jbrowse-plugin-graphgenomeviewer 8.7.2 → 8.8.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jbrowse-plugin-graphgenomeviewer",
-  "version": "8.7.2",
+  "version": "8.8.0",
   "description": "JBrowse 2 graph genome (pangenome) view: rGFA reference-anchored layouts, the Bandage force-directed engine, and haplotype lanes read from a gbz-base database",
   "license": "GPL-3.0-or-later",
   "repository": {

package/src/GraphGenomeView/components/GraphSettingsDialog.test.tsx

@@ -16,7 +16,7 @@ function shown(layoutEngine: string) {
     repeatTrackChoices: [],
     hasGraph: true,
     usesLayoutEngine: true,
-    layoutEngine,
+    chosenLayoutEngine: layoutEngine,
     layoutQuality: 2,
     bubbleSpread: 'auto',
     linearLayout: false,

package/src/GraphGenomeView/components/GraphSettingsDialog.tsx

@@ -308,7 +308,7 @@ const GraphSettingsDialog = observer(function GraphSettingsDialog(props: {
 
           <SettingSelect
             label="Engine"
-            value={model.layoutEngine}
+            value={model.chosenLayoutEngine}
             options={LAYOUT_ENGINES}
             testId="graph-layout-engine-select"
             onChange={engine => {
@@ -350,7 +350,7 @@ const GraphSettingsDialog = observer(function GraphSettingsDialog(props: {
             <Caption>How far the layout opens a bubble</Caption>
           </SettingSelect>
 
-          {model.layoutEngine === 'stress' ? null : (
+          {model.chosenLayoutEngine === 'stress' ? null : (
             <SettingSwitch
               label="Linear layout"
               checked={model.linearLayout}

package/src/GraphGenomeView/pane/graphViews.ts

@@ -113,6 +113,7 @@ import type {
 } from '@jbrowse/bandage-core/colorSchemes'
 import type { EdgeWidth } from '@jbrowse/bandage-core/edgeWidths'
 import type { FacetInput, FacetSetting } from '@jbrowse/bandage-core/facetGrid'
+import type { LayoutEngineKind } from '@jbrowse/bandage-core/layoutEngines'
 import type { LayoutModeValue } from '@jbrowse/bandage-core/layoutModes'
 import type { NodeWidth } from '@jbrowse/bandage-core/nodeWidths'
 import type { AssemblyNames } from '@jbrowse/bandage-core/reference'
@@ -169,6 +170,7 @@ function spanIn(
 // as props, a track display in its config
 export interface GraphGrammar {
   layoutMode?: LayoutModeValue
+  layoutEngine?: LayoutEngineKind
   encoding?: GraphEncoding
   size?: NodeSize
   layers?: GraphLayers
@@ -232,6 +234,9 @@ export const withGraphViews = paneBase
       get chosenLayoutMode(): LayoutModeValue {
         return self.grammar.layoutMode ?? 'force'
       },
+      get chosenLayoutEngine(): LayoutEngineKind {
+        return self.grammar.layoutEngine ?? 'fmmm'
+      },
       get chosenColorScheme(): ColorScheme {
         return schemeOfColor(self.grammar.encoding?.color)
       },

package/src/GraphGenomeView/pane/launchActions.ts

@@ -472,7 +472,9 @@ export const withLaunchActions = withRenderingActions
     graphMenuItems(): MenuItem[] {
       const options = this.layoutOptionMenuItems()
       const mode = layoutModeByValue(self.chosenLayoutMode)
-      const engine = ENGINE_NAMES.find(([e]) => e === self.layoutEngine)![1]
+      const engine = ENGINE_NAMES.find(
+        ([e]) => e === self.chosenLayoutEngine,
+      )![1]
       return [
         {
           label: `Layout: ${layoutMenuLabel(mode)}${mode.value === 'force' ? ` (${engine})` : ''}`,
@@ -490,7 +492,7 @@ export const withLaunchActions = withRenderingActions
                     label: `${layoutMenuLabel(mode)} (${name})`,
                     checked:
                       self.chosenLayoutMode === mode.value &&
-                      self.layoutEngine === engine,
+                      self.chosenLayoutEngine === engine,
                     onClick: () => {
                       void self.switchForceEngine(engine)
                     },

package/src/GraphGenomeView/pane/loadActions.ts

@@ -61,7 +61,7 @@ import type { FileLocation } from '@jbrowse/core/util/types'
 const withEngineSettings = withSettingActions.views(self => ({
   get engineSettings() {
     return engineSettingsOf({
-      engine: self.layoutEngine,
+      engine: self.chosenLayoutEngine,
       quality: self.layoutQuality,
       linearLayout: self.linearLayout,
       bubbleSpread: self.bubbleSpread,

package/src/GraphGenomeView/pane/paneBase.ts

@@ -2,7 +2,6 @@ import { lazy } from 'react'
 
 import { BUBBLE_SPREAD_VALUES } from '@jbrowse/bandage-core/bubbleSpreads'
 import { createForceLayoutCache } from '@jbrowse/bandage-core/layout/forceCache'
-import { LAYOUT_ENGINE_VALUES } from '@jbrowse/bandage-core/layoutEngines'
 import { viewportOf } from '@jbrowse/bandage-core/viewport'
 import { types } from '@jbrowse/mobx-state-tree'
 import { RenderLifecycleMixin } from '@jbrowse/render-core/RenderLifecycleMixin'
@@ -246,9 +245,6 @@ export const paneBase = types
       // Cost at the sizes this view draws is milliseconds, and the header
       // states the layout time.
       layoutQuality: types.optional(types.number, 2),
-      // Which engine draws the force layout: Bandage's FMMM, or the stress
-      // layout, which reads the reference straight. See LAYOUT_ENGINES.
-      layoutEngine: lenientOptionalEnum(LAYOUT_ENGINE_VALUES, 'fmmm'),
       linearLayout: types.optional(types.boolean, false),
       // How far the force layout opens a bubble, which on a variation graph is
       // the difference between a legible drawing and a rope. See

package/src/GraphGenomeView/pane/settingActions.ts

@@ -130,7 +130,7 @@ export const withSettingActions = withTubeMapViews
       self.layoutQuality = quality
     },
     setLayoutEngine(engine: LayoutEngineKind) {
-      self.layoutEngine = engine
+      self.writeGrammar({ layoutEngine: engine })
     },
     setLinearLayout(linear: boolean) {
       self.linearLayout = linear

package/src/GraphGenomeView/viewModel.ts

@@ -1,3 +1,4 @@
+import { LAYOUT_ENGINE_VALUES } from '@jbrowse/bandage-core/layoutEngines'
 import { LAYOUT_MODE_VALUES } from '@jbrowse/bandage-core/layoutModes'
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models'
 import { getSession } from '@jbrowse/core/util'
@@ -5,7 +6,7 @@ import { addDisposer, isAlive, types } from '@jbrowse/mobx-state-tree'
 import { reaction } from 'mobx'
 
 import { HOVER_HIGHLIGHT_VALUES } from './hoverHighlight'
-import { lenientMaybeEnum } from './lenientEnum'
+import { lenientMaybeEnum, lenientOptionalEnum } from './lenientEnum'
 import { GraphPane, fileName, formatSpanBp } from './model'
 import { liftFlatNodeColor } from './retiredNodeColor'
 import { canonicalRegion } from '../launchFromGraph/launchFromGraph'
@@ -40,6 +41,9 @@ export default function stateModelFactory() {
         loadedTrackId: types.optional(types.string, ''),
         // unset is force
         layoutMode: lenientMaybeEnum(LAYOUT_MODE_VALUES),
+        // Which engine draws the force layout: Bandage's FMMM, or the stress
+        // layout, which reads the reference straight. See LAYOUT_ENGINES.
+        layoutEngine: lenientOptionalEnum(LAYOUT_ENGINE_VALUES, 'fmmm'),
         color: types.maybe(types.frozen<NodeColor>()),
         size: types.maybe(types.frozen<NodeSize>()),
         layers: types.maybe(types.frozen<GraphLayers>()),
@@ -58,6 +62,7 @@ export default function stateModelFactory() {
       get grammar(): GraphGrammar {
         return {
           layoutMode: self.layoutMode,
+          layoutEngine: self.layoutEngine,
           encoding: { color: self.color },
           size: self.size,
           layers: self.layers,

package/src/LinearGraphDisplay/LinearGraphDisplay.test.ts

@@ -247,8 +247,14 @@ function createEnvironment({
         uri: 'graph',
         ...(tiered ? { coarse } : {}),
       },
+      // anchored, the layout whose cut margins and genomic x most tests here
+      // pin; a track naming no layout opens force-directed
       displays: [
-        { type: 'LinearGraphDisplay', displayId: 'graph-LinearGraphDisplay' },
+        {
+          type: 'LinearGraphDisplay',
+          displayId: 'graph-LinearGraphDisplay',
+          layoutMode: 'auto',
+        },
       ],
     },
     { pluginManager },
@@ -260,8 +266,14 @@ function createEnvironment({
       name: 'walks',
       assemblyNames: [ASM, 'HG1.1', 'HG2.1'],
       adapter: { type: 'GbzBaseSyntenyAdapter', assemblyNames: [ASM] },
+      // anchored, whose margined cut is what the refusal tests' dense
+      // thresholds are set against
       displays: [
-        { type: 'LinearGraphDisplay', displayId: 'walks-LinearGraphDisplay' },
+        {
+          type: 'LinearGraphDisplay',
+          displayId: 'walks-LinearGraphDisplay',
+          layoutMode: 'auto',
+        },
       ],
     },
     { pluginManager },
@@ -1108,6 +1120,7 @@ test('a launch that states one choice takes the rest from the config', async ()
 test('each grammar setter writes the track config, and the pane reads it back', async () => {
   const { display } = await shownGraph()
   display.setLayoutMode('ordered')
+  display.setLayoutEngine('fmmm')
   display.setColorScheme('depth')
   display.setNodeWidth('uniform')
   display.setLinkWidth('walks')
@@ -1116,7 +1129,14 @@ test('each grammar setter writes the track config, and the pane reads it back',
   display.setWalkRowSamples(['HG1'])
   display.setWalkRowOrder('shared')
   display.setHover('off')
-  const slots = ['layoutMode', 'encoding', 'size', 'layers', 'rows'] as const
+  const slots = [
+    'layoutMode',
+    'layoutEngine',
+    'encoding',
+    'size',
+    'layers',
+    'rows',
+  ] as const
   expect(
     Object.fromEntries(
       [...slots, 'hover' as const].map(s => [
@@ -1126,6 +1146,7 @@ test('each grammar setter writes the track config, and the pane reads it back',
     ),
   ).toEqual({
     layoutMode: 'ordered',
+    layoutEngine: 'fmmm',
     encoding: { color: { field: 'depth' } },
     size: { value: 6, links: 'walks' },
     layers: { bubbles: true },
@@ -1135,6 +1156,7 @@ test('each grammar setter writes the track config, and the pane reads it back',
   expect(readConfObject(display.configuration, ['facet', 'field'])).toBe('walk')
   expect([
     display.chosenLayoutMode,
+    display.chosenLayoutEngine,
     display.chosenColorScheme,
     display.nodeWidth,
     display.linkWidth,
@@ -1144,6 +1166,7 @@ test('each grammar setter writes the track config, and the pane reads it back',
     display.chosenHover,
   ]).toEqual([
     'ordered',
+    'fmmm',
     'depth',
     'uniform',
     'walks',
@@ -1199,6 +1222,35 @@ test('a 4.0 FeatureTrack config still opens as the graph', async () => {
   expect(display.hasGraph).toBe(true)
 })
 
