired with, or in any linear view holding it when the graph was never\n// paired (a hand-written session), the same rule the hover sync uses.\nexport function sourceLaneDisplay(\n  views: unknown[],\n  connectedViewId: string | undefined,\n  trackId: string,\n) {\n  for (const view of views) {\n    if (\n      isLaneView(view) &&\n      (connectedViewId === undefined || view.id === connectedViewId)\n    ) {\n      const track = view.tracks?.find(t => t.configuration.trackId === trackId)\n      const display = track?.displays[0]\n      if (display?.type === 'LinearBasicDisplay') {\n        return display\n      }\n    }\n  }\n  return undefined\n}\n\n// Idempotent, since the autorun that calls this re-fires on every domain read.\n// A host at 5.0.0-beta.9 or later keeps `color` as a channel object whose\n// `value` holds the expression; earlier hosts keep the bare string.\nexport function paintSourceLane(display: LaneDisplay, color: string) {\n  const { color: current } = getSnapshot(display.configuration) as {\n    color?: unknown\n  }\n  const painted =\n    typeof current === 'object' && current !== null && 'value' in current\n      ? current.value\n      : current\n  if (painted !== color) {\n    setConf(display, 'color', color)\n  }\n}\n", "import { isBackbone } from '../anchoredNodes'\n\nimport type { Graph, NodeSegment } from '../types'\n\ntype Positions = Record<string, NodeSegment[]>\n\n// Turn a finished force layout so the reference runs left to right: the\n// rotation that best maps backbone midpoints onto their reference coordinate\n// (a one-dimensional orthogonal Procrustes fit, weighted by segment length),\n// then a reflection so the off-reference mass sits below the axis. A rigid\n// transform, so the drawing FMMM made is unchanged; only its frame moves.\n//\n// About the length-weighted centroid, and translated back, so a drawing that is\n// already oriented comes back where it was rather than recentred on the origin.\nexport function orientToReference(graph: Graph, positions: Positions) {\n  const backbone = graph.nodes.filter(\n    node => isBackbone(node) && (positions[node.id]?.length ?? 0) > 0,\n  )\n  if (backbone.length < 2) {\n    return positions\n  }\n  const points = backbone.map(node => {\n    const segments = positions[node.id]!\n    const mid = segments[Math.floor(segments.length / 2)]!\n    return {\n      x: mid.x,\n      y: mid.y,\n      r: node.stable!.start + node.length / 2,\n      w: node.length,\n    }\n  })\n  const weight = points.reduce((sum, p) => sum + p.w, 0)\n  const cx = points.reduce((sum, p) => sum + p.x * p.w, 0) / weight\n  const cy = points.reduce((sum, p) => sum + p.y * p.w, 0) / weight\n  const cr = points.reduce((sum, p) => sum + p.r * p.w, 0) / weight\n  // cross-covariance of (x, y) against (r, 0); only the first row is non-zero\n  let sxr = 0\n  let syr = 0\n  for (const p of points) {\n    sxr += p.w * (p.x - cx) * (p.r - cr)\n    syr += p.w * (p.y - cy) * (p.r - cr)\n  }\n  // the rotation taking the direction (sxr, syr) onto +x\n  const angle = -Math.atan2(syr, sxr)\n  const c = Math.cos(angle)\n  const s = Math.sin(angle)\n\n  const out: Positions = {}\n  for (const [id, segments] of Object.entries(positions)) {\n    out[id] = segments.map(p => {\n      const x = p.x - cx\n      const y = p.y - cy\n      return { x: cx + c * x - s * y, y: cy + s * x + c * y }\n    })\n  }\n\n  let below = 0\n  let above = 0\n  for (const node of graph.nodes) {\n    if (isBackbone(node)) {\n      continue\n    }\n    for (const p of out[node.id] ?? []) {\n      if (p.y > cy) {\n        below++\n      } else {\n        above++\n      }\n    }\n  }\n  if (above > below) {\n    for (const segments of Object.values(out)) {\n      for (const p of segments) {\n        p.y = 2 * cy - p.y\n      }\n    }\n  }\n  return out\n}\n", "import { isBackbone } from '../anchoredNodes'\nimport { buildNeighbors } from '../referenceSpan'\nimport { drawnNodeLength } from './drawnScale'\n\nimport type { LayoutScaling } from './drawnScale'\nimport type { Graph, GraphNode } from '../types'\n\n// A node as the engine takes it: an optional `x`/`y` is where FMMM starts the\n// node's chain (`addToOgdfGraph`, graphlayout.cpp).\nexport type LayoutNode = GraphNode & { x?: number; y?: number }\n\nexport interface Seed {\n  x: number\n  y: number\n}\n\n// y per BFS step off the backbone. FMMM keeps only the coarse shape of these\n// (OGDF applies the initial placement at its coarsest multilevel graph), so\n// the gap needs to say \"below the line\", not to place a lane.\nconst LANE_GAP = 30\n\n// Initial positions for a reference-anchored graph: the backbone end to end\n// along x at drawn length, each off-reference node at the midpoint of the node\n// a BFS from the backbone reached it from, a lane lower per step. Two alleles\n// off one anchor share a seed; FMMM separates them. Nodes no backbone reaches\n// spread along x below everything rather than piling on one point.\n//\n// Lengths come from `scaling.nodes`, not the graph's bp: under a compressing\n// spread a node's `length` crosses the RPC as drawn units times 1000 with a\n// matching `nodeLengthPerMegabase`, and a seed from bp would misplace every\n// chain against the one the engine builds.\nexport function referenceSeeds(\n  graph: Graph,\n  scaling: LayoutScaling,\n): Map<string, Seed> {\n  const { opts } = scaling\n  const drawn = new Map(\n    scaling.nodes.map(node => [node.id, drawnNodeLength(opts, node.length)]),\n  )\n  const drawnOf = (id: string) => drawn.get(id) ?? opts.minimumNodeLength\n  const backbone = graph.nodes\n    .filter(isBackbone)\n    .sort((a, b) => a.stable.start - b.stable.start)\n\n  const seeds = new Map<string, Seed>()\n  let x = 0\n  for (const node of backbone) {\n    seeds.set(node.id, { x, y: 0 })\n    x += drawnOf(node.id) + opts.edgeLength\n  }\n\n  const adjacent = buildNeighbors(graph)\n\n  const depth = new Map(backbone.map(node => [node.id, 0]))\n  // for-of over an array that grows as it goes: the iterator reads the live\n  // length, so nodes pushed here are visited\n  const queue = backbone.map(node => node.id)\n  for (const id of queue) {\n    const at = seeds.get(id)!\n    const next = depth.get(id)! + 1\n    for (const neighbour of adjacent.get(id) ?? []) {\n      if (depth.has(neighbour)) {\n        continue\n      }\n      depth.set(neighbour, next)\n      seeds.set(neighbour, { x: at.x + drawnOf(id) / 2, y: LANE_GAP * next })\n      queue.push(neighbour)\n    }\n  }\n\n  let unreached = 0\n  for (const node of graph.nodes) {\n    if (!seeds.has(node.id)) {\n      seeds.set(node.id, {\n        x: (unreached++ * x) / graph.nodes.length,\n        y: LANE_GAP * 3,\n      })\n    }\n  }\n  return seeds\n}\n\nexport function seededNodes(\n  graph: Graph,\n  scaling: LayoutScaling,\n): LayoutNode[] {\n  const seeds = referenceSeeds(graph, scaling)\n  return scaling.nodes.map(node => ({ ...node, ...seeds.get(node.id) }))\n}\n", "import type { Feature } from '@jbrowse/core/util'\n\nexport interface RepeatCall {\n  bp: number\n  // TRGT's `SD`. Zero means the allele is a copy of the one the reads did\n  // support, so its length states nothing about a second haplotype; absent\n  // where the genotyper writes no such field.\n  spanningReads?: number\n}\n\n// A tandem repeat array as the walk rows need it: its span on the reference,\n// which is what the bars measure between, and its unit length, which is what\n// they tile by. Read off whatever repeat annotation the session has, since the\n// tools all state the same two facts under different names: VCF 4.5's\n// `<CNV:TR>` allele gives `RUL` and `RUS` (one entry per repeat sequence,\n// grouped by `RN`), UCSC simpleRepeat and TRF give `period` and the consensus\n// `sequence`, TRGT gives `MOTIFS` and `TRID`, ExpansionHunter `RU` and `REPID`,\n// HipSTR and GangSTR `PERIOD`, vamos its `motifs`. A VCF record's INFO is\n// searched as well as its top level, and a list's first entry is the unit the\n// bars tile by: for a compound array that is the first repeat sequence, which\n// is the expanding one at every such locus in the common catalogues.\nexport interface RepeatArray {\n  key: string\n  name: string\n  refName: string\n  start: number\n  end: number\n  unit: number\n  motif?: string\n  // Each sample's genotyped alleles, from a genotyper's per-sample `AL`\n  // (TRGT); absent from a catalogue.\n  calls?: Record<string, RepeatCall[]>\n}\n\nexport const REPEAT_ADAPTER_TYPES = new Set([\n  'BedAdapter',\n  'BedTabixAdapter',\n  'BigBedAdapter',\n  'VcfAdapter',\n  'VcfTabixAdapter',\n])\n\nconst REPEAT_TRACK_HINT =\n  /repeat|tandem|\\bstr\\b|vntr|trf|trgt|vamos|expansion|microsat/i\n\nexport function pickRepeatTrack<\n  T extends { trackId: string; name?: string; adapterType: string },\n>(tracks: T[], named: string) {\n  if (named) {\n    return tracks.find(t => t.trackId === named)\n  }\n  const candidates = tracks.filter(t => REPEAT_ADAPTER_TYPES.has(t.adapterType))\n  return candidates.find(t =>\n    REPEAT_TRACK_HINT.test(`${t.trackId} ${t.name ?? ''}`),\n  )\n}\n\ntype FeatureLike = Feature | Record<string, unknown>\n\nfunction own(f: FeatureLike, name: string): unknown {\n  return typeof (f as Feature).get === 'function'\n    ? (f as Feature).get(name)\n    : (f as Record<string, unknown>)[name]\n}\n\n// A TRGT repeat catalogue is a BED whose name column packs the record:\n// `ID=HTT;MOTIFS=CAG,CCG;STRUC=(CAG)nCAACAG(CCG)n`. Read as fields when it\n// has that shape.\nconst PACKED_NAME = /^\\w+=[^;]*(;\\w+=[^;]*)*$/\n\nfunction packedName(f: FeatureLike) {\n  const name = own(f, 'name')\n  if (typeof name !== 'string' || !PACKED_NAME.test(name)) {\n    return undefined\n  }\n  return Object.fromEntries(\n    name.split(';').map(pair => {\n      const i = pair.indexOf('=')\n      return [pair.slice(0, i), pair.slice(i + 1)]\n    }),\n  )\n}\n\n// A field at the feature's top level, in a VCF record's INFO, or in a packed\n// name column, in that order.\nfunction field(f: FeatureLike, name: string): unknown {\n  const top = own(f, name)\n  if (top !== undefined) {\n    return top\n  }\n  const info = own(f, 'INFO') as Record<string, unknown> | undefined\n  return info?.[name] ?? packedName(f)?.[name]\n}\n\nconst MOTIF_FIELDS = [\n  'RUS',\n  'MOTIFS',\n  'RU',\n  'motifs',\n  'motif',\n  'sequence',\n  'consensus',\n]\nconst PERIOD_FIELDS = [\n  'RUL',\n  'period',\n  'PERIOD',\n  'consensusSize',\n  'unit',\n  'unitLength',\n]\nconst NAME_FIELDS = ['TRID', 'REPID', 'VARID', 'ID', 'name', 'id']\n\n// The first entry of a list-valued field, whether it arrived parsed or as\n// the comma-joined text a VCF INFO or a BED column holds; VCF's missing \".\"\n// counts as absent.\nfunction first(f: FeatureLike, names: string[]) {\n  for (const name of names) {\n    const value = field(f, name)\n    const one = String((Array.isArray(value) ? value[0] : value) ?? '')\n      .split(',')[0]!\n      .trim()\n    if (one !== '' && one !== '.') {\n      return one\n    }\n  }\n  return undefined\n}\n\nconst IUPAC = /^[ACGTURYSWKMBDHVN]+$/i\n\n// The unit in bp: a stated period, else the length of the first motif.\nexport function repeatUnitOf(f: FeatureLike) {\n  const period = Number(first(f, PERIOD_FIELDS))\n  if (Number.isFinite(period) && period > 0) {\n    return Math.round(period)\n  }\n  const motif = first(f, MOTIF_FIELDS)\n  return motif && IUPAC.test(motif) ? motif.length : undefined\n}\n\n// A per-sample list field, parsed or as the comma-joined text a VCF column\n// holds. A missing entry stays missing: read as 0, an absent `SD` would make\n// every allele of every genotyper that writes no such field unspanned.\nfunction numbers(value: unknown) {\n  const raw: unknown[] = Array.isArray(value)\n    ? value\n    : String(value ?? '').split(',')\n  return raw.map(one => {\n    const n =\n      one === '' || one === null || one === undefined ? NaN : Number(one)\n    return Number.isFinite(n) ? n : undefined\n  })\n}\n\nfunction callsOf(f: FeatureLike) {\n  const samples = own(f, 'samples') as\n    Record<string, Record<string, unknown>> | undefined\n  const called: Record<string, RepeatCall[]> = {}\n  for (const [sample, fields] of Object.entries(samples ?? {})) {\n    const reads = numbers(fields.SD)\n    const alleles = numbers(fields.AL).flatMap((bp, i) =>\n      bp !== undefined && bp > 0\n        ? [reads[i] === undefined ? { bp } : { bp, spanningReads: reads[i] }]\n        : [],\n    )\n    if (alleles.length > 0) {\n      called[sample] = alleles\n    }\n  }\n  return Object.keys(called).length > 0 ? called : undefined\n}\n\nexport function repeatArraysFrom(features: FeatureLike[]): RepeatArray[] {\n  const arrays: RepeatArray[] = []\n  for (const f of features) {\n    const start = field(f, 'start') as number\n    const end = field(f, 'end') as number\n    const unit = repeatUnitOf(f)\n    if (!(end > start) || unit === undefined) {\n      continue\n    }\n    const refName = field(f, 'refName') as string\n    const motif = first(f, MOTIF_FIELDS)\n    const stated = first(f, NAME_FIELDS)\n    arrays.push({\n      key: `${refName}:${start}-${end}`,\n      name:\n        (stated && !PACKED_NAME.test(stated) ? stated : undefined) ??\n        (motif && motif.length <= 12\n          ? `(${motif})n`\n          : `${refName}:${(start + 1).toLocaleString()}-${end.toLocaleString()}`),\n      refName,\n      start,\n      end,\n      unit,\n      motif,\n      calls: callsOf(f),\n    })\n  }\n  return arrays.sort((a, b) => a.start - b.start)\n}\n", "import { pathOrigin } from './pathAnchoring'\n\nimport type { Graph } from './types'\n\n// One walk lifted out of the drawing: the nodes it visits and the links it\n// takes, so the geometry can fade everything else, plus what it carries\n// through the window against the reference walk.\nexport interface WalkHighlight {\n  name: string\n  nodeIds: Set<string>\n  edgeIndexes: Set<number>\n  steps: number\n  bp: number\n  referenceBp?: number\n}\n\nexport function walkHighlight(\n  graph: Graph,\n  name: string,\n): WalkHighlight | undefined {\n  const path = graph.paths?.find(p => p.name === name)\n  if (!path) {\n    return undefined\n  }\n  const byId = new Map(graph.nodes.map(n => [n.id, n]))\n  const edgeAt = new Map<string, number>()\n  graph.edges.forEach((e, i) => {\n    edgeAt.set(`${e.from}>${e.to}`, i)\n  })\n  const nodeIds = new Set(path.nodeIds)\n  const edgeIndexes = new Set<number>()\n  for (let i = 1; i < path.nodeIds.length; i++) {\n    const a = path.nodeIds[i - 1]!\n    const b = path.nodeIds[i]!\n    const index = edgeAt.get(`${a}>${b}`) ?? edgeAt.get(`${b}>${a}`)\n    if (index !== undefined) {\n      edgeIndexes.add(index)\n    }\n  }\n  const bpOf = (ids: string[]) =>\n    ids.reduce((sum, id) => sum + (byId.get(id)?.length ?? 0), 0)\n  // `referencePath` is the anchor name, which pathOrigin has stripped of the\n  // range suffix odgi leaves on a P record's name\n  const reference = graph.referencePath\n    ? graph.paths!.find(p => pathOrigin(p.name).name === graph.referencePath)\n    : undefined\n  return {\n    name,\n    nodeIds,\n    edgeIndexes,\n    steps: path.nodeIds.length,\n    bp: bpOf(path.nodeIds),\n    referenceBp:\n      reference && reference !== path ? bpOf(reference.nodeIds) : undefined,\n  }\n}\n", "import { isBackbone } from '../GraphGenomeView/anchoredNodes'\n\nimport type { GraphNode } from '../GraphGenomeView/types'\n\n// What a LinearGenomeView writes to `session.hovered` on every mousemove (see\n// LinearGenomeViewContainer): the bp under the cursor, plus the feature under it\n// if the topmost track had one. Nothing names the source VIEW, so a graph view\n// filters by whether the position falls in the region it was cut from \u2014 but the\n// position does name the source ASSEMBLY, and that turns out to be the half\n// that matters.\nexport interface LgvHover {\n  refName: string\n  // The 0-based base under the pointer, the convention `stable.start` and the\n  // cut region are in. Not the LGV's own `coord`, which is 1-based for display.\n  coord: number\n  // The assembly the hovered view is showing. `hoverPosition` is a\n  // `PxToBpResult`, i.e. the displayed region the pointer landed in spread flat,\n  // so this is that region's own `assemblyName`.\n  //\n  // Read because refName alone does not identify a locus in a session holding\n  // several assemblies, which is every session these graphs are launched in. A\n  // PanSN name reduces to a bare contig \u2014 the E. coli pangenome loads five\n  // strains each with one refName `chr`, and HPRC's hg38 and a GenArk haplotype\n  // both call it `chr6` \u2014 so a synteny stack's rows all answer to the same\n  // name at unrelated coordinates. Without this the hover on ANY row lit up a\n  // node in the graph, and the node then published its own reference interval\n  // back into every linear view.\n  //\n  // Optional because the channel is typed `unknown` and read structurally: a\n  // hover that states no assembly is taken at its word rather than dropped.\n  assemblyName?: string\n  featureName?: string\n}\n\nfunction isRecord(value: unknown): value is Record<string, unknown> {\n  return typeof value === 'object' && value !== null\n}\n\ninterface FeatureLike {\n  get: (key: string) => unknown\n}\n\nfunction isFeatureLike(value: unknown): value is FeatureLike {\n  return isRecord(value) && typeof value.get === 'function'\n}\n\n// A display hovers either a Feature, read with `get`, or a plain hit item with\n// a `name` of its own, which is what the canvas feature display hands over.\n// Reading only the first left the exact segment match dead on that display.\nfunction hoveredName(feature: unknown) {\n  const name = isFeatureLike(feature)\n    ? feature.get('name')\n    : isRecord(feature)\n      ? feature.name\n      : undefined\n  return typeof name === 'string' ? name : undefined\n}\n\n// `hovered` is typed `unknown` on the session by design \u2014 it is a shared channel\n// every view writes its own shape to \u2014 so this reads the LGV's shape out of it\n// structurally rather than asserting a type onto it.\nexport function readLgvHover(hovered: unknown): LgvHover | undefined {\n  let result: LgvHover | undefined\n  if (isRecord(hovered) && isRecord(hovered.hoverPosition)) {\n    const { refName, coord, coord0, assemblyName } = hovered.hoverPosition\n    if (typeof refName === 'string' && typeof coord === 'number') {\n      result = {\n        refName,\n        // `coord` is 1-based; a host that states the 0-based `coord0` is\n        // taken at its word. Read as 0-based, the last base of every node lit\n        // the next one, and a 1 bp node could not be reached at all.\n        coord: typeof coord0 === 'number' ? coord0 : coord - 1,\n        assemblyName:\n          typeof assemblyName === 'string' ? assemblyName : undefined,\n        featureName: hoveredName(hovered.hoverFeature),\n      }\n    }\n  }\n  return result\n}\n\n// Whether a hover is one this graph can answer: the same assembly, the same\n// stable sequence, and inside the window the cut was made for.\n//\n// The assembly is checked FIRST and is the whole reason this is not just a\n// coordinate test. See LgvHover.assemblyName: a graph cut from K12 and a\n// synteny row on Sakai both call their sequence `chr`, so on refName and\n// coordinate alone every row of the stack matched and the graph highlighted a\n// K12 node at Sakai's offset. A hover that names no assembly still passes,\n// which is what a hand-written channel writer and the older LGVs get.\nexport function hoverInRegion(\n  hover: LgvHover,\n  region: { refName: string; assemblyName: string; start: number; end: number },\n) {\n  return (\n    (hover.assemblyName === undefined ||\n      hover.assemblyName === region.assemblyName) &&\n    hover.refName === region.refName &&\n    hover.coord >= region.start &&\n    hover.coord < region.end\n  )\n}\n\n// The graph node a linear-view hover points at.\n//\n// The feature under the cursor is the exact answer when the graph's own segments\n// track is what's hovered: an RgfaTabixAdapter feature's name is the segment id,\n// which is `GraphNode.name` (`GraphNode.id` carries a strand suffix, so the\n// match has to be on name). Any other track \u2014 genes, bubbles \u2014 supplies only a\n// coordinate, which still identifies the backbone segment covering it: the\n// backbone tiles the reference exactly once, whether rGFA's rank 0 declared it\n// or a reference path's own steps did.\nexport function nodeForLgvHover({\n  hover,\n  nodes,\n}: {\n  hover: LgvHover\n  nodes: GraphNode[]\n}) {\n  let byName: string | undefined\n  let byCoord: string | undefined\n  for (const node of nodes) {\n    if (node.name === hover.featureName) {\n      byName = node.id\n    } else if (\n      byCoord === undefined &&\n      isBackbone(node) &&\n      hover.coord >= node.stable.start &&\n      hover.coord < node.stable.start + node.length\n    ) {\n      byCoord = node.id\n    }\n  }\n  // An exact segment match wins over the coordinate it happens to sit at.\n  return byName ?? byCoord ?? null\n}\n", "import { readConfObject } from '@jbrowse/core/configuration'\n\nimport { locLabel, locString } from './contributors'\nimport { linearViewTarget } from './linearViewTarget'\n\nimport type { Contributor, GraphLocation } from './contributors'\nimport type { TrackScanSession } from '../launchSubgraph/subgraphTracks'\n\nexport interface GraphLaunchSession extends TrackScanSession {\n  addView: (type: string, snapshot?: Record<string, unknown>) => { id: string }\n  // The session's own loader for a view whose state model is registered\n  // lazily (JBrowse 4's LinearSyntenyView); absent on an older core, where\n  // addView is enough\n  launchView?: (\n    type: string,\n    snapshot?: Record<string, unknown>,\n  ) => Promise<{ id: string }>\n  assemblyNames: string[]\n  views: unknown[]\n  // optional, as a hand-built session in a test has none\n  notifyError?: (message: string, error?: unknown) => void\n}\n\n// A launch is a promise nothing waits on. Let go, a refusal moved nothing and\n// said nothing; this is where it is told to the user instead.\nfunction reportFailure(\n  session: GraphLaunchSession,\n  what: string,\n  launch: Promise<unknown>,\n) {\n  launch.catch((error: unknown) => {\n    console.error(`[GraphGenomeView] ${what}`, error)\n    session.notifyError?.(`${what}: ${error}`, error)\n  })\n}\n\n// A node is often shorter than a line of text \u2014 a base-level allele can be a\n// handful of bp \u2014 and a linear view opened on exactly that span shows the span\n// and no context at all. Padding to a minimum window puts the node in the middle\n// of something readable.\nconst MIN_LAUNCH_SPAN_BP = 1000\n\nexport function paddedLocation(\n  loc: GraphLocation,\n  minSpan = MIN_LAUNCH_SPAN_BP,\n): GraphLocation {\n  const pad = Math.max(0, Math.ceil((minSpan - (loc.end - loc.start)) / 2))\n  return { ...loc, start: Math.max(0, loc.start - pad), end: loc.end + pad }\n}\n\n// Restate the rank-0 contributor in the terms of the region the graph was cut\n// from. Two separate corrections, both required:\n//\n//   - the *assembly*. A backbone segment's SN is the graph's own spelling of the\n//     reference, which need not be the name of any loaded assembly: the HPRC\n//     graph says `GRCh38#0#chr6` in a session whose assembly is `hg38`. Taking\n//     the PanSN sample there resolves to nothing and the graph offers no way out\n//     at all. `loadedRegion` is authoritative \u2014 the adapter resolved that\n//     assembly to that stable sequence to cut the subgraph in the first place.\n//     The backbone's `haplotype` (`GRCh38#0`) goes with it, since\n//     resolveLocationAssembly tries that before the sample.\n//   - the *locus*. The cut region is what the user framed in the linear view, and\n//     it is the span every other panel of a synteny launch is compared against;\n//     the union of backbone segments differs from it whenever the window ends\n//     inside a bubble.\n//\n// A subgraph is cut on one reference, so there is at most one rank-0\n// contributor. Must run before contributors are resolved against the session's\n// assemblies, or the reference is filtered out by the name this replaces.\nexport function withReferenceRegion(\n  contributors: Contributor[],\n  region:\n    | { refName: string; assemblyName: string; start: number; end: number }\n    | undefined,\n): Contributor[] {\n  return region\n    ? contributors.map(c =>\n        c.rank === 0\n          ? {\n              ...c,\n              sample: region.assemblyName,\n              haplotype: undefined,\n              refName: region.refName,\n              start: region.start,\n              end: region.end,\n            }\n          : c,\n      )\n    : contributors\n}\n\n// Show a location in a linear view: move the one already on screen if there is\n// one to move, open a pane only if there isn't.\n//\n// This is the difference between \"flip to the linear view\" and \"accumulate\n// panes\". The pangenome sessions this ships in are a linear view above a graph,\n// and there the answer to \"where is this node?\" should be that the linear view\n// scrolls to it \u2014 see linearViewTarget for which view counts as the one to move.\n//\n// `tracks` is only applied to a view being created; a view already open keeps\n// whatever the user has turned on. Returns the id of the view that ended up\n// showing the location, so the graph can pair with it for the hover sync.\nexport function showInLinearView({\n  session,\n  location,\n  assembly,\n  connectedViewId,\n  tracks = [],\n}: {\n  session: GraphLaunchSession\n  location: GraphLocation\n  assembly: string\n  connectedViewId?: string\n  tracks?: string[]\n}) {\n  const existing = linearViewTarget({\n    views: session.views,\n    connectedViewId,\n    assemblyName: assembly,\n  })\n  let viewId: string\n  if (existing) {\n    reportFailure(\n      session,\n      `Could not show ${assembly} ${locLabel(location)}`,\n      Promise.resolve(existing.navToLocString(locString(location), assembly)),\n    )\n    viewId = existing.id\n  } else {\n    viewId = session.addView('LinearGenomeView', {\n      displayName: `${assembly} \u2014 ${locLabel(location)}`,\n      init: { assembly, loc: locString(location), tracks },\n    }).id\n  }\n  return viewId\n}\n\n// Mark where a node sits on the reference, in the linear view already on\n// screen, instead of scrolling that view to it. Review: \"need to be able to\n// just highlight lineargenomeview coords\".\n//\n// The other half of the pair above, and the half that survives being let go of:\n// hover sync draws a band for as long as the pointer is over the node, where a\n// highlight is written into the view's own list and stays until it is removed.\n// It also keeps the reader's frame \u2014 the interesting comparison at a pangenome\n// locus is usually the whole window, not the 200 bp the node occupies.\n//\n// Nothing to mark when no linear view on that assembly is ours to move (see\n// linearViewTarget); the caller offers the item only when there is.\nexport function highlightInLinearView({\n  session,\n  location,\n  assembly,\n  connectedViewId,\n}: {\n  session: GraphLaunchSession\n  location: GraphLocation\n  assembly: string\n  connectedViewId?: string\n}) {\n  const target = linearViewTarget({\n    views: session.views,\n    connectedViewId,\n    assemblyName: assembly,\n  })\n  target?.addToHighlights?.({\n    refName: location.refName,\n    start: location.start,\n    end: location.end,\n    assemblyName: assembly,\n  })\n  return target !== undefined\n}\n\n// Which assemblies a track config says it covers, for deciding whether a panel\n// can draw it at all. A trackId naming nothing in the session reads as covering\n// nothing, so a stale id drops the lane rather than adding one the panel would\n// fail to load.\nfunction assemblyNamesOfTrack(\n  session: GraphLaunchSession,\n  trackId: string | undefined,\n) {\n  if (trackId === undefined) {\n    return []\n  }\n  const track = session.tracks.find(\n    t => readConfObject(t, 'trackId') === trackId,\n  )\n  const names: unknown = track ? readConfObject(track, 'assemblyNames') : []\n  return Array.isArray(names) ? names.filter(n => typeof n === 'string') : []\n}\n\n// One panel per contributing assembly, each framed on the locus that assembly\n// contributes here, with the graph's own reference panel on top.\n//\n// The panel loci come from the graph rather than from the synteny track: rGFA\n// states where each contributor's sequence sits on its own coordinates, so the\n// launch needs no mate discovery, no PAF lookup and no dialog. That is the whole\n// point of launching from the graph instead of from a linear view.\n//\n// Panels carry THE GRAPH'S OWN TRACK and nothing else, which is a narrower rule\n// than the single-view launch's (see launchTracks, which scans the session for\n// the assembly's annotation). Tried that here: a gene track per panel takes\n// about 160px of a row that is otherwise a ruler, so on five strains the\n// annotation is most of the viewport and the ribbons \u2014 the thing the launch\n// exists to draw \u2014 are squeezed into the gaps, and `collapseEmptyRows` is here\n// to prevent exactly that.\n//\n// The graph's own track does not have that shape. It goes only in the panels\n// whose assembly its config declares, which is where the graph HAS coordinates:\n// the HPRC segments track names two, so both its panels get one lane, while the\n// E. coli one names K12 alone and a five-strain launch adds a single lane rather\n// than five. And it is the lane that makes the band readable, since the ribbons\n// otherwise connect two bare rulers and the reader has nothing to match across\n// them.\nexport function launchSyntenyView({\n  session,\n  contributors,\n  trackId,\n  graphTrackId,\n}: {\n  session: GraphLaunchSession\n  contributors: Contributor[]\n  trackId?: string\n  graphTrackId?: string\n}) {\n  const graphTrackAssemblies = assemblyNamesOfTrack(session, graphTrackId)\n  // The panels the chosen track aligns, in the order given. A pairwise track is\n  // offered beside an all-vs-all, two assemblies being a synteny view, and over\n  // every contributor it sat on each level and could draw on one at most. A\n  // track that states no assemblies keeps them all.\n  const aligned = assemblyNamesOfTrack(session, trackId)\n  const covered = contributors.filter(c => aligned.includes(c.sample))\n  const panels = covered.length >= 2 ? covered : contributors\n  const snapshot = {\n    init: {\n      views: panels.map(c => ({\n        assembly: c.sample,\n        loc: locString(c),\n        ...(graphTrackId !== undefined &&\n        graphTrackAssemblies.includes(c.sample)\n          ? { tracks: [graphTrackId] }\n          : {}),\n      })),\n      // One entry per LEVEL, not one for the track. `init.tracks` is 2D \u2014 the\n      // gap between views[i] and views[i+1] \u2014 and a flat `[trackId]` is read as\n      // the level-0 shorthand, so on a five-strain launch only the top band got\n      // the alignment and the four below it opened as bare rulers. The same\n      // all-vs-all track fills every level: it carries all the pairs.\n      tracks: trackId ? panels.slice(1).map(() => [trackId]) : [],\n      collapseEmptyRows: true,\n    },\n  }\n  // launchView where the session has it: a synteny view's state model is\n  // loaded on demand and addView throws until it is\n  if (session.launchView) {\n    reportFailure(\n      session,\n      'Could not open the synteny view',\n      session.launchView('LinearSyntenyView', snapshot),\n    )\n  } else {\n    session.addView('LinearSyntenyView', snapshot)\n  }\n}\n", "export interface NavigableLinearView {\n  id: string\n  assemblyNames: string[]\n  navToLocString: (locString: string, assemblyName?: string) => unknown\n  // The other way of answering \"where is this node\": mark it rather than scroll\n  // to it. Optional, and not part of isLinearView's test \u2014 navigating is what\n  // makes a view a target here, and a view that cannot be marked can still be\n  // moved.\n  addToHighlights?: (highlight: {\n    refName: string\n    start: number\n    end: number\n    assemblyName: string\n  }) => unknown\n}\n\nfunction isRecord(value: unknown): value is Record<string, unknown> {\n  return typeof value === 'object' && value !== null\n}\n\n// Reads `session.views` structurally, the same way graphViewHighlights does: the\n// members needed here are declared by LinearGenomeView, not by the\n// AbstractViewModel the session array is typed as.\nfunction isLinearView(view: unknown): view is NavigableLinearView {\n  return (\n    isRecord(view) &&\n    view.type === 'LinearGenomeView' &&\n    typeof view.id === 'string' &&\n    typeof view.navToLocString === 'function' &&\n    Array.isArray(view.assemblyNames)\n  )\n}\n\n// The view a graph was launched from is not always in `session.views`: a row of\n// a LinearSyntenyView, LinearComparativeView or BreakpointSplitView sits in\n// that view's own `views[]`, so the candidates are the session's views plus one\n// level of rows.\nexport function withRows(views: unknown[]) {\n  return views.flatMap(view =>\n    isRecord(view) && Array.isArray(view.views)\n      ? [view, ...view.views]\n      : [view],\n  )\n}\n\n// The linear view a \"show me this\" from the graph should move, rather than\n// opening a pane beside it. Three cases, in order:\n//\n//   - the view this graph is paired with (`connectedViewId`), which is either\n//     the view the graph was launched from or the one it later opened itself.\n//     Explicit, so it wins.\n//   - failing that, the only linear view in the session showing this assembly.\n//     The pangenome sessions this view ships in are a linear view above a graph\n//     with no pairing recorded, and there \"the linear view\" is unambiguous \u2014 the\n//     same reasoning hoverSync's isConnected already applies to highlights.\n//   - two or more candidates and no pairing: nothing. Guessing which of the\n//     user's views to scroll is worse than opening one that is ours to move.\n//\n// Assembly-gated throughout: a linear view on a different assembly cannot show\n// this location at all.\nexport function linearViewTarget({\n  views,\n  connectedViewId,\n  assemblyName,\n}: {\n  views: unknown[]\n  connectedViewId: string | undefined\n  assemblyName: string\n}) {\n  const candidates = withRows(views)\n    .filter(view => isLinearView(view))\n    .filter(view => view.assemblyNames.includes(assemblyName))\n  const connected = candidates.find(view => view.id === connectedViewId)\n  return connected ?? (candidates.length === 1 ? candidates[0] : undefined)\n}\n", "import { readConfObject } from '@jbrowse/core/configuration'\n\nimport type { TrackScanSession } from '../launchSubgraph/subgraphTracks'\n\nconst ANNOTATION_TRACK_TYPE = 'FeatureTrack'\n\n// What to turn on in a linear view the graph opens on `assemblyName`.\n//\n// A launch used to carry the graph's own track and nothing else, and that track\n// is configured for the reference alone \u2014 so `Launch view` \u2192 `CFT073 chr:\u2026`\n// landed on `No tracks active`, which answers \"where is this strain's sequence?\"\n// with an empty pane. What the session does hold for a contributing assembly is\n// that assembly's own annotation, and on a pangenome config that is one track\n// per strain (`CFT073_genes`), which is exactly what makes the landing readable.\n//\n// Annotation tracks only, not everything configured for the assembly. A launch\n// is a jump to a locus, and an alignments or coverage track turned on behind the\n// user's back fetches data nobody asked for; a FeatureTrack at a 50 kb window is\n// a tabix range query. The graph's own segments track is a FeatureTrack too, so\n// the reference case still gets it from the same scan.\n//\n// `first` is the graph's own track when the launch is on the reference, so the\n// segments the graph drew sit at the top of the view rather than wherever config\n// order puts them.\nexport function launchTracks({\n  session,\n  assemblyName,\n  first,\n}: {\n  session: TrackScanSession\n  assemblyName: string\n  first?: string\n}) {\n  const found: string[] = []\n  for (const track of session.tracks) {\n    const type: unknown = readConfObject(track, 'type')\n    const assemblyNames: unknown = readConfObject(track, 'assemblyNames')\n    const trackId: unknown = readConfObject(track, 'trackId')\n    if (\n      type === ANNOTATION_TRACK_TYPE &&\n      Array.isArray(assemblyNames) &&\n      assemblyNames.includes(assemblyName) &&\n      typeof trackId === 'string' &&\n      trackId !== first\n    ) {\n      found.push(trackId)\n    }\n  }\n  return first ? [first, ...found] : found\n}\n", "import { readConfObject } from '@jbrowse/core/configuration'\nimport { getTrackName } from '@jbrowse/core/util/tracks'\n\nimport type { TrackScanSession } from '../launchSubgraph/subgraphTracks'\n\nexport interface LaunchableSyntenyTrack {\n  trackId: string\n  name: string\n  // how many of the requested assemblies this track covers, so a whole-set\n  // all-vs-all sorts above a pairwise alignment covering two of them\n  coverage: number\n}\n\nconst SYNTENY_TRACK_TYPE = 'SyntenyTrack'\n\n// Synteny datasets in the session that align at least two of `assemblyNames`.\n//\n// Track type rather than adapter name: SyntenyTrack is the core track type every\n// synteny adapter is configured under, so this does not go stale when an adapter\n// is added or renamed the way naming PAF adapters would.\n//\n// Two is the floor because that is the floor for a synteny view; more is better,\n// and an all-vs-all covering every contributing assembly is what makes the\n// multi-panel launch worth offering at all.\nexport function launchableSyntenyTracks(\n  session: TrackScanSession,\n  assemblyNames: string[],\n) {\n  const wanted = new Set(assemblyNames)\n  const found: LaunchableSyntenyTrack[] = []\n  for (const track of session.tracks) {\n    const type: unknown = readConfObject(track, 'type')\n    const trackAssemblies: unknown = readConfObject(track, 'assemblyNames')\n    const trackId: unknown = readConfObject(track, 'trackId')\n    if (\n      type === SYNTENY_TRACK_TYPE &&\n      typeof trackId === 'string' &&\n      Array.isArray(trackAssemblies)\n    ) {\n      const coverage = trackAssemblies.filter(name => wanted.has(name)).length\n      if (coverage >= 2) {\n        found.push({ trackId, name: getTrackName(track, session), coverage })\n      }\n    }\n  }\n  return found.sort((a, b) => b.coverage - a.coverage)\n}\n", "import { readConfObject } from '@jbrowse/core/configuration'\nimport { getTrackName } from '@jbrowse/core/util/tracks'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { AnyConfigurationModel } from '@jbrowse/core/configuration'\n\nexport interface SubgraphTrack {\n  trackId: string\n  name: string\n  // The assembly a cut has to be on; see graphReferenceAssembly.\n  referenceAssembly: string | undefined\n  // The lanes the cut is for; undefined is every haplotype.\n  haplotypes: string[] | undefined\n}\n\nexport interface TrackScanSession {\n  tracks: AnyConfigurationModel[]\n  assemblies: AnyConfigurationModel[]\n}\n\n// The linear view a launch is offered from, as far as the lanes go.\nexport interface LaunchingView {\n  tracks: readonly {\n    configuration: AnyConfigurationModel\n    displays: readonly unknown[]\n  }[]\n}\n\ninterface LaneSelectingDisplay {\n  laneSelection: readonly string[] | undefined\n  hiddenLanes: readonly string[]\n}\n\n// Whether an adapter declares it can cut a local subgraph. Discovery is by\n// declared capability, not adapter name: the old launcher hardcoded\n// `GfaTabixAdapter`/`GfaServerAdapter`, which is exactly what left it dead when\n// those were removed.\n//\n// `getAdapterType` throws for a type that was never registered, and a session\n// can hold tracks whose plugin isn't loaded, so registration is checked first \u2014\n// a session-wide scan reaches tracks a single display's menu never would.\nexport function adapterCanCutSubgraph(\n  pluginManager: PluginManager,\n  adapterType: unknown,\n) {\n  return (\n    typeof adapterType === 'string' &&\n    pluginManager.adapterTypes.has(adapterType) &&\n    pluginManager\n      .getAdapterType(adapterType)\n      .adapterCapabilities.includes('getSubgraph')\n  )\n}\n\nfunction isStringArray(value: unknown): value is string[] {\n  return Array.isArray(value) && value.every(item => typeof item === 'string')\n}\n\nfunction isLaneSelecting(display: unknown): display is LaneSelectingDisplay {\n  return (\n    typeof display === 'object' &&\n    display !== null &&\n    'laneSelection' in display &&\n    'hiddenLanes' in display\n  )\n}\n\n// The assemblies the track names after its reference, which is what core's\n// MultiWaySyntenyDisplay opens a lane-declaring source on.\nexport function trackLanes(track: AnyConfigurationModel) {\n  const assemblyNames: unknown = readConfObject(track, 'assemblyNames')\n  const lanes = isStringArray(assemblyNames) ? assemblyNames.slice(1) : []\n  return lanes.length > 0 ? lanes : undefined\n}\n\n// A graph is cut on the first assembly its track names, the rule\n// GbzBaseSyntenyAdapter states for its anchor. Every other assembly the track\n// names holds its sequence as rank>0 alleles off that reference's backbone, so\n// a window on one has no reference coordinates to frame the cut by.\nexport function graphReferenceAssembly(track: AnyConfigurationModel) {\n  const assemblyNames: unknown = readConfObject(track, 'assemblyNames')\n  return isStringArray(assemblyNames) ? assemblyNames[0] : undefined\n}\n\nexport function offReferenceProblem(\n  referenceAssembly: string | undefined,\n  assemblyName: string,\n) {\n  return referenceAssembly === undefined || referenceAssembly === assemblyName\n    ? undefined\n    : `The graph is cut on its reference, ${referenceAssembly}: open it from a view of ${referenceAssembly}`\n}\n\n// The lanes the track draws in `view`: the ones in force there less any the\n// reader hid. A track not on screen there has its own assemblies to go by.\nfunction lanesToCut(\n  track: AnyConfigurationModel,\n  trackId: string,\n  view: LaunchingView | undefined,\n) {\n  const shown = view?.tracks\n    .find(t => readConfObject(t.configuration, 'trackId') === trackId)\n    ?.displays.find(isLaneSelecting)\n  return shown\n    ? shown.laneSelection?.filter(name => !shown.hiddenLanes.includes(name))\n    : trackLanes(track)\n}\n\nexport function subgraphTrack(\n  track: AnyConfigurationModel,\n  trackId: string,\n  session: TrackScanSession,\n  view?: LaunchingView,\n): SubgraphTrack {\n  return {\n    trackId,\n    name: getTrackName(track, session),\n    referenceAssembly: graphReferenceAssembly(track),\n    haplotypes: lanesToCut(track, trackId, view),\n  }\n}\n\n// Tracks anywhere in the session that can cut a subgraph on `assemblyName`, so\n// the launch can be offered from a linear view that doesn't have the graph track\n// in it. The entry point no longer has to be the graph track's own menu \u2014 which\n// was the whole problem: a user browsing genes had no way in.\nexport function subgraphTracks(\n  pluginManager: PluginManager,\n  session: TrackScanSession,\n  assemblyName: string,\n  view?: LaunchingView,\n) {\n  const found: SubgraphTrack[] = []\n  for (const track of session.tracks) {\n    const assemblyNames: unknown = readConfObject(track, 'assemblyNames')\n    const adapter: unknown = readConfObject(track, 'adapter')\n    const trackId: unknown = readConfObject(track, 'trackId')\n    if (\n      Array.isArray(assemblyNames) &&\n      assemblyNames.includes(assemblyName) &&\n      typeof trackId === 'string' &&\n      typeof adapter === 'object' &&\n      adapter !== null &&\n      'type' in adapter &&\n      adapterCanCutSubgraph(pluginManager, adapter.type)\n    ) {\n      found.push(subgraphTrack(track, trackId, session, view))\n    }\n  }\n  return found\n}\n", "import type modelFactory from './GraphGenomeView/model'\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { AbstractSessionModel } from '@jbrowse/core/util'\nimport type { SnapshotIn } from '@jbrowse/mobx-state-tree'\n\n// GraphGenomeView has no assembly/track resolution \u2014 every field is a plain\n// persisted view prop, so the launch spec forwards straight onto the view\n// snapshot. `afterAttach` loads `gfaLocation`, or refetches the\n// `loadedTrackId`/`loadedRegion` pair, once the view is created.\n//\n// **Taken off the model rather than listed by hand**, which is the whole point.