jbrowse-plugin-graphgenomeviewer 6.27.0 → 7.1.0

package/README.md

@@ -2,222 +2,106 @@
 
 Pangenome graphs in JBrowse 2.
 
-## Do it yourself
-
-Tutorials in the [JBrowse 2 docs](https://jbrowse.org/jb2/docs/tutorials/), each
-with commands you can run:
-
-- **[Hosting your own graph](https://jbrowse.org/jb2/docs/tutorials/pangenome_prepare_graph)**
-  — start here. One script turns an rGFA or GFA into indexed files and a track
-  config; later sections add haplotype walks and gbz-base
-- [pggb](https://jbrowse.org/jb2/docs/tutorials/pangenome_ecoli) — five _E.
-  coli_ strains from FASTA to graph, index, synteny and variants
-- [Minigraph-Cactus](https://jbrowse.org/jb2/docs/tutorials/pangenome_cactus) —
-  the same from `cactus-pangenome`
-- [Cattle](https://jbrowse.org/jb2/docs/tutorials/pangenome_cattle) and
-  [mouse](https://jbrowse.org/jb2/docs/tutorials/pangenome_mouse) — published
-  graphs: `vg deconstruct` one, rank the bubbles of another
-- HPRC release 2:
-  [graph alleles](https://jbrowse.org/jb2/docs/tutorials/pangenome_hprc),
-  [haplotypes against each other](https://jbrowse.org/jb2/docs/tutorials/pangenome_hprc_haplotypes),
-  [repeat lengths](https://jbrowse.org/jb2/docs/tutorials/pangenome_hprc_repeats)
-- [Graph genome view user guide](https://jbrowse.org/jb2/docs/user_guides/graph_genome_view)
-
-## What data to use
-
-The plugin reads a graph as tabix files or a gbz-base database, one window at a
-time. A GFA small enough to load whole opens with **Add → Graph genome view**.
-
-Build the graph with [minigraph](https://github.com/lh3/minigraph) (rGFA),
-[pggb](https://github.com/pangenome/pggb) or
-[Minigraph-Cactus](https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md)
-(GFA and GBZ), then index what you have:
-
-- **rGFA** — `gfa-to-tabix build graph.rgfa.gz -o out` (0.11.0+). It calls
-  [gfatools](https://github.com/lh3/gfatools) for the bubbles and writes
-  `.segs.bed.gz`, `.links.bed.gz`, `.bubbles.bed.gz`, `.alleles.bed.gz`, a
-  coarse tier, a `.graph.json` manifest and a track config. Opening
-  `out.segs.bed.gz` in **Add pangenome graph track** reads the manifest.
-  Adapter: `RgfaTabixAdapter`
-- **Plain GFA** (pggb, odgi, vg, base-level Minigraph-Cactus) — the same
-  command, with `--reference`, `--assembly` and `--snarls`, a VCF from
-  `vg deconstruct -a` or `pggb -V`
-- **Alleles, with a CIGAR each** — `build` writes `.alleles.bed.gz`, which an
-  alignments track draws; `gfa-to-tabix alleles <prefix>` makes one from a
-  `--layout contig` index
-- **Haplotype walks, as tabix files** — `vg convert -f graph.gbz`, then
-  `gfa-to-tabix --walks`. Adapter: `WalkTabixSyntenyAdapter`, or
-  `RgfaTabixAdapter` with `walksUri`
-- **Haplotype walks, as one database** — `vg chains`, `gbz-base construct`,
-  `gbz-haplotype-index` make `.gbz.db` and `.haplotype-index.db`. Adapter:
-  `GbzBaseSyntenyAdapter`
-- **Reads** — `vg giraffe -o gaf`, `vg gamsort -G`, `bgzip`, `tabix` make a
-  `.gaf.gz` for a gbz-base adapter's `reads`
-- **Minigraph paths per assembly** — `minigraph -cxasm --call` per sample, then
-  `gfa-to-tabix paths` (0.9.0+) writes one row per bubble and sample
-
-[vg](https://github.com/vgteam/vg) 1.69.0 or later covers the GBZ steps.
-
-## As a track of a linear view
-
-A `GraphTrack` cuts the graph for the view's window and redraws it as you pan. A
-force-directed track draws a strip of the reference segments at their bp above
-the graph, each in its node's colour, so the graph reads against the tracks
-above it.
-
-- **LPA's KIV-2 repeat.** The goldenrod outlines on the graph are the gene
-  track's LPA exons. The charcoal loops, sequence off the reference, hang inside
-  the array the curated VNTR track marks.
+- **In:** a GFA, rGFA, GBZ or walk-indexed graph
+- **Out:** a graph track in a linear view, or a view of its own, with
+  haplotypes, bubbles and genes marked
 
 ![KIV-2 as a graph track under RefSeq genes and the curated KIV-2 annotation, its reference segments on a strip at their bp](img/force_kiv2.png)
 
-- **Each haplotype takes its own loops.** Side by side, one walk per panel:
-  HG01960 skips most of GRCh38's loops for the big one, and HG00133 takes both.
+## Quick start
+
+1. Add the plugin to your JBrowse 5.0.0-beta.11 or later config:
+
+   ```json
+   {
+     "plugins": [
+       {
+         "name": "GraphGenomeView",
+         "esmUrl": "https://jbrowse.org/plugins/jbrowse-plugin-graphgenomeviewer/latest/dist/jbrowse-plugin-graphgenomeviewer.esm.js"
+       }
+     ]
+   }
+   ```
+
+2. Open a graph:
+   - **A small GFA:** Add → **Graph genome view** opens the whole file
+   - **A large graph:** index it with
+     [gfa-to-tabix](https://github.com/GMOD/gfa-to-tabix) or build a gbz-base
+     database, then File → **Open track**. The track redraws the graph for the
+     view's window as you pan. See [docs/data.md](docs/data.md)
+
+3. Explore:
+   - Pick a layout from the track menu: force-directed, ordered, anchored,
+     sample rows, walk rows or tube map ([docs/layouts.md](docs/layouts.md))
+   - Lift haplotypes or show a panel per haplotype
+     ([docs/haplotypes.md](docs/haplotypes.md))
+   - Launch → **Graph genome view** on a track opens its cut as a view, where
+     hovering a node bands its bp in the linear view
+   - Export SVG from the track or the view
+
+The [JBrowse tutorials](#tutorials) walk through the whole process with commands
+you can run.
+
+## What it draws
 
 ![The KIV-2 array side by side: GRCh38, HG00097, HG01960 and HG00133 each followed start to end](img/force_kiv2_facet.png)
 
-- **Copy number off a bar.** Walk rows tile each haplotype by the 5,548 bp
-  kringle: GRCh38's six units are the six LPA exon pairs above, and HG00133
-  has 27.
-
 ![KIV-2 walk rows under LPA and the curated KIV-2 annotation](img/walk_rows_kiv2.png)
 
-- **Allele frequency as a tube map.** A tube per route, as wide as the
-  haplotypes taking it, coloured by superpopulation. Over C4's RCCX module, 35
-  of 60 haplotypes skip the 6.4 kb HERV-K in C4B, so their C4B is short; thin
-  tubes skip a whole 33 kb module, keeping one C4, or add one. Panels split the
-  map by sample or a sample table column.
-
-![C4A and C4B as a tube per route coloured by superpopulation, the main route's five strands stepping round C4B's HERV-K and thin tubes round or through whole modules](img/tube_map_c4_routes_by_population.png)
-
-## As its own view
-
-**Add → Graph genome view** opens a whole GFA file. A graph track's **Launch →
-Graph genome view** opens the cut on screen, drawn as the track draws it; a
-session spec does the same with `loadedTrackId` and `loadedRegion`. Hovering a
-node in the view bands its bp in the linear view:
-
-![The MICB cut as a view under its linear view, a variant's box hovered and its bp banded in exon 2](img/tube_map_micb.png)
-
-## Features
-
-- Seven layouts: force-directed (Bandage FMMM, or stress in a track), ordered,
-  anchored, sample rows, walk rows, and sequenceTubeMap's tube map on its own
-  axis or the reference's
-- Genes from the session's annotation track, drawn on the graph
-- Hovering a callset or MAF row in the same view lifts that haplotype's walk
-- Bubbles from `gfatools bubble` or the graph itself, opened level by level
-- gbz-base haplotypes as walks: the number of walks through a node as its
-  thickness, walks lifted out as metro-map lanes or side by side, a panel per
-  walk or a row per sample, each shading from its start to its end
-- Tube maps split into a panel per sample, haplotype or sample table column,
-  drawn as a tube per route and coloured by a sample table column
-- GAF reads in the tube map, with their mismatches, from a gbz-base track
-- Figures as SVG: the graph track in the linear view's Export SVG, the graph
-  genome view's own Export SVG, or a JSON spec with no browser
-  ([docs/figures.md](https://github.com/GMOD/bandage-core/blob/main/docs/figures.md))
-
-## Usage
-
-Needs JBrowse 5.0.0-beta.11 or later.
-
-```json
-{
-  "plugins": [
-    {
-      "name": "GraphGenomeView",
-      "esmUrl": "https://jbrowse.org/plugins/jbrowse-plugin-graphgenomeviewer/latest/dist/jbrowse-plugin-graphgenomeviewer.esm.js"
-    }
-  ]
-}
-```
-
-- **File → Open track** opens an rGFA index (`.segs.bed.gz` from
-  [gfa-to-tabix](https://github.com/GMOD/gfa-to-tabix)) or a gbz-base database
-  (`.gbz.db`) as a `GraphTrack`. It finds the links and indexes beside the url,
-  which a presigned url's signature doesn't cover; spell out each location in a
-  config instead
-- Open track's **Add pangenome graph track** workflow also reads
-  `<prefix>.graph.json` beside a `<prefix>.segs.bed.gz` (written by
-  `gfa-to-tabix build`) for the coarse tier and the reference's PanSN sample;
-  without one, the track has no coarse tier
-- A hand-written track needs only the adapter:
-
-```json
-{
-  "type": "GraphTrack",
-  "trackId": "hprc_graph",
-  "name": "HPRC release 2 graph",
-  "assemblyNames": ["hg38"],
-  "adapter": {
-    "type": "RgfaTabixAdapter",
-    "uri": "https://example.com/hprc",
-    "coarse": {
-      "uri": "https://example.com/hprc.fold10000",
-      "foldBelowBp": 10000
-    }
-  }
-}
-```
-
-- The track menu picks layout, colour and highlighted haplotypes, and switches
-  to the segments lane or, for gbz-base and walk-indexed graphs, the haplotype
-  lanes
-- Cuts the window plus a window each side, up to 5 Mb; past `aboveBpPerPx`
-  (default `foldBelowBp / 10`), the `coarse` tier (`gfa-to-tabix fold`)
-- Past the cut (5 Mb, or a gbz-base adapter's `nodeLimit`) the track asks you to
-  zoom in. For a population view of a wide window, add the graph's VCF as a
-  variant track (`vg deconstruct` makes one from a GBZ)
-- gbz-base swaps in `{ "type": "GbzBaseSyntenyAdapter", "uri": "….gbz.db" }`; an
-  `hg38` or `hs1` track finds the graph's GRCh38 or CHM13 reference sample, and
-  `assemblyNameToPanSN` covers other names. A haplotype's lane draws on the
-  assembly aliased by its PanSN name (`HG002#1`) with no map entry
-- A walk-indexed graph (`gfa-to-tabix --walks`) swaps in
-  `{ "type": "WalkTabixSyntenyAdapter", "walksUri": "….GRCh38", "assemblyNames": ["hg38"] }`
-  and draws the same haplotype lanes from the walk files, with no database
-- `"reads": "….gaf.gz"` on the gbz-base adapter draws GAF reads in the tube map
-  layouts, fetched through its tabix index;
-  [docs/layouts.md](docs/layouts.md#reads) has the config and how to make one
+![C4A and C4B as a tube per route coloured by superpopulation](img/tube_map_c4_routes_by_population.png)
+
+## Tutorials
+
+In the [JBrowse 2 docs](https://jbrowse.org/jb2/docs/tutorials/):
+
+- **[Hosting your own graph](https://jbrowse.org/jb2/docs/tutorials/pangenome_prepare_graph):**
+  start here
+- [pggb](https://jbrowse.org/jb2/docs/tutorials/pangenome_ecoli) and
+  [Minigraph-Cactus](https://jbrowse.org/jb2/docs/tutorials/pangenome_cactus)
+- [Cattle](https://jbrowse.org/jb2/docs/tutorials/pangenome_cattle) and
+  [mouse](https://jbrowse.org/jb2/docs/tutorials/pangenome_mouse)
+- HPRC release 2:
+  [graph alleles](https://jbrowse.org/jb2/docs/tutorials/pangenome_hprc),
+  [haplotypes](https://jbrowse.org/jb2/docs/tutorials/pangenome_hprc_haplotypes),
+  [repeat lengths](https://jbrowse.org/jb2/docs/tutorials/pangenome_hprc_repeats)
+- [User guide](https://jbrowse.org/jb2/docs/user_guides/graph_genome_view)
 
 ## Docs
 
-- [docs/layouts.md](docs/layouts.md) — layouts, bubbles, walks, genes, loci
-- [docs/developing.md](docs/developing.md) — building, testing, `host-compat`
+In reading order:
 
-## See also
+1. [Data and track config](docs/data.md): index a graph and write the track
+2. [Layouts](docs/layouts.md): the seven layouts, colour, the reference strip
+3. [Haplotypes](docs/haplotypes.md): lifting, panels, colouring, walk rows
+4. [Tube maps](docs/tube-maps.md): panels, routes, reads
+5. [Bubbles](docs/bubbles.md) and [genes](docs/genes.md)
+6. [Developing](docs/developing.md): build, test, release
 
-Apps and figures
+## See also
 
-- [BandageJS](https://github.com/cmdcolin/BandageJS) - standalone page with the
-  same layouts, outside JBrowse
-- [ggbandage](https://github.com/GMOD/ggbandage) - R port of the Bandage layout,
-  as ggplot2 layers
-- [ggtubemap](https://github.com/GMOD/ggtubemap) - R port of the tube map, as
-  ggplot2 layers
-- [sequenceTubeMap, MemPanG26 edition](https://github.com/cmdcolin/sequenceTubeMap) -
+- [BandageJS](https://github.com/cmdcolin/BandageJS): standalone page with the
+  same layouts
+- [sequenceTubeMap, MemPanG26 edition](https://github.com/cmdcolin/sequenceTubeMap):
   our fork of the tube map app
 
-Libraries
+### Programmatic usage
 
-- [@jbrowse/bandage-core](https://github.com/GMOD/bandage-core) - the layout and
-  drawing engine behind this plugin
-- [@jbrowse/graph-stress-layout](https://github.com/GMOD/graph-stress-layout) -
-  stress layout that straightens the reference
-- [@jbrowse/tubemap-core](https://github.com/GMOD/tubemap-core) - tube map
+- [@jbrowse/bandage-core](https://github.com/GMOD/bandage-core) (npm): layout
+  and drawing engine, plus `bandage-figure` for SVGs with no browser
+- [@jbrowse/graph-stress-layout](https://github.com/GMOD/graph-stress-layout)
+  (npm): stress layout
+- [@jbrowse/tubemap-core](https://github.com/GMOD/tubemap-core) (npm): tube map
   layout
-- [@gmod/gbz-base](https://github.com/GMOD/gbz-base-js) - range-request reader
-  for `.gbz.db` databases
-
-Preparing data
-
-- [gfa-to-tabix](https://github.com/GMOD/gfa-to-tabix) - indexes a GFA for the
-  graph track
-- [gbz-haplotype-index](https://github.com/GMOD/gbz-haplotype-index) - names
+- [@gmod/gbz-base](https://github.com/GMOD/gbz-base-js) (npm): `.gbz.db` reader
+- [ggbandage](https://github.com/GMOD/ggbandage) (R): Bandage layout as ggplot2
+  layers
+- [ggtubemap](https://github.com/GMOD/ggtubemap) (R): tube map as ggplot2 layers
+- [gfa-to-tabix](https://github.com/GMOD/gfa-to-tabix): indexes a GFA
+- [gbz-haplotype-index](https://github.com/GMOD/gbz-haplotype-index): names
   every walk in a gbz-base cut
-- [gfa-to-pairwise-paf](https://github.com/cmdcolin/gfa-to-pairwise-paf-rs) -
+- [gfa-to-pairwise-paf](https://github.com/cmdcolin/gfa-to-pairwise-paf-rs):
   graph to PAF, for synteny views
 
 ## License
 
-GPL-3.0-or-later (this module is based on work from Bandage and ODGF graph
-drawing algorithms which are both GPL).
+GPL-3.0-or-later, based on work from Bandage and OGDF, both GPL.