+test('a track whose config names no layout opens force-directed, drawn by stress', async () => {
+  const { view } = createEnvironment()
+  view.zoomTo(60_000 / WIDTH_PX)
+  view.scrollTo(1_000_000 / view.bpPerPx)
+  view.showTrack('graph-as-feature', {}, { type: 'LinearGraphDisplay' })
+  const display = view.tracks[0]!.displays[0] as LinearGraphDisplayModel
+  display.startRenderingBackend(fakeRenderer())
+  await wait(SETTLE_MS)
+  expect(display.chosenLayoutMode).toBe('force')
+  expect(display.chosenLayoutEngine).toBe('stress')
+  expect(display.usesLayoutEngine).toBe(true)
+})
+
+test('a config that picks FMMM opens with it, and the graph view it launches keeps it', async () => {
+  const { view } = createEnvironment()
+  view.zoomTo(60_000 / WIDTH_PX)
+  view.scrollTo(1_000_000 / view.bpPerPx)
+  view.showTrack(
+    'graph-as-feature',
+    {},
+    { type: 'LinearGraphDisplay', layoutEngine: 'fmmm' },
+  )
+  const display = view.tracks[0]!.displays[0] as LinearGraphDisplayModel
+  display.startRenderingBackend(fakeRenderer())
+  await wait(SETTLE_MS)
+  expect(display.chosenLayoutEngine).toBe('fmmm')
+  expect(display.graphViewSpec).toMatchObject({ layoutEngine: 'fmmm' })
+})
+
 test("a track naming its reference by an alias of the view's assembly cuts the window", async () => {
   const { view, cuts } = createEnvironment()
   view.zoomTo(60_000 / WIDTH_PX)

package/src/LinearGraphDisplay/configSchema.ts

@@ -1,3 +1,4 @@
+import { LAYOUT_ENGINE_VALUES } from '@jbrowse/bandage-core/layoutEngines'
 import { LAYOUT_MODE_VALUES } from '@jbrowse/bandage-core/layoutModes'
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 import { trackHeightConfigSchemaFields } from '@jbrowse/display-kit/trackHeightConfigSchemaFields'
@@ -20,12 +21,24 @@ export function configSchemaFactory() {
     {
       /**
        * #slot
-       * the layout the track opens in
+       * the layout the track opens in: `force`, which the stress engine draws
+       * in reference order and keeps steady across a pan (ADR-046), or `auto`
+       * for the anchored layout, whose x is reference bp
        */
       layoutMode: {
         type: 'stringEnum',
         model: types.enumeration('LayoutMode', LAYOUT_MODE_VALUES),
-        defaultValue: 'auto',
+        defaultValue: 'force',
+      },
+      /**
+       * #slot
+       * the engine that draws `force`: `stress`, which keeps a re-cut's
+       * drawing in place (ADR-044), or Bandage's `fmmm`
+       */
+      layoutEngine: {
+        type: 'stringEnum',
+        model: types.enumeration('LayoutEngine', LAYOUT_ENGINE_VALUES),
+        defaultValue: 'stress',
       },
       /**
        * #slot

package/src/LinearGraphDisplay/model.ts

@@ -1,7 +1,6 @@
 import { lazy } from 'react'
 import type { ReactNode } from 'react'
 
-import { LAYOUT_ENGINE_VALUES } from '@jbrowse/bandage-core/layoutEngines'
 import { layoutModeByValue } from '@jbrowse/bandage-core/layoutModes'
 import {
   ConfigurationReference,
@@ -26,7 +25,6 @@ import { reaction } from 'mobx'
 import { isNodeLimitError } from '../nodeLimitError'
 import { denseCovers } from './denseWindow'
 import { cutHolds, hostCut, hostWindow } from '../GraphGenomeView/host'
-import { lenientOptionalEnum } from '../GraphGenomeView/lenientEnum'
 import { GraphPane, formatSpanBp } from '../GraphGenomeView/model'
 import { FACET_KEY_PX } from '../GraphGenomeView/pane/fitViews'
 import { paneBase } from '../GraphGenomeView/pane/paneBase'
@@ -103,9 +101,6 @@ export function stateModelFactory(configSchema: LinearGraphDisplayConfigModel) {
       types.model({
         type: types.literal('LinearGraphDisplay'),
         configuration: ConfigurationReference(configSchema),
-        // a zoom re-cuts the graph, and stress keeps the drawing's
-        // orientation across re-cuts where FMMM turns it (ADR-044)
-        layoutEngine: lenientOptionalEnum(LAYOUT_ENGINE_VALUES, 'stress'),
         // the window the graph on screen was asked for, so a restored
         // session cuts it again
         cutRegion: types.maybe(types.frozen<SubgraphRegion>()),
@@ -129,6 +124,7 @@ export function stateModelFactory(configSchema: LinearGraphDisplayConfigModel) {
       get grammar(): GraphGrammar {
         return {
           layoutMode: getConf(self, 'layoutMode'),
+          layoutEngine: getConf(self, 'layoutEngine'),
           encoding: getConf(self, 'encoding'),
           size: getConf(self, 'size'),
           layers: getConf(self, 'layers') as GraphLayers,

package/src/version.ts

@@ -1 +1 @@
-export const version = '8.7.2'
+export const version = '8.8.0'

package/dist/chunks/chunk-64OSFJLE.js

@@ -1,2 +0,0 @@
-import{d as A}from"./chunk-QUDJ7AM3.js";import{a as x,d as O}from"./chunk-TMM73K4C.js";import{f as I}from"./chunk-6VNDP3UB.js";function G(e){return Array.isArray(e)&&e.every(t=>typeof t=="string")}function se(e){let t=x(e).slice(1);return t.length>0?t:void 0}function M(e){return e.type==="WalkTabixSyntenyAdapter"||e.type==="RgfaTabixAdapter"&&(typeof e.walksUri=="string"&&e.walksUri!==""||I(e.walksLocation))}function oe(e){return e.type==="GbzBaseSyntenyAdapter"||M(e)}function ie(e){let{defaultHaplotypes:t}=e;return M(e)&&G(t)&&t.length>0?t:void 0}function ae(e){return x(e)[0]}function ce(e){return O(e).adapter}function ue(e,t){return e===void 0||e===t?void 0:`The graph is cut on its reference, ${e}: open it from a view of ${e}`}function i(e,t){return typeof e.get=="function"?e.get(t):e[t]}function b(e,t){return e.find(n=>n.trackId===t)}function l(e){return`${e.trackId} ${e.name??""}`}var U=new Set(["BedAdapter","BedTabixAdapter","BigBedAdapter","VcfAdapter","VcfTabixAdapter"]),R=/repeat|tandem|\bstr\b|vntr|trf|trgt|vamos|expansion|microsat/i;function Ge(e,t){let n=t?b(e,t):void 0;return n||e.filter(s=>U.has(s.adapterType)).find(s=>R.test(l(s)))}var B=/^\w+=[^;]*(;\w+=[^;]*)*$/;function H(e){let t=i(e,"name");if(!(typeof t!="string"||!B.test(t)))return Object.fromEntries(t.split(";").map(n=>{let r=n.indexOf("=");return[n.slice(0,r),n.slice(r+1)]}))}function d(e,t){let n=i(e,t);return n!==void 0?n:i(e,"INFO")?.[t]??H(e)?.[t]}var P=["RUS","MOTIFS","RU","motifs","motif","sequence","consensus"],v=["RUL","period","PERIOD","consensusSize","unit","unitLength"],j=["TRID","REPID","VARID","ID","name","id"];function h(e,t){for(let n of t){let r=d(e,n),s=String((Array.isArray(r)?r[0]:r)??"").split(",")[0].trim();if(s!==""&&s!==".")return s}}var $=/^[ACGTURYSWKMBDHVN]+$/i;function V(e){let t=Number(h(e,v));if(Number.isFinite(t)&&t>0)return Math.round(t);let n=h(e,P);return n&&$.test(n)?n.length:void 0}function m(e){return(Array.isArray(e)?e:String(e??"").split(",")).map(n=>{let r=n===""||n===null||n===void 0?NaN:Number(n);return Number.isFinite(r)?r:void 0})}function N(e){return(Array.isArray(e)?e:String(e??"").split(",")).map(n=>{let r=String(n??"").trim();return r===""||r==="."?void 0:r})}var w="<CNV:TR>";function K(e){let t=N(i(e,"ALT"));if(!t.includes(w))return;let n=m(d(e,"RN")),r=N(d(e,"RUS")),s=m(d(e,"RUL")),o=m(d(e,"RUC")),a=m(d(e,"RB")),c=0;return t.map((u,f)=>{let p=n[f]??(u===w?1:0),k=0,S=0;for(let F=0;F<p;F++,c++){let y=r[c],L=s[c]??(y&&$.test(y)?y.length:void 0),_=o[c],C=a[c]??(L&&_!==void 0?Math.round(L*_):void 0);C!==void 0&&(k+=C,S++)}return u===w&&p>0&&S===p?k:void 0})}function Y(e,t,n){let r=e?.includes("|");return(e??"").split(/[/|]/).flatMap((s,o)=>{let a=s===""?NaN:Number(s),c=a>0?t[a-1]:n;return!Number.isInteger(a)||c===void 0?[]:[{bp:c,...r?{haplotype:o+1}:{}}]})}function W(e,t,n){let r=i(e,"samples"),s={};for(let[o,a]of Object.entries(r??{})){let c=m(a.SD),u=m(a.AL).flatMap((p,k)=>p!==void 0&&p>0?[c[k]===void 0?{bp:p}:{bp:p,spanningReads:c[k]}]:[]),f=u.length>0||!t?u:Y(N(a.GT)[0],t,n);f.length>0&&(s[o]=f)}return Object.keys(s).length>0?s:void 0}function J(e,t){let n=d(e,"start"),r=d(e,"end"),s=m(d(e,"SVLEN"))[0];return t&&s!==void 0?{start:n+1,end:n+1+s}:{start:n,end:r}}function Ue(e){let t=[];for(let n of e){let r=K(n),{start:s,end:o}=J(n,r!==void 0),a=V(n);if(!(o>s)||a===void 0)continue;let c=d(n,"refName"),u=h(n,P),f=h(n,j);t.push({key:`${c}:${s}-${o}`,name:(f&&!B.test(f)?f:void 0)??(u&&u.length<=12?`(${u})n`:`${c}:${(s+1).toLocaleString("en-US")}-${o.toLocaleString("en-US")}`),refName:c,start:s,end:o,unit:a,motif:u,calls:W(n,r,o-s)})}return t.sort((n,r)=>n.start-r.start)}function T(e){let t=[];for(let n of[...e].sort((r,s)=>r.start-s.start)){let r=t.at(-1);r&&n.start<=r.end?r.end=Math.max(r.end,n.end):t.push({...n})}return t}function E(e){let t=[],n=new Map;for(let r of[...e].sort((s,o)=>s.start-o.start)){let s=`${r.refName}	${r.strand}	${r.name}`,o=n.get(s);if(o&&r.start<o.end)o.end=Math.max(o.end,r.end),o.exons=T([...o.exons,...r.exons]);else{let a={...r,exons:T(r.exons)};t.push(a),n.set(s,a)}}return t}var q=new Set(["Gff3TabixAdapter","Gff3Adapter","BedTabixAdapter","BedAdapter","GtfTabixAdapter","GtfAdapter","BigBedAdapter","NCListAdapter"]),z=/gene|refseq|gencode|ensembl|annotation/i,X=new Set(["BedTabixAdapter","BedAdapter"]);function Qe(e,t){let n=t?b(e,t):void 0;if(n)return n;let r=e.filter(s=>q.has(s.adapterType)&&!R.test(l(s)));return r.find(s=>z.test(l(s)))??r.find(s=>!X.has(s.adapterType))}var Q=/\bTEs?\b|transpos/i;function Ze(e){return e&&Q.test(l(e))?"TE":"gene"}function en(e,t){let n=e.tracks?.find(r=>A(r.configuration,"trackId")===t)?.displays[0];return n?A(n.configuration,"filter")??[]:[]}var Z=new Set(["chromosome","region","contig","supercontig","scaffold"]),ee=new Set(["exon","CDS","five_prime_UTR","three_prime_UTR","UTR"]);function D(e,t){let n=i(e,"type");typeof n=="string"&&ee.has(n)&&t.push({start:i(e,"start"),end:i(e,"end")});let r=i(e,"subfeatures");for(let s of r??[])D(s,t)}function nn(e){let t=[];for(let n of e){let r=i(n,"gene_name")??i(n,"name")??i(n,"gene")??i(n,"gene_id"),s=i(n,"start"),o=i(n,"end");if(!r||!(o>s)||Z.has(i(n,"type")))continue;let a=[];D(n,a),t.push({name:r,refName:i(n,"refName"),start:s,end:o,strand:i(n,"strand")??0,exons:a.length?T(a):[{start:s,end:o}]})}return E(t)}var g=JBrowseExports["tss-react/mui"],ne=e=>g!=null&&e in Object(g)?g[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from 'tss-react/mui' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e});var rn=ne("makeStyles"),sn=g&&g.__esModule?g.default:g;export{se as a,M as b,oe as c,ie as d,ae as e,ce as f,ue as g,U as h,Ge as i,Ue as j,q as k,Qe as l,Ze as m,en as n,nn as o,rn as p};
-//# sourceMappingURL=chunk-64OSFJLE.js.map

