jbrowse2: x/static/js/3578.058bdae5.chunk.js.map comparison

comparison x/static/js/3578.058bdae5.chunk.js.map @ 125:49f3d3878413 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566

author	fubar
date	Sat, 05 Oct 2024 23:58:05 +0000
parents
children

comparison

equal deleted inserted replaced

124:137e08517410	125:49f3d3878413
	1 {"version":3,"file":"static/js/3578.058bdae5.chunk.js","mappings":"kNA8Be,MAAMA,UAA8BC,EAAAA,oBAKjD,iBAAaC,CAAYC,GACvB,MAAM,MAAEC,SAAgBC,KAAKC,MAAMH,GACnC,MAAO,IAAIC,EAAMG,OACnB,CAEA,gBAAaC,CAAWL,GACtB,MAAM,MAAEC,SAAgBC,KAAKC,MAAMH,GACnC,MAAO,IAAIC,EAAMK,WAAWC,KAAI,EAAEC,EAASC,MAAU,CACnDD,UACAE,MAAO,EACPC,IAAKF,EAAKG,SAASC,UAEvB,CAEA,cAAaC,CAASC,GACpB,MAAMC,EAAgBd,KAAKe,QAAQ,iBAC7BC,GAzCeC,QA0CbC,EAAAA,EAAAA,cAAaJ,EAAed,KAAKmB,eAAeC,SAAS,QAzC5D,IAAIC,IACTJ,EACGK,MAAM,KACNC,QAAOC,GAAK,KAAKC,KAAKD,KACtBnB,KAAIqB,IACH,MAAOC,KAAYC,GAAYF,EAAUJ,MAAM,OACxCO,KAAOC,GAAeH,EAASL,MAAM,KACtCZ,EAAWkB,EAASG,KAAK,IAAIC,QAAQ,MAAO,IAClD,MAAO,CACLH,EACA,CACEC,YAAaA,EAAYC,KAAK,KAC9BrB,YAEH,MAfT,IAAyBO,EA6CrB,MAAO,CACLlB,MAAO,IAAIsB,IACT,IAAIL,EAAIZ,WAAWC,KAAI,EAAEC,EAAS2B,KACzB,EACLC,EAAAA,EAAAA,gBAAelC,KAAKmC,OAAQ,kBAAmB,CAAE7B,aAC/CA,EACF2B,MAKV,CAEA,eAAaG,GACX,MAAMC,EAAMrC,KAAKe,QAAQ,oBACzB,MAAmB,KAAZsB,EAAIC,KAA0B,8BAAZD,EAAIC,IACzB,MACApB,EAAAA,EAAAA,cAAamB,EAAKrC,KAAKmB,eAAeC,SAAS,OACrD,CAEA,WAAanB,CAAMH,GAOjB,OANKE,KAAKuC,SACRvC,KAAKuC,OAASvC,KAAKY,SAASd,GAAM0C,OAAOC,IAEvC,MADAzC,KAAKuC,YAASG,EACRD,CAAC,KAGJzC,KAAKuC,MACd,CAEOI,WAAAA,CAAYC,EAA0B9C,GAC3C,MAAM,QAAEQ,EAAO,MAAEE,EAAK,IAAEC,GAAQmC,EAChC,OAAOC,EAAAA,EAAAA,mBAA0BC,UAC/B,MAAM,MAAE/C,SAAgBC,KAAKC,MAAMH,GAC7BiD,EAAQhD,EAAMiD,IAAI1C,GACpByC,GACFE,EAASC,KACP,IAAIC,EAAAA,cAAc,CAChBtB,GAAI,GAAGvB,KAAWE,KAASC,IAC3BF,KAAM,CACJD,UACAE,QACAC,MACA2C,IAAKL,EAAMrC,SAAS2C,MAAM7C,EAAOC,OAKzCwC,EAASK,UAAU,GAEvB,CAEOC,aAAAA,GAAuC,E","sources":["../../../plugins/sequence/src/UnindexedFastaAdapter/UnindexedFastaAdapter.ts"],"sourcesContent":["import {\n BaseSequenceAdapter,\n BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { FileLocation, NoAssemblyRegion } from '@jbrowse/core/util/types'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { SimpleFeature, Feature } from '@jbrowse/core/util'\nimport { readConfObject } from '@jbrowse/core/configuration'\n\nfunction parseSmallFasta(text: string) {\n return new Map(\n text\n .split('>')\n .filter(t => /\\S/.test(t))\n .map(entryText => {\n const [defLine, ...seqLines] = entryText.split('\\n')\n const [id, ...description] = defLine!.split(' ')\n const sequence = seqLines.join('').replace(/\\s/g, '')\n return [\n id!,\n {\n description: description.join(' '),\n sequence,\n },\n ] as const\n }),\n )\n}\n\nexport default class UnindexedFastaAdapter extends BaseSequenceAdapter {\n protected setupP?: Promise<{\n fasta: ReturnType<typeof parseSmallFasta>\n }>\n\n public async getRefNames(opts?: BaseOptions) {\n const { fasta } = await this.setup(opts)\n return [...fasta.keys()]\n }\n\n public async getRegions(opts?: BaseOptions) {\n const { fasta } = await this.setup(opts)\n return [...fasta.entries()].map(([refName, data]) => ({\n refName,\n start: 0,\n end: data.sequence.length,\n }))\n }\n\n public async setupPre(_opts?: BaseOptions) {\n const fastaLocation = this.getConf('fastaLocation') as FileLocation\n const res = parseSmallFasta(\n await openLocation(fastaLocation, this.pluginManager).readFile('utf8'),\n )\n\n return {\n fasta: new Map(\n [...res.entries()].map(([refName, val]) => {\n return [\n readConfObject(this.config, 'rewriteRefNames', { refName }) \|\|\n refName,\n val,\n ]\n }),\n ),\n }\n }\n\n public async getHeader() {\n const loc = this.getConf('metadataLocation')\n return loc.uri === '' \|\| loc.uri === '/path/to/fa.metadata.yaml'\n ? null\n : openLocation(loc, this.pluginManager).readFile('utf8')\n }\n\n public async setup(opts?: BaseOptions) {\n if (!this.setupP) {\n this.setupP = this.setupPre(opts).catch((e: unknown) => {\n this.setupP = undefined\n throw e\n })\n }\n return this.setupP\n }\n\n public getFeatures(region: NoAssemblyRegion, opts?: BaseOptions) {\n const { refName, start, end } = region\n return ObservableCreate<Feature>(async observer => {\n const { fasta } = await this.setup(opts)\n const entry = fasta.get(refName)\n if (entry) {\n observer.next(\n new SimpleFeature({\n id: `${refName}-${start}-${end}`,\n data: {\n refName,\n start,\n end,\n seq: entry.sequence.slice(start, end),\n },\n }),\n )\n }\n observer.complete()\n })\n }\n\n public freeResources(/* { region } */): void {}\n}\n"],"names":["UnindexedFastaAdapter","BaseSequenceAdapter","getRefNames","opts","fasta","this","setup","keys","getRegions","entries","map","refName","data","start","end","sequence","length","setupPre","_opts","fastaLocation","getConf","res","text","openLocation","pluginManager","readFile","Map","split","filter","t","test","entryText","defLine","seqLines","id","description","join","replace","val","readConfObject","config","getHeader","loc","uri","setupP","catch","e","undefined","getFeatures","region","ObservableCreate","async","entry","get","observer","next","SimpleFeature","seq","slice","complete","freeResources"],"sourceRoot":""}

