jbrowse-plugin-graphgenomeviewer 7.4.3 → 7.5.0

package/dist/chunks/chunk-ZAYC5OMQ.js

@@ -1,2 +0,0 @@
-import{h as B,k as M,n as F}from"./chunk-TGSDXZXI.js";import{b as O,h as _}from"./chunk-CXOMX2I6.js";import{H as b,N as A}from"./chunk-WGTLNVST.js";import{e as R}from"./chunk-YU7T5WOQ.js";import{D as P,E,H as m,d as v,o as T,q as I,r as L,s as w,t as N,w as x,y as D,z as G}from"./chunk-UGCNPRKC.js";import{b as t,c as i,d as k}from"./chunk-JMBDTNUR.js";var S=[{value:0,label:"Fastest"},{value:1,label:"Fast"},{value:2,label:"Default"},{value:3,label:"Fine"},{value:4,label:"Best"}];function f({label:o,value:n,options:e,testId:s,size:c,sx:d,disabled:a,title:h,shown:g,onChange:Q}){let C=R();return i(w,{size:c,sx:d,disabled:a,title:h,children:[t(x,{id:C,shrink:!0,children:o}),t(P,{labelId:C,value:n,label:o,notched:!0,displayEmpty:!0,"data-testid":s,renderValue:l=>g??e.find(z=>z.value===l)?.label??l,onChange:l=>{Q(l.target.value)},children:e.map(l=>t(G,{value:l.value,disabled:l.disabled,title:l.disabled?void 0:l.description,children:t(D,{primary:l.label,secondary:l.disabled?l.description:void 0})},l.value))})]})}var u=F()({section:{marginBottom:24},group:{marginBottom:16},heading:{marginBottom:8}});function r({warn:o=!1,children:n}){return t(m,{variant:"caption",component:"div",color:o?"warning.main":"text.secondary",children:n})}function y({title:o,children:n}){let{classes:e}=u();return i("section",{className:e.group,children:[t(m,{variant:"subtitle1",className:e.heading,children:o}),n]})}function U({label:o,checked:n,onChange:e,children:s}){let{classes:c}=u();return i("div",{className:c.section,children:[t(N,{control:t(E,{checked:n,onChange:d=>{e(d.target.checked)}}),label:o}),s]})}function p({children:o,...n}){let{classes:e}=u();return i("div",{className:e.section,children:[t(f,{sx:{minWidth:200},...n}),o]})}var Y=[5e3,2e4,5e4,1e5];function H(o){return[...new Set([...Y,o])].sort((n,e)=>n-e).map(n=>({value:String(n),label:n.toLocaleString()}))}function W({label:o,choices:n,stored:e,auto:s,testId:c,onChange:d,children:a}){return n.length>0?t(p,{label:o,value:n.some(h=>h.trackId===e)?e:"",options:[{value:"",label:`Automatic (${s?.name??"none"})`},...n.map(({trackId:h,name:g})=>({value:h,label:g}))],testId:c,onChange:d,children:a}):null}var $=k(function(n){let{model:e,onClose:s,children:c}=n,{classes:d}=u();return i(v,{open:!0,onClose:s,title:"Graph settings",children:[i(L,{children:[i(y,{title:"Subgraph",children:[c,t(p,{label:"Node limit",value:String(e.maxGraphNodes),options:H(e.maxGraphNodes),testId:"graph-node-limit-select",onChange:a=>{e.setMaxGraphNodes(Number(a))},children:t(r,{children:"The most nodes a layout draws; past it the graph is declined. Walk rows take no limit."