package/dist/chunks/chunk-64OSFJLE.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../src/graphTrackConfig.ts", "../../src/GraphGenomeView/trackFeatures.ts", "../../src/GraphGenomeView/repeats/repeatFeatures.ts", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.6.2/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-EQDQ7P4Y.js", "../../src/GraphGenomeView/genes/geneFeatures.ts", "jbrowse-host:tss-react/mui"],
-  "sourcesContent": ["import {\n  getConfAssemblyNamesOrNone,\n  toTrackConfigEntry,\n} from '@jbrowse/core/util/tracks'\n\nimport { snapshotNamesFile } from './locationName.ts'\n\nimport type { AnyTrackConfig } from '@jbrowse/core/configuration'\n\nfunction isStringArray(value: unknown): value is string[] {\n  return Array.isArray(value) && value.every(item => typeof item === 'string')\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: AnyTrackConfig) {\n  const lanes = getConfAssemblyNamesOrNone(track).slice(1)\n  return lanes.length > 0 ? lanes : undefined\n}\n\n// Whether a track names a walk file, by the `walksUri` shorthand as written\n// or the location it expands to: an rGFA track may, and a\n// WalkTabixSyntenyAdapter one does\nexport function walkIndexed(adapterConfig: Record<string, unknown>) {\n  return (\n    adapterConfig.type === 'WalkTabixSyntenyAdapter' ||\n    (adapterConfig.type === 'RgfaTabixAdapter' &&\n      ((typeof adapterConfig.walksUri === 'string' &&\n        adapterConfig.walksUri !== '') ||\n        snapshotNamesFile(adapterConfig.walksLocation)))\n  )\n}\n\n// Whether a track's cut reads `haplotypes`: a GBZ cut does, and so does an\n// rGFA one with a walk file\nexport function cutsByHaplotype(adapterConfig: Record<string, unknown>) {\n  return (\n    adapterConfig.type === 'GbzBaseSyntenyAdapter' || walkIndexed(adapterConfig)\n  )\n}\n\n// The haplotypes a walk-indexed track's config names to cut for until the\n// user picks others\nexport function configHaplotypes(adapterConfig: Record<string, unknown>) {\n  const { defaultHaplotypes } = adapterConfig\n  return walkIndexed(adapterConfig) &&\n    isStringArray(defaultHaplotypes) &&\n    defaultHaplotypes.length > 0\n    ? defaultHaplotypes\n    : 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: AnyTrackConfig) {\n  return getConfAssemblyNamesOrNone(track)[0]\n}\n\n// A track's adapter config, from a live node or a session's frozen entry\nexport function trackAdapterSnapshot(track: AnyTrackConfig) {\n  return toTrackConfigEntry(track).adapter as Record<string, unknown>\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 ${referenceAssembly}`\n}\n", "import type { Feature } from '@jbrowse/core/util'\n\nexport type FeatureLike = Feature | Record<string, unknown>\n\nexport function ownField(f: FeatureLike, name: string): unknown {\n  return typeof (f as Feature).get === 'function'\n    ? (f as Feature).get(name)\n    : (f as Record<string, unknown>)[name]\n}\n\nexport interface TrackChoice {\n  trackId: string\n  name?: string\n  adapterType: string\n}\n\nexport function namedTrack<T extends TrackChoice>(tracks: T[], named: string) {\n  return tracks.find(t => t.trackId === named)\n}\n\n// what a track-name hint such as /repeat|tandem/ is matched against\nexport function trackLabel(t: TrackChoice) {\n  return `${t.trackId} ${t.name ?? ''}`\n}\n", "import { namedTrack, ownField, trackLabel } from '../trackFeatures'\n\nimport type { FeatureLike, TrackChoice } from '../trackFeatures'\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  // the PanSN haplotype a phased genotype puts this allele on\n  haplotype?: 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) or a genotype over VCF 4.5 <CNV:TR> alleles; absent from a\n  // 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\nexport const REPEAT_TRACK_HINT =\n  /repeat|tandem|\\bstr\\b|vntr|trf|trgt|vamos|expansion|microsat/i\n\nexport function pickRepeatTrack<T extends TrackChoice>(\n  tracks: T[],\n  named: string,\n) {\n  const chosen = named ? namedTrack(tracks, named) : undefined\n  if (chosen) {\n    return chosen\n  }\n  const candidates = tracks.filter(t => REPEAT_ADAPTER_TYPES.has(t.adapterType))\n  return candidates.find(t => REPEAT_TRACK_HINT.test(trackLabel(t)))\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 = ownField(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 = ownField(f, name)\n  if (top !== undefined) {\n    return top\n  }\n  const info = ownField(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 strings(value: unknown) {\n  const raw: unknown[] = Array.isArray(value)\n    ? value\n    : String(value ?? '').split(',')\n  return raw.map(one => {\n    const text = String(one ?? '').trim()\n    return text === '' || text === '.' ? undefined : text\n  })\n}\n\nconst TANDEM_REPEAT = '<CNV:TR>'\n\n// Each ALT allele's length, off VCF 4.5's flattened list-of-lists: RN says how\n// many RUS/RUL/RUC/RB entries each allele takes, and the allele's bases are\n// its runs' RB, or unit length times count where RB is missing. An allele that\n// is not <CNV:TR>, or has a run stating neither, has none.\nfunction tandemAlleleBp(f: FeatureLike) {\n  const alts = strings(ownField(f, 'ALT'))\n  if (!alts.includes(TANDEM_REPEAT)) {\n    return undefined\n  }\n  const rn = numbers(field(f, 'RN'))\n  const rus = strings(field(f, 'RUS'))\n  const rul = numbers(field(f, 'RUL'))\n  const ruc = numbers(field(f, 'RUC'))\n  const rb = numbers(field(f, 'RB'))\n  let k = 0\n  return alts.map((alt, i) => {\n    const n = rn[i] ?? (alt === TANDEM_REPEAT ? 1 : 0)\n    let bp = 0\n    let known = 0\n    for (let j = 0; j < n; j++, k++) {\n      const motif = rus[k]\n      const unitLength =\n        rul[k] ?? (motif && IUPAC.test(motif) ? motif.length : undefined)\n      const count = ruc[k]\n      const runBp =\n        rb[k] ??\n        (unitLength && count !== undefined\n          ? Math.round(unitLength * count)\n          : undefined)\n      if (runBp !== undefined) {\n        bp += runBp\n        known++\n      }\n    }\n    return alt === TANDEM_REPEAT && n > 0 && known === n ? bp : undefined\n  })\n}\n\n// A sample's alleles through its genotype: 0 is the reference's, an index\n// past it the ALT allele's. A phased genotype's k-th allele is PanSN\n// haplotype k, the order vg deconstruct writes an assembly's haplotypes in.\nfunction genotyped(\n  gt: string | undefined,\n  alleleBp: (number | undefined)[],\n  referenceBp: number,\n) {\n  const phased = gt?.includes('|')\n  return (gt ?? '').split(/[/|]/).flatMap((index, k): RepeatCall[] => {\n    const i = index === '' ? NaN : Number(index)\n    const bp = i > 0 ? alleleBp[i - 1] : referenceBp\n    if (!Number.isInteger(i) || bp === undefined) {\n      return []\n    }\n    return [{ bp, ...(phased ? { haplotype: k + 1 } : {}) }]\n  })\n}\n\nfunction callsOf(\n  f: FeatureLike,\n  alleleBp: (number | undefined)[] | undefined,\n  referenceBp: number,\n) {\n  const samples = ownField(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 lengths = numbers(fields.AL).flatMap((bp, i) =>\n      bp !== undefined && bp > 0\n        ? [reads[i] === undefined ? { bp } : { bp, spanningReads: reads[i] }]\n        : [],\n    )\n    const calls =\n      lengths.length > 0 || !alleleBp\n        ? lengths\n        : genotyped(strings(fields.GT)[0], alleleBp, referenceBp)\n    if (calls.length > 0) {\n      called[sample] = calls\n    }\n  }\n  return Object.keys(called).length > 0 ? called : undefined\n}\n\n// A <CNV:TR> record's POS is the base before the array and SVLEN the\n// reference allele's length, while a VCF feature starts at that padding base.