\n// This named four props (`gfaLocation`, `colorScheme`, `linearLayout`,\n// `drawPaths`) while the extension point spreads whatever it is handed \u2014 so the\n// runtime accepted every prop and the DECLARED contract accepted a third of\n// them. The docs' own figure specs launch with thirteen: `loadedTrackId`,\n// `loadedRegion`, `layoutMode`, `colorDomain`, `paneHeight`, `referencePath`,\n// `layoutQuality`, `maxRegionBp` and `bubbleSpread` among them, none of which\n// this said were allowed. It carries a `#extensionPoint` tag, so the published\n// API docs said so too.\n//\n// Derived, so adding a view prop widens the launch with it. `type` is the\n// dispatch key rather than a setting \u2014 loadSessionSpec strips it before calling\n// this \u2014 and is the one field a caller may not supply.\nexport type LaunchGraphGenomeViewArgs = Partial<\n  Omit<SnapshotIn<ReturnType<typeof modelFactory>>, 'type'>\n> & {\n  session: AbstractSessionModel\n}\n\ndeclare module '@jbrowse/core/PluginManager' {\n  interface ExtensionPointRegistry {\n    'LaunchView-GraphGenomeView': {\n      args: LaunchGraphGenomeViewArgs\n      result: LaunchGraphGenomeViewArgs\n    }\n  }\n}\n\nexport default function LaunchGraphGenomeViewF(pluginManager: PluginManager) {\n  /** #extensionPoint LaunchView-GraphGenomeView | async | Programmatically launch a graph genome view */\n  pluginManager.addToExtensionPoint('LaunchView-GraphGenomeView', args => {\n    const { session, ...spec } = args\n    session.addView('GraphGenomeView', spec)\n    return args\n  })\n}\n", "import { lazy } from 'react'\n\nimport DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'\n\nimport { configSchemaFactory } from './configSchema'\nimport { stateModelFactory } from './model'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\n\nexport default function LinearGraphDisplayF(pluginManager: PluginManager) {\n  pluginManager.addDisplayType(() => {\n    const configSchema = configSchemaFactory()\n    return new DisplayType({\n      name: 'LinearGraphDisplay',\n      displayName: 'Graph',\n      configSchema,\n      stateModel: stateModelFactory(configSchema),\n      trackType: ['FeatureTrack', 'SyntenyTrack'],\n      viewType: 'LinearGenomeView',\n      ReactComponent: lazy(() => import('./components/LinearGraphDisplay')),\n    })\n  })\n}\n", "import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { trackHeightConfigSchemaFields } from '@jbrowse/display-kit/trackHeightConfigSchemaFields'\nimport { types } from '@jbrowse/mobx-state-tree'\n\nimport { COLOR_SCHEME_VALUES } from '../GraphGenomeView/colorSchemes'\nimport { LAYOUT_MODE_VALUES } from '../GraphGenomeView/layoutModes'\n\nimport type { Instance } from '@jbrowse/mobx-state-tree'\n\n/**\n * #config LinearGraphDisplay\n * The graph drawn as a track of the linear genome view. A layout whose x is\n * reference bp draws under the view's coordinates and re-cuts as the view\n * moves; force, ordered and walk rows draw in their own coordinates, fitted to\n * the track.\n */\nexport function configSchemaFactory() {\n  return ConfigurationSchema(\n    'LinearGraphDisplay',\n    {\n      /**\n       * #slot\n       * the layout the track opens in\n       */\n      layoutMode: {\n        type: 'stringEnum',\n        model: types.enumeration('LayoutMode', LAYOUT_MODE_VALUES),\n        defaultValue: 'auto',\n      },\n      /**\n       * #slot\n       */\n      colorScheme: {\n        type: 'stringEnum',\n        model: types.enumeration('ColorScheme', COLOR_SCHEME_VALUES),\n        defaultValue: 'auto',\n      },\n      ...trackHeightConfigSchemaFields({\n        defaultHeight: 300,\n        height:\n          'the most the track takes; a layout shorter than it takes only what it needs',\n      }),\n    },\n    { explicitlyTyped: true, explicitIdentifier: 'displayId' },\n  )\n}\n\nexport type LinearGraphDisplayConfigModel = ReturnType<\n  typeof configSchemaFactory\n>\nexport type LinearGraphDisplayConfig = Instance<LinearGraphDisplayConfigModel>\n", "import { lazy } from 'react'\n\nimport { ConfigurationReference, getConf } from '@jbrowse/core/configuration'\nimport { BaseDisplay } from '@jbrowse/core/pluggableElementTypes'\nimport { getContainingView, getSession } from '@jbrowse/core/util'\nimport TrackHeightMixin from '@jbrowse/display-kit/TrackHeightMixin'\nimport { addDisposer, types } from '@jbrowse/mobx-state-tree'\nimport SettingsIcon from '@mui/icons-material/Settings'\nimport { autorun } from 'mobx'\n\nimport { COLOR_SCHEMES } from '../GraphGenomeView/colorSchemes'\nimport { isLinearHost } from '../GraphGenomeView/host'\nimport { LAYOUT_MODES } from '../GraphGenomeView/layoutModes'\nimport paneModelFactory from '../GraphGenomeView/model'\n\nimport type { LinearGraphDisplayConfigModel } from './configSchema'\nimport type { MenuItem } from '@jbrowse/core/ui'\nimport type { Instance } from '@jbrowse/mobx-state-tree'\n\nconst GraphSettingsDialog = lazy(\n  () => import('../GraphGenomeView/components/GraphSettingsDialog'),\n)\n\nexport function stateModelFactory(configSchema: LinearGraphDisplayConfigModel) {\n  const Pane = paneModelFactory()\n  return types\n    .compose(\n      'LinearGraphDisplay',\n      BaseDisplay,\n      TrackHeightMixin(),\n      types.model({\n        type: types.literal('LinearGraphDisplay'),\n        configuration: ConfigurationReference(configSchema),\n        // The graph pane, the same model the standalone view is. Here the\n        // linear view above is its host: x is that view's window for a layout\n        // whose x is reference bp, and the cut is re-made when the window\n        // leaves it (pane.host).\n        pane: types.optional(Pane, () => ({\n          type: 'GraphGenomeView' as const,\n        })),\n        // The config's layout and colour reach the pane once, so a choice made\n        // in the track menu survives a reload.\n        configured: types.optional(types.boolean, false),\n      }),\n    )\n    .views(self => ({\n      get host() {\n        let view: unknown\n        try {\n          view = getContainingView(self)\n        } catch {\n          return undefined\n        }\n        return isLinearHost(view) ? view : undefined\n      },\n      get trackId(): string {\n        return getConf(self.parentTrack, 'trackId')\n      },\n    }))\n    .views(self => ({\n      trackMenuItems(): MenuItem[] {\n        const { pane } = self\n        const { graph } = pane\n        const walks = pane.walkChoices\n        return [\n          {\n            label: 'Layout',\n            subMenu: LAYOUT_MODES.map(mode => ({\n              type: 'radio' as const,\n              label: mode.label,\n              checked: pane.layoutMode === mode.value,\n              disabled: graph ? !mode.available(graph) : false,\n              onClick: () => {\n                void pane.switchLayout(mode.value)\n              },\n            })),\n          },\n          {\n            label: 'Color',\n            subMenu: COLOR_SCHEMES.map(scheme => ({\n              type: 'radio' as const,\n              label: scheme.label,\n              checked: pane.colorScheme === scheme.value,\n              onClick: () => {\n                pane.setColorScheme(scheme.value)\n              },\n            })),\n          },\n          ...(walks.length > 0\n            ? [\n                {\n                  label: 'Walk',\n                  subMenu: [\n                    {\n                      type: 'radio' as const,\n                      label: 'None',\n                      checked: pane.highlightedPath === '',\n                      onClick: () => {\n                        pane.setHighlightedPath('')\n                      },\n                    },\n                    ...walks.map(walk => ({\n                      type: 'radio' as const,\n                      label: walk.label,\n                      checked: pane.highlightedPath === walk.name,\n                      onClick: () => {\n                        pane.setHighlightedPath(walk.name)\n                      },\n                    })),\n                  ],\n                },\n              ]\n            : []),\n          ...(pane.hostPlacesX\n            ? []\n            : [\n                {\n                  label: 'Zoom in',\n                  onClick: () => {\n                    pane.zoom(1.5, pane.width / 2, pane.canvasHeight / 2)\n                  },\n                },\n                {\n                  label: 'Zoom out',\n                  onClick: () => {\n                    pane.zoom(1 / 1.5, pane.width / 2, pane.canvasHeight / 2)\n                  },\n                },\n                {\n                  label: 'Zoom to fit',\n                  onClick: () => {\n                    pane.zoomToFit()\n                  },\n                },\n              ]),\n          {\n            type: 'checkbox',\n            label: 'Mark bubbles',\n            checked: pane.showBubbles,\n            onClick: () => {\n              pane.setShowBubbles(!pane.showBubbles)\n            },\n          },\n          {\n            type: 'checkbox',\n            label: 'Show deletion edges',\n            checked: pane.showDeletionEdges,\n            onClick: () => {\n              pane.setShowDeletionEdges(!pane.showDeletionEdges)\n            },\n          },\n          {\n            type: 'checkbox',\n            label: 'Genes on the backbone',\n            checked: pane.showGenes,\n            onClick: () => {\n              pane.setShowGenes(!pane.showGenes)\n            },\n          },\n          {\n            label: 'Settings',\n            icon: SettingsIcon,\n            onClick: () => {\n              getSession(self).queueDialog(onClose => [\n                GraphSettingsDialog,\n                { model: pane, open: true, onClose },\n              ])\n            },\n          },\n        ]\n      },\n    }))\n    .actions(self => ({\n      setConfigured() {\n        self.configured = true\n      },\n      // The track's height is the pane's ceiling: a layout shorter than it\n      // takes only what it needs, and a drag on the handle moves the ceiling.\n      resizeHeight(distance: number) {\n        const before = self.height\n        const target = Math.max(before + distance, 40)\n        self.pane.setPaneHeight(target)\n        return target - before\n      },\n    }))\n    .actions(self => ({\n      afterAttach() {\n        const { pane } = self\n        if (!self.configured) {\n          pane.setLayoutMode(getConf(self, 'layoutMode'))\n          pane.setColorScheme(getConf(self, 'colorScheme'))\n          pane.setPaneHeight(getConf(self, 'height'))\n          self.setConfigured()\n        }\n        pane.adoptTrack(self.trackId)\n        pane.startHosting()\n        addDisposer(\n          self,\n          autorun(\n            () => {\n              const { host } = self\n              if (host) {\n                pane.setWidth(host.width)\n                pane.pairWithLinearView(host.id)\n              }\n            },\n            { name: 'LinearGraphDisplayHost' },\n          ),\n        )\n        addDisposer(\n          self,\n          autorun(\n            () => {\n              const height = pane.canvasHeight\n              if (self.height !== height) {\n                self.setHeight(height)\n              }\n            },\n            { name: 'LinearGraphDisplayHeight' },\n          ),\n        )\n      },\n    }))\n}\n\nexport type LinearGraphDisplayStateModel = ReturnType<typeof stateModelFactory>\nexport type LinearGraphDisplayModel = Instance<LinearGraphDisplayStateModel>\n", "import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'\n\nimport configSchema, { normalizeSnapshot } from './configSchema.ts'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\n\nexport default function MinigraphBubbleAdapterF(pluginManager: PluginManager) {\n  pluginManager.addAdapterType(\n    () =>\n      new AdapterType({\n        name: 'MinigraphBubbleAdapter',\n        displayName: 'Minigraph bubble BED adapter',\n        normalizeSnapshot,\n        configSchema,\n        adapterMetadata: {\n          category: 'Graph adapters',\n        },\n        getAdapterClass: () =>\n          import('./MinigraphBubbleAdapter.ts').then(r => r.default),\n      }),\n  )\n}\n", "import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { types } from '@jbrowse/mobx-state-tree'\n\nimport type { Instance } from '@jbrowse/mobx-state-tree'\n\n/**\n * #config MinigraphBubbleAdapter\n * #trackType FeatureTrack\n * #fileFormat graph | Minigraph bubble BED | `gfatools bubble` output; HPRC publishes one ready-made, so no preprocessing at all\n * the tabix-indexed BED `gfatools bubble` writes for a minigraph graph: one row\n * per bubble, on the reference's own coordinates. Unlike\n * [RgfaTabixAdapter](/docs/config/rgfatabixadapter) this needs no index build of\n * your own, because HPRC publishes this file beside its minigraph graph.\n *\n * It shows *where* the graph varies and by how much, not the graph itself.\n *\n * #example\n * ```js\n * {\n *   type: 'MinigraphBubbleAdapter',\n *   uri: 'https://jbrowse.org/demos/hprc/hprc-v2.0-mc-grch38.bubbles.bed.gz',\n *   assemblyNameToPanSN: { hg38: 'GRCh38' },\n * }\n * ```\n */\n\nexport function normalizeSnapshot(snap: Record<string, unknown>) {\n  const { uri, baseUri, csi } = snap\n  return typeof uri === 'string'\n    ? {\n        ...snap,\n        bubblesLocation: { uri, baseUri },\n        index: {\n          indexType: csi ? 'CSI' : 'TBI',\n          location: { uri: `${uri}.${csi ? 'csi' : 'tbi'}`, baseUri },\n        },\n      }\n    : snap\n}\n\nconst MinigraphBubbleAdapter = ConfigurationSchema(\n  'MinigraphBubbleAdapter',\n  {\n    /**\n     * #slot\n     */\n    bubblesLocation: {\n      type: 'fileLocation',\n      defaultValue: {\n        uri: '/path/to/graph.bb.bed.gz',\n        locationType: 'UriLocation',\n      },\n    },\n    /**\n     * #slot\n     */\n    index: ConfigurationSchema('MinigraphBubbleIndex', {\n      /**\n       * #slot index.indexType\n       */\n      indexType: {\n        model: types.enumeration('IndexType', ['TBI', 'CSI']),\n        type: 'stringEnum',\n        defaultValue: 'TBI',\n      },\n      /**\n       * #slot index.location\n       */\n      location: {\n        type: 'fileLocation',\n        defaultValue: {\n          uri: '/path/to/graph.bb.bed.gz.tbi',\n          locationType: 'UriLocation',\n        },\n      },\n    }),\n    /**\n     * #slot\n     * Maps a JBrowse assembly name to its PanSN sample prefix, for when they\n     * differ. `gfatools bubble` names each row after the graph's stable\n     * sequence, so a Minigraph-Cactus graph yields `GRCh38#0#chr6` and an\n     * `hg38` assembly needs `{ hg38: 'GRCh38' }`; HPRC's published v1.0\n     * minigraph bubbles are bare (`chr6`) and need nothing.\n     */\n    assemblyNameToPanSN: {\n      type: 'frozen',\n      defaultValue: {},\n    },\n  },\n  {\n    explicitlyTyped: true,\n\n    /**\n     * #preProcessSnapshot\n     *\n     * preprocessor to allow the minimal config\n     * ```json\n     * { \"type\": \"MinigraphBubbleAdapter\", \"uri\": \"graph.bb.bed.gz\" }\n     * ```\n     */\n    preProcessSnapshot: normalizeSnapshot,\n  },\n)\n\nexport type MinigraphBubbleAdapterConfig = Instance<\n  typeof MinigraphBubbleAdapter\n>\n\nexport default MinigraphBubbleAdapter\n", "import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'\n\nimport configSchema, { normalizeSnapshot } from './configSchema.ts'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\n\nexport default function RgfaTabixAdapterF(pluginManager: PluginManager) {\n  pluginManager.addAdapterType(\n    () =>\n      new AdapterType({\n        name: 'RgfaTabixAdapter',\n        displayName: 'Indexed rGFA adapter',\n        normalizeSnapshot,\n        configSchema,\n        // what the launch menus look for (launchSubgraph/subgraphTracks.ts)\n        adapterCapabilities: ['getSubgraph'],\n        adapterMetadata: {\n          category: 'Graph adapters',\n        },\n        getAdapterClass: () =>\n          import('./RgfaTabixAdapter.ts').then(r => r.default),\n      }),\n  )\n}\n", "import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { types } from '@jbrowse/mobx-state-tree'\n\nimport type { Instance } from '@jbrowse/mobx-state-tree'\n\n/**\n * #config RgfaTabixAdapter\n * #trackType FeatureTrack\n * #fileFormat graph | Indexed rGFA | Built by `scripts/build_rgfa_tabix.sh`; serves segments as features and extracts local subgraphs\n * two tabix-indexed BED projections of an rGFA (minigraph). rGFA tags every\n * segment with `SN`/`SO`/`SR`, so both files record coordinates the graph\n * already states rather than inventing any. Plain GFA (pggb, odgi,\n * Minigraph-Cactus) has no such tags and is not supported.\n *\n * The `uri` shorthand takes the prefix the build script was given and resolves\n * `<uri>.segs.bed.gz`, `<uri>.links.bed.gz` and their `.tbi` indexes. `coarse`\n * takes the same shorthand for a second pair at one node per bubble, built by\n * `build_bubble_tier.sh` in jbrowse-components, plus the zoom past which a\n * graph view following a linear view cuts it.\n *\n * #example\n * ```js\n * {\n *   type: 'RgfaTabixAdapter',\n *   uri: 'https://example.com/hprc.rgfa',\n *   coarse: { uri: 'https://example.com/hprc.tier10000', aboveBpPerPx: 1000 },\n * }\n * ```\n */\n\nfunction tbi(uri: string, baseUri: unknown, csi: unknown) {\n  return {\n    indexType: csi ? 'CSI' : 'TBI',\n    location: { uri: `${uri}.${csi ? 'csi' : 'tbi'}`, baseUri },\n  }\n}\n\nfunction prefixLocations(snap: Record<string, unknown>) {\n  const { uri, baseUri, csi } = snap\n  return typeof uri === 'string'\n    ? {\n        ...snap,\n        segmentsLocation: { uri: `${uri}.segs.bed.gz`, baseUri },\n        segmentsIndex: tbi(`${uri}.segs.bed.gz`, baseUri, csi),\n        linksLocation: { uri: `${uri}.links.bed.gz`, baseUri },\n        linksIndex: tbi(`${uri}.links.bed.gz`, baseUri, csi),\n      }\n    : snap\n}\n\nexport function normalizeSnapshot(snap: Record<string, unknown>) {\n  const { coarse, baseUri } = snap\n  return prefixLocations(\n    typeof coarse === 'object' && coarse !== null\n      ? { ...snap, coarse: prefixLocations({ baseUri, ...coarse }) }\n      : snap,\n  )\n}\n\nconst indexSchema = (name: string, defaultUri: string) =>\n  ConfigurationSchema(name, {\n    /**\n     * #slot\n     */\n    indexType: {\n      model: types.enumeration('IndexType', ['TBI', 'CSI']),\n      type: 'stringEnum',\n      defaultValue: 'TBI',\n    },\n    /**\n     * #slot\n     */\n    location: {\n      type: 'fileLocation',\n      defaultValue: { uri: defaultUri, locationType: 'UriLocation' },\n    },\n  })\n\nconst RgfaTabixCoarseTier = ConfigurationSchema('RgfaTabixCoarseTier', {\n  /**\n   * #slot\n   * The linear view's bp per px past which a graph following it cuts this\n   * pair. Unset means the track has no coarse tier. There is no default,\n   * because the zoom a fine cut stays drawable to depends on the graph's\n   * density: a minigraph graph averages ~7 kb per segment, a base-level pggb\n   * graph ~17 bp.\n   */\n  aboveBpPerPx: { type: 'maybeNumber' },\n  /**\n   * #slot\n   */\n  segmentsLocation: {\n    type: 'fileLocation',\n    defaultValue: {\n      uri: '/path/to/graph.tier.segs.bed.gz',\n      locationType: 'UriLocation',\n    },\n  },\n  /**\n   * #slot\n   */\n  segmentsIndex: indexSchema(\n    'RgfaCoarseSegmentsIndex',\n    '/path/to/graph.tier.segs.bed.gz.tbi',\n  ),\n  /**\n   * #slot\n   */\n  linksLocation: {\n    type: 'fileLocation',\n    defaultValue: {\n      uri: '/path/to/graph.tier.links.bed.gz',\n      locationType: 'UriLocation',\n    },\n  },\n  /**\n   * #slot\n   */\n  linksIndex: indexSchema(\n    'RgfaCoarseLinksIndex',\n    '/path/to/graph.tier.links.bed.gz.tbi',\n  ),\n})\n\nconst RgfaTabixAdapter = ConfigurationSchema(\n  'RgfaTabixAdapter',\n  {\n    /**\n     * #slot\n     * one row per segment: `stableName start end segmentId rank`, as emitted by\n     * `gfatools gfa2bed -m`\n     */\n    segmentsLocation: {\n      type: 'fileLocation',\n      defaultValue: {\n        uri: '/path/to/graph.segs.bed.gz',\n        locationType: 'UriLocation',\n      },\n    },\n    /**\n     * #slot\n     */\n    segmentsIndex: indexSchema(\n      'RgfaSegmentsIndex',\n      '/path/to/graph.segs.bed.gz.tbi',\n    ),\n    /**\n     * #slot\n     * one row per link per endpoint, each carrying both endpoints in full so a\n     * neighbour on another stable sequence needs no segment-id lookup\n     */\n    linksLocation: {\n      type: 'fileLocation',\n      defaultValue: {\n        uri: '/path/to/graph.links.bed.gz',\n        locationType: 'UriLocation',\n      },\n    },\n    /**\n     * #slot\n     */\n    linksIndex: indexSchema(\n      'RgfaLinksIndex',\n      '/path/to/graph.links.bed.gz.tbi',\n    ),\n    /**\n     * #slot\n     * Maps a JBrowse assembly name to its PanSN sample prefix in the graph, for\n     * when they differ. Defaults to identity: the assembly name is assumed to be\n     * the PanSN sample name, and a graph whose stable names are bare (minigraph\n     * writes `chr1`) needs nothing here at all.\n     *\n     * Minigraph-Cactus writes PanSN stable names, so HPRC's release-2 graph\n     * calls the reference `GRCh38#0#chr1` and an `hg38` assembly needs\n     * `{ hg38: 'GRCh38' }`. The prefix is what disambiguates: that same graph\n     * also contains `CHM13#0#chr1`, so matching on the contig alone would\n     * silently resolve to the wrong sample.\n     */\n    assemblyNameToPanSN: {\n      type: 'frozen',\n      defaultValue: {},\n    },\n    /**\n     * #slot\n     * The same graph at one node per bubble, which a graph view following a\n     * linear view cuts once that view is zoomed out past `aboveBpPerPx`, and\n     * which no bp cap applies to. `{ uri, aboveBpPerPx }`, where `uri` is a\n     * prefix as the adapter's own is.\n     */\n    coarse: RgfaTabixCoarseTier,\n  },\n  {\n    explicitlyTyped: true,\n\n    /**\n     * #preProcessSnapshot\n     *\n     * preprocessor to allow the minimal config\n     * ```json\n     * { \"type\": \"RgfaTabixAdapter\", \"uri\": \"graph.rgfa\" }\n     * ```\n     */\n    preProcessSnapshot: normalizeSnapshot,\n  },\n)\n\nexport type RgfaTabixAdapterConfig = Instance<typeof RgfaTabixAdapter>\n\nexport default RgfaTabixAdapter\n", "import { getSession } from '@jbrowse/core/util'\nimport { alpha } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport { graphViewHighlights } from './graphViewHighlights'\n\nimport type { HighlightRegion } from './graphViewHighlights'\nimport type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'\n\nconst useStyles = makeStyles()(theme => ({\n  highlight: {\n    height: '100%',\n    position: 'absolute',\n    background: alpha(theme.palette.primary.main, 0.25),\n    borderLeft: `2px solid ${theme.palette.primary.main}`,\n    borderRight: `2px solid ${theme.palette.primary.main}`,\n    pointerEvents: 'none',\n    zIndex: 10,\n  },\n}))\n\n// One band over the linear view for a hovered graph node. `getHighlightCoords`\n// is the LGV's own projection \u2014 it canonicalizes the refName and floors the\n// width to 3 px, so a pure insertion (a zero-length reference span) still shows\n// as a mark rather than vanishing.\nconst Highlight = observer(function Highlight({\n  model,\n  region,\n}: {\n  model: LinearGenomeViewModel\n  region: HighlightRegion\n}) {\n  const { classes } = useStyles()\n  const coords = model.getHighlightCoords(region)\n  return coords ? (\n    <div\n      data-testid=\"graph-node-highlight\"\n      className={classes.highlight}\n      style={{ left: coords.left, width: coords.width }}\n    />\n  ) : null\n})\n\nconst GraphNodeHighlight = observer(function GraphNodeHighlight({\n  model,\n}: {\n  model: LinearGenomeViewModel\n}) {\n  const { views } = getSession(model)\n  return (\n    <>\n      {graphViewHighlights([...views], model.id, model.assemblyNames).map(\n        ({ key, region }) => (\n          <Highlight key={`graph-hover-${key}`} model={model} region={region} />\n        ),\n      )}\n    </>\n  )\n})\n\nexport default GraphNodeHighlight\n", "import { withRows } from '../launchFromGraph/linearViewTarget'\n\nexport interface HighlightRegion {\n  refName: string\n  start: number\n  end: number\n  assemblyName?: string\n}\n\nexport interface GraphViewHighlight {\n  key: string\n  region: HighlightRegion\n}\n\nfunction isRecord(value: unknown): value is Record<string, unknown> {\n  return typeof value === 'object' && value !== null\n}\n\nfunction readRegion(value: unknown): HighlightRegion | undefined {\n  let region: HighlightRegion | undefined\n  if (isRecord(value)) {\n    const { refName, start, end, assemblyName } = value\n    if (\n      typeof refName === 'string' &&\n      typeof start === 'number' &&\n      typeof end === 'number'\n    ) {\n      region = {\n        refName,\n        start,\n        end,\n        assemblyName:\n          typeof assemblyName === 'string' ? assemblyName : undefined,\n      }\n    }\n  }\n  return region\n}\n\n// Whether a graph view's highlights belong on a given linear view.\n// `connectedViewId` is written by the launch menu, so a launched pair is\n// explicit. A graph view without one \u2014 a hand-written session snapshot, or\n// `Add > Graph genome view` followed by a subgraph load \u2014 matches any linear\n// view, because the alternative is silently drawing nothing.\n//\n// So does one whose linear view has been closed. Held to an id nothing answers\n// to, it matched no view and its hover drew nowhere for the rest of the\n// session, the view it next opened included.\nfunction isConnected(\n  view: Record<string, unknown>,\n  linearViewId: string,\n  liveViewIds: ReadonlySet<unknown>,\n) {\n  const connectedViewId = view.connectedViewId\n  return (\n    connectedViewId === undefined ||\n    connectedViewId === linearViewId ||\n    !liveViewIds.has(connectedViewId)\n  )\n}\n\n// ...and whether the view can mean anything by it. `getHighlightCoords`\n// canonicalizes a refName against the region's OWN assembly and then lays it\n// out against this view's displayed regions, without ever asking whether the\n// two are the same assembly \u2014 so a band handed to the wrong view is drawn, at\n// coordinates that belong to somebody else's genome.\n//\n// That is not hypothetical for an unpaired graph, which by the rule above\n// matches every linear view in the session. A synteny stack's rows are LGVs on\n// different assemblies, and a PanSN name reduces to a bare contig: the five\n// E. coli strains each have one refName `chr`, so a graph cut from K12 painted\n// its K12 interval across Sakai's row and CFT073's at their own offsets. With\n// the assembly checked the reference row keeps the band and the rest correctly\n// draw nothing.\n//\n// A region stating no assembly still passes \u2014 `readRegion` leaves it optional,\n// and the fallback is the behaviour every existing snapshot has.\nfunction isOnAssembly(\n  region: HighlightRegion,\n  assemblyNames: string[] | undefined,\n) {\n  return (\n    region.assemblyName === undefined ||\n    assemblyNames === undefined ||\n    assemblyNames.includes(region.assemblyName)\n  )\n}\n\n// The highlights a linear view should draw for the graph views connected to it.\n// Reads `session.views` structurally: the members it needs are declared by\n// GraphGenomeView, not by the AbstractViewModel the session array is typed as.\nexport function graphViewHighlights(\n  views: unknown[],\n  linearViewId: string,\n  // the drawing view's own assemblies, so a band is only drawn where its\n  // coordinates mean something \u2014 see isOnAssembly\n  linearAssemblyNames?: string[],\n): GraphViewHighlight[] {\n  const highlights: GraphViewHighlight[] = []\n  const liveViewIds = new Set(\n    withRows(views).map(view => (isRecord(view) ? view.id : undefined)),\n  )\n  for (const view of views) {\n    if (\n      isRecord(view) &&\n      view.type === 'GraphGenomeView' &&\n      isConnected(view, linearViewId, liveViewIds)\n    ) {\n      const region = readRegion(view.hoverHighlight)\n      if (region && isOnAssembly(region, linearAssemblyNames)) {\n        highlights.push({\n          key: typeof view.id === 'string' ? view.id : 'graph',\n          region,\n        })\n      }\n    }\n  }\n  return highlights\n}\n", "import GraphNodeHighlight from './GraphNodeHighlight'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\n\n// The graph-to-linear half of the hover sync. The reverse half needs no mount\n// point: an LGV already publishes its hover to `session.hovered`, and the graph\n// view's own autorun reads it (see GraphGenomeView/model.ts).\n//\n// Mounted through the extension point rather than imported by the LGV, so this\n// plugin never imports @jbrowse/plugin-linear-genome-view at runtime: it is not\n// one of JBrowse's shared globals, so a value import would bundle a second copy\n// of that whole plugin.\nconst POINT = 'LinearGenomeView-TracksContainerComponent'\n\nexport default function GraphHoverSyncF(pluginManager: PluginManager) {\n  pluginManager.contributeToExtensionPoint(POINT, ({ model }) => (\n    <GraphNodeHighlight key=\"graphgenomeview-hover-highlight\" model={model} />\n  ))\n}\n", "// The name JBrowse knows this plugin by, which a config's `plugins` entry\n// states beside its `esmUrl`.\nexport const PLUGIN_NAME = 'GraphGenomeView'\n", "export const version = '4.0.0'\n"],
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"walkLabel", "name", "byName", "n", "halos", "bubble", "parts", "top", "nodeIds", "ends", "bubbleSegmentIds", "node", "line", "isBackbone", "svgPath", "p", "anchor", "s", "sharing", "route", "id", "routes", "rarest", "at", "far", "d", "routeText", "classifyBubble", "names", "shown", "more", "formatBp", "bubblesFromGraph", "graph", "isBackbone", "byId", "n", "order", "referenceOrder", "indexOf", "id", "i", "reach", "succ", "linked", "e", "a", "lo", "hi", "from", "to", "backbone", "b", "ends", "boundaries", "node", "ia", "ib", "walkIndex", "at", "bubbles", "start", "i0", "end", "i1", "interior", "best", "cur", "t", "add", "prev", "SATURATED_PATH_COUNT", "walked", "walkRoutes", "crossed", "routes", "walksLeave", "refStart", "refEnd", "chain", "chainBroken", "k", "partial", "fallback", "startId", "endId", "seen", "min", "max", "left", "p", "steps", "bp", "key", "route", "bubbleSubgraph", "graph", "segmentIds", "keep", "nodes", "n", "ids", "paths", "p", "id", "e", "GENE_ADAPTER_TYPES", "GENE_TRACK_HINT", "pickGeneTrack", "tracks", "named", "t", "candidates", "field", "f", "name", "exonsOf", "into", "children", "child", "merged", "intervals", "sorted", "a", "b", "out", "iv", "last", "geneModelsFrom", "features", "genes", "start", "end", "exons", "contig", "name", "genePins", "graph", "genes", "positions", "byContig", "contigOf", "node", "isBackbone", "refName", "entry", "nodes", "a", "b", "pins", "gene", "backbone", "parts", "at", "atDistance", "covered", "mid", "reach", "i", "firstNodeAtOrAfter", "nodeStart", "nodeEnd", "line", "exon", "stretch", "polylineSlice", "svgPath", "pinBp", "distance", "p", "parseTag", "tag", "tags", "nameEnd", "typeEnd", "name", "type", "val", "parseTags", "fields", "field", "stableCoordinate", "node", "SN", "SO", "SR", "GT", "LT", "parseWalkBody", "body", "segments", "strand", "start", "push", "end", "i", "ch", "parseGFA", "file", "graph", "rawLine", "line", "rest", "len", "seq", "tagfields", "gfa1", "first", "source", "target", "cigar", "strand1", "strand2", "sample", "hap", "contig", "path", "surveySegments", "gfaGraph", "canonical", "traversals", "claim", "id", "strand", "traverse", "link", "gfaPath", "segment", "walk", "seg", "anchorablePaths", "p", "pathOrigin", "w", "s", "carriedSamples", "gfaNode", "sm", "samples", "positive", "v", "statedDepth", "tags", "length", "count", "makeNode", "depth", "stableCoordinate", "convertGFAToGraph", "name", "nodes", "edges", "nodeId", "segmentId", "paths", "edgeToPathsMap", "edgeKey", "a", "recordPathEdges", "nodeIds", "i", "key", "edge", "pathIds", "lengths", "n", "anchoring", "surveyPaths", "isLinearHost", "view", "v", "widest", "blocks", "best", "b", "hostFrame", "region", "block", "bpPerPx", "hostWindow", "displayed", "hostCut", "window", "capBp", "visible", "margin", "cutHolds", "cut", "import_configuration", "import_mobx_state_tree", "OFF_REFERENCE_COLOR", "referencePositionColor", "start", "end", "hue", "isLaneView", "view", "sourceLaneDisplay", "views", "connectedViewId", "trackId", "display", "t", "paintSourceLane", "color", "current", "orientToReference", "graph", "positions", "backbone", "node", "isBackbone", "points", "segments", "mid", "weight", "sum", "p", "cx", "cy", "cr", "sxr", "syr", "angle", "c", "s", "out", "id", "x", "y", "below", "above", "LANE_GAP", "referenceSeeds", "graph", "scaling", "opts", "drawn", "node", "drawnNodeLength", "drawnOf", "id", "backbone", "isBackbone", "a", "b", "seeds", "x", "adjacent", "buildNeighbors", "depth", "queue", "at", "next", "neighbour", "unreached", "seededNodes", "REPEAT_ADAPTER_TYPES", "REPEAT_TRACK_HINT", "pickRepeatTrack", "tracks", "named", "t", "own", "f", "name", "PACKED_NAME", "packedName", "pair", "i", "field", "top", "MOTIF_FIELDS", "PERIOD_FIELDS", "NAME_FIELDS", "first", "names", "value", "one", "IUPAC", "repeatUnitOf", "period", "motif", "numbers", "n", "callsOf", "samples", "called", "sample", "fields", "reads", "alleles", "bp", "repeatArraysFrom", "features", "arrays", "start", "end", "unit", "refName", "stated", "a", "b", "walkHighlight", "graph", "name", "path", "p", "byId", "n", "edgeAt", "e", "i", "nodeIds", "edgeIndexes", "a", "b", "index", "bpOf", "ids", "sum", "id", "reference", "pathOrigin", "isRecord", "value", "isFeatureLike", "hoveredName", "feature", "name", "readLgvHover", "hovered", "result", "refName", "coord", "coord0", "assemblyName", "hoverInRegion", "hover", "region", "nodeForLgvHover", "nodes", "byName", "byCoord", "node", "isBackbone", "import_configuration", "isRecord", "value", "isLinearView", "view", "withRows", "views", "linearViewTarget", "connectedViewId", "assemblyName", "candidates", "reportFailure", "session", "what", "launch", "error", "MIN_LAUNCH_SPAN_BP", "paddedLocation", "loc", "minSpan", "pad", "withReferenceRegion", "contributors", "region", "c", "showInLinearView", "location", "assembly", "connectedViewId", "tracks", "existing", "linearViewTarget", "viewId", "locLabel", "locString", "highlightInLinearView", "target", "assemblyNamesOfTrack", "trackId", "track", "t", "names", "n", "launchSyntenyView", "graphTrackId", "graphTrackAssemblies", "aligned", "covered", "panels", "snapshot", "import_configuration", "ANNOTATION_TRACK_TYPE", "launchTracks", "session", "assemblyName", "first", "found", "track", "type", "assemblyNames", "trackId", "import_configuration", "import_tracks", "SYNTENY_TRACK_TYPE", "launchableSyntenyTracks", "session", "assemblyNames", "wanted", "found", "track", "type", "trackAssemblies", "trackId", "coverage", "name", "a", "b", "import_configuration", "import_tracks", "isStringArray", "value", "item", "graphReferenceAssembly", "track", "assemblyNames", "isStringArray", "offReferenceProblem", "referenceAssembly", "assemblyName", "MAX_CANVAS_HEIGHT", "MIN_CANVAS_HEIGHT", "VARIANT_MAP_HEIGHT", "SEGMENTS_SUFFIX", "bubblePrefix", "adapterConfig", "uri", "FIT_PADDING", "HOVER_BRIGHTEN", "SELECT_BRIGHTEN", "VIEWPORT_DEBOUNCE_MS", "VIEWPORT_PANES_BUILT", "dependOn", "_values", "MAX_GRAPH_REGION_BP", "formatSpanBp", "bp", "DEFAULT_MAX_GRAPH_NODES", "MIN_ZOOM", "MAX_ZOOM", "clampZoom", "zoom", "axisScaleOf", "scale", "pixelRows", "viewportOf", "model", "padded", "v", "panes", "w", "h", "fittedTranslateY", "bounds", "usableHeight", "yScale", "leftoverY", "contains", "outer", "inner", "forceLayouts", "FORCE_LAYOUT_CACHE_SIZE", "forceLayoutsOf", "graph", "cache", "inheritForceLayouts", "from", "to", "remember", "key", "result", "stateModelFactory", "LAYOUT_MODE_VALUES", "COLOR_SCHEME_VALUES", "BUBBLE_SPREAD_VALUES", "NODE_WIDTH_VALUES", "self", "m", "modeUsesLayoutEngine", "n", "paths", "pathColorsLegible", "pathLegend", "walkHighlight", "bubblesFromGraph", "track", "t", "region", "GENE_ADAPTER_TYPES", "REPEAT_ADAPTER_TYPES", "pickRepeatTrack", "r", "buildNeighbors", "contigThickness", "nodeWidth", "nodeById", "mean", "meanDepth", "maxNodeWidthPx", "id", "node", "nodeWidthPx", "deletionEdges", "repeat", "bars", "walkRows", "samples", "rows", "b", "withCalls", "row", "i", "bubble", "classifyBubble", "positions", "genePins", "labels", "c", "bubbleHalos", "name", "computeReferenceRamp", "minX", "minY", "maxX", "maxY", "segments", "seg", "extent", "walkRowsExtent", "usableWidth", "ceiling", "floor", "pickGeneTrack", "d", "ramp", "nodeId", "neighbors", "span", "nodeReferenceSpan", "backbone", "backboneNodes", "contributingAssemblies", "backboneSpan", "assemblyManager", "panSN", "byPrefix", "asm", "prefix", "loaded", "sample", "resolveContributors", "withReferenceRegion", "linearViewTarget", "own", "nodeOwnLocation", "ownAssembly", "resolveLocationAssembly", "onReference", "paddedLocation", "above", "view", "isLinearHost", "host", "layout", "loadedRegion", "hostFrame", "error", "message", "ms", "strokeCount", "built", "quality", "linear", "mode", "reanchored", "anchorFromPaths", "draw", "show", "scheme", "spread", "width", "trackId", "px", "hops", "haplotypes", "viewId", "paired", "withRows", "edgeIdx", "panning", "session", "s", "tx", "ty", "factor", "centerX", "centerY", "newScale", "ratio", "fitX", "fitY", "translateX", "engaging", "scheduleViewportDirty", "requestPositionsDirtyFrame", "dx", "dy", "loadController", "callLayout", "scaling", "rpcManager", "sessionId", "anchored", "isBackbone", "seededNodes", "status", "forceLayoutKey", "computeLayout", "start", "local", "layoutModeByValue", "hit", "spreadFor", "merged", "mergeRuns", "duration", "layoutScaling", "drawn", "drawnNodeLength", "splitRuns", "oriented", "orientToReference", "liveRequest", "layoutInto", "request", "isLive", "signal", "computed", "e", "live", "parseAndLayout", "text", "keepSelection", "gfaGraph", "parseGFA", "anchorGraph", "convertGFAToGraph", "selected", "liveLoad", "beginLoad", "load", "loadedTrack", "loadBubbles", "features", "f", "trackFeatures", "what", "config", "loadGenes", "geneModelsFrom", "loadRepeats", "repeatArraysFrom", "doSubgraphLoad", "opts", "regionSize", "refusal", "offReferenceProblem", "graphReferenceAssembly", "fetchStart", "gfaText", "label", "locLabel", "cutFromLoadedTrack", "coarse", "loadWholeGFA", "source", "location", "stated", "sub", "bubbleSubgraph", "bubbleSegmentIds", "BUBBLE_KIND_NAMES", "seen", "tier", "cap", "visible", "cutHolds", "hostCut", "places", "frame", "a", "blocks", "hostWindow", "backend", "domain", "display", "sourceLaneDisplay", "paintSourceLane", "referencePositionColor", "hover", "readLgvHover", "hoverInRegion", "nodeForLgvHover", "firstViewport", "viewport", "hoveredNode", "hoveredEdge", "selectedNode", "nodes", "geometryStart", "viewportBounds", "batch", "buildGeometry", "dpr", "target", "showInLinearView", "launchTracks", "highlightInLinearView", "launchSyntenyView", "launchableSyntenyTracks", "items", "item", "graphLaunchMenuItems", "graphLaunchKeys", "GraphGenomeViewF", "pluginManager", "ViewType", "stateModelFactory", "LaunchGraphGenomeViewF", "pluginManager", "args", "session", "spec", "import_react", "import_DisplayType", "import_configuration", "import_trackHeightConfigSchemaFields", "import_mobx_state_tree", "configSchemaFactory", "LAYOUT_MODE_VALUES", "COLOR_SCHEME_VALUES", "import_react", "import_configuration", "import_pluggableElementTypes", "import_util", "import_TrackHeightMixin", "import_mobx_state_tree", "import_mobx", "GraphSettingsDialog", "stateModelFactory", "configSchema", "Pane", "TrackHeightMixin", "self", "view", "isLinearHost", "pane", "graph", "walks", "LAYOUT_MODES", "mode", "COLOR_SCHEMES", "scheme", "walk", "Settings_default", "onClose", "distance", "before", "target", "host", "height", "LinearGraphDisplayF", "pluginManager", "configSchema", "configSchemaFactory", "DisplayType", "stateModelFactory", "import_AdapterType", "import_configuration", "import_mobx_state_tree", "normalizeSnapshot", "snap", "uri", "baseUri", "csi", "MinigraphBubbleAdapter", "configSchema_default", "MinigraphBubbleAdapterF", "pluginManager", "AdapterType", "normalizeSnapshot", "configSchema_default", "r", "import_AdapterType", "import_configuration", "import_mobx_state_tree", "tbi", "uri", "baseUri", "csi", "prefixLocations", "snap", "normalizeSnapshot", "coarse", "indexSchema", "name", "defaultUri", "RgfaTabixCoarseTier", "RgfaTabixAdapter", "configSchema_default", "RgfaTabixAdapterF", "pluginManager", "AdapterType", "normalizeSnapshot", "configSchema_default", "r", "import_util", "import_material", "import_mobx_react", "import_mui", "isRecord", "value", "readRegion", "region", "refName", "start", "end", "assemblyName", "isConnected", "view", "linearViewId", "liveViewIds", "connectedViewId", "isOnAssembly", "assemblyNames", "graphViewHighlights", "views", "linearAssemblyNames", "highlights", "withRows", "import_jsx_runtime", "useStyles", "theme", "Highlight", "model", "region", "classes", "coords", "GraphNodeHighlight", "views", "graphViewHighlights", "key", "GraphNodeHighlight_default", "import_jsx_runtime", "POINT", "GraphHoverSyncF", "pluginManager", "model", "GraphNodeHighlight_default", "PLUGIN_NAME", "version", "GraphGenomeViewPlugin", "Plugin", "PLUGIN_NAME", "version", "pluginManager", "GraphGenomeViewF", "LinearGraphDisplayF", "LaunchGraphGenomeViewF", "GraphHoverSyncF", "RgfaTabixAdapterF", "MinigraphBubbleAdapterF", "GbzBaseSyntenyAdapterF", "GraphAddTrackWorkflowF", "GraphComputeLayout", "GetSubgraph", "BubbleChart_default", "session", "e"]