package/dist/chunks/GbzBaseSyntenyAdapter-TIXR4Y3J.js

@@ -0,0 +1,2 @@
+import{a as q,b as re,c as de,d as oe,e as T}from"./chunk-SAMJE6GH.js";import{a as ne}from"./chunk-KOB7YIMR.js";import{a as Z,b as U,c as X,d as g,e as C,f as M,g as k,h as E,i as z,k as Y}from"./chunk-YJHYBDYF.js";import"./chunk-EWFJBQDV.js";import{a as O,b as H}from"./chunk-3Q4RBDCL.js";import"./chunk-AU73K7LX.js";import"./chunk-IXQK7JAW.js";import{a as ae}from"./chunk-TXI43PEN.js";import{a as ee,c as L,f as te}from"./chunk-AMFIBQVR.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import{e as A,f as P,g as B}from"./chunk-446RWIA3.js";import"./chunk-E7J6SB5P.js";import{b as G,e as J,f as K,g as V}from"./chunk-5OI6LO4I.js";import"./chunk-7WIBGKBU.js";import{a as N}from"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{e as W,o as $}from"./chunk-TENPGIPX.js";function F(n){let i=/\.gbz\.db$/i;return i.test(n)?n.replace(i,".haplotype-index.db"):void 0}function fe(n){return K(n)&&F(J(n))?V(n,i=>F(i)):void 0}function he(n){return n instanceof Error&&(/\bHTTP 40[34]\b/.test(n.message)||n.code==="ENOENT")}async function se(n,i){let t=fe(n);if(!t)return{};try{return await N(t,i).stat(),{location:t}}catch(e){return he(e)?{}:{unreadable:String(e)}}}var ge=5e3,ue=50*2**20,_=class extends Error{constructor(t){super(`this GAF is ${(t/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function ye(n,i){if(n.length<=i)return n;let t=n.length/i;return Array.from({length:i},(e,a)=>n[Math.floor(a*t)])}var ie=(n,i)=>n.path.some(t=>i.has(t.name)),v=class{constructor(i,t){this.file=i;this.tabix=t;this.whole=L({setup:async({signal:i})=>{let{size:t}=await this.file.stat();if(t>ue)throw new _(t);let e=await this.file.readFile({signal:i}),a=new TextDecoder().decode(e[0]===31&&e[1]===139?await ee(e):e);return H(a)}})}async readIndexed(i,t,e){let a=1/0,r=-1/0;for(let c of t){let s=Number(c);Number.isInteger(s)&&(a=Math.min(a,s),r=Math.max(r,s))}let o=[];return a<=r&&await i.getLines("{node}",a,r+1,{signal:e,lineCallback:c=>{let s=O(c);s&&ie(s,t)&&o.push(s)}}),o}async readsOver(i,{signal:t}={}){let e=this.tabix?await this.readIndexed(this.tabix,i,t):(await this.whole({signal:t})).filter(a=>ie(a,i));return{records:ye(e,ge),total:e.length}}};var I=class extends Error{constructor(t){super(t===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${t}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},D=class extends Error{constructor(t,e){super(`the graph is cut on its reference, ${e}; a window on ${t} has no reference coordinates to cut at. Open the graph from a ${e} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function be(n,i){return`${g(n)}#${n.contig}@${i.start.node}.${i.start.offset}`}function we({alignment:n,assemblyName:i,refName:t,lane:e}){let{refStart:a,refEnd:r,strand:o,cigar:c}=n;if(!(r<=a)){let{name:s,hapStart:p,hapEnd:l}=n,f=be(s,n),u={uniqueId:f,assemblyName:i,refName:t,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:c,syntenyId:f,mate:{refName:s.contig,start:p,end:l,assemblyName:e}};return new q(u)}}function xe({pair:n,lane:i,mateLane:t}){let e=`${g(n.target)}#${n.target.contig}:${n.targetStart}-${n.targetEnd}|${g(n.query)}#${n.query.contig}:${n.queryStart}-${n.queryEnd}`;return new q({uniqueId:e,assemblyName:i,refName:n.target.contig,start:n.targetStart,end:n.targetEnd,type:"match",strand:n.strand==="-"?-1:1,CIGAR:n.cigar,syntenyId:e,identity:n.matches/Math.max(n.columns,1),numMatches:n.matches,blockLen:n.columns,mate:{refName:n.query.contig,start:n.queryStart,end:n.queryEnd,assemblyName:t}})}var Se=12e4;function Pe(n,i){let t=new Map;for(let a of n)for(let{name:r,start:o,end:c}of a.walkSpans()){let s=g(r);if(i.has(s)){let p=`${s}#${r.contig}`,l=t.get(p);l?l.push([o,c]):t.set(p,[[o,c]])}}let e=0;for(let a of t.values()){a.sort((r,o)=>r[0]-o[0]);for(let r=1;r<a.length;r++){let o=a[r][0]-a[r-1][1];o>0&&o<=Se&&(e=Math.max(e,o))}}return e}function Q(n,i){return n instanceof X&&(n.message=`Zoom in to about ${W(n.fitsBp)} to see ${i}`),n}var ce=n=>({...n,start:Math.floor(n.start),end:Math.ceil(n.end)}),j=class extends re{constructor(){super(...arguments);this.graph=L({label:"Opening pangenome database",setup:async()=>{let t=this.getConf("gbzDbLocation"),e=this.getConf("haplotypeIndexLocation"),a=G(e)?{location:e}:await se(t,this.pluginManager),r=a.location,o=await U.open({source:N(t,this.pluginManager),haplotypeIndex:r?N(r,this.pluginManager):void 0}),c=this.getConf("assemblyNames")[0];if(c===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let s=await M(o),p=k({configured:this.getConf("referenceSample"),anchorPrefix:P(this,c),referenceSamples:s});return{db:o,anchor:c,referenceSample:p,referenceSamples:s,unreadableIndex:a.unreadable}}});this.gaf=L({label:"Opening reads",setup:async()=>{let t=this.getConf("readsLocation"),e=this.getConf(["readsIndex","location"]);return G(t)?new v(N(t,this.pluginManager),G(e)?te(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(t,e){let{db:a,referenceSample:r}=await this.graph(e);return E(a,r,t)}async getHaplotypes(t={}){let{db:e,referenceSamples:a}=await this.graph(t),r=new Map;for(let o of await e.paths()){let c=g(o.name),s=r.get(c);s?s.contigs.includes(o.name.contig)||s.contigs.push(o.name.contig):r.set(c,{prefix:c,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(t={}){let{anchor:e,referenceSample:a,referenceSamples:r}=await this.graph(t),o=B(this),c=[];for(let s of await this.getHaplotypes(t))s.sample!==a&&c.push({name:T(o,s.prefix),label:s.prefix,group:s.sample});return{hasCoarseTier:!1,anchorAssemblyName:e,referenceSample:a,referenceSamples:r,lanes:c}}async getRefNames(t={}){let{db:e,anchor:a,referenceSample:r}=await this.graph(t),{assemblyName:o}=t,c=o===a?void 0:P(this,o),s=(await e.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:A(g(p.name),c)).map(p=>p.name.contig);return[...new Set(s)]}keepPredicate(t,e){let a=t===void 0||t.length===0?void 0:t.map(r=>P(this,r));return a===void 0&&e===void 0?void 0:r=>C(r,a)&&(e===void 0||A(g(r),e))}async getSubgraph(t,e={}){let{signal:a}=e,{db:r,anchor:o,referenceSample:c,unreadableIndex:s}=await this.graph({signal:a}),{assemblyName:p,refName:l,start:f,end:u}=ce(t);if(p!==o)throw new D(p,o);let y=await this.referenceQuery(l,{signal:a});if(!y)throw new Error(`${c} has no indexed path ${l} in this graph`);let x=this.keepPredicate(e.haplotypes);if(x!==void 0&&!r.hasHaplotypeIndex)throw new I(s);let m=await Y(r,y,f,u,{context:this.getConf("context"),snarls:e.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:e.signal,keep:x}).catch(b=>{throw Q(b,"the graph")});return typeof m=="string"?m:ae(m,{start:f,end:u},e.walkRows)}async getReads(t,e={}){let a=await this.gaf(e);return a?a.readsOver(new Set(t),e):{records:[],total:0}}async laneHaplotypes(t,e){let a=P(this,t);return(await this.getHaplotypes(e)).filter(r=>A(r.prefix,a))}async anchorFeatures(t,e){let{db:a}=await this.graph(e),{assemblyName:r,refName:o,start:c,end:s}=t,p=P(this,e.targetAssemblyName),l=B(this),f=this.keepPredicate(e.haplotypes,p),u=await this.referenceQuery(o,e),y=this.getConf("nodeLimit");return(u?await $(`Reading graph ${o}:${c.toLocaleString()}-${s.toLocaleString()}`,e.statusCallback,()=>a.getAlignments({path:u,start:c,end:s,context:this.getConf("context"),haplotypes:"all",limit:y,signal:e.signal,keep:f}).catch(m=>{throw Q(z(m,y,s-c)??m,"lanes")})):[]).flatMap(m=>{let b=m.resolved?we({alignment:m,assemblyName:r,refName:o,lane:T(l,g(m.name))}):void 0;return b===void 0?[]:[b]})}async pairFeatures(t,e,a){let{db:r}=await this.graph(a),{refName:o,start:c,end:s}=t,l=(await Promise.all(e.map(async d=>({pair:d,featureSide:await this.laneHaplotypes(d.queryAssemblyName,a),mateSide:await this.laneHaplotypes(d.targetAssemblyName,a)})))).filter(({featureSide:d,mateSide:h})=>d.length>0&&h.length>0),f=new Set(l.flatMap(({featureSide:d,mateSide:h})=>[...d,...h].map(g))),u=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),x=this.getConf("context"),[m]=e,b=(d,h)=>r.getSubgraphs({path:d,start:c,end:s,context:h,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:S=>f.has(g(S))}),pe=async d=>{let h=await b(d,x).catch(w=>{throw Q(z(w,y,s-c)??w,"lanes")}),S=Pe(h,f),R=Math.ceil(S/2)+2e3;return S>0&&R>x?b(d,R).catch(w=>{if(w instanceof Z)return h;throw w}):h};return(u&&m&&l.length>0?await $(e.length===1?`Reading ${m.queryAssemblyName} against ${m.targetAssemblyName}`:`Reading ${e.length} lane pairs`,a.statusCallback,()=>pe(u)):[]).flatMap(d=>l.flatMap(({pair:h,featureSide:S,mateSide:R})=>S.flatMap(w=>R.flatMap(le=>d.pairAlignments({target:w,query:le,bases:!1}).map(me=>xe({pair:me,lane:h.queryAssemblyName,mateLane:h.targetAssemblyName}))))))}getFeatures(t,e={}){let a=ce(t);return ne(async r=>{let{db:o,anchor:c,unreadableIndex:s}=await this.graph(e);if(!o.hasHaplotypeIndex)throw new I(s);if(a.assemblyName===c){let p=oe(e),l=p.length>0?await this.pairFeatures(a,p,e):await this.anchorFeatures(a,e);for(let f of l)r.next(f)}r.complete()},e.signal)}};export{D as HaplotypeWindowError,I as NoHaplotypeIndexError,de as PairTargetError,j as default,we as fragmentFeature,xe as pairFeature,Pe as widestWalkGap};
+//# sourceMappingURL=GbzBaseSyntenyAdapter-TIXR4Y3J.js.map