\nfunction spanOf(f: FeatureLike, tandem: boolean) {\n  const start = field(f, 'start') as number\n  const end = field(f, 'end') as number\n  const svlen = numbers(field(f, 'SVLEN'))[0]\n  return tandem && svlen !== undefined\n    ? { start: start + 1, end: start + 1 + svlen }\n    : { start, end }\n}\n\nexport function repeatArraysFrom(features: FeatureLike[]): RepeatArray[] {\n  const arrays: RepeatArray[] = []\n  for (const f of features) {\n    const alleleBp = tandemAlleleBp(f)\n    const { start, end } = spanOf(f, alleleBp !== undefined)\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}:${(start + 1).toLocaleString('en-US')}-${end.toLocaleString('en-US')}`),\n      refName,\n      start,\n      end,\n      unit,\n      motif,\n      calls: callsOf(f, alleleBp, end - start),\n    })\n  }\n  return arrays.sort((a, b) => a.start - b.start)\n}\n", "// src/genes/geneFiles.ts\nvar GENE_TYPE = /(gene|gene_segment|RNA|transcript)$/i;\nvar isGene = (type) => GENE_TYPE.test(type) || type === \"CDS\" || type === \"exon\";\nfunction mergedIntervals(intervals) {\n  const out = [];\n  for (const iv of [...intervals].sort((a, b) => a.start - b.start)) {\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}\nfunction strandOf(s) {\n  return s === \"+\" ? 1 : s === \"-\" ? -1 : 0;\n}\nfunction unescape(value) {\n  try {\n    return decodeURIComponent(value);\n  } catch {\n    return value;\n  }\n}\nfunction attributes(column) {\n  const out = /* @__PURE__ */ new Map();\n  for (const pair of column.split(\";\")) {\n    const eq = pair.indexOf(\"=\");\n    if (eq > 0) {\n      out.set(pair.slice(0, eq).trim(), unescape(pair.slice(eq + 1).trim()));\n    }\n  }\n  return out;\n}\nfunction gff3Row(line) {\n  const cols = line.split(\"\t\");\n  const start = Number(cols[3]);\n  const end = Number(cols[4]);\n  if (cols.length < 9 || !Number.isInteger(start) || !Number.isInteger(end)) {\n    return void 0;\n  }\n  return {\n    refName: cols[0],\n    type: cols[2],\n    start: start - 1,\n    end,\n    strand: strandOf(cols[6]),\n    attrs: attributes(cols[8])\n  };\n}\nfunction genesFromGff3Lines(lines) {\n  const rows = [];\n  for (const line of lines) {\n    if (line.startsWith(\"##FASTA\")) {\n      break;\n    }\n    const row = line.startsWith(\"#\") ? void 0 : gff3Row(line);\n    if (row) {\n      rows.push(row);\n    }\n  }\n  const parentOf = /* @__PURE__ */ new Map();\n  for (const { attrs } of rows) {\n    const id = attrs.get(\"ID\");\n    const parent = attrs.get(\"Parent\")?.split(\",\")[0];\n    if (id && parent) {\n      parentOf.set(id, parent);\n    }\n  }\n  const rootOf = (row) => {\n    let id = row.attrs.get(\"Parent\")?.split(\",\")[0] ?? row.attrs.get(\"ID\");\n    if (!id) {\n      return row.attrs.get(\"gene_id\");\n    }\n    const seen = /* @__PURE__ */ new Set();\n    while (id && parentOf.has(id) && !seen.has(id)) {\n      seen.add(id);\n      id = parentOf.get(id);\n    }\n    return id;\n  };\n  const groups = /* @__PURE__ */ new Map();\n  rows.forEach((row, i) => {\n    const root = rootOf(row) ?? `#${i}`;\n    const key = `${row.refName}\t${root}`;\n    const group = groups.get(key) ?? groups.set(key, { rows: [] }).get(key);\n    group.rows.push(row);\n    if (!row.attrs.has(\"Parent\") && !group.top) {\n      group.top = row;\n    }\n  });\n  const genes = [];\n  for (const [key, { top, rows: rows2 }] of groups) {\n    if (top && !isGene(top.type)) {\n      continue;\n    }\n    const first = top ?? rows2[0];\n    const start = top?.start ?? Math.min(...rows2.map((r) => r.start));\n    const end = top?.end ?? Math.max(...rows2.map((r) => r.end));\n    const a = first.attrs;\n    const spans = (type) => rows2.filter((r) => r.type === type).map((r) => ({ start: r.start, end: r.end }));\n    const exons = spans(\"exon\");\n    const coding = spans(\"CDS\");\n    const transcribed = rows2.some(\n      (r) => r !== top && r.type !== \"exon\" && r.type !== \"CDS\"\n    );\n    genes.push({\n      name: a.get(\"Name\") ?? a.get(\"gene_name\") ?? a.get(\"gene\") ?? a.get(\"gene_id\") ?? key.split(\"\t\")[1],\n      refName: first.refName,\n      start,\n      end,\n      strand: first.strand,\n      // A range read holds only the rows over its window, so a gene with\n      // transcripts but no exon or CDS there is intronic in it. Only a gene\n      // with no transcripts, as a bacterium's gene and CDS, is one exon.\n      exons: exons.length ? mergedIntervals(exons) : transcribed ? mergedIntervals(coding) : [{ start, end }]\n    });\n  }\n  return genes;\n}\nfunction mergeOverlappingByName(genes) {\n  const out = [];\n  const open = /* @__PURE__ */ new Map();\n  for (const g of [...genes].sort((a, b) => a.start - b.start)) {\n    const key = `${g.refName}\t${g.strand}\t${g.name}`;\n    const last = open.get(key);\n    if (last && g.start < last.end) {\n      last.end = Math.max(last.end, g.end);\n      last.exons = mergedIntervals([...last.exons, ...g.exons]);\n    } else {\n      const gene = { ...g, exons: mergedIntervals(g.exons) };\n      out.push(gene);\n      open.set(key, gene);\n    }\n  }\n  return out;\n}\nvar BED_HEADER = /^(#|track\\s|browser\\s)/;\nfunction genesFromBed(text) {\n  const rows = [];\n  for (const line of text.split(\"\\n\")) {\n    const cols = line.replace(/\\r$/, \"\").split(\"\t\");\n    const start = Number(cols[1]);\n    const end = Number(cols[2]);\n    if (BED_HEADER.test(line) || cols.length < 3 || !Number.isInteger(start) || !(end > start)) {\n      continue;\n    }\n    const refName = cols[0];\n    const name = cols[3] && cols[3] !== \".\" ? cols[3] : `${refName}:${start + 1}-${end}`;\n    const sizes = cols[10]?.split(\",\").filter((s) => s !== \"\").map(Number);\n    const starts = cols[11]?.split(\",\").filter((s) => s !== \"\").map(Number);\n    const blocks = sizes?.length && sizes.length === starts?.length ? sizes.map((size, i) => ({\n      start: start + starts[i],\n      end: start + starts[i] + size\n    })) : [{ start, end }];\n    rows.push({\n      name,\n      refName,\n      start,\n      end,\n      strand: strandOf(cols[5]),\n      exons: blocks\n    });\n  }\n  return mergeOverlappingByName(rows);\n}\nfunction sniffedFormat(text) {\n  const first = text.split(\"\\n\", 1e3).find((l) => l.trim() !== \"\" && !BED_HEADER.test(l));\n  const cols = first?.split(\"\t\") ?? [];\n  return /^\\d+$/.test(cols[1] ?? \"\") && /^\\d+$/.test(cols[2] ?? \"\") ? \"bed\" : \"gff3\";\n}\nfunction genesFromText(text, format = sniffedFormat(text)) {\n  return format === \"bed\" ? genesFromBed(text) : genesFromGff3Lines(text.split(/\\r?\\n/));\n}\n\nexport {\n  mergedIntervals,\n  genesFromGff3Lines,\n  mergeOverlappingByName,\n  genesFromBed,\n  genesFromText\n};\n", "import {\n  mergeOverlappingByName,\n  mergedIntervals,\n} from '@jbrowse/bandage-core/genes/geneFiles'\nimport { readConfObject } from '@jbrowse/core/configuration'\n\nimport { REPEAT_TRACK_HINT } from '../repeats/repeatFeatures'\nimport { namedTrack, ownField, trackLabel } from '../trackFeatures'\n\nimport type { FeatureLike, TrackChoice } from '../trackFeatures'\nimport type { GeneModel } from '@jbrowse/bandage-core/genes/genePins'\nimport type { AnyConfigurationModel } from '@jbrowse/core/configuration'\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  'BedTabixAdapter',\n  'BedAdapter',\n  'GtfTabixAdapter',\n  'GtfAdapter',\n  'BigBedAdapter',\n  'NCListAdapter',\n])\n\nconst GENE_TRACK_HINT = /gene|refseq|gencode|ensembl|annotation/i\n\n// A BED track is as often peaks or repeats as genes, so one counts only where\n// its name says it is annotation\nconst BED_ADAPTER_TYPES = new Set(['BedTabixAdapter', 'BedAdapter'])\n\n// Which of the session's tracks to read genes from: the named one while the\n// assembly has it (a saved pick can name a track since removed), else the\n// first gene-bearing track on the assembly whose name says it is annotation,\n// else the first non-BED gene-bearing track. A track whose name says repeats is\n// never picked unnamed, as \"RepeatMasker annotation\" would be.