+  "sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/core/Plugin\"];", "module.exports = JBrowseExports[\"@jbrowse/core/pluggableElementTypes/AdapterType\"];", "module.exports = JBrowseExports[\"@jbrowse/core/configuration\"];", "module.exports = JBrowseExports[\"@jbrowse/core/data_adapters/dataAdapterCache\"];", "module.exports = JBrowseExports[\"@jbrowse/core/pluggableElementTypes\"];", "module.exports = JBrowseExports[\"@jbrowse/core/pluggableElementTypes/ViewType\"];", "module.exports = JBrowseExports[\"@jbrowse/core/util/withLaunchInput\"];", "module.exports = JBrowseExports[\"@jbrowse/core/pluggableElementTypes/models\"];", "module.exports = JBrowseExports[\"@jbrowse/render-core/RenderLifecycleMixin\"];", "module.exports = JBrowseExports[\"mobx\"];", "module.exports = JBrowseExports[\"@jbrowse/core/pluggableElementTypes/DisplayType\"];", "module.exports = JBrowseExports[\"@jbrowse/display-kit/trackHeightConfigSchemaFields\"];", "module.exports = JBrowseExports[\"@jbrowse/display-kit/TrackHeightMixin\"];", "import Plugin from '@jbrowse/core/Plugin'\nimport { isAbstractMenuManager } from '@jbrowse/core/util'\nimport BubbleChartIcon from '@mui/icons-material/BubbleChart'\n\nimport GbzBaseSyntenyAdapterF from './GbzBaseSyntenyAdapter/index'\nimport GetSubgraph from './GetSubgraph'\nimport GraphAddTrackWorkflowF from './GraphAddTrackWorkflow/index'\nimport GraphComputeLayout from './GraphComputeLayout'\nimport GraphGenomeViewF from './GraphGenomeView/index'\nimport LaunchGraphGenomeViewF from './LaunchGraphGenomeView'\nimport LinearGraphDisplayF from './LinearGraphDisplay/index'\nimport MinigraphBubbleAdapterF from './MinigraphBubbleAdapter/index'\nimport RgfaTabixAdapterF from './RgfaTabixAdapter/index'\nimport GraphHoverSyncF from './hoverSync/index'\nimport { PLUGIN_NAME } from './pluginName'\nimport { version } from './version'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { AbstractSessionModel } from '@jbrowse/core/util'\n\nexport default class GraphGenomeViewPlugin extends Plugin {\n  name = PLUGIN_NAME\n  version = version\n\n  install(pluginManager: PluginManager) {\n    GraphGenomeViewF(pluginManager)\n    LinearGraphDisplayF(pluginManager)\n    LaunchGraphGenomeViewF(pluginManager)\n    GraphHoverSyncF(pluginManager)\n    RgfaTabixAdapterF(pluginManager)\n    MinigraphBubbleAdapterF(pluginManager)\n    GbzBaseSyntenyAdapterF(pluginManager)\n    GraphAddTrackWorkflowF(pluginManager)\n    pluginManager.addRpcMethod(() => new GraphComputeLayout(pluginManager))\n    pluginManager.addRpcMethod(() => new GetSubgraph(pluginManager))\n  }\n\n  // A throw from configure() takes the whole session to its error page, and a\n  // menu entry is not worth that: hubs 1.0.9 did exactly this to every\n  // jbrowse.org/ucsc launch by appending to a menu a released host defines as\n  // a function. The view is still reachable without the entry.\n  configure(pluginManager: PluginManager) {\n    try {\n      if (isAbstractMenuManager(pluginManager.rootModel)) {\n        pluginManager.rootModel.appendToSubMenu(['Add'], {\n          label: 'Graph genome view',\n          icon: BubbleChartIcon,\n          onClick: (session: AbstractSessionModel) => {\n            session.addView('GraphGenomeView', {})\n          },\n        })\n      }\n    } catch (e) {\n      console.warn('[GraphGenomeView] could not add the Add menu entry', e)\n    }\n  }\n}\n", "\"use client\";\n\nimport createSvgIcon from \"./utils/createSvgIcon.mjs\";\nimport { jsx as _jsx } from \"react/jsx-runtime\";\nexport default createSvgIcon([/*#__PURE__*/_jsx(\"circle\", {\n  cx: \"7.2\",\n  cy: \"14.4\",\n  r: \"3.2\"\n}, \"0\"), /*#__PURE__*/_jsx(\"circle\", {\n  cx: \"14.8\",\n  cy: \"18\",\n  r: \"2\"\n}, \"1\"), /*#__PURE__*/_jsx(\"circle\", {\n  cx: \"15.2\",\n  cy: \"8.8\",\n  r: \"4.8\"\n}, \"2\")], 'BubbleChart');", "import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'\n\nimport configSchema from './configSchema.ts'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\n\nexport default function GbzBaseSyntenyAdapterF(pluginManager: PluginManager) {\n  pluginManager.addAdapterType(\n    () =>\n      new AdapterType({\n        name: 'GbzBaseSyntenyAdapter',\n        displayName: 'gbz-base pangenome adapter',\n        configSchema,\n        // The same opened database serves the graph view's subgraph, so the\n        // launch menu offers this track too (launchSubgraph/subgraphTracks).\n        // headerLanes: getHeader declares every haplotype as a lane, which is\n        // what makes MultiWaySyntenyDisplay read the header of an untiered\n        // adapter and offer its lane picker over the whole graph.\n        // lanePairsOnAnchor: a window of the anchor answers any two lanes'\n        // alignment to each other, so the display fetches each adjacent pair\n        // rather than composing it through the reference\n        adapterCapabilities: [\n          'getSubgraph',\n          'headerLanes',\n          'lanePairsOnAnchor',\n        ],\n        adapterMetadata: {\n          category: 'Synteny adapters',\n        },\n        getAdapterClass: () =>\n          import('./GbzBaseSyntenyAdapter.ts').then(r => r.default),\n      }),\n  )\n}\n", "import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { types } from '@jbrowse/mobx-state-tree'\n\nimport type { Instance } from '@jbrowse/mobx-state-tree'\n\n/**\n * #config GbzBaseSyntenyAdapter\n * #trackType SyntenyTrack\n * #fileFormat synteny | gbz-base pangenome database | Haplotype alignments read from the graph at query time, no PAF conversion\n * Serves a pangenome graph stored as a gbz-base SQLite database (`.gbz.db`) as\n * haplotype-versus-reference alignments, the shape `MultiWaySyntenyDisplay`\n * draws as one lane per haplotype. A window on the reference is located on the\n * graph's reference path, every haplotype's walk through the nodes it covers\n * is recovered and named, and each haplotype becomes one alignment record with\n * a CIGAR, so the graph is read through HTTP range requests with no offline\n * conversion. The database has to carry the `HaplotypeSamples` and\n * `HaplotypeLengths` side tables that `gbz-haplotype-index` (shipped with\n * `@gmod/gbz-base`) writes into an upstream-built database; without them the\n * graph cannot say which haplotype a walk belongs to.\n *\n * Only the fine tier exists: a whole-chromosome view stays on a PIF's coarse\n * tier. A query on a haplotype lane answers nothing, so the multi-way display\n * composes its lane-to-lane links through the reference.\n *\n * #example\n * ```js\n * {\n *   type: 'GbzBaseSyntenyAdapter',\n *   uri: 'hprc-v2.gbz.db',\n *   assemblyNames: ['hg38'],\n *   assemblyNameToPanSN: { hg38: 'GRCh38#0' },\n * }\n * ```\n */\nconst GbzBaseSyntenyAdapter = ConfigurationSchema(\n  'GbzBaseSyntenyAdapter',\n  {\n    /**\n     * #slot\n     * The first entry is the anchor: the JBrowse assembly the graph's reference\n     * sample is loaded as. Further entries are haplotypes loaded as JBrowse\n     * assemblies under their PanSN prefix (`HG002#1`); one loaded under another\n     * name only needs its `assemblyNameToPanSN` entry. A haplotype named in\n     * neither is still a lane, labelled by its PanSN prefix.\n     */\n    assemblyNames: {\n      type: 'stringArray',\n      defaultValue: [],\n    },\n    /**\n     * #slot\n     * The `.gbz.db` written by `gbz-base construct` and augmented by\n     * `gbz-haplotype-index`; read by HTTP range requests, so it can be large.\n     */\n    gbzDbLocation: {\n      type: 'fileLocation',\n      defaultValue: {\n        uri: '/path/to/graph.gbz.db',\n        locationType: 'UriLocation',\n      },\n    },\n    /**\n     * #slot\n     * A companion database written by `gbz-haplotype-index --output`, holding\n     * the `HaplotypeSamples` and `HaplotypeLengths` tables for a graph database\n     * that does not carry them itself, such as the one HPRC publishes. One\n     * built with anchor rows (the tool's default) lets a fetch for a chosen\n     * set of lanes walk only those haplotypes. Empty means the graph database\n     * carries the tables.\n     */\n    haplotypeIndexLocation: {\n      type: 'fileLocation',\n      defaultValue: {\n        uri: '',\n        locationType: 'UriLocation',\n      },\n    },\n    /**\n     * #slot\n     * How the graph view's subgraph is extended past the nodes the reference\n     * window touches. `contained` adds every top-level snarl with both\n     * boundary nodes in the window, which is what brings back the bubbles a\n     * reference-only walk leaves out; a haplotype still breaks into a new W\n     * line wherever it leaves the window's nodes (a 60 kb C4 window on the\n     * HPRC graph: 2,703 nodes, 8,083 walks for 464 haplotypes). `overlapping`\n     * also follows snarls that leave the window, so every haplotype is one\n     * walk (464), at the price of every node in those snarls (4,184 there,\n     * 24,547 across the KIV-2 repeat). `none` leaves only the bp `context`.\n     */\n    subgraphSnarls: {\n      type: 'stringEnum',\n      model: types.enumeration('SnarlOutput', [\n        'none',\n        'contained',\n        'overlapping',\n      ]),\n      defaultValue: 'contained',\n    },\n    /**\n     * #slot\n     * The graph sample the anchor window is located on. Empty means the sample\n     * the anchor's PanSN prefix names, or the database's one reference sample\n     * (`gbwt_reference_samples`) when the anchor names none; a database with\n     * several reference samples then needs this set.\n     */\n    referenceSample: {\n      type: 'string',\n      defaultValue: '',\n    },\n    /**\n     * #slot\n     * Maps a JBrowse assembly name to its PanSN prefix in the graph, sample or\n     * haplotype level (`{ hg38: 'GRCh38#0', 'HG002.1': 'HG002#1' }`). Defaults\n     * to identity.\n     */\n    assemblyNameToPanSN: {\n      type: 'frozen',\n      defaultValue: {},\n    },\n    /**\n     * #slot\n     * Graph context around the reference walk, in bp, on top of\n     * `subgraphSnarls`. Since `@gmod/gbz-base` joins the pieces of a walk that\n     * leaves the window's nodes and comes back (the private stretch becomes the\n     * record's insertion, the skipped reference its deletion), a lane's record\n     * count is one per haplotype at any context; what context trades is nodes\n     * read against pieces to identify and join. A window inside a snarl far\n     * larger than itself (MHC class II on the HPRC graph, 90 kb) is 1.1M pieces\n     * at 0 and 464 walks at 1000, three times faster; a window whose private\n     * stretches are short bubbles costs about the same either way. For the\n     * graph view's cut it is simply how far past the window the cut extends.\n     */\n    context: {\n      type: 'number',\n      defaultValue: 1000,\n      advanced: true,\n    },\n    /**\n     * #slot\n     * The most graph nodes one window may load before the query fails rather\n     * than reading a whole chromosome into the worker.\n     */\n    nodeLimit: {\n      type: 'number',\n      defaultValue: 100000,\n      advanced: true,\n    },\n  },\n  {\n    explicitlyTyped: true,\n\n    /**\n     * #preProcessSnapshot\n     *\n     *\n     * preprocessor to allow minimal config:\n     * ```json\n     * {\n     *   \"type\": \"GbzBaseSyntenyAdapter\",\n     *   \"uri\": \"graph.gbz.db\",\n     *   \"assemblyNames\": [\"hg38\"]\n     * }\n     * ```\n     */\n    preProcessSnapshot: snap => {\n      return snap.uri\n        ? {\n            ...snap,\n            gbzDbLocation: {\n              uri: snap.uri,\n              baseUri: snap.baseUri,\n            },\n          }\n        : snap\n    },\n  },\n)\n\nexport type GbzBaseSyntenyAdapterConfig = Instance<typeof GbzBaseSyntenyAdapter>\n\nexport default GbzBaseSyntenyAdapter\n", "import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'\nimport { RpcMethodTypeWithRenameRegion } from '@jbrowse/core/pluggableElementTypes'\n\nimport type { RpcExecuteArgs } from '@jbrowse/core/rpc/RpcRegistry'\nimport type { Region } from '@jbrowse/core/util'\n\n// No `sessionId`, `signal` or `statusCallback` here: those belong to the\n// CALL, not to this payload, and core's `EntriesDeclaringCallLevelFields` fails\n// the build for a registry entry that declares one. `execute` still receives\n// them, because `RpcExecuteArgs` intersects `RpcCallContext` in.\n// `hops` is how far past the window a cut follows links, which only the rGFA\n// cut reads; the GBZ cut has its own bp `context` slot. `haplotypes` is the\n// set the cut is for, lane assembly names or PanSN prefixes, which only the GBZ\n// cut reads: it keeps those walks and the nodes they visit. Undefined or empty\n// is every haplotype. `tier` picks which of an rGFA track's two index pairs the\n// cut reads, the adapter's own or its `coarse` one; fine when absent.\nexport type SubgraphTier = 'fine' | 'coarse'\n\nexport interface SubgraphCutOptions {\n  hops?: number\n  haplotypes?: string[]\n  tier?: SubgraphTier\n}\n\n// What an adapter's cut is handed: the payload, plus the call's own signal so\n// a cut the view has moved on from stops reading.\nexport interface SubgraphAdapterOptions extends SubgraphCutOptions {\n  signal?: AbortSignal\n}\n\nexport interface GetSubgraphArgs {\n  adapterConfig: Record<string, unknown>\n  region: Region\n  opts?: SubgraphCutOptions\n}\n\ndeclare module '@jbrowse/core/rpc/RpcRegistry' {\n  interface RpcRegistry {\n    GetSubgraph: {\n      args: GetSubgraphArgs\n      return: string\n    }\n  }\n}\n\n// Adapters that can cut a local subgraph out of a graph file implement this:\n// RgfaTabixAdapter and GbzBaseSyntenyAdapter today.\ninterface SubgraphAdapter {\n  getSubgraph(region: Region, opts?: SubgraphAdapterOptions): Promise<string>\n}\n\nfunction isSubgraphAdapter(adapter: object): adapter is SubgraphAdapter {\n  return (\n    'getSubgraph' in adapter &&\n    typeof (adapter as SubgraphAdapter).getSubgraph === 'function'\n  )\n}\n\n// RpcMethodTypeWithRenameRegion, not the plain RpcMethodType: the base class is\n// what maps `region.refName` from the assembly's spelling onto the adapter's own\n// before the call crosses to the worker. Without it a launch on an hg38 whose\n// contigs are bare (`6`, which is what every GRCh38 FASTA on jbrowse.org uses)\n// asked RgfaTabixAdapter for `GRCh38#0#6`, matched nothing, and opened a view\n// reading \"0 nodes, 0 edges\" with no error. The segments track drew the whole\n// time, because CoreGetFeatures renames and this did not, so the graph looked\n// broken while its own track looked fine. `assemblyNameToPanSN` covers the\n// sample half of a PanSN name only; the contig half is refName aliasing, which\n// the assembly already knows and this now consults.\nexport default class GetSubgraph extends RpcMethodTypeWithRenameRegion<'GetSubgraph'> {\n  name = 'GetSubgraph' as const\n\n  // Parameterized by the registry key, not left at the default `string`: a bare\n  // RpcMethodTypeWithRenameRegion resolves RpcExecuteArgs to `unknown`, so\n  // `execute` type-checks against nothing at all. `invoke` has already run\n  // `deserializeArguments` by the time this is called, so it does not.\n  async execute(args: RpcExecuteArgs<'GetSubgraph'>) {\n    // `signal` arrives on every call and has to be named to be forwarded:\n    // unnamed, a cut the view had replaced went on querying to the end, one\n    // tabix read per off-reference segment per hop.\n    const { adapterConfig, region, sessionId, opts, signal } = args\n\n    const { dataAdapter } = await getAdapter(\n      this.pluginManager,\n      sessionId,\n      adapterConfig,\n    )\n    if (isSubgraphAdapter(dataAdapter)) {\n      return dataAdapter.getSubgraph(region, { ...opts, signal })\n    }\n    // An empty result is how the view and the launch menu detect \"this track\n    // can't do subgraphs\" \u2014 see GraphGenomeView.loadFromTabixSubgraph.\n    console.warn(\n      `[GetSubgraph] ${dataAdapter.constructor.name} does not implement getSubgraph`,\n    )\n    return ''\n  }\n}\n", "import { lazy } from 'react'\n\nimport { AddTrackWorkflowType } from '@jbrowse/core/pluggableElementTypes'\nimport { types } from '@jbrowse/mobx-state-tree'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\n\nconst GraphAddTrackWidget = lazy(() => import('./AddTrackWorkflow'))\n\nexport default function GraphAddTrackWorkflowF(pluginManager: PluginManager) {\n  pluginManager.addAddTrackWorkflowType(\n    () =>\n      new AddTrackWorkflowType({\n        name: 'Pangenome graph track',\n        displayName: 'Add pangenome graph track',\n        ReactComponent: GraphAddTrackWidget,\n        stateModel: types.model({}),\n      }),\n  )\n}\n", "import { RpcMethodType } from '@jbrowse/core/pluggableElementTypes'\n\nimport loadBandage from './loadBandage'\n\nimport type { LayoutNode } from './GraphGenomeView/layout/referenceSeeds'\nimport type { Graph, LayoutResult } from './GraphGenomeView/types'\nimport type { RpcExecuteArgs } from '@jbrowse/core/rpc/RpcRegistry'\n\n// `sessionId` and `statusCallback` are the CALL's, not this payload's \u2014 core's\n// `EntriesDeclaringCallLevelFields` fails the build for a registry entry that\n// declares either, on the grounds that a field one method owns is a field the\n// other forty cannot be passed. `execute` still receives both, through\n// `RpcExecuteArgs`'s intersection with `RpcCallContext`.\nexport interface GraphComputeLayoutArgs {\n  // a node may carry an `x`/`y` seed, which the engine reads as where its\n  // chain starts (referenceSeeds.ts)\n  graph: { nodes: LayoutNode[]; edges: Graph['edges'] }\n  options: Record<string, unknown>\n}\n\ndeclare module '@jbrowse/core/rpc/RpcRegistry' {\n  interface RpcRegistry {\n    GraphComputeLayout: {\n      args: GraphComputeLayoutArgs\n      return: { result: LayoutResult; duration: number }\n    }\n  }\n}\n\nexport default class GraphComputeLayout extends RpcMethodType<'GraphComputeLayout'> {\n  name = 'GraphComputeLayout' as const\n\n  async execute(args: RpcExecuteArgs<'GraphComputeLayout'>) {\n    const { graph, options, statusCallback } = args\n\n    statusCallback?.('Loading layout engine')\n    const module = await loadBandage()\n\n    statusCallback?.('Computing layout')\n    const startTime = performance.now()\n    const result = module.computeLayout(graph, options)\n    const duration = performance.now() - startTime\n\n    return { result, duration }\n  }\n}\n", "export type { BandageModule } from './bandage/bandage-layout'\n\nimport type { BandageModule } from './bandage/bandage-layout'\n\n// The Bandage engine is a ~425kb self-contained ES module (Emscripten\n// -sSINGLE_FILE=1, wasm inlined as base64). A plain dynamic import lets the\n// bundler emit it as a sibling chunk that the browser resolves relative to this\n// module's own url via import.meta.url \u2014 so it downloads only when a\n// force-directed layout is requested, and works identically on the main thread\n// and in the RPC worker with no url plumbing.\nlet cached: Promise<BandageModule> | undefined\n\nexport default function loadBandage() {\n  cached ??= import('./bandage/bandage-layout')\n    .then(mod => mod.default())\n    .catch((e: unknown) => {\n      // let a later attempt retry rather than caching the failure forever\n      cached = undefined\n      throw e\n    })\n  return cached\n}\n", "import { lazy } from 'react'\n\nimport ViewType from '@jbrowse/core/pluggableElementTypes/ViewType'\nimport { defineLaunchKeys } from '@jbrowse/core/util/withLaunchInput'\n\nimport modelFactory from './model'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\n\n// This view has NO launch keys, and saying so is what turns the check on.\n//\n// A launch key is a spec field the launcher interprets rather than assigns \u2014 an\n// LGV's `assembly` and `loc`, resolved into `displayedRegions`. Every field of\n// a graph launch is a plain persisted prop instead (see\n// LaunchGraphGenomeView), so the registration is empty; what it buys is\n// `ViewType.acceptedKeys`, which is `undefined` until a view declares its\n// launch vocabulary, and which `loadSessionSpec` needs to report\n// `ignored unknown key(s)`.\n//\n// Without it a session spec's typo in a GraphGenomeView entry is silent: the\n// key lands in the snapshot, MST drops it, and the view opens on the import\n// form with nothing said. That surface is written by hand with no compiler\n// behind it \u2014 `sessionSpec()` takes a bare `object` \u2014 and the docs build two\n// dozen graph figures through it, `loadedRegion` and `loadedTrackId` among the\n// fields a misspelling would silently cost.\n//\n// Ignored by a host that predates `acceptedKeys`: its ViewType constructor\n// reads the options it knows and this is not one of them.\nconst graphLaunchKeys = defineLaunchKeys<object>()({})\n\nexport default function GraphGenomeViewF(pluginManager: PluginManager) {\n  pluginManager.addViewType(() => {\n    return new ViewType({\n      name: 'GraphGenomeView',\n      displayName: 'Graph genome view',\n      stateModel: modelFactory(),\n      launchKeys: graphLaunchKeys,\n      ReactComponent: lazy(() => import('./components/GraphGenomeView')),\n    })\n  })\n}\n", "import { readConfObject } from '@jbrowse/core/configuration'\nimport { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models'\nimport { pushLaunchViewMenuItem } from '@jbrowse/core/ui'\nimport {\n  getContainingView,\n  getSession,\n  isSessionModelWithWidgets,\n  statusMessageText,\n} from '@jbrowse/core/util'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { addDisposer, flow, isAlive, types } from '@jbrowse/mobx-state-tree'\nimport { RenderLifecycleMixin } from '@jbrowse/render-core/RenderLifecycleMixin'\nimport { getDpr } from '@jbrowse/render-core/canvas2dUtils'\nimport { autorun, reaction, untracked } from 'mobx'\n\nimport { backboneNodes, backboneSpan, isBackbone } from './anchoredNodes'\nimport { BUBBLE_SPREAD_VALUES, spreadFor } from './bubbleSpreads'\nimport { bubbleHalos } from './bubbles/bubbleHalos'\nimport { bubblesFromGraph } from './bubbles/bubblesFromGraph'\nimport {\n  BUBBLE_KIND_NAMES,\n  bubbleSegmentIds,\n  classifyBubble,\n} from './bubbles/classifyBubble'\nimport { bubbleSubgraph } from './bubbles/popBubble'\nimport { COLOR_SCHEME_VALUES } from './colorSchemes'\nimport { deletionEdges } from './deletionEdges'\nimport {\n  GENE_ADAPTER_TYPES,\n  geneModelsFrom,\n  pickGeneTrack,\n} from './genes/geneFeatures'\nimport { genePins } from './genes/genePins'\nimport { convertGFAToGraph } from './gfa/gfaConverter'\nimport { cutHolds, hostCut, hostFrame, hostWindow, isLinearHost } from './host'\nimport {\n  paintSourceLane,\n  referencePositionColor,\n  sourceLaneDisplay,\n} from './laneRamp'\nimport { drawnNodeLength, layoutScaling } from './layout/drawnScale'\nimport { mergeRuns, splitRuns } from './layout/mergeRuns'\nimport { orientToReference } from './layout/orientToReference'\nimport { seededNodes } from './layout/referenceSeeds'\nimport { ROW_HEIGHT_PX } from './layout/rowSpacing'\nimport { walkRowsExtent } from './layout/walkRowLayout'\nimport { walkRows } from './layout/walkRows'\nimport {\n  LAYOUT_MODE_VALUES,\n  layoutModeByValue,\n  modeUsesLayoutEngine,\n} from './layoutModes'\nimport {\n  NODE_WIDTH_VALUES,\n  maxNodeWidthPx,\n  meanDepth,\n  nodeWidthPx,\n} from './nodeWidths'\nimport { anchorFromPaths, anchorGraph } from './pathAnchoring'\nimport { pathColorsLegible, pathLegend } from './pathColors'\nimport { buildNeighbors, nodeReferenceSpan } from './referenceSpan'\nimport { buildGeometry, computeReferenceRamp } from './renderer/GeometryBuilder'\nimport {\n  REPEAT_ADAPTER_TYPES,\n  pickRepeatTrack,\n  repeatArraysFrom,\n} from './repeats/repeatFeatures'\nimport { withCalls } from './repeats/walkCalls'\nimport { walkHighlight } from './walkHighlight'\nimport { parseGFA } from '../gfa-core/index'\nimport {\n  hoverInRegion,\n  nodeForLgvHover,\n  readLgvHover,\n} from '../hoverSync/lgvHover'\nimport {\n  contributingAssemblies,\n  locLabel,\n  nodeOwnLocation,\n  resolveContributors,\n  resolveLocationAssembly,\n} from '../launchFromGraph/contributors'\nimport { graphLaunchMenuItems } from '../launchFromGraph/graphMenuItems'\nimport {\n  highlightInLinearView,\n  launchSyntenyView,\n  paddedLocation,\n  showInLinearView,\n  withReferenceRegion,\n} from '../launchFromGraph/launchFromGraph'\nimport { launchTracks } from '../launchFromGraph/launchTracks'\nimport { linearViewTarget, withRows } from '../launchFromGraph/linearViewTarget'\nimport { launchableSyntenyTracks } from '../launchFromGraph/syntenyTracks'\nimport {\n  graphReferenceAssembly,\n  offReferenceProblem,\n} from '../launchSubgraph/subgraphTracks'\n\nimport type { BubbleSpread } from './bubbleSpreads'\nimport type { ColorScheme, ResolvedColorScheme } from './colorSchemes'\nimport type { GeneModel } from './genes/geneFeatures'\nimport type { HostWindow, LinearHost } from './host'\nimport type { LayoutScaling } from './layout/drawnScale'\nimport type { LayoutModeValue } from './layoutModes'\nimport type { NodeWidth } from './nodeWidths'\nimport type { Renderer } from './renderer/types'\nimport type { RepeatArray } from './repeats/repeatFeatures'\nimport type { Graph, GraphNode, LayoutResult } from './types'\nimport type { SubgraphCutOptions, SubgraphTier } from '../GetSubgraph'\nimport type { NodeInk } from './util/hitDetection'\nimport type { MinigraphBubble } from '../MinigraphBubbleAdapter/bubbleLine'\nimport type { AxisScale } from './util/geometry'\nimport type { GraphLocation } from '../launchFromGraph/contributors'\nimport type { SubgraphRegion } from '../launchSubgraph/launchSubgraphView'\nimport type { MenuItem } from '@jbrowse/core/ui'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { FileLocation } from '@jbrowse/core/util/types'\n\n// Ceiling on the pane, and what it falls back to before there is a layout to\n// size against. A roughly square drawing (FMMM) hits this and keeps the\n// scrollable pane it has always had.\nconst MAX_CANVAS_HEIGHT = 600\n// Floor, so a window holding only backbone \u2014 one row, no height at all \u2014 still\n// leaves room to hover a node and read its tooltip.\nconst MIN_CANVAS_HEIGHT = 160\nconst VARIANT_MAP_HEIGHT = 340\n\nconst SEGMENTS_SUFFIX = '.segs.bed.gz'\n\n// The rGFA index prefix an adapter config names, from either spelling the\n// config schema accepts: the `uri` shorthand or an explicit segments location.\nfunction bubblePrefix(adapterConfig: Record<string, unknown>) {\n  if (typeof adapterConfig.uri === 'string') {\n    return adapterConfig.uri\n  }\n  const segments = adapterConfig.segmentsLocation as\n    { uri?: string } | undefined\n  const uri = segments?.uri\n  return typeof uri === 'string' && uri.endsWith(SEGMENTS_SUFFIX)\n    ? uri.slice(0, -SEGMENTS_SUFFIX.length)\n    : undefined\n}\n// Gap between the drawing and the edge of the pane, on all four sides.\nconst FIT_PADDING = 40\nconst HOVER_BRIGHTEN = 1.4\nconst SELECT_BRIGHTEN = 1.6\nconst VIEWPORT_DEBOUNCE_MS = 150\nconst VIEWPORT_PANES_BUILT = 1\n\n// MobX tracks every observable read while a computed or autorun runs, so\n// passing values here registers them as dependencies without otherwise using\n// them.\nfunction dependOn(..._values: unknown[]) {}\n\n// Hard size cap for the single-mode graph view. Past it the view declines with a\n// \"zoom in\" message rather than switching to a degraded rendering mode \u2014 one mode\n// only, since the large-region case is a linear synteny view, not a graph.\n// (The `adr-027` citation this used to carry was stale: that number was reused\n// for wheel-input semantics after the large-mode ADR was removed in 9d8102f0b5.)\n//\n// This bounds the *fetch*, and it is the only cap that can be applied before one\n// happens. It is a poor proxy for cost, because cost tracks node count, so the\n// number is chosen against the density of the graphs it can actually guard: a\n// region is fetched through `getSubgraph`, and the rGFA cut is what this number\n// was chosen against (the GBZ cut is base-level and has its own `nodeLimit`,\n// which trips long before 5 Mb). Both measured rGFAs are sparse, and at 5 Mb\n// both land at or under the ~2k nodes that redraw in under 10 ms (see agent-docs/GRAPH_SCALE_AND_LOD.md):\n//\n//   HPRC MC GRCh38   ~7,000 bp/segment   whole 4.9 Mb MHC   1,173 nodes\n//   ecoli minigraph   3,078 bp/segment   whole 4.6 Mb genome 2,415 nodes\n//\n// Fetch cost does not scale with the window either: against the hosted HPRC\n// index a 4.9 Mb links query and a 100 kb one both cost ~1.3 s, being dominated\n// by HTTP setup. FMMM is the slowest consumer at this size and stays tolerable,\n// ~0.1-3 s for ~1k nodes depending on layout quality (bandage-layout-js), and it\n// runs off the main thread.\n//\n// A dense graph is what this cannot protect against, because bp per node varies\n// by orders of magnitude between graph types \u2014 a base-level pggb graph runs ~17\n// bp/node, where 5 Mb would be hundreds of thousands. Such a graph has no region\n// query to reach this check with today, and the node budget below is the cap that\n// catches it if one ever does.\nexport const MAX_GRAPH_REGION_BP = 5_000_000\n\n// The cap in a message, in the unit that reads: `5 Mb`, not `5000 kb`.\nexport function formatSpanBp(bp: number) {\n  return bp >= 1_000_000\n    ? `${+(bp / 1_000_000).toFixed(1)} Mb`\n    : `${Math.round(bp / 1000)} kb`\n}\n\n// What the view will actually draw, checked once the graph is parsed and so\n// applying to a whole-file import as much as to a subgraph fetch. Measured on\n// bubble-chain graphs: ~1-2k nodes redraws in under 10 ms, 10k takes ~43 ms of\n// geometry and ~125k canvas draw calls per frame (single-digit fps while\n// panning), and 100k needs 632 ms and 75 MB of vertex buffers. So this is set\n// where the tab stops being usable rather than where it stops being smooth, and\n// it is a view prop rather than a constant so a session can raise it \u2014 the same\n// escape hatch strangepg gives with `-T N`.\nexport const DEFAULT_MAX_GRAPH_NODES = 20_000\n\n// The floor exists to keep a scale positive and finite, not to express a useful\n// zoom level, so it has to clear the smallest scale a real layout asks for. In\n// the reference-anchored layouts world units are bp: fitting a chromosome-scale\n// rGFA (250 Mbp) into ~720 px needs ~3e-6, and the old 0.001 floor clamped that\n// to 7x too wide \u2014 zoomToFit could not fit a whole-file import at all.\nconst MIN_ZOOM = 1e-6\nconst MAX_ZOOM = 100\n\nfunction clampZoom(zoom: number) {\n  return Math.max(MIN_ZOOM, Math.min(MAX_ZOOM, zoom))\n}\n\n// The zoom as a pair of axis scales. One expression, read by all three getters\n// below: they sit in one `.views()` block and so cannot reach each other through\n// `self`, which had each of them restating the `pixelRows ? 1 : scale` rule that\n// AxisScale exists to keep in one place.\nfunction axisScaleOf(scale: number, pixelRows: boolean): AxisScale {\n  // pixelRows rides along rather than being derived downstream: the deletion\n  // bow is capped in a row layout and not in the isotropic one, and `scaleY !==\n  // scaleX` coincides at one zoom level. See AxisScale.\n  return { scaleX: scale, scaleY: pixelRows ? 1 : scale, pixelRows }\n}\n\ntype ViewportOwner = 'fit' | 'user' | 'host'\n\ninterface Bounds {\n  minX: number\n  minY: number\n  maxX: number\n  maxY: number\n}\n\n// What the pane shows, in layout units.\nfunction viewportOf(model: {\n  translateX: number\n  translateY: number\n  width: number\n  scaleX: number\n  scaleY: number\n  canvasHeight: number\n}): Bounds {\n  return {\n    minX: -model.translateX / model.scaleX,\n    minY: -model.translateY / model.scaleY,\n    maxX: (model.width - model.translateX) / model.scaleX,\n    maxY: (model.canvasHeight - model.translateY) / model.scaleY,\n  }\n}\n\n// The window a geometry build covers: the pane plus a whole pane on every\n// side, so a pan has that far to go before the drawing runs out and a rebuild\n// is due. Drawing three panes' worth is cheap now that a redraw is a few\n// batched strokes; what it buys is that an ordinary pan never blanks its\n// margins for the debounce and never rebuilds at all.\nfunction padded(v: Bounds, panes: number): Bounds {\n  const w = (v.maxX - v.minX) * panes\n  const h = (v.maxY - v.minY) * panes\n  return {\n    minX: v.minX - w,\n    minY: v.minY - h,\n    maxX: v.maxX + w,\n    maxY: v.maxY + h,\n  }\n}\n\n// Centre the leftover, but only when there IS leftover. A row layout fits on x\n// alone, so its drawing is routinely taller than the pane \u2014 that is the case\n// rowSpacing.ts means by \"reached by panning\" \u2014 and centring an overflow splits\n// the loss across both ends: at 41 rows the top row landed 100 px above the\n// pane. The top row is the reference backbone, i.e. the axis the whole layout\n// exists to put under the linear view, so it is the one row that must not be\n// the first thing to go. Pinned at the padding it opens where a fitting drawing\n// opens, and the rows past the ceiling are below, which is the direction a\n// reader already scrolls a track in.\nfunction fittedTranslateY(\n  bounds: { minY: number; h: number },\n  usableHeight: number,\n  yScale: number,\n) {\n  const leftoverY = usableHeight - bounds.h * yScale\n  return FIT_PADDING - bounds.minY * yScale + Math.max(0, leftoverY) / 2\n}\n\nfunction contains(outer: Bounds, inner: Bounds) {\n  return (\n    inner.minX >= outer.minX &&\n    inner.maxX <= outer.maxX &&\n    inner.minY >= outer.minY &&\n    inner.maxY <= outer.maxY\n  )\n}\n\n// Force layouts already computed for a graph, keyed by the view props the\n// engine reads. Every layout mode is local and costs a millisecond except this\n// one, which is seconds: measured on the committed engine, a 1,201-node bubble\n// chain is 0.6 s proportional, 4.3 s at 'Wide bubbles' and 3.4 s at the highest\n// quality.\n//\n// Worth keeping because a session revisits the same layout. The two drawings\n// answer different questions and the README's own figure is one subgraph in\n// both, so Anchored <-> Force is a round trip a reader makes repeatedly \u2014 and\n// every control in the settings dialog calls `recomputeLayout` on change\n// whether or not the current mode reads what it changed, which made picking a\n// reference path in force mode a multi-second re-run of an identical layout.\n// Both are hits.\n//\n// Entries are the live position objects rather than copies, which a node drag\n// mutates in place (see moveNode), so a layout comes back arranged the way it\n// was left rather than snapping back.\n//\n// Weak on the graph so nothing has to invalidate it: a graph is rebuilt by\n// every load and dropped by `clearGraph`, and its layouts go with it.\nconst forceLayouts = new WeakMap<Graph, Map<string, LayoutResult>>()\n\n// Enough to hold the settings a comparison moves between; past that the oldest\n// goes, since a big graph's positions are megabytes.\nconst FORCE_LAYOUT_CACHE_SIZE = 4\n\nfunction forceLayoutsOf(graph: Graph) {\n  let cache = forceLayouts.get(graph)\n  if (!cache) {\n    cache = new Map()\n    forceLayouts.set(graph, cache)\n  }\n  return cache\n}\n\n// Re-anchoring builds a new Graph, and the force layout of it is the same\n// drawing: `anchorFromPaths` rewrites each node's `stable` and `samples` and\n// touches neither the ids, the lengths, the depths nor the edges, which are all\n// the engine reads. So the layouts follow the graph they were computed for\n// rather than being thrown away with it.\nfunction inheritForceLayouts(from: Graph, to: Graph) {\n  const cache = forceLayouts.get(from)\n  if (cache && from !== to) {\n    forceLayouts.set(to, cache)\n  }\n}\n\nfunction remember(\n  cache: Map<string, LayoutResult>,\n  key: string,\n  result: LayoutResult,\n) {\n  if (cache.size >= FORCE_LAYOUT_CACHE_SIZE) {\n    cache.delete(cache.keys().next().value!)\n  }\n  cache.set(key, result)\n}\n\nexport default function stateModelFactory() {\n  return types\n    .compose(\n      'GraphGenomeView',\n      BaseViewModel,\n      RenderLifecycleMixin(),\n      types.model({\n        type: types.literal('GraphGenomeView'),\n        // FMMM's iteration budget, 0-4, the same scale Bandage's own settings\n        // dialog exposes: 3+1 iterations at 0, 15+10 at 1, 30+20 at 2, 60+40 at\n        // 3, 120+60 at 4 (BandageNG layout/graphlayoutworker.cpp).\n        //\n        // 2 because that is what the engine we vendor ships as its default\n        // (`graphLayoutQuality = IntSetting(2, 0, 4)`, program/settings.cpp).\n        // This was 1 for no recorded reason, i.e. one step BELOW upstream, and a\n        // first sight of any graph is the default: review kept asking whether\n        // the drawing could be iterated more (\"are you sure you can't iterate it\n        // more times for better layout?\") of figures that were simply on a lower\n        // setting than the tool they come from. Cost at the sizes this view\n        // draws is milliseconds, and the header states the layout time so the\n        // difference is visible rather than asserted.\n        layoutQuality: types.optional(types.number, 2),\n        linearLayout: types.optional(types.boolean, false),\n        // Which drawing to use; the modes and their fallbacks are described in\n        // LAYOUT_MODES. Default 'force' is the Bandage FMMM drawing, i.e. what\n        // someone who has seen a pangenome graph before expects to see.\n        //\n        // The default used to be 'auto', the reference-anchored layout, on the\n        // argument that lining the graph's x axis up with a linear view above it\n        // is what this view can do and Bandage cannot. Docs review disagreed\n        // twice, on figure after figure \u2014 \"the linear backbone is just\n        // confusing\", \"default to showing the bandage graphs over linear\n        // backbone in almost all cases\" \u2014 and the reason is that the anchored\n        // drawing looks like a track rather than a graph: a bubble collapses onto\n        // the reference axis, so the alternative alleles read as short bars\n        // hanging under a line rather than as two routes through the same locus.\n        // The anchored modes stay one dropdown click away, and are what the\n        // hover-sync and one-row-per-strain figures select deliberately.\n        layoutMode: types.optional(\n          types.enumeration(LAYOUT_MODE_VALUES),\n          'force',\n        ),\n        // 'auto' rather than a colour, resolved by `effectiveColorScheme`. See\n        // COLOR_SCHEMES for why the default is not 'uniform' any more. A session\n        // that names a scheme keeps it \u2014 this only decides what an unstated one\n        // opens as.\n        colorScheme: types.optional(\n          types.enumeration(COLOR_SCHEME_VALUES),\n          'auto',\n        ),\n        // How far the force layout opens a bubble, which on a variation graph is\n        // the difference between a legible drawing and a rope. See\n        // BUBBLE_SPREADS; no effect on the reference-anchored layouts, which\n        // place a node from its coordinates rather than from a force sim.\n        bubbleSpread: types.optional(\n          types.enumeration(BUBBLE_SPREAD_VALUES),\n          'auto',\n        ),\n        // Node thickness by depth, Bandage's own device; see NODE_WIDTHS.\n        nodeWidth: types.optional(\n          types.enumeration(NODE_WIDTH_VALUES),\n          'depth',\n        ),\n        // Whether the node layouts draw each bubble as a halo along its nodes\n        // with a label that opens it. The variant map draws glyphs instead.\n        showBubbles: types.optional(types.boolean, true),\n        showDeletionEdges: types.optional(types.boolean, false),\n        // The session's genes drawn onto the backbone: exons along the nodes\n        // that carry them, names pinned at their midpoints. See genes/.\n        showGenes: types.optional(types.boolean, true),\n        // Which track the genes come from; empty picks the assembly's\n        // annotation track (pickGeneTrack).\n        geneTrackId: types.optional(types.string, ''),\n        // Which track the walk rows read tandem repeat arrays from; empty\n        // picks a track whose name says repeats (pickRepeatTrack).\n        repeatTrackId: types.optional(types.string, ''),\n        // The array the walk rows measure between and tile by, as\n        // RepeatArray.key; empty measures the whole window untiled.\n        repeatKey: types.optional(types.string, ''),\n        // Samples whose walks the walk rows show, by the name before the\n        // haplotype number; undefined shows every walk the cut holds.\n        walkRowSamples: types.maybe(types.frozen<string[]>()),\n        // One walk, by its path name, lifted out of the drawing: its nodes and\n        // links keep their ink and the rest fades. Empty lifts none.\n        highlightedPath: types.optional(types.string, ''),\n        // Which of a general GFA's paths the anchored layouts put on x. A path\n        // GFA's names are arbitrary and none of them is marked as the\n        // reference, so this is a choice; empty means \"infer\", which is the\n        // assembly a subgraph was cut against, and the first path in the file\n        // for a whole-file import. No effect on an rGFA, whose segments carry\n        // their own coordinates. See pathAnchoring.ts.\n        referencePath: types.optional(types.string, ''),\n        // Whether the toolbar spells out `fetch 12371ms \u00B7 layout 4ms \u00B7 geom 9ms`.\n        // Off by default because it was in the toolbar of every published graph\n        // figure, where a machine's fetch time is noise a reader has to skip\n        // past. The numbers themselves are always on the element as `data-*`\n        // attributes, which is what browser tests assert against, so hiding the\n        // text costs no coverage.\n        showPerf: types.optional(types.boolean, false),\n        contigThickness: types.optional(types.number, 6),\n        connectorThickness: types.optional(types.number, 2),\n        darkMode: types.optional(types.boolean, false),\n        scale: types.optional(types.number, 1),\n        translateX: types.optional(types.number, 0),\n        translateY: types.optional(types.number, 0),\n        drawPaths: types.optional(types.boolean, false),\n        // Ceiling on the drawing pane, in css px, for a session or a figure that\n        // wants a shorter one than the drawing asks for. Unset means the built-in\n        // MAX_CANVAS_HEIGHT, which is what every existing session gets.\n        //\n        // Why this is a knob rather than a smaller default: the pane is as tall\n        // as the drawing's own aspect ratio (see canvasHeight), which is right \u2014\n        // a graph that is twice as tall as it is wide should not be squeezed\n        // into a strip. But one very long node in a cut of short ones makes that\n        // aspect ratio all arc: the HPRC CHM13 figure draws a 142 kb allele\n        // among sub-kb backbone segments, pins the 600 px ceiling and spends\n        // most of it on the loop, with the chain squashed along the bottom edge.\n        // Lowering the ceiling there scales the whole drawing down, which is\n        // exactly the trade that figure wants and the wrong default for a graph\n        // whose height is carrying information.\n        paneHeight: types.maybe(types.number),\n        // Raise to draw a bigger graph than the default budget allows; see\n        // DEFAULT_MAX_GRAPH_NODES for what the numbers cost.\n        maxGraphNodes: types.optional(types.number, DEFAULT_MAX_GRAPH_NODES),\n        // The bp ceiling on a cut, which is a PROXY for node count and only a\n        // good one at fine granularity: on a base-level index 5 Mb is already\n        // thousands of segments, so refusing by span is refusing by cost. A\n        // level-of-detail tier breaks the proxy \u2014 a whole 249 Mb human\n        // chromosome is 474 nodes off the hosted HPRC tier \u2014 so a session that\n        // knows which granularity it is pointed at can raise this. The real\n        // backstop stays `maxGraphNodes`, which counts what actually came back.\n        //\n        // The launch MENUS keep the constant deliberately (launchSubgraphView):\n        // a user rubber-banding 249 Mb over a fine index should still be told\n        // no, because nothing there has said the track is coarse.\n        maxRegionBp: types.optional(types.number, MAX_GRAPH_REGION_BP),\n        loadedTrackId: types.optional(types.string, ''),\n        loadedRegion: types.maybe(\n          types.frozen<{\n            refName: string\n            assemblyName: string\n            start: number\n            end: number\n          }>(),\n        ),\n        // The haplotypes the cut is for, lane assembly names or PanSN\n        // prefixes, beside the region so a re-cut asks for the same set;\n        // undefined is every haplotype. Only the GBZ cut reads it.\n        subgraphHaplotypes: types.maybe(types.frozen<string[]>()),\n        // How far the cut follows links past the segments the region's own\n        // links name, defaulting to one hop because at 0 the drawing is wrong\n        // rather than merely sparse. A detour that leaves the backbone before\n        // the window and rejoins after it has its interior indexed only under\n        // its own stable sequence, which no query on the reference reaches, so an\n        // arm that bypasses 21 kb of reference arrives as a 43 bp fragment: the\n        // one bubble draws as two unrelated small insertions, and nothing on\n        // screen says they are the same event. One hop closes those, and that is\n        // the whole of what a reader means by seeing the local graph.\n        //\n        // The cost is queries rather than nodes, and a hop only follows alleles\n        // (offReference in RgfaTabixAdapter, which is gfabase's stop-at-cutpoints\n        // rule read off the rank tag), so it is bounded by the off-reference\n        // segments the cut already reached and it does not walk the backbone out\n        // of the window. Measured: the E. coli paa locus goes 14 segments at 0 to\n        // 17 at 1 and stays at 17 at 2, so the cut closes and stays closed.\n        // HPRC's amylase window goes 63 to 78 to 92, because there the alleles\n        // have alleles; wall-clock is flat across all three, the remote index\n        // dominating. 0 stays available for a graph where even that is too much.\n        //\n        // Still not a graph-aware cut: a complete one needs the bubble\n        // decomposition (`gfatools view -R`, whose bubble rows state their own\n        // member segments) rather than a frontier, which is the follow-up noted\n        // in the adapter.\n        subgraphContext: types.optional(types.number, 1),\n        // Whole-GFA source loaded on attach \u2014 lets a GraphGenomeView be\n        // instantiated declaratively from a session/config snapshot.\n        gfaLocation: types.maybe(types.frozen<FileLocation>()),\n        // The reference span the reference-position ramp runs over. A graph cut\n        // from a track already states one as `loadedRegion`; a file-loaded graph\n        // has no region at all, and this is how its snapshot can still put a\n        // linear track beside it on the same ramp \u2014 both painted from one pair\n        // of numbers rather than from the file's own measured extent.\n        colorDomain: types.maybe(\n          types.frozen<{ start: number; end: number }>(),\n        ),\n        // The linear view this graph was launched from, so a hovered node can\n        // draw its reference span there and vice versa. Written by the launch\n        // menu; see hoverSync/.\n        connectedViewId: types.maybe(types.string),\n        // Whether the cut came from the source track's `coarse` pair\n        // (RgfaTabixAdapter), so a restored session re-makes the cut it saved.\n        // No bp cap applies to that pair; maxGraphNodes counts what came back.