package/dist/chunks/GbzBaseSyntenyAdapter-TIXR4Y3J.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@10.2.4/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-VQWHMWLF.js", "../../src/GbzBaseSyntenyAdapter/companion.ts", "../../src/gaf/gafFile.ts", "../../src/GbzBaseSyntenyAdapter/GbzBaseSyntenyAdapter.ts"],
+  "sourcesContent": ["import {\n  GBZ_CUT_DEFAULTS,\n  cutWindowGFA,\n  haplotypeWanted,\n  referencePathQuery,\n  referenceSamplesOf,\n  resolveReferenceSample\n} from \"./chunk-Q7LYHGGQ.js\";\n\n// src/gbzCut.ts\nimport { GBZBase } from \"@gmod/gbz-base\";\nvar HPRC_GBZ = {\n  db: \"https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/v2.1/hprc-v2.1-mc-grch38/hprc-v2.1-mc-grch38.gbz.db\",\n  index: \"https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38.haplotype-index.f3.db\"\n};\nfunction haplotypeIndexBeside(db) {\n  const GBZ_DB = /\\.gbz\\.db$/i;\n  return GBZ_DB.test(db) ? db.replace(GBZ_DB, \".haplotype-index.db\") : void 0;\n}\nfunction parseRegion(text) {\n  const m = /^\\s*([^:\\s]+):([\\d,]+)-([\\d,]+)\\s*$/.exec(text);\n  if (!m) {\n    throw new Error(\n      `\"${text}\" is not a region like chr6:160,614,798-160,647,758`\n    );\n  }\n  const n = (s) => Number(s.replaceAll(\",\", \"\"));\n  const region = { refName: m[1], start: n(m[2]), end: n(m[3]) };\n  if (region.end <= region.start) {\n    throw new Error(`\"${text}\" ends at or before it starts`);\n  }\n  return region;\n}\nasync function openGbz(db, index) {\n  const base = await GBZBase.open({ source: db, haplotypeIndex: index });\n  return { base, referenceSamples: await referenceSamplesOf(base) };\n}\nfunction referenceSample(ref, samples) {\n  try {\n    return resolveReferenceSample({\n      configured: \"\",\n      anchorPrefix: ref ?? samples[0] ?? \"\",\n      referenceSamples: samples\n    });\n  } catch (e) {\n    if (ref) {\n      return ref;\n    }\n    throw e;\n  }\n}\nasync function cutGbzRegion({ base, referenceSamples }, src, signal) {\n  const region = parseRegion(src.region);\n  const sample = referenceSample(src.referenceSample, referenceSamples);\n  const query = await referencePathQuery(base, sample, region.refName);\n  if (!query) {\n    throw new Error(`${sample} has no indexed path named ${region.refName}`);\n  }\n  signal?.throwIfAborted();\n  const wanted = src.haplotypes?.length ? src.haplotypes : void 0;\n  const text = await cutWindowGFA(base, query, region.start, region.end, {\n    context: src.context ?? GBZ_CUT_DEFAULTS.context,\n    snarls: src.snarls ?? GBZ_CUT_DEFAULTS.snarls,\n    limit: GBZ_CUT_DEFAULTS.limit,\n    signal,\n    keep: wanted ? (name) => haplotypeWanted(name, wanted) : void 0\n  });\n  return { text, region, sample };\n}\n\nexport {\n  HPRC_GBZ,\n  haplotypeIndexBeside,\n  parseRegion,\n  openGbz,\n  cutGbzRegion\n};\n", "import { haplotypeIndexBeside } from '@jbrowse/bandage-core/gbzCut'\nimport { openLocation } from '@jbrowse/core/util/io'\n\nimport { locationName, readsSiblings, renamed } from '../locationName'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { FileLocation } from '@jbrowse/core/util/types'\n\nexport function siblingCompanion(gbzDb: FileLocation) {\n  return readsSiblings(gbzDb) && haplotypeIndexBeside(locationName(gbzDb))\n    ? renamed(gbzDb, name => haplotypeIndexBeside(name)!)\n    : undefined\n}\n\n// 404 is a missing file, and so is 403 from a bucket that does not let a\n// reader list it; anything else leaves the file's presence unknown\nfunction isMissing(error: unknown) {\n  return (\n    error instanceof Error &&\n    (/\\bHTTP 40[34]\\b/.test(error.message) ||\n      (error as { code?: unknown }).code === 'ENOENT')\n  )\n}\n\n// `unreadable` is why a companion that may be there could not be checked, such\n// as a network error, or a server that answers a missing file without CORS\nexport async function findCompanion(\n  gbzDb: FileLocation,\n  pluginManager?: PluginManager,\n): Promise<{ location?: FileLocation; unreadable?: string }> {\n  const candidate = siblingCompanion(gbzDb)\n  if (!candidate) {\n    return {}\n  }\n  try {\n    await openLocation(candidate, pluginManager).stat()\n    return { location: candidate }\n  } catch (error) {\n    return isMissing(error) ? {} : { unreadable: String(error) }\n  }\n}\n", "import { unzip } from '@gmod/bgzf-filehandle'\nimport { parseGaf, parseGafLine } from '@jbrowse/bandage-core/gaf/parseGaf'\nimport { cachedSetup } from '@jbrowse/core/data_adapters/BaseAdapter'\n\nimport type { TabixIndexedFile } from '@gmod/tabix'\nimport type { GafRecord } from '@jbrowse/bandage-core/gaf/parseGaf'\n\ninterface WholeFile {\n  stat(): Promise<{ size: number }>\n  readFile(opts?: { signal?: AbortSignal }): Promise<Uint8Array>\n}\n\nexport interface GafReads {\n  records: GafRecord[]\n  // reads over the nodes before sampling\n  total: number\n}\n\n// The tube map lays reads out on the main thread at about 40 ms per thousand\nexport const MAX_READS = 5000\n\n// An unindexed GAF is read whole, once, into the worker\nconst MAX_UNINDEXED_BYTES = 50 * 2 ** 20\n\nexport class UnindexedGafTooLargeError extends Error {\n  override name = 'UnindexedGafTooLargeError'\n\n  constructor(size: number) {\n    super(\n      `this GAF is ${(size / 2 ** 20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`,\n    )\n  }\n}\n\n// Evenly spaced, so a pileup thins out rather than losing its right half\nfunction sample(records: GafRecord[], max: number) {\n  if (records.length <= max) {\n    return records\n  }\n  const stride = records.length / max\n  return Array.from({ length: max }, (_, k) => records[Math.floor(k * stride)]!)\n}\n\nconst touches = (record: GafRecord, names: ReadonlySet<string>) =>\n  record.path.some(step => names.has(step.name))\n\n// A GAF over a graph's segments: bgzipped and indexed with `tabix -p gaf`,\n// which keys each line by its lowest and highest node id and so needs numeric\n// segment names, or plain or gzipped and read whole.\nexport class GafFile {\n  // Shared by every window, so the signal is cachedSetup's own, which aborts\n  // once no caller is left waiting\n  private whole = cachedSetup({\n    setup: async ({ signal }) => {\n      const { size } = await this.file.stat()\n      if (size > MAX_UNINDEXED_BYTES) {\n        throw new UnindexedGafTooLargeError(size)\n      }\n      const bytes = await this.file.readFile({ signal })\n      const text = new TextDecoder().decode(\n        bytes[0] === 0x1f && bytes[1] === 0x8b ? await unzip(bytes) : bytes,\n      )\n      return parseGaf(text)\n    },\n  })\n\n  constructor(\n    private file: WholeFile,\n    private tabix?: TabixIndexedFile,\n  ) {}\n\n  private async readIndexed(\n    tabix: TabixIndexedFile,\n    names: ReadonlySet<string>,\n    signal?: AbortSignal,\n  ) {\n    let lo = Infinity\n    let hi = -Infinity\n    for (const name of names) {\n      const id = Number(name)\n      if (Number.isInteger(id)) {\n        lo = Math.min(lo, id)\n        hi = Math.max(hi, id)\n      }\n    }\n    const records: GafRecord[] = []\n    if (lo <= hi) {\n      // a GAF index ignores the refName, and getLines keeps a read whose node\n      // ids span min..max when min < end && max >= start, hence hi + 1\n      await tabix.getLines('{node}', lo, hi + 1, {\n        signal,\n        lineCallback: line => {\n          const record = parseGafLine(line)\n          if (record && touches(record, names)) {\n            records.push(record)\n          }\n        },\n      })\n    }\n    return records\n  }\n\n  async readsOver(\n    names: ReadonlySet<string>,\n    { signal }: { signal?: AbortSignal } = {},\n  ): Promise<GafReads> {\n    const records = this.tabix\n      ? await this.readIndexed(this.tabix, names, signal)\n      : (await this.whole({ signal })).filter(r => touches(r, names))\n    return { records: sample(records, MAX_READS), total: records.length }\n  }\n}\n", "import { GBZBase, SubgraphLimitError } from '@gmod/gbz-base'\nimport {\n  NodeLimitError,\n  cutWindowTables,\n  haplotypePrefix,\n  haplotypeWanted,\n  nodeLimitError,\n  referencePathQuery,\n  referenceSamplesOf,\n  resolveReferenceSample,\n} from '@jbrowse/bandage-core/gbzWindow'\nimport {\n  assemblyByPanSNPrefix,\n  panSNMatchesPrefix,\n  resolvePanSNPrefix,\n} from '@jbrowse/bandage-core/pansn'\nimport { cachedSetup } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { getBpDisplayStr, updateStatus } from '@jbrowse/core/util'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\n\nimport { findCompanion } from './companion.ts'\nimport { walkCutFor } from '../RgfaTabixAdapter/walkRowRuns.ts'\nimport { GafFile } from '../gaf/gafFile.ts'\nimport { locationIsSet } from '../locationName.ts'\nimport { openTabixSlot } from '../panSNTabix.ts'\nimport { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'\nimport SyntenyFeature from '../synteny/SyntenyFeature.ts'\nimport { laneAssemblyName, requestedPairs } from '../synteny/lanePairs.ts'\n\nimport type { GbzBaseSyntenyAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions } from '../GetSubgraph.ts'\nimport type { GafReads } from '../gaf/gafFile.ts'\nimport type { LaneFeatureOptions, LanePair } from '../synteny/lanePairs.ts'\nimport type {\n  HaplotypeAlignment,\n  HaplotypeRef,\n  PairAlignment,\n  PathName,\n  PathQuery,\n  Subgraph,\n} from '@gmod/gbz-base'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util'\nimport type { FileLocation, Region } from '@jbrowse/core/util/types'\n\nexport class NoHaplotypeIndexError extends Error {\n  override name = 'NoHaplotypeIndexError'\n\n  constructor(unreadable?: string) {\n    super(\n      unreadable === undefined\n        ? 'no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation'\n        : `the haplotype index beside the graph database could not be checked (${unreadable}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`,\n    )\n  }\n}\n\nexport interface GbzHaplotype {\n  prefix: string\n  sample: string\n  haplotype: number\n  contigs: string[]\n  isReference: boolean\n}\n\n/**\n * One lane the header declares, in the shape MultiWaySyntenyDisplay's lane\n * picker reads: `name` is the lane's assembly name, the same string the\n * fetched features' mates carry, `label` its PanSN prefix and `group` its\n * sample, so a diploid sample's two lanes sit together\n */\ninterface GbzHeaderLane {\n  name: string\n  label: string\n  group: string\n}\n\nexport { PairTargetError } from '../synteny/lanePairs.ts'\nexport type { LanePair } from '../synteny/lanePairs.ts'\n\nexport class HaplotypeWindowError extends Error {\n  override name = 'HaplotypeWindowError'\n\n  constructor(assemblyName: string, anchor: string) {\n    super(\n      `the graph is cut on its reference, ${anchor}; a window on ${assemblyName} has no reference coordinates to cut at. Open the graph from a ${anchor} view, and find this haplotype's lane there`,\n    )\n  }\n}\n\ntype ResolvedAlignment = Extract<HaplotypeAlignment, { resolved: true }>\n\n/**\n * The id of one haplotype fragment: the walk's GBWT position at its first node\n * in the window, which is a property of the graph, so the same fragment gets\n * the same id on a refetch of the same window and the display's hover and\n * selection survive it. `clipToRegion` suffixes the window.\n */\nfunction fragmentId(name: PathName, alignment: ResolvedAlignment) {\n  return `${haplotypePrefix(name)}#${name.contig}@${alignment.start.node}.${alignment.start.offset}`\n}\n\nexport function fragmentFeature({\n  alignment,\n  assemblyName,\n  refName,\n  lane,\n}: {\n  alignment: ResolvedAlignment\n  assemblyName: string\n  refName: string\n  lane: string\n}) {\n  const { refStart, refEnd, strand, cigar } = alignment\n  if (refEnd <= refStart) {\n    return undefined\n  } else {\n    const { name, hapStart, hapEnd } = alignment\n    const id = fragmentId(name, alignment)\n    const data: SimpleFeatureSerialized = {\n      uniqueId: id,\n      assemblyName,\n      refName,\n      start: refStart,\n      end: refEnd,\n      type: 'match',\n      strand: strand === '-' ? -1 : 1,\n      CIGAR: cigar,\n      syntenyId: id,\n      mate: {\n        refName: name.contig,\n        start: hapStart,\n        end: hapEnd,\n        assemblyName: lane,\n      },\n    }\n    return new SyntenyFeature(data)\n  }\n}\n\n/**\n * One record of a lane pair, on the target walk's own contig with the query\n * walk as its mate. gbz-base writes the CIGAR along the target, a `D` being\n * target bases the query lacks, which is the side a JBrowse feature is, so it\n * passes through unchanged.\n */\nexport function pairFeature({\n  pair,\n  lane,\n  mateLane,\n}: {\n  pair: PairAlignment\n  lane: string\n  mateLane: string\n}) {\n  const id = `${haplotypePrefix(pair.target)}#${pair.target.contig}:${pair.targetStart}-${pair.targetEnd}|${haplotypePrefix(pair.query)}#${pair.query.contig}:${pair.queryStart}-${pair.queryEnd}`\n  return new SyntenyFeature({\n    uniqueId: id,\n    assemblyName: lane,\n    refName: pair.target.contig,\n    start: pair.targetStart,\n    end: pair.targetEnd,\n    type: 'match',\n    strand: pair.strand === '-' ? -1 : 1,\n    CIGAR: pair.cigar,\n    syntenyId: id,\n    identity: pair.matches / Math.max(pair.columns, 1),\n    numMatches: pair.matches,\n    blockLen: pair.columns,\n    mate: {\n      refName: pair.query.contig,\n      start: pair.queryStart,\n      end: pair.queryEnd,\n      assemblyName: mateLane,\n    },\n  })\n}\n\n// The longest detour a pair cut widens its context to take in\nconst BRIDGE_MAX_BP = 120_000\n\n/**\n * The widest gap, up to `BRIDGE_MAX_BP`, between two pieces of one kept walk:\n * a haplotype that left the cut's nodes for sequence the reference lacks and\n * came back. Two kept haplotypes that share that sequence only align across it\n * once its nodes are in the cut.\n */\nexport function widestWalkGap(subgraphs: Subgraph[], kept: Set<string>) {\n  const byPath = new Map<string, [number, number][]>()\n  for (const subgraph of subgraphs) {\n    for (const { name, start, end } of subgraph.walkSpans()) {\n      const prefix = haplotypePrefix(name)\n      if (kept.has(prefix)) {\n        const key = `${prefix}#${name.contig}`\n        const spans = byPath.get(key)\n        if (spans) {\n          spans.push([start, end])\n        } else {\n          byPath.set(key, [[start, end]])\n        }\n      }\n    }\n  }\n  let widest = 0\n  for (const spans of byPath.values()) {\n    spans.sort((a, b) => a[0] - b[0])\n    for (let i = 1; i < spans.length; i++) {\n      const gap = spans[i]![0] - spans[i - 1]![1]\n      if (gap > 0 && gap <= BRIDGE_MAX_BP) {\n        widest = Math.max(widest, gap)\n      }\n    }\n  }\n  return widest\n}\n\n// A window past the node limit fails as a zoom-in notice naming a span that\n// fits\nfunction zoomInNotice(error: unknown, what: string) {\n  if (error instanceof NodeLimitError) {\n    error.message = `Zoom in to about ${getBpDisplayStr(error.fitsBp)} to see ${what}`\n  }\n  return error\n}\n\n// gbz-base reads whole bp; a view asks at fractional ones\nconst wholeBp = (region: Region) => ({\n  ...region,\n  start: Math.floor(region.start),\n  end: Math.ceil(region.end),\n})\n\nexport default class GbzBaseSyntenyAdapter extends ComparativeAdapterBase<GbzBaseSyntenyAdapterConfig> {\n  private graph = cachedSetup({\n    label: 'Opening pangenome database',\n    setup: async () => {\n      const gbzDb: FileLocation = this.getConf('gbzDbLocation')\n      const configured: FileLocation = this.getConf('haplotypeIndexLocation')\n      const companion = locationIsSet(configured)\n        ? { location: configured }\n        : await findCompanion(gbzDb, this.pluginManager)\n      const indexLocation = companion.location\n      const db = await GBZBase.open({\n        source: openLocation(gbzDb, this.pluginManager),\n        haplotypeIndex: indexLocation\n          ? openLocation(indexLocation, this.pluginManager)\n          : undefined,\n      })\n      const anchor = this.getConf('assemblyNames')[0]\n      if (anchor === undefined) {\n        throw new Error(\n          'GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as',\n        )\n      }\n      const referenceSamples = await referenceSamplesOf(db)\n      const referenceSample = resolveReferenceSample({\n        configured: this.getConf('referenceSample'),\n        anchorPrefix: resolvePanSNPrefix(this, anchor),\n        referenceSamples,\n      })\n      return {\n        db,\n        anchor,\n        referenceSample,\n        referenceSamples,\n        unreadableIndex: companion.unreadable,\n      }\n    },\n  })\n\n  /**\n   * The indexed reference path a window on `refName` resolves against, or\n   * undefined when the reference sample has no indexed path by that contig.\n   */\n  private async referenceQuery(\n    refName: string,\n    opts: BaseOptions,\n  ): Promise<PathQuery | undefined> {\n    const { db, referenceSample } = await this.graph(opts)\n    return referencePathQuery(db, referenceSample, refName)\n  }\n\n  /**\n   * Every haplotype the graph carries a walk for, `sample#haplotype` with its\n   * contigs, from the Paths scan the adapter already makes; the lane picker's\n   * source list. Reference samples are included and flagged.\n   */\n  async getHaplotypes(opts: BaseOptions = {}): Promise<GbzHaplotype[]> {\n    const { db, referenceSamples } = await this.graph(opts)\n    const byPrefix = new Map<string, GbzHaplotype>()\n    for (const path of await db.paths()) {\n      const prefix = haplotypePrefix(path.name)\n      const entry = byPrefix.get(prefix)\n      if (entry) {\n        if (!entry.contigs.includes(path.name.contig)) {\n          entry.contigs.push(path.name.contig)\n        }\n      } else {\n        byPrefix.set(prefix, {\n          prefix,\n          sample: path.name.sample,\n          haplotype: path.name.haplotype,\n          contigs: [path.name.contig],\n          isReference: referenceSamples.includes(path.name.sample),\n        })\n      }\n    }\n    return [...byPrefix.values()]\n  }\n\n  /**\n   * `lanes` is every haplotype but the reference sample's own, which is the\n   * anchor rather than a lane, declared up front so the display can offer the\n   * whole graph's haplotypes before a fetch has placed any of them.\n   */\n  async getHeader(opts: BaseOptions = {}) {\n    const { anchor, referenceSample, referenceSamples } = await this.graph(opts)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const lanes: GbzHeaderLane[] = []\n    for (const haplotype of await this.getHaplotypes(opts)) {\n      if (haplotype.sample !== referenceSample) {\n        lanes.push({\n          name: laneAssemblyName(asmByPrefix, haplotype.prefix),\n          label: haplotype.prefix,\n          group: haplotype.sample,\n        })\n      }\n    }\n    return {\n      hasCoarseTier: false,\n      anchorAssemblyName: anchor,\n      referenceSample,\n      referenceSamples,\n      lanes,\n    }\n  }\n\n  async getRefNames(opts: BaseOptions = {}) {\n    const { db, anchor, referenceSample } = await this.graph(opts)\n    const { assemblyName } = opts\n    const prefix =\n      assemblyName === anchor\n        ? undefined\n        : resolvePanSNPrefix(this, assemblyName)\n    const contigs = (await db.paths())\n      .filter(path =>\n        assemblyName === anchor\n          ? path.isIndexed && path.name.sample === referenceSample\n          : panSNMatchesPrefix(haplotypePrefix(path.name), prefix),\n      )\n      .map(path => path.name.contig)\n    return [...new Set(contigs)]\n  }\n\n  /**\n   * The predicate gbz-base builds a window for, from the lanes a fetch asks\n   * for. With a companion whose stray rows cover the window gbz-base walks\n   * only the wanted haplotypes; otherwise it names every walk and keeps the\n   * ones the predicate accepts, and throws rather than guess when a walk has\n   * no name. Either way a cut holds those walks, the reference, and the nodes\n   * they visit. Undefined when every haplotype is wanted.\n   */\n  //\n  // `targetPrefix` is a pairwise view's one lane, and it belongs in here: left\n  // to filter what came back, it handed gbz-base no predicate, and every\n  // haplotype in the graph was walked for one to be kept.\n  private keepPredicate(\n    haplotypes: string[] | undefined,\n    targetPrefix?: string,\n  ) {\n    const wantedPrefixes =\n      haplotypes === undefined || haplotypes.length === 0\n        ? undefined\n        : haplotypes.map(lane => resolvePanSNPrefix(this, lane))\n    return wantedPrefixes === undefined && targetPrefix === undefined\n      ? undefined\n      : (name: PathName) =>\n          haplotypeWanted(name, wantedPrefixes) &&\n          (targetPrefix === undefined ||\n            panSNMatchesPrefix(haplotypePrefix(name), targetPrefix))\n  }\n\n  /**\n   * The graph view's cut of the window, as tables: the reference walk, every\n   * top-level snarl contained in it, and one walk per haplotype, PanSN-named\n   * when the database (or its companion) carries the haplotype index and\n   * `unknown#N` otherwise. The reference walk is the first, which is the one\n   * the view anchors on by default. With `haplotypes` the walks are that\n   * set's and the nodes those walks visit, the reference walk kept. With\n   * `walkRows` the rows' runs come along, as on a walk-file cut.\n   *\n   * Only a window on the anchor can be cut: a haplotype lane's coordinates\n   * are its own contig's, and the graph is indexed for random access on the\n   * reference sample's paths alone.\n   */\n  async getSubgraph(region: Region, opts: SubgraphAdapterOptions = {}) {\n    const { signal } = opts\n    const { db, anchor, referenceSample, unreadableIndex } = await this.graph({\n      signal,\n    })\n    const { assemblyName, refName, start, end } = wholeBp(region)\n    if (assemblyName !