})})]}),i(y,{title:"Drawing",children:[e.anchorPaths.length>1?t(p,{label:"Reference path",value:e.activeReferencePath??"",options:e.anchorPaths.map(({name:a})=>({value:a,label:a})),testId:"graph-reference-path-select",onChange:a=>{e.setReferencePath(a),e.recomputeLayout()},children:t(r,{children:"The path the anchored layouts place x along"})}):null,t(p,{label:"Node width",value:e.nodeWidth,options:A,testId:"graph-node-width-select",onChange:a=>{e.setNodeWidth(a)},children:t(r,{children:"Depth as width. In a cut with walks, depth is how many haplotypes carry the node."})}),i(U,{label:"Draw paths",checked:e.drawPaths,onChange:a=>{e.setLayer("paths",a)},children:[t(r,{children:"Color each node by the paths through it, one lane per path"}),e.drawPaths&&!e.effectiveDrawPaths?t(r,{warn:!0,children:e.pathCount>b?`Off: ${e.pathCount.toLocaleString()} paths is past the ${b} this can tell apart`:"Off: this graph states no paths"}):null]}),t(W,{label:"Gene track",choices:e.geneTrackChoices,stored:e.geneTrackId,auto:M(e.geneTrackChoices,""),testId:"graph-gene-track-select",onChange:a=>{e.setGeneTrackId(a)},children:t(r,{children:"Where genes on the backbone come from"})}),t(W,{label:"Repeat track",choices:e.repeatTrackChoices,stored:e.repeatTrackId,auto:B(e.repeatTrackChoices,""),testId:"graph-repeat-track-select",onChange:a=>{e.setRepeatTrackId(a)},children:t(r,{children:"The tandem repeat annotation walk rows measure and tile by"})})]}),i(y,{title:"Force-directed layout",children:[e.hasGraph&&!e.usesLayoutEngine?t("div",{className:d.section,children:t(r,{warn:!0,children:"No effect on the current layout until Layout is Force-directed"})}):null,t(p,{label:"Engine",value:e.layoutEngine,options:O,testId:"graph-layout-engine-select",onChange:a=>{e.setLayoutEngine(a)},children:t(r,{children:"Stress keeps the reference straight, so a zoom keeps the picture; FMMM lets the whole graph settle."})}),t(p,{label:"Layout quality",value:String(e.layoutQuality),options:S.map(a=>({value:String(a.value),label:a.label})),testId:"graph-layout-quality-select",onChange:a=>{e.setLayoutQuality(Number(a))},children:t(r,{children:"The engine's iteration budget; higher is slower"})}),t(p,{label:"Bubble spread",value:e.bubbleSpread,options:_,testId:"graph-bubble-spread-select",onChange:a=>{e.setBubbleSpread(a)},children:t(r,{children:"How far the layout opens a bubble"})}),e.layoutEngine==="stress"?null:t(U,{label:"Linear layout",checked:e.linearLayout,onChange:a=>{e.setLinearLayout(a)},children:t(r,{children:"Keeps a chain of nodes on one line where it can"})})]})]}),t(I,{children:t(T,{variant:"contained",color:"primary",onClick:s,children:"Close"})})]})}),he=$;export{f as a,he as b};
-//# sourceMappingURL=chunk-ZAYC5OMQ.js.map