\n        coarseCut: types.optional(types.boolean, false),\n      }),\n    )\n    .volatile(() => ({\n      graph: undefined as Graph | undefined,\n      layoutResult: undefined as LayoutResult | undefined,\n      // The bubble index rows over the cut window, when the source track has\n      // one beside its segments. Undefined for a graph with no index, which the\n      // variant map draws from `derivedBubbles` instead.\n      indexBubbles: undefined as MinigraphBubble[] | undefined,\n      // the genes over the cut window, read once per cut from the gene track\n      geneFeatures: undefined as GeneModel[] | undefined,\n      // the tandem repeat arrays over the cut window, from the repeat track\n      repeatArrays: undefined as RepeatArray[] | undefined,\n      // The graphs the open bubble was popped out of, outermost first, each\n      // with what closing back to it restores without a refetch. A stack so a\n      // popped superbubble can be mapped and popped again.\n      popStack: [] as {\n        graph: Graph\n        layoutMode: LayoutModeValue\n        label: string\n        indexBubbles: MinigraphBubble[] | undefined\n      }[],\n\n      // eslint-disable-next-line @typescript-eslint/no-unnecessary-type-assertion\n      error: undefined as unknown,\n      isLoading: false,\n      loadCanceled: false,\n      statusMessage: '',\n      hoveredNode: null as string | null,\n      hoveredEdge: null as number | null,\n      selectedNode: null as string | null,\n      viewportDirty: 0,\n      // Bumped when the layout's positions are mutated IN PLACE, which only a\n      // node drag does. Separate from `viewportDirty` because that one also\n      // fires on pan and zoom, and the things keyed off this \u2014 the two hit\n      // indexes and the label placement's per-layout caches \u2014 do not depend on\n      // the transform at all. Rebuilding a 12k-edge hit index because the user\n      // panned cost ~14 ms of the first mousemove after every gesture.\n      positionsVersion: 0,\n      // Bumped per upload, so the hover autorun re-states its highlights\n      // against the batch the renderer now holds.\n      geometryVersion: 0,\n      // The zoom and the window the current batch was built for; a pan that\n      // stays inside it needs no rebuild.\n      builtViewport: undefined as { scale: number; bounds: Bounds } | undefined,\n      draggingNode: null as string | null,\n      // Dragging the background rather than a node. Lives here beside\n      // draggingNode instead of in a component ref+state pair, so the two\n      // mutually exclusive drag modes are one piece of state read from one place.\n      isPanning: false,\n      // Who places the view. 'fit' refits it to every new layout, 'user' leaves\n      // it where a gesture or a restored session put it, and 'host' takes x\n      // from the linear view the pane sits in. Not derived from\n      // `isDefaultViewport`, which zoomToFit itself invalidates on its first\n      // run \u2014 that made the fit fire once against not-yet-measured dimensions\n      // and then never re-fit.\n      // eslint-disable-next-line @typescript-eslint/no-unnecessary-type-assertion\n      viewportOwner: 'fit' as ViewportOwner,\n      // the pane height a host holds, so a re-cut with more rows does not\n      // move the pane while the linear view above it is being dragged\n      hostPaneHeight: undefined as number | undefined,\n      cutNote: undefined as string | undefined,\n      recuts: 0,\n      viewportDirtyTimer: undefined as\n        ReturnType<typeof setTimeout> | undefined,\n      // 0 is never a live rAF handle, so it doubles as \"nothing pending\"\n      positionsDirtyFrame: 0,\n      // Performance instrumentation, surfaced in GraphStats for browser tests\n      // to assert against budgets. `fetchMs` is the GetSubgraph RPC round-trip,\n      // `layoutMs` is the Bandage FMMM compute time reported by the\n      // GraphComputeLayout RPC, `geometryMs` is the main-thread buildGeometry\n      // pass and `geometryStrokeCount` the node strokes it produced.\n      lastFetchMs: undefined as number | undefined,\n      lastLayoutMs: undefined as number | undefined,\n      lastGeometryMs: undefined as number | undefined,\n      lastGeometryStrokeCount: undefined as number | undefined,\n    }))\n    .views(self => ({\n      get nodeById() {\n        if (self.graph) {\n          const m = new Map<string, GraphNode>()\n          for (const n of self.graph.nodes) {\n            m.set(n.id, n)\n          }\n          return m\n        }\n        return undefined\n      },\n      // bp per node id, which is all the label overlay needs of a GraphNode.\n      // Held here rather than rebuilt in the component: that render runs on\n      // every pan, and the map is a fact about the graph (measured 6.9 ms an\n      // allocation on a 30k-node cut).\n      get nodeLengths() {\n        const m = new Map<string, number>()\n        for (const n of self.graph?.nodes ?? []) {\n          m.set(n.id, n.length)\n        }\n        return m\n      },\n      get nodeCount() {\n        return self.graph?.nodes.length ?? 0\n      },\n      get edgeCount() {\n        return self.graph?.edges.length ?? 0\n      },\n      get pathCount() {\n        return self.graph?.paths?.length ?? 0\n      },\n      get hasGraph() {\n        return self.graph !== undefined\n      },\n      // The app-wide readiness contract (AppReadyMarker, @jbrowse/capture)\n      // reads this: a declared source still fetching, or a graph whose\n      // geometry has not been built yet.\n      get showLoading() {\n        return (\n          self.error === undefined &&\n          (self.isLoading ||\n            ((self.graph !== undefined ||\n              !!(self.loadedTrackId && self.loadedRegion) ||\n              !!self.gfaLocation) &&\n              self.lastGeometryStrokeCount === undefined))\n        )\n      },\n      get canRetryLoad() {\n        return !!(self.loadedTrackId && self.loadedRegion) || !!self.gfaLocation\n      },\n      // Only before anything is drawn: past that point a reload is superseded\n      // by the next setting change, and stopping one midway would leave a new\n      // graph under the previous graph's layout.\n      get canCancelLoad() {\n        return self.isLoading && !self.layoutResult\n      },\n      // Whether the drawing on screen is the FMMM engine's. False before there\n      // is a graph, since nothing is drawn by anything yet.\n      //\n      // Read by the settings that only the engine looks at: the layout quality\n      // and the bubble spread do nothing at all to an anchored drawing, which\n      // places a node from its coordinates, and the guide says so in prose\n      // precisely because the dialog did not. A control that silently does\n      // nothing is worse than one that says it cannot \u2014 the same rule the\n      // `drawPaths` switch already follows.\n      get usesLayoutEngine() {\n        return self.graph\n          ? modeUsesLayoutEngine(self.layoutMode, self.graph)\n          : false\n      },\n      // A rank-0 backbone to draw x against, whether the segments declared it\n      // (rGFA) or a path walk derived it. Only a GFA with neither tags nor\n      // paths has no backbone at all, and there force is the one honest layout.\n      get canAnchorLayout() {\n        return self.graph?.nodes.some(n => n.stable?.rank === 0) ?? false\n      },\n      // The paths this graph could be anchored on, for the picker. Empty for an\n      // rGFA, which has no P/W records and needs none.\n      get anchorPaths() {\n        return self.graph?.anchorPaths ?? []\n      },\n      // Which haplotype each ribbon colour belongs to, in the order the file\n      // states the paths \u2014 the same list and the same order the geometry keys\n      // its colours off, so the key cannot name a colour that is not drawn.\n      // Empty unless the ribbons are actually on: a colour key beside a drawing\n      // with no colours in it is a legend for nothing.\n      get pathLegend() {\n        const paths = self.graph?.paths\n        return self.drawPaths && paths && pathColorsLegible(paths.length)\n          ? pathLegend(paths)\n          : []\n      },\n      // Every walk the graph carries, named for a picker, whatever the count.\n      get walkChoices() {\n        const paths = self.graph?.paths\n        return paths?.length ? pathLegend(paths) : []\n      },\n      // The lifted walk, or undefined when none is named or the graph on\n      // screen does not carry the one that was.\n      get walkHighlight() {\n        return self.graph && self.highlightedPath\n          ? walkHighlight(self.graph, self.highlightedPath)\n          : undefined\n      },\n      // Whether the drawing is actually painted per path, which is not the same\n      // question as whether the user asked for it: past MAX_PATH_COLORS the\n      // colours say nothing and cost a stroke per path per edge. A bare getter\n      // returning a resolved value, the same shape and for the same reason as\n      // `effectiveColorScheme` \u2014 every consumer of a path colour reads this\n      // one, so the geometry, the hit index and the key cannot disagree about\n      // whether there are any. The switch in the settings dialog reads the raw\n      // `drawPaths`, so the user's choice stays visible as the choice it is.\n      get effectiveDrawPaths() {\n        return (\n          self.drawPaths && pathColorsLegible(self.graph?.paths?.length ?? 0)\n        )\n      },\n      // The path x is currently drawn on, which is not necessarily the one\n      // `referencePath` asked for: an unmatched name falls back rather than\n      // leaving the graph unanchored, and the picker has to show what happened.\n      get activeReferencePath() {\n        return self.graph?.referencePath\n      },\n      // What to anchor on. An explicit choice wins; otherwise a graph cut from\n      // a track is anchored on the assembly it was cut against, which is the\n      // one the linear view beside it is showing.\n      get preferredReferencePath() {\n        return self.referencePath === ''\n          ? self.loadedRegion?.assemblyName\n          : self.referencePath\n      },\n      // The span the reference-position ramp runs over: what the snapshot\n      // stated, else the region the graph was cut from. Undefined only for a\n      // file-loaded graph that states neither, where the ramp falls back to the\n      // drawn extent (computeReferenceRamp). A follow's re-cut moves\n      // loadedRegion, so the ramp re-spans every new cut, and the lane above\n      // with it.\n      get rampDomain() {\n        return self.colorDomain ?? self.loadedRegion\n      },\n      // The scheme the renderer actually paints with, which is the raw prop\n      // unless it is 'auto'. A bare getter returns a resolved value (root\n      // CLAUDE.md): every consumer of a colour reads this one, and the two\n      // dropdowns read `colorScheme` so \"Auto\" stays visible as the choice it\n      // is.\n      //\n      // 'auto' asks the GRAPH, not the layout. A hue along the reference is\n      // meaningful whenever the segments have reference coordinates \u2014\n      // `anchoredBy` is exactly that question \u2014 and a force-directed drawing of\n      // an rGFA is the case that proves it: the layout has no reference axis and\n      // the ramp still says where on the reference each node came from, which is\n      // the only quantity a linear track beside it can be painted with too.\n      get effectiveColorScheme(): ResolvedColorScheme {\n        return self.colorScheme !== 'auto'\n          ? self.colorScheme\n          : self.graph?.anchoredBy\n            ? 'reference-position'\n            : 'uniform'\n      },\n      get nodePositions() {\n        return self.layoutResult?.nodePositions\n      },\n      // Empty rather than undefined: every consumer maps over it, and a layout\n      // with no row structure (FMMM) is a normal state, not a missing one.\n      get rowLabels() {\n        return self.layoutResult?.rowLabels ?? []\n      },\n      // Deletions the layout found inside an allele, empty for the same reason\n      // rowLabels is: a layout drawn at sequence scale states none, because\n      // there a node's drawn extent already IS its length. `deletions` beside\n      // this one is the bare-edge kind, which every layout has.\n      get alleleDeletions() {\n        return self.layoutResult?.alleleDeletions ?? []\n      },\n      // Whether the current layout states y in screen px rather than in the same\n      // units as x (LayoutResult.pixelRows). Everything that has to put the two\n      // axes in one expression reads this through scaleX/scaleY.\n      get pixelRows() {\n        return self.layoutResult?.pixelRows ?? false\n      },\n      get zoomPercent() {\n        return `${(self.scale * 100).toFixed(1)}%`\n      },\n      // True while the persisted transform is still the schema default, i.e.\n      // neither a restored session nor the user has positioned this view yet,\n      // so an incoming layout is free to zoom-to-fit.\n      get isDefaultViewport() {\n        return (\n          self.scale === 1 && self.translateX === 0 && self.translateY === 0\n        )\n      },\n    }))\n    .views(self => ({\n      get poppedFrom() {\n        return self.popStack.at(-1)\n      },\n      // The bubbles the graph itself states, for a graph with no index: a GBZ\n      // cut, a pggb file, the inside of a popped bubble.\n      get derivedBubbles() {\n        return self.graph ? bubblesFromGraph(self.graph) : []\n      },\n    }))\n    .views(self => ({\n      // What the variant map draws. Index rows win where both exist: gfatools\n      // measured every allele, the layered order only bounds them.\n      get bubbles() {\n        return self.indexBubbles?.length\n          ? self.indexBubbles\n          : self.derivedBubbles\n      },\n    }))\n    .views(self => ({\n      // As written: a session track is a plain object until something\n      // hydrates it, so a slot left at its default reads undefined here.\n      get sourceAdapter() {\n        const track = getSession(self).tracks.find(\n          t => t.trackId === self.loadedTrackId,\n        )\n        return track\n          ? (readConfObject(track, 'adapter') as Record<string, unknown>)\n          : undefined\n      },\n      get assemblyTrackChoices() {\n        const region = self.loadedRegion\n        if (!region) {\n          return []\n        }\n        return getSession(self)\n          .tracks.filter(t =>\n            (readConfObject(t, 'assemblyNames') as string[]).includes(\n              region.assemblyName,\n            ),\n          )\n          .map(t => ({\n            trackId: t.trackId as string,\n            name: readConfObject(t, 'name') as string,\n            adapterType: (readConfObject(t, 'adapter') as { type: string })\n              .type,\n          }))\n      },\n    }))\n    .views(self => ({\n      get geneTrackChoices() {\n        return self.assemblyTrackChoices.filter(t =>\n          GENE_ADAPTER_TYPES.has(t.adapterType),\n        )\n      },\n      // The session's feature tracks a repeat annotation could be, for the\n      // picker; which one is read is pickRepeatTrack's choice.\n      get repeatTrackChoices() {\n        return self.assemblyTrackChoices.filter(t =>\n          REPEAT_ADAPTER_TYPES.has(t.adapterType),\n        )\n      },\n      // The arrays over the window that state a unit, for the Repeat picker.\n      get repeatChoices() {\n        return self.repeatArrays ?? []\n      },\n    }))\n    .views(self => ({\n      get repeatTrack() {\n        return pickRepeatTrack(self.repeatTrackChoices, self.repeatTrackId)\n      },\n      get selectedRepeat() {\n        return self.repeatChoices.find(r => r.key === self.repeatKey)\n      },\n    }))\n    .views(self => ({\n      get nodeNeighbors() {\n        return self.graph ? buildNeighbors(self.graph) : undefined\n      },\n      // How far each node's ink reaches from its centreline, for the hit test:\n      // the widths the geometry draws with, from the same function.\n      get nodeInk(): NodeInk {\n        const { contigThickness, nodeWidth, nodeById } = self\n        const mean = self.graph ? meanDepth(self.graph) : 0\n        return {\n          maxHalfWidthPx: maxNodeWidthPx(contigThickness, nodeWidth) / 2,\n          halfWidthPx: id => {\n            const node = nodeById?.get(id)\n            return node\n              ? nodeWidthPx(node, contigThickness, nodeWidth, mean) / 2\n              : contigThickness / 2\n          },\n        }\n      },\n      // Links that skip reference sequence, i.e. the deletions this graph\n      // holds. Computed once per graph rather than per geometry rebuild: it is\n      // a pass over the edges and the drawing rebuilds on every pan.\n      // Walk rows state what each walk skips as its own bar length, so the arcs\n      // over the backbone would only say it again, across the bars.\n      get deletions() {\n        return self.graph && self.layoutMode !== 'walkrows'\n          ? deletionEdges(self.graph)\n          : []\n      },\n      // One bar per haplotype walk on its own bp axis, for the walk-rows\n      // overlay. Empty under every other layout.\n      get walkRowBars() {\n        if (self.layoutMode !== 'walkrows' || !self.graph) {\n          return undefined\n        }\n        const repeat = self.selectedRepeat\n        const bars = repeat\n          ? walkRows(self.graph, repeat, repeat.unit)\n          : walkRows(self.graph, self.loadedRegion)\n        if (!bars) {\n          return undefined\n        }\n        const samples = self.walkRowSamples\n        const rows = samples\n          ? bars.rows\n              .filter(r => samples.includes(r.sample))\n              .sort(\n                (a, b) =>\n                  samples.indexOf(a.sample) - samples.indexOf(b.sample) ||\n                  a.label.localeCompare(b.label),\n              )\n          : bars.rows\n        return { ...bars, rows: withCalls(rows, repeat?.calls) }\n      },\n      // The labels drawn beside the rows. Walk rows label from the bars\n      // themselves, which follow the selected repeat and sample filter that\n      // the layout, run once per cut, cannot.\n      get drawnRowLabels() {\n        const bars = this.walkRowBars\n        return bars\n          ? [bars.reference, ...bars.rows].map((row, i) => ({\n              label: row.label,\n              y: i * ROW_HEIGHT_PX,\n            }))\n          : self.rowLabels\n      },\n      // Each bubble in the window with what it is, for the variant map's\n      // glyphs on the reference line.\n      get bubbleGlyphs() {\n        const bubbles = self.layoutMode === 'variants' ? self.bubbles : []\n        return bubbles.map(bubble => ({\n          bubble,\n          ...classifyBubble(bubble),\n        }))\n      },\n      // Exons and names on the backbone, in layout units. Reads\n      // positionsVersion so a dragged node takes its exons with it.\n      get genePins() {\n        dependOn(self.positionsVersion)\n        const positions = self.layoutResult?.nodePositions\n        return self.showGenes &&\n          self.layoutMode !== 'variants' &&\n          self.layoutMode !== 'walkrows' &&\n          self.graph &&\n          self.geneFeatures &&\n          positions\n          ? genePins(self.graph, self.geneFeatures, positions)\n          : []\n      },\n      // The same bubbles over every other layout, as halos along their nodes.\n      // Reads positionsVersion so a dragged node takes its halo with it.\n      get bubbleHalos() {\n        dependOn(self.positionsVersion)\n        const positions = self.layoutResult?.nodePositions\n        if (\n          !self.showBubbles ||\n          self.layoutMode === 'variants' ||\n          self.layoutMode === 'walkrows' ||\n          !self.graph ||\n          !positions\n        ) {\n          return []\n        }\n        const labels = new Map(self.walkChoices.map(c => [c.name, c.label]))\n        return bubbleHalos(\n          self.graph,\n          self.bubbles,\n          positions,\n          name => labels.get(name) ?? name,\n        )\n      },\n      // Every node's midpoint on the reference plus the interval the hue ramps\n      // over \u2014 what `reference-position` paints from, and undefined under every\n      // other scheme so the walk is never run for a colouring that ignores it.\n      //\n      // Here for the same reason `deletions` is, only more so: deriving it is a\n      // bounded neighbour walk PER NODE (referenceMidpoints), it depends on\n      // nothing the transform touches, and it was being redone inside every\n      // geometry rebuild \u2014 1.6 ms at 1.5k nodes, 45 ms at 30k, on a pass that\n      // reruns on each debounced pan and each drag frame. `reference-position`\n      // is also what `auto` resolves to on any anchored graph, so this was the\n      // default path rather than an opt-in one.\n      get referenceRamp() {\n        return self.effectiveColorScheme === 'reference-position' && self.graph\n          ? computeReferenceRamp(self.graph, self.rampDomain)\n          : undefined\n      },\n      // The assemblies this view is showing, which is the interface every\n      // assembly-aware piece of the app looks for \u2014 `viewTitle` first among\n      // them, which falls back through it and otherwise names the view\n      // \"Untitled view\". Every published HPRC figure showed that.\n      // `launchSubgraphView` only avoids it by writing `displayName`, so a\n      // declaratively-instantiated view (a session snapshot, a figure spec) got\n      // the fallback.\n      //\n      // A whole-file import has none: its stable names are a GFA's business and\n      // need not name anything the session has loaded. Empty rather than\n      // undefined, matching what an LGV with no displayed regions reports.\n      get assemblyNames() {\n        const region = self.loadedRegion\n        return region ? [region.assemblyName] : []\n      },\n      // Screen px per layout unit, per axis. `scale` is the x zoom and the whole\n      // of what a user's wheel moves; y is a second question the layout answers\n      // for itself.\n      //\n      // On a row layout the pitch is already in screen px (rowSpacing.ts), so\n      // scaleY is 1 and stays 1: rows are a track's row height, unchanged by\n      // zoom, and the backbone under them zooms the way the ruler above it does.\n      // On an isotropic layout (FMMM) x and y are one simulation space and one\n      // number scales both, exactly as before.\n      //\n      // Everything that mixes the two axes takes their ratio as `yToX`\n      // (scaleY / scaleX) \u2014 see computeEdgeCurves.\n      get scaleX() {\n        return axisScaleOf(self.scale, self.pixelRows).scaleX\n      },\n      get scaleY() {\n        return axisScaleOf(self.scale, self.pixelRows).scaleY\n      },\n      // The pair, for everything that draws or hit-tests. Handed over as one\n      // value on purpose: every consumer needs both, and passing them separately\n      // let a caller supply the x scale and default y, which compiles and draws\n      // a wrong picture. See AxisScale.\n      get axisScale() {\n        return axisScaleOf(self.scale, self.pixelRows)\n      },\n      // Extent of the drawing in layout units, shared by the pane height and\n      // zoomToFit. On a reference-bp layout x is the cut window rather than\n      // how far the drawing reaches: an allele anchored far outside it is a\n      // fact about the graph, not a reason to draw the window at 6% of the\n      // frame. A popped bubble fits to what it drew. Walk rows reach as far as\n      // the bars on screen, which a repeat pick or a sample filter narrows\n      // after the layout ran.\n      get layoutBounds() {\n        let bounds:\n          { minX: number; minY: number; w: number; h: number } | undefined\n        if (self.layoutResult) {\n          let minX = Infinity\n          let minY = Infinity\n          let maxX = -Infinity\n          let maxY = -Infinity\n          for (const segments of Object.values(\n            self.layoutResult.nodePositions,\n          )) {\n            for (const seg of segments) {\n              minX = Math.min(minX, seg.x)\n              minY = Math.min(minY, seg.y)\n              maxX = Math.max(maxX, seg.x)\n              maxY = Math.max(maxY, seg.y)\n            }\n          }\n          const region =\n            self.layoutResult.referenceAxis && self.popStack.length === 0\n              ? self.loadedRegion\n              : undefined\n          if (region && region.end > region.start) {\n            minX = region.start\n            maxX = region.end\n          }\n          const bars = this.walkRowBars\n          const extent =\n            bars && self.layoutResult.extent\n              ? walkRowsExtent(bars)\n              : self.layoutResult.extent\n          if (extent) {\n            maxX = Math.max(maxX, extent.maxX)\n            maxY = Math.max(maxY, extent.maxY)\n          }\n          bounds = { minX, minY, w: maxX - minX, h: maxY - minY }\n        }\n        return bounds\n      },\n      // The pane is as tall as the drawing, rather than a fixed box the drawing\n      // floats in the middle of.\n      //\n      // A row layout says how tall it is outright: rows are px, so the drawing's\n      // height is the row count times the pitch and this is a sum, not a\n      // derivation. It used to be derived from the drawing's ASPECT RATIO\n      // against the x-fit scale, because y was in bp and a height in px did not\n      // exist until a scale was chosen \u2014 which is also why a ceiling had to be\n      // put on the row pitch to stop tall graphs from binding the fit on the\n      // wrong axis. Both are gone with the unit.\n      //\n      // An isotropic layout still has no height of its own and keeps the aspect\n      // derivation. It reads neither `scale` nor the height it is replacing, so\n      // zoomToFit consumes this without feeding back into it.\n      get canvasHeight() {\n        if (\n          self.viewportOwner === 'host' &&\n          self.hostPaneHeight !== undefined\n        ) {\n          return self.hostPaneHeight\n        }\n        const bounds = this.layoutBounds\n        const usableWidth = self.width - FIT_PADDING * 2\n        // `paneHeight` replaces the built-in ceiling rather than adding a\n        // second clamp under it, and the floor still wins: a pane shorter than\n        // MIN_CANVAS_HEIGHT leaves no room to hover a node and read its\n        // tooltip, which is the reason that floor exists.\n        const ceiling = Math.max(\n          MIN_CANVAS_HEIGHT,\n          self.paneHeight ?? MAX_CANVAS_HEIGHT,\n        )\n        if (!bounds) {\n          return ceiling\n        }\n        if (self.pixelRows) {\n          // The variant map's drawing is one line; its glyphs and labels are\n          // painted above it by the overlay and need the room a row layout\n          // would give to rows.\n          const floor =\n            self.layoutMode === 'variants'\n              ? VARIANT_MAP_HEIGHT\n              : MIN_CANVAS_HEIGHT\n          return Math.min(ceiling, Math.max(floor, bounds.h + FIT_PADDING * 2))\n        }\n        return bounds.w > 0 && usableWidth > 0\n          ? Math.min(\n              ceiling,\n              Math.max(\n                MIN_CANVAS_HEIGHT,\n                (bounds.h * usableWidth) / bounds.w + FIT_PADDING * 2,\n              ),\n            )\n          : ceiling\n      },\n    }))\n    .views(self => ({\n      get geneTrack() {\n        return pickGeneTrack(self.geneTrackChoices, self.geneTrackId)\n      },\n      // Which of `graph.edges` are deletions, and what each one bypasses, keyed\n      // the way the geometry and the hit index address an edge. One map per\n      // graph rather than per rebuild, since both of those take it on every\n      // pan.\n      get deletionEdgeIndexes() {\n        return new Map(self.deletions.map(d => [d.edgeIndex, d.bypassed]))\n      },\n      get hiddenEdgeIndexes() {\n        return new Set(\n          self.showDeletionEdges ? [] : self.deletions.map(d => d.edgeIndex),\n        )\n      },\n      // The interval the reference-position ramp runs over, for the key beside\n      // the drawing, and undefined when no key should be drawn. Two tutorials\n      // carry \"red to magenta is left to right of the cut window\" as a sentence\n      // in prose because nothing on screen said it.\n      //\n      // Read off the ramp the drawing is actually painted with rather than\n      // re-derived from the domain, so the key cannot come to describe a\n      // different interval from the hues beside it \u2014 and so a graph that states\n      // no domain, whose interval has to be measured, does not pay for a second\n      // neighbour walk to say what the first one already worked out.\n      get referenceRampDomain() {\n        const ramp = self.referenceRamp\n        return ramp\n          ? { start: ramp.start, end: ramp.start + ramp.span }\n          : undefined\n      },\n      // The reference interval of the hovered node, for a connected linear view\n      // to highlight. Only a graph cut from a track has one: a whole-file import\n      // has no region, and its stable names need not name anything in a loaded\n      // assembly.\n      get hoverHighlight() {\n        let result:\n          | {\n              refName: string\n              assemblyName: string\n              start: number\n              end: number\n            }\n          | undefined\n        const region = self.loadedRegion\n        const nodeId = self.hoveredNode\n        const nodeById = self.nodeById\n        const neighbors = self.nodeNeighbors\n        if (region && nodeId !== null && nodeById && neighbors) {\n          const span = nodeReferenceSpan({ nodeId, nodeById, neighbors })\n          if (span) {\n            result = {\n              refName: region.refName,\n              assemblyName: region.assemblyName,\n              ...span,\n            }\n          }\n        }\n        return result\n      },\n    }))\n    .views(self => ({\n      // Every assembly this graph names a segment from, with the locus each one\n      // contributes here. rGFA's SN tag is what makes this knowable: the graph\n      // states its own contributors, so the view can offer a way out to each of\n      // them without consulting an alignment.\n      //\n      // Gaps larger than the backbone span split a contributor's segments into\n      // separate loci and the widest wins, so a sample that also contributes\n      // sequence from a distant duplication is launched at the locus on screen\n      // rather than at the union of the two.\n      get contributingAssemblies() {\n        const graph = self.graph\n        const backbone = graph ? backboneNodes(graph) : []\n        return graph\n          ? contributingAssemblies(graph, {\n              maxGap: backbone.length > 0 ? backboneSpan(backbone) : Infinity,\n            })\n          : []\n      },\n    }))\n    .views(self => ({\n      // A node's PanSN sample as an assembly this session can open, or\n      // undefined. The graph's spelling and the assembly's need not agree:\n      // HPRC writes `CHM13` where the assembly is UCSC's `hs1`. The track the\n      // graph was cut from states that pairing in its `assemblyNameToPanSN`,\n      // so its map is read first, then `assemblyManager`'s names and aliases.\n      //\n      // `has` before `get`, deliberately: `get` reports an unknown name to\n      // `Core-handleUnrecognizedAssembly`, which asks every installed plugin to\n      // go supply it, and this is a probe run for hundreds of haplotypes per\n      // graph.\n      get assemblyResolver() {\n        const { assemblyManager } = getSession(self)\n        const panSN = self.sourceAdapter?.assemblyNameToPanSN as\n          Record<string, string> | undefined\n        const byPrefix = new Map(\n          Object.entries(panSN ?? {}).map(([asm, prefix]) => [prefix, asm]),\n        )\n        const loaded = (name: string | undefined) =>\n          name !== undefined && assemblyManager.has(name)\n            ? (assemblyManager.get(name)?.name ?? name)\n            : undefined\n        return (sample: string) =>\n          loaded(byPrefix.get(sample)) ?? loaded(sample)\n      },\n    }))\n    .views(self => ({\n      // The contributors a view can actually be opened on: those naming an\n      // assembly this session has loaded. Every strain of an E. coli pangenome\n      // demo is its own assembly, so all of them resolve; an HPRC graph names\n      // hundreds of haplotypes that no session loads, so only the reference\n      // does.\n      get launchableAssemblies() {\n        return resolveContributors(\n          withReferenceRegion(self.contributingAssemblies, self.loadedRegion),\n          self.assemblyResolver,\n        )\n      },\n      // Whether there is a linear view this graph may draw a highlight into \u2014\n      // the paired one, or the session's only one on the reference assembly.\n      // Read by the node menu, which offers the item only when it would land\n      // somewhere.\n      get canHighlightInLinearView() {\n        const region = self.loadedRegion\n        return (\n          region !== undefined &&\n          linearViewTarget({\n            views: [...getSession(self).views],\n            connectedViewId: self.connectedViewId,\n            assemblyName: region.assemblyName,\n          }) !== undefined\n        )\n      },\n      // Where one node can be opened: on its own assembly, and on the reference\n      // the graph was cut against. Both are padded to a readable window \u2014 a\n      // base-level allele is a few bp, and a linear view framed on exactly that\n      // shows no context at all.\n      nodeLaunchTargets(nodeId: string) {\n        const node = self.nodeById?.get(nodeId)\n        const own = node ? nodeOwnLocation(node) : undefined\n        const ownAssembly = own\n          ? resolveLocationAssembly(self.assemblyResolver, own)\n          : undefined\n        const region = self.loadedRegion\n        const nodeById = self.nodeById\n        const neighbors = self.nodeNeighbors\n        const span =\n          region && nodeById && neighbors\n            ? nodeReferenceSpan({ nodeId, nodeById, neighbors })\n            : undefined\n        const onReference =\n          region && span\n            ? {\n                sample: region.assemblyName,\n                haplotype: undefined,\n                refName: region.refName,\n                ...span,\n              }\n            : undefined\n        return {\n          own:\n            own && ownAssembly\n              ? { location: paddedLocation(own), assembly: ownAssembly }\n              : undefined,\n          reference:\n            region && onReference\n              ? {\n                  location: paddedLocation(onReference),\n                  assembly: region.assemblyName,\n                }\n              : undefined,\n          // Unpadded: a mark is of the node, the same span its hover band\n          // draws. The padding above is room to read a view opened on it.\n          highlight:\n            region && onReference\n              ? { location: onReference, assembly: region.assemblyName }\n              : undefined,\n        }\n      },\n    }))\n    .views(self => ({\n      // The linear view's zoom past which a follow cuts the source track's\n      // coarse pair, or undefined for a track with none.\n      get coarseAboveBpPerPx() {\n        const coarse = self.sourceAdapter?.coarse as\n          { aboveBpPerPx?: unknown } | undefined\n        const above = coarse?.aboveBpPerPx\n        return typeof above === 'number' ? above : undefined\n      },\n    }))\n    .views(self => ({\n      get cutTier(): SubgraphTier {\n        return self.coarseCut && self.coarseAboveBpPerPx !== undefined\n          ? 'coarse'\n          : 'fine'\n      },\n    }))\n    .views(self => ({\n      get regionCapBp() {\n        return self.cutTier === 'coarse' ? Infinity : self.maxRegionBp\n      },\n    }))\n    .views(self => ({\n      // The linear view this pane draws inside, when a display hosts it: x is\n      // that view's window and the cut is re-made when the window leaves it.\n      // A pane that is a view of its own has none.\n      get host(): LinearHost | undefined {\n        let view: unknown\n        try {\n          view = getContainingView(self)\n        } catch {\n          return undefined\n        }\n        return view !== self && isLinearHost(view) ? view : undefined\n      },\n    }))\n    .views(self => ({\n      // Whether the host places x. Only a layout whose x is reference bp can\n      // take the window's transform; force, ordered and walk rows draw in\n      // their own coordinates inside the track, and a popped bubble is a\n      // picture of its own.\n      get hostPlacesX() {\n        const { host, loadedRegion: region, layoutResult: layout } = self\n        return (\n          host !== undefined &&\n          host.initialized &&\n          region !== undefined &&\n          layout?.referenceAxis === true &&\n          self.popStack.length === 0 &&\n          !host.dynamicBlocks.contentBlocks.some(\n            b => b.refName === region.refName && b.reversed,\n          )\n        )\n      },\n    }))\n    .views(self => ({\n      get hostFrame() {\n        const { host, loadedRegion } = self\n        return self.hostPlacesX && host && loadedRegion\n          ? hostFrame(host, loadedRegion)\n          : undefined\n      },\n    }))\n    .actions(self => ({\n      setError(error: unknown) {\n        self.error = error\n        self.isLoading = false\n      },\n      setStatusMessage(message: string) {\n        self.statusMessage = message\n      },\n      setFetchMs(ms: number) {\n        self.lastFetchMs = ms\n      },\n      setLayoutMs(ms: number) {\n        self.lastLayoutMs = ms\n      },\n      setGeometryMetrics(\n        ms: number,\n        strokeCount: number,\n        built: { scale: number; bounds: Bounds },\n      ) {\n        self.lastGeometryMs = ms\n        self.lastGeometryStrokeCount = strokeCount\n        self.builtViewport = built\n        self.geometryVersion++\n      },\n      setLayoutQuality(quality: number) {\n        self.layoutQuality = quality\n      },\n      setLinearLayout(linear: boolean) {\n        self.linearLayout = linear\n      },\n      setLayoutMode(mode: LayoutModeValue) {\n        self.layoutMode = mode\n      },\n      // Re-anchor in place rather than re-parsing: the coordinate walk is\n      // already recorded on the graph, and only which path counts as rank 0\n      // changes. The caller recomputes the layout, the same way it does after\n      // setLayoutMode. An rGFA is left alone \u2014 its coordinates are not derived.\n      setReferencePath(name: string) {\n        self.referencePath = name\n        const graph = self.graph\n        if (graph?.anchoredBy === 'paths') {\n          const reanchored = anchorFromPaths(graph, name)\n          inheritForceLayouts(graph, reanchored)\n          self.graph = reanchored\n        }\n      },\n      setDrawPaths(draw: boolean) {\n        self.drawPaths = draw\n      },\n      setShowPerf(show: boolean) {\n        self.showPerf = show\n      },\n      setColorScheme(scheme: ColorScheme) {\n        self.colorScheme = scheme\n      },\n      setBubbleSpread(spread: BubbleSpread) {\n        self.bubbleSpread = spread\n      },\n      setNodeWidth(width: NodeWidth) {\n        self.nodeWidth = width\n      },\n      setShowBubbles(show: boolean) {\n        self.showBubbles = show\n      },\n      setShowDeletionEdges(show: boolean) {\n        self.showDeletionEdges = show\n      },\n      setShowGenes(show: boolean) {\n        self.showGenes = show\n      },\n      setGeneTrackId(trackId: string) {\n        self.geneTrackId = trackId\n      },\n      setRepeatTrackId(trackId: string) {\n        self.repeatTrackId = trackId\n      },\n      setRepeatKey(key: string) {\n        self.repeatKey = key\n      },\n      setHighlightedPath(name: string) {\n        self.highlightedPath = name\n      },\n      // Undefined restores the built-in ceiling. Nothing recomputes: the pane\n      // reads canvasHeight and the drawing is placed by zoomToFit, which the\n      // caller runs if it wants the drawing refitted into the new pane.\n      setPaneHeight(px: number | undefined) {\n        self.paneHeight = px\n        if (self.viewportOwner === 'host') {\n          self.hostPaneHeight = px\n        }\n      },\n      // The track a hosted pane cuts from. The first settle makes the cut.\n      adoptTrack(trackId: string) {\n        if (self.loadedTrackId !== trackId) {\n          self.loadedTrackId = trackId\n          self.loadedRegion = undefined\n          self.coarseCut = false\n          self.graph = undefined\n          self.layoutResult = undefined\n        }\n      },\n      // The caller refetches \u2014 the number only describes how the next cut is\n      // made, and the graph on screen was cut with the old one.\n      setSubgraphContext(hops: number) {\n        self.subgraphContext = hops\n      },\n      // Same contract: the caller refetches, since the set describes the next\n      // cut and the graph on screen was cut for the old one.\n      setWalkRowSamples(samples: string[] | undefined) {\n        self.walkRowSamples = samples\n      },\n      setSubgraphHaplotypes(haplotypes: string[] | undefined) {\n        self.subgraphHaplotypes = haplotypes\n      },\n      // Same contract as setSubgraphContext: describes how the NEXT cut is\n      // gated, so the caller refetches. See the prop for why a session is\n      // allowed to move this and the launch menus are not.\n      setMaxRegionBp(bp: number) {\n        self.maxRegionBp = bp\n      },\n      // Pair with a linear view for the hover sync, without ever repointing an\n      // existing pairing: a graph launched *from* an LGV is already paired with\n      // it, and stealing that would break the sync the user came in on. So a\n      // launch out of the graph only claims the slot when it is empty.\n      //\n      // A slot naming a view that has been closed is empty too. Held, the view\n      // the graph opened next never got its hover, since a highlight is drawn\n      // only in the paired view.\n      pairWithLinearView(viewId: string) {\n        const paired = self.connectedViewId\n        const stillOpen =\n          paired !== undefined &&\n          withRows([...getSession(self).views]).some(\n            view => (view as { id?: unknown }).id === paired,\n          )\n        if (!stillOpen) {\n          self.connectedViewId = viewId\n        }\n      },\n      setHoveredNode(nodeId: string | null) {\n        self.hoveredNode = nodeId\n      },\n      setHoveredEdge(edgeIdx: number | null) {\n        self.hoveredEdge = edgeIdx\n      },\n      setSelectedNode(nodeId: string | null) {\n        self.selectedNode = nodeId\n      },\n      setDraggingNode(nodeId: string | null) {\n        self.draggingNode = nodeId\n      },\n      setPanning(panning: boolean) {\n        self.isPanning = panning\n      },\n      stopDragging() {\n        self.draggingNode = null\n        self.isPanning = false\n      },\n      // Everything that names a part of the current graph. Reset when the graph\n      // is replaced, and by clearGraph.\n      clearInteractionState() {\n        self.hoveredNode = null\n        self.hoveredEdge = null\n        self.selectedNode = null\n        self.draggingNode = null\n        self.isPanning = false\n      },\n      showNodeDetails(nodeId: string) {\n        const node = self.nodeById?.get(nodeId)\n        const nodeById = self.nodeById\n        const neighbors = self.nodeNeighbors\n        if (node && nodeById && neighbors) {\n          const session = getSession(self)\n          const region = self.loadedRegion\n          // refName/start/end are what makes the widget show a location rather\n          // than a bare id, and they are the same span the linear view\n          // highlights on hover.\n          const span = region\n            ? nodeReferenceSpan({ nodeId, nodeById, neighbors })\n            : undefined\n          if (isSessionModelWithWidgets(session)) {\n            session.showWidget(\n              session.addWidget('BaseFeatureWidget', 'baseFeature', {\n                featureData: {\n                  id: node.id,\n                  name: node.name,\n                  length: node.length,\n                  depth: node.depth,\n                  rank: node.stable?.rank,\n                  stableName: node.stable?.refName,\n                  // The assembly that contributed this segment, split off the\n                  // stable name. On an HPRC graph this is the only thing that\n                  // says which of 400-odd haplotypes an allele came from.