== anchor) {\n      throw new HaplotypeWindowError(assemblyName, anchor)\n    }\n    const query = await this.referenceQuery(refName, { signal })\n    if (!query) {\n      throw new Error(\n        `${referenceSample} has no indexed path ${refName} in this graph`,\n      )\n    }\n    const keep = this.keepPredicate(opts.haplotypes)\n    if (keep !== undefined && !db.hasHaplotypeIndex) {\n      throw new NoHaplotypeIndexError(unreadableIndex)\n    }\n    const cut = await cutWindowTables(db, query, start, end, {\n      context: this.getConf('context'),\n      snarls: opts.snarls ?? this.getConf('subgraphSnarls'),\n      limit: this.getConf('nodeLimit'),\n      signal: opts.signal,\n      keep,\n    }).catch((error: unknown) => {\n      throw zoomInNotice(error, 'the graph')\n    })\n    return typeof cut === 'string'\n      ? cut\n      : walkCutFor(cut, { start, end }, opts.walkRows)\n  }\n\n  private gaf = cachedSetup({\n    label: 'Opening reads',\n    setup: async () => {\n      const location: FileLocation = this.getConf('readsLocation')\n      const index: FileLocation = this.getConf(['readsIndex', 'location'])\n      return locationIsSet(location)\n        ? new GafFile(\n            openLocation(location, this.pluginManager),\n            locationIsSet(index)\n              ? openTabixSlot(this, ['readsLocation'], ['readsIndex'])\n              : undefined,\n          )\n        : undefined\n    },\n  })\n\n  /**\n   * The reads over a cut's segments, from `readsLocation`, sampled down to\n   * what the tube map lays out at interactive speed\n   */\n  async getReads(\n    nodeNames: string[],\n    opts: BaseOptions = {},\n  ): Promise<GafReads> {\n    const gaf = await this.gaf(opts)\n    return gaf\n      ? gaf.readsOver(new Set(nodeNames), opts)\n      : { records: [], total: 0 }\n  }\n\n  private async laneHaplotypes(\n    assemblyName: string,\n    opts: BaseOptions,\n  ): Promise<HaplotypeRef[]> {\n    const prefix = resolvePanSNPrefix(this, assemblyName)\n    return (await this.getHaplotypes(opts)).filter(haplotype =>\n      panSNMatchesPrefix(haplotype.prefix, prefix),\n    )\n  }\n\n  private async anchorFeatures(region: Region, opts: LaneFeatureOptions) {\n    const { db } = await this.graph(opts)\n    const { assemblyName, refName, start, end } = region\n    const targetPrefix = resolvePanSNPrefix(this, opts.targetAssemblyName)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const keep = this.keepPredicate(opts.haplotypes, targetPrefix)\n    const query = await this.referenceQuery(refName, opts)\n    const nodeLimit: number = this.getConf('nodeLimit')\n    const alignments = query\n      ? await updateStatus(\n          `Reading graph ${refName}:${start.toLocaleString()}-${end.toLocaleString()}`,\n          opts.statusCallback,\n          () =>\n            db\n              .getAlignments({\n                path: query,\n                start,\n                end,\n                context: this.getConf('context'),\n                haplotypes: 'all',\n                limit: nodeLimit,\n                signal: opts.signal,\n                keep,\n              })\n              .catch((error: unknown) => {\n                throw zoomInNotice(\n                  nodeLimitError(error, nodeLimit, end - start) ?? error,\n                  'lanes',\n                )\n              }),\n        )\n      : []\n    return alignments.flatMap(alignment => {\n      const feature = alignment.resolved\n        ? fragmentFeature({\n            alignment,\n            assemblyName,\n            refName,\n            lane: laneAssemblyName(\n              asmByPrefix,\n              haplotypePrefix(alignment.name),\n            ),\n          })\n        : undefined\n      return feature === undefined ? [] : [feature]\n    })\n  }\n\n  /**\n   * Each pair's two lanes cut out of the anchor window alone, all pairs in one\n   * cut, and each walk of a pair's query lane aligned to each walk of its\n   * target lane on the nodes both visit, with no base compared. A pair's\n   * records sit on its query lane's contigs, the lane the display draws on top.\n   *\n   * Whether the index has anchor rows changes only how fast gbz-base finds\n   * the walks: both routes cut the same pieces.\n   */\n  private async pairFeatures(\n    region: Region,\n    pairs: LanePair[],\n    opts: LaneFeatureOptions,\n  ) {\n    const { db } = await this.graph(opts)\n    const { refName, start, end } = region\n    const sides = await Promise.all(\n      pairs.map(async pair => ({\n        pair,\n        featureSide: await this.laneHaplotypes(pair.queryAssemblyName, opts),\n        mateSide: await this.laneHaplotypes(pair.targetAssemblyName, opts),\n      })),\n    )\n    const answerable = sides.filter(\n      ({ featureSide, mateSide }) =>\n        featureSide.length > 0 && mateSide.length > 0,\n    )\n    const kept = new Set(\n      answerable.flatMap(({ featureSide, mateSide }) =>\n        [...featureSide, ...mateSide].map(haplotypePrefix),\n      ),\n    )\n    const query = await this.referenceQuery(refName, opts)\n    const nodeLimit: number = this.getConf('nodeLimit')\n    const baseContext: number = this.getConf('context')\n    const [first] = pairs\n    const cut = (path: PathQuery, context: number) =>\n      db.getSubgraphs({\n        path,\n        start,\n        end,\n        context,\n        snarls: this.getConf('subgraphSnarls'),\n        haplotypes: 'all',\n        limit: nodeLimit,\n        signal: opts.signal,\n        keep: name => kept.has(haplotypePrefix(name)),\n      })\n    // a cut past the node limit for the wider context keeps the first one\n    const bridged = async (path: PathQuery) => {\n      const subgraphs = await cut(path, baseContext).catch((error: unknown) => {\n        throw zoomInNotice(\n          nodeLimitError(error, nodeLimit, end - start) ?? error,\n          'lanes',\n        )\n      })\n      const gap = widestWalkGap(subgraphs, kept)\n      const context = Math.ceil(gap / 2) + 2000\n      return gap > 0 && context > baseContext\n        ? cut(path, context).catch((error: unknown) => {\n            if (error instanceof SubgraphLimitError) {\n              return subgraphs\n            }\n            throw error\n          })\n        : subgraphs\n    }\n    const subgraphs =\n      query && first && answerable.length > 0\n        ? await updateStatus(\n            pairs.length === 1\n              ? `Reading ${first.queryAssemblyName} against ${first.targetAssemblyName}`\n              : `Reading ${pairs.length} lane pairs`,\n            opts.statusCallback,\n            () => bridged(query),\n          )\n        : []\n    return subgraphs.flatMap(subgraph =>\n      answerable.flatMap(({ pair, featureSide, mateSide }) =>\n        featureSide.flatMap(target =>\n          mateSide.flatMap(mate =>\n            subgraph\n              .pairAlignments({ target, query: mate, bases: false })\n              .map(alignment =>\n                pairFeature({\n                  pair: alignment,\n                  lane: pair.queryAssemblyName,\n                  mateLane: pair.targetAssemblyName,\n                }),\n              ),\n          ),\n        ),\n      ),\n    )\n  }\n\n  getFeatures(asked: Region, opts: LaneFeatureOptions = {}) {\n    const region = wholeBp(asked)\n    return ObservableCreate<Feature>(async observer => {\n      const { db, anchor, unreadableIndex } = await this.graph(opts)\n      if (!db.hasHaplotypeIndex) {\n        throw new NoHaplotypeIndexError(unreadableIndex)\n      }\n      // the graph is indexed on its reference alone, so a window on a\n      // haplotype lane has no answer: a lane pair is read inside the anchor's\n      if (region.assemblyName === anchor) {\n        const pairs = requestedPairs(opts)\n        const features =\n          pairs.length > 0\n            ? await this.pairFeatures(region, pairs, opts)\n            : await this.anchorFeatures(region, opts)\n        for (const feature of features) {\n          observer.next(feature)\n        }\n      }\n      observer.complete()\n    }, opts.signal)\n  }\n}\n"],
+  "mappings": "ixBAeA,SAASA,EAAqBC,EAAI,CAChC,IAAMC,EAAS,cACf,OAAOA,EAAO,KAAKD,CAAE,EAAIA,EAAG,QAAQC,EAAQ,qBAAqB,EAAI,MACvE,CCVO,SAASC,GAAiBC,EAAqB,CACpD,OAAOC,EAAcD,CAAK,GAAKE,EAAqBC,EAAaH,CAAK,CAAC,EACnEI,EAAQJ,EAAOK,GAAQH,EAAqBG,CAAI,CAAE,EAClD,MACN,CAIA,SAASC,GAAUC,EAAgB,CACjC,OACEA,aAAiB,QAChB,kBAAkB,KAAKA,EAAM,OAAO,GAClCA,EAA6B,OAAS,SAE7C,CAIA,eAAsBC,GACpBR,EACAS,EAC2D,CAC3D,IAAMC,EAAYX,GAAiBC,CAAK,EACxC,GAAI,CAACU,EACH,MAAO,CAAC,EAEV,GAAI,CACF,aAAMC,EAAaD,EAAWD,CAAa,EAAE,KAAK,EAC3C,CAAE,SAAUC,CAAU,CAC/B,OAASH,EAAO,CACd,OAAOD,GAAUC,CAAK,EAAI,CAAC,EAAI,CAAE,WAAY,OAAOA,CAAK,CAAE,CAC7D,CACF,CCrBO,IAAMK,GAAY,IAGnBC,GAAsB,GAAK,GAAK,GAEzBC,EAAN,cAAwC,KAAM,CAGnD,YAAYC,EAAc,CACxB,MACE,gBAAgBA,EAAO,GAAK,IAAI,QAAQ,CAAC,CAAC,+DAC5C,EALF,KAAS,KAAO,2BAMhB,CACF,EAGA,SAASC,GAAOC,EAAsBC,EAAa,CACjD,GAAID,EAAQ,QAAUC,EACpB,OAAOD,EAET,IAAME,EAASF,EAAQ,OAASC,EAChC,OAAO,MAAM,KAAK,CAAE,OAAQA,CAAI,EAAG,CAACE,EAAGC,IAAMJ,EAAQ,KAAK,MAAMI,EAAIF,CAAM,CAAC,CAAE,CAC/E,CAEA,IAAMG,GAAU,CAACC,EAAmBC,IAClCD,EAAO,KAAK,KAAKE,GAAQD,EAAM,IAAIC,EAAK,IAAI,CAAC,EAKlCC,EAAN,KAAc,CAiBnB,YACUC,EACAC,EACR,CAFQ,UAAAD,EACA,WAAAC,EAhBV,KAAQ,MAAQC,EAAY,CAC1B,MAAO,MAAO,CAAE,OAAAC,CAAO,IAAM,CAC3B,GAAM,CAAE,KAAAf,CAAK,EAAI,MAAM,KAAK,KAAK,KAAK,EACtC,GAAIA,EAAOF,GACT,MAAM,IAAIC,EAA0BC,CAAI,EAE1C,IAAMgB,EAAQ,MAAM,KAAK,KAAK,SAAS,CAAE,OAAAD,CAAO,CAAC,EAC3CE,EAAO,IAAI,YAAY,EAAE,OAC7BD,EAAM,CAAC,IAAM,IAAQA,EAAM,CAAC,IAAM,IAAO,MAAME,GAAMF,CAAK,EAAIA,CAChE,EACA,OAAOG,EAASF,CAAI,CACtB,CACF,CAAC,CAKE,CAEH,MAAc,YACZJ,EACAJ,EACAM,EACA,CACA,IAAIK,EAAK,IACLC,EAAK,KACT,QAAWC,KAAQb,EAAO,CACxB,IAAMc,EAAK,OAAOD,CAAI,EAClB,OAAO,UAAUC,CAAE,IACrBH,EAAK,KAAK,IAAIA,EAAIG,CAAE,EACpBF,EAAK,KAAK,IAAIA,EAAIE,CAAE,EAExB,CACA,IAAMrB,EAAuB,CAAC,EAC9B,OAAIkB,GAAMC,GAGR,MAAMR,EAAM,SAAS,SAAUO,EAAIC,EAAK,EAAG,CACzC,OAAAN,EACA,aAAcS,GAAQ,CACpB,IAAMhB,EAASiB,EAAaD,CAAI,EAC5BhB,GAAUD,GAAQC,EAAQC,CAAK,GACjCP,EAAQ,KAAKM,CAAM,CAEvB,CACF,CAAC,EAEIN,CACT,CAEA,MAAM,UACJO,EACA,CAAE,OAAAM,CAAO,EAA8B,CAAC,EACrB,CACnB,IAAMb,EAAU,KAAK,MACjB,MAAM,KAAK,YAAY,KAAK,MAAOO,EAAOM,CAAM,GAC/C,MAAM,KAAK,MAAM,CAAE,OAAAA,CAAO,CAAC,GAAG,OAAOW,GAAKnB,GAAQmB,EAAGjB,CAAK,CAAC,EAChE,MAAO,CAAE,QAASR,GAAOC,EAASL,EAAS,EAAG,MAAOK,EAAQ,MAAO,CACtE,CACF,ECjEO,IAAMyB,EAAN,cAAoC,KAAM,CAG/C,YAAYC,EAAqB,CAC/B,MACEA,IAAe,OACX,uKACA,uEAAuEA,CAAU,qGACvF,EAPF,KAAS,KAAO,uBAQhB,CACF,EAyBaC,EAAN,cAAmC,KAAM,CAG9C,YAAYC,EAAsBC,EAAgB,CAChD,MACE,sCAAsCA,CAAM,iBAAiBD,CAAY,kEAAkEC,CAAM,6CACnJ,EALF,KAAS,KAAO,sBAMhB,CACF,EAUA,SAASC,GAAWC,EAAgBC,EAA8B,CAChE,MAAO,GAAGC,EAAgBF,CAAI,CAAC,IAAIA,EAAK,MAAM,IAAIC,EAAU,MAAM,IAAI,IAAIA,EAAU,MAAM,MAAM,EAClG,CAEO,SAASE,GAAgB,CAC9B,UAAAF,EACA,aAAAJ,EACA,QAAAO,EACA,KAAAC,CACF,EAKG,CACD,GAAM,CAAE,SAAAC,EAAU,OAAAC,EAAQ,OAAAC,EAAQ,MAAAC,CAAM,EAAIR,EAC5C,GAAI,EAAAM,GAAUD,GAEP,CACL,GAAM,CAAE,KAAAN,EAAM,SAAAU,EAAU,OAAAC,CAAO,EAAIV,EAC7BW,EAAKb,GAAWC,EAAMC,CAAS,EAC/BY,EAAgC,CACpC,SAAUD,EACV,aAAAf,EACA,QAAAO,EACA,MAAOE,EACP,IAAKC,EACL,KAAM,QACN,OAAQC,IAAW,IAAM,GAAK,EAC9B,MAAOC,EACP,UAAWG,EACX,KAAM,CACJ,QAASZ,EAAK,OACd,MAAOU,EACP,IAAKC,EACL,aAAcN,CAChB,CACF,EACA,OAAO,IAAIS,EAAeD,CAAI,CAChC,CACF,CAQO,SAASE,GAAY,CAC1B,KAAAC,EACA,KAAAX,EACA,SAAAY,CACF,EAIG,CACD,IAAML,EAAK,GAAGV,EAAgBc,EAAK,MAAM,CAAC,IAAIA,EAAK,OAAO,MAAM,IAAIA,EAAK,WAAW,IAAIA,EAAK,SAAS,IAAId,EAAgBc,EAAK,KAAK,CAAC,IAAIA,EAAK,MAAM,MAAM,IAAIA,EAAK,UAAU,IAAIA,EAAK,QAAQ,GAC9L,OAAO,IAAIF,EAAe,CACxB,SAAUF,EACV,aAAcP,EACd,QAASW,EAAK,OAAO,OACrB,MAAOA,EAAK,YACZ,IAAKA,EAAK,UACV,KAAM,QACN,OAAQA,EAAK,SAAW,IAAM,GAAK,EACnC,MAAOA,EAAK,MACZ,UAAWJ,EACX,SAAUI,EAAK,QAAU,KAAK,IAAIA,EAAK,QAAS,CAAC,EACjD,WAAYA,EAAK,QACjB,SAAUA,EAAK,QACf,KAAM,CACJ,QAASA,EAAK,MAAM,OACpB,MAAOA,EAAK,WACZ,IAAKA,EAAK,SACV,aAAcC,CAChB,CACF,CAAC,CACH,CAGA,IAAMC,GAAgB,KAQf,SAASC,GAAcC,EAAuBC,EAAmB,CACtE,IAAMC,EAAS,IAAI,IACnB,QAAWC,KAAYH,EACrB,OAAW,CAAE,KAAApB,EAAM,MAAAwB,EAAO,IAAAC,CAAI,IAAKF,EAAS,UAAU,EAAG,CACvD,IAAMG,EAASxB,EAAgBF,CAAI,EACnC,GAAIqB,EAAK,IAAIK,CAAM,EAAG,CACpB,IAAMC,EAAM,GAAGD,CAAM,IAAI1B,EAAK,MAAM,GAC9B4B,EAAQN,EAAO,IAAIK,CAAG,EACxBC,EACFA,EAAM,KAAK,CAACJ,EAAOC,CAAG,CAAC,EAEvBH,EAAO,IAAIK,EAAK,CAAC,CAACH,EAAOC,CAAG,CAAC,CAAC,CAElC,CACF,CAEF,IAAII,EAAS,EACb,QAAWD,KAASN,EAAO,OAAO,EAAG,CACnCM,EAAM,KAAK,CAACE,EAAGC,IAAMD,EAAE,CAAC,EAAIC,EAAE,CAAC,CAAC,EAChC,QAASC,EAAI,EAAGA,EAAIJ,EAAM,OAAQI,IAAK,CACrC,IAAMC,EAAML,EAAMI,CAAC,EAAG,CAAC,EAAIJ,EAAMI,EAAI,CAAC,EAAG,CAAC,EACtCC,EAAM,GAAKA,GAAOf,KACpBW,EAAS,KAAK,IAAIA,EAAQI,CAAG,EAEjC,CACF,CACA,OAAOJ,CACT,CAIA,SAASK,EAAaC,EAAgBC,EAAc,CAClD,OAAID,aAAiBE,IACnBF,EAAM,QAAU,oBAAoBG,EAAgBH,EAAM,MAAM,CAAC,WAAWC,CAAI,IAE3ED,CACT,CAGA,IAAMI,GAAWC,IAAoB,CACnC,GAAGA,EACH,MAAO,KAAK,MAAMA,EAAO,KAAK,EAC9B,IAAK,KAAK,KAAKA,EAAO,GAAG,CAC3B,GAEqBC,EAArB,cAAmDC,EAAoD,CAAvG,kCACE,KAAQ,MAAQC,EAAY,CAC1B,MAAO,6BACP,MAAO,SAAY,CACjB,IAAMC,EAAsB,KAAK,QAAQ,eAAe,EAClDC,EAA2B,KAAK,QAAQ,wBAAwB,EAChEC,EAAYC,EAAcF,CAAU,EACtC,CAAE,SAAUA,CAAW,EACvB,MAAMG,GAAcJ,EAAO,KAAK,aAAa,EAC3CK,EAAgBH,EAAU,SAC1BI,EAAK,MAAMC,EAAQ,KAAK,CAC5B,OAAQC,EAAaR,EAAO,KAAK,aAAa,EAC9C,eAAgBK,EACZG,EAAaH,EAAe,KAAK,aAAa,EAC9C,MACN,CAAC,EACKnD,EAAS,KAAK,QAAQ,eAAe,EAAE,CAAC,EAC9C,GAAIA,IAAW,OACb,MAAM,IAAI,MACR,8GACF,EAEF,IAAMuD,EAAmB,MAAMC,EAAmBJ,CAAE,EAC9CK,EAAkBC,EAAuB,CAC7C,WAAY,KAAK,QAAQ,iBAAiB,EAC1C,aAAcC,EAAmB,KAAM3D,CAAM,EAC7C,iBAAAuD,CACF,CAAC,EACD,MAAO,CACL,GAAAH,EACA,OAAApD,EACA,gBAAAyD,EACA,iBAAAF,EACA,gBAAiBP,EAAU,UAC7B,CACF,CACF,CAAC,EAgKD,KAAQ,IAAMH,EAAY,CACxB,MAAO,gBACP,MAAO,SAAY,CACjB,IAAMe,EAAyB,KAAK,QAAQ,eAAe,EACrDC,EAAsB,KAAK,QAAQ,CAAC,aAAc,UAAU,CAAC,EACnE,OAAOZ,EAAcW,CAAQ,EACzB,IAAIE,EACFR,EAAaM,EAAU,KAAK,aAAa,EACzCX,EAAcY,CAAK,EACfE,GAAc,KAAM,CAAC,eAAe,EAAG,CAAC,YAAY,CAAC,EACrD,MACN,EACA,MACN,CACF,CAAC,EAxKD,MAAc,eACZzD,EACA0D,EACgC,CAChC,GAAM,CAAE,GAAAZ,EAAI,gBAAAK,CAAgB,EAAI,MAAM,KAAK,MAAMO,CAAI,EACrD,OAAOC,EAAmBb,EAAIK,EAAiBnD,CAAO,CACxD,CAOA,MAAM,cAAc0D,EAAoB,CAAC,EAA4B,CACnE,GAAM,CAAE,GAAAZ,EAAI,iBAAAG,CAAiB,EAAI,MAAM,KAAK,MAAMS,CAAI,EAChDE,EAAW,IAAI,IACrB,QAAWC,KAAQ,MAAMf,EAAG,MAAM,EAAG,CACnC,IAAMxB,EAASxB,EAAgB+D,EAAK,IAAI,EAClCC,EAAQF,EAAS,IAAItC,CAAM,EAC7BwC,EACGA,EAAM,QAAQ,SAASD,EAAK,KAAK,MAAM,GAC1CC,EAAM,QAAQ,KAAKD,EAAK,KAAK,MAAM,EAGrCD,EAAS,IAAItC,EAAQ,CACnB,OAAAA,EACA,OAAQuC,EAAK,KAAK,OAClB,UAAWA,EAAK,KAAK,UACrB,QAAS,CAACA,EAAK,KAAK,MAAM,EAC1B,YAAaZ,EAAiB,SAASY,EAAK,KAAK,MAAM,CACzD,CAAC,CAEL,CACA,MAAO,CAAC,GAAGD,EAAS,OAAO,CAAC,CAC9B,CAOA,MAAM,UAAUF,EAAoB,CAAC,EAAG,CACtC,GAAM,CAAE,OAAAhE,EAAQ,gBAAAyD,EAAiB,iBAAAF,CAAiB,EAAI,MAAM,KAAK,MAAMS,CAAI,EACrEK,EAAcC,EAAsB,IAAI,EACxCC,EAAyB,CAAC,EAChC,QAAWC,KAAa,MAAM,KAAK,cAAcR,CAAI,EAC/CQ,EAAU,SAAWf,GACvBc,EAAM,KAAK,CACT,KAAME,EAAiBJ,EAAaG,EAAU,MAAM,EACpD,MAAOA,EAAU,OACjB,MAAOA,EAAU,MACnB,CAAC,EAGL,MAAO,CACL,cAAe,GACf,mBAAoBxE,EACpB,gBAAAyD,EACA,iBAAAF,EACA,MAAAgB,CACF,CACF,CAEA,MAAM,YAAYP,EAAoB,CAAC,EAAG,CACxC,GAAM,CAAE,GAAAZ,EAAI,OAAApD,EAAQ,gBAAAyD,CAAgB,EAAI,MAAM,KAAK,MAAMO,CAAI,EACvD,CAAE,aAAAjE,CAAa,EAAIiE,EACnBpC,EACJ7B,IAAiBC,EACb,OACA2D,EAAmB,KAAM5D,CAAY,EACrC2E,GAAW,MAAMtB,EAAG,MAAM,GAC7B,OAAOe,GACNpE,IAAiBC,EACbmE,EAAK,WAAaA,EAAK,KAAK,SAAWV,EACvCkB,EAAmBvE,EAAgB+D,EAAK,IAAI,EAAGvC,CAAM,CAC3D,EACC,IAAIuC,GAAQA,EAAK,KAAK,MAAM,EAC/B,MAAO,CAAC,GAAG,IAAI,IAAIO,CAAO,CAAC,CAC7B,CAcQ,cACNE,EACAC,EACA,CACA,IAAMC,EACJF,IAAe,QAAaA,EAAW,SAAW,EAC9C,OACAA,EAAW,IAAIrE,GAAQoD,EAAmB,KAAMpD,CAAI,CAAC,EAC3D,OAAOuE,IAAmB,QAAaD,IAAiB,OACpD,OACC3E,GACC6E,EAAgB7E,EAAM4E,CAAc,IACnCD,IAAiB,QAChBF,EAAmBvE,EAAgBF,CAAI,EAAG2E,CAAY,EAChE,CAeA,MAAM,YAAYnC,EAAgBsB,EAA+B,CAAC,EAAG,CACnE,GAAM,CAAE,OAAAgB,CAAO,EAAIhB,EACb,CAAE,GAAAZ,EAAI,OAAApD,EAAQ,gBAAAyD,EAAiB,gBAAAwB,CAAgB,EAAI,MAAM,KAAK,MAAM,CACxE,OAAAD,CACF,CAAC,EACK,CAAE,aAAAjF,EAAc,QAAAO,EAAS,MAAAoB,EAAO,IAAAC,CAAI,EAAIc,GAAQC,CAAM,EAC5D,GAAI3C,IAAiBC,EACnB,MAAM,IAAIF,EAAqBC,EAAcC,CAAM,EAErD,IAAMkF,EAAQ,MAAM,KAAK,eAAe5E,EAAS,CAAE,OAAA0E,CAAO,CAAC,EAC3D,GAAI,CAACE,EACH,MAAM,IAAI,MACR,GAAGzB,CAAe,wBAAwBnD,CAAO,gBACnD,EAEF,IAAM6E,EAAO,KAAK,cAAcnB,EAAK,UAAU,EAC/C,GAAImB,IAAS,QAAa,CAAC/B,EAAG,kBAC5B,MAAM,IAAIxD,EAAsBqF,CAAe,EAEjD,IAAMG,EAAM,MAAMC,EAAgBjC,EAAI8B,EAAOxD,EAAOC,EAAK,CACvD,QAAS,KAAK,QAAQ,SAAS,EAC/B,OAAQqC,EAAK,QAAU,KAAK,QAAQ,gBAAgB,EACpD,MAAO,KAAK,QAAQ,WAAW,EAC/B,OAAQA,EAAK,OACb,KAAAmB,CACF,CAAC,EAAE,MAAO9C,GAAmB,CAC3B,MAAMD,EAAaC,EAAO,WAAW,CACvC,CAAC,EACD,OAAO,OAAO+C,GAAQ,SAClBA,EACAE,GAAWF,EAAK,CAAE,MAAA1D,EAAO,IAAAC,CAAI,EAAGqC,EAAK,QAAQ,CACnD,CAsBA,MAAM,SACJuB,EACAvB,EAAoB,CAAC,EACF,CACnB,IAAMwB,EAAM,MAAM,KAAK,IAAIxB,CAAI,EAC/B,OAAOwB,EACHA,EAAI,UAAU,IAAI,IAAID,CAAS,EAAGvB,CAAI,EACtC,CAAE,QAAS,CAAC,EAAG,MAAO,CAAE,CAC9B,CAEA,MAAc,eACZjE,EACAiE,EACyB,CACzB,IAAMpC,EAAS+B,EAAmB,KAAM5D,CAAY,EACpD,OAAQ,MAAM,KAAK,cAAciE,CAAI,GAAG,OAAOQ,GAC7CG,EAAmBH,EAAU,OAAQ5C,CAAM,CAC7C,CACF,CAEA,MAAc,eAAec,EAAgBsB,EAA0B,CACrE,GAAM,CAAE,GAAAZ,CAAG,EAAI,MAAM,KAAK,MAAMY,CAAI,EAC9B,CAAE,aAAAjE,EAAc,QAAAO,EAAS,MAAAoB,EAAO,IAAAC,CAAI,EAAIe,EACxCmC,EAAelB,EAAmB,KAAMK,EAAK,kBAAkB,EAC/DK,EAAcC,EAAsB,IAAI,EACxCa,EAAO,KAAK,cAAcnB,EAAK,WAAYa,CAAY,EACvDK,EAAQ,MAAM,KAAK,eAAe5E,EAAS0D,CAAI,EAC/CyB,EAAoB,KAAK,QAAQ,WAAW,EAyBlD,OAxBmBP,EACf,MAAMQ,EACJ,iBAAiBpF,CAAO,IAAIoB,EAAM,eAAe,CAAC,IAAIC,EAAI,eAAe,CAAC,GAC1EqC,EAAK,eACL,IACEZ,EACG,cAAc,CACb,KAAM8B,EACN,MAAAxD,EACA,IAAAC,EACA,QAAS,KAAK,QAAQ,SAAS,EAC/B,WAAY,MACZ,MAAO8D,EACP,OAAQzB,EAAK,OACb,KAAAmB,CACF,CAAC,EACA,MAAO9C,GAAmB,CACzB,MAAMD,EACJuD,EAAetD,EAAOoD,EAAW9D,EAAMD,CAAK,GAAKW,EACjD,OACF,CACF,CAAC,CACP,EACA,CAAC,GACa,QAAQlC,GAAa,CACrC,IAAMyF,EAAUzF,EAAU,SACtBE,GAAgB,CACd,UAAAF,EACA,aAAAJ,EACA,QAAAO,EACA,KAAMmE,EACJJ,EACAjE,EAAgBD,EAAU,IAAI,CAChC,CACF,CAAC,EACD,OACJ,OAAOyF,IAAY,OAAY,CAAC,EAAI,CAACA,CAAO,CAC9C,CAAC,CACH,CAWA,MAAc,aACZlD,EACAmD,EACA7B,EACA,CACA,GAAM,CAAE,GAAAZ,CAAG,EAAI,MAAM,KAAK,MAAMY,CAAI,EAC9B,CAAE,QAAA1D,EAAS,MAAAoB,EAAO,IAAAC,CAAI,EAAIe,EAQ1BoD,GAPQ,MAAM,QAAQ,IAC1BD,EAAM,IAAI,MAAM3E,IAAS,CACvB,KAAAA,EACA,YAAa,MAAM,KAAK,eAAeA,EAAK,kBAAmB8C,CAAI,EACnE,SAAU,MAAM,KAAK,eAAe9C,EAAK,mBAAoB8C,CAAI,CACnE,EAAE,CACJ,GACyB,OACvB,CAAC,CAAE,YAAA+B,EAAa,SAAAC,CAAS,IACvBD,EAAY,OAAS,GAAKC,EAAS,OAAS,CAChD,EACMzE,EAAO,IAAI,IACfuE,EAAW,QAAQ,CAAC,CAAE,YAAAC,EAAa,SAAAC,CAAS,IAC1C,CAAC,GAAGD,EAAa,GAAGC,CAAQ,EAAE,IAAI5F,CAAe,CACnD,CACF,EACM8E,EAAQ,MAAM,KAAK,eAAe5E,EAAS0D,CAAI,EAC/CyB,EAAoB,KAAK,QAAQ,WAAW,EAC5CQ,EAAsB,KAAK,QAAQ,SAAS,EAC5C,CAACC,CAAK,EAAIL,EACVT,EAAM,CAACjB,EAAiBgC,IAC5B/C,EAAG,aAAa,CACd,KAAAe,EACA,MAAAzC,EACA,IAAAC,EACA,QAAAwE,EACA,OAAQ,KAAK,QAAQ,gBAAgB,EACrC,WAAY,MACZ,MAAOV,EACP,OAAQzB,EAAK,OACb,KAAM9D,GAAQqB,EAAK,IAAInB,EAAgBF,CAAI,CAAC,CAC9C,CAAC,EAEGkG,GAAU,MAAOjC,GAAoB,CACzC,IAAM7C,EAAY,MAAM8D,EAAIjB,EAAM8B,CAAW,EAAE,MAAO5D,GAAmB,CACvE,MAAMD,EACJuD,EAAetD,EAAOoD,EAAW9D,EAAMD,CAAK,GAAKW,EACjD,OACF,CACF,CAAC,EACKF,EAAMd,GAAcC,EAAWC,CAAI,EACnC4E,EAAU,KAAK,KAAKhE,EAAM,CAAC,EAAI,IACrC,OAAOA,EAAM,GAAKgE,EAAUF,EACxBb,EAAIjB,EAAMgC,CAAO,EAAE,MAAO9D,GAAmB,CAC3C,GAAIA,aAAiBgE,EACnB,OAAO/E,EAET,MAAMe,CACR,CAAC,EACDf,CACN,EAWA,OATE4D,GAASgB,GAASJ,EAAW,OAAS,EAClC,MAAMJ,EACJG,EAAM,SAAW,EACb,WAAWK,EAAM,iBAAiB,YAAYA,EAAM,kBAAkB,GACtE,WAAWL,EAAM,MAAM,cAC3B7B,EAAK,eACL,IAAMoC,GAAQlB,CAAK,CACrB,EACA,CAAC,GACU,QAAQzD,GACvBqE,EAAW,QAAQ,CAAC,CAAE,KAAA5E,EAAM,YAAA6E,EAAa,SAAAC,CAAS,IAChDD,EAAY,QAAQO,GAClBN,EAAS,QAAQO,IACf9E,EACG,eAAe,CAAE,OAAA6E,EAAQ,MAAOC,GAAM,MAAO,EAAM,CAAC,EACpD,IAAIpG,IACHc,GAAY,CACV,KAAMd,GACN,KAAMe,EAAK,kBACX,SAAUA,EAAK,kBACjB,CAAC,CACH,CACJ,CACF,CACF,CACF,CACF,CAEA,YAAYsF,EAAexC,EAA2B,CAAC,EAAG,CACxD,IAAMtB,EAASD,GAAQ+D,CAAK,EAC5B,OAAOC,GAA0B,MAAMC,GAAY,CACjD,GAAM,CAAE,GAAAtD,EAAI,OAAApD,EAAQ,gBAAAiF,CAAgB,EAAI,MAAM,KAAK,MAAMjB,CAAI,EAC7D,GAAI,CAACZ,EAAG,kBACN,MAAM,IAAIxD,EAAsBqF,CAAe,EAIjD,GAAIvC,EAAO,eAAiB1C,EAAQ,CAClC,IAAM6F,EAAQc,GAAe3C,CAAI,EAC3B4C,EACJf,EAAM,OAAS,EACX,MAAM,KAAK,aAAanD,EAAQmD,EAAO7B,CAAI,EAC3C,MAAM,KAAK,eAAetB,EAAQsB,CAAI,EAC5C,QAAW4B,KAAWgB,EACpBF,EAAS,KAAKd,CAAO,CAEzB,CACAc,EAAS,SAAS,CACpB,EAAG1C,EAAK,MAAM,CAChB,CACF",
+  "names": ["haplotypeIndexBeside", "db", "GBZ_DB", "siblingCompanion", "gbzDb", "readsSiblings", "haplotypeIndexBeside", "locationName", "renamed", "name", "isMissing", "error", "findCompanion", "pluginManager", "candidate", "openLocation", "MAX_READS", "MAX_UNINDEXED_BYTES", "UnindexedGafTooLargeError", "size", "sample", "records", "max", "stride", "_", "k", "touches", "record", "names", "step", "GafFile", "file", "tabix", "cachedSetup", "signal", "bytes", "text", "unzip", "parseGaf", "lo", "hi", "name", "id", "line", "parseGafLine", "r", "NoHaplotypeIndexError", "unreadable", "HaplotypeWindowError", "assemblyName", "anchor", "fragmentId", "name", "alignment", "haplotypePrefix", "fragmentFeature", "refName", "lane", "refStart", "refEnd", "strand", "cigar", "hapStart", "hapEnd", "id", "data", "SyntenyFeature", "pairFeature", "pair", "mateLane", "BRIDGE_MAX_BP", "widestWalkGap", "subgraphs", "kept", "byPath", "subgraph", "start", "end", "prefix", "key", "spans", "widest", "a", "b", "i", "gap", "zoomInNotice", "error", "what", "NodeLimitError", "getBpDisplayStr", "wholeBp", "region", "GbzBaseSyntenyAdapter", "ComparativeAdapterBase", "cachedSetup", "gbzDb", "configured", "companion", "locationIsSet", "findCompanion", "indexLocation", "db", "GBZBase", "openLocation", "referenceSamples", "referenceSamplesOf", "referenceSample", "resolveReferenceSample", "resolvePanSNPrefix", "location", "index", "GafFile", "openTabixSlot", "opts", "referencePathQuery", "byPrefix", "path", "entry", "asmByPrefix", "assemblyByPanSNPrefix", "lanes", "haplotype", "laneAssemblyName", "contigs", "panSNMatchesPrefix", "haplotypes", "targetPrefix", "wantedPrefixes", "haplotypeWanted", "signal", "unreadableIndex", "query", "keep", "cut", "cutWindowTables", "walkCutFor", "nodeNames", "gaf", "nodeLimit", "updateStatus", "nodeLimitError", "feature", "pairs", "answerable", "featureSide", "mateSide", "baseContext", "first", "context", "bridged", "SubgraphLimitError", "target", "mate", "asked", "ObservableCreate", "observer", "requestedPairs", "features"]
+}