package/src/launchFromGraph/launchTracks.test.ts

@@ -1,95 +0,0 @@
-import { expect, test } from 'vitest'
-
-import { launchTracks } from './launchTracks'
-
-// Plain objects rather than config models: readConfObject returns a non-MST
-// object's own fields unchanged, so this exercises the same read path.
-function track(props: Record<string, unknown>) {
-  return props as never
-}
-
-const TRACKS = [
-  track({
-    type: 'FeatureTrack',
-    trackId: 'K12_genes',
-    assemblyNames: ['K12'],
-  }),
-  track({
-    type: 'FeatureTrack',
-    trackId: 'CFT073_genes',
-    assemblyNames: ['CFT073'],
-  }),
-  track({
-    type: 'FeatureTrack',
-    trackId: 'ecoli_minigraph_segments',
-    assemblyNames: ['K12'],
-  }),
-  track({
-    type: 'SyntenyTrack',
-    trackId: 'ecoli_pggb_ava',
-    assemblyNames: ['K12', 'CFT073'],
-  }),
-  track({
-    type: 'AlignmentsTrack',
-    trackId: 'K12_reads',
-    assemblyNames: ['K12'],
-  }),
-]
-
-const session = { tracks: TRACKS, assemblies: [] }
-
-// The bug this exists for: the graph's own track is configured for the
-// reference alone, so a per-strain launch carrying only that landed on
-// `No tracks active`.
-test("a non-reference launch gets that strain's own annotation", () => {
-  expect(launchTracks({ session, assemblyName: 'CFT073' })).toEqual([
-    'CFT073_genes',
-  ])
-})
-
-test("the graph's own track leads a launch on the reference", () => {
-  expect(
-    launchTracks({
-      session,
-      assemblyName: 'K12',
-      first: 'ecoli_minigraph_segments',
-    }),
-  ).toEqual(['ecoli_minigraph_segments', 'K12_genes'])
-})
-
-// A launch is a jump to a locus, not a session restore: an alignments track
-// turned on behind the user fetches data nobody asked for, and a synteny track
-// is what the launch beside this one opens as a view of its own.
-test('only annotation tracks are carried', () => {
-  expect(launchTracks({ session, assemblyName: 'K12' })).toEqual([
-    'K12_genes',
-    'ecoli_minigraph_segments',
-  ])
-})
-
-test('an assembly the session has no annotation for gets none', () => {
-  expect(launchTracks({ session, assemblyName: 'IAI39' })).toEqual([])
-})
-
-test('a track naming the assembly by an alias is carried', () => {
-  const aliased = {
-    tracks: [
-      track({
-        type: 'FeatureTrack',
-        trackId: 'ncbi_genes',
-        assemblyNames: ['GRCh38'],
-      }),
-    ],
-    assemblies: [],
-    assemblyManager: {
-      has: (name: string) => name === 'GRCh38' || name === 'hg38',
-      get: () => ({ name: 'hg38' }),
-    },
-  }
-  expect(launchTracks({ session: aliased, assemblyName: 'hg38' })).toEqual([
-    'ncbi_genes',
-  ])
-  expect(launchTracks({ session: aliased, assemblyName: 'GRCh38' })).toEqual([
-    'ncbi_genes',
-  ])
-})

package/src/launchFromGraph/launchTracks.ts

@@ -1,49 +0,0 @@
-import { readConfObject } from '@jbrowse/core/configuration'
-
-import { canonicalAssemblyName, trackAssemblies } from './launchFromGraph'
-
-import type { TrackScanSession } from './launchFromGraph'
-
-const ANNOTATION_TRACK_TYPE = 'FeatureTrack'
-
-// What to turn on in a linear view the graph opens on `assemblyName`.
-//
-// A launch used to carry the graph's own track and nothing else, and that track
-// is configured for the reference alone — so `Launch view` → `CFT073 chr:…`
-// landed on `No tracks active`, which answers "where is this strain's sequence?"
-// with an empty pane. What the session does hold for a contributing assembly is
-// that assembly's own annotation, and on a pangenome config that is one track
-// per strain (`CFT073_genes`), which is exactly what makes the landing readable.
-//
-// Annotation tracks only, not everything configured for the assembly. A launch
-// is a jump to a locus, and an alignments or coverage track turned on behind the
-// user's back fetches data nobody asked for; a FeatureTrack at a 50 kb window is
-// a tabix range query.
-//
-// `first` is the graph's own track when the launch is on the reference, so the
-// segments the graph drew sit at the top of the view rather than wherever config
-// order puts them.
-export function launchTracks({
-  session,
-  assemblyName,
-  first,
-}: {
-  session: TrackScanSession
-  assemblyName: string
-  first?: string
-}) {
-  const wanted = canonicalAssemblyName(session, assemblyName)
-  const found: string[] = []
-  for (const track of session.tracks) {
-    const trackId: unknown = readConfObject(track, 'trackId')
-    if (
-      readConfObject(track, 'type') === ANNOTATION_TRACK_TYPE &&
-      typeof trackId === 'string' &&
-      trackId !== first &&
-      trackAssemblies(session, track).includes(wanted)
-    ) {
-      found.push(trackId)
-    }
-  }
-  return first ? [first, ...found] : found
-}