\n                  contributingAssembly: nodeOwnLocation(node)?.sample,\n                  // and the haplotype, where the graph's names state one:\n                  // the assembly to load to open this node on its own\n                  // coordinates\n                  contributingHaplotype: nodeOwnLocation(node)?.haplotype,\n                  // Every assembly that traverses it, which is a different\n                  // question and one only a path GFA can answer. Absent on an\n                  // rGFA rather than approximated, so the two are never\n                  // confused: there `contributingAssembly` is first-seen, not\n                  // carriage.\n                  carriedBy: node.samples?.join(', '),\n                  ...(region && span\n                    ? {\n                        refName: region.refName,\n                        assemblyName: region.assemblyName,\n                        start: span.start,\n                        end: span.end,\n                      }\n                    : {}),\n                },\n              }),\n            )\n          }\n        }\n      },\n\n      // A gesture on a hosted graph moves the linear view, and the frame\n      // clock brings x back here; y stays the pane's own.\n      setTransform(s: number, tx: number, ty: number) {\n        const { host } = self\n        if (self.viewportOwner === 'host' && host) {\n          host.horizontalScroll(self.translateX - tx)\n        } else {\n          self.viewportOwner = 'user'\n          self.scale = clampZoom(s)\n          self.translateX = tx\n        }\n        self.translateY = ty\n      },\n      zoom(factor: number, centerX: number, centerY: number) {\n        const { host } = self\n        if (self.viewportOwner === 'host' && host) {\n          host.zoomTo(host.bpPerPx / factor, centerX)\n          return\n        }\n        self.viewportOwner = 'user'\n        const newScale = clampZoom(self.scale * factor)\n        const ratio = newScale / self.scale\n        self.scale = newScale\n        self.translateX = centerX - (centerX - self.translateX) * ratio\n        // y only follows when it is on the same scale. A row layout's y is\n        // screen px (scaleY === 1), so nothing about it changes as x zooms \u2014\n        // moving translateY by the ratio there would slide the rows off under\n        // the cursor while their pitch stayed put.\n        if (!self.pixelRows) {\n          self.translateY = centerY - (centerY - self.translateY) * ratio\n        }\n      },\n      setViewportDirty() {\n        self.viewportDirty++\n      },\n      // The positions themselves moved, as opposed to the window onto them.\n      setPositionsDirty() {\n        self.positionsVersion++\n      },\n      zoomToFit() {\n        // A layout is routinely degenerate on one axis: an anchored window\n        // holding only backbone segments puts every node on row 0. So each axis\n        // constrains the scale only when it has extent, and only a layout with\n        // no extent at all is unfittable. Requiring extent on both axes left\n        // that window at scale 1 with the graph off-screen entirely, since x\n        // there is reference bp.\n        const bounds = self.layoutBounds\n        const usableWidth = self.width - FIT_PADDING * 2\n        const usableHeight = self.canvasHeight - FIT_PADDING * 2\n        // A host owns x, so a fit while hosted places the rows only.\n        if (self.viewportOwner === 'host') {\n          if (bounds && usableHeight > 0) {\n            self.translateY = fittedTranslateY(\n              bounds,\n              usableHeight,\n              self.scaleY,\n            )\n          }\n          return\n        }\n        // Nothing to fit into before the canvas is measured. The autorun re-runs\n        // once width lands, so skipping here beats computing a negative scale\n        // and persisting that transform into the session snapshot.\n        if (\n          bounds &&\n          usableWidth > 0 &&\n          usableHeight > 0 &&\n          // A row layout needs x extent specifically: y cannot stand in for it\n          // there, having no scale left to solve for.\n          (bounds.w > 0 || (!self.pixelRows && bounds.h > 0))\n        ) {\n          // A row layout fits on x ALONE, which is the point of it: the pane is\n          // as tall as the rows are and the rows are as tall as they need to be,\n          // so there is no height to fit into and nothing that can make the\n          // backbone narrower than the pane it is supposed to line up with. That\n          // is the bug this axis change is for \u2014 past ~12 rows the drawing was\n          // taller than it was wide, the vertical axis bound the fit, and the\n          // backbone stopped matching the linear view above it.\n          //\n          // An isotropic layout still fits on whichever axis binds, and the\n          // leftover on the other is split evenly.\n          const fitX = bounds.w > 0 ? usableWidth / bounds.w : Infinity\n          const fitY = bounds.h > 0 ? usableHeight / bounds.h : Infinity\n          const newScale = clampZoom(\n            self.pixelRows ? fitX : Math.min(fitX, fitY),\n          )\n          self.scale = newScale\n          self.translateX =\n            FIT_PADDING -\n            bounds.minX * newScale +\n            (usableWidth - bounds.w * newScale) / 2\n          // scaleY, which a row layout pins at 1\n          self.translateY = fittedTranslateY(\n            bounds,\n            usableHeight,\n            self.pixelRows ? 1 : newScale,\n          )\n        }\n      },\n      clearPerfMetrics() {\n        self.lastFetchMs = undefined\n        self.lastLayoutMs = undefined\n        self.lastGeometryMs = undefined\n        self.lastGeometryStrokeCount = undefined\n        self.builtViewport = undefined\n      },\n    }))\n    .actions(self => ({\n      // The frame clock. Unclamped, since clampZoom's floor is there to keep a\n      // scale finite and 1 / bpPerPx already is; clamped, a whole-chromosome\n      // window would stop lining up.\n      hostTransform(scale: number, translateX: number) {\n        const engaging = self.viewportOwner !== 'host'\n        if (engaging) {\n          self.hostPaneHeight = self.canvasHeight\n          self.viewportOwner = 'host'\n        }\n        self.scale = scale\n        self.translateX = translateX\n        if (engaging) {\n          self.zoomToFit()\n        }\n      },\n      // A drawing still on the reference stays where the host left it; one\n      // whose x no longer means bp is refit.\n      releaseHost() {\n        if (self.viewportOwner === 'host') {\n          self.hostPaneHeight = undefined\n          if (self.layoutResult?.referenceAxis) {\n            self.viewportOwner = 'user'\n          } else {\n            self.viewportOwner = 'fit'\n            self.zoomToFit()\n          }\n        }\n      },\n    }))\n    .actions(self => {\n      // Pan/zoom can wait: the geometry on screen is still correct while the\n      // gesture runs (the viewport bounds carry 20% overscan), so rebuilding is\n      // deferred until the user settles.\n      function scheduleViewportDirty() {\n        clearTimeout(self.viewportDirtyTimer)\n        self.viewportDirtyTimer = setTimeout(() => {\n          if (isAlive(self)) {\n            self.setViewportDirty()\n          }\n        }, VIEWPORT_DEBOUNCE_MS)\n      }\n\n      // A node drag cannot wait \u2014 the node only moves on screen when its\n      // geometry is rebuilt \u2014 but a bump costs a full geometry rebuild plus\n      // invalidation of both hit-detection indexes, and mousemove fires in\n      // bursts well above the frame rate. Coalescing to the next frame keeps the\n      // drag live while bounding that work to once per frame instead of once\n      // per event.\n      function requestPositionsDirtyFrame() {\n        cancelAnimationFrame(self.positionsDirtyFrame)\n        self.positionsDirtyFrame = requestAnimationFrame(() => {\n          if (isAlive(self)) {\n            self.setPositionsDirty()\n          }\n        })\n      }\n\n      return {\n        // Moves the position objects IN PLACE, which is the one thing\n        // jbrowse-components' upload invariant says not to do (\"per-region\n        // upload values must be freshly constructed, never mutated \u2014 backends\n        // diff by reference identity\"), so it is worth saying why this is not\n        // that case and what it costs instead.\n        //\n        // Nothing here diffs by identity: the geometry is rebuilt wholesale and\n        // handed over as one batch, so `nodePositions` identity is not a\n        // protocol between the model and the backend the way a per-region map\n        // is. What identity DOES drive is the fit: the zoom-to-fit autorun and\n        // `layoutBounds` \u2014 and so `canvasHeight` \u2014 key off `layoutResult`, and\n        // they mean \"a new LAYOUT arrived\", not \"a node moved\". Publishing a\n        // fresh positions record per frame of a drag would refit the drawing\n        // and resize the pane under the cursor, sixty times a second.\n        //\n        // So the change is announced by `positionsVersion` instead, and every\n        // cache that would otherwise trust identity takes it as a key. The cost\n        // of that trade is that the version is a thing to remember: a caller\n        // that mutates here and does not bump it gets stale curves, stale hit\n        // boxes and stale labels, silently. Everything downstream of it is\n        // reached from this one action.\n        moveNode(nodeId: string, dx: number, dy: number) {\n          const positions = self.layoutResult?.nodePositions\n          if (positions?.[nodeId]) {\n            for (const seg of positions[nodeId]) {\n              seg.x += dx\n              seg.y += dy\n            }\n            requestPositionsDirtyFrame()\n          }\n        },\n        scheduleViewportDirty,\n      }\n    })\n    .actions(self => {\n      let loadController: AbortController | undefined\n\n      // `scaling.nodes` rather than the graph's own: under a compressing\n      // drawn-length law a node's `length` crosses this boundary as a drawn\n      // length, which is all the engine ever reads it as.\n      //\n      // An anchored graph also carries a seed per node, the backbone along x,\n      // and asks the engine not to rotate components: FMMM then keeps the\n      // reference's coarse shape instead of curling it into a C\n      // (docs/layout-experiments.md, experiment 2).\n      function callLayout(graph: Graph, scaling: LayoutScaling) {\n        const session = getSession(self)\n        const { rpcManager } = session\n        // Stable grouping key for the layout RPC; a view has no display-level\n        // rpcSessionId. `rpcManager.call` injects sessionId into the args.\n        const sessionId = 'graph'\n        const anchored = graph.nodes.some(isBackbone)\n        return rpcManager.call(sessionId, 'GraphComputeLayout', {\n          graph: {\n            nodes: anchored ? seededNodes(graph, scaling) : scaling.nodes,\n            edges: graph.edges,\n          },\n          options: {\n            quality: self.layoutQuality,\n            linearLayout: self.linearLayout,\n            ...scaling.opts,\n            ...(anchored ? { rotateComponents: false } : {}),\n          },\n          signal: loadController?.signal,\n          // A StatusCallback takes an RpcStatus, not a string \u2014 it may be a\n          // bare label, a phase, or a phase that threw. `statusMessageText` is\n          // core's reader for the human-facing line.\n          statusCallback: status => {\n            self.setStatusMessage(statusMessageText(status) ?? '')\n          },\n        }) as Promise<{ result: LayoutResult; duration: number }>\n      }\n\n      // The engine's inputs, and only those: the graph, plus what `callLayout`\n      // puts in `options`. The reference path is there because the seeds are a\n      // function of it; the colour scheme and the anchored modes' own settings\n      // are absent because none of them reaches the engine.\n      function forceLayoutKey(graph: Graph) {\n        const anchored = graph.nodes.some(isBackbone)\n        return `${self.layoutQuality}|${self.linearLayout}|${self.bubbleSpread}|${anchored}|${graph.referencePath ?? ''}`\n      }\n\n      // Single dispatch point for every layout mode. A mode that returns a\n      // result computed it locally; one that returns undefined can't draw this\n      // graph and hands off to the remote FMMM engine, which is also how\n      // 'force' is expressed. See LAYOUT_MODES.\n      function* computeLayout(graph: Graph) {\n        const start = performance.now()\n        const local = layoutModeByValue(self.layoutMode).run(\n          graph,\n          self.loadedRegion,\n          self.host ? self.layoutResult?.sampleRows : undefined,\n        )\n        if (local) {\n          return { result: local, duration: performance.now() - start }\n        }\n        const cache = forceLayoutsOf(graph)\n        const key = forceLayoutKey(graph)\n        const hit = cache.get(key)\n        if (hit) {\n          return { result: hit, duration: performance.now() - start }\n        }\n        // The engine lays out the runs, not the nodes: a base-level cut is\n        // thousands of nodes in unbranching chains, and one chain per run is\n        // the same drawing at a third of the time. Members take their share of\n        // the run's polyline by drawn length, so the picture is per node again\n        // before anything else sees it.\n        const spread = spreadFor(self.bubbleSpread)\n        const merged = mergeRuns(graph)\n        const { result, duration } = (yield callLayout(\n          merged.graph,\n          layoutScaling(merged.graph, spread),\n        )) as { result: LayoutResult; duration: number }\n        const scaling = layoutScaling(graph, spread)\n        const drawn = new Map(\n          scaling.nodes.map(n => [\n            n.id,\n            drawnNodeLength(scaling.opts, n.length),\n          ]),\n        )\n        const positions = splitRuns(\n          result.nodePositions,\n          merged.runs,\n          id => drawn.get(id) ?? 0,\n        )\n        // Turned so the reference reads left to right, like the linear view\n        // above it. Before `remember`, so the cache hands back the drawing as\n        // it was shown.\n        const oriented = {\n          ...result,\n          nodePositions: graph.nodes.some(isBackbone)\n            ? orientToReference(graph, positions)\n            : positions,\n        }\n        // Under the key read BEFORE the call: the settings that produced this\n        // drawing are not necessarily the ones on screen now, and filing it\n        // under the current ones would serve it up as a layout it is not.\n        remember(cache, key, oriented)\n        return { result: oriented, duration }\n      }\n\n      // Which layout request is the live one. A layout is async and nothing in\n      // the UI waits for it, so several are routinely in flight: every control\n      // in the settings dialog fires `recomputeLayout` on change, and a force\n      // layout takes seconds where an anchored one is instant.\n      //\n      // The graph identity below is not enough to order them, because the\n      // competing requests are usually layouts of the SAME graph. Left to\n      // resolve order the last one to FINISH won rather than the last one\n      // asked for, so switching away from a slow force layout \u2014 to an anchored\n      // mode, a cheaper bubble spread, a lower quality \u2014 drew the abandoned\n      // one over the top of the chosen one seconds later, with the dropdown\n      // still naming the choice that was discarded.\n      let liveRequest = 0\n\n      // Applied under a guard because a layout is async and the user can load a\n      // different graph, or ask for a different layout of it, while one is in\n      // flight; the stale result must not land.\n      function* layoutInto(graph: Graph) {\n        const request = ++liveRequest\n        const isLive = () => self.graph === graph && request === liveRequest\n        const signal = loadController?.signal\n        let computed\n        try {\n          computed = yield* computeLayout(graph)\n        } catch (e) {\n          // A discarded layout's failure is not the user's problem: the drawing\n          // they asked for is on screen or on its way, and raising a banner\n          // over it reports a graph as broken because a setting they moved on\n          // from could not be drawn. An aborted one was discarded by the load\n          // that replaced it, even when the graph is still the same object.\n          if (!isLive() || signal?.aborted) {\n            return false\n          }\n          throw e\n        }\n        const live = isLive()\n        if (live) {\n          self.layoutResult = computed.result\n          self.setLayoutMs(computed.duration)\n        }\n        return live\n      }\n\n      // `keepSelection` for a re-cut of the same source: node ids survive one\n      // where edge indexes do not, so the selection is found again by id.\n      function* parseAndLayout(\n        text: string,\n        name: string,\n        keepSelection = false,\n      ) {\n        self.setStatusMessage('Parsing GFA')\n        const gfaGraph = parseGFA(text)\n        // A general GFA states its coordinates only in its P/W lines, so the\n        // walk that recovers them happens before anything reads `stable` \u2014\n        // otherwise the anchored layouts see an unanchored graph and hand off\n        // to force.\n        const graph = anchorGraph(\n          convertGFAToGraph(gfaGraph, name),\n          self.preferredReferencePath,\n        )\n        // Checked here, between parsing and laying out, because this is the one\n        // point both load paths pass through and it is upstream of everything\n        // expensive: the layout, the geometry and the per-frame draw calls all\n        // scale with this number. The whole-file import path had no cap at all,\n        // so a chromosome-scale GFA would parse and then freeze the tab.\n        if (graph.nodes.length === 0) {\n          throw new Error(`No graph segments in ${name}`)\n        }\n        if (graph.nodes.length > self.maxGraphNodes) {\n          throw new Error(\n            `Graph too large to draw: ${graph.nodes.length.toLocaleString()} nodes (limit ${self.maxGraphNodes.toLocaleString()}). Zoom in to a smaller region, or raise maxGraphNodes on this view.`,\n          )\n        }\n        const selected = keepSelection ? self.selectedNode : null\n        self.graph = graph\n        self.indexBubbles = undefined\n        self.geneFeatures = undefined\n        self.repeatArrays = undefined\n        self.popStack = []\n        // hoveredEdge is an index into graph.edges and hoveredNode/selectedNode\n        // are ids, so all three address the graph being replaced here. Carrying\n        // them over points the tooltip and the highlight at whatever now happens\n        // to sit at that index.\n        self.clearInteractionState()\n        if (selected !== null && self.nodeById?.has(selected)) {\n          self.selectedNode = selected\n        }\n        self.setStatusMessage('Computing layout')\n        yield* layoutInto(graph)\n      }\n\n      // Which load is the live one, for the reason liveRequest orders layouts:\n      // every change in the settings dialog re-cuts, a remote cut takes seconds,\n      // and the last one to finish is not the last one asked for.\n      let liveLoad = 0\n\n      function beginLoad() {\n        const load = ++liveLoad\n        loadController?.abort()\n        loadController = new AbortController()\n        self.loadCanceled = false\n        return {\n          isLive: () => load === liveLoad,\n          signal: loadController.signal,\n        }\n      }\n\n      function loadedTrack() {\n        return self.loadedTrackId\n          ? getSession(self).tracks.find(t => t.trackId === self.loadedTrackId)\n          : undefined\n      }\n\n      // The bubble index that the hosted HPRC build keeps beside its segments,\n      // `<prefix>.bubbles.bed.gz`, read through the bubble adapter over the same\n      // window. A graph whose source has no such file, the ordinary case for a\n      // graph of one's own, keeps its derived bubbles, so a failure here is not\n      // the graph's problem. A coarse cut reads none: its nodes are the\n      // bubbles, and the index over its window can run to a chromosome's rows.\n      function* loadBubbles(\n        adapterConfig: Record<string, unknown>,\n        region: SubgraphRegion,\n        isLive: () => boolean,\n      ) {\n        // The track config arrives as written, so the prefix is either the\n        // `uri` shorthand or the segments location it expands to.\n        const prefix = bubblePrefix(adapterConfig)\n        if (\n          adapterConfig.type !== 'RgfaTabixAdapter' ||\n          prefix === undefined ||\n          self.cutTier === 'coarse'\n        ) {\n          return\n        }\n        try {\n          const features = (yield getSession(self).rpcManager.call(\n            'graph',\n            'CoreGetFeatures',\n            {\n              adapterConfig: {\n                type: 'MinigraphBubbleAdapter',\n                uri: `${prefix}.bubbles.bed.gz`,\n                baseUri: adapterConfig.baseUri,\n                assemblyNameToPanSN: adapterConfig.assemblyNameToPanSN,\n              },\n              regions: [region],\n            },\n          )) as Feature[]\n          if (isLive()) {\n            self.indexBubbles = features.map(f => ({\n              refName: region.refName,\n              start: f.get('start'),\n              end: f.get('end'),\n              segmentCount: f.get('segmentCount') as number,\n              pathCount: (f.get('pathCount') as number | undefined) ?? 0,\n              inversion: f.get('inversion') as boolean,\n              shortestAlleleLength: f.get('shortestAlleleLength') as number,\n              longestAlleleLength: f.get('longestAlleleLength') as number,\n              segments: f.get('segments') as string,\n              shortestAllele: undefined,\n              longestAllele: undefined,\n            }))\n          }\n        } catch (e) {\n          console.warn('[GraphGenomeView] no bubble index for this graph', e)\n        }\n      }\n\n      // A session track's features over the cut. Undefined when the session\n      // has no such track or the read fails: an annotation is never the\n      // graph's problem.\n      function* trackFeatures(\n        trackId: string | undefined,\n        region: SubgraphRegion,\n        what: string,\n      ) {\n        const session = getSession(self)\n        const config = trackId\n          ? session.tracks.find(t => t.trackId === trackId)\n          : undefined\n        if (!config) {\n          return undefined\n        }\n        try {\n          return (yield session.rpcManager.call('graph', 'CoreGetFeatures', {\n            adapterConfig: readConfObject(config, 'adapter'),\n            regions: [region],\n          })) as Feature[]\n        } catch (e) {\n          console.warn(`[GraphGenomeView] no ${what} for this graph`, e)\n          return undefined\n        }\n      }\n\n      // The genes over the cut, from the session's annotation track for the\n      // assembly, so the backbone can carry its exons and names.\n      function* loadGenes(region: SubgraphRegion, isLive: () => boolean) {\n        const features = yield* trackFeatures(\n          self.geneTrack?.trackId,\n          region,\n          'genes',\n        )\n        if (features && isLive()) {\n          self.geneFeatures = geneModelsFrom(features)\n        }\n      }\n\n      // The tandem repeat arrays over the cut, from the session's repeat\n      // track, for the walk rows to measure between and tile by.\n      function* loadRepeats(region: SubgraphRegion, isLive: () => boolean) {\n        const features = yield* trackFeatures(\n          self.repeatTrack?.trackId,\n          region,\n          'repeats',\n        )\n        if (features && isLive()) {\n          self.repeatArrays = repeatArraysFrom(features)\n        }\n      }\n\n      // Inner loading logic shared by loadFromTabixSubgraph and refetchIfNeeded\n      function* doSubgraphLoad(\n        adapterConfig: Record<string, unknown>,\n        region: SubgraphRegion,\n        opts: SubgraphCutOptions = {},\n      ) {\n        const { isLive, signal } = beginLoad()\n        const track = loadedTrack()\n        const regionSize = region.end - region.start\n        // Past the size cap the graph view declines rather than degrading to a\n        // non-graph rectangle rendering; large-region and full-genome\n        // comparison is a linear synteny view instead.\n        const refusal =\n          (track &&\n            offReferenceProblem(\n              graphReferenceAssembly(track),\n              region.assemblyName,\n            )) ??\n          (regionSize > self.regionCapBp\n            ? `Region too large (${formatSpanBp(regionSize)}) \u2014 zoom in to view graph (max ${formatSpanBp(self.regionCapBp)})`\n            : undefined)\n        if (refusal !== undefined) {\n          self.graph = undefined\n          self.layoutResult = undefined\n          self.isLoading = false\n          self.error = new Error(refusal)\n          return\n        }\n        self.isLoading = true\n        self.error = undefined\n        self.setStatusMessage('Fetching subgraph')\n        try {\n          const session = getSession(self)\n          const { rpcManager } = session\n          const sessionId = 'graph' // getRpcSessionId(self) no rpcSessionId getter\n          const fetchStart = performance.now()\n          const gfaText = (yield rpcManager.call(sessionId, 'GetSubgraph', {\n            adapterConfig,\n            region,\n            opts,\n            signal,\n          })) as string\n          if (!isLive()) {\n            return\n          }\n          self.setFetchMs(performance.now() - fetchStart)\n          if (!gfaText) {\n            throw new Error(\n              'Adapter returned no GFA \u2014 region may be outside indexed data or the adapter does not implement getSubgraph',\n            )\n          }\n          const label = locLabel(region)\n          yield* parseAndLayout(gfaText, label, true)\n          if (!isLive()) {\n            return\n          }\n          // Three independent remote reads, each landing as it arrives: in\n          // turn they held the overlay over a drawn graph for the sum of their\n          // round trips.\n          self.setStatusMessage('Reading annotations')\n          yield Promise.all([\n            flow(loadBubbles)(adapterConfig, region, isLive),\n            flow(loadGenes)(region, isLive),\n            flow(loadRepeats)(region, isLive),\n          ])\n        } catch (e) {\n          if (isLive()) {\n            console.error('[GraphGenomeView.loadFromTabixSubgraph]', e)\n            self.error = e\n          }\n        } finally {\n          if (isLive()) {\n            self.isLoading = false\n          }\n        }\n      }\n\n      // The cut behind a graph whose source is a track in this session, which is\n      // what both a launch snapshot and a restored session carry. Silent when\n      // there is no such pair, which is the whole-file case. A pair naming a\n      // track the session lacks is reported, because otherwise the view sits on\n      // an empty import form with nothing saying why.\n      //\n      // Nothing here saves and restores the transform: `viewportOwner` is\n      // what protects a restored session's pan/zoom, and it gates the fit\n      // autorun \u2014 the only thing in this flow that would otherwise move the\n      // view. A save/restore pair around the load wrote back the values it had\n      // just read.\n      function* cutFromLoadedTrack() {\n        const region = self.loadedRegion\n        const track = loadedTrack()\n        if (region && self.loadedTrackId && !track) {\n          self.error = new Error(\n            `The track this graph was cut from, \"${self.loadedTrackId}\", is not in this session`,\n          )\n        } else if (track && region) {\n          // A hop past a coarse cut reaches nothing new: every bubble node's\n          // two links are indexed under the backbone either side of it.\n          const coarse = self.cutTier === 'coarse'\n          yield* doSubgraphLoad(readConfObject(track, 'adapter'), region, {\n            hops: coarse ? 0 : self.subgraphContext,\n            haplotypes: self.subgraphHaplotypes,\n            tier: coarse ? 'coarse' : undefined,\n          })\n        }\n      }\n\n      // Raises `isLoading` before any fetch, so a view waiting on a remote file\n      // shows its loading state instead of the import form. Text already in\n      // hand is parsed without yielding first.\n      // `region` is the window a declared file was stated beside. Held through\n      // the load rather than restored after it, so the parse anchors on that\n      // assembly's path and a failed or canceled load can still be retried\n      // with it.\n      function* loadWholeGFA(\n        name: string,\n        source: string | ((signal: AbortSignal) => Promise<string>),\n        region?: SubgraphRegion,\n      ) {\n        const { isLive, signal } = beginLoad()\n        self.loadedTrackId = ''\n        self.loadedRegion = region\n        self.coarseCut = false\n        self.isLoading = true\n        self.error = undefined\n        try {\n          const text =\n            typeof source === 'string'\n              ? source\n              : ((yield source(signal)) as string)\n          if (isLive()) {\n            yield* parseAndLayout(text, name)\n          }\n        } catch (e) {\n          if (isLive()) {\n            console.error('[GraphGenomeView.loadWholeGFA]', e)\n            self.error = e\n          }\n        } finally {\n          if (isLive()) {\n            self.isLoading = false\n          }\n        }\n        return isLive()\n      }\n\n      return {\n        // Back to the import form: drop the graph, everything derived from it,\n        // and the source it came from. Leaving the source declared kept\n        // `showLoading` true over the import form and had a reloaded session\n        // cut the dismissed graph again. Any load in flight ends here too,\n        // or it would land its graph afterwards.\n        clearGraph() {\n          loadController?.abort()\n          loadController = undefined\n          liveLoad++\n          liveRequest++\n          self.graph = undefined\n          self.layoutResult = undefined\n          self.loadedTrackId = ''\n          self.loadedRegion = undefined\n          self.coarseCut = false\n          self.cutNote = undefined\n          self.gfaLocation = undefined\n          self.indexBubbles = undefined\n          self.geneFeatures = undefined\n          self.repeatArrays = undefined\n          self.popStack = []\n          self.error = undefined\n          self.isLoading = false\n          self.loadCanceled = false\n          self.statusMessage = ''\n          self.clearInteractionState()\n          self.clearPerfMetrics()\n        },\n        cancelLoad() {\n          if (self.canCancelLoad) {\n            loadController?.abort()\n            loadController = undefined\n            liveLoad++\n            liveRequest++\n            self.graph = undefined\n            self.isLoading = false\n            self.statusMessage = ''\n            self.loadCanceled = true\n          }\n        },\n        loadGFA: flow(function* (text: string, name = 'Imported GFA') {\n          yield* loadWholeGFA(name, text)\n        }),\n        loadGFAFromLocation: flow(function* (location: FileLocation) {\n          self.setStatusMessage('Fetching GFA')\n          const stated = self.loadedRegion\n          const live = yield* loadWholeGFA(\n            'uri' in location\n              ? (location.uri.split('/').pop() ?? 'GFA')\n              : 'GFA',\n            signal =>\n              openLocation(location).readFile({ encoding: 'utf8', signal }),\n            stated,\n          )\n          if (stated && live && self.graph) {\n            yield* loadRepeats(stated, () => self.loadedRegion === stated)\n          }\n        }),\n        loadFromTabixSubgraph: flow(function* (\n          adapterConfig: Record<string, unknown>,\n          region: SubgraphRegion,\n          opts: {\n            trackId?: string\n          } = {},\n        ) {\n          self.loadedTrackId = opts.trackId ?? ''\n          self.loadedRegion = opts.trackId ? region : undefined\n          self.coarseCut = false\n          yield* doSubgraphLoad(adapterConfig, region, {\n            hops: self.subgraphContext,\n            haplotypes: self.subgraphHaplotypes,\n          })\n        }),\n        // Cut on attach only \u2014 a graph already on screen is either the user's\n        // own or one this just drew.\n        refetchIfNeeded: flow(function* () {\n          if (!self.graph) {\n            yield* cutFromLoadedTrack()\n          }\n        }),\n        // Cut the same region again, for a change to what the cut returns\n        // rather than to how it is drawn (subgraphContext).\n        reloadSubgraph: flow(function* () {\n          yield* cutFromLoadedTrack()\n        }),\n        // Re-read one annotation track alone, for a track change or a graph\n        // that came from a whole file beside a stated region. The graph, its\n        // layout and any open bubble stay as they are. Live only while the\n        // track it read is still the one chosen, so a slow read cannot land\n        // over the pick that followed it.\n        reloadRepeats: flow(function* () {\n          const region = self.loadedRegion\n          const trackId = self.repeatTrack?.trackId\n          if (region) {\n            yield* loadRepeats(\n              region,\n              () =>\n                self.loadedRegion === region &&\n                self.repeatTrack?.trackId === trackId,\n            )\n          }\n        }),\n        reloadGenes: flow(function* () {\n          const region = self.loadedRegion\n          const trackId = self.geneTrack?.trackId\n          if (region) {\n            yield* loadGenes(\n              region,\n              () =>\n                self.loadedRegion === region &&\n                self.geneTrack?.trackId === trackId,\n            )\n          }\n        }),\n        // Open one bubble: the graph becomes the segments the bubble row names,\n        // drawn in the layout the reader is in, or force-directed from the\n        // variant map. The graph it came from stays behind it, one click away,\n        // and the popped graph gets its own derived bubbles, so a superbubble\n        // opens progressively.\n        popBubble: flow(function* (bubble: MinigraphBubble) {\n          const graph = self.graph\n          if (!graph) {\n            return\n          }\n          const sub = bubbleSubgraph(graph, bubbleSegmentIds(bubble))\n          if (sub.nodes.length === 0) {\n            getSession(self).notify(\n              'None of the segments of this bubble are in the cut; widen the graph context to open it',\n              'info',\n            )\n            return\n          }\n          const { isLive } = beginLoad()\n          self.popStack = [\n            ...self.popStack,\n            {\n              graph,\n              layoutMode: self.layoutMode,\n              label: graph.name,\n              indexBubbles: self.indexBubbles,\n            },\n          ]\n          self.indexBubbles = undefined\n          const label = `${BUBBLE_KIND_NAMES[classifyBubble(bubble).kind]} at ${bubble.refName}:${bubble.start.toLocaleString()}`\n          self.graph = { ...sub, name: label }\n          if (self.layoutMode === 'variants') {\n            self.layoutMode = 'force'\n          }\n          self.clearInteractionState()\n          self.viewportOwner = 'fit'\n          self.isLoading = true\n          try {\n            if (yield* layoutInto(self.graph)) {\n              self.isLoading = false\n            }\n          } catch (e) {\n            if (isLive()) {\n              self.error = e\n              self.isLoading = false\n            }\n          }\n        }),\n        unpopBubble: flow(function* () {\n          const from = self.poppedFrom\n          if (!from) {\n            return\n          }\n          self.popStack = self.popStack.slice(0, -1)\n          self.graph = from.graph\n          self.layoutMode = from.layoutMode\n          self.indexBubbles = from.indexBubbles\n          self.clearInteractionState()\n          self.viewportOwner = 'fit'\n          self.isLoading = true\n          try {\n            if (yield* layoutInto(from.graph)) {\n              self.isLoading = false\n            }\n          } catch (e) {\n            self.error = e\n            self.isLoading = false\n          }\n        }),\n        recomputeLayout: flow(function* () {\n          const graph = self.graph\n          if (!graph) {\n            return\n          }\n          self.isLoading = true\n          self.setStatusMessage('Computing layout')\n\n          try {\n            // A superseded request leaves the spinner to the request that\n            // replaced it: clearing it here reports \"done\" while the layout the\n            // user actually asked for is still being computed, which is the\n            // common case when a cheap choice follows an expensive one.\n            if (yield* layoutInto(graph)) {\n              self.isLoading = false\n            }\n          } catch (e) {\n            console.error('[GraphGenomeView.recomputeLayout]', e)\n            self.error = e\n            self.isLoading = false\n          }\n        }),\n      }\n    })\n    .actions(self => ({\n      // The settle clock. A pan the cut still holds fetches nothing; one past\n      // its edge re-cuts the window plus a window-width each side, on the tier\n      // the zoom asks for. Overlapping re-cuts are ordered by doSubgraphLoad's\n      // liveLoad, so the latest window wins.\n      settleOn(seen: HostWindow) {\n        const above = self.coarseAboveBpPerPx\n        const tier =\n          above !== undefined && seen.bpPerPx > above ? 'coarse' : 'fine'\n        const cap = tier === 'coarse' ? Infinity : self.maxRegionBp\n        const visible = seen.end - seen.start\n        self.cutNote =\n          visible > cap\n            ? `Holding the last cut: ${formatSpanBp(visible)} is past the ${formatSpanBp(cap)} a cut may span`\n            : undefined\n        if (\n          self.cutNote !== undefined ||\n          (tier === self.cutTier && cutHolds(self.loadedRegion, seen))\n        ) {\n          return\n        }\n        self.coarseCut = tier === 'coarse'\n        self.loadedRegion = hostCut(seen, cap)\n        self.recuts++\n        void self.reloadSubgraph()\n      },\n    }))\n    .actions(self => ({\n      // The host's two clocks, started by the display that hosts the pane.\n      // The frame clock moves x with every frame of the linear view and\n      // fetches nothing; the settle clock wakes on its debounced blocks and\n      // re-cuts only when the window has left the cut, whatever the layout.\n      startHosting() {\n        addDisposer(\n          self,\n          reaction(\n            () => self.hostPlacesX,\n            places => {\n              if (!places) {\n                self.releaseHost()\n              }\n            },\n            { name: 'GraphHostPlacesX' },\n          ),\n        )\n        addDisposer(\n          self,\n          reaction(\n            () => self.hostFrame,\n            frame => {\n              if (frame) {\n                self.hostTransform(frame.scale, frame.translateX)\n              }\n            },\n            {\n              equals: (a, b) =>\n                a?.scale === b?.scale && a?.translateX === b?.translateX,\n              fireImmediately: true,\n              name: 'GraphHostFrame',\n            },\n          ),\n        )\n        addDisposer(\n          self,\n          reaction(\n            () => self.host?.coarseDynamicBlocks,\n            blocks => {\n              const { host } = self\n              const seen = blocks && host ? hostWindow(host) : undefined\n              if (seen) {\n                self.settleOn(seen)\n              }\n            },\n            { fireImmediately: true, name: 'GraphHostSettle' },\n          ),\n        )\n      },\n    }))\n    .actions(self => ({\n      startRenderingBackend(backend: Renderer) {\n        if (!self.autorunsInstalled) {\n          // Autorun: paint the lane this graph was cut from in the graph's own\n          // reference-position ramp, so a block above and its node below share\n          // a hue with nothing configured. Follows the domain, so a re-cut or\n          // an opened bubble moves the lane's ramp with the drawing.\n          addDisposer(\n            self,\n            autorun(() => {\n              const domain = self.rampDomain\n              const trackId = self.loadedTrackId\n              if (\n                domain &&\n                trackId &&\n                self.effectiveColorScheme === 'reference-position'\n              ) {\n                const display = untracked(() =>\n                  sourceLaneDisplay(\n                    getSession(self).views,\n                    self.connectedViewId,\n                    trackId,\n                  ),\n                )\n                if (display) {\n                  paintSourceLane(display, referencePositionColor(domain))\n                }\n              }\n            }),\n          )\n\n          // Autorun: keep the view fitted to the graph until the user moves it.\n          // Reads layoutResult plus (via zoomToFit) width/canvasHeight, so it\n          // re-fires \u2014 and re-fits \u2014 as the layout arrives and the canvas is\n          // measured, rather than firing once against not-yet-known dimensions.\n          // A manual pan/zoom (or a restored-session transform) makes the\n          // viewport the user's, and a host makes it the linear view's.\n          addDisposer(\n            self,\n            autorun(() => {\n              if (\n                self.layoutResult &&\n                untracked(() => self.viewportOwner === 'fit')\n              ) {\n                self.zoomToFit()\n              }\n            }),\n          )\n\n          // Autorun: mirror a connected linear view's hover onto the graph. An\n          // LGV writes `{hoverPosition, hoverFeature}` to session.hovered on\n          // every mousemove; neither field names the source view, so the guard\n          // is that the position lies in the region this graph was cut from.\n          //\n          // Only `hovered` is tracked \u2014 the graph reads are untracked, so a\n          // geometry rebuild can't re-fire this and clobber a hover the canvas\n          // itself set. Assigning an unchanged id doesn't notify, so a hover\n          // that travels within one segment costs nothing downstream.\n          addDisposer(\n            self,\n            autorun(() => {\n              const hover = readLgvHover(getSession(self).hovered)\n              untracked(() => {\n                const region = self.loadedRegion\n                const graph = self.graph\n                if (region && graph) {\n                  self.setHoveredNode(\n                    hover && hoverInRegion(hover, region)\n                      ? nodeForLgvHover({ hover, nodes: graph.nodes })\n                      : null,\n                  )\n                }\n              })\n            }),\n          )\n\n          // Reaction: drop a hover the pointer cannot still be over.\n          //\n          // A hover is set by a mousemove on the canvas, and here the drawing\n          // moves under a STATIONARY cursor on three axes \u2014 the wheel zoom, the\n          // toolbar's zoom and fit buttons, and a pan \u2014 none of which fire a\n          // pointer event. Left alone the tooltip goes on naming the node that\n          // used to be under the cursor, `hoverHighlight` goes on publishing its\n          // span, and the paired linear view paints a band over the wrong\n          // sequence until the mouse happens to move.