package/dist/chunks/{GraphGenomeView-T4YQMLAX.js → GraphGenomeView-Z2WZKEEO.js}

@@ -1,4 +1,4 @@
-import{a as C}from"./chunk-V4YHDVV3.js";import"./chunk-Z4B6RZGP.js";import"./chunk-2APZWSYD.js";import"./chunk-STTY74OG.js";import{k as d}from"./chunk-ZWMYT35X.js";import"./chunk-CH2E7TRS.js";import"./chunk-XJDTSPBL.js";import"./chunk-G73A6PEI.js";import"./chunk-TOT4S3TG.js";import"./chunk-56V22DVI.js";import"./chunk-G57N55FV.js";import"./chunk-HW4LIGPA.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import"./chunk-OUN4BNWJ.js";import"./chunk-5OI6LO4I.js";import"./chunk-NDRLCGPC.js";import"./chunk-TENPGIPX.js";import{g as x}from"./chunk-6OPB7FOJ.js";import{A as l,F as L,H as p,d as s,i as v,o as n,x as G}from"./chunk-E3WYW7Z6.js";import{a as y,b as a,c as r,d as i}from"./chunk-JMBDTNUR.js";var w=d()({paper:{padding:16,margin:8,maxWidth:560,marginInline:"auto",display:"flex",flexDirection:"column",gap:12},row:{display:"flex",alignItems:"center",justifyContent:"space-between",gap:8}}),E=i(function({model:e}){let{classes:t}=w();return e.isLoading?r(l,{className:t.paper,"data-testid":"graph-genome-loading",children:[r("div",{className:t.row,children:[a(v,{variant:"h6",message:e.statusMessage}),a(n,{size:"small","data-testid":"graph-genome-cancel",onClick:()=>{e.cancelLoad()},children:"Cancel"})]}),a(G,{variant:"indeterminate"})]}):e.error?a(l,{className:t.paper,children:a(s,{error:e.error,onReset:()=>{e.retryLoad()}})}):a(l,{className:t.paper,"data-testid":"graph-genome-load-canceled",children:r("div",{className:t.row,children:[a(p,{variant:"h6",children:"Loading canceled"}),a(n,{variant:"contained",size:"small","data-testid":"graph-genome-retry",onClick:()=>{e.retryLoad()},children:"Retry"})]})})}),g=E;var F=`H	VN:Z:1.0
+import{a as C}from"./chunk-BJMRBVG3.js";import"./chunk-J6NZIAZF.js";import"./chunk-GOFS7BXK.js";import"./chunk-IJQTSJGT.js";import{k as d}from"./chunk-YSTMDXXX.js";import"./chunk-5SFGHDQA.js";import"./chunk-DZ4OUKQV.js";import"./chunk-MHPJB22Z.js";import"./chunk-XT766CZ5.js";import"./chunk-EWFJBQDV.js";import"./chunk-3Q4RBDCL.js";import"./chunk-AU73K7LX.js";import"./chunk-TXI43PEN.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import"./chunk-446RWIA3.js";import"./chunk-5OI6LO4I.js";import"./chunk-NDRLCGPC.js";import"./chunk-TENPGIPX.js";import{g as x}from"./chunk-6OPB7FOJ.js";import{A as l,F as L,H as p,d as s,i as v,o as n,x as G}from"./chunk-E3WYW7Z6.js";import{a as y,b as a,c as r,d as i}from"./chunk-JMBDTNUR.js";var w=d()({paper:{padding:16,margin:8,maxWidth:560,marginInline:"auto",display:"flex",flexDirection:"column",gap:12},row:{display:"flex",alignItems:"center",justifyContent:"space-between",gap:8}}),E=i(function({model:e}){let{classes:t}=w();return e.isLoading?r(l,{className:t.paper,"data-testid":"graph-genome-loading",children:[r("div",{className:t.row,children:[a(v,{variant:"h6",message:e.statusMessage}),a(n,{size:"small","data-testid":"graph-genome-cancel",onClick:()=>{e.cancelLoad()},children:"Cancel"})]}),a(G,{variant:"indeterminate"})]}):e.error?a(l,{className:t.paper,children:a(s,{error:e.error,onReset:()=>{e.retryLoad()}})}):a(l,{className:t.paper,"data-testid":"graph-genome-load-canceled",children:r("div",{className:t.row,children:[a(p,{variant:"h6",children:"Loading canceled"}),a(n,{variant:"contained",size:"small","data-testid":"graph-genome-retry",onClick:()=>{e.retryLoad()},children:"Retry"})]})})}),g=E;var F=`H	VN:Z:1.0
 S	1	ACGT
 S	2	GGCC
 S	3	TTAA
@@ -7,4 +7,4 @@ L	1	+	2	+	0M
 L	1	+	3	+	0M
 L	2	+	4	+	0M
 L	3	+	4	+	0M`,S=d()({column:{display:"flex",flexDirection:"column",gap:8},rowEnd:{display:"flex",gap:8,alignItems:"flex-end"},rowCenter:{display:"flex",gap:8,alignItems:"center"},flex1:{flex:1},paper:{padding:16,margin:8,maxWidth:560,marginInline:"auto"},header:{marginBottom:12},footer:{marginTop:12,display:"flex",justifyContent:"flex-end"}}),T=i(function({model:e}){let{classes:t}=S(),[m,M]=x("");function u(){let o=m.trim();o&&e.loadGFAFromLocation({uri:o,locationType:"UriLocation"})}function N(o){let c=o.target.files?.[0];o.target.value="",c&&c.text().then(f=>e.loadGFA(f,c.name)).catch(f=>{e.setError(f)})}return r(l,{className:t.paper,children:[a("div",{className:t.header,children:a(p,{variant:"h6",children:"Load a GFA graph"})}),r("div",{className:t.column,children:[r("div",{className:t.rowCenter,children:[r(n,{variant:"outlined",component:"label",size:"small",children:["Choose file",a("input",{type:"file",accept:".gfa,.gfa1,.gfa2",hidden:!0,onChange:o=>{N(o)}})]}),a(p,{variant:"caption",color:"text.secondary",children:"Whole-file GFA; best for small/medium graphs."})]}),r("div",{className:t.rowEnd,children:[a(L,{size:"small",label:"URL",placeholder:"https://example.com/graph.gfa",value:m,onChange:o=>{M(o.target.value)},onKeyDown:o=>{o.key==="Enter"&&u()},className:t.flex1}),a(n,{variant:"contained",onClick:()=>{u()},disabled:!m.trim(),children:"Open"})]})]}),a("div",{className:t.footer,children:a(n,{size:"small",onClick:()=>{e.loadGFA(F,"Example graph")},children:"Load 4-node example"})}),e.error?a(s,{error:e.error}):null]})}),P=T;var A=i(function({model:e}){return e.hasGraph?a(C,{model:e}):e.canRetryLoad&&(e.error||e.loadCanceled)?a(g,{model:e}):r(y,{children:[e.isLoading?a(g,{model:e}):null,a("div",{hidden:e.isLoading,children:a(P,{model:e})})]})}),J=A;export{J as default};
-//# sourceMappingURL=GraphGenomeView-T4YQMLAX.js.map
+//# sourceMappingURL=GraphGenomeView-Z2WZKEEO.js.map

package/dist/chunks/{GraphGenomeView-T4YQMLAX.js.map → GraphGenomeView-Z2WZKEEO.js.map}