1 {"version":3,"file":"static/js/3578.058bdae5.chunk.js","mappings":"kNA8Be,MAAMA,UAA8BC,EAAAA,oBAKjD,iBAAaC,CAAYC,GACvB,MAAM,MAAEC,SAAgBC,KAAKC,MAAMH,GACnC,MAAO,IAAIC,EAAMG,OACnB,CAEA,gBAAaC,CAAWL,GACtB,MAAM,MAAEC,SAAgBC,KAAKC,MAAMH,GACnC,MAAO,IAAIC,EAAMK,WAAWC,KAAI,EAAEC,EAASC,MAAU,CACnDD,UACAE,MAAO,EACPC,IAAKF,EAAKG,SAASC,UAEvB,CAEA,cAAaC,CAASC,GACpB,MAAMC,EAAgBd,KAAKe,QAAQ,iBAC7BC,GAzCeC,QA0CbC,EAAAA,EAAAA,cAAaJ,EAAed,KAAKmB,eAAeC,SAAS,QAzC5D,IAAIC,IACTJ,EACGK,MAAM,KACNC,QAAOC,GAAK,KAAKC,KAAKD,KACtBnB,KAAIqB,IACH,MAAOC,KAAYC,GAAYF,EAAUJ,MAAM,OACxCO,KAAOC,GAAeH,EAASL,MAAM,KACtCZ,EAAWkB,EAASG,KAAK,IAAIC,QAAQ,MAAO,IAClD,MAAO,CACLH,EACA,CACEC,YAAaA,EAAYC,KAAK,KAC9BrB,YAEH,MAfT,IAAyBO,EA6CrB,MAAO,CACLlB,MAAO,IAAIsB,IACT,IAAIL,EAAIZ,WAAWC,KAAI,EAAEC,EAAS2B,KACzB,EACLC,EAAAA,EAAAA,gBAAelC,KAAKmC,OAAQ,kBAAmB,CAAE7B,aAC/CA,EACF2B,MAKV,CAEA,eAAaG,GACX,MAAMC,EAAMrC,KAAKe,QAAQ,oBACzB,MAAmB,KAAZsB,EAAIC,KAA0B,8BAAZD,EAAIC,IACzB,MACApB,EAAAA,EAAAA,cAAamB,EAAKrC,KAAKmB,eAAeC,SAAS,OACrD,CAEA,WAAanB,CAAMH,GAOjB,OANKE,KAAKuC,SACRvC,KAAKuC,OAASvC,KAAKY,SAASd,GAAM0C,OAAOC,IAEvC,MADAzC,KAAKuC,YAASG,EACRD,CAAC,KAGJzC,KAAKuC,MACd,CAEOI,WAAAA,CAAYC,EAA0B9C,GAC3C,MAAM,QAAEQ,EAAO,MAAEE,EAAK,IAAEC,GAAQmC,EAChC,OAAOC,EAAAA,EAAAA,mBAA0BC,UAC/B,MAAM,MAAE/C,SAAgBC,KAAKC,MAAMH,GAC7BiD,EAAQhD,EAAMiD,IAAI1C,GACpByC,GACFE,EAASC,KACP,IAAIC,EAAAA,cAAc,CAChBtB,GAAI,GAAGvB,KAAWE,KAASC,IAC3BF,KAAM,CACJD,UACAE,QACAC,MACA2C,IAAKL,EAAMrC,SAAS2C,MAAM7C,EAAOC,OAKzCwC,EAASK,UAAU,GAEvB,CAEOC,aAAAA,GAAuC,E","sources":["../../../plugins/sequence/src/UnindexedFastaAdapter/UnindexedFastaAdapter.ts"],"sourcesContent":["import {\n BaseSequenceAdapter,\n BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { FileLocation, NoAssemblyRegion } from '@jbrowse/core/util/types'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { SimpleFeature, Feature } from '@jbrowse/core/util'\nimport { readConfObject } from '@jbrowse/core/configuration'\n\nfunction parseSmallFasta(text: string) {\n return new Map(\n text\n .split('>')\n .filter(t => /\\S/.test(t))\n .map(entryText => {\n const [defLine, ...seqLines] = entryText.split('\\n')\n const [id, ...description] = defLine!.split(' ')\n const sequence = seqLines.join('').replace(/\\s/g, '')\n return [\n id!,\n {\n description: description.join(' '),\n sequence,\n },\n ] as const\n }),\n )\n}\n\nexport default class UnindexedFastaAdapter extends BaseSequenceAdapter {\n protected setupP?: Promise<{\n fasta: ReturnType<typeof parseSmallFasta>\n }>\n\n public async getRefNames(opts?: BaseOptions) {\n const { fasta } = await this.setup(opts)\n return [...fasta.keys()]\n }\n\n public async getRegions(opts?: BaseOptions) {\n const { fasta } = await this.setup(opts)\n return [...fasta.entries()].map(([refName, data]) => ({\n refName,\n start: 0,\n end: data.sequence.length,\n }))\n }\n\n public async setupPre(_opts?: BaseOptions) {\n const fastaLocation = this.getConf('fastaLocation') as FileLocation\n const res = parseSmallFasta(\n await openLocation(fastaLocation, this.pluginManager).readFile('utf8'),\n )\n\n return {\n fasta: new Map(\n [...res.entries()].map(([refName, val]) => {\n return [\n readConfObject(this.config, 'rewriteRefNames', { refName }) ||\n refName,\n val,\n ]\n }),\n ),\n }\n }\n\n public async getHeader() {\n const loc = this.getConf('metadataLocation')\n return loc.uri === '' || loc.uri === '/path/to/fa.metadata.yaml'\n ? null\n : openLocation(loc, this.pluginManager).readFile('utf8')\n }\n\n public async setup(opts?: BaseOptions) {\n if (!this.setupP) {\n this.setupP = this.setupPre(opts).catch((e: unknown) => {\n this.setupP = undefined\n throw e\n })\n }\n return this.setupP\n }\n\n public getFeatures(region: NoAssemblyRegion, opts?: BaseOptions) {\n const { refName, start, end } = region\n return ObservableCreate<Feature>(async observer => {\n const { fasta } = await this.setup(opts)\n const entry = fasta.get(refName)\n if (entry) {\n observer.next(\n new SimpleFeature({\n id: `${refName}-${start}-${end}`,\n data: {\n refName,\n start,\n end,\n seq: entry.sequence.slice(start, end),\n },\n }),\n )\n }\n observer.complete()\n })\n }\n\n public freeResources(/* { region } */): void {}\n}\n"],"names":["UnindexedFastaAdapter","BaseSequenceAdapter","getRefNames","opts","fasta","this","setup","keys","getRegions","entries","map","refName","data","start","end","sequence","length","setupPre","_opts","fastaLocation","getConf","res","text","openLocation","pluginManager","readFile","Map","split","filter","t","test","entryText","defLine","seqLines","id","description","join","replace","val","readConfObject","config","getHeader","loc","uri","setupP","catch","e","undefined","getFeatures","region","ObservableCreate","async","entry","get","observer","next","SimpleFeature","seq","slice","complete","freeResources"],"sourceRoot":""}

Mercurial > repos > fubar > jbrowse2

comparison x/static/js/3578.058bdae5.chunk.js.map @ 125:49f3d3878413 draft