\nexport function pickGeneTrack<T extends TrackChoice>(\n  tracks: T[],\n  named: string,\n) {\n  const chosen = named ? namedTrack(tracks, named) : undefined\n  if (chosen) {\n    return chosen\n  }\n  const candidates = tracks.filter(\n    t =>\n      GENE_ADAPTER_TYPES.has(t.adapterType) &&\n      !REPEAT_TRACK_HINT.test(trackLabel(t)),\n  )\n  return (\n    candidates.find(t => GENE_TRACK_HINT.test(trackLabel(t))) ??\n    candidates.find(t => !BED_ADAPTER_TYPES.has(t.adapterType))\n  )\n}\n\nconst TE_TRACK_HINT = /\\bTEs?\\b|transpos/i\n\n// What a walk row's boxes are, for the key: TEs where the annotation track's\n// name says so, else genes\nexport function annotationNoun(track: TrackChoice | undefined) {\n  return track && TE_TRACK_HINT.test(trackLabel(track)) ? 'TE' : 'gene'\n}\n\ninterface LaneView {\n  tracks?: readonly {\n    configuration: AnyConfigurationModel\n    displays: readonly { configuration: AnyConfigurationModel }[]\n  }[]\n}\n\n// The `filter` of the gene track's lane in the view the graph is drawn in, so\n// the chips name what the lane draws. None where the view shows no such lane,\n// or has no tracks, as a graph genome view of its own.\nexport function laneFilters(view: object, trackId: string | undefined) {\n  const lane = (view as LaneView).tracks?.find(\n    t => readConfObject(t.configuration, 'trackId') === trackId,\n  )?.displays[0]\n  return lane\n    ? ((readConfObject(lane.configuration, 'filter') as string[] | undefined) ??\n        [])\n    : []\n}\n\n// Records spanning a whole sequence, the types the GFF3 adapter declines to\n// widen a fetch for. RefSeq opens every molecule with a `region` named\n// ANONYMOUS.\nconst WHOLE_SEQUENCE_TYPES = new Set([\n  'chromosome',\n  'region',\n  'contig',\n  'supercontig',\n  'scaffold',\n])\n\n// JBrowse's BED parser splits a coding BED12 block into CDS and UTR parts and\n// keeps `exon` for non-coding ones, so all of them are exon\nconst EXON_PARTS = new Set([\n  'exon',\n  'CDS',\n  'five_prime_UTR',\n  'three_prime_UTR',\n  'UTR',\n])\n\nfunction exonsOf(f: FeatureLike, into: { start: number; end: number }[]) {\n  const type = ownField(f, 'type')\n  if (typeof type === 'string' && EXON_PARTS.has(type)) {\n    into.push({\n      start: ownField(f, 'start') as number,\n      end: ownField(f, 'end') as number,\n    })\n  }\n  const children = ownField(f, 'subfeatures') as FeatureLike[] | undefined\n  for (const child of children ?? []) {\n    exonsOf(child, into)\n  }\n}\n\n// Genes from a track's features: every top-level feature but a whole-sequence\n// record, named by the first of gene_name, name, gene and gene_id it carries,\n// with the exons found anywhere under it merged. A feature with no exons is one exon,\n// its whole span. A BED track gives one feature per transcript, so a name's\n// overlapping features merge, while its copies down the contig stay apart.\n// UCSC's ncbiRefSeq.gff gene records carry their symbol only as gene_id. A\n// feature with none of those names is left out: its raw ID, RefSeq's\n// `id-NC_000913.3:1978503..1979270`, only restates where it is.\nexport function geneModelsFrom(features: FeatureLike[]): GeneModel[] {\n  const genes: GeneModel[] = []\n  for (const f of features) {\n    const name =\n      (ownField(f, 'gene_name') as string | undefined) ??\n      (ownField(f, 'name') as string | undefined) ??\n      (ownField(f, 'gene') as string | undefined) ??\n      (ownField(f, 'gene_id') as string | undefined)\n    const start = ownField(f, 'start') as number\n    const end = ownField(f, 'end') as number\n    if (\n      !name ||\n      !(end > start) ||\n      WHOLE_SEQUENCE_TYPES.has(ownField(f, 'type') as string)\n    ) {\n      continue\n    }\n    const exons: { start: number; end: number }[] = []\n    exonsOf(f, exons)\n    genes.push({\n      name,\n      refName: ownField(f, 'refName') as string,\n      start,\n      end,\n      strand: (ownField(f, 'strand') as number | undefined) ?? 0,\n      exons: exons.length ? mergedIntervals(exons) : [{ start, end }],\n    })\n  }\n  return mergeOverlappingByName(genes)\n}\n", "const host = JBrowseExports[\"tss-react/mui\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\"This JBrowse does not provide '\" + name + \"' from '\" + \"tss-react/mui\" + \"' to plugins: \" + \"GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\")\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const cx = /* @__PURE__ */ read(\"cx\")\nexport const keyframes = /* @__PURE__ */ read(\"keyframes\")\nexport const makeStyles = /* @__PURE__ */ read(\"makeStyles\")\nexport default host && host.__esModule ? host.default : host"],
-  "mappings": "+HASA,SAASA,EAAcC,EAAmC,CACxD,OAAO,MAAM,QAAQA,CAAK,GAAKA,EAAM,MAAMC,GAAQ,OAAOA,GAAS,QAAQ,CAC7E,CAIO,SAASC,GAAWC,EAAuB,CAChD,IAAMC,EAAQC,EAA2BF,CAAK,EAAE,MAAM,CAAC,EACvD,OAAOC,EAAM,OAAS,EAAIA,EAAQ,MACpC,CAKO,SAASE,EAAYC,EAAwC,CAClE,OACEA,EAAc,OAAS,2BACtBA,EAAc,OAAS,qBACpB,OAAOA,EAAc,UAAa,UAClCA,EAAc,WAAa,IAC3BC,EAAkBD,EAAc,aAAa,EAErD,CAIO,SAASE,GAAgBF,EAAwC,CACtE,OACEA,EAAc,OAAS,yBAA2BD,EAAYC,CAAa,CAE/E,CAIO,SAASG,GAAiBH,EAAwC,CACvE,GAAM,CAAE,kBAAAI,CAAkB,EAAIJ,EAC9B,OAAOD,EAAYC,CAAa,GAC9BR,EAAcY,CAAiB,GAC/BA,EAAkB,OAAS,EACzBA,EACA,MACN,CAMO,SAASC,GAAuBT,EAAuB,CAC5D,OAAOE,EAA2BF,CAAK,EAAE,CAAC,CAC5C,CAGO,SAASU,GAAqBV,EAAuB,CAC1D,OAAOW,EAAmBX,CAAK,EAAE,OACnC,CAEO,SAASY,GACdC,EACAC,EACA,CACA,OAAOD,IAAsB,QAAaA,IAAsBC,EAC5D,OACA,sCAAsCD,CAAiB,4BAA4BA,CAAiB,EAC1G,CCpEO,SAASE,EAASC,EAAgBC,EAAuB,CAC9D,OAAO,OAAQD,EAAc,KAAQ,WAChCA,EAAc,IAAIC,CAAI,EACtBD,EAA8BC,CAAI,CACzC,CAQO,SAASC,EAAkCC,EAAaC,EAAe,CAC5E,OAAOD,EAAO,KAAKE,GAAKA,EAAE,UAAYD,CAAK,CAC7C,CAGO,SAASE,EAAWD,EAAgB,CACzC,MAAO,GAAGA,EAAE,OAAO,IAAIA,EAAE,MAAQ,EAAE,EACrC,CCgBO,IAAME,EAAuB,IAAI,IAAI,CAC1C,aACA,kBACA,gBACA,aACA,iBACF,CAAC,EAEYC,EACX,gEAEK,SAASC,GACdC,EACAC,EACA,CACA,IAAMC,EAASD,EAAQE,EAAWH,EAAQC,CAAK,EAAI,OACnD,OAAIC,GAGeF,EAAO,OAAOI,GAAKP,EAAqB,IAAIO,EAAE,WAAW,CAAC,EAC3D,KAAKA,GAAKN,EAAkB,KAAKO,EAAWD,CAAC,CAAC,CAAC,CACnE,CAKA,IAAME,EAAc,2BAEpB,SAASC,EAAWC,EAAgB,CAClC,IAAMC,EAAOC,EAASF,EAAG,MAAM,EAC/B,GAAI,SAAOC,GAAS,UAAY,CAACH,EAAY,KAAKG,CAAI,GAGtD,OAAO,OAAO,YACZA,EAAK,MAAM,GAAG,EAAE,IAAIE,GAAQ,CAC1B,IAAMC,EAAID,EAAK,QAAQ,GAAG,EAC1B,MAAO,CAACA,EAAK,MAAM,EAAGC,CAAC,EAAGD,EAAK,MAAMC,EAAI,CAAC,CAAC,CAC7C,CAAC,CACH,CACF,CAIA,SAASC,EAAML,EAAgBC,EAAuB,CACpD,IAAMK,EAAMJ,EAASF,EAAGC,CAAI,EAC5B,OAAIK,IAAQ,OACHA,EAEIJ,EAASF,EAAG,MAAM,IACjBC,CAAI,GAAKF,EAAWC,CAAC,IAAIC,CAAI,CAC7C,CAEA,IAAMM,EAAe,CACnB,MACA,SACA,KACA,SACA,QACA,WACA,WACF,EACMC,EAAgB,CACpB,MACA,SACA,SACA,gBACA,OACA,YACF,EACMC,EAAc,CAAC,OAAQ,QAAS,QAAS,KAAM,OAAQ,IAAI,EAKjE,SAASC,EAAMV,EAAgBW,EAAiB,CAC9C,QAAWV,KAAQU,EAAO,CACxB,IAAMC,EAAQP,EAAML,EAAGC,CAAI,EACrBY,EAAM,QAAQ,MAAM,QAAQD,CAAK,EAAIA,EAAM,CAAC,EAAIA,IAAU,EAAE,EAC/D,MAAM,GAAG,EAAE,CAAC,EACZ,KAAK,EACR,GAAIC,IAAQ,IAAMA,IAAQ,IACxB,OAAOA,CAEX,CAEF,CAEA,IAAMC,EAAQ,yBAGP,SAASC,EAAaf,EAAgB,CAC3C,IAAMgB,EAAS,OAAON,EAAMV,EAAGQ,CAAa,CAAC,EAC7C,GAAI,OAAO,SAASQ,CAAM,GAAKA,EAAS,EACtC,OAAO,KAAK,MAAMA,CAAM,EAE1B,IAAMC,EAAQP,EAAMV,EAAGO,CAAY,EACnC,OAAOU,GAASH,EAAM,KAAKG,CAAK,EAAIA,EAAM,OAAS,MACrD,CAKA,SAASC,EAAQN,EAAgB,CAI/B,OAHuB,MAAM,QAAQA,CAAK,EACtCA,EACA,OAAOA,GAAS,EAAE,EAAE,MAAM,GAAG,GACtB,IAAIC,GAAO,CACpB,IAAMM,EACJN,IAAQ,IAAMA,IAAQ,MAAQA,IAAQ,OAAY,IAAM,OAAOA,CAAG,EACpE,OAAO,OAAO,SAASM,CAAC,EAAIA,EAAI,MAClC,CAAC,CACH,CAEA,SAASC,EAAQR,EAAgB,CAI/B,OAHuB,MAAM,QAAQA,CAAK,EACtCA,EACA,OAAOA,GAAS,EAAE,EAAE,MAAM,GAAG,GACtB,IAAIC,GAAO,CACpB,IAAMQ,EAAO,OAAOR,GAAO,EAAE,EAAE,KAAK,EACpC,OAAOQ,IAAS,IAAMA,IAAS,IAAM,OAAYA,CACnD,CAAC,CACH,CAEA,IAAMC,EAAgB,WAMtB,SAASC,EAAevB,EAAgB,CACtC,IAAMwB,EAAOJ,EAAQlB,EAASF,EAAG,KAAK,CAAC,EACvC,GAAI,CAACwB,EAAK,SAASF,CAAa,EAC9B,OAEF,IAAMG,EAAKP,EAAQb,EAAML,EAAG,IAAI,CAAC,EAC3B0B,EAAMN,EAAQf,EAAML,EAAG,KAAK,CAAC,EAC7B2B,EAAMT,EAAQb,EAAML,EAAG,KAAK,CAAC,EAC7B4B,EAAMV,EAAQb,EAAML,EAAG,KAAK,CAAC,EAC7B6B,EAAKX,EAAQb,EAAML,EAAG,IAAI,CAAC,EAC7B8B,EAAI,EACR,OAAON,EAAK,IAAI,CAACO,EAAK3B,IAAM,CAC1B,IAAMe,EAAIM,EAAGrB,CAAC,IAAM2B,IAAQT,EAAgB,EAAI,GAC5CU,EAAK,EACLC,EAAQ,EACZ,QAASC,EAAI,EAAGA,EAAIf,EAAGe,IAAKJ,IAAK,CAC/B,IAAMb,EAAQS,EAAII,CAAC,EACbK,EACJR,EAAIG,CAAC,IAAMb,GAASH,EAAM,KAAKG,CAAK,EAAIA,EAAM,OAAS,QACnDmB,EAAQR,EAAIE,CAAC,EACbO,EACJR,EAAGC,CAAC,IACHK,GAAcC,IAAU,OACrB,KAAK,MAAMD,EAAaC,CAAK,EAC7B,QACFC,IAAU,SACZL,GAAMK,EACNJ,IAEJ,CACA,OAAOF,IAAQT,GAAiBH,EAAI,GAAKc,IAAUd,EAAIa,EAAK,MAC9D,CAAC,CACH,CAKA,SAASM,EACPC,EACAC,EACAC,EACA,CACA,IAAMC,EAASH,GAAI,SAAS,GAAG,EAC/B,OAAQA,GAAM,IAAI,MAAM,MAAM,EAAE,QAAQ,CAACI,EAAOb,IAAoB,CAClE,IAAM1B,EAAIuC,IAAU,GAAK,IAAM,OAAOA,CAAK,EACrCX,EAAK5B,EAAI,EAAIoC,EAASpC,EAAI,CAAC,EAAIqC,EACrC,MAAI,CAAC,OAAO,UAAUrC,CAAC,GAAK4B,IAAO,OAC1B,CAAC,EAEH,CAAC,CAAE,GAAAA,EAAI,GAAIU,EAAS,CAAE,UAAWZ,EAAI,CAAE,EAAI,CAAC,CAAG,CAAC,CACzD,CAAC,CACH,CAEA,SAASc,EACP5C,EACAwC,EACAC,EACA,CACA,IAAMI,EAAU3C,EAASF,EAAG,SAAS,EAE/B8C,EAAuC,CAAC,EAC9C,OAAW,CAACC,EAAQC,CAAM,IAAK,OAAO,QAAQH,GAAW,CAAC,CAAC,EAAG,CAC5D,IAAMI,EAAQ/B,EAAQ8B,EAAO,EAAE,EACzBE,EAAUhC,EAAQ8B,EAAO,EAAE,EAAE,QAAQ,CAAChB,EAAI5B,IAC9C4B,IAAO,QAAaA,EAAK,EACrB,CAACiB,EAAM7C,CAAC,IAAM,OAAY,CAAE,GAAA4B,CAAG,EAAI,CAAE,GAAAA,EAAI,cAAeiB,EAAM7C,CAAC,CAAE,CAAC,EAClE,CAAC,CACP,EACM+C,EACJD,EAAQ,OAAS,GAAK,CAACV,EACnBU,EACAZ,EAAUlB,EAAQ4B,EAAO,EAAE,EAAE,CAAC,EAAGR,EAAUC,CAAW,EACxDU,EAAM,OAAS,IACjBL,EAAOC,CAAM,EAAII,EAErB,CACA,OAAO,OAAO,KAAKL,CAAM,EAAE,OAAS,EAAIA,EAAS,MACnD,CAIA,SAASM,EAAOpD,EAAgBqD,EAAiB,CAC/C,IAAMC,EAAQjD,EAAML,EAAG,OAAO,EACxBuD,EAAMlD,EAAML,EAAG,KAAK,EACpBwD,EAAQtC,EAAQb,EAAML,EAAG,OAAO,CAAC,EAAE,CAAC,EAC1C,OAAOqD,GAAUG,IAAU,OACvB,CAAE,MAAOF,EAAQ,EAAG,IAAKA,EAAQ,EAAIE,CAAM,EAC3C,CAAE,MAAAF,EAAO,IAAAC,CAAI,CACnB,CAEO,SAASE,GAAiBC,EAAwC,CACvE,IAAMC,EAAwB,CAAC,EAC/B,QAAW3D,KAAK0D,EAAU,CACxB,IAAMlB,EAAWjB,EAAevB,CAAC,EAC3B,CAAE,MAAAsD,EAAO,IAAAC,CAAI,EAAIH,EAAOpD,EAAGwC,IAAa,MAAS,EACjDoB,EAAO7C,EAAaf,CAAC,EAC3B,GAAI,EAAEuD,EAAMD,IAAUM,IAAS,OAC7B,SAEF,IAAMC,EAAUxD,EAAML,EAAG,SAAS,EAC5BiB,EAAQP,EAAMV,EAAGO,CAAY,EAC7BuD,EAASpD,EAAMV,EAAGS,CAAW,EACnCkD,EAAO,KAAK,CACV,IAAK,GAAGE,CAAO,IAAIP,CAAK,IAAIC,CAAG,GAC/B,MACGO,GAAU,CAAChE,EAAY,KAAKgE,CAAM,EAAIA,EAAS,UAC/C7C,GAASA,EAAM,QAAU,GACtB,IAAIA,CAAK,KACT,GAAG4C,CAAO,KAAKP,EAAQ,GAAG,eAAe,OAAO,CAAC,IAAIC,EAAI,eAAe,OAAO,CAAC,IACtF,QAAAM,EACA,MAAAP,EACA,IAAAC,EACA,KAAAK,EACA,MAAA3C,EACA,MAAO2B,EAAQ5C,EAAGwC,EAAUe,EAAMD,CAAK,CACzC,CAAC,CACH,CACA,OAAOK,EAAO,KAAK,CAACI,EAAGC,IAAMD,EAAE,MAAQC,EAAE,KAAK,CAChD,CC3RA,SAASC,EAAgBC,EAAW,CAClC,IAAMC,EAAM,CAAC,EACb,QAAWC,IAAM,CAAC,GAAGF,CAAS,EAAE,KAAK,CAACG,EAAGC,IAAMD,EAAE,MAAQC,EAAE,KAAK,EAAG,CACjE,IAAMC,EAAOJ,EAAI,GAAG,EAAE,EAClBI,GAAQH,EAAG,OAASG,EAAK,IAC3BA,EAAK,IAAM,KAAK,IAAIA,EAAK,IAAKH,EAAG,GAAG,EAEpCD,EAAI,KAAK,CAAE,GAAGC,CAAG,CAAC,CAEtB,CACA,OAAOD,CACT,CA2GA,SAASK,EAAuBC,EAAO,CACrC,IAAMC,EAAM,CAAC,EACPC,EAAuB,IAAI,IACjC,QAAWC,IAAK,CAAC,GAAGH,CAAK,EAAE,KAAK,CAACI,EAAGC,IAAMD,EAAE,MAAQC,EAAE,KAAK,EAAG,CAC5D,IAAMC,EAAM,GAAGH,EAAE,OAAO,IAAIA,EAAE,MAAM,IAAIA,EAAE,IAAI,GACxCI,EAAOL,EAAK,IAAII,CAAG,EACzB,GAAIC,GAAQJ,EAAE,MAAQI,EAAK,IACzBA,EAAK,IAAM,KAAK,IAAIA,EAAK,IAAKJ,EAAE,GAAG,EACnCI,EAAK,MAAQC,EAAgB,CAAC,GAAGD,EAAK,MAAO,GAAGJ,EAAE,KAAK,CAAC,MACnD,CACL,IAAMM,EAAO,CAAE,GAAGN,EAAG,MAAOK,EAAgBL,EAAE,KAAK,CAAE,EACrDF,EAAI,KAAKQ,CAAI,EACbP,EAAK,IAAII,EAAKG,CAAI,CACpB,CACF,CACA,OAAOR,CACT,CC1HO,IAAMS,EAAqB,IAAI,IAAI,CACxC,mBACA,cACA,kBACA,aACA,kBACA,aACA,gBACA,eACF,CAAC,EAEKC,EAAkB,0CAIlBC,EAAoB,IAAI,IAAI,CAAC,kBAAmB,YAAY,CAAC,EAO5D,SAASC,GACdC,EACAC,EACA,CACA,IAAMC,EAASD,EAAQE,EAAWH,EAAQC,CAAK,EAAI,OACnD,GAAIC,EACF,OAAOA,EAET,IAAME,EAAaJ,EAAO,OACxBK,GACET,EAAmB,IAAIS,EAAE,WAAW,GACpC,CAACC,EAAkB,KAAKC,EAAWF,CAAC,CAAC,CACzC,EACA,OACED,EAAW,KAAKC,GAAKR,EAAgB,KAAKU,EAAWF,CAAC,CAAC,CAAC,GACxDD,EAAW,KAAKC,GAAK,CAACP,EAAkB,IAAIO,EAAE,WAAW,CAAC,CAE9D,CAEA,IAAMG,EAAgB,qBAIf,SAASC,GAAeC,EAAgC,CAC7D,OAAOA,GAASF,EAAc,KAAKD,EAAWG,CAAK,CAAC,EAAI,KAAO,MACjE,CAYO,SAASC,GAAYC,EAAcC,EAA6B,CACrE,IAAMC,EAAQF,EAAkB,QAAQ,KACtCP,GAAKU,EAAeV,EAAE,cAAe,SAAS,IAAMQ,CACtD,GAAG,SAAS,CAAC,EACb,OAAOC,EACDC,EAAeD,EAAK,cAAe,QAAQ,GAC3C,CAAC,EACH,CAAC,CACP,CAKA,IAAME,EAAuB,IAAI,IAAI,CACnC,aACA,SACA,SACA,cACA,UACF,CAAC,EAIKC,GAAa,IAAI,IAAI,CACzB,OACA,MACA,iBACA,kBACA,KACF,CAAC,EAED,SAASC,EAAQC,EAAgBC,EAAwC,CACvE,IAAMC,EAAOC,EAASH,EAAG,MAAM,EAC3B,OAAOE,GAAS,UAAYJ,GAAW,IAAII,CAAI,GACjDD,EAAK,KAAK,CACR,MAAOE,EAASH,EAAG,OAAO,EAC1B,IAAKG,EAASH,EAAG,KAAK,CACxB,CAAC,EAEH,IAAMI,EAAWD,EAASH,EAAG,aAAa,EAC1C,QAAWK,KAASD,GAAY,CAAC,EAC/BL,EAAQM,EAAOJ,CAAI,CAEvB,CAUO,SAASK,GAAeC,EAAsC,CACnE,IAAMC,EAAqB,CAAC,EAC5B,QAAWR,KAAKO,EAAU,CACxB,IAAME,EACHN,EAASH,EAAG,WAAW,GACvBG,EAASH,EAAG,MAAM,GAClBG,EAASH,EAAG,MAAM,GAClBG,EAASH,EAAG,SAAS,EAClBU,EAAQP,EAASH,EAAG,OAAO,EAC3BW,EAAMR,EAASH,EAAG,KAAK,EAC7B,GACE,CAACS,GACD,EAAEE,EAAMD,IACRb,EAAqB,IAAIM,EAASH,EAAG,MAAM,CAAW,EAEtD,SAEF,IAAMY,EAA0C,CAAC,EACjDb,EAAQC,EAAGY,CAAK,EAChBJ,EAAM,KAAK,CACT,KAAAC,EACA,QAASN,EAASH,EAAG,SAAS,EAC9B,MAAAU,EACA,IAAAC,EACA,OAASR,EAASH,EAAG,QAAQ,GAA4B,EACzD,MAAOY,EAAM,OAASC,EAAgBD,CAAK,EAAI,CAAC,CAAE,MAAAF,EAAO,IAAAC,CAAI,CAAC,CAChE,CAAC,CACH,CACA,OAAOG,EAAuBN,CAAK,CACrC,CC5JA,IAAMO,EAAO,eAAe,eAAe,EACrCC,GAAOC,GACXF,GAAQ,MAAQE,KAAQ,OAAOF,CAAI,EAC/BA,EAAKE,CAAI,EACT,OAAO,OACL,UAAY,CACV,MAAM,IAAI,MAAM,kCAAoCA,EAAO,+HAA8I,CAC3M,EACA,CAAE,mBAAoBA,CAAK,CAC7B,EAGC,IAAMC,GAA6BC,GAAK,YAAY,EACpDC,GAAQC,GAAQA,EAAK,WAAaA,EAAK,QAAUA",
-  "names": ["isStringArray", "value", "item", "trackLanes", "track", "lanes", "getConfAssemblyNamesOrNone", "walkIndexed", "adapterConfig", "snapshotNamesFile", "cutsByHaplotype", "configHaplotypes", "defaultHaplotypes", "graphReferenceAssembly", "trackAdapterSnapshot", "toTrackConfigEntry", "offReferenceProblem", "referenceAssembly", "assemblyName", "ownField", "f", "name", "namedTrack", "tracks", "named", "t", "trackLabel", "REPEAT_ADAPTER_TYPES", "REPEAT_TRACK_HINT", "pickRepeatTrack", "tracks", "named", "chosen", "namedTrack", "t", "trackLabel", "PACKED_NAME", "packedName", "f", "name", "ownField", "pair", "i", "field", "top", "MOTIF_FIELDS", "PERIOD_FIELDS", "NAME_FIELDS", "first", "names", "value", "one", "IUPAC", "repeatUnitOf", "period", "motif", "numbers", "n", "strings", "text", "TANDEM_REPEAT", "tandemAlleleBp", "alts", "rn", "rus", "rul", "ruc", "rb", "k", "alt", "bp", "known", "j", "unitLength", "count", "runBp", "genotyped", "gt", "alleleBp", "referenceBp", "phased", "index", "callsOf", "samples", "called", "sample", "fields", "reads", "lengths", "calls", "spanOf", "tandem", "start", "end", "svlen", "repeatArraysFrom", "features", "arrays", "unit", "refName", "stated", "a", "b", "mergedIntervals", "intervals", "out", "iv", "a", "b", "last", "mergeOverlappingByName", "genes", "out", "open", "g", "a", "b", "key", "last", "mergedIntervals", "gene", "GENE_ADAPTER_TYPES", "GENE_TRACK_HINT", "BED_ADAPTER_TYPES", "pickGeneTrack", "tracks", "named", "chosen", "namedTrack", "candidates", "t", "REPEAT_TRACK_HINT", "trackLabel", "TE_TRACK_HINT", "annotationNoun", "track", "laneFilters", "view", "trackId", "lane", "readConfObject", "WHOLE_SEQUENCE_TYPES", "EXON_PARTS", "exonsOf", "f", "into", "type", "ownField", "children", "child", "geneModelsFrom", "features", "genes", "name", "start", "end", "exons", "mergedIntervals", "mergeOverlappingByName", "host", "read", "name", "makeStyles", "read", "mui_default", "host"]
-}