@@ -2,6 +2,6 @@
   "version": 3,
   "sources": ["../../src/GraphGenomeView/components/GraphLoadStatus.tsx", "../../src/GraphGenomeView/components/ImportForm.tsx", "../../src/GraphGenomeView/components/GraphGenomeView.tsx"],
   "sourcesContent": ["import { ErrorBanner, LoadingEllipses } from '@jbrowse/core/ui'\nimport { Button, LinearProgress, Paper, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport type { GraphPaneModel } from '../model'\n\nconst useStyles = makeStyles()({\n  paper: {\n    padding: 16,\n    margin: 8,\n    maxWidth: 560,\n    marginInline: 'auto',\n    display: 'flex',\n    flexDirection: 'column',\n    gap: 12,\n  },\n  row: {\n    display: 'flex',\n    alignItems: 'center',\n    justifyContent: 'space-between',\n    gap: 8,\n  },\n})\n\n// What a view with no graph on screen shows while its load runs, and after a\n// load of a source it can retry was canceled or failed.\nconst GraphLoadStatus = observer(function GraphLoadStatus({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const { classes } = useStyles()\n  if (model.isLoading) {\n    return (\n      <Paper className={classes.paper} data-testid=\"graph-genome-loading\">\n        <div className={classes.row}>\n          <LoadingEllipses variant=\"h6\" message={model.statusMessage} />\n          <Button\n            size=\"small\"\n            data-testid=\"graph-genome-cancel\"\n            onClick={() => {\n              model.cancelLoad()\n            }}\n          >\n            Cancel\n          </Button>\n        </div>\n        <LinearProgress variant=\"indeterminate\" />\n      </Paper>\n    )\n  }\n  if (model.error) {\n    return (\n      <Paper className={classes.paper}>\n        <ErrorBanner\n          error={model.error}\n          onReset={() => {\n            model.retryLoad()\n          }}\n        />\n      </Paper>\n    )\n  }\n  return (\n    <Paper className={classes.paper} data-testid=\"graph-genome-load-canceled\">\n      <div className={classes.row}>\n        <Typography variant=\"h6\">Loading canceled</Typography>\n        <Button\n          variant=\"contained\"\n          size=\"small\"\n          data-testid=\"graph-genome-retry\"\n          onClick={() => {\n            model.retryLoad()\n          }}\n        >\n          Retry\n        </Button>\n      </div>\n    </Paper>\n  )\n})\n\nexport default GraphLoadStatus\n", "import { useState } from 'react'\n\nimport { ErrorBanner } from '@jbrowse/core/ui'\nimport { Button, Paper, TextField, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport type { GraphPaneModel } from '../model'\n\nconst EXAMPLE_GFA = `H\\tVN:Z:1.0\nS\\t1\\tACGT\nS\\t2\\tGGCC\nS\\t3\\tTTAA\nS\\t4\\tCCGG\nL\\t1\\t+\\t2\\t+\\t0M\nL\\t1\\t+\\t3\\t+\\t0M\nL\\t2\\t+\\t4\\t+\\t0M\nL\\t3\\t+\\t4\\t+\\t0M`\n\nconst useStyles = makeStyles()({\n  column: { display: 'flex', flexDirection: 'column', gap: 8 },\n  rowEnd: { display: 'flex', gap: 8, alignItems: 'flex-end' },\n  rowCenter: { display: 'flex', gap: 8, alignItems: 'center' },\n  flex1: { flex: 1 },\n  paper: { padding: 16, margin: 8, maxWidth: 560, marginInline: 'auto' },\n  header: { marginBottom: 12 },\n  footer: { marginTop: 12, display: 'flex', justifyContent: 'flex-end' },\n})\n\nconst ImportForm = observer(function ImportForm({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const { classes } = useStyles()\n  const [url, setUrl] = useState('')\n\n  function handleUrlLoad() {\n    const uri = url.trim()\n    if (uri) {\n      void model.loadGFAFromLocation({ uri, locationType: 'UriLocation' })\n    }\n  }\n\n  function handleFileUpload(event: React.ChangeEvent<HTMLInputElement>) {\n    const file = event.target.files?.[0]\n    // or picking the same file again fires no change\n    event.target.value = ''\n    if (file) {\n      file\n        .text()\n        .then(text => model.loadGFA(text, file.name))\n        .catch((err: unknown) => {\n          model.setError(err)\n        })\n    }\n  }\n\n  return (\n    <Paper className={classes.paper}>\n      <div className={classes.header}>\n        <Typography variant=\"h6\">Load a GFA graph</Typography>\n      </div>\n\n      <div className={classes.column}>\n        <div className={classes.rowCenter}>\n          <Button variant=\"outlined\" component=\"label\" size=\"small\">\n            Choose file\n            <input\n              type=\"file\"\n              accept=\".gfa,.gfa1,.gfa2\"\n              hidden\n              onChange={event => {\n                handleFileUpload(event)\n              }}\n            />\n          </Button>\n          <Typography variant=\"caption\" color=\"text.secondary\">\n            Whole-file GFA; best for small/medium graphs.\n          </Typography>\n        </div>\n\n        <div className={classes.rowEnd}>\n          <TextField\n            size=\"small\"\n            label=\"URL\"\n            placeholder=\"https://example.com/graph.gfa\"\n            value={url}\n            onChange={e => {\n              setUrl(e.target.value)\n            }}\n            onKeyDown={e => {\n              if (e.key === 'Enter') {\n                handleUrlLoad()\n              }\n            }}\n            className={classes.flex1}\n          />\n          <Button\n            variant=\"contained\"\n            onClick={() => {\n              handleUrlLoad()\n            }}\n            disabled={!url.trim()}\n          >\n            Open\n          </Button>\n        </div>\n      </div>\n\n      <div className={classes.footer}>\n        <Button\n          size=\"small\"\n          onClick={() => {\n            void model.loadGFA(EXAMPLE_GFA, 'Example graph')\n          }}\n        >\n          Load 4-node example\n        </Button>\n      </div>\n\n      {model.error ? <ErrorBanner error={model.error} /> : null}\n    </Paper>\n  )\n})\n\nexport default ImportForm\n", "import { observer } from 'mobx-react'\n\nimport GraphCanvas from './GraphCanvas'\nimport GraphLoadStatus from './GraphLoadStatus'\nimport ImportForm from './ImportForm'\n\nimport type { GraphPaneModel } from '../model'\n\nconst GraphGenomeView = observer(function GraphGenomeView({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  if (model.hasGraph) {\n    return <GraphCanvas model={model} />\n  }\n  // A launched or restored view has a source of its own, so the import form\n  // has nothing to offer it when that source fails\n  if (model.canRetryLoad && (model.error || model.loadCanceled)) {\n    return <GraphLoadStatus model={model} />\n  }\n  // Hidden rather than unmounted, so a typed URL survives a failed load\n  return (\n    <>\n      {model.isLoading ? <GraphLoadStatus model={model} /> : null}\n      <div hidden={model.isLoading}>\n        <ImportForm model={model} />\n      </div>\n    </>\n  )\n})\n\nexport default GraphGenomeView\n"],
-  "mappings": "usBAOA,IAAMA,EAAYC,EAAW,EAAE,CAC7B,MAAO,CACL,QAAS,GACT,OAAQ,EACR,SAAU,IACV,aAAc,OACd,QAAS,OACT,cAAe,SACf,IAAK,EACP,EACA,IAAK,CACH,QAAS,OACT,WAAY,SACZ,eAAgB,gBAChB,IAAK,CACP,CACF,CAAC,EAIKC,EAAkBC,EAAS,SAAyB,CACxD,MAAAC,CACF,EAEG,CACD,GAAM,CAAE,QAAAC,CAAQ,EAAIL,EAAU,EAC9B,OAAII,EAAM,UAENE,EAACC,EAAA,CAAM,UAAWF,EAAQ,MAAO,cAAY,uBAC3C,UAAAC,EAAC,OAAI,UAAWD,EAAQ,IACtB,UAAAG,EAACC,EAAA,CAAgB,QAAQ,KAAK,QAASL,EAAM,cAAe,EAC5DI,EAACE,EAAA,CACC,KAAK,QACL,cAAY,sBACZ,QAAS,IAAM,CACbN,EAAM,WAAW,CACnB,EACD,kBAED,GACF,EACAI,EAACG,EAAA,CAAe,QAAQ,gBAAgB,GAC1C,EAGAP,EAAM,MAENI,EAACD,EAAA,CAAM,UAAWF,EAAQ,MACxB,SAAAG,EAACI,EAAA,CACC,MAAOR,EAAM,MACb,QAAS,IAAM,CACbA,EAAM,UAAU,CAClB,EACF,EACF,EAIFI,EAACD,EAAA,CAAM,UAAWF,EAAQ,MAAO,cAAY,6BAC3C,SAAAC,EAAC,OAAI,UAAWD,EAAQ,IACtB,UAAAG,EAACK,EAAA,CAAW,QAAQ,KAAK,4BAAgB,EACzCL,EAACE,EAAA,CACC,QAAQ,YACR,KAAK,QACL,cAAY,qBACZ,QAAS,IAAM,CACbN,EAAM,UAAU,CAClB,EACD,iBAED,GACF,EACF,CAEJ,CAAC,EAEMU,EAAQZ,EC1Ef,IAAMa,EAAc;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA,cAUdC,EAAYC,EAAW,EAAE,CAC7B,OAAQ,CAAE,QAAS,OAAQ,cAAe,SAAU,IAAK,CAAE,EAC3D,OAAQ,CAAE,QAAS,OAAQ,IAAK,EAAG,WAAY,UAAW,EAC1D,UAAW,CAAE,QAAS,OAAQ,IAAK,EAAG,WAAY,QAAS,EAC3D,MAAO,CAAE,KAAM,CAAE,EACjB,MAAO,CAAE,QAAS,GAAI,OAAQ,EAAG,SAAU,IAAK,aAAc,MAAO,EACrE,OAAQ,CAAE,aAAc,EAAG,EAC3B,OAAQ,CAAE,UAAW,GAAI,QAAS,OAAQ,eAAgB,UAAW,CACvE,CAAC,EAEKC,EAAaC,EAAS,SAAoB,CAC9C,MAAAC,CACF,EAEG,CACD,GAAM,CAAE,QAAAC,CAAQ,EAAIL,EAAU,EACxB,CAACM,EAAKC,CAAM,EAAIC,EAAS,EAAE,EAEjC,SAASC,GAAgB,CACvB,IAAMC,EAAMJ,EAAI,KAAK,EACjBI,GACGN,EAAM,oBAAoB,CAAE,IAAAM,EAAK,aAAc,aAAc,CAAC,CAEvE,CAEA,SAASC,EAAiBC,EAA4C,CACpE,IAAMC,EAAOD,EAAM,OAAO,QAAQ,CAAC,EAEnCA,EAAM,OAAO,MAAQ,GACjBC,GACFA,EACG,KAAK,EACL,KAAKC,GAAQV,EAAM,QAAQU,EAAMD,EAAK,IAAI,CAAC,EAC3C,MAAOE,GAAiB,CACvBX,EAAM,SAASW,CAAG,CACpB,CAAC,CAEP,CAEA,OACEC,EAACC,EAAA,CAAM,UAAWZ,EAAQ,MACxB,UAAAa,EAAC,OAAI,UAAWb,EAAQ,OACtB,SAAAa,EAACC,EAAA,CAAW,QAAQ,KAAK,4BAAgB,EAC3C,EAEAH,EAAC,OAAI,UAAWX,EAAQ,OACtB,UAAAW,EAAC,OAAI,UAAWX,EAAQ,UACtB,UAAAW,EAACI,EAAA,CAAO,QAAQ,WAAW,UAAU,QAAQ,KAAK,QAAQ,wBAExDF,EAAC,SACC,KAAK,OACL,OAAO,mBACP,OAAM,GACN,SAAUN,GAAS,CACjBD,EAAiBC,CAAK,CACxB,EACF,GACF,EACAM,EAACC,EAAA,CAAW,QAAQ,UAAU,MAAM,iBAAiB,yDAErD,GACF,EAEAH,EAAC,OAAI,UAAWX,EAAQ,OACtB,UAAAa,EAACG,EAAA,CACC,KAAK,QACL,MAAM,MACN,YAAY,gCACZ,MAAOf,EACP,SAAUgB,GAAK,CACbf,EAAOe,EAAE,OAAO,KAAK,CACvB,EACA,UAAWA,GAAK,CACVA,EAAE,MAAQ,SACZb,EAAc,CAElB,EACA,UAAWJ,EAAQ,MACrB,EACAa,EAACE,EAAA,CACC,QAAQ,YACR,QAAS,IAAM,CACbX,EAAc,CAChB,EACA,SAAU,CAACH,EAAI,KAAK,EACrB,gBAED,GACF,GACF,EAEAY,EAAC,OAAI,UAAWb,EAAQ,OACtB,SAAAa,EAACE,EAAA,CACC,KAAK,QACL,QAAS,IAAM,CACRhB,EAAM,QAAQL,EAAa,eAAe,CACjD,EACD,+BAED,EACF,EAECK,EAAM,MAAQc,EAACK,EAAA,CAAY,MAAOnB,EAAM,MAAO,EAAK,MACvD,CAEJ,CAAC,EAEMoB,EAAQtB,ECtHf,IAAMuB,EAAkBC,EAAS,SAAyB,CACxD,MAAAC,CACF,EAEG,CACD,OAAIA,EAAM,SACDC,EAACC,EAAA,CAAY,MAAOF,EAAO,EAIhCA,EAAM,eAAiBA,EAAM,OAASA,EAAM,cACvCC,EAACE,EAAA,CAAgB,MAAOH,EAAO,EAItCI,EAAAC,EAAA,CACG,UAAAL,EAAM,UAAYC,EAACE,EAAA,CAAgB,MAAOH,EAAO,EAAK,KACvDC,EAAC,OAAI,OAAQD,EAAM,UACjB,SAAAC,EAACK,EAAA,CAAW,MAAON,EAAO,EAC5B,GACF,CAEJ,CAAC,EAEMO,EAAQT",
+  "mappings": "muBAOA,IAAMA,EAAYC,EAAW,EAAE,CAC7B,MAAO,CACL,QAAS,GACT,OAAQ,EACR,SAAU,IACV,aAAc,OACd,QAAS,OACT,cAAe,SACf,IAAK,EACP,EACA,IAAK,CACH,QAAS,OACT,WAAY,SACZ,eAAgB,gBAChB,IAAK,CACP,CACF,CAAC,EAIKC,EAAkBC,EAAS,SAAyB,CACxD,MAAAC,CACF,EAEG,CACD,GAAM,CAAE,QAAAC,CAAQ,EAAIL,EAAU,EAC9B,OAAII,EAAM,UAENE,EAACC,EAAA,CAAM,UAAWF,EAAQ,MAAO,cAAY,uBAC3C,UAAAC,EAAC,OAAI,UAAWD,EAAQ,IACtB,UAAAG,EAACC,EAAA,CAAgB,QAAQ,KAAK,QAASL,EAAM,cAAe,EAC5DI,EAACE,EAAA,CACC,KAAK,QACL,cAAY,sBACZ,QAAS,IAAM,CACbN,EAAM,WAAW,CACnB,EACD,kBAED,GACF,EACAI,EAACG,EAAA,CAAe,QAAQ,gBAAgB,GAC1C,EAGAP,EAAM,MAENI,EAACD,EAAA,CAAM,UAAWF,EAAQ,MACxB,SAAAG,EAACI,EAAA,CACC,MAAOR,EAAM,MACb,QAAS,IAAM,CACbA,EAAM,UAAU,CAClB,EACF,EACF,EAIFI,EAACD,EAAA,CAAM,UAAWF,EAAQ,MAAO,cAAY,6BAC3C,SAAAC,EAAC,OAAI,UAAWD,EAAQ,IACtB,UAAAG,EAACK,EAAA,CAAW,QAAQ,KAAK,4BAAgB,EACzCL,EAACE,EAAA,CACC,QAAQ,YACR,KAAK,QACL,cAAY,qBACZ,QAAS,IAAM,CACbN,EAAM,UAAU,CAClB,EACD,iBAED,GACF,EACF,CAEJ,CAAC,EAEMU,EAAQZ,EC1Ef,IAAMa,EAAc;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA,cAUdC,EAAYC,EAAW,EAAE,CAC7B,OAAQ,CAAE,QAAS,OAAQ,cAAe,SAAU,IAAK,CAAE,EAC3D,OAAQ,CAAE,QAAS,OAAQ,IAAK,EAAG,WAAY,UAAW,EAC1D,UAAW,CAAE,QAAS,OAAQ,IAAK,EAAG,WAAY,QAAS,EAC3D,MAAO,CAAE,KAAM,CAAE,EACjB,MAAO,CAAE,QAAS,GAAI,OAAQ,EAAG,SAAU,IAAK,aAAc,MAAO,EACrE,OAAQ,CAAE,aAAc,EAAG,EAC3B,OAAQ,CAAE,UAAW,GAAI,QAAS,OAAQ,eAAgB,UAAW,CACvE,CAAC,EAEKC,EAAaC,EAAS,SAAoB,CAC9C,MAAAC,CACF,EAEG,CACD,GAAM,CAAE,QAAAC,CAAQ,EAAIL,EAAU,EACxB,CAACM,EAAKC,CAAM,EAAIC,EAAS,EAAE,EAEjC,SAASC,GAAgB,CACvB,IAAMC,EAAMJ,EAAI,KAAK,EACjBI,GACGN,EAAM,oBAAoB,CAAE,IAAAM,EAAK,aAAc,aAAc,CAAC,CAEvE,CAEA,SAASC,EAAiBC,EAA4C,CACpE,IAAMC,EAAOD,EAAM,OAAO,QAAQ,CAAC,EAEnCA,EAAM,OAAO,MAAQ,GACjBC,GACFA,EACG,KAAK,EACL,KAAKC,GAAQV,EAAM,QAAQU,EAAMD,EAAK,IAAI,CAAC,EAC3C,MAAOE,GAAiB,CACvBX,EAAM,SAASW,CAAG,CACpB,CAAC,CAEP,CAEA,OACEC,EAACC,EAAA,CAAM,UAAWZ,EAAQ,MACxB,UAAAa,EAAC,OAAI,UAAWb,EAAQ,OACtB,SAAAa,EAACC,EAAA,CAAW,QAAQ,KAAK,4BAAgB,EAC3C,EAEAH,EAAC,OAAI,UAAWX,EAAQ,OACtB,UAAAW,EAAC,OAAI,UAAWX,EAAQ,UACtB,UAAAW,EAACI,EAAA,CAAO,QAAQ,WAAW,UAAU,QAAQ,KAAK,QAAQ,wBAExDF,EAAC,SACC,KAAK,OACL,OAAO,mBACP,OAAM,GACN,SAAUN,GAAS,CACjBD,EAAiBC,CAAK,CACxB,EACF,GACF,EACAM,EAACC,EAAA,CAAW,QAAQ,UAAU,MAAM,iBAAiB,yDAErD,GACF,EAEAH,EAAC,OAAI,UAAWX,EAAQ,OACtB,UAAAa,EAACG,EAAA,CACC,KAAK,QACL,MAAM,MACN,YAAY,gCACZ,MAAOf,EACP,SAAUgB,GAAK,CACbf,EAAOe,EAAE,OAAO,KAAK,CACvB,EACA,UAAWA,GAAK,CACVA,EAAE,MAAQ,SACZb,EAAc,CAElB,EACA,UAAWJ,EAAQ,MACrB,EACAa,EAACE,EAAA,CACC,QAAQ,YACR,QAAS,IAAM,CACbX,EAAc,CAChB,EACA,SAAU,CAACH,EAAI,KAAK,EACrB,gBAED,GACF,GACF,EAEAY,EAAC,OAAI,UAAWb,EAAQ,OACtB,SAAAa,EAACE,EAAA,CACC,KAAK,QACL,QAAS,IAAM,CACRhB,EAAM,QAAQL,EAAa,eAAe,CACjD,EACD,+BAED,EACF,EAECK,EAAM,MAAQc,EAACK,EAAA,CAAY,MAAOnB,EAAM,MAAO,EAAK,MACvD,CAEJ,CAAC,EAEMoB,EAAQtB,ECtHf,IAAMuB,EAAkBC,EAAS,SAAyB,CACxD,MAAAC,CACF,EAEG,CACD,OAAIA,EAAM,SACDC,EAACC,EAAA,CAAY,MAAOF,EAAO,EAIhCA,EAAM,eAAiBA,EAAM,OAASA,EAAM,cACvCC,EAACE,EAAA,CAAgB,MAAOH,EAAO,EAItCI,EAAAC,EAAA,CACG,UAAAL,EAAM,UAAYC,EAACE,EAAA,CAAgB,MAAOH,EAAO,EAAK,KACvDC,EAAC,OAAI,OAAQD,EAAM,UACjB,SAAAC,EAACK,EAAA,CAAW,MAAON,EAAO,EAC5B,GACF,CAEJ,CAAC,EAEMO,EAAQT",
   "names": ["useStyles", "makeStyles", "GraphLoadStatus", "observer", "model", "classes", "jsxs", "Paper", "jsx", "LoadingEllipses", "Button", "LinearProgress", "ErrorBanner", "Typography", "GraphLoadStatus_default", "EXAMPLE_GFA", "useStyles", "makeStyles", "ImportForm", "observer", "model", "classes", "url", "setUrl", "useState", "handleUrlLoad", "uri", "handleFileUpload", "event", "file", "text", "err", "jsxs", "Paper", "jsx", "Typography", "Button", "TextField", "e", "ErrorBanner", "ImportForm_default", "GraphGenomeView", "observer", "model", "jsx", "GraphCanvas_default", "GraphLoadStatus_default", "jsxs", "Fragment", "ImportForm_default", "GraphGenomeView_default"]
 }

package/dist/chunks/{GraphTrackSettingsDialog-EQ5W5KTL.js → GraphTrackSettingsDialog-TAM6PMXD.js}