\n          //\n          // This is jbrowse-components' `installClearHoverOnViewportChange`\n          // (BaseLinearDisplay), whose three axes are bpPerPx / offsetPx /\n          // scrollTop; a graph view's are its own transform. Its rule is worth\n          // restating rather than just citing: a sticky canvas gets no\n          // mousemove and no mouseleave for any of them. Not imported because\n          // it lives in the LGV plugin and reads a containing LGV, and this\n          // plugin deliberately takes no runtime dependency on that plugin\n          // (see hoverSync/index.tsx).\n          //\n          // A `reaction`, not an autorun, for the reason stated there: the\n          // effect touches hover state, and an autorun would re-enter itself.\n          // Selection is untouched \u2014 a click is a choice, and the content\n          // moving does not unmake it.\n          addDisposer(\n            self,\n            reaction(\n              () => `${self.scale}-${self.translateX}-${self.translateY}`,\n              () => {\n                self.setHoveredNode(null)\n                self.setHoveredEdge(null)\n              },\n              { name: 'GraphClearHoverOnViewportChange' },\n            ),\n          )\n\n          // Autorun: a zoom, or a pan that leaves the window the last build\n          // covered, schedules a debounced rebuild. A pan inside it costs a\n          // repaint and nothing else. Skips the first run.\n          let firstViewport = true\n          addDisposer(\n            self,\n            autorun(() => {\n              const { scale } = self\n              const viewport = viewportOf(self)\n              if (firstViewport) {\n                firstViewport = false\n                return\n              }\n              const built = untracked(() => self.builtViewport)\n              if (built?.scale === scale && contains(built.bounds, viewport)) {\n                return\n              }\n              self.scheduleViewportDirty()\n            }),\n          )\n\n          // Autorun: hover/select are draw-time colour overrides, stated whole\n          // on every change, so there is nothing to restore and nothing to go\n          // stale when a rebuild renumbers the batch. Tracks `geometryVersion`\n          // because an upload drops the renderer's edge highlight.\n          addDisposer(\n            self,\n            autorun(() => {\n              const b = self.currentRenderingBackend as Renderer | undefined\n              const hoveredNode = self.hoveredNode\n              const hoveredEdge = self.hoveredEdge\n              const selectedNode = self.selectedNode\n              dependOn(self.geometryVersion)\n              if (b) {\n                const nodes = new Map<string, number>()\n                if (selectedNode !== null) {\n                  nodes.set(selectedNode, SELECT_BRIGHTEN)\n                }\n                if (hoveredNode !== null && hoveredNode !== selectedNode) {\n                  nodes.set(hoveredNode, HOVER_BRIGHTEN)\n                }\n                b.setNodeHighlights(nodes)\n                b.setEdgeHighlight(hoveredEdge, HOVER_BRIGHTEN)\n                self.renderNow()\n              }\n            }),\n          )\n        }\n\n        // The second argument is a SETUP THUNK, not the callbacks themselves:\n        // anything it closes over lives exactly as long as the callbacks that\n        // read it, which is what lets a per-backend memo work.\n        self.attachRenderingBackend<Renderer>(backend, () => ({\n          // Autorun: rebuild geometry when graph data or display options\n          // change. scale/translate are untracked so they don't trigger a full\n          // rebuild \u2014 only the debounced viewportDirty flag does.\n          upload: (b: Renderer) => {\n            b.resize(self.width, self.canvasHeight)\n            const nodeById = self.nodeById\n            if (self.nodePositions && self.graph && nodeById) {\n              // The window moved (debounced pan/zoom), or the positions did (a\n              // node drag, coalesced to a frame). Both change the drawing;\n              // everything below reads them untracked or not at all.\n              dependOn(self.viewportDirty, self.positionsVersion)\n              const geometryStart = performance.now()\n              const viewportBounds = untracked(() =>\n                padded(viewportOf(self), VIEWPORT_PANES_BUILT),\n              )\n              const batch = buildGeometry({\n                nodePositions: self.nodePositions,\n                graph: self.graph,\n                nodeById,\n                colorScheme: self.effectiveColorScheme,\n                contigThickness: self.contigThickness,\n                connectorThickness: self.connectorThickness,\n                drawPaths: self.effectiveDrawPaths,\n                nodeWidth: self.nodeWidth,\n                highlight: self.walkHighlight,\n                // Untracked, so a zoom does not eagerly rebuild geometry \u2014 the\n                // debounced viewportDirty bump drives the scale-dependent\n                // rebuild (flatness, arrow visibility, viewport culling), same\n                // as pan.\n                axis: untracked(() => self.axisScale),\n                linearLayout: self.linearLayout,\n                viewportBounds,\n                // Where each node sits on the reference and what interval the\n                // hue spans. Held against the graph rather than derived here,\n                // the same way `deletions` is and for the same reason \u2014 see\n                // the `referenceRamp` view.\n                referenceRamp: self.referenceRamp,\n                deletions: self.deletionEdgeIndexes,\n                hiddenEdges: self.hiddenEdgeIndexes,\n                // Read tracked above; passed here so the shared edge-curve\n                // cache can tell a drag from a pan.\n                version: self.positionsVersion,\n              })\n              b.uploadGeometry(batch)\n              self.setGeometryMetrics(\n                performance.now() - geometryStart,\n                batch.nodeStrokes.length,\n                { scale: untracked(() => self.scale), bounds: viewportBounds },\n              )\n              return true\n            }\n            // Nothing reached the backend, so the autorun may skip the redraw\n            // it would otherwise force. Safe despite the resize above: with no\n            // positions there is nothing to draw, which is the same case\n            // `render` below returns false for.\n            return false\n          },\n          // Autorun: re-render on pan/zoom/darkMode without rebuilding geometry\n          render: (b: Renderer) => {\n            if (!self.nodePositions) {\n              return false\n            }\n            // getDpr(), never a bare `devicePixelRatio`: it is capped at\n            // MAX_DPR so this canvas costs what every other canvas in the app\n            // costs on a 3x display (the square of the ratio, i.e. 9x the\n            // pixels of 1x against the 4x everything else pays), and it is the\n            // same read `syncCanvasSize` sizes the backing store with \u2014 two\n            // call sites reading the global separately can disagree, and then\n            // the geometry lands at a different scale from the canvas under it.\n            const dpr = getDpr()\n            b.updateTransform({\n              scaleX: self.scaleX * dpr,\n              scaleY: self.scaleY * dpr,\n              translateX: self.translateX * dpr,\n              translateY: self.translateY * dpr,\n              // Handed over rather than read again by the backend: the\n              // thicknesses in the vertex buffer are css px and are expanded\n              // after this transform, so they need the same ratio the fields\n              // above were already multiplied by. See TransformUniform.dpr.\n              dpr,\n            })\n            b.render(self.darkMode ? [0.12, 0.12, 0.12, 1] : [1, 1, 1, 1])\n            return true\n          },\n        }))\n      },\n    }))\n    .actions(self => ({\n      // A layout picked from a menu: the mode, then the drawing it makes.\n      switchLayout(mode: LayoutModeValue) {\n        self.setLayoutMode(mode)\n        return self.recomputeLayout()\n      },\n      retryLoad() {\n        if (self.loadedTrackId && self.loadedRegion) {\n          void self.reloadSubgraph()\n        } else if (self.gfaLocation) {\n          void self.loadGFAFromLocation(self.gfaLocation)\n        }\n      },\n      // A declaratively-instantiated view loads itself on attach, from either\n      // declarative source: a whole-GFA `gfaLocation`, or the\n      // `loadedTrackId`/`loadedRegion` pair the launch menu writes and a\n      // reloaded session restores.\n      //\n      // This has to happen here rather than when the rendering backend starts:\n      // the canvas only mounts once `hasGraph` is true, so a view whose graph\n      // must be fetched would never fetch it.\n      afterAttach() {\n        // A restored session that already carries a non-default transform is\n        // the user's own view \u2014 mark it so the fit autorun leaves it alone.\n        if (!self.isDefaultViewport) {\n          self.viewportOwner = 'user'\n        }\n        // loadGFAFromLocation leaves `gfaLocation` intact, so the source\n        // round-trips through a session snapshot.\n        if (self.gfaLocation && !self.graph) {\n          void self.loadGFAFromLocation(self.gfaLocation)\n        }\n        void self.refetchIfNeeded()\n      },\n    }))\n    .actions(self => ({\n      // Move the linear view already on screen, or open one if there is none,\n      // and pair with whichever it was. A view being created gets the session's\n      // annotation for the assembly it opens on (see launchTracks), led by the\n      // graph's own segments track when the launch is on the reference \u2014 the one\n      // assembly that track is configured for.\n      //\n      // Only a view on the reference is paired with. A node's hover band is on\n      // that assembly, so paired with a view on another the band fails that\n      // view's assembly check and the reference view's id check, and is drawn\n      // nowhere.\n      showInLinearView(target: { location: GraphLocation; assembly: string }) {\n        const session = getSession(self)\n        const onReference = target.assembly === self.loadedRegion?.assemblyName\n        const viewId = showInLinearView({\n          session,\n          location: target.location,\n          assembly: target.assembly,\n          connectedViewId: self.connectedViewId,\n          tracks: launchTracks({\n            session,\n            assemblyName: target.assembly,\n            first:\n              self.loadedTrackId && onReference\n                ? self.loadedTrackId\n                : undefined,\n          }),\n        })\n        if (onReference) {\n          self.pairWithLinearView(viewId)\n        }\n      },\n      // Mark the node's reference interval in the linear view beside the graph.\n      // Not an action that opens anything: with no view to mark, the menu does\n      // not offer it (see nodeLaunchMenuItems).\n      highlightInLinearView(target: {\n        location: GraphLocation\n        assembly: string\n      }) {\n        highlightInLinearView({\n          session: getSession(self),\n          location: target.location,\n          assembly: target.assembly,\n          connectedViewId: self.connectedViewId,\n        })\n      },\n      showSyntenyView(trackId: string) {\n        launchSyntenyView({\n          session: getSession(self),\n          contributors: self.launchableAssemblies,\n          trackId,\n          graphTrackId: self.loadedTrackId || undefined,\n        })\n      },\n    }))\n    .views(self => ({\n      // Synteny datasets that could fill the panels of a multi-genome launch.\n      // Below two openable contributors there is nothing to compare, so the scan\n      // is skipped rather than run and discarded.\n      get syntenyLaunchTracks() {\n        const samples = self.launchableAssemblies.map(c => c.sample)\n        return samples.length >= 2\n          ? launchableSyntenyTracks(getSession(self), samples)\n          : []\n      },\n    }))\n    .views(self => ({\n      // The graph's way out, in the same shared \"Launch view\" submenu every\n      // other view contributes to. Until this existed the triangle had two edges:\n      // a linear view could open a graph or a synteny view of a locus, and the\n      // graph could open nothing at all.\n      menuItems(): MenuItem[] {\n        const items: MenuItem[] = []\n        for (const item of graphLaunchMenuItems({\n          contributors: self.launchableAssemblies,\n          syntenyTracks: self.syntenyLaunchTracks,\n          onShowLinear: target => {\n            self.showInLinearView(target)\n          },\n          onShowSynteny: trackId => {\n            self.showSyntenyView(trackId)\n          },\n        })) {\n          pushLaunchViewMenuItem(items, item)\n        }\n        return items\n      },\n    }))\n}\n\nexport type GraphGenomeViewModel = ReturnType<\n  ReturnType<typeof stateModelFactory>['create']\n>\n", "import { bubbleSegmentIds, classifyBubble, formatBp } from './classifyBubble'\nimport { isBackbone } from '../anchoredNodes'\nimport { svgPath } from '../util/geometry'\n\nimport type { BubbleKind } from './classifyBubble'\nimport type {\n  BubbleRoute,\n  MinigraphBubble,\n} from '../../MinigraphBubbleAdapter/bubbleLine'\nimport type { Graph, NodeSegment } from '../types'\n\n// A bubble drawn over the graph itself: a wide translucent stroke along the\n// nodes inside it, in layout coordinates, so the same halo follows the nodes\n// through the force layout's loops as through the ordered layout's lenses. The\n// two backbone nodes a bubble hangs between are not inside it, and are left\n// out so neighbouring halos do not touch.\nexport interface BubbleHalo {\n  bubble: MinigraphBubble\n  kind: BubbleKind\n  label: string\n  // an SVG path in layout units; a drawing transform puts it on screen\n  path: string\n  // where the label goes: the highest point of the halo, in layout units\n  top: NodeSegment\n  members: number\n  // the ids of those nodes, so a lifted walk can say which bubbles it enters\n  nodeIds: string[]\n  // the bubble is the whole drawing, as a popped bubble's own row is: its\n  // label still names it, but a halo around everything marks nothing\n  whole: boolean\n  // each route the walks take through the bubble, the reference's own\n  // included, named for the haplotypes that take it; a route with no steps, a\n  // deletion, has nowhere to carry a chip\n  routes: RouteLabel[]\n}\n\nexport interface RouteLabel {\n  route: BubbleRoute\n  at: NodeSegment\n  text: string\n}\n\nconst WHOLE_FRACTION = 0.9\nconst NAMED_WALKS = 2\n// a SNP's routes are a dot each; chips are for loops a reader can see\nconst MIN_CHIPPED_BP = 1000\n\nexport function bubbleHalos(\n  graph: Graph,\n  bubbles: MinigraphBubble[],\n  positions: Record<string, NodeSegment[]>,\n  walkLabel: (name: string) => string = name => name,\n): BubbleHalo[] {\n  const byName = new Map(graph.nodes.map(n => [n.name, n]))\n  const halos: BubbleHalo[] = []\n  for (const bubble of bubbles) {\n    const parts: string[] = []\n    let top: NodeSegment | undefined\n    const nodeIds: string[] = []\n    const ends: NodeSegment[] = []\n    for (const name of bubbleSegmentIds(bubble)) {\n      const node = byName.get(name)\n      const line = node && positions[node.id]\n      if (!node || !line?.length) {\n        continue\n      }\n      if (\n        isBackbone(node) &&\n        (node.stable.start < bubble.start || node.stable.start >= bubble.end)\n      ) {\n        ends.push(line[Math.floor(line.length / 2)]!)\n        continue\n      }\n      nodeIds.push(node.id)\n      // a one-point line still needs a segment to stroke as a dot\n      parts.push(svgPath(line.length === 1 ? [line[0]!, line[0]!] : line))\n      for (const p of line) {\n        if (!top || p.y < top.y) {\n          top = p\n        }\n      }\n    }\n    if (!top) {\n      continue\n    }\n    const anchor = ends.length\n      ? {\n          x: ends.reduce((s, p) => s + p.x, 0) / ends.length,\n          y: ends.reduce((s, p) => s + p.y, 0) / ends.length,\n        }\n      : top\n    // A chip goes on the stretch that is the route's own: among the nodes the\n    // fewest other routes share, the point farthest from the bubble's ends.\n    // Routes through a repeat array share most of their copies, and the far\n    // point of a shared copy would put every chip on one loop.\n    const sharing = new Map<string, number>()\n    for (const route of bubble.routes ?? []) {\n      for (const id of new Set(route.steps)) {\n        sharing.set(id, (sharing.get(id) ?? 0) + 1)\n      }\n    }\n    const routes: RouteLabel[] = []\n    for (const route of bubble.routes ?? []) {\n      if (bubble.longestAlleleLength < MIN_CHIPPED_BP) {\n        break\n      }\n      if (route.steps.length === 0) {\n        continue\n      }\n      const rarest = Math.min(...route.steps.map(id => sharing.get(id)!))\n      let at: NodeSegment | undefined\n      let far = -1\n      for (const id of route.steps) {\n        if (sharing.get(id) !== rarest) {\n          continue\n        }\n        for (const p of positions[id] ?? []) {\n          const d = Math.hypot(p.x - anchor.x, p.y - anchor.y)\n          if (d > far) {\n            far = d\n            at = p\n          }\n        }\n      }\n      if (at) {\n        routes.push({ route, at, text: routeText(route, walkLabel) })\n      }\n    }\n    halos.push({\n      bubble,\n      ...classifyBubble(bubble),\n      path: parts.join(''),\n      top,\n      members: nodeIds.length,\n      nodeIds,\n      whole: nodeIds.length >= WHOLE_FRACTION * graph.nodes.length,\n      routes,\n    })\n  }\n  return halos\n}\n\nfunction routeText(route: BubbleRoute, walkLabel: (name: string) => string) {\n  const names = [...new Set(route.walks.map(walkLabel))].sort()\n  const shown = names.slice(0, NAMED_WALKS).join(', ')\n  const more =\n    names.length > NAMED_WALKS ? ` +${names.length - NAMED_WALKS}` : ''\n  return `${shown}${more} \u00B7 ${formatBp(route.bp)}`\n}\n", "import { SATURATED_PATH_COUNT } from '../../MinigraphBubbleAdapter/bubbleLine'\nimport { isBackbone } from '../anchoredNodes'\nimport { referenceOrder } from '../layout/orderedLayout'\n\nimport type {\n  BubbleRoute,\n  MinigraphBubble,\n} from '../../MinigraphBubbleAdapter/bubbleLine'\nimport type { Graph, GraphNode } from '../types'\n\n// Bubbles from the graph alone, off the reference order the ordered layout is\n// also drawn from (referenceOrder): a backbone node no link reaches across is a\n// bubble boundary, and whatever sorts between two consecutive boundaries is a\n// bubble. Needs a reference, not an index, so it works on a GBZ cut, a pggb\n// file and the inside of a popped superbubble alike.\n//\n// Read off the order itself, not off the layers the drawing puts it in. A\n// layer is where a node is drawn, and one nothing leads into is drawn in the\n// first layer wherever it sorts. That is every node a walk enters the cut at,\n// the ordinary shape of a GBZ cut whose context stops short of a haplotype's\n// walk: its link into the backbone then crossed every layer between, and the\n// bubbles on either side of those boundaries fused into one.\n//\n// Route statistics come from the walks when the graph has paths (exact, and\n// immune to a repeat array whose copies the order cannot direct), and from a\n// DP over the ordered DAG otherwise. A reversed stretch comes out as one\n// bubble whose interior runs against the reference, not as an inversion flag.\n\ninterface Routes {\n  min: number\n  max: number\n  n: number\n}\n\nexport function bubblesFromGraph(graph: Graph): MinigraphBubble[] {\n  if (!graph.nodes.some(isBackbone)) {\n    return []\n  }\n  const byId = new Map(graph.nodes.map(n => [n.id, n]))\n  const order = referenceOrder(graph)\n  const indexOf = new Map(order.map((id, i) => [id, i]))\n  // how many links reach across each place in the order, as a running sum of\n  // where each one starts and stops\n  const reach = new Int32Array(order.length + 1)\n  // successors as a set: a repeat's back edge is the same DAG edge as its\n  // forward one, and counting it twice doubles every route through the copy\n  const succ = new Map<string, Set<string>>()\n  const linked = new Set<string>()\n  for (const e of graph.edges) {\n    const a = indexOf.get(e.from)\n    const b = indexOf.get(e.to)\n    if (a === undefined || b === undefined || a === b) {\n      continue\n    }\n    linked.add(`${e.from}>${e.to}`).add(`${e.to}>${e.from}`)\n    const [lo, hi] = a < b ? [a, b] : [b, a]\n    reach[lo + 1]!++\n    reach[hi]!--\n    const [from, to] = a < b ? [e.from, e.to] : [e.to, e.from]\n    ;(succ.get(from) ?? succ.set(from, new Set()).get(from)!).add(to)\n  }\n  for (let i = 1; i < reach.length; i++) {\n    reach[i]! += reach[i - 1]!\n  }\n  // Boundaries are nodes: every backbone node no link reaches across, plus the\n  // window's first and last backbone node whatever reaches across them, since a\n  // repeat array whose copies reach the last backbone node would otherwise\n  // never close.\n  const backbone = graph.nodes\n    .filter(isBackbone)\n    .sort((a, b) => a.stable.start - b.stable.start)\n  const ends = new Set([backbone[0]!.id, backbone.at(-1)!.id])\n  const boundaries = backbone\n    .map(node => [node, indexOf.get(node.id)!] as const)\n    .filter(([node, i]) => ends.has(node.id) || reach[i] === 0)\n    .sort(([a, ia], [b, ib]) => ia - ib || a.stable.start - b.stable.start)\n  const walkIndex = graph.paths?.map(p => {\n    const at = new Map<string, number>()\n    p.nodeIds.forEach((id, i) => {\n      if (!at.has(id)) {\n        at.set(id, i)\n      }\n    })\n    return at\n  })\n\n  const bubbles: MinigraphBubble[] = []\n  for (let i = 0; i + 1 < boundaries.length; i++) {\n    const [start, i0] = boundaries[i]!\n    const [end, i1] = boundaries[i + 1]!\n    const interior = order.slice(i0 + 1, i1)\n    if (interior.length === 0) {\n      continue\n    }\n\n    const best = new Map<string, Routes>([[start.id, { min: 0, max: 0, n: 1 }]])\n    for (const id of [start.id, ...interior]) {\n      const cur = best.get(id)\n      if (!cur) {\n        continue\n      }\n      for (const t of succ.get(id) ?? []) {\n        const ti = indexOf.get(t)!\n        if (ti > i1) {\n          continue\n        }\n        const add = t === end.id ? 0 : byId.get(t)!.length\n        const prev = best.get(t)\n        best.set(t, {\n          min: Math.min(prev?.min ?? Infinity, cur.min + add),\n          max: Math.max(prev?.max ?? -Infinity, cur.max + add),\n          n: Math.min(SATURATED_PATH_COUNT, cur.n + (prev?.n ?? 0)),\n        })\n      }\n    }\n    const walked =\n      walkIndex && walkRoutes(graph, byId, walkIndex, start.id, end.id)\n    const crossed = walked?.n ? walked : undefined\n    const routes = crossed ?? best.get(end.id) ?? { min: 0, max: 0, n: 0 }\n    // A walk that enters the bubble and never reaches its other end left the\n    // cut: a GBZ cut of a repeat array at 1 kb of context splits each\n    // haplotype's walk into pieces, and the routes seen are then a floor.\n    const walksLeave = walked !== undefined && walked.left > 0\n\n    const refStart = start.stable.start + start.length\n    const refEnd = end.stable.start\n    // The reference route exists in the cut only if every backbone pair inside\n    // is linked; a flank the hop reached from an allele is not.\n    const chain = [\n      start.id,\n      ...interior.filter(id => isBackbone(byId.get(id)!)),\n      end.id,\n    ]\n    const chainBroken = chain.some(\n      (id, k) => k > 0 && !linked.has(`${chain[k - 1]}>${id}`),\n    )\n    const partial = chainBroken || walksLeave\n    const fallback = chainBroken && !crossed\n    bubbles.push({\n      refName: start.stable.refName,\n      start: refStart,\n      end: refEnd,\n      segmentCount: interior.length + 2,\n      pathCount: routes.n,\n      // a real inversion test needs each walk's direction relative to the\n      // reference; the first visit's strand is just whichever path anchored the\n      // node\n      inversion: false,\n      shortestAlleleLength: fallback ? refEnd - refStart : routes.min,\n      longestAlleleLength: fallback ? refEnd - refStart : routes.max,\n      segments: [start, ...interior.map(id => byId.get(id)!), end]\n        .map(n => n.name)\n        .join(','),\n      shortestAllele: undefined,\n      longestAllele: undefined,\n      partial,\n      routes: crossed?.routes,\n    })\n  }\n  return bubbles\n}\n\n// For every walk that passes both boundary nodes, the bp between them and the\n// step sequence, so routes are distinct sequences and lengths are the true\n// haplotype lengths. `left` counts the walks that pass one boundary and end\n// before the other.\n//\n// `byId` is the caller's: this runs once per bubble, and a map of every node\n// built here made the whole pass quadratic, seven seconds at 15k nodes.\nfunction walkRoutes(\n  graph: Graph,\n  byId: Map<string, GraphNode>,\n  walkIndex: Map<string, number>[],\n  startId: string,\n  endId: string,\n): (Routes & { left: number; routes: BubbleRoute[] }) | undefined {\n  const seen = new Map<string, BubbleRoute>()\n  let min = Infinity\n  let max = -Infinity\n  let left = 0\n  graph.paths!.forEach((p, k) => {\n    const i0 = walkIndex[k]!.get(startId)\n    const i1 = walkIndex[k]!.get(endId)\n    if (i0 === undefined || i1 === undefined) {\n      if (i0 !== undefined || i1 !== undefined) {\n        left++\n      }\n      return\n    }\n    // Start to end, whichever way the walk crosses: a contig on the reverse\n    // strand takes the same route, and read end-first it keyed as a second one.\n    const steps = p.nodeIds.slice(Math.min(i0, i1) + 1, Math.max(i0, i1))\n    if (i1 < i0) {\n      steps.reverse()\n    }\n    let bp = 0\n    for (const id of steps) {\n      bp += byId.get(id)?.length ?? 0\n    }\n    const key = steps.join(',')\n    const route = seen.get(key) ?? { steps, bp, walks: [] }\n    route.walks.push(p.name)\n    seen.set(key, route)\n    min = Math.min(min, bp)\n    max = Math.max(max, bp)\n  })\n  return seen.size || left\n    ? { min, max, n: seen.size, left, routes: [...seen.values()] }\n    : undefined\n}\n", "import type { Graph } from '../types'\n\n// The graph inside one bubble: the segments the bubble row names, with the\n// links among them. The row's list includes the two backbone segments the\n// bubble hangs between, so the cut keeps its anchors and every layout that\n// needs a backbone still has one. A walk keeps the steps it takes inside the\n// bubble, so the bubbles derived inside it still read their routes and\n// lengths off the haplotypes, and carriage still sets node width.\nexport function bubbleSubgraph(graph: Graph, segmentIds: string[]): Graph {\n  const keep = new Set(segmentIds)\n  const nodes = graph.nodes.filter(n => keep.has(n.name))\n  const ids = new Set(nodes.map(n => n.id))\n  const paths = graph.paths\n    ?.map(p => ({ ...p, nodeIds: p.nodeIds.filter(id => ids.has(id)) }))\n    .filter(p => p.nodeIds.length > 0)\n  return {\n    name: graph.name,\n    nodes,\n    edges: graph.edges.filter(e => ids.has(e.from) && ids.has(e.to)),\n    ...(paths?.length ? { paths } : {}),\n    anchorPaths: graph.anchorPaths,\n    pathVisits: graph.pathVisits,\n    anchoredBy: graph.anchoredBy,\n    referencePath: graph.referencePath,\n  }\n}\n", "import type { Feature } from '@jbrowse/core/util'\n\n// A gene as the pins need it: its name, its span on the reference, and the\n// exons of all its transcripts merged into one set of intervals.\nexport interface GeneModel {\n  name: string\n  refName: string\n  start: number\n  end: number\n  strand: number\n  exons: { start: number; end: number }[]\n}\n\n// The adapters whose tracks hold gene models, in the order the session's\n// tracks are searched when no track is named.\nexport const GENE_ADAPTER_TYPES = new Set([\n  'Gff3TabixAdapter',\n  'Gff3Adapter',\n  'GtfTabixAdapter',\n  'GtfAdapter',\n  'BigBedAdapter',\n  'NCListAdapter',\n])\n\nconst GENE_TRACK_HINT = /gene|refseq|gencode|ensembl|annotation/i\n\n// Which of the session's tracks to read genes from: the named one, else the\n// first gene-bearing track on the assembly whose name says it is annotation,\n// else the first gene-bearing track at all.\nexport function pickGeneTrack<\n  T extends { trackId: string; name?: string; adapterType: string },\n>(tracks: T[], named: string) {\n  if (named) {\n    return tracks.find(t => t.trackId === named)\n  }\n  const candidates = tracks.filter(t => GENE_ADAPTER_TYPES.has(t.adapterType))\n  return (\n    candidates.find(t =>\n      GENE_TRACK_HINT.test(`${t.trackId} ${t.name ?? ''}`),\n    ) ?? candidates[0]\n  )\n}\n\ntype FeatureLike = Feature | Record<string, unknown>\n\nfunction field(f: FeatureLike, name: string): unknown {\n  return typeof (f as Feature).get === 'function'\n    ? (f as Feature).get(name)\n    : (f as Record<string, unknown>)[name]\n}\n\nfunction exonsOf(f: FeatureLike, into: { start: number; end: number }[]) {\n  const type = field(f, 'type')\n  if (type === 'exon') {\n    into.push({\n      start: field(f, 'start') as number,\n      end: field(f, 'end') as number,\n    })\n  }\n  const children = field(f, 'subfeatures') as FeatureLike[] | undefined\n  for (const child of children ?? []) {\n    exonsOf(child, into)\n  }\n}\n\nfunction merged(intervals: { start: number; end: number }[]) {\n  const sorted = [...intervals].sort((a, b) => a.start - b.start)\n  const out: { start: number; end: number }[] = []\n  for (const iv of sorted) {\n    const last = out.at(-1)\n    if (last && iv.start <= last.end) {\n      last.end = Math.max(last.end, iv.end)\n    } else {\n      out.push({ ...iv })\n    }\n  }\n  return out\n}\n\n// Genes from a track's features: every top-level feature, named by the first\n// of gene_name, name and id it carries, with the exons found anywhere under it\n// merged. A feature with no exons is one exon, its whole span.\nexport function geneModelsFrom(features: FeatureLike[]): GeneModel[] {\n  const genes: GeneModel[] = []\n  for (const f of features) {\n    const name =\n      (field(f, 'gene_name') as string | undefined) ??\n      (field(f, 'name') as string | undefined) ??\n      (field(f, 'id') as string | undefined)\n    const start = field(f, 'start') as number\n    const end = field(f, 'end') as number\n    if (!name || !(end > start)) {\n      continue\n    }\n    const exons: { start: number; end: number }[] = []\n    exonsOf(f, exons)\n    genes.push({\n      name,\n      refName: field(f, 'refName') as string,\n      start,\n      end,\n      strand: (field(f, 'strand') as number | undefined) ?? 0,\n      exons: exons.length ? merged(exons) : [{ start, end }],\n    })\n  }\n  return genes\n}\n", "import { firstNodeAtOrAfter, isBackbone } from '../anchoredNodes'\nimport { polylineSlice } from '../layout/mergeRuns'\nimport { svgPath } from '../util/geometry'\n\nimport type { GeneModel } from './geneFeatures'\nimport type { AnchoredNode } from '../anchoredNodes'\nimport type { Graph, NodeSegment } from '../types'\n\n// A gene drawn onto the graph: its exons as stretches of the backbone nodes\n// that carry them, in layout units, and one point on the backbone to pin its\n// name to. Only the backbone has coordinates, so an allele shows no exon even\n// where a haplotype's own annotation would put one.\nexport interface GenePin {\n  gene: GeneModel\n  // an SVG path of the exon stretches, in layout units\n  exons: string\n  // where the name goes: the backbone point at the gene's midpoint, or the\n  // nearest backbone point inside the gene where the midpoint is not in the cut\n  at: NodeSegment\n  // how much of the gene's span the cut's backbone covers, so a label can say\n  // when a gene runs off the cut\n  covered: number\n}\n\n// A backbone node names its sequence the way the graph does, `GRCh38#0#chr6`,\n// and a gene the way the assembly does, `chr6`; the contig is the part they\n// share.\nfunction contig(name: string) {\n  return name.split('#').at(-1)!\n}\n\n// The backbone of one contig in offset order, for finding the nodes a gene\n// lies over without reading the rest. `reach` is the longest node: a node over\n// a gene's start begins no further before it than that.\ninterface ContigBackbone {\n  nodes: AnchoredNode[]\n  reach: number\n}\n\nexport function genePins(\n  graph: Graph,\n  genes: GeneModel[],\n  positions: Record<string, NodeSegment[]>,\n): GenePin[] {\n  // Per contig and sorted once, so a gene reads the few nodes it lies over.\n  // Every gene used to read every backbone node, splitting both names each\n  // time, on each frame of a node drag: 199 ms for 100 genes over 15k nodes,\n  // now 12.\n  const byContig = new Map<string, ContigBackbone>()\n  const contigOf = new Map<string, string>()\n  for (const node of graph.nodes) {\n    if (isBackbone(node) && positions[node.id]?.length) {\n      const { refName } = node.stable\n      const name =\n        contigOf.get(refName) ??\n        contigOf.set(refName, contig(refName)).get(refName)!\n      const entry =\n        byContig.get(name) ??\n        byContig.set(name, { nodes: [], reach: 0 }).get(name)!\n      entry.nodes.push(node)\n      entry.reach = Math.max(entry.reach, node.length)\n    }\n  }\n  for (const { nodes } of byContig.values()) {\n    nodes.sort((a, b) => a.stable.start - b.stable.start)\n  }\n  const pins: GenePin[] = []\n  for (const gene of genes) {\n    const backbone = byContig.get(contig(gene.refName))\n    if (!backbone) {\n      continue\n    }\n    const parts: string[] = []\n    let at: NodeSegment | undefined\n    let atDistance = Infinity\n    let covered = 0\n    const mid = (gene.start + gene.end) / 2\n    const { nodes, reach } = backbone\n    for (\n      let i = firstNodeAtOrAfter(nodes, gene.start - reach);\n      i < nodes.length && nodes[i]!.stable.start < gene.end;\n      i++\n    ) {\n      const node = nodes[i]!\n      const nodeStart = node.stable.start\n      const nodeEnd = nodeStart + node.length\n      if (nodeEnd <= gene.start) {\n        continue\n      }\n      const line = positions[node.id]!\n      covered += Math.min(nodeEnd, gene.end) - Math.max(nodeStart, gene.start)\n      for (const exon of gene.exons) {\n        const a = Math.max(exon.start, nodeStart)\n        const b = Math.min(exon.end, nodeEnd)\n        if (b <= a) {\n          continue\n        }\n        const stretch = polylineSlice(\n          line,\n          (a - nodeStart) / node.length,\n          (b - nodeStart) / node.length,\n        )\n        if (stretch.length === 1) {\n          stretch.push({ ...stretch[0]! })\n        }\n        parts.push(svgPath(stretch))\n      }\n      const pinBp = Math.min(Math.max(mid, nodeStart), nodeEnd)\n      const distance = Math.abs(pinBp - mid)\n      if (distance < atDistance) {\n        atDistance = distance\n        const [p] = polylineSlice(\n          line,\n          (pinBp - nodeStart) / node.length,\n          (pinBp - nodeStart) / node.length,\n        )\n        at = p\n      }\n    }\n    if (at) {\n      pins.push({\n        gene,\n        exons: parts.join(''),\n        at,\n        covered: covered / (gene.end - gene.start),\n      })\n    }\n  }\n  return pins\n}\n", "// Minimal GFA (Graphical Fragment Assembly) text parser shared by the graph\n// pangenome plugins (GraphGenomeView, TubeMapView). Handles GFA1/GFA2 segment,\n// link, edge, path and walk records plus header tags.\n\n// Only the first two colons delimit a tag; everything after them is the value.\n// A Z value may contain colons of its own, and rGFA stable names routinely do\n// (`SN:Z:chr1:1-1000` from a sliced reference), where splitting on every colon\n// silently truncates the name to `chr1` and mis-anchors the whole layout.\nfunction parseTag(tag: string, tags: Record<string, string | number>) {\n  const nameEnd = tag.indexOf(':')\n  const typeEnd = tag.indexOf(':', nameEnd + 1)\n  if (nameEnd !== -1 && typeEnd !== -1) {\n    const name = tag.slice(0, nameEnd)\n    const type = tag.slice(nameEnd + 1, typeEnd)\n    const val = tag.slice(typeEnd + 1)\n    if (type === 'i' || type === 'f') {\n      tags[name] = +val\n    } else if (type === 'Z') {\n      tags[name] = val\n    }\n  }\n}\n\nfunction parseTags(fields: string[]) {\n  const tags: Record<string, string | number> = {}\n  for (const field of fields) {\n    parseTag(field, tags)\n  }\n  return tags\n}\n\nexport interface GFANode {\n  id: string\n  length: number\n  sequence: string\n  tags: Record<string, string | number>\n}\n\n// rGFA (minigraph) anchors every segment to a reference coordinate: SN is the\n// stable sequence name, SO the offset on it, and SR the stable rank, where 0 is\n// the reference backbone and higher ranks are the sequence that diverges from\n// it. Plain GFA (pggb, odgi, Minigraph-Cactus) carries none of these, which is\n// why coordinates there exist only inside the P/W lines.\nexport interface StableCoordinate {\n  refName: string\n  start: number\n  rank: number\n  // How the anchoring path reads this segment. Only path-derived coordinates\n  // set it: an rGFA segment is by construction forward on the sequence SN\n  // names, so there is nothing there for it to say.\n  strand?: '+' | '-'\n}\n\nexport function stableCoordinate(node: GFANode): StableCoordinate | undefined {\n  const { SN, SO, SR } = node.tags\n  return typeof SN === 'string' &&\n    typeof SO === 'number' &&\n    typeof SR === 'number'\n    ? { refName: SN, start: SO, rank: SR }\n    : undefined\n}\n\nexport interface GFALink {\n  source: string\n  target: string\n  strand1?: string\n  strand2?: string\n  cigar: string\n  tags: Record<string, string | number>\n}\n\nexport interface GFAPath {\n  name: string\n  path: string\n  rest: string[]\n}\n\nexport interface GFAWalkSegment {\n  id: string\n  strand: string\n}\n\nexport interface GFAWalk {\n  sample: string\n  haplotype: number\n  contig: string\n  start: number\n  end: number\n  segments: GFAWalkSegment[]\n  tags: Record<string, string | number>\n}\n\nconst GT = 62 // '>'\nconst LT = 60 // '<'\n\n// A W record's body is `>s1<s2>s3\u2026`, and on a Minigraph-Cactus graph one record\n// is the whole walk of one haplotype across a chromosome \u2014 hundreds of\n// thousands of steps in a single field.\n//\n// So the ids are cut out by index rather than accumulated a character at a\n// time. `current += ch` builds and discards one string per character of every\n// id, and it dominated the parse: a file whose single W record walks 200k steps\n// went from ~55 ms to ~24 ms by slicing instead. `pnpm bench` keeps the number.\nfunction parseWalkBody(body: string) {\n  const segments: GFAWalkSegment[] = []\n  let strand = '+'\n  let start = 0\n  // An empty run \u2014 a leading delimiter, or two in a row \u2014 names no segment.\n  function push(end: number) {\n    if (end > start) {\n      segments.push({ id: body.slice(start, end), strand })\n    }\n  }\n  for (let i = 0; i < body.length; i++) {\n    const ch = body.charCodeAt(i)\n    if (ch === GT || ch === LT) {\n      push(i)\n      strand = ch === GT ? '+' : '-'\n      start = i + 1\n    }\n  }\n  push(body.length)\n  return segments\n}\n\nexport interface GFAGraph {\n  nodes: GFANode[]\n  links: GFALink[]\n  paths: GFAPath[]\n  walks: GFAWalk[]\n  header: Record<string, string | number>[]\n  id: string\n}\n\nexport function parseGFA(file: string) {\n  const graph: GFAGraph = {\n    nodes: [],\n    links: [],\n    paths: [],\n    walks: [],\n    header: [],\n    id: '',\n  }\n\n  // \\r is stripped rather than split on, so a CRLF file does not leave it on\n  // whichever field happens to be last: a trailing Z tag would carry it into a\n  // stable name and a trailing cigar into the CIGAR string.\n  //\n  // Stripped per line inside the loop rather than with a .map() over the split,\n  // which would hold a second copy of every line in the file at once.\n  for (const rawLine of file.split('\\n')) {\n    const line = rawLine.endsWith('\\r') ? rawLine.slice(0, -1) : rawLine\n    if (line.startsWith('H')) {\n      const [, ...rest] = line.split('\\t')\n      graph.header.push(parseTags(rest))\n    } else if (line.startsWith('S')) {\n      const [, name, ...rest] = line.split('\\t')\n      let len: number\n      let seq: string\n      let tagfields: string[]\n      let gfa1 = false\n      // A truncated record has no field to read; `*` is what the spec writes for\n      // a segment whose sequence is absent, so treating a missing one the same\n      // way yields a 0 bp segment instead of throwing partway through the file.\n      const first = rest[0] ?? '*'\n      // GFA2 puts an integer length in this field, GFA1 the sequence. Testing\n      // the digits rather than the coerced number keeps a GFA2 `S sid 0 *` from\n      // being read as a GFA1 sequence of \"0\".\n      if (/^\\d+$/.test(first)) {\n        len = +first\n        seq = rest[1] ?? '*'\n        tagfields = rest.slice(2)\n      } else {\n        gfa1 = true\n        seq = first\n        // `*` is GFA1's \"no sequence here\"; its length is whatever LN says\n        // below, and 0 if the file states none. Counting the placeholder's own\n        // character instead reports every such segment as 1 bp.\n        len = seq === '*' ? 0 : seq.length\n        tagfields = rest.slice(1)\n      }\n      const tags = parseTags(tagfields)\n      if (gfa1 && 'LN' in tags) {\n        len = +tags.LN\n      }\n      graph.nodes.push({ id: name!, length: len, sequence: seq, tags })\n    } else if (line.startsWith('E')) {\n      // From here down, a record cut off before the fields that make it a\n      // link, walk or path states nothing drawable and is dropped; the file\n      // around it still reads. A link missing only its overlap is kept.\n      const [, , source, target, , , , , cigar, ...rest] = line.split('\\t')\n      if (source && target) {\n        graph.links.push({\n          source: source.slice(0, -1),\n          target: target.slice(0, -1),\n          strand1: source.at(-1),\n          strand2: target.at(-1),\n          cigar: cigar ?? '*',\n          tags: parseTags(rest),\n        })\n      }\n    } else if (line.startsWith('L')) {\n      const [, source, strand1, target, strand2, cigar, ...rest] =\n        line.split('\\t')\n      if (source && target && strand2) {\n        graph.links.push({\n          source,\n          target,\n          strand1,\n          strand2,\n          cigar: cigar ?? '*',\n          tags: parseTags(rest),\n        })\n      }\n    } else if (line.startsWith('W')) {\n      const [, sample, hap, contig, start, end, body, ...rest] =\n        line.split('\\t')\n      if (sample && hap && contig && start && end && body) {\n        graph.walks.push({\n          sample,\n          haplotype: +hap,\n          contig,\n          start: start === '*' ? -1 : +start,\n          end: end === '*' ? -1 : +end,\n          segments: parseWalkBody(body),\n          tags: parseTags(rest),\n        })\n      }\n    } else if (line.startsWith('P')) {\n      const [, name, path, ...rest] = line.split('\\t')\n      if (name && path) {\n        graph.paths.push({ name, path, rest })\n      }\n    }\n  }\n  return graph\n}\n", "import { stableCoordinate } from '../../gfa-core/index'\nimport { pathOrigin, surveyPaths } from '../pathAnchoring'\n\nimport type { GFAGraph, GFANode } from '../../gfa-core/index'\nimport type { PathSteps } from '../pathAnchoring'\nimport type { Graph, GraphEdge, GraphNode, GraphPath } from '../types'\n\n// Single pass over every reference a GFA makes to a segment, collecting the two\n// things the drawn graph needs from them.\n//\n// `canonical` is the one orientation each segment is drawn in, which is what\n// Bandage calls single-node mode. A segment is the same sequence read either\n// way (`L 1 + 2 +` is the same edge as `L 2 - 1 -`), so `1+` and `1-` are one\n// node, not two: drawing both doubles every segment, and since the L lines only\n// wire one of the pair, the other copy has no edges at all and scatters loose\n// across the layout. Links carry the topology, so their orientation wins; a\n// segment only paths mention takes the orientation they walk it in.\n//\n// `traversals` is how many paths cross each segment. Assembly GFAs carry read\n// depth in a dp/RC/FC/KC tag, but a pangenome GFA (odgi, vg) carries none \u2014\n// there the meaningful depth is how many samples go through the segment, i.e.\n// core versus accessory sequence.\nfunction surveySegments(gfaGraph: GFAGraph) {\n  const canonical = new Map<string, '+' | '-'>()\n  const traversals = new Map<string, number>()\n  function claim(id: string, strand: '+' | '-') {\n    if (!canonical.has(id)) {\n      canonical.set(id, strand)\n    }\n  }\n  function traverse(id: string, strand: '+' | '-') {\n    claim(id, strand)\n    traversals.set(id, (traversals.get(id) ?? 