package/dist/chunks/chunk-S7DQGZX2.js

@@ -1,2 +0,0 @@
-var tt;function ut(){return tt??(tt=import("./bandage-layout-UZEOCKMS.js").then(o=>o.default()).catch(o=>{throw tt=void 0,o})),tt}async function dt(o){return(await ut()).computeLayout(o.graph,o.options)}var Bt="\0deletion:";var kt=25*Math.PI/180,Pt=.25,St=150,nn=[0,-.35,.35,-.7,.7,-1.05,1.05,-1.4,1.4],pt=[0,1];function _t(o){return o?0:1}function lt(o,t){let n=t.x-o.x,e=t.y-o.y,s=Math.hypot(n,e)||1;return{x:n/s,y:e/s}}function gt(o,t,n){return{x:o.x+(t.x-o.x)*n,y:o.y+(t.y-o.y)*n}}function Dt(o){let t=0,n=0;for(let e of o)t+=e.x,n+=e.y;return{x:t/o.length,y:n/o.length}}function Gt(o){let t=new Float64Array(o.length);for(let n=1;n<o.length;n++)t[n]=t[n-1]+Math.hypot(o[n].x-o[n-1].x,o[n].y-o[n-1].y);return t}function Ut(o){var t;return(t=Gt(o)[o.length-1])!==null&&t!==void 0?t:0}var at=new Map;function en(o){let t=at.get(o);if(t!==void 0)return t;let n=on(o);return at.size>1e4&&at.clear(),at.set(o,n),n}function on(o){let t=1e-6,n=2*Math.PI-1e-6;for(let e=0;e<60;e++){let s=(t+n)/2;s/(2*Math.sin(s/2))<o?t=s:n=s}return(t+n)/2}function sn(o,t){if(o<1e-9)return Math.PI*t;let n=(o*o/4+t*t)/(2*t),e=2*Math.asin(Math.min(1,o/(2*n)));return n*(t>n?2*Math.PI-e:e)}function mt(o,t,n,e){let s=t-2*n,i=o<1e-9?2*Math.PI:en(s/o),r=s/i,l=Math.cos(i/2),d=o/2,c=e+n-r*l;return{at:a=>{if(a<=n)return{u:0,v:e+a};if(a>=t-n)return{u:o,v:e+t-a};let h=(a-n)/r-i/2;return{u:d+r*Math.sin(h),v:c+r*Math.cos(h)}},apex:e+n+r*(1-l),length:t}}function It(o,t,n){if(!n)return o;let e=Math.cos(n),s=Math.sin(n);return{...o,at:i=>{let{u:r,v:l}=o.at(i),d=r-t/2;return{u:t/2+d*e-l*s,v:d*s+l*e}}}}function rn(o){for(let t=0;t<=32;t++)if(o.at(o.length*t/32).v<-1e-6)return!0;return!1}function Ot(o,t,n,e,s){return{at:i=>({u:o+n*i,v:t+e*i}),apex:t+Math.max(0,e)*s,length:s}}var ot=class{constructor(t,n,e=!1){var s;this.pts=t,this.normals=n,this.straight=e,this.arc=Gt(t),this.total=(s=this.arc[t.length-1])!==null&&s!==void 0?s:0}segment(t){let{arc:n}=this,e=1,s=n.length-1;for(;e<s;){let i=e+s>>1;n[i]<t?e=i+1:s=i}return e}fraction(t,n){let e=this.arc[t]-this.arc[t-1];return e>0?(n-this.arc[t-1])/e:0}pointAt(t){let{pts:n}=this,e=n.length-1;if(e===0)return{...n[0]};if(t<=0){let i=lt(n[0],n[1]);return{x:n[0].x+i.x*t,y:n[0].y+i.y*t}}if(t>=this.total){let i=lt(n[e-1],n[e]),r=t-this.total;return{x:n[e].x+i.x*r,y:n[e].y+i.y*r}}let s=this.segment(t);return gt(n[s-1],n[s],this.fraction(s,t))}normalAt(t){let{normals:n}=this;if(n.length===1||t<=0)return n[0];if(t>=this.total)return n[n.length-1];let e=this.segment(t),{x:s,y:i}=gt(n[e-1],n[e],this.fraction(e,t)),r=Math.hypot(s,i)||1;return{x:s/r,y:i/r}}};function an(o,t){let n=Dt(o);return o.map((e,s)=>{let i=lt(o[Math.max(0,s-1)],o[Math.min(o.length-1,s+1)]),r={x:-i.y,y:i.x},l=e.x-n.x,d=e.y-n.y,c=Math.hypot(l,d),a=r.x*l+r.y*d,h=t[s],f=c>1e-9&&Math.abs(a)>.3*c?Math.sign(a):Math.sign(r.x*h.x+r.y*h.y)||1;return{x:r.x*f,y:r.y*f}})}function xt(o,t,n,e,s){let i=Math.min(s,Math.max(e.length/24,.5)),r=[],l=[];for(let d=0;d<=e.length+1e-9;d+=i){let{u:c,v:a}=e.at(Math.min(d,e.length)),h=o.pointAt(t+c),f=o.normalAt(t+c),u=f.x*n,g=f.y*n;r.push({x:h.x+u*a,y:h.y+g*a}),l.push({x:u,y:g})}return{pts:r,refs:l}}var Ft=5,cn=10.5/2;function yt(o,t,n,e,s,i){let r=s,l=xt(o,t,n,e(r),i);if(o.straight)return l;for(let d=0;d<6;d++){let c=Ut(l.pts);if(!(c>0)||Math.abs(c/s-1)<.001)break;r*=s/c,l=xt(o,t,n,e(r),i)}return l}function ct(o,t){return Array.from({length:t},(n,e)=>o+e*15/2)}function Tt(o){if(o.length===0)return 1/0;let t=1/0,n=-1/0;for(let e of o)t=Math.min(t,e.point.x),n=Math.max(n,e.point.x);return n-t}function Rt(o,t){return o*73856093^t*19349663}var ht=class{constructor(t){this.c=t,this.grid=new Map;let{ids:n,first:e,count:s,per:i,seedX:r,seedY:l,backbone:d}=t,c=n.length;this.points=Array.from({length:c},()=>{}),this.params=Array.from({length:c},()=>{}),this.curves=Array.from({length:c},()=>{}),this.links=t.links.map((f,u)=>f.map(g=>g.filter(([M])=>M!==u))),this.route=n.map(f=>f.startsWith(Bt));let a=1/0,h=-1/0;for(let f=0;f<c;f++){let u=e[f];!d[u]||Number.isNaN(r[u])||(a=Math.min(a,r[u]),h=Math.max(h,r[u]+i[f]*(s[f]-1)))}this.backbone=new ot([{x:a,y:0},{x:h,y:0}],[{x:0,y:1},{x:0,y:1}],!0),this.backboneCentroid={x:(a+h)/2,y:0};for(let f=0;f<c;f++){let u=e[f];if(!d[u]||Number.isNaN(r[u]))continue;let g=[],M=[];for(let b=0;b<s[f];b++){let U=r[u]+b*i[f];g.push({x:U,y:l[u]}),M.push(U-a)}this.points[f]=g,this.params[f]=M,this.curves[f]=this.backbone,this.occupy(g,this.backbone)}}static hasBackbone(t){for(let n=0;n<t.ids.length;n++){let e=t.first[n];if(t.backbone[e]&&!Number.isNaN(t.seedX[e]))return!0}return!1}run(){let t=[];for(let e=0;e<this.points.length;e++)this.points[e]||t.push(e);let n=this.componentsOf(t).map(e=>({members:e,anchors:this.anchorsOf(e)})).filter(e=>e.anchors.length).map(e=>({members:e.members,span:Tt(e.anchors),drawn:e.members.reduce((s,i)=>s+this.drawn(i),0),feet:e.anchors.map(s=>`${s.point.x},${s.point.y}`).sort().join(" ")})).sort((e,s)=>e.span-s.span||(e.feet===s.feet?s.drawn-e.drawn:e.drawn-s.drawn));for(let e of n)this.placePiece(e.members,this.backboneCentroid)}write(t,n){let{first:e}=this.c;this.points.forEach((s,i)=>{s?.forEach((r,l)=>{t[e[i]+l]=r.x,n[e[i]+l]=r.y})})}drawn(t){return this.c.per[t]*(this.c.count[t]-1)}endIndex(t,n){return n?this.c.count[t]-1:0}occupy(t,n){for(let e of t){let s=Rt(Math.floor(e.x/10.5),Math.floor(e.y/10.5)),i=this.grid.get(s),r={x:e.x,y:e.y,curve:n};i?i.push(r):this.grid.set(s,[r])}}violations(t,n,e,s){var i;let r=0;for(let l of t){if(e.some(a=>Math.hypot(l.x-a.x,l.y-a.y)<15))continue;let d=Math.floor(l.x/10.5),c=Math.floor(l.y/10.5);for(let a=d-1;a<=d+1;a++)for(let h=c-1;h<=c+1;h++)for(let f of(i=this.grid.get(Rt(a,h)))!==null&&i!==void 0?i:[])if(f.curve!==n&&Math.hypot(l.x-f.x,l.y-f.y)<10.5&&(r++,r>=s))return r}return r}choose(t,n,e){let s,i=1/0;for(let r of t){let l=this.violations(r(cn).pts,n,e,i);if(l===0)return r(Ft);l<i&&(i=l,s=r)}return s(Ft)}anchorsOf(t){let n=new Set(t),e=[];for(let s of t)for(let i of pt)for(let[r,l]of this.links[s][i]){let d=this.points[r];if(n.has(r)||!d)continue;let c=this.endIndex(r,l);e.push({u:s,uSide:i,v:r,vSide:l,point:d[c],curve:this.curves[r],t:this.params[r][c]})}return e}componentsOf(t){let n=new Set(t),e=new Set,s=[];for(let i of t){if(e.has(i))continue;let r=[i];e.add(i);for(let l of r)for(let d of pt)for(let[c]of this.links[l][d])n.has(c)&&!e.has(c)&&(e.add(c),r.push(c));s.push(r)}return s}spinePath(t,n,e,s,i){let r=new Set(t),l=(u,g)=>u*2+g,d=(u,g)=>u===s&&_t(g)===i,c=new Map([[l(n,e),-1]]),a=[[n,e]],h=[n,e];for(let[u,g]of a){if(h=[u,g],s!==void 0&&d(u,g))break;for(let[M,b]of this.links[u][_t(g)])!r.has(M)||c.has(l(M,b))||(c.set(l(M,b),l(u,g)),a.push([M,b]))}if(s!==void 0&&!d(h[0],h[1]))return;let f=[];for(let u=l(h[0],h[1]);u!==-1;u=c.get(u))f.push({k:u>>1,enter:u&1});return f.reverse()}loosePath(t,n,e){let s=new Set(t),i=new Map([[n,-1]]),r=new Map([[n,0]]),l=[n];for(let c of l){if(c===e)break;for(let a of pt)for(let[h,f]of this.links[c][a])!s.has(h)||i.has(h)||(i.set(h,c),r.set(h,f),l.push(h))}let d=[];for(let c=e;c!==-1;c=i.get(c))d.push({k:c,enter:r.get(c)});return d.reverse()}spineLength(t){let{link:n}=this.c;return t.reduce((e,{k:s})=>e+this.drawn(s)+n,n)}layAlong(t,n,e,s){let{count:i,per:r,link:l}=this.c,d=e,c=[];for(let{k:a,enter:h}of t){let f=s??r[a],u=[],g=[];for(let M=0;M<i[a];M++)u.push(n.pointAt(d+M*f)),g.push(d+M*f);h===1&&(u.reverse(),g.reverse()),this.points[a]=u,this.params[a]=g,this.curves[a]=n,c.push(...u),d+=f*(i[a]-1)+l}return c}arcCandidates(t,n,e,s,i){let r=(i-s)/2-1e-6,l=i>2*s?nn:[0],d=[];for(let c of ct(0,8))for(let a of l)for(let h=0;h<=16;h++){let f=r*h/16,u=It(mt(s,i,f,c),s,a);h<16&&u.apex<12||rn(u)||d.push(g=>yt(t,n,e,M=>It(mt(s,M,Math.min(f,(M-s)/2-1e-6),c),s,a),i,g))}return d}placePiece(t,n){var e;let{count:s,link:i}=this.c,r=this.anchorsOf(t);if(r.length===0)return;let l=t.every(x=>this.route[x]),d=r.every(x=>x.curve===r[0].curve)?r[0].curve:void 0,c,a,h,f;if(d)r.sort((x,T)=>x.t-T.t),c=d,a=r[0].t,h=r[r.length-1].t,f=c===this.backbone&&l?-1:1;else{r.sort((q,Q)=>q.point.x-Q.point.x||q.point.y-Q.point.y);let x=r[0].point,T=r[r.length-1].point,W=Math.hypot(T.x-x.x,T.y-x.y),B=W>1e-9?lt(x,T):{x:1,y:0},D={x:-B.y,y:B.x},H=gt(x,T,.5);f=r.some(q=>q.curve===this.backbone)?(l?-1:1)*(Math.sign(D.y)||1):(H.x-n.x)*D.x+(H.y-n.y)*D.y>=0?1:-1,c=new ot([x,T],[D,D],!0),a=0,h=W}let u=r[0],g=r[r.length-1],M=h-a,b=r.length===1||u.u===g.u&&u.uSide===g.uSide&&M<1e-9,U=[u.point,g.point],v=x=>this.choose(x,d,U),N,y,L=i,w;if(b){N=this.spinePath(t,u.u,u.uSide);let x=this.spineLength(N),T=u.vSide?Math.max(0,s[u.v]-2):Math.min(1,s[u.v]-1),B=(u.t>=this.params[u.v][T]?1:-1)*Math.cos(kt),D=Math.sin(kt);y=v(ct(0,12).map(H=>q=>yt(c,a,f,Q=>Ot(0,H,B,D,Q),x,q)))}else{N=(e=this.spinePath(t,u.u,u.uSide,g.u,g.uSide))!==null&&e!==void 0?e:this.loosePath(t,u.u,g.u);let x=this.spineLength(N);if(l){let T=Math.max(12,Math.min(Pt*M,St));y=v(ct(T,12).map(B=>D=>xt(c,a,f,mt(M,sn(M,B),0,0),D)));let W=Ut(y.pts);w=Math.max(.001,(W-2*i)/(s[N[0].k]-1))}else if(x>M+1e-6)y=v(this.arcCandidates(c,a,f,M,x));else{let T=x-2*i,W=Math.max(12,Math.min(Pt*(M-T),St));y=v(ct(W,12).map(B=>D=>yt(c,a,f,H=>Ot(M/2-H/2,B,1,0,H),T,D))),L=0}}let E=new ot(y.pts,an(y.pts,y.refs)),O=this.layAlong(N,E,L,w);this.occupy(O,E);let _=Dt(O),R=t.filter(x=>!this.points[x]),F=this.componentsOf(R).map(x=>({members:x,span:Tt(this.anchorsOf(x))})).sort((x,T)=>x.span-T.span);for(let x of F)this.placePiece(x.members,_)}};function Mt(o){let t=new Float64Array(o.n).fill(NaN),n=new Float64Array(o.n).fill(NaN);if(ht.hasBackbone(o)){let e=new ht(o);e.run(),e.write(t,n)}return{X:t,Y:n}}var ln=[{walks:2,iterations:15},{walks:4,iterations:30},{walks:8,iterations:60},{walks:12,iterations:90},{walks:16,iterations:120}],hn=20,fn=3,wt=.3,un=2,dn=200,pn=.1,mn=.5,yn=o=>{var t;return((t=o.stable)===null||t===void 0?void 0:t.rank)===0};function Ht(o,t){let n=t.at(-1);return(o==="+"||o==="-")&&(n==="+"||n==="-")&&o!