@@ -1,6 +1,6 @@
-import{b as G}from"./chunk-Z4B6RZGP.js";import{b as H,c as x}from"./chunk-E2QPSDQL.js";import{k as h}from"./chunk-ZWMYT35X.js";import"./chunk-G73A6PEI.js";import"./chunk-HW4LIGPA.js";import"./chunk-MVVXRZXV.js";import"./chunk-OUN4BNWJ.js";import"./chunk-5OI6LO4I.js";import{g as u}from"./chunk-6OPB7FOJ.js";import{D as v,F as f,H as c,n as g,s as b,w as S,z as C}from"./chunk-E3WYW7Z6.js";import{b as a,c as l,d as i}from"./chunk-JMBDTNUR.js";var F=h()({section:{marginBottom:24},formControl:{minWidth:200}}),M=[{value:0,label:"None"},{value:1,label:"1 hop"},{value:2,label:"2 hops"}],I=i(function({model:t}){let{classes:e}=F();return t.adapterConfig.type==="RgfaTabixAdapter"&&!H(t.adapterConfig)?l("div",{className:e.section,children:[l(b,{className:e.formControl,children:[a(S,{children:"Graph context"}),a(v,{value:t.subgraphContext,label:"Graph context","data-testid":"graph-context-select",onChange:o=>{t.setSubgraphContext(o.target.value),t.cut()},children:M.map(({value:o,label:p})=>a(C,{value:o,children:p},o))})]}),a(c,{variant:"caption",component:"div",color:"text.secondary",children:"How far the cut follows links out of the region. At none, a detour that leaves the window draws as two stubs. No effect on gfa-to-tabix's default anchored index."})]}):null}),L=I;var N=h()({section:{marginBottom:24}});function P(n){let t=n.split(/[\s,]+/).map(e=>e.trim()).filter(e=>e!=="");return t.length===0?void 0:t}var T=i(function({model:t}){let[e,o]=u(t.cutHaplotypes?.join(", ")??""),p=()=>{let r=P(e)??[];r.join(`
+import{b as G}from"./chunk-J6NZIAZF.js";import{b as H,c as x}from"./chunk-E2QPSDQL.js";import{k as h}from"./chunk-YSTMDXXX.js";import"./chunk-MHPJB22Z.js";import"./chunk-AU73K7LX.js";import"./chunk-MVVXRZXV.js";import"./chunk-446RWIA3.js";import"./chunk-5OI6LO4I.js";import{g as u}from"./chunk-6OPB7FOJ.js";import{D as v,F as f,H as c,n as g,s as b,w as S,z as C}from"./chunk-E3WYW7Z6.js";import{b as a,c as l,d as i}from"./chunk-JMBDTNUR.js";var F=h()({section:{marginBottom:24},formControl:{minWidth:200}}),M=[{value:0,label:"None"},{value:1,label:"1 hop"},{value:2,label:"2 hops"}],I=i(function({model:t}){let{classes:e}=F();return t.adapterConfig.type==="RgfaTabixAdapter"&&!H(t.adapterConfig)?l("div",{className:e.section,children:[l(b,{className:e.formControl,children:[a(S,{children:"Graph context"}),a(v,{value:t.subgraphContext,label:"Graph context","data-testid":"graph-context-select",onChange:o=>{t.setSubgraphContext(o.target.value),t.cut()},children:M.map(({value:o,label:p})=>a(C,{value:o,children:p},o))})]}),a(c,{variant:"caption",component:"div",color:"text.secondary",children:"How far the cut follows links out of the region. At none, a detour that leaves the window draws as two stubs. No effect on gfa-to-tabix's default anchored index."})]}):null}),L=I;var N=h()({section:{marginBottom:24}});function P(n){let t=n.split(/[\s,]+/).map(e=>e.trim()).filter(e=>e!=="");return t.length===0?void 0:t}var T=i(function({model:t}){let[e,o]=u(t.cutHaplotypes?.join(", ")??""),p=()=>{let r=P(e)??[];r.join(`
 `)===(t.cutHaplotypes??[]).join(`
 `)||(t.setSubgraphHaplotypes(r),t.cut())};return a(f,{fullWidth:!0,label:"Haplotypes",placeholder:"every haplotype",value:e,slotProps:{htmlInput:{"data-testid":"graph-haplotypes-field"}},onChange:r=>{o(r.target.value)},onBlur:()=>{p()},onKeyDown:r=>{r.key==="Enter"&&p()}})}),w=i(function({model:t,names:e}){let[o,p]=u(t.cutHaplotypes??[]),[r,d]=u(!1),m=s=>{s.join(`
 `)!==(t.cutHaplotypes??[]).join(`
 `)&&(t.setSubgraphHaplotypes(s),t.cut())};return a(g,{multiple:!0,freeSolo:!0,disableCloseOnSelect:!0,options:e,value:o,open:r,onOpen:()=>{d(!0)},onClose:()=>{d(!1),m(o)},onChange:(s,y)=>{p(y),r||m(y)},renderInput:s=>a(f,{...s,label:"Haplotypes",placeholder:o.length===0?"every haplotype":void 0,slotProps:{...s.slotProps,htmlInput:{...s.slotProps.htmlInput,"data-testid":"graph-haplotypes-field"}}})})}),D=i(function({model:t}){let{classes:e}=N(),o=t.haplotypeNames,p=t.cutHaplotypes?.join(",")??"";return x(t.adapterConfig)?l("div",{className:e.section,children:[o?a(w,{model:t,names:o},p):a(T,{model:t},p),l(c,{variant:"caption",component:"div",color:"text.secondary",children:[o?`Which of the graph's ${o.length.toLocaleString()} haplotypes to cut, or a PanSN prefix (HG002 for both).`:"Which haplotypes to cut, as lane assembly names or PanSN prefixes (HG002#1, or HG002 for both) separated by commas."," ","Empty is every haplotype."]})]}):null}),k=D;function B({model:n,open:t,onClose:e}){return l(G,{model:n,open:t,onClose:e,children:[a(L,{model:n}),a(k,{model:n})]})}export{B as default};
-//# sourceMappingURL=GraphTrackSettingsDialog-EQ5W5KTL.js.map
+//# sourceMappingURL=GraphTrackSettingsDialog-TAM6PMXD.js.map

package/dist/chunks/{HighlightColorDialog-3BONNNBR.js → HighlightColorDialog-EYBKFSJU.js}

@@ -1,2 +1,2 @@
-import{o as v,p as C}from"./chunk-XJDTSPBL.js";import"./chunk-G73A6PEI.js";import"./chunk-HW4LIGPA.js";import"./chunk-OUN4BNWJ.js";import{F as g,H as t,c as u,o as y,q as c,r as d,z as s}from"./chunk-E3WYW7Z6.js";import{a as h,b as l,c as p,d as m}from"./chunk-JMBDTNUR.js";var b=m(function({model:o,onClose:r}){return p(u,{open:!0,onClose:r,title:"Color highlighted haplotypes",children:[p(d,{sx:{display:"grid",gridTemplateColumns:"auto 1fr 1fr",alignItems:"center",gap:1.5},children:[l(t,{variant:"subtitle2",children:"Haplotype"}),l(t,{variant:"subtitle2",children:"Color by"}),l(t,{variant:"subtitle2",children:"Palette"}),o.drawnWalks.map(({name:a,encoding:n})=>l(f,{label:o.walkLabel(a),field:n.field,scheme:n.scheme,onField:e=>{o.setWalkColor(a,{field:e})},onScheme:e=>{o.setWalkColor(a,{scheme:e})}},a))]}),l(c,{children:l(y,{variant:"contained",onClick:r,children:"Done"})})]})});function f({label:i,field:o,scheme:r,onField:a,onScheme:n}){return p(h,{children:[l(t,{variant:"body2",children:i}),l(g,{select:!0,size:"small",value:o,slotProps:{select:{SelectDisplayProps:{"aria-label":`Color ${i} by`}}},onChange:e=>{a(e.target.value)},children:v.map(e=>l(s,{value:e.value,children:e.label},e.value))}),l(g,{select:!0,size:"small",value:r,slotProps:{select:{SelectDisplayProps:{"aria-label":`Palette for ${i}`}}},onChange:e=>{n(e.target.value)},children:C.filter(e=>e.value!=="rainbow"||o==="reference").map(e=>l(s,{value:e.value,children:e.label},e.value))})]})}var P=b;export{P as default};
-//# sourceMappingURL=HighlightColorDialog-3BONNNBR.js.map
+import{o as v,p as C}from"./chunk-DZ4OUKQV.js";import"./chunk-MHPJB22Z.js";import"./chunk-AU73K7LX.js";import"./chunk-446RWIA3.js";import{F as g,H as t,c as u,o as y,q as c,r as d,z as s}from"./chunk-E3WYW7Z6.js";import{a as h,b as l,c as p,d as m}from"./chunk-JMBDTNUR.js";var b=m(function({model:o,onClose:r}){return p(u,{open:!0,onClose:r,title:"Color highlighted haplotypes",children:[p(d,{sx:{display:"grid",gridTemplateColumns:"auto 1fr 1fr",alignItems:"center",gap:1.5},children:[l(t,{variant:"subtitle2",children:"Haplotype"}),l(t,{variant:"subtitle2",children:"Color by"}),l(t,{variant:"subtitle2",children:"Palette"}),o.drawnWalks.map(({name:a,encoding:n})=>l(f,{label:o.walkLabel(a),field:n.field,scheme:n.scheme,onField:e=>{o.setWalkColor(a,{field:e})},onScheme:e=>{o.setWalkColor(a,{scheme:e})}},a))]}),l(c,{children:l(y,{variant:"contained",onClick:r,children:"Done"})})]})});function f({label:i,field:o,scheme:r,onField:a,onScheme:n}){return p(h,{children:[l(t,{variant:"body2",children:i}),l(g,{select:!0,size:"small",value:o,slotProps:{select:{SelectDisplayProps:{"aria-label":`Color ${i} by`}}},onChange:e=>{a(e.target.value)},children:v.map(e=>l(s,{value:e.value,children:e.label},e.value))}),l(g,{select:!0,size:"small",value:r,slotProps:{select:{SelectDisplayProps:{"aria-label":`Palette for ${i}`}}},onChange:e=>{n(e.target.value)},children:C.filter(e=>e.value!=="rainbow"||o==="reference").map(e=>l(s,{value:e.value,children:e.label},e.value))})]})}var P=b;export{P as default};
+//# sourceMappingURL=HighlightColorDialog-EYBKFSJU.js.map

package/dist/chunks/LinearGraphDisplay-WIBVWRQE.js

@@ -0,0 +1,2 @@
+import{a as g}from"./chunk-BJMRBVG3.js";import"./chunk-J6NZIAZF.js";import"./chunk-GOFS7BXK.js";import"./chunk-IJQTSJGT.js";import"./chunk-YSTMDXXX.js";import"./chunk-5SFGHDQA.js";import"./chunk-DZ4OUKQV.js";import"./chunk-MHPJB22Z.js";import"./chunk-XT766CZ5.js";import"./chunk-EWFJBQDV.js";import"./chunk-3Q4RBDCL.js";import"./chunk-AU73K7LX.js";import"./chunk-TXI43PEN.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import"./chunk-446RWIA3.js";import"./chunk-5OI6LO4I.js";import"./chunk-NDRLCGPC.js";import"./chunk-TENPGIPX.js";import{g as y}from"./chunk-6OPB7FOJ.js";import"./chunk-E3WYW7Z6.js";import{b as e,c as l,d as T}from"./chunk-JMBDTNUR.js";var s=JBrowseExports["@jbrowse/display-kit/DisplayBackgroundProgress"];var v=s&&s.__esModule?s.default:s;var i=JBrowseExports["@jbrowse/display-kit/DisplayErrorBar"];var h=i&&i.__esModule?i.default:i;var a=JBrowseExports["@jbrowse/display-kit/DisplayLoadingOverlay"];var O=a&&a.__esModule?a.default:a;var n=JBrowseExports["@jbrowse/display-kit/TooLargeMessage"];var f=n&&n.__esModule?n.default:n;var t=JBrowseExports["@jbrowse/display-ui"],p=r=>t!=null&&r in Object(t)?t[r]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+r+"' from '@jbrowse/display-ui' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:r});var w=p("BottomRightCornerContext");var c=p("TrackOverlayPortal");var L=p("useChromeOverlayOverride");var j=t&&t.__esModule?t.default:t;var D={TooLarge:f,ErrorBar:h,Loading:O,BackgroundProgress:v};function d({model:r,phase:o,drawn:u,testid:_,style:C,children:E,...B}){let{TooLarge:G,ErrorBar:S,Loading:b,BackgroundProgress:m}=L()??D,[P,A]=y(null),x={...B,"data-testid":_,"data-display-id":r.configuration.displayId,"data-display-drawn":u,"data-display-phase":o};return o==="tooLarge"?e("div",{style:{display:"contents"},...x,children:e(c,{children:e("div",{style:{pointerEvents:"auto"},children:e(G,{model:r})})})}):l("div",{style:{position:"relative",height:r.height,...C},...x,children:[e(w,{value:P,children:E}),l(c,{children:[e(S,{model:r,visible:o==="error"}),e(b,{model:r,visible:o==="loading"||o==="canceled",immediate:!u}),e("div",{ref:A,style:{position:"absolute",bottom:2,right:2,display:"flex",flexDirection:"column",alignItems:"flex-end",gap:4,pointerEvents:"none"},children:e(m,{model:r,visible:o==="ready"})})]})]})}var I=T(function({model:o}){return e(d,{model:o,phase:o.displayPhase,drawn:o.painted&&o.geometryPainted,testid:"linear-graph-display","data-layout":o.chosenLayoutMode,"data-cut-tier":o.cutTier,"data-recuts":o.recuts,"data-node-count":o.hasGraph?o.nodeCount:void 0,"data-loading":o.isLoading?"":void 0,style:{width:o.paneWidth,height:o.height,overflow:"hidden"},children:e(g,{model:o,ownChrome:!1})})}),Q=I;export{Q as default};
+//# sourceMappingURL=LinearGraphDisplay-WIBVWRQE.js.map

package/dist/chunks/{LinearGraphDisplay-MQ4LD2RQ.js.map → LinearGraphDisplay-WIBVWRQE.js.map}