0) + 1)\n  }\n  for (const link of gfaGraph.links) {\n    claim(link.source, link.strand1 === '-' ? '-' : '+')\n    claim(link.target, link.strand2 === '-' ? '-' : '+')\n  }\n  for (const gfaPath of gfaGraph.paths) {\n    for (const segment of gfaPath.path.split(',')) {\n      traverse(segment.slice(0, -1), segment.endsWith('-') ? '-' : '+')\n    }\n  }\n  for (const walk of gfaGraph.walks) {\n    for (const seg of walk.segments) {\n      traverse(seg.id, seg.strand === '-' ? '-' : '+')\n    }\n  }\n  return { canonical, traversals }\n}\n\n// P and W state the same thing in different shapes: a P body is a comma-joined\n// `<id><strand>` list whose start offset lives in the record's *name*, a W\n// record arrives already split into steps and states its start as a field.\n// Normalized here so the coordinate walk sees one kind of path.\nfunction anchorablePaths(gfaGraph: GFAGraph): PathSteps[] {\n  return [\n    ...gfaGraph.paths.map(p => ({\n      ...pathOrigin(p.name),\n      steps: p.path.split(',').map(segment => ({\n        id: segment.slice(0, -1),\n        strand: segment.endsWith('-') ? ('-' as const) : ('+' as const),\n      })),\n    })),\n    ...gfaGraph.walks.map(w => ({\n      name: `${w.sample}#${w.haplotype}#${w.contig}`,\n      // `*` parses to -1, meaning the record declines to say; 0 is then the\n      // only offset that can be assumed, and it makes the walk self-relative\n      // rather than wrong\n      start: w.start === -1 ? 0 : w.start,\n      steps: w.segments.map(s => ({\n        id: s.id,\n        strand: s.strand === '-' ? ('-' as const) : ('+' as const),\n      })),\n    })),\n  ]\n}\n\n// Carriage stated as a tag rather than derived from a walk. `RgfaTabixAdapter`\n// synthesizes its S-lines from a segs.bed whose sixth column is a list of GFA\n// tags, and `scripts/pggb_gfa_to_bed.py` in jbrowse-components puts every\n// haplotype that visits a segment there as `SM:Z:K12.1,Sakai.1`. That is the\n// only way carriage reaches an INDEXED graph: the cut has no P or W lines to\n// walk, so `pathAnchoring` has no visits to derive it from.\n//\n// It does not compete with that walk. `pathAnchoring.anchorNode` rebuilds\n// `samples` from the visits whenever there are any, so a graph loaded as a file\n// keeps the authoritative path-derived set and this is what a tabix cut falls\n// back to.\nfunction carriedSamples(gfaNode: GFANode) {\n  const sm = gfaNode.tags.SM\n  if (typeof sm !== 'string') {\n    return undefined\n  }\n  const samples = sm\n    .split(',')\n    .map(s => s.trim())\n    .filter(Boolean)\n  return samples.length > 0 ? samples : undefined\n}\n\nconst positive = (v: unknown) =>\n  typeof v === 'number' && v > 0 ? v : undefined\n\n// The depth a segment states, or undefined. DP is a depth in either case it is\n// written. RC, FC and KC are read, fragment and k-mer counts, so depth is the\n// count over the length: taken raw, a 100 kb node at 5x outweighed a 1 kb node\n// at 50x tenfold in every width drawn from it.\nfunction statedDepth({ tags, length }: GFANode) {\n  const count = positive(tags.RC) ?? positive(tags.FC) ?? positive(tags.KC)\n  return (\n    positive(tags.dp) ??\n    positive(tags.DP) ??\n    (count !== undefined && length > 0 ? count / length : undefined)\n  )\n}\n\nfunction makeNode(\n  gfaNode: GFANode,\n  strand: '+' | '-',\n  depth: number,\n): GraphNode {\n  return {\n    id: `${gfaNode.id}${strand}`,\n    name: gfaNode.id,\n    length: gfaNode.length,\n    depth,\n    stable: stableCoordinate(gfaNode),\n    samples: carriedSamples(gfaNode),\n  }\n}\n\nexport function convertGFAToGraph(gfaGraph: GFAGraph, name = 'Imported GFA') {\n  const nodes: GraphNode[] = []\n  const edges: GraphEdge[] = []\n\n  const { canonical, traversals } = surveySegments(gfaGraph)\n  // segments no link, path, or walk mentions are drawn forward-strand\n  const nodeId = (segmentId: string) =>\n    `${segmentId}${canonical.get(segmentId) ?? '+'}`\n\n  for (const gfaNode of gfaGraph.nodes) {\n    const depth =\n      statedDepth(gfaNode) ?? Math.max(traversals.get(gfaNode.id) ?? 1, 1)\n    nodes.push(makeNode(gfaNode, canonical.get(gfaNode.id) ?? '+', depth))\n  }\n\n  for (const link of gfaGraph.links) {\n    edges.push({\n      from: nodeId(link.source),\n      to: nodeId(link.target),\n      fromStrand: link.strand1 === '-' ? '-' : '+',\n      toStrand: link.strand2 === '-' ? '-' : '+',\n    })\n  }\n\n  const paths: GraphPath[] = []\n  const edgeToPathsMap = new Map<string, Set<string>>()\n\n  // A path that walks the graph on the reverse strand visits an edge's nodes in\n  // the opposite order to the L line that declared it, so the key is unordered.\n  const edgeKey = (a: string, b: string) => [a, b].sort().join('--')\n\n  function recordPathEdges(nodeIds: string[], name: string) {\n    for (let i = 0; i < nodeIds.length - 1; i++) {\n      const key = edgeKey(nodeIds[i]!, nodeIds[i + 1]!)\n      if (!edgeToPathsMap.has(key)) {\n        edgeToPathsMap.set(key, new Set())\n      }\n      edgeToPathsMap.get(key)!.add(name)\n    }\n  }\n\n  for (const gfaPath of gfaGraph.paths) {\n    // path segments arrive as `<id><strand>`; the node they land on is the\n    // segment's canonical orientation, whichever way this path reads it\n    const nodeIds = gfaPath.path\n      .split(',')\n      .map(segment => nodeId(segment.slice(0, -1)))\n    paths.push({ name: gfaPath.name, nodeIds } satisfies GraphPath)\n    recordPathEdges(nodeIds, gfaPath.name)\n  }\n\n  for (const walk of gfaGraph.walks) {\n    const nodeIds = walk.segments.map(seg => nodeId(seg.id))\n    // The full PanSN name, contig included, which is also what `anchorablePaths`\n    // above calls the same record. Dropping the contig made a path's name an\n    // ASSEMBLY's name, and one assembly walks one W record per contig: two walks\n    // of `HG00438#1` then shared an identity, so `edgeToPathsMap` merged them,\n    // `pathColors` (keyed by name) kept only the last colour written while the\n    // node stripes kept the first, and the key drew one haplotype twice in two\n    // colours. That is the ordinary Minigraph-Cactus shape, not a corner case.\n    //\n    // The legend narrows it back: `labelTiers` tries sample, then sample and\n    // haplotype, then the whole name, so a graph with one contig per haplotype\n    // is labelled exactly as before and only a colliding one widens.\n    const name = `${walk.sample}#${walk.haplotype}#${walk.contig}`\n    paths.push({\n      name,\n      nodeIds,\n      sample: walk.sample,\n      haplotype: walk.haplotype,\n      contig: walk.contig,\n    } satisfies GraphPath)\n    recordPathEdges(nodeIds, name)\n  }\n\n  for (const edge of edges) {\n    const pathIds = edgeToPathsMap.get(edgeKey(edge.from, edge.to))\n    if (pathIds && pathIds.size > 0) {\n      edge.pathIds = [...pathIds]\n    }\n  }\n\n  // Only walked when the file has paths to walk, so an rGFA \u2014 which has none at\n  // all \u2014 pays nothing for it. `lengthOf` reads the segment table rather than\n  // the nodes just built, because a path may name a segment no S line declared.\n  const lengths = new Map(gfaGraph.nodes.map(n => [n.id, n.length]))\n  const anchoring =\n    gfaGraph.paths.length > 0 || gfaGraph.walks.length > 0\n      ? surveyPaths(anchorablePaths(gfaGraph), id => lengths.get(id) ?? 0)\n      : undefined\n\n  return {\n    name,\n    nodes,\n    edges,\n    paths: paths.length > 0 ? paths : undefined,\n    anchorPaths: anchoring?.anchorPaths,\n    pathVisits: anchoring?.pathVisits,\n    // rGFA's own tags win wherever they are present; pathAnchoring only ever\n    // fills in for a graph that carries none.\n    anchoredBy: nodes.some(n => n.stable) ? 'tags' : undefined,\n  } satisfies Graph\n}\n", "import type { SubgraphRegion } from '../launchSubgraph/launchSubgraphView'\n\n// The members of a LinearGenomeView a hosted pane reads and drives.\n// Structural, because this plugin takes no runtime dependency on the LGV\n// plugin (see hoverSync/index.tsx).\nexport interface HostBlock {\n  refName: string\n  assemblyName: string\n  start: number\n  end: number\n  offsetPx: number\n  reversed?: boolean\n  displayedRegionIndex?: number\n}\n\nexport interface LinearHost {\n  id: string\n  initialized: boolean\n  bpPerPx: number\n  offsetPx: number\n  width: number\n  displayedRegions: readonly { start: number; end: number }[]\n  dynamicBlocks: { contentBlocks: readonly HostBlock[] }\n  coarseDynamicBlocks: readonly HostBlock[]\n  horizontalScroll: (distance: number) => number\n  zoomTo: (bpPerPx: number, offset?: number) => number\n}\n\nexport function isLinearHost(view: unknown): view is LinearHost {\n  if (typeof view !== 'object' || view === null) {\n    return false\n  }\n  const v = view as Record<string, unknown>\n  return (\n    typeof v.horizontalScroll === 'function' &&\n    typeof v.zoomTo === 'function' &&\n    'coarseDynamicBlocks' in v &&\n    'dynamicBlocks' in v\n  )\n}\n\n// launchSubgraphView's widestBlock, restated rather than imported: that module\n// imports the model, which imports this.\nfunction widest(blocks: readonly HostBlock[]) {\n  return blocks.reduce<HostBlock | undefined>(\n    (best, b) => (best && best.end - best.start >= b.end - b.start ? best : b),\n    undefined,\n  )\n}\n\nexport interface HostWindow {\n  refName: string\n  assemblyName: string\n  start: number\n  end: number\n  bpPerPx: number\n  // the view's width in bp, which the margin is sized by: a block at a contig\n  // end is clipped, the zoom is not\n  span: number\n  regionStart: number\n  regionEnd: number\n}\n\n// x is reference bp on an anchored layout, so the graph shows what the linear\n// view shows when one bp is as many px in both and the cut's refName sits at\n// the same screen x. Undefined when the linear view shows no block of that\n// refName, which is a re-cut's job rather than the frame's.\nexport function hostFrame(view: LinearHost, region: SubgraphRegion) {\n  const block = widest(\n    view.dynamicBlocks.contentBlocks.filter(\n      b =>\n        b.refName === region.refName && b.assemblyName === region.assemblyName,\n    ),\n  )\n  const { bpPerPx } = view\n  return block && bpPerPx > 0\n    ? {\n        scale: 1 / bpPerPx,\n        translateX: block.offsetPx - view.offsetPx - block.start / bpPerPx,\n      }\n    : undefined\n}\n\n// Read off the LIVE blocks even when the coarse ones woke the caller: those\n// name where the window was half a second ago (SyntenyFollow/CLAUDE.md).\nexport function hostWindow(view: LinearHost): HostWindow | undefined {\n  const block = widest(view.dynamicBlocks.contentBlocks)\n  const displayed =\n    block?.displayedRegionIndex === undefined\n      ? undefined\n      : view.displayedRegions[block.displayedRegionIndex]\n  return block && view.bpPerPx > 0\n    ? {\n        refName: block.refName,\n        assemblyName: block.assemblyName,\n        start: block.start,\n        end: block.end,\n        bpPerPx: view.bpPerPx,\n        span: view.bpPerPx * view.width,\n        regionStart: displayed?.start ?? block.start,\n        regionEnd: displayed?.end ?? block.end,\n      }\n    : undefined\n}\n\n// The window plus one window-width each side, clamped to the displayed\n// region, with the margins narrowed until the whole cut fits under `capBp`.\nexport function hostCut(window: HostWindow, capBp: number): SubgraphRegion {\n  const visible = window.end - window.start\n  const margin = Math.max(0, Math.min(window.span, (capBp - visible) / 2))\n  return {\n    refName: window.refName,\n    assemblyName: window.assemblyName,\n    start: Math.max(window.regionStart, Math.floor(window.start - margin)),\n    end: Math.min(window.regionEnd, Math.ceil(window.end + margin)),\n  }\n}\n\nexport function cutHolds(cut: SubgraphRegion | undefined, window: HostWindow) {\n  return (\n    cut?.refName === window.refName &&\n    cut.assemblyName === window.assemblyName &&\n    cut.start <= window.start &&\n    window.end <= cut.end\n  )\n}\n", "import { setConf } from '@jbrowse/core/configuration'\nimport { getSnapshot } from '@jbrowse/mobx-state-tree'\n\nimport type { AnyConfigurationModel } from '@jbrowse/core/configuration'\n\n// The graph's own off-ramp charcoal, for a segment with no reference\n// coordinate (GeometryBuilder's REFERENCE_RAMP_ALT_COLOR).\nexport const OFF_REFERENCE_COLOR = 'rgb(60,65,72)'\n\n// The reference-position ramp as a `color` expression a linear track can run:\n// hue 0 to 300 over the domain by the feature's reference midpoint, the same\n// function of the same two numbers the graph paints its nodes with. `rank` is\n// what RgfaTabixAdapter puts on a feature; a track carrying none reads\n// `undefined > 0` as false and stays on the ramp.\nexport function referencePositionColor({\n  start,\n  end,\n}: {\n  start: number\n  end: number\n}) {\n  const mid = \"(get(feature,'start')+get(feature,'end'))/2\"\n  const hue = `min(300, max(0, (${mid} - ${start}) / ${end - start} * 300))`\n  return `jexl:get(feature,'rank')>0 ? '${OFF_REFERENCE_COLOR}' : 'hsl(' + ${hue} + ',70%,50%)'`\n}\n\nexport interface LaneDisplay {\n  type: string\n  configuration: AnyConfigurationModel\n}\n\ninterface LaneTrack {\n  configuration: { trackId: string }\n  displays: LaneDisplay[]\n}\n\ninterface LaneView {\n  id: string\n  tracks?: LaneTrack[]\n}\n\nfunction isLaneView(view: unknown): view is LaneView {\n  return (\n    typeof view === 'object' &&\n    view !== null &&\n    'id' in view &&\n    Array.isArray((view as { tracks?: unknown }).tracks)\n  )\n}\n\n// The display a graph was cut from: the track by id in the linear view it is\n// paired with, or in any linear view holding it when the graph was never\n// paired (a hand-written session), the same rule the hover sync uses.\nexport function sourceLaneDisplay(\n  views: unknown[],\n  connectedViewId: string | undefined,\n  trackId: string,\n) {\n  for (const view of views) {\n    if (\n      isLaneView(view) &&\n      (connectedViewId === undefined || view.id === connectedViewId)\n    ) {\n      const track = view.tracks?.find(t => t.configuration.trackId === trackId)\n      const display = track?.displays[0]\n      if (display?.type === 'LinearBasicDisplay') {\n        return display\n      }\n    }\n  }\n  return undefined\n}\n\n// Idempotent, since the autorun that calls this re-fires on every domain read.\n// A host at 5.0.0-beta.9 or later keeps `color` as a channel object whose\n// `value` holds the expression; earlier hosts keep the bare string.\nexport function paintSourceLane(display: LaneDisplay, color: string) {\n  const { color: current } = getSnapshot(display.configuration) as {\n    color?: unknown\n  }\n  const painted =\n    typeof current === 'object' && current !== null && 'value' in current\n      ? current.value\n      : current\n  if (painted !== color) {\n    setConf(display, 'color', color)\n  }\n}\n", "import { isBackbone } from '../anchoredNodes'\n\nimport type { Graph, NodeSegment } from '../types'\n\ntype Positions = Record<string, NodeSegment[]>\n\n// Turn a finished force layout so the reference runs left to right: the\n// rotation that best maps backbone midpoints onto their reference coordinate\n// (a one-dimensional orthogonal Procrustes fit, weighted by segment length),\n// then a reflection so the off-reference mass sits below the axis. A rigid\n// transform, so the drawing FMMM made is unchanged; only its frame moves.\n//\n// About the length-weighted centroid, and translated back, so a drawing that is\n// already oriented comes back where it was rather than recentred on the origin.\nexport function orientToReference(graph: Graph, positions: Positions) {\n  const backbone = graph.nodes.filter(\n    node => isBackbone(node) && (positions[node.id]?.length ?? 0) > 0,\n  )\n  if (backbone.length < 2) {\n    return positions\n  }\n  const points = backbone.map(node => {\n    const segments = positions[node.id]!\n    const mid = segments[Math.floor(segments.length / 2)]!\n    return {\n      x: mid.x,\n      y: mid.y,\n      r: node.stable!.start + node.length / 2,\n      w: node.length,\n    }\n  })\n  const weight = points.reduce((sum, p) => sum + p.w, 0)\n  const cx = points.reduce((sum, p) => sum + p.x * p.w, 0) / weight\n  const cy = points.reduce((sum, p) => sum + p.y * p.w, 0) / weight\n  const cr = points.reduce((sum, p) => sum + p.r * p.w, 0) / weight\n  // cross-covariance of (x, y) against (r, 0); only the first row is non-zero\n  let sxr = 0\n  let syr = 0\n  for (const p of points) {\n    sxr += p.w * (p.x - cx) * (p.r - cr)\n    syr += p.w * (p.y - cy) * (p.r - cr)\n  }\n  // the rotation taking the direction (sxr, syr) onto +x\n  const angle = -Math.atan2(syr, sxr)\n  const c = Math.cos(angle)\n  const s = Math.sin(angle)\n\n  const out: Positions = {}\n  for (const [id, segments] of Object.entries(positions)) {\n    out[id] = segments.map(p => {\n      const x = p.x - cx\n      const y = p.y - cy\n      return { x: cx + c * x - s * y, y: cy + s * x + c * y }\n    })\n  }\n\n  let below = 0\n  let above = 0\n  for (const node of graph.nodes) {\n    if (isBackbone(node)) {\n      continue\n    }\n    for (const p of out[node.id] ?? []) {\n      if (p.y > cy) {\n        below++\n      } else {\n        above++\n      }\n    }\n  }\n  if (above > below) {\n    for (const segments of Object.values(out)) {\n      for (const p of segments) {\n        p.y = 2 * cy - p.y\n      }\n    }\n  }\n  return out\n}\n", "import { isBackbone } from '../anchoredNodes'\nimport { buildNeighbors } from '../referenceSpan'\nimport { drawnNodeLength } from './drawnScale'\n\nimport type { LayoutScaling } from './drawnScale'\nimport type { Graph, GraphNode } from '../types'\n\n// A node as the engine takes it: an optional `x`/`y` is where FMMM starts the\n// node's chain (`addToOgdfGraph`, graphlayout.cpp).\nexport type LayoutNode = GraphNode & { x?: number; y?: number }\n\nexport interface Seed {\n  x: number\n  y: number\n}\n\n// y per BFS step off the backbone. FMMM keeps only the coarse shape of these\n// (OGDF applies the initial placement at its coarsest multilevel graph), so\n// the gap needs to say \"below the line\", not to place a lane.\nconst LANE_GAP = 30\n\n// Initial positions for a reference-anchored graph: the backbone end to end\n// along x at drawn length, each off-reference node at the midpoint of the node\n// a BFS from the backbone reached it from, a lane lower per step. Two alleles\n// off one anchor share a seed; FMMM separates them. Nodes no backbone reaches\n// spread along x below everything rather than piling on one point.\n//\n// Lengths come from `scaling.nodes`, not the graph's bp: under a compressing\n// spread a node's `length` crosses the RPC as drawn units times 1000 with a\n// matching `nodeLengthPerMegabase`, and a seed from bp would misplace every\n// chain against the one the engine builds.\nexport function referenceSeeds(\n  graph: Graph,\n  scaling: LayoutScaling,\n): Map<string, Seed> {\n  const { opts } = scaling\n  const drawn = new Map(\n    scaling.nodes.map(node => [node.id, drawnNodeLength(opts, node.length)]),\n  )\n  const drawnOf = (id: string) => drawn.get(id) ?? opts.minimumNodeLength\n  const backbone = graph.nodes\n    .filter(isBackbone)\n    .sort((a, b) => a.stable.start - b.stable.start)\n\n  const seeds = new Map<string, Seed>()\n  let x = 0\n  for (const node of backbone) {\n    seeds.set(node.id, { x, y: 0 })\n    x += drawnOf(node.id) + opts.edgeLength\n  }\n\n  const adjacent = buildNeighbors(graph)\n\n  const depth = new Map(backbone.map(node => [node.id, 0]))\n  // for-of over an array that grows as it goes: the iterator reads the live\n  // length, so nodes pushed here are visited\n  const queue = backbone.map(node => node.id)\n  for (const id of queue) {\n    const at = seeds.get(id)!\n    const next = depth.get(id)! + 1\n    for (const neighbour of adjacent.get(id) ?? []) {\n      if (depth.has(neighbour)) {\n        continue\n      }\n      depth.set(neighbour, next)\n      seeds.set(neighbour, { x: at.x + drawnOf(id) / 2, y: LANE_GAP * next })\n      queue.push(neighbour)\n    }\n  }\n\n  let unreached = 0\n  for (const node of graph.nodes) {\n    if (!seeds.has(node.id)) {\n      seeds.set(node.id, {\n        x: (unreached++ * x) / graph.nodes.length,\n        y: LANE_GAP * 3,\n      })\n    }\n  }\n  return seeds\n}\n\nexport function seededNodes(\n  graph: Graph,\n  scaling: LayoutScaling,\n): LayoutNode[] {\n  const seeds = referenceSeeds(graph, scaling)\n  return scaling.nodes.map(node => ({ ...node, ...seeds.get(node.id) }))\n}\n", "import type { Feature } from '@jbrowse/core/util'\n\nexport interface RepeatCall {\n  bp: number\n  // TRGT's `SD`. Zero means the allele is a copy of the one the reads did\n  // support, so its length states nothing about a second haplotype; absent\n  // where the genotyper writes no such field.\n  spanningReads?: number\n}\n\n// A tandem repeat array as the walk rows need it: its span on the reference,\n// which is what the bars measure between, and its unit length, which is what\n// they tile by. Read off whatever repeat annotation the session has, since the\n// tools all state the same two facts under different names: VCF 4.5's\n// `<CNV:TR>` allele gives `RUL` and `RUS` (one entry per repeat sequence,\n// grouped by `RN`), UCSC simpleRepeat and TRF give `period` and the consensus\n// `sequence`, TRGT gives `MOTIFS` and `TRID`, ExpansionHunter `RU` and `REPID`,\n// HipSTR and GangSTR `PERIOD`, vamos its `motifs`. A VCF record's INFO is\n// searched as well as its top level, and a list's first entry is the unit the\n// bars tile by: for a compound array that is the first repeat sequence, which\n// is the expanding one at every such locus in the common catalogues.\nexport interface RepeatArray {\n  key: string\n  name: string\n  refName: string\n  start: number\n  end: number\n  unit: number\n  motif?: string\n  // Each sample's genotyped alleles, from a genotyper's per-sample `AL`\n  // (TRGT); absent from a catalogue.\n  calls?: Record<string, RepeatCall[]>\n}\n\nexport const REPEAT_ADAPTER_TYPES = new Set([\n  'BedAdapter',\n  'BedTabixAdapter',\n  'BigBedAdapter',\n  'VcfAdapter',\n  'VcfTabixAdapter',\n])\n\nconst REPEAT_TRACK_HINT =\n  /repeat|tandem|\\bstr\\b|vntr|trf|trgt|vamos|expansion|microsat/i\n\nexport function pickRepeatTrack<\n  T extends { trackId: string; name?: string; adapterType: string },\n>(tracks: T[], named: string) {\n  if (named) {\n    return tracks.find(t => t.trackId === named)\n  }\n  const candidates = tracks.filter(t => REPEAT_ADAPTER_TYPES.has(t.adapterType))\n  return candidates.find(t =>\n    REPEAT_TRACK_HINT.test(`${t.trackId} ${t.name ?? ''}`),\n  )\n}\n\ntype FeatureLike = Feature | Record<string, unknown>\n\nfunction own(f: FeatureLike, name: string): unknown {\n  return typeof (f as Feature).get === 'function'\n    ? (f as Feature).get(name)\n    : (f as Record<string, unknown>)[name]\n}\n\n// A TRGT repeat catalogue is a BED whose name column packs the record:\n// `ID=HTT;MOTIFS=CAG,CCG;STRUC=(CAG)nCAACAG(CCG)n`. Read as fields when it\n// has that shape.\nconst PACKED_NAME = /^\\w+=[^;]*(;\\w+=[^;]*)*$/\n\nfunction packedName(f: FeatureLike) {\n  const name = own(f, 'name')\n  if (typeof name !== 'string' || !PACKED_NAME.test(name)) {\n    return undefined\n  }\n  return Object.fromEntries(\n    name.split(';').map(pair => {\n      const i = pair.indexOf('=')\n      return [pair.slice(0, i), pair.slice(i + 1)]\n    }),\n  )\n}\n\n// A field at the feature's top level, in a VCF record's INFO, or in a packed\n// name column, in that order.\nfunction field(f: FeatureLike, name: string): unknown {\n  const top = own(f, name)\n  if (top !== undefined) {\n    return top\n  }\n  const info = own(f, 'INFO') as Record<string, unknown> | undefined\n  return info?.[name] ?? packedName(f)?.[name]\n}\n\nconst MOTIF_FIELDS = [\n  'RUS',\n  'MOTIFS',\n  'RU',\n  'motifs',\n  'motif',\n  'sequence',\n  'consensus',\n]\nconst PERIOD_FIELDS = [\n  'RUL',\n  'period',\n  'PERIOD',\n  'consensusSize',\n  'unit',\n  'unitLength',\n]\nconst NAME_FIELDS = ['TRID', 'REPID', 'VARID', 'ID', 'name', 'id']\n\n// The first entry of a list-valued field, whether it arrived parsed or as\n// the comma-joined text a VCF INFO or a BED column holds; VCF's missing \".\"\n// counts as absent.\nfunction first(f: FeatureLike, names: string[]) {\n  for (const name of names) {\n    const value = field(f, name)\n    const one = String((Array.isArray(value) ? value[0] : value) ?? '')\n      .split(',')[0]!\n      .trim()\n    if (one !== '' && one !== '.') {\n      return one\n    }\n  }\n  return undefined\n}\n\nconst IUPAC = /^[ACGTURYSWKMBDHVN]+$/i\n\n// The unit in bp: a stated period, else the length of the first motif.\nexport function repeatUnitOf(f: FeatureLike) {\n  const period = Number(first(f, PERIOD_FIELDS))\n  if (Number.isFinite(period) && period > 0) {\n    return Math.round(period)\n  }\n  const motif = first(f, MOTIF_FIELDS)\n  return motif && IUPAC.test(motif) ? motif.length : undefined\n}\n\n// A per-sample list field, parsed or as the comma-joined text a VCF column\n// holds. A missing entry stays missing: read as 0, an absent `SD` would make\n// every allele of every genotyper that writes no such field unspanned.\nfunction numbers(value: unknown) {\n  const raw: unknown[] = Array.isArray(value)\n    ? value\n    : String(value ?? '').split(',')\n  return raw.map(one => {\n    const n =\n      one === '' || one === null || one === undefined ? NaN : Number(one)\n    return Number.isFinite(n) ? n : undefined\n  })\n}\n\nfunction callsOf(f: FeatureLike) {\n  const samples = own(f, 'samples') as\n    Record<string, Record<string, unknown>> | undefined\n  const called: Record<string, RepeatCall[]> = {}\n  for (const [sample, fields] of Object.entries(samples ?? {})) {\n    const reads = numbers(fields.SD)\n    const alleles = numbers(fields.AL).flatMap((bp, i) =>\n      bp !== undefined && bp > 0\n        ? [reads[i] === undefined ? { bp } : { bp, spanningReads: reads[i] }]\n        : [],\n    )\n    if (alleles.length > 0) {\n      called[sample] = alleles\n    }\n  }\n  return Object.keys(called).length > 0 ? called : undefined\n}\n\nexport function repeatArraysFrom(features: FeatureLike[]): RepeatArray[] {\n  const arrays: RepeatArray[] = []\n  for (const f of features) {\n    const start = field(f, 'start') as number\n    const end = field(f, 'end') as number\n    const unit = repeatUnitOf(f)\n    if (!(end > start) || unit === undefined) {\n      continue\n    }\n    const refName = field(f, 'refName') as string\n    const motif = first(f, MOTIF_FIELDS)\n    const stated = first(f, NAME_FIELDS)\n    arrays.push({\n      key: `${refName}:${start}-${end}`,\n      name:\n        (stated && !PACKED_NAME.test(stated) ? stated : undefined) ??\n        (motif && motif.length <= 12\n          ? `(${motif})n`\n          : `${refName}:${(start + 1).toLocaleString()}-${end.toLocaleString()}`),\n      refName,\n      start,\n      end,\n      unit,\n      motif,\n      calls: callsOf(f),\n    })\n  }\n  return arrays.sort((a, b) => a.start - b.start)\n}\n", "import { pathOrigin } from './pathAnchoring'\n\nimport type { Graph } from './types'\n\n// One walk lifted out of the drawing: the nodes it visits and the links it\n// takes, so the geometry can fade everything else, plus what it carries\n// through the window against the reference walk.\nexport interface WalkHighlight {\n  name: string\n  nodeIds: Set<string>\n  edgeIndexes: Set<number>\n  steps: number\n  bp: number\n  referenceBp?: number\n}\n\nexport function walkHighlight(\n  graph: Graph,\n  name: string,\n): WalkHighlight | undefined {\n  const path = graph.paths?.find(p => p.name === name)\n  if (!path) {\n    return undefined\n  }\n  const byId = new Map(graph.nodes.map(n => [n.id, n]))\n  const edgeAt = new Map<string, number>()\n  graph.edges.forEach((e, i) => {\n    edgeAt.set(`${e.from}>${e.to}`, i)\n  })\n  const nodeIds = new Set(path.nodeIds)\n  const edgeIndexes = new Set<number>()\n  for (let i = 1; i < path.nodeIds.length; i++) {\n    const a = path.nodeIds[i - 1]!\n    const b = path.nodeIds[i]!\n    const index = edgeAt.get(`${a}>${b}`) ?? edgeAt.get(`${b}>${a}`)\n    if (index !== undefined) {\n      edgeIndexes.add(index)\n    }\n  }\n  const bpOf = (ids: string[]) =>\n    ids.reduce((sum, id) => sum + (byId.get(id)?.length ?? 0), 0)\n  // `referencePath` is the anchor name, which pathOrigin has stripped of the\n  // range suffix odgi leaves on a P record's name\n  const reference = graph.referencePath\n    ? graph.paths!.find(p => pathOrigin(p.name).name === graph.referencePath)\n    : undefined\n  return {\n    name,\n    nodeIds,\n    edgeIndexes,\n    steps: path.nodeIds.length,\n    bp: bpOf(path.nodeIds),\n    referenceBp:\n      reference && reference !== path ? bpOf(reference.nodeIds) : undefined,\n  }\n}\n", "import { isBackbone } from '../GraphGenomeView/anchoredNodes'\n\nimport type { GraphNode } from '../GraphGenomeView/types'\n\n// What a LinearGenomeView writes to `session.hovered` on every mousemove (see\n// LinearGenomeViewContainer): the bp under the cursor, plus the feature under it\n// if the topmost track had one. Nothing names the source VIEW, so a graph view\n// filters by whether the position falls in the region it was cut from \u2014 but the\n// position does name the source ASSEMBLY, and that turns out to be the half\n// that matters.\nexport interface LgvHover {\n  refName: string\n  // The 0-based base under the pointer, the convention `stable.start` and the\n  // cut region are in. Not the LGV's own `coord`, which is 1-based for display.\n  coord: number\n  // The assembly the hovered view is showing. `hoverPosition` is a\n  // `PxToBpResult`, i.e. the displayed region the pointer landed in spread flat,\n  // so this is that region's own `assemblyName`.\n  //\n  // Read because refName alone does not identify a locus in a session holding\n  // several assemblies, which is every session these graphs are launched in. A\n  // PanSN name reduces to a bare contig \u2014 the E. coli pangenome loads five\n  // strains each with one refName `chr`, and HPRC's hg38 and a GenArk haplotype\n  // both call it `chr6` \u2014 so a synteny stack's rows all answer to the same\n  // name at unrelated coordinates. Without this the hover on ANY row lit up a\n  // node in the graph, and the node then published its own reference interval\n  // back into every linear view.\n  //\n  // Optional because the channel is typed `unknown` and read structurally: a\n  // hover that states no assembly is taken at its word rather than dropped.\n  assemblyName?: string\n  featureName?: string\n}\n\nfunction isRecord(value: unknown): value is Record<string, unknown> {\n  return typeof value === 'object' && value !== null\n}\n\ninterface FeatureLike {\n  get: (key: string) => unknown\n}\n\nfunction isFeatureLike(value: unknown): value is FeatureLike {\n  return isRecord(value) && typeof value.get === 'function'\n}\n\n// A display hovers either a Feature, read with `get`, or a plain hit item with\n// a `name` of its own, which is what the canvas feature display hands over.\n// Reading only the first left the exact segment match dead on that display.\nfunction hoveredName(feature: unknown) {\n  const name = isFeatureLike(feature)\n    ? feature.get('name')\n    : isRecord(feature)\n      ? feature.name\n      : undefined\n  return typeof name === 'string' ? name : undefined\n}\n\n// `hovered` is typed `unknown` on the session by design \u2014 it is a shared channel\n// every view writes its own shape to \u2014 so this reads the LGV's shape out of it\n// structurally rather than asserting a type onto it.\nexport function readLgvHover(hovered: unknown): LgvHover | undefined {\n  let result: LgvHover | undefined\n  if (isRecord(hovered) && isRecord(hovered.hoverPosition)) {\n    const { refName, coord, coord0, assemblyName } = hovered.hoverPosition\n    if (typeof refName === 'string' && typeof coord === 'number') {\n      result = {\n        refName,\n        // `coord` is 1-based; a host that states the 0-based `coord0` is\n        // taken at its word. Read as 0-based, the last base of every node lit\n        // the next one, and a 1 bp node could not be reached at all.\n        coord: typeof coord0 === 'number' ? coord0 : coord - 1,\n        assemblyName:\n          typeof assemblyName === 'string' ? assemblyName : undefined,\n        featureName: hoveredName(hovered.hoverFeature),\n      }\n    }\n  }\n  return result\n}\n\n// Whether a hover is one this graph can answer: the same assembly, the same\n// stable sequence, and inside the window the cut was made for.\n//\n// The assembly is checked FIRST and is the whole reason this is not just a\n// coordinate test. See LgvHover.assemblyName: a graph cut from K12 and a\n// synteny row on Sakai both call their sequence `chr`, so on refName and\n// coordinate alone every row of the stack matched and the graph highlighted a\n// K12 node at Sakai's offset. A hover that names no assembly still passes,\n// which is what a hand-written channel writer and the older LGVs get.\nexport function hoverInRegion(\n  hover: LgvHover,\n  region: { refName: string; assemblyName: string; start: number; end: number },\n) {\n  return (\n    (hover.assemblyName === undefined ||\n      hover.assemblyName === region.assemblyName) &&\n    hover.refName === region.refName &&\n    hover.coord >= region.start &&\n    hover.coord < region.end\n  )\n}\n\n// The graph node a linear-view hover points at.\n//\n// The feature under the cursor is the exact answer when the graph's own segments\n// track is what's hovered: an RgfaTabixAdapter feature's name is the segment id,\n// which is `GraphNode.name` (`GraphNode.id` carries a strand suffix, so the\n// match has to be on name). Any other track \u2014 genes, bubbles \u2014 supplies only a\n// coordinate, which still identifies the backbone segment covering it: the\n// backbone tiles the reference exactly once, whether rGFA's rank 0 declared it\n// or a reference path's own steps did.\nexport function nodeForLgvHover({\n  hover,\n  nodes,\n}: {\n  hover: LgvHover\n  nodes: GraphNode[]\n}) {\n  let byName: string | undefined\n  let byCoord: string | undefined\n  for (const node of nodes) {\n    if (node.name === hover.featureName) {\n      byName = node.id\n    } else if (\n      byCoord === undefined &&\n      isBackbone(node) &&\n      hover.coord >= node.stable.start &&\n      hover.coord < node.stable.start + node.length\n    ) {\n      byCoord = node.id\n    }\n  }\n  // An exact segment match wins over the coordinate it happens to sit at.\n  return byName ?? byCoord ?? null\n}\n", "import { readConfObject } from '@jbrowse/core/configuration'\n\nimport { locLabel, locString } from './contributors'\nimport { linearViewTarget } from './linearViewTarget'\n\nimport type { Contributor, GraphLocation } from './contributors'\nimport type { TrackScanSession } from '../launchSubgraph/subgraphTracks'\n\nexport interface GraphLaunchSession extends TrackScanSession {\n  addView: (type: string, snapshot?: Record<string, unknown>) => { id: string }\n  // The session's own loader for a view whose state model is registered\n  // lazily (JBrowse 4's LinearSyntenyView); absent on an older core, where\n  // addView is enough\n  launchView?: (\n    type: string,\n    snapshot?: Record<string, unknown>,\n  ) => Promise<{ id: string }>\n  assemblyNames: string[]\n  views: unknown[]\n  // optional, as a hand-built session in a test has none\n  notifyError?: (message: string, error?: unknown) => void\n}\n\n// A launch is a promise nothing waits on. Let go, a refusal moved nothing and\n// said nothing; this is where it is told to the user instead.\nfunction reportFailure(\n  session: GraphLaunchSession,\n  what: string,\n  launch: Promise<unknown>,\n) {\n  launch.catch((error: unknown) => {\n    console.error(`[GraphGenomeView] ${what}`, error)\n    session.notifyError?.(`${what}: ${error}`, error)\n  })\n}\n\n// A node is often shorter than a line of text \u2014 a base-level allele can be a\n// handful of bp \u2014 and a linear view opened on exactly that span shows the span\n// and no context at all. Padding to a minimum window puts the node in the middle\n// of something readable.\nconst MIN_LAUNCH_SPAN_BP = 1000\n\nexport function paddedLocation(\n  loc: GraphLocation,\n  minSpan = MIN_LAUNCH_SPAN_BP,\n): GraphLocation {\n  const pad = Math.max(0, Math.ceil((minSpan - (loc.end - loc.start)) / 2))\n  return { ...loc, start: Math.max(0, loc.start - pad), end: loc.end + pad }\n}\n\n// Restate the rank-0 contributor in the terms of the region the graph was cut\n// from. Two separate corrections, both required:\n//\n//   - the *assembly*. A backbone segment's SN is the graph's own spelling of the\n//     reference, which need not be the name of any loaded assembly: the HPRC\n//     graph says `GRCh38#0#chr6` in a session whose assembly is `hg38`. Taking\n//     the PanSN sample there resolves to nothing and the graph offers no way out\n//     at all. `loadedRegion` is authoritative \u2014 the adapter resolved that\n//     assembly to that stable sequence to cut the subgraph in the first place.\n//     The backbone's `haplotype` (`GRCh38#0`) goes with it, since\n//     resolveLocationAssembly tries that before the sample.\n//   - the *locus*. The cut region is what the user framed in the linear view, and\n//     it is the span every other panel of a synteny launch is compared against;\n//     the union of backbone segments differs from it whenever the window ends\n//     inside a bubble.\n//\n// A subgraph is cut on one reference, so there is at most one rank-0\n// contributor. Must run before contributors are resolved against the session's\n// assemblies, or the reference is filtered out by the name this replaces.\nexport function withReferenceRegion(\n  contributors: Contributor[],\n  region:\n    | { refName: string; assemblyName: string; start: number; end: number }\n    | undefined,\n): Contributor[] {\n  return region\n    ? contributors.map(c =>\n        c.rank === 0\n          ? {\n              ...c,\n              sample: region.assemblyName,\n              haplotype: undefined,\n              refName: region.refName,\n              start: region.start,\n              end: region.end,\n            }\n          : c,\n      )\n    : contributors\n}\n\n// Show a location in a linear view: move the one already on screen if there is\n// one to move, open a pane only if there isn't.\n//\n// This is the difference between \"flip to the linear view\" and \"accumulate\n// panes\". The pangenome sessions this ships in are a linear view above a graph,\n// and there the answer to \"where is this node?\" should be that the linear view\n// scrolls to it \u2014 see linearViewTarget for which view counts as the one to move.\n//\n// `tracks` is only applied to a view being created; a view already open keeps\n// whatever the user has turned on. Returns the id of the view that ended up\n// showing the location, so the graph can pair with it for the hover sync.\nexport function showInLinearView({\n  session,\n  location,\n  assembly,\n  connectedViewId,\n  tracks = [],\n}: {\n  session: GraphLaunchSession\n  location: GraphLocation\n  assembly: string\n  connectedViewId?: string\n  tracks?: string[]\n}) {\n  const existing = linearViewTarget({\n    views: session.views,\n    connectedViewId,\n    assemblyName: assembly,\n  })\n  let viewId: string\n  if (existing) {\n    reportFailure(\n      session,\n      `Could not show ${assembly} ${locLabel(location)}`,\n      Promise.resolve(existing.navToLocString(locString(location), assembly)),\n    )\n    viewId = existing.id\n  } else {\n    viewId = session.addView('LinearGenomeView', {\n      displayName: `${assembly} \u2014 ${locLabel(location)}`,\n      init: { assembly, loc: locString(location), tracks },\n    }).id\n  }\n  return viewId\n}\n\n// Mark where a node sits on the reference, in the linear view already on\n// screen, instead of scrolling that view to it. Review: \"need to be able to\n// just highlight lineargenomeview coords\".\n//\n// The other half of the pair above, and the half that survives being let go of:\n// hover sync draws a band for as long as the pointer is over the node, where a\n// highlight is written into the view's own list and stays until it is removed.\n// It also keeps the reader's frame \u2014 the interesting comparison at a pangenome\n// locus is usually the whole window, not the 200 bp the node occupies.\n//\n// Nothing to mark when no linear view on that assembly is ours to move (see\n// linearViewTarget); the caller offers the item only when there is.\nexport function highlightInLinearView({\n  session,\n  location,\n  assembly,\n  connectedViewId,\n}: {\n  session: GraphLaunchSession\n  location: GraphLocation\n  assembly: string\n  connectedViewId?: string\n}) {\n  const target = linearViewTarget({\n    views: session.views,\n    connectedViewId,\n    assemblyName: assembly,\n  })\n  target?.addToHighlights?.({\n    refName: location.refName,\n    start: location.start,\n    end: location.end,\n    assemblyName: assembly,\n  })\n  return target !== undefined\n}\n\n// Which assemblies a track config says it covers, for deciding whether a panel\n// can draw it at all. A trackId naming nothing in the session reads as covering\n// nothing, so a stale id drops the lane rather than adding one the panel would\n// fail to load.\nfunction assemblyNamesOfTrack(\n  session: GraphLaunchSession,\n  trackId: string | undefined,\n) {\n  if (trackId === undefined) {\n    return []\n  }\n  const track = session.tracks.find(\n    t => readConfObject(t, 'trackId') === trackId,\n  )\n  const names: unknown = track ? readConfObject(track, 'assemblyNames') : []\n  return Array.isArray(names) ? names.filter(n => typeof n === 'string') : []\n}\n\n// One panel per contributing assembly, each framed on the locus that assembly\n// contributes here, with the graph's own reference panel on top.\n//\n// The panel loci come from the graph rather than from the synteny track: rGFA\n// states where each contributor's sequence sits on its own coordinates, so the\n// launch needs no mate discovery, no PAF lookup and no dialog. That is the whole\n// point of launching from the graph instead of from a linear view.\n//\n// Panels carry THE GRAPH'S OWN TRACK and nothing else, which is a narrower rule\n// than the single-view launch's (see launchTracks, which scans the session for\n// the assembly's annotation). Tried that here: a gene track per panel takes\n// about 160px of a row that is otherwise a ruler, so on five strains the\n// annotation is most of the viewport and the ribbons \u2014 the thing the launch\n// exists to draw \u2014 are squeezed into the gaps, and `collapseEmptyRows` is here\n// to prevent exactly that.\n//\n// The graph's own track does not have that shape. It goes only in the panels\n// whose assembly its config declares, which is where the graph HAS coordinates:\n// the HPRC segments track names two, so both its panels get one lane, while the\n// E. coli one names K12 alone and a five-strain launch adds a single lane rather\n// than five. And it is the lane that makes the band readable, since the ribbons\n// otherwise connect two bare rulers and the reader has nothing to match across\n// them.\nexport function launchSyntenyView({\n  session,\n  contributors,\n  trackId,\n  graphTrackId,\n}: {\n  session: GraphLaunchSession\n  contributors: Contributor[]\n  trackId?: string\n  graphTrackId?: string\n}) {\n  const graphTrackAssemblies = assemblyNamesOfTrack(session, graphTrackId)\n  // The panels the chosen track aligns, in the order given. A pairwise track is\n  // offered beside an all-vs-all, two assemblies being a synteny view, and over\n  // every contributor it sat on each level and could draw on one at most. A\n  // track that states no assemblies keeps them all.\n  const aligned = assemblyNamesOfTrack(session, trackId)\n  const covered = contributors.filter(c => aligned.includes(c.sample))\n  const panels = covered.length >= 2 ? covered : contributors\n  const snapshot = {\n    init: {\n      views: panels.map(c => ({\n        assembly: c.sample,\n        loc: locString(c),\n        ...(graphTrackId !== undefined &&\n        graphTrackAssemblies.includes(c.sample)\n          ? { tracks: [graphTrackId] }\n          : {}),\n      })),\n      // One entry per LEVEL, not one for the track. `init.tracks` is 2D \u2014 the\n      // gap between views[i] and views[i+1] \u2014 and a flat `[trackId]` is read as\n      // the level-0 shorthand, so on a five-strain launch only the top band got\n      // the alignment and the four below it opened as bare rulers. The same\n      // all-vs-all track fills every level: it carries all the pairs.