==n}function gn(o){let t=Math.imul(o,2654435761)>>>0||1;return()=>(t^=t<<13,t>>>=0,t^=t>>>17,t^=t<<5,t>>>=0,t/4294967296)}function z(o,t){return typeof o=="number"&&Number.isFinite(o)?o:t}function Nt(o,t){return Math.max(z(o.nodeLengthPerMegabase,1e3)*t/1e6,z(o.minimumNodeLength,1))}function Ct(o){let{nodes:t,edges:n}=o.graph,e=o.options,s=z(e.nodeSegmentLength,1),i=z(e.edgeLength,1),r=t.map(w=>w.id),l=new Int32Array(t.length),d=new Int32Array(t.length),c=new Float64Array(t.length),a=0;t.forEach((w,E)=>{let O=Nt(e,w.length),_=Math.max(1,Math.ceil(O/s));l[E]=a,d[E]=_+1,c[E]=O/_,a+=_+1});let h=new Int32Array(a),f=new Int32Array(a),u=new Float64Array(a).fill(NaN),g=new Float64Array(a).fill(NaN),M=new Uint8Array(a),b=Array.from({length:a},()=>[]);t.forEach((w,E)=>{let O=typeof w.x=="number"&&typeof w.y=="number",_=yn(w)?1:0;for(let R=0;R<d[E];R++){let F=l[E]+R;h[F]=E,f[F]=R,M[F]=_,O&&(u[F]=w.x+R*c[E],g[F]=w.y),R>0&&(b[F-1].push([F,c[E]]),b[F].push([F-1,c[E]]))}});let U=new Map(r.map((w,E)=>[w,E])),v=t.map(()=>[[],[]]);for(let w of n){let E=U.get(w.from),O=U.get(w.to);if(E===void 0||O===void 0||E===O&&d[E]<=2)continue;let _=Ht(w.fromStrand,w.from)?0:1,R=Ht(w.toStrand,w.to)?1:0,F=l[E]+(_?d[E]-1:0),x=l[O]+(R?d[O]-1:0);b[F].push([x,i]),b[x].push([F,i]),v[E][_].push([O,R]),v[O][R].push([E,_])}let N=new Int32Array(a+1);for(let w=0;w<a;w++)N[w+1]=N[w]+b[w].length;let y=new Int32Array(N[a]),L=new Float64Array(N[a]);for(let w=0;w<a;w++)b[w].forEach(([E,O],_)=>{y[N[w]+_]=E,L[N[w]+_]=O});return{ids:r,first:l,count:d,per:c,links:v,chainOf:h,indexOf:f,seedX:u,seedY:g,backbone:M,off:N,nb:y,wt:L,n:a,link:i}}function xn(o){let{n:t,off:n,nb:e}=o,s=new Int32Array(t).fill(-1),i=[];for(let r=0;r<t;r++){if(s[r]>=0)continue;let l=[r];s[r]=i.length;for(let d of l)for(let c=n[d];c<n[d+1];c++){let a=e[c];s[a]<0&&(s[a]=i.length,l.push(a))}i.push(l)}return{comp:s,members:i}}function At(o,t={}){var n,e,s;let i=Ct(o),{n:r,off:l,nb:d,wt:c,seedX:a,seedY:h,first:f,count:u,per:g,link:M}=i,b=o.options,U=ln[Math.max(0,Math.min(4,z((n=t.quality)!==null&&n!==void 0?n:b.quality,2)))],v=z((e=t.componentSeparation)!==null&&e!==void 0?e:b.componentSeparation,15),N=gn(z((s=t.seed)!==null&&s!==void 0?s:b.seed,1)),y=new Float64Array(r),L=new Float64Array(r),w={};if(r===0)return{nodePositions:w};let{comp:E,members:O}=xn(i),_=1/0,R=0;for(let p=0;p<d.length;p++)_=Math.min(_,c[p]),R+=c[p];R/=2;let F=!1;for(let p=0;p<r;p++)if(!Number.isNaN(a[p])){F=!0;break}let x=F?Mt(i):void 0,T=Math.sqrt(r)*20;for(let p=0;p<r;p++)x&&!Number.isNaN(x.X[p])?(y[p]=x.X[p],L[p]=x.Y[p]):F&&!Number.isNaN(a[p])?(y[p]=a[p]+N()-.5,L[p]=h[p]+N()-.5):(y[p]=N()*T,L[p]=N()*T);let W=O.map(p=>x!==void 0&&p.every(A=>!Number.isNaN(x.X[A]))),B=[],D=!0;for(let p=0;p<r;p++)W[E[p]]||(B.push(p),D&&(D=!Number.isNaN(a[p])));let H=Math.max(R/4,_*10),q=H*H,Q=pn*_*_,{walks:Jt,iterations:rt}=U,Qt=Math.log(q/Q)/Math.max(1,rt-1),bt=Math.log(_),Zt=Math.log(H),Lt=(p,A,m,k)=>{let S=k/(m*m);S>1&&(S=1);let P=y[p]-y[A],I=L[p]-L[A],V=Math.sqrt(P*P+I*I)||1e-9,G=S*(V-m)/(2*V),j=G*P,C=G*I;y[p]=y[p]-j,L[p]=L[p]-C,y[A]=y[A]+j,L[A]=L[A]+C},et=0,Yt=(p,A)=>{let m=i.chainOf[p],k=i.indexOf[p],S=N()<.5?-1:1,P=A;for(let I=0;I<dn;I++){let V=u[m],G=g[m],j=(S>0?V-1-k:k)*G;if(P<=j){let J=Math.round(P/G);return et=A-P+J*G,f[m]+k+S*J}P-=j;let C=i.links[m][S>0?1:0];if(C.length===0)return et=A-P,f[m]+(S>0?V-1:0);let[Y,$]=C[Math.floor(N()*C.length)];if(P-=M,m=Y,S=$===0?1:-1,k=$===0?0:u[Y]-1,P<=0)return et=A-P,f[m]+k}return-1},Et=(p,A)=>{for(let m=l[p];m<l[p+1];m++){let k=d[m];k>p&&Lt(p,k,c[m],A)}},Z=Int32Array.from(B),Xt=D?Math.floor(mn*rt):0;for(let p=B.length?Xt:rt;p<rt;p++){let A=q*Math.exp(-Qt*p);for(let m=Z.length-1;m>0;m--){let k=Math.floor(N()*(m+1)),S=Z[m];Z[m]=Z[k],Z[k]=S}for(let m of Z){Et(m,A);for(let k=0;k<Jt;k++){let S=Math.exp(bt+N()*(Zt-bt)),P=Yt(m,S);P>=0&&P!==m&&et>0&&Lt(m,P,et,A)}}}let K=fn*M,tn=(p,A)=>Math.floor(p/K)*73856093^Math.floor(A/K)*19349663;for(let p=0;p<(B.length?hn:0);p++){let A=new Map;for(let m of B){let k=tn(y[m],L[m]),S=A.get(k);S?S.push(m):A.set(k,[m])}for(let m of B){let k=Math.floor(y[m]/K),S=Math.floor(L[m]/K);for(let P=k-1;P<=k+1;P++)for(let I=S-1;I<=S+1;I++){let V=A.get(P*73856093^I*19349663);if(V)for(let G of V){if(G<=m)continue;let j=!1;for(let X=l[m];X<l[m+1];X++)if(d[X]===G){j=!0;break}if(j)continue;let C=y[m]-y[G],Y=L[m]-L[G],$=Math.sqrt(C*C+Y*Y);if($>=K)continue;let J,it;if($>1e-6){let X=wt*(K-$)/(2*$);J=X*C,it=X*Y}else J=wt*K*(N()-.5),it=wt*K*(N()-.5);y[m]=y[m]+J,L[m]=L[m]+it,y[G]=y[G]-J,L[G]=L[G]-it}}}for(let m of B)Et(m,1/0)}for(let p=0;p<u.length;p++){let A=f[p],m=u[p];if(!(m<3)){for(let k=0;k<un;k++){let S=y.slice(A,A+m),P=L.slice(A,A+m);for(let I=1;I+1<m;I++)y[A+I]=.5*S[I]+.25*(S[I-1]+S[I+1]),L[A+I]=.5*P[I]+.25*(P[I-1]+P[I+1])}Mn(y,L,A,m,g[p])}}Nn(E,O,y,L,F,v);for(let p=0;p<i.ids.length;p++){let A=[];for(let m=0;m<u[p];m++)A.push({x:y[f[p]+m],y:L[f[p]+m]});w[i.ids[p]]=A}return{nodePositions:w}}function Mn(o,t,n,e,s){wn(o,t,n,e,s*(e-1));let i=new Float64Array(e);for(let a=1;a<e;a++)i[a]=i[a-1]+Math.hypot(o[n+a]-o[n+a-1],t[n+a]-t[n+a-1]);if(!i[e-1])return;let r=i[e-1],l=o.slice(n,n+e),d=t.slice(n,n+e),c=1;for(let a=1;a+1<e;a++){let h=r*a/(e-1);for(;c<e-1&&i[c]<h;)c++;let f=i[c]-i[c-1],u=f>0?(h-i[c-1])/f:0;o[n+a]=l[c-1]+(l[c]-l[c-1])*u,t[n+a]=d[c-1]+(d[c]-d[c-1])*u}}function wn(o,t,n,e,s){let i=n+e-1,r=o[n],l=t[n],d=Math.hypot(o[i]-r,t[i]-l),c=d>1e-9?(o[i]-r)/d:1,a=d>1e-9?(t[i]-l)/d:0,h=new Float64Array(e),f=new Float64Array(e),u=!0;for(let v=0;v<e;v++){let N=o[n+v]-r,y=t[n+v]-l;h[v]=N*c+y*a,f[v]=y*c-N*a,u&&(u=Math.abs(f[v])<1e-6)}let g=v=>{let N=0;for(let y=1;y<e;y++)N+=Math.hypot(h[y]-h[y-1],v*(f[y]-f[y-1]));return N};if(u||g(1)>=s)return;let M=1,b=2;for(;g(b)<s&&b<1e6;)M=b,b*=2;for(let v=0;v<40;v++){let N=(M+b)/2;g(N)<s?M=N:b=N}let U=(M+b)/2;for(let v=1;v+1<e;v++)o[n+v]=r+h[v]*c-U*f[v]*a,t[n+v]=l+h[v]*a+U*f[v]*c}function Nn(o,t,n,e,s,i){if(!s)for(let h of t)An(n,e,h);if(t.length<2)return;let r=new Float64Array(t.length).fill(1/0),l=new Float64Array(t.length).fill(1/0),d=new Float64Array(t.length).fill(-1/0);for(let h=0;h<n.length;h++){let f=o[h];r[f]=Math.min(r[f],n[h]),l[f]=Math.min(l[f],e[h]),d[f]=Math.max(d[f],e[h])}let c=new Float64Array(t.length),a=0;for(let h=0;h<t.length;h++)c[h]=a-l[h],a+=d[h]-l[h]+i;for(let h=0;h<n.length;h++){let f=o[h];n[h]=n[h]-r[f],e[h]=e[h]+c[f]}}function An(o,t,n){if(n.length<3)return;let e=0,s=0;for(let h of n)e+=o[h],s+=t[h];e/=n.length,s/=n.length;let i=0,r=0,l=0;for(let h of n){let f=o[h]-e,u=t[h]-s;i+=f*f,r+=u*u,l+=f*u}let d=-.5*Math.atan2(2*l,i-r),c=Math.cos(d),a=Math.sin(d);for(let h of n){let f=o[h]-e,u=t[h]-s;o[h]=e+c*f-a*u,t[h]=s+a*f+c*u}}var Wt=[{value:"fmmm",label:"Bandage (FMMM)",description:"Bandage's force-directed layout: OGDF's fast multipole multilevel method, compiled to wasm."},{value:"stress",label:"Stress",description:"Plain JS: the reference drawn straight and each variant placed against it, an allele as a lens, a repeat loop as a ring, a deletion as an arch; stress by stochastic gradient descent for components with no reference."}],vn=Wt.map(o=>o.value);var bn=async o=>{let t=performance.now();return{result:o.options.engine==="stress"?At(o):await dt(o),duration:performance.now()-t}};var st=40,Kt=500,ft=5;function Ln(o,t){return Math.max(o.nodeLengthPerMegabase*t/1e6,o.minimumNodeLength)}function Vt(o,t=ft){let e=o.nodes.reduce((i,r)=>i+r.length,0)/1e6,s=Math.max(o.nodes.length*st,Kt);return{nodeLengthPerMegabase:e>0?s/e:1e4,minimumNodeLength:Math.max(ft,t),edgeLength:5,nodeSegmentLength:20}}var nt={power:1,effect:1};function jt(o){return o.power===1&&o.effect===1}function zt(o,t){let n=o.nodes.length,e=o.nodes.reduce((r,l)=>r+l.length,0),s=n>0?e/n:0,i=n>0?Math.max(n*st,Kt)/n:st;return r=>{if(s<=0)return i;let l=(r/s)**t.power;return Math.max(i*((l-1)*t.effect+1),ft)}}var qt=1e3,$t={law:nt,minNodeLength:0};function Qn(o,t=$t){let{law:n,minNodeLength:e}=t,s=Vt(o,e);if(jt(n))return{nodes:o.nodes,opts:s};let i=zt(o,n);return{nodes:o.nodes.map(r=>({...r,length:Math.round(i(r.length)*qt)})),opts:{...s,nodeLengthPerMegabase:1e6/qt,minimumNodeLength:ft}}}function Zn(o,t=$t){if(jt(t.law)){let n=Vt(o,t.minNodeLength);return e=>Ln(n,e)}return zt(o,t.law)}var vt=[{value:"auto",label:"Proportional",description:"Bandage's own scale: a node draws proportional to its length, so a 1 bp allele is a speck.",law:nt,minNodeFactor:0},{value:"open",label:"Open bubbles",description:"Give every allele a drawn length, so a bubble reads as two arms rather than a knot.",law:nt,minNodeFactor:2.5},{value:"wide",label:"Wide bubbles",description:"As open, spread further. Best on a window of a dozen bubbles.",law:nt,minNodeFactor:10},{value:"compress",label:"Compress lengths",description:"Pull the longest and shortest nodes towards the graph\u2019s mean, so a cut spanning kb and bp fits one pane.",law:{power:.5,effect:.5},minNodeFactor:0}],En=vt.map(o=>o.value);function kn(o){let t=vt.find(n=>n.value===o);return{law:t?.law??nt,minNodeLength:(t?.minNodeFactor??0)*st}}export{Bt as a,Wt as b,vn as c,bn as d,Ln as e,Qn as f,Zn as g,vt as h,En as i,kn as j};
-//# sourceMappingURL=chunk-S7DQGZX2.js.map