@@ -2,6 +2,6 @@
   "version": 3,
   "sources": ["host:@jbrowse/display-kit/DisplayBackgroundProgress", "host:@jbrowse/display-kit/DisplayErrorBar", "host:@jbrowse/display-kit/DisplayLoadingOverlay", "host:@jbrowse/display-kit/TooLargeMessage", "host:@jbrowse/display-ui", "../../src/LinearGraphDisplay/components/GraphStatusChrome.tsx", "../../src/LinearGraphDisplay/components/LinearGraphDisplay.tsx"],
   "sourcesContent": ["const host = JBrowseExports[\"@jbrowse/display-kit/DisplayBackgroundProgress\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/display-kit/DisplayBackgroundProgress\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport default host && host.__esModule ? host.default : host", "const host = JBrowseExports[\"@jbrowse/display-kit/DisplayErrorBar\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/display-kit/DisplayErrorBar\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport default host && host.__esModule ? host.default : host", "const host = JBrowseExports[\"@jbrowse/display-kit/DisplayLoadingOverlay\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/display-kit/DisplayLoadingOverlay\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport default host && host.__esModule ? host.default : host", "const host = JBrowseExports[\"@jbrowse/display-kit/TooLargeMessage\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/display-kit/TooLargeMessage\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport default host && host.__esModule ? host.default : host", "const host = JBrowseExports[\"@jbrowse/display-ui\"]\nconst read = name =>\n  host != null && name in Object(host)\n    ? host[name]\n    : Object.assign(\n        function () {\n          throw new Error(\n            \"This JBrowse does not provide '\" + name + \"' from '\" + \"@jbrowse/display-ui\" + \"' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse\",\n          )\n        },\n        { jbrowseHostMissing: name },\n      )\nexport const AXIS_GUTTER_WIDTH_PX = /* @__PURE__ */ read(\"AXIS_GUTTER_WIDTH_PX\")\nexport const AXIS_RIGHT_INSET_PX = /* @__PURE__ */ read(\"AXIS_RIGHT_INSET_PX\")\nexport const AxisCaption = /* @__PURE__ */ read(\"AxisCaption\")\nexport const AxisCaptionOverlay = /* @__PURE__ */ read(\"AxisCaptionOverlay\")\nexport const AxisGutter = /* @__PURE__ */ read(\"AxisGutter\")\nexport const BOTTOM_RIGHT_CONTROLS_ORDER = /* @__PURE__ */ read(\"BOTTOM_RIGHT_CONTROLS_ORDER\")\nexport const BottomRightCornerContext = /* @__PURE__ */ read(\"BottomRightCornerContext\")\nexport const COMPACT_AXIS_HEIGHT = /* @__PURE__ */ read(\"COMPACT_AXIS_HEIGHT\")\nexport const CrossHatchLines = /* @__PURE__ */ read(\"CrossHatchLines\")\nexport const CrossHatches = /* @__PURE__ */ read(\"CrossHatches\")\nexport const DEFAULT_RULE_COLOR = /* @__PURE__ */ read(\"DEFAULT_RULE_COLOR\")\nexport const DisplayChromeOverlayProvider = /* @__PURE__ */ read(\"DisplayChromeOverlayProvider\")\nexport const DisplayUIProvider = /* @__PURE__ */ read(\"DisplayUIProvider\")\nexport const FLOATING_LEGEND_RIGHT_PX = /* @__PURE__ */ read(\"FLOATING_LEGEND_RIGHT_PX\")\nexport const FLOATING_LEGEND_TOP_PX = /* @__PURE__ */ read(\"FLOATING_LEGEND_TOP_PX\")\nexport const FloatingLegend = /* @__PURE__ */ read(\"FloatingLegend\")\nexport const FloatingSvgOverlay = /* @__PURE__ */ read(\"FloatingSvgOverlay\")\nexport const FloatingText = /* @__PURE__ */ read(\"FloatingText\")\nexport const PointerLayer = /* @__PURE__ */ read(\"PointerLayer\")\nexport const SCORE_CAPTION_HEIGHT = /* @__PURE__ */ read(\"SCORE_CAPTION_HEIGHT\")\nexport const ScoreDomainCaption = /* @__PURE__ */ read(\"ScoreDomainCaption\")\nexport const ScoreRuleLines = /* @__PURE__ */ read(\"ScoreRuleLines\")\nexport const ScoreRules = /* @__PURE__ */ read(\"ScoreRules\")\nexport const SvgHaloText = /* @__PURE__ */ read(\"SvgHaloText\")\nexport const TEXT_BASELINE_RATIO = /* @__PURE__ */ read(\"TEXT_BASELINE_RATIO\")\nexport const Tooltip = /* @__PURE__ */ read(\"Tooltip\")\nexport const TrackControlProvider = /* @__PURE__ */ read(\"TrackControlProvider\")\nexport const TrackOverlayContext = /* @__PURE__ */ read(\"TrackOverlayContext\")\nexport const TrackOverlayPortal = /* @__PURE__ */ read(\"TrackOverlayPortal\")\nexport const TrackOverlaySlot = /* @__PURE__ */ read(\"TrackOverlaySlot\")\nexport const YSCALEBAR_LABEL_OFFSET = /* @__PURE__ */ read(\"YSCALEBAR_LABEL_OFFSET\")\nexport const YScaleBar = /* @__PURE__ */ read(\"YScaleBar\")\nexport const YScaleBarOverlay = /* @__PURE__ */ read(\"YScaleBarOverlay\")\nexport const axisDrawn = /* @__PURE__ */ read(\"axisDrawn\")\nexport const axisGutterLeft = /* @__PURE__ */ read(\"axisGutterLeft\")\nexport const axisGutterWidth = /* @__PURE__ */ read(\"axisGutterWidth\")\nexport const axisPlotBox = /* @__PURE__ */ read(\"axisPlotBox\")\nexport const clampStrokeInsideAxis = /* @__PURE__ */ read(\"clampStrokeInsideAxis\")\nexport const cullOverlappingLabels = /* @__PURE__ */ read(\"cullOverlappingLabels\")\nexport const formatScore = /* @__PURE__ */ read(\"formatScore\")\nexport const isLiveModel = /* @__PURE__ */ read(\"isLiveModel\")\nexport const leftAxisGutterWidth = /* @__PURE__ */ read(\"leftAxisGutterWidth\")\nexport const plainChromeOverlays = /* @__PURE__ */ read(\"plainChromeOverlays\")\nexport const plainTrackControl = /* @__PURE__ */ read(\"plainTrackControl\")\nexport const resolveOverlays = /* @__PURE__ */ read(\"resolveOverlays\")\nexport const scoreToAxisY = /* @__PURE__ */ read(\"scoreToAxisY\")\nexport const textHalo = /* @__PURE__ */ read(\"textHalo\")\nexport const tooLargeBannerText = /* @__PURE__ */ read(\"tooLargeBannerText\")\nexport const useChromeOverlayOverride = /* @__PURE__ */ read(\"useChromeOverlayOverride\")\nexport const useTooltip = /* @__PURE__ */ read(\"useTooltip\")\nexport const useTrackControlMenu = /* @__PURE__ */ read(\"useTrackControlMenu\")\nexport const useTrackControlOverride = /* @__PURE__ */ read(\"useTrackControlOverride\")\nexport default host && host.__esModule ? host.default : host", "import { useState } from 'react'\nimport type { CSSProperties, ReactNode } from 'react'\n\nimport DisplayBackgroundProgress from '@jbrowse/display-kit/DisplayBackgroundProgress'\nimport DisplayErrorBar from '@jbrowse/display-kit/DisplayErrorBar'\nimport DisplayLoadingOverlay from '@jbrowse/display-kit/DisplayLoadingOverlay'\nimport TooLargeMessage from '@jbrowse/display-kit/TooLargeMessage'\nimport {\n  BottomRightCornerContext,\n  TrackOverlayPortal,\n  useChromeOverlayOverride,\n} from '@jbrowse/display-ui'\n\nimport type { LinearGraphDisplayModel } from '../model'\nimport type { DisplayStatusPhase } from '@jbrowse/render-core/displayPhase'\n\nconst muiOverlays = {\n  TooLarge: TooLargeMessage,\n  ErrorBar: DisplayErrorBar,\n  Loading: DisplayLoadingOverlay,\n  BackgroundProgress: DisplayBackgroundProgress,\n}\n\n/**\n * The status chrome of a display that owns its canvas: the zoom-in notice in\n * place of the display, and the error bar, loading overlay and progress chip\n * over it in the track's overlay layer. Core's `DisplayStatusChrome` drew this\n * until jbrowse-web main removed it on 2026-10-08 (d8db736896), and its named\n * import came back undefined there, failing the track with React error #130.\n * Built here from the overlays every host from 5.0.0-beta.11 serves.\n */\nexport default function GraphStatusChrome({\n  model,\n  phase,\n  drawn,\n  testid,\n  style,\n  children,\n  ...dataProps\n}: {\n  model: LinearGraphDisplayModel\n  phase: DisplayStatusPhase\n  drawn: boolean\n  testid: string\n  style?: CSSProperties\n  children: ReactNode\n} & Record<`data-${string}`, unknown>) {\n  const { TooLarge, ErrorBar, Loading, BackgroundProgress } =\n    useChromeOverlayOverride() ?? muiOverlays\n  const [corner, setCorner] = useState<HTMLDivElement | null>(null)\n  const attributes = {\n    ...dataProps,\n    'data-testid': testid,\n    'data-display-id': model.configuration.displayId,\n    'data-display-drawn': drawn,\n    'data-display-phase': phase,\n  }\n  if (phase === 'tooLarge') {\n    return (\n      <div style={{ display: 'contents' }} {...attributes}>\n        <TrackOverlayPortal>\n          <div style={{ pointerEvents: 'auto' }}>\n            <TooLarge model={model} />\n          </div>\n        </TrackOverlayPortal>\n      </div>\n    )\n  }\n  return (\n    <div\n      style={{ position: 'relative', height: model.height, ...style }}\n      {...attributes}\n    >\n      <BottomRightCornerContext value={corner}>\n        {children}\n      </BottomRightCornerContext>\n      <TrackOverlayPortal>\n        <ErrorBar model={model} visible={phase === 'error'} />\n        <Loading\n          model={model}\n          visible={phase === 'loading' || phase === 'canceled'}\n          immediate={!drawn}\n        />\n        <div\n          ref={setCorner}\n          style={{\n            position: 'absolute',\n            bottom: 2,\n            right: 2,\n            display: 'flex',\n            flexDirection: 'column',\n            alignItems: 'flex-end',\n            gap: 4,\n            pointerEvents: 'none',\n          }}\n        >\n          <BackgroundProgress model={model} visible={phase === 'ready'} />\n        </div>\n      </TrackOverlayPortal>\n    </div>\n  )\n}\n", "import { observer } from 'mobx-react'\n\nimport GraphStatusChrome from './GraphStatusChrome'\nimport GraphCanvas from '../../GraphGenomeView/components/GraphCanvas'\n\nimport type { LinearGraphDisplayModel } from '../model'\n\nconst LinearGraphDisplay = observer(function LinearGraphDisplay({\n  model,\n}: {\n  model: LinearGraphDisplayModel\n}) {\n  return (\n    <GraphStatusChrome\n      model={model}\n      phase={model.displayPhase}\n      drawn={model.painted && model.geometryPainted}\n      testid=\"linear-graph-display\"\n      data-layout={model.chosenLayoutMode}\n      data-cut-tier={model.cutTier}\n      data-recuts={model.recuts}\n      data-node-count={model.hasGraph ? model.nodeCount : undefined}\n      data-loading={model.isLoading ? '' : undefined}\n      style={{\n        width: model.paneWidth,\n        height: model.height,\n        overflow: 'hidden',\n      }}\n    >\n      <GraphCanvas model={model} ownChrome={false} />\n    </GraphStatusChrome>\n  )\n})\n\nexport default LinearGraphDisplay\n"],
-  "mappings": "8nBAAA,IAAMA,EAAO,eAAe,gDAAgD,EAY5E,IAAOC,EAAQC,GAAQA,EAAK,WAAaA,EAAK,QAAUA,ECZxD,IAAMC,EAAO,eAAe,sCAAsC,EAYlE,IAAOC,EAAQC,GAAQA,EAAK,WAAaA,EAAK,QAAUA,ECZxD,IAAMC,EAAO,eAAe,4CAA4C,EAYxE,IAAOC,EAAQC,GAAQA,EAAK,WAAaA,EAAK,QAAUA,ECZxD,IAAMC,EAAO,eAAe,sCAAsC,EAYlE,IAAOC,EAAQC,GAAQA,EAAK,WAAaA,EAAK,QAAUA,ECZxD,IAAMC,EAAO,eAAe,qBAAqB,EAC3CC,EAAOC,GACXF,GAAQ,MAAQE,KAAQ,OAAOF,CAAI,EAC/BA,EAAKE,CAAI,EACT,OAAO,OACL,UAAY,CACV,MAAM,IAAI,MACR,kCAAoCA,EAAO,qIAC7C,CACF,EACA,CAAE,mBAAoBA,CAAK,CAC7B,EAOC,IAAMC,EAA2CC,EAAK,0BAA0B,EAsBhF,IAAMC,EAAqCC,EAAK,oBAAoB,EAoBpE,IAAMC,EAA2CC,EAAK,0BAA0B,EAIvF,IAAOC,EAAQC,GAAQA,EAAK,WAAaA,EAAK,QAAUA,EChDxD,IAAMC,EAAc,CAClB,SAAUC,EACV,SAAUC,EACV,QAASC,EACT,mBAAoBC,CACtB,EAUe,SAARC,EAAmC,CACxC,MAAAC,EACA,MAAAC,EACA,MAAAC,EACA,OAAAC,EACA,MAAAC,EACA,SAAAC,EACA,GAAGC,CACL,EAOuC,CACrC,GAAM,CAAE,SAAAC,EAAU,SAAAC,EAAU,QAAAC,EAAS,mBAAAC,CAAmB,EACtDC,EAAyB,GAAKjB,EAC1B,CAACkB,EAAQC,CAAS,EAAIC,EAAgC,IAAI,EAC1DC,EAAa,CACjB,GAAGT,EACH,cAAeH,EACf,kBAAmBH,EAAM,cAAc,UACvC,qBAAsBE,EACtB,qBAAsBD,CACxB,EACA,OAAIA,IAAU,WAEVe,EAAC,OAAI,MAAO,CAAE,QAAS,UAAW,EAAI,GAAGD,EACvC,SAAAC,EAACC,EAAA,CACC,SAAAD,EAAC,OAAI,MAAO,CAAE,cAAe,MAAO,EAClC,SAAAA,EAACT,EAAA,CAAS,MAAOP,EAAO,EAC1B,EACF,EACF,EAIFkB,EAAC,OACC,MAAO,CAAE,SAAU,WAAY,OAAQlB,EAAM,OAAQ,GAAGI,CAAM,EAC7D,GAAGW,EAEJ,UAAAC,EAACG,EAAA,CAAyB,MAAOP,EAC9B,SAAAP,EACH,EACAa,EAACD,EAAA,CACC,UAAAD,EAACR,EAAA,CAAS,MAAOR,EAAO,QAASC,IAAU,QAAS,EACpDe,EAACP,EAAA,CACC,MAAOT,EACP,QAASC,IAAU,WAAaA,IAAU,WAC1C,UAAW,CAACC,EACd,EACAc,EAAC,OACC,IAAKH,EACL,MAAO,CACL,SAAU,WACV,OAAQ,EACR,MAAO,EACP,QAAS,OACT,cAAe,SACf,WAAY,WACZ,IAAK,EACL,cAAe,MACjB,EAEA,SAAAG,EAACN,EAAA,CAAmB,MAAOV,EAAO,QAASC,IAAU,QAAS,EAChE,GACF,GACF,CAEJ,CC9FA,IAAMmB,EAAqBC,EAAS,SAA4B,CAC9D,MAAAC,CACF,EAEG,CACD,OACEC,EAACC,EAAA,CACC,MAAOF,EACP,MAAOA,EAAM,aACb,MAAOA,EAAM,SAAWA,EAAM,gBAC9B,OAAO,uBACP,cAAaA,EAAM,iBACnB,gBAAeA,EAAM,QACrB,cAAaA,EAAM,OACnB,kBAAiBA,EAAM,SAAWA,EAAM,UAAY,OACpD,eAAcA,EAAM,UAAY,GAAK,OACrC,MAAO,CACL,MAAOA,EAAM,UACb,OAAQA,EAAM,OACd,SAAU,QACZ,EAEA,SAAAC,EAACE,EAAA,CAAY,MAAOH,EAAO,UAAW,GAAO,EAC/C,CAEJ,CAAC,EAEMI,EAAQN",
+  "mappings": "0pBAAA,IAAMA,EAAO,eAAe,gDAAgD,EAY5E,IAAOC,EAAQC,GAAQA,EAAK,WAAaA,EAAK,QAAUA,ECZxD,IAAMC,EAAO,eAAe,sCAAsC,EAYlE,IAAOC,EAAQC,GAAQA,EAAK,WAAaA,EAAK,QAAUA,ECZxD,IAAMC,EAAO,eAAe,4CAA4C,EAYxE,IAAOC,EAAQC,GAAQA,EAAK,WAAaA,EAAK,QAAUA,ECZxD,IAAMC,EAAO,eAAe,sCAAsC,EAYlE,IAAOC,EAAQC,GAAQA,EAAK,WAAaA,EAAK,QAAUA,ECZxD,IAAMC,EAAO,eAAe,qBAAqB,EAC3CC,EAAOC,GACXF,GAAQ,MAAQE,KAAQ,OAAOF,CAAI,EAC/BA,EAAKE,CAAI,EACT,OAAO,OACL,UAAY,CACV,MAAM,IAAI,MACR,kCAAoCA,EAAO,qIAC7C,CACF,EACA,CAAE,mBAAoBA,CAAK,CAC7B,EAOC,IAAMC,EAA2CC,EAAK,0BAA0B,EAsBhF,IAAMC,EAAqCC,EAAK,oBAAoB,EAoBpE,IAAMC,EAA2CC,EAAK,0BAA0B,EAIvF,IAAOC,EAAQC,GAAQA,EAAK,WAAaA,EAAK,QAAUA,EChDxD,IAAMC,EAAc,CAClB,SAAUC,EACV,SAAUC,EACV,QAASC,EACT,mBAAoBC,CACtB,EAUe,SAARC,EAAmC,CACxC,MAAAC,EACA,MAAAC,EACA,MAAAC,EACA,OAAAC,EACA,MAAAC,EACA,SAAAC,EACA,GAAGC,CACL,EAOuC,CACrC,GAAM,CAAE,SAAAC,EAAU,SAAAC,EAAU,QAAAC,EAAS,mBAAAC,CAAmB,EACtDC,EAAyB,GAAKjB,EAC1B,CAACkB,EAAQC,CAAS,EAAIC,EAAgC,IAAI,EAC1DC,EAAa,CACjB,GAAGT,EACH,cAAeH,EACf,kBAAmBH,EAAM,cAAc,UACvC,qBAAsBE,EACtB,qBAAsBD,CACxB,EACA,OAAIA,IAAU,WAEVe,EAAC,OAAI,MAAO,CAAE,QAAS,UAAW,EAAI,GAAGD,EACvC,SAAAC,EAACC,EAAA,CACC,SAAAD,EAAC,OAAI,MAAO,CAAE,cAAe,MAAO,EAClC,SAAAA,EAACT,EAAA,CAAS,MAAOP,EAAO,EAC1B,EACF,EACF,EAIFkB,EAAC,OACC,MAAO,CAAE,SAAU,WAAY,OAAQlB,EAAM,OAAQ,GAAGI,CAAM,EAC7D,GAAGW,EAEJ,UAAAC,EAACG,EAAA,CAAyB,MAAOP,EAC9B,SAAAP,EACH,EACAa,EAACD,EAAA,CACC,UAAAD,EAACR,EAAA,CAAS,MAAOR,EAAO,QAASC,IAAU,QAAS,EACpDe,EAACP,EAAA,CACC,MAAOT,EACP,QAASC,IAAU,WAAaA,IAAU,WAC1C,UAAW,CAACC,EACd,EACAc,EAAC,OACC,IAAKH,EACL,MAAO,CACL,SAAU,WACV,OAAQ,EACR,MAAO,EACP,QAAS,OACT,cAAe,SACf,WAAY,WACZ,IAAK,EACL,cAAe,MACjB,EAEA,SAAAG,EAACN,EAAA,CAAmB,MAAOV,EAAO,QAASC,IAAU,QAAS,EAChE,GACF,GACF,CAEJ,CC9FA,IAAMmB,EAAqBC,EAAS,SAA4B,CAC9D,MAAAC,CACF,EAEG,CACD,OACEC,EAACC,EAAA,CACC,MAAOF,EACP,MAAOA,EAAM,aACb,MAAOA,EAAM,SAAWA,EAAM,gBAC9B,OAAO,uBACP,cAAaA,EAAM,iBACnB,gBAAeA,EAAM,QACrB,cAAaA,EAAM,OACnB,kBAAiBA,EAAM,SAAWA,EAAM,UAAY,OACpD,eAAcA,EAAM,UAAY,GAAK,OACrC,MAAO,CACL,MAAOA,EAAM,UACb,OAAQA,EAAM,OACd,SAAU,QACZ,EAEA,SAAAC,EAACE,EAAA,CAAY,MAAOH,EAAO,UAAW,GAAO,EAC/C,CAEJ,CAAC,EAEMI,EAAQN",
   "names": ["host", "DisplayBackgroundProgress_default", "host", "host", "DisplayErrorBar_default", "host", "host", "DisplayLoadingOverlay_default", "host", "host", "TooLargeMessage_default", "host", "host", "read", "name", "BottomRightCornerContext", "read", "TrackOverlayPortal", "read", "useChromeOverlayOverride", "read", "display_ui_default", "host", "muiOverlays", "TooLargeMessage_default", "DisplayErrorBar_default", "DisplayLoadingOverlay_default", "DisplayBackgroundProgress_default", "GraphStatusChrome", "model", "phase", "drawn", "testid", "style", "children", "dataProps", "TooLarge", "ErrorBar", "Loading", "BackgroundProgress", "useChromeOverlayOverride", "corner", "setCorner", "useState", "attributes", "jsx", "TrackOverlayPortal", "jsxs", "BottomRightCornerContext", "LinearGraphDisplay", "observer", "model", "jsx", "GraphStatusChrome", "GraphCanvas_default", "LinearGraphDisplay_default"]
 }