\n      tracks: trackId ? panels.slice(1).map(() => [trackId]) : [],\n      collapseEmptyRows: true,\n    },\n  }\n  // launchView where the session has it: a synteny view's state model is\n  // loaded on demand and addView throws until it is\n  if (session.launchView) {\n    reportFailure(\n      session,\n      'Could not open the synteny view',\n      session.launchView('LinearSyntenyView', snapshot),\n    )\n  } else {\n    session.addView('LinearSyntenyView', snapshot)\n  }\n}\n", "export interface NavigableLinearView {\n  id: string\n  assemblyNames: string[]\n  navToLocString: (locString: string, assemblyName?: string) => unknown\n  // The other way of answering \"where is this node\": mark it rather than scroll\n  // to it. Optional, and not part of isLinearView's test \u2014 navigating is what\n  // makes a view a target here, and a view that cannot be marked can still be\n  // moved.\n  addToHighlights?: (highlight: {\n    refName: string\n    start: number\n    end: number\n    assemblyName: string\n  }) => unknown\n}\n\nfunction isRecord(value: unknown): value is Record<string, unknown> {\n  return typeof value === 'object' && value !== null\n}\n\n// Reads `session.views` structurally, the same way graphViewHighlights does: the\n// members needed here are declared by LinearGenomeView, not by the\n// AbstractViewModel the session array is typed as.\nfunction isLinearView(view: unknown): view is NavigableLinearView {\n  return (\n    isRecord(view) &&\n    view.type === 'LinearGenomeView' &&\n    typeof view.id === 'string' &&\n    typeof view.navToLocString === 'function' &&\n    Array.isArray(view.assemblyNames)\n  )\n}\n\n// The view a graph was launched from is not always in `session.views`: a row of\n// a LinearSyntenyView, LinearComparativeView or BreakpointSplitView sits in\n// that view's own `views[]`, so the candidates are the session's views plus one\n// level of rows.\nexport function withRows(views: unknown[]) {\n  return views.flatMap(view =>\n    isRecord(view) && Array.isArray(view.views)\n      ? [view, ...view.views]\n      : [view],\n  )\n}\n\n// The linear view a \"show me this\" from the graph should move, rather than\n// opening a pane beside it. Three cases, in order:\n//\n//   - the view this graph is paired with (`connectedViewId`), which is either\n//     the view the graph was launched from or the one it later opened itself.\n//     Explicit, so it wins.\n//   - failing that, the only linear view in the session showing this assembly.\n//     The pangenome sessions this view ships in are a linear view above a graph\n//     with no pairing recorded, and there \"the linear view\" is unambiguous \u2014 the\n//     same reasoning hoverSync's isConnected already applies to highlights.\n//   - two or more candidates and no pairing: nothing. Guessing which of the\n//     user's views to scroll is worse than opening one that is ours to move.\n//\n// Assembly-gated throughout: a linear view on a different assembly cannot show\n// this location at all.\nexport function linearViewTarget({\n  views,\n  connectedViewId,\n  assemblyName,\n}: {\n  views: unknown[]\n  connectedViewId: string | undefined\n  assemblyName: string\n}) {\n  const candidates = withRows(views)\n    .filter(view => isLinearView(view))\n    .filter(view => view.assemblyNames.includes(assemblyName))\n  const connected = candidates.find(view => view.id === connectedViewId)\n  return connected ?? (candidates.length === 1 ? candidates[0] : undefined)\n}\n", "import { readConfObject } from '@jbrowse/core/configuration'\n\nimport type { TrackScanSession } from '../launchSubgraph/subgraphTracks'\n\nconst ANNOTATION_TRACK_TYPE = 'FeatureTrack'\n\n// What to turn on in a linear view the graph opens on `assemblyName`.\n//\n// A launch used to carry the graph's own track and nothing else, and that track\n// is configured for the reference alone \u2014 so `Launch view` \u2192 `CFT073 chr:\u2026`\n// landed on `No tracks active`, which answers \"where is this strain's sequence?\"\n// with an empty pane. What the session does hold for a contributing assembly is\n// that assembly's own annotation, and on a pangenome config that is one track\n// per strain (`CFT073_genes`), which is exactly what makes the landing readable.\n//\n// Annotation tracks only, not everything configured for the assembly. A launch\n// is a jump to a locus, and an alignments or coverage track turned on behind the\n// user's back fetches data nobody asked for; a FeatureTrack at a 50 kb window is\n// a tabix range query. The graph's own segments track is a FeatureTrack too, so\n// the reference case still gets it from the same scan.\n//\n// `first` is the graph's own track when the launch is on the reference, so the\n// segments the graph drew sit at the top of the view rather than wherever config\n// order puts them.\nexport function launchTracks({\n  session,\n  assemblyName,\n  first,\n}: {\n  session: TrackScanSession\n  assemblyName: string\n  first?: string\n}) {\n  const found: string[] = []\n  for (const track of session.tracks) {\n    const type: unknown = readConfObject(track, 'type')\n    const assemblyNames: unknown = readConfObject(track, 'assemblyNames')\n    const trackId: unknown = readConfObject(track, 'trackId')\n    if (\n      type === ANNOTATION_TRACK_TYPE &&\n      Array.isArray(assemblyNames) &&\n      assemblyNames.includes(assemblyName) &&\n      typeof trackId === 'string' &&\n      trackId !== first\n    ) {\n      found.push(trackId)\n    }\n  }\n  return first ? [first, ...found] : found\n}\n", "import { readConfObject } from '@jbrowse/core/configuration'\nimport { getTrackName } from '@jbrowse/core/util/tracks'\n\nimport type { TrackScanSession } from '../launchSubgraph/subgraphTracks'\n\nexport interface LaunchableSyntenyTrack {\n  trackId: string\n  name: string\n  // how many of the requested assemblies this track covers, so a whole-set\n  // all-vs-all sorts above a pairwise alignment covering two of them\n  coverage: number\n}\n\nconst SYNTENY_TRACK_TYPE = 'SyntenyTrack'\n\n// Synteny datasets in the session that align at least two of `assemblyNames`.\n//\n// Track type rather than adapter name: SyntenyTrack is the core track type every\n// synteny adapter is configured under, so this does not go stale when an adapter\n// is added or renamed the way naming PAF adapters would.\n//\n// Two is the floor because that is the floor for a synteny view; more is better,\n// and an all-vs-all covering every contributing assembly is what makes the\n// multi-panel launch worth offering at all.\nexport function launchableSyntenyTracks(\n  session: TrackScanSession,\n  assemblyNames: string[],\n) {\n  const wanted = new Set(assemblyNames)\n  const found: LaunchableSyntenyTrack[] = []\n  for (const track of session.tracks) {\n    const type: unknown = readConfObject(track, 'type')\n    const trackAssemblies: unknown = readConfObject(track, 'assemblyNames')\n    const trackId: unknown = readConfObject(track, 'trackId')\n    if (\n      type === SYNTENY_TRACK_TYPE &&\n      typeof trackId === 'string' &&\n      Array.isArray(trackAssemblies)\n    ) {\n      const coverage = trackAssemblies.filter(name => wanted.has(name)).length\n      if (coverage >= 2) {\n        found.push({ trackId, name: getTrackName(track, session), coverage })\n      }\n    }\n  }\n  return found.sort((a, b) => b.coverage - a.coverage)\n}\n", "import { readConfObject } from '@jbrowse/core/configuration'\nimport { getTrackName } from '@jbrowse/core/util/tracks'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { AnyConfigurationModel } from '@jbrowse/core/configuration'\n\nexport interface SubgraphTrack {\n  trackId: string\n  name: string\n  // The assembly a cut has to be on; see graphReferenceAssembly.\n  referenceAssembly: string | undefined\n  // The lanes the cut is for; undefined is every haplotype.\n  haplotypes: string[] | undefined\n}\n\nexport interface TrackScanSession {\n  tracks: AnyConfigurationModel[]\n  assemblies: AnyConfigurationModel[]\n}\n\n// The linear view a launch is offered from, as far as the lanes go.\nexport interface LaunchingView {\n  tracks: readonly {\n    configuration: AnyConfigurationModel\n    displays: readonly unknown[]\n  }[]\n}\n\ninterface LaneSelectingDisplay {\n  laneSelection: readonly string[] | undefined\n  hiddenLanes: readonly string[]\n}\n\n// Whether an adapter declares it can cut a local subgraph. Discovery is by\n// declared capability, not adapter name: the old launcher hardcoded\n// `GfaTabixAdapter`/`GfaServerAdapter`, which is exactly what left it dead when\n// those were removed.\n//\n// `getAdapterType` throws for a type that was never registered, and a session\n// can hold tracks whose plugin isn't loaded, so registration is checked first \u2014\n// a session-wide scan reaches tracks a single display's menu never would.\nexport function adapterCanCutSubgraph(\n  pluginManager: PluginManager,\n  adapterType: unknown,\n) {\n  return (\n    typeof adapterType === 'string' &&\n    pluginManager.adapterTypes.has(adapterType) &&\n    pluginManager\n      .getAdapterType(adapterType)\n      .adapterCapabilities.includes('getSubgraph')\n  )\n}\n\nfunction isStringArray(value: unknown): value is string[] {\n  return Array.isArray(value) && value.every(item => typeof item === 'string')\n}\n\nfunction isLaneSelecting(display: unknown): display is LaneSelectingDisplay {\n  return (\n    typeof display === 'object' &&\n    display !== null &&\n    'laneSelection' in display &&\n    'hiddenLanes' in display\n  )\n}\n\n// The assemblies the track names after its reference, which is what core's\n// MultiWaySyntenyDisplay opens a lane-declaring source on.\nexport function trackLanes(track: AnyConfigurationModel) {\n  const assemblyNames: unknown = readConfObject(track, 'assemblyNames')\n  const lanes = isStringArray(assemblyNames) ? assemblyNames.slice(1) : []\n  return lanes.length > 0 ? lanes : undefined\n}\n\n// A graph is cut on the first assembly its track names, the rule\n// GbzBaseSyntenyAdapter states for its anchor. Every other assembly the track\n// names holds its sequence as rank>0 alleles off that reference's backbone, so\n// a window on one has no reference coordinates to frame the cut by.\nexport function graphReferenceAssembly(track: AnyConfigurationModel) {\n  const assemblyNames: unknown = readConfObject(track, 'assemblyNames')\n  return isStringArray(assemblyNames) ? assemblyNames[0] : undefined\n}\n\nexport function offReferenceProblem(\n  referenceAssembly: string | undefined,\n  assemblyName: string,\n) {\n  return referenceAssembly === undefined || referenceAssembly === assemblyName\n    ? undefined\n    : `The graph is cut on its reference, ${referenceAssembly}: open it from a view of ${referenceAssembly}`\n}\n\n// The lanes the track draws in `view`: the ones in force there less any the\n// reader hid. A track not on screen there has its own assemblies to go by.\nfunction lanesToCut(\n  track: AnyConfigurationModel,\n  trackId: string,\n  view: LaunchingView | undefined,\n) {\n  const shown = view?.tracks\n    .find(t => readConfObject(t.configuration, 'trackId') === trackId)\n    ?.displays.find(isLaneSelecting)\n  return shown\n    ? shown.laneSelection?.filter(name => !shown.hiddenLanes.includes(name))\n    : trackLanes(track)\n}\n\nexport function subgraphTrack(\n  track: AnyConfigurationModel,\n  trackId: string,\n  session: TrackScanSession,\n  view?: LaunchingView,\n): SubgraphTrack {\n  return {\n    trackId,\n    name: getTrackName(track, session),\n    referenceAssembly: graphReferenceAssembly(track),\n    haplotypes: lanesToCut(track, trackId, view),\n  }\n}\n\n// Tracks anywhere in the session that can cut a subgraph on `assemblyName`, so\n// the launch can be offered from a linear view that doesn't have the graph track\n// in it. The entry point no longer has to be the graph track's own menu \u2014 which\n// was the whole problem: a user browsing genes had no way in.\nexport function subgraphTracks(\n  pluginManager: PluginManager,\n  session: TrackScanSession,\n  assemblyName: string,\n  view?: LaunchingView,\n) {\n  const found: SubgraphTrack[] = []\n  for (const track of session.tracks) {\n    const assemblyNames: unknown = readConfObject(track, 'assemblyNames')\n    const adapter: unknown = readConfObject(track, 'adapter')\n    const trackId: unknown = readConfObject(track, 'trackId')\n    if (\n      Array.isArray(assemblyNames) &&\n      assemblyNames.includes(assemblyName) &&\n      typeof trackId === 'string' &&\n      typeof adapter === 'object' &&\n      adapter !== null &&\n      'type' in adapter &&\n      adapterCanCutSubgraph(pluginManager, adapter.type)\n    ) {\n      found.push(subgraphTrack(track, trackId, session, view))\n    }\n  }\n  return found\n}\n", "import type modelFactory from './GraphGenomeView/model'\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { AbstractSessionModel } from '@jbrowse/core/util'\nimport type { SnapshotIn } from '@jbrowse/mobx-state-tree'\n\n// GraphGenomeView has no assembly/track resolution \u2014 every field is a plain\n// persisted view prop, so the launch spec forwards straight onto the view\n// snapshot. `afterAttach` loads `gfaLocation`, or refetches the\n// `loadedTrackId`/`loadedRegion` pair, once the view is created.\n//\n// **Taken off the model rather than listed by hand**, which is the whole point.\n// This named four props (`gfaLocation`, `colorScheme`, `linearLayout`,\n// `drawPaths`) while the extension point spreads whatever it is handed \u2014 so the\n// runtime accepted every prop and the DECLARED contract accepted a third of\n// them. The docs' own figure specs launch with thirteen: `loadedTrackId`,\n// `loadedRegion`, `layoutMode`, `colorDomain`, `paneHeight`, `referencePath`,\n// `layoutQuality`, `maxRegionBp` and `bubbleSpread` among them, none of which\n// this said were allowed. It carries a `#extensionPoint` tag, so the published\n// API docs said so too.\n//\n// Derived, so adding a view prop widens the launch with it. `type` is the\n// dispatch key rather than a setting \u2014 loadSessionSpec strips it before calling\n// this \u2014 and is the one field a caller may not supply.\nexport type LaunchGraphGenomeViewArgs = Partial<\n  Omit<SnapshotIn<ReturnType<typeof modelFactory>>, 'type'>\n> & {\n  session: AbstractSessionModel\n}\n\ndeclare module '@jbrowse/core/PluginManager' {\n  interface ExtensionPointRegistry {\n    'LaunchView-GraphGenomeView': {\n      args: LaunchGraphGenomeViewArgs\n      result: LaunchGraphGenomeViewArgs\n    }\n  }\n}\n\nexport default function LaunchGraphGenomeViewF(pluginManager: PluginManager) {\n  /** #extensionPoint LaunchView-GraphGenomeView | async | Programmatically launch a graph genome view */\n  pluginManager.addToExtensionPoint('LaunchView-GraphGenomeView', args => {\n    const { session, ...spec } = args\n    session.addView('GraphGenomeView', spec)\n    return args\n  })\n}\n", "import { lazy } from 'react'\n\nimport DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'\n\nimport { configSchemaFactory } from './configSchema'\nimport { stateModelFactory } from './model'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\n\nexport default function LinearGraphDisplayF(pluginManager: PluginManager) {\n  pluginManager.addDisplayType(() => {\n    const configSchema = configSchemaFactory()\n    return new DisplayType({\n      name: 'LinearGraphDisplay',\n      displayName: 'Graph',\n      configSchema,\n      stateModel: stateModelFactory(configSchema),\n      trackType: ['FeatureTrack', 'SyntenyTrack'],\n      viewType: 'LinearGenomeView',\n      ReactComponent: lazy(() => import('./components/LinearGraphDisplay')),\n    })\n  })\n}\n", "import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { trackHeightConfigSchemaFields } from '@jbrowse/display-kit/trackHeightConfigSchemaFields'\nimport { types } from '@jbrowse/mobx-state-tree'\n\nimport { COLOR_SCHEME_VALUES } from '../GraphGenomeView/colorSchemes'\nimport { LAYOUT_MODE_VALUES } from '../GraphGenomeView/layoutModes'\n\nimport type { Instance } from '@jbrowse/mobx-state-tree'\n\n/**\n * #config LinearGraphDisplay\n * The graph drawn as a track of the linear genome view. A layout whose x is\n * reference bp draws under the view's coordinates and re-cuts as the view\n * moves; force, ordered and walk rows draw in their own coordinates, fitted to\n * the track.\n */\nexport function configSchemaFactory() {\n  return ConfigurationSchema(\n    'LinearGraphDisplay',\n    {\n      /**\n       * #slot\n       * the layout the track opens in\n       */\n      layoutMode: {\n        type: 'stringEnum',\n        model: types.enumeration('LayoutMode', LAYOUT_MODE_VALUES),\n        defaultValue: 'auto',\n      },\n      /**\n       * #slot\n       */\n      colorScheme: {\n        type: 'stringEnum',\n        model: types.enumeration('ColorScheme', COLOR_SCHEME_VALUES),\n        defaultValue: 'auto',\n      },\n      ...trackHeightConfigSchemaFields({\n        defaultHeight: 300,\n        height:\n          'the most the track takes; a layout shorter than it takes only what it needs',\n      }),\n    },\n    { explicitlyTyped: true, explicitIdentifier: 'displayId' },\n  )\n}\n\nexport type LinearGraphDisplayConfigModel = ReturnType<\n  typeof configSchemaFactory\n>\nexport type LinearGraphDisplayConfig = Instance<LinearGraphDisplayConfigModel>\n", "import { lazy } from 'react'\n\nimport { ConfigurationReference, getConf } from '@jbrowse/core/configuration'\nimport { BaseDisplay } from '@jbrowse/core/pluggableElementTypes'\nimport { getContainingView, getSession } from '@jbrowse/core/util'\nimport TrackHeightMixin from '@jbrowse/display-kit/TrackHeightMixin'\nimport { addDisposer, types } from '@jbrowse/mobx-state-tree'\nimport SettingsIcon from '@mui/icons-material/Settings'\nimport { autorun } from 'mobx'\n\nimport { COLOR_SCHEMES } from '../GraphGenomeView/colorSchemes'\nimport { isLinearHost } from '../GraphGenomeView/host'\nimport { LAYOUT_MODES } from '../GraphGenomeView/layoutModes'\nimport paneModelFactory from '../GraphGenomeView/model'\n\nimport type { LinearGraphDisplayConfigModel } from './configSchema'\nimport type { MenuItem } from '@jbrowse/core/ui'\nimport type { Instance } from '@jbrowse/mobx-state-tree'\n\nconst GraphSettingsDialog = lazy(\n  () => import('../GraphGenomeView/components/GraphSettingsDialog'),\n)\n\ntype ConfiguredSlot = 'layoutMode' | 'colorScheme' | 'height'\n\nexport function stateModelFactory(configSchema: LinearGraphDisplayConfigModel) {\n  const Pane = paneModelFactory()\n  return (\n    types\n      .compose(\n        'LinearGraphDisplay',\n        BaseDisplay,\n        TrackHeightMixin(),\n        types.model({\n          type: types.literal('LinearGraphDisplay'),\n          configuration: ConfigurationReference(configSchema),\n          // The graph pane, the same model the standalone view is. Here the\n          // linear view above is its host: x is that view's window for a layout\n          // whose x is reference bp, and the cut is re-made when the window\n          // leaves it (pane.host).\n          pane: types.optional(Pane, () => ({\n            type: 'GraphGenomeView' as const,\n          })),\n          // Which of the config's slots have reached the pane. Each reaches it\n          // once, so a choice made in the track menu survives a reload, and a\n          // launch that states a pane prop keeps it over the config's.\n          configured: types.optional(\n            types.frozen<Partial<Record<ConfiguredSlot, boolean>>>(),\n            {},\n          ),\n        }),\n      )\n      // A launch names the pane's props without the pane's own type, and what\n      // it states is what the config does not set.\n      .preProcessSnapshot(snapshot => {\n        const { pane, configured } = snapshot as {\n          pane?: Record<string, unknown>\n          configured?: Partial<Record<ConfiguredSlot, boolean>>\n        }\n        return pane\n          ? ({\n              ...snapshot,\n              configured: {\n                layoutMode: pane.layoutMode !== undefined,\n                colorScheme: pane.colorScheme !== undefined,\n                height: pane.paneHeight !== undefined,\n                ...configured,\n              },\n              pane:\n                pane.type === undefined\n                  ? { type: 'GraphGenomeView', ...pane }\n                  : pane,\n            } as typeof snapshot)\n          : snapshot\n      })\n      .views(self => ({\n        get host() {\n          let view: unknown\n          try {\n            view = getContainingView(self)\n          } catch {\n            return undefined\n          }\n          return isLinearHost(view) ? view : undefined\n        },\n        get trackId(): string {\n          return getConf(self.parentTrack, 'trackId')\n        },\n      }))\n      .views(self => ({\n        trackMenuItems(): MenuItem[] {\n          const { pane } = self\n          const { graph } = pane\n          const walks = pane.walkChoices\n          return [\n            {\n              label: 'Layout',\n              subMenu: LAYOUT_MODES.map(mode => ({\n                type: 'radio' as const,\n                label: mode.label,\n                checked: pane.layoutMode === mode.value,\n                disabled: graph ? !mode.available(graph) : false,\n                onClick: () => {\n                  void pane.switchLayout(mode.value)\n                },\n              })),\n            },\n            {\n              label: 'Color',\n              subMenu: COLOR_SCHEMES.map(scheme => ({\n                type: 'radio' as const,\n                label: scheme.label,\n                checked: pane.colorScheme === scheme.value,\n                onClick: () => {\n                  pane.setColorScheme(scheme.value)\n                },\n              })),\n            },\n            ...(walks.length > 0\n              ? [\n                  {\n                    label: 'Walk',\n                    subMenu: [\n                      {\n                        type: 'radio' as const,\n                        label: 'None',\n                        checked: pane.highlightedPath === '',\n                        onClick: () => {\n                          pane.setHighlightedPath('')\n                        },\n                      },\n                      ...walks.map(walk => ({\n                        type: 'radio' as const,\n                        label: walk.label,\n                        checked: pane.highlightedPath === walk.name,\n                        onClick: () => {\n                          pane.setHighlightedPath(walk.name)\n                        },\n                      })),\n                    ],\n                  },\n                ]\n              : []),\n            ...(pane.hostPlacesX\n              ? []\n              : [\n                  {\n                    label: 'Zoom in',\n                    onClick: () => {\n                      pane.zoom(1.5, pane.width / 2, pane.canvasHeight / 2)\n                    },\n                  },\n                  {\n                    label: 'Zoom out',\n                    onClick: () => {\n                      pane.zoom(1 / 1.5, pane.width / 2, pane.canvasHeight / 2)\n                    },\n                  },\n                  {\n                    label: 'Zoom to fit',\n                    onClick: () => {\n                      pane.zoomToFit()\n                    },\n                  },\n                ]),\n            {\n              type: 'checkbox',\n              label: 'Mark bubbles',\n              checked: pane.showBubbles,\n              onClick: () => {\n                pane.setShowBubbles(!pane.showBubbles)\n              },\n            },\n            {\n              type: 'checkbox',\n              label: 'Show deletion edges',\n              checked: pane.showDeletionEdges,\n              onClick: () => {\n                pane.setShowDeletionEdges(!pane.showDeletionEdges)\n              },\n            },\n            {\n              type: 'checkbox',\n              label: 'Genes on the backbone',\n              checked: pane.showGenes,\n              onClick: () => {\n                pane.setShowGenes(!pane.showGenes)\n              },\n            },\n            {\n              label: 'Settings',\n              icon: SettingsIcon,\n              onClick: () => {\n                getSession(self).queueDialog(onClose => [\n                  GraphSettingsDialog,\n                  { model: pane, open: true, onClose },\n                ])\n              },\n            },\n          ]\n        },\n      }))\n      .actions(self => ({\n        // The config's slots the pane has not yet taken, then all of them.\n        applyConfig() {\n          const { pane, configured } = self\n          if (!configured.layoutMode) {\n            pane.setLayoutMode(getConf(self, 'layoutMode'))\n          }\n          if (!configured.colorScheme) {\n            pane.setColorScheme(getConf(self, 'colorScheme'))\n          }\n          if (!configured.height) {\n            pane.setPaneHeight(getConf(self, 'height'))\n          }\n          self.configured = {\n            layoutMode: true,\n            colorScheme: true,\n            height: true,\n          }\n        },\n        // The track's height is the pane's ceiling: a layout shorter than it\n        // takes only what it needs, and a drag on the handle moves the ceiling.\n        resizeHeight(distance: number) {\n          const before = self.height\n          const target = Math.max(before + distance, 40)\n          self.pane.setPaneHeight(target)\n          return target - before\n        },\n      }))\n      .actions(self => ({\n        afterAttach() {\n          const { pane } = self\n          self.applyConfig()\n          pane.adoptTrack(self.trackId)\n          pane.startHosting()\n          addDisposer(\n            self,\n            autorun(\n              () => {\n                const { host } = self\n                if (host) {\n                  pane.setWidth(host.width)\n                  pane.pairWithLinearView(host.id)\n                }\n              },\n              { name: 'LinearGraphDisplayHost' },\n            ),\n          )\n          addDisposer(\n            self,\n            autorun(\n              () => {\n                const height = pane.canvasHeight\n                if (self.height !== height) {\n                  self.setHeight(height)\n                }\n              },\n              { name: 'LinearGraphDisplayHeight' },\n            ),\n          )\n        },\n      }))\n  )\n}\n\nexport type LinearGraphDisplayStateModel = ReturnType<typeof stateModelFactory>\nexport type LinearGraphDisplayModel = Instance<LinearGraphDisplayStateModel>\n", "import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'\n\nimport configSchema, { normalizeSnapshot } from './configSchema.ts'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\n\nexport default function MinigraphBubbleAdapterF(pluginManager: PluginManager) {\n  pluginManager.addAdapterType(\n    () =>\n      new AdapterType({\n        name: 'MinigraphBubbleAdapter',\n        displayName: 'Minigraph bubble BED adapter',\n        normalizeSnapshot,\n        configSchema,\n        adapterMetadata: {\n          category: 'Graph adapters',\n        },\n        getAdapterClass: () =>\n          import('./MinigraphBubbleAdapter.ts').then(r => r.default),\n      }),\n  )\n}\n", "import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { types } from '@jbrowse/mobx-state-tree'\n\nimport type { Instance } from '@jbrowse/mobx-state-tree'\n\n/**\n * #config MinigraphBubbleAdapter\n * #trackType FeatureTrack\n * #fileFormat graph | Minigraph bubble BED | `gfatools bubble` output; HPRC publishes one ready-made, so no preprocessing at all\n * the tabix-indexed BED `gfatools bubble` writes for a minigraph graph: one row\n * per bubble, on the reference's own coordinates. Unlike\n * [RgfaTabixAdapter](/docs/config/rgfatabixadapter) this needs no index build of\n * your own, because HPRC publishes this file beside its minigraph graph.\n *\n * It shows *where* the graph varies and by how much, not the graph itself.\n *\n * #example\n * ```js\n * {\n *   type: 'MinigraphBubbleAdapter',\n *   uri: 'https://jbrowse.org/demos/hprc/hprc-v2.0-mc-grch38.bubbles.bed.gz',\n *   assemblyNameToPanSN: { hg38: 'GRCh38' },\n * }\n * ```\n */\n\nexport function normalizeSnapshot(snap: Record<string, unknown>) {\n  const { uri, baseUri, csi } = snap\n  return typeof uri === 'string'\n    ? {\n        ...snap,\n        bubblesLocation: { uri, baseUri },\n        index: {\n          indexType: csi ? 'CSI' : 'TBI',\n          location: { uri: `${uri}.${csi ? 'csi' : 'tbi'}`, baseUri },\n        },\n      }\n    : snap\n}\n\nconst MinigraphBubbleAdapter = ConfigurationSchema(\n  'MinigraphBubbleAdapter',\n  {\n    /**\n     * #slot\n     */\n    bubblesLocation: {\n      type: 'fileLocation',\n      defaultValue: {\n        uri: '/path/to/graph.bb.bed.gz',\n        locationType: 'UriLocation',\n      },\n    },\n    /**\n     * #slot\n     */\n    index: ConfigurationSchema('MinigraphBubbleIndex', {\n      /**\n       * #slot index.indexType\n       */\n      indexType: {\n        model: types.enumeration('IndexType', ['TBI', 'CSI']),\n        type: 'stringEnum',\n        defaultValue: 'TBI',\n      },\n      /**\n       * #slot index.location\n       */\n      location: {\n        type: 'fileLocation',\n        defaultValue: {\n          uri: '/path/to/graph.bb.bed.gz.tbi',\n          locationType: 'UriLocation',\n        },\n      },\n    }),\n    /**\n     * #slot\n     * Maps a JBrowse assembly name to its PanSN sample prefix, for when they\n     * differ. `gfatools bubble` names each row after the graph's stable\n     * sequence, so a Minigraph-Cactus graph yields `GRCh38#0#chr6` and an\n     * `hg38` assembly needs `{ hg38: 'GRCh38' }`; HPRC's published v1.0\n     * minigraph bubbles are bare (`chr6`) and need nothing.\n     */\n    assemblyNameToPanSN: {\n      type: 'frozen',\n      defaultValue: {},\n    },\n  },\n  {\n    explicitlyTyped: true,\n\n    /**\n     * #preProcessSnapshot\n     *\n     * preprocessor to allow the minimal config\n     * ```json\n     * { \"type\": \"MinigraphBubbleAdapter\", \"uri\": \"graph.bb.bed.gz\" }\n     * ```\n     */\n    preProcessSnapshot: normalizeSnapshot,\n  },\n)\n\nexport type MinigraphBubbleAdapterConfig = Instance<\n  typeof MinigraphBubbleAdapter\n>\n\nexport default MinigraphBubbleAdapter\n", "import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'\n\nimport configSchema, { normalizeSnapshot } from './configSchema.ts'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\n\nexport default function RgfaTabixAdapterF(pluginManager: PluginManager) {\n  pluginManager.addAdapterType(\n    () =>\n      new AdapterType({\n        name: 'RgfaTabixAdapter',\n        displayName: 'Indexed rGFA adapter',\n        normalizeSnapshot,\n        configSchema,\n        // what the launch menus look for (launchSubgraph/subgraphTracks.ts)\n        adapterCapabilities: ['getSubgraph'],\n        adapterMetadata: {\n          category: 'Graph adapters',\n        },\n        getAdapterClass: () =>\n          import('./RgfaTabixAdapter.ts').then(r => r.default),\n      }),\n  )\n}\n", "import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { types } from '@jbrowse/mobx-state-tree'\n\nimport type { Instance } from '@jbrowse/mobx-state-tree'\n\n/**\n * #config RgfaTabixAdapter\n * #trackType FeatureTrack\n * #fileFormat graph | Indexed rGFA | Built by `scripts/build_rgfa_tabix.sh`; serves segments as features and extracts local subgraphs\n * two tabix-indexed BED projections of an rGFA (minigraph). rGFA tags every\n * segment with `SN`/`SO`/`SR`, so both files record coordinates the graph\n * already states rather than inventing any. Plain GFA (pggb, odgi,\n * Minigraph-Cactus) has no such tags and is not supported.\n *\n * The `uri` shorthand takes the prefix the build script was given and resolves\n * `<uri>.segs.bed.gz`, `<uri>.links.bed.gz` and their `.tbi` indexes. `coarse`\n * takes the same shorthand for a second pair at one node per bubble, built by\n * `build_bubble_tier.sh` in jbrowse-components, plus the zoom past which a\n * graph view following a linear view cuts it.\n *\n * #example\n * ```js\n * {\n *   type: 'RgfaTabixAdapter',\n *   uri: 'https://example.com/hprc.rgfa',\n *   coarse: { uri: 'https://example.com/hprc.tier10000', aboveBpPerPx: 1000 },\n * }\n * ```\n */\n\nfunction tbi(uri: string, baseUri: unknown, csi: unknown) {\n  return {\n    indexType: csi ? 'CSI' : 'TBI',\n    location: { uri: `${uri}.${csi ? 'csi' : 'tbi'}`, baseUri },\n  }\n}\n\nfunction prefixLocations(snap: Record<string, unknown>) {\n  const { uri, baseUri, csi } = snap\n  return typeof uri === 'string'\n    ? {\n        ...snap,\n        segmentsLocation: { uri: `${uri}.segs.bed.gz`, baseUri },\n        segmentsIndex: tbi(`${uri}.segs.bed.gz`, baseUri, csi),\n        linksLocation: { uri: `${uri}.links.bed.gz`, baseUri },\n        linksIndex: tbi(`${uri}.links.bed.gz`, baseUri, csi),\n      }\n    : snap\n}\n\nexport function normalizeSnapshot(snap: Record<string, unknown>) {\n  const { coarse, baseUri } = snap\n  return prefixLocations(\n    typeof coarse === 'object' && coarse !== null\n      ? { ...snap, coarse: prefixLocations({ baseUri, ...coarse }) }\n      : snap,\n  )\n}\n\nconst indexSchema = (name: string, defaultUri: string) =>\n  ConfigurationSchema(name, {\n    /**\n     * #slot\n     */\n    indexType: {\n      model: types.enumeration('IndexType', ['TBI', 'CSI']),\n      type: 'stringEnum',\n      defaultValue: 'TBI',\n    },\n    /**\n     * #slot\n     */\n    location: {\n      type: 'fileLocation',\n      defaultValue: { uri: defaultUri, locationType: 'UriLocation' },\n    },\n  })\n\nconst RgfaTabixCoarseTier = ConfigurationSchema('RgfaTabixCoarseTier', {\n  /**\n   * #slot\n   * The linear view's bp per px past which a graph following it cuts this\n   * pair. Unset means the track has no coarse tier. There is no default,\n   * because the zoom a fine cut stays drawable to depends on the graph's\n   * density: a minigraph graph averages ~7 kb per segment, a base-level pggb\n   * graph ~17 bp.\n   */\n  aboveBpPerPx: { type: 'maybeNumber' },\n  /**\n   * #slot\n   */\n  segmentsLocation: {\n    type: 'fileLocation',\n    defaultValue: {\n      uri: '/path/to/graph.tier.segs.bed.gz',\n      locationType: 'UriLocation',\n    },\n  },\n  /**\n   * #slot\n   */\n  segmentsIndex: indexSchema(\n    'RgfaCoarseSegmentsIndex',\n    '/path/to/graph.tier.segs.bed.gz.tbi',\n  ),\n  /**\n   * #slot\n   */\n  linksLocation: {\n    type: 'fileLocation',\n    defaultValue: {\n      uri: '/path/to/graph.tier.links.bed.gz',\n      locationType: 'UriLocation',\n    },\n  },\n  /**\n   * #slot\n   */\n  linksIndex: indexSchema(\n    'RgfaCoarseLinksIndex',\n    '/path/to/graph.tier.links.bed.gz.tbi',\n  ),\n})\n\nconst RgfaTabixAdapter = ConfigurationSchema(\n  'RgfaTabixAdapter',\n  {\n    /**\n     * #slot\n     * one row per segment: `stableName start end segmentId rank`, as emitted by\n     * `gfatools gfa2bed -m`\n     */\n    segmentsLocation: {\n      type: 'fileLocation',\n      defaultValue: {\n        uri: '/path/to/graph.segs.bed.gz',\n        locationType: 'UriLocation',\n      },\n    },\n    /**\n     * #slot\n     */\n    segmentsIndex: indexSchema(\n      'RgfaSegmentsIndex',\n      '/path/to/graph.segs.bed.gz.tbi',\n    ),\n    /**\n     * #slot\n     * one row per link per endpoint, each carrying both endpoints in full so a\n     * neighbour on another stable sequence needs no segment-id lookup\n     */\n    linksLocation: {\n      type: 'fileLocation',\n      defaultValue: {\n        uri: '/path/to/graph.links.bed.gz',\n        locationType: 'UriLocation',\n      },\n    },\n    /**\n     * #slot\n     */\n    linksIndex: indexSchema(\n      'RgfaLinksIndex',\n      '/path/to/graph.links.bed.gz.tbi',\n    ),\n    /**\n     * #slot\n     * Maps a JBrowse assembly name to its PanSN sample prefix in the graph, for\n     * when they differ. Defaults to identity: the assembly name is assumed to be\n     * the PanSN sample name, and a graph whose stable names are bare (minigraph\n     * writes `chr1`) needs nothing here at all.\n     *\n     * Minigraph-Cactus writes PanSN stable names, so HPRC's release-2 graph\n     * calls the reference `GRCh38#0#chr1` and an `hg38` assembly needs\n     * `{ hg38: 'GRCh38' }`. The prefix is what disambiguates: that same graph\n     * also contains `CHM13#0#chr1`, so matching on the contig alone would\n     * silently resolve to the wrong sample.\n     */\n    assemblyNameToPanSN: {\n      type: 'frozen',\n      defaultValue: {},\n    },\n    /**\n     * #slot\n     * The same graph at one node per bubble, which a graph view following a\n     * linear view cuts once that view is zoomed out past `aboveBpPerPx`, and\n     * which no bp cap applies to. `{ uri, aboveBpPerPx }`, where `uri` is a\n     * prefix as the adapter's own is.\n     */\n    coarse: RgfaTabixCoarseTier,\n  },\n  {\n    explicitlyTyped: true,\n\n    /**\n     * #preProcessSnapshot\n     *\n     * preprocessor to allow the minimal config\n     * ```json\n     * { \"type\": \"RgfaTabixAdapter\", \"uri\": \"graph.rgfa\" }\n     * ```\n     */\n    preProcessSnapshot: normalizeSnapshot,\n  },\n)\n\nexport type RgfaTabixAdapterConfig = Instance<typeof RgfaTabixAdapter>\n\nexport default RgfaTabixAdapter\n", "import { getSession } from '@jbrowse/core/util'\nimport { alpha } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport { graphViewHighlights } from './graphViewHighlights'\n\nimport type { HighlightRegion } from './graphViewHighlights'\nimport type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'\n\nconst useStyles = makeStyles()(theme => ({\n  highlight: {\n    height: '100%',\n    position: 'absolute',\n    background: alpha(theme.palette.primary.main, 0.25),\n    borderLeft: `2px solid ${theme.palette.primary.main}`,\n    borderRight: `2px solid ${theme.palette.primary.main}`,\n    pointerEvents: 'none',\n    zIndex: 10,\n  },\n}))\n\n// One band over the linear view for a hovered graph node. `getHighlightCoords`\n// is the LGV's own projection \u2014 it canonicalizes the refName and floors the\n// width to 3 px, so a pure insertion (a zero-length reference span) still shows\n// as a mark rather than vanishing.\nconst Highlight = observer(function Highlight({\n  model,\n  region,\n}: {\n  model: LinearGenomeViewModel\n  region: HighlightRegion\n}) {\n  const { classes } = useStyles()\n  const coords = model.getHighlightCoords(region)\n  return coords ? (\n    <div\n      data-testid=\"graph-node-highlight\"\n      className={classes.highlight}\n      style={{ left: coords.left, width: coords.width }}\n    />\n  ) : null\n})\n\nconst GraphNodeHighlight = observer(function GraphNodeHighlight({\n  model,\n}: {\n  model: LinearGenomeViewModel\n}) {\n  const { views } = getSession(model)\n  return (\n    <>\n      {graphViewHighlights([...views], model.id, model.assemblyNames).map(\n        ({ key, region }) => (\n          <Highlight key={`graph-hover-${key}`} model={model} region={region} />\n        ),\n      )}\n    </>\n  )\n})\n\nexport default GraphNodeHighlight\n", "import { withRows } from '../launchFromGraph/linearViewTarget'\n\nexport interface HighlightRegion {\n  refName: string\n  start: number\n  end: number\n  assemblyName?: string\n}\n\nexport interface GraphViewHighlight {\n  key: string\n  region: HighlightRegion\n}\n\nfunction isRecord(value: unknown): value is Record<string, unknown> {\n  return typeof value === 'object' && value !== null\n}\n\nfunction readRegion(value: unknown): HighlightRegion | undefined {\n  let region: HighlightRegion | undefined\n  if (isRecord(value)) {\n    const { refName, start, end, assemblyName } = value\n    if (\n      typeof refName === 'string' &&\n      typeof start === 'number' &&\n      typeof end === 'number'\n    ) {\n      region = {\n        refName,\n        start,\n        end,\n        assemblyName:\n          typeof assemblyName === 'string' ? assemblyName : undefined,\n      }\n    }\n  }\n  return region\n}\n\n// Whether a graph view's highlights belong on a given linear view.\n// `connectedViewId` is written by the launch menu, so a launched pair is\n// explicit. A graph view without one \u2014 a hand-written session snapshot, or\n// `Add > Graph genome view` followed by a subgraph load \u2014 matches any linear\n// view, because the alternative is silently drawing nothing.\n//\n// So does one whose linear view has been closed. Held to an id nothing answers\n// to, it matched no view and its hover drew nowhere for the rest of the\n// session, the view it next opened included.\nfunction isConnected(\n  view: Record<string, unknown>,\n  linearViewId: string,\n  liveViewIds: ReadonlySet<unknown>,\n) {\n  const connectedViewId = view.connectedViewId\n  return (\n    connectedViewId === undefined ||\n    connectedViewId === linearViewId ||\n    !liveViewIds.has(connectedViewId)\n  )\n}\n\n// ...and whether the view can mean anything by it. `getHighlightCoords`\n// canonicalizes a refName against the region's OWN assembly and then lays it\n// out against this view's displayed regions, without ever asking whether the\n// two are the same assembly \u2014 so a band handed to the wrong view is drawn, at\n// coordinates that belong to somebody else's genome.\n//\n// That is not hypothetical for an unpaired graph, which by the rule above\n// matches every linear view in the session. A synteny stack's rows are LGVs on\n// different assemblies, and a PanSN name reduces to a bare contig: the five\n// E. coli strains each have one refName `chr`, so a graph cut from K12 painted\n// its K12 interval across Sakai's row and CFT073's at their own offsets. With\n// the assembly checked the reference row keeps the band and the rest correctly\n// draw nothing.\n//\n// A region stating no assembly still passes \u2014 `readRegion` leaves it optional,\n// and the fallback is the behaviour every existing snapshot has.\nfunction isOnAssembly(\n  region: HighlightRegion,\n  assemblyNames: string[] | undefined,\n) {\n  return (\n    region.assemblyName === undefined ||\n    assemblyNames === undefined ||\n    assemblyNames.includes(region.assemblyName)\n  )\n}\n\n// The highlights a linear view should draw for the graph views connected to it.\n// Reads `session.views` structurally: the members it needs are declared by\n// GraphGenomeView, not by the AbstractViewModel the session array is typed as.\nexport function graphViewHighlights(\n  views: unknown[],\n  linearViewId: string,\n  // the drawing view's own assemblies, so a band is only drawn where its\n  // coordinates mean something \u2014 see isOnAssembly\n  linearAssemblyNames?: string[],\n): GraphViewHighlight[] {\n  const highlights: GraphViewHighlight[] = []\n  const liveViewIds = new Set(\n    withRows(views).map(view => (isRecord(view) ? view.id : undefined)),\n  )\n  for (const view of views) {\n    if (\n      isRecord(view) &&\n      view.type === 'GraphGenomeView' &&\n      isConnected(view, linearViewId, liveViewIds)\n    ) {\n      const region = readRegion(view.hoverHighlight)\n      if (region && isOnAssembly(region, linearAssemblyNames)) {\n        highlights.push({\n          key: typeof view.id === 'string' ? view.id : 'graph',\n          region,\n        })\n      }\n    }\n  }\n  return highlights\n}\n", "import GraphNodeHighlight from './GraphNodeHighlight'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\n\n// The graph-to-linear half of the hover sync. The reverse half needs no mount\n// point: an LGV already publishes its hover to `session.hovered`, and the graph\n// view's own autorun reads it (see GraphGenomeView/model.ts).\n//\n// Mounted through the extension point rather than imported by the LGV, so this\n// plugin never imports @jbrowse/plugin-linear-genome-view at runtime: it is not\n// one of JBrowse's shared globals, so a value import would bundle a second copy\n// of that whole plugin.\nconst POINT = 'LinearGenomeView-TracksContainerComponent'\n\nexport default function GraphHoverSyncF(pluginManager: PluginManager) {\n  pluginManager.contributeToExtensionPoint(POINT, ({ model }) => (\n    <GraphNodeHighlight key=\"graphgenomeview-hover-highlight\" model={model} />\n  ))\n}\n", "// The name JBrowse knows this plugin by, which a config's `plugins` entry\n// states beside its `esmUrl`.\nexport const PLUGIN_NAME = 'GraphGenomeView'\n", "export const version = '4.0.2'\n"],
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