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b.get('start'))\n  }\n\n  return features\n}\n\nexport default class FromConfigAdapter extends BaseFeatureDataAdapter {\n  protected features: Map<string, Feature[]>\n\n  constructor(\n    conf: AnyConfigurationModel,\n    getSubAdapter?: getSubAdapterType,\n    pluginManager?: PluginManager,\n  ) {\n    super(conf, getSubAdapter, pluginManager)\n    const feats = readConfObject(conf, 'features') as SimpleFeatureSerialized[]\n    this.features = makeFeatures(feats)\n  }\n\n  async getRefNames() {\n    return [...this.features.keys()]\n  }\n\n  async getRefNameAliases() {\n    return [...this.features.values()].map(featureArray => ({\n      refName: featureArray[0]!.get('refName'),\n      aliases: featureArray[0]!.get('aliases'),\n    }))\n  }\n\n  getFeatures(region: NoAssemblyRegion) {\n    const { refName, start, end } = region\n\n    return ObservableCreate<Feature>(async observer => {\n      const features = this.features.get(refName) || []\n      for (const f of features) {\n        if (f.get('end') > start && f.get('start') < end) {\n          observer.next(f)\n        }\n      }\n      observer.complete()\n    })\n  }\n\n  freeResources(/* { region } */): void {}\n}\n","import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { NoAssemblyRegion } from '@jbrowse/core/util/types'\nimport { toArray } from 'rxjs/operators'\nimport { RegionsAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\n\n// locals\nimport FromConfigAdapter from '../FromConfigAdapter/FromConfigAdapter'\nimport { firstValueFrom } from 'rxjs'\n\nexport default class FromConfigSequenceAdapter\n  extends FromConfigAdapter\n  implements RegionsAdapter\n{\n  /**\n   * Fetch features for a certain region\n   * @param region - Region\n   * @returns Observable of Feature objects in the region\n   */\n  getFeatures(region: NoAssemblyRegion) {\n    return ObservableCreate<Feature>(async observer => {\n      const feats = await firstValueFrom(\n        super.getFeatures(region).pipe(toArray()),\n      )\n      const feat = feats[0]!\n      observer.next(\n        new SimpleFeature({\n          ...feat.toJSON(),\n          uniqueId: `${feat.id()}:${region.start}-${region.end}`,\n          end: region.end,\n          start: region.start,\n          seq: feat\n            .get('seq')\n            .slice(\n              Math.max(region.start - feat.get('start'), 0),\n              Math.max(region.end - feat.get('start'), 0),\n            ),\n        }),\n      )\n\n      observer.complete()\n    })\n  }\n\n  /**\n   * Get refName, start, and end for all features after collapsing any overlaps\n   */\n  async getRegions() {\n    const regions = []\n\n    // recall: features are stored in this object sorted by start coordinate\n    for (const [refName, features] of this.features) {\n      let currentRegion:\n        | { start: number; end: number; refName: string }\n        | undefined\n      for (const feature of features) {\n        if (\n          currentRegion &&\n          currentRegion.end >= feature.get('start') &&\n          currentRegion.start <= feature.get('end')\n        ) {\n          currentRegion.end = feature.get('end')\n        } else {\n          if (currentRegion) {\n            regions.push(currentRegion)\n          }\n          currentRegion = {\n            refName,\n            start: feature.get('start'),\n            end: feature.get('end'),\n          }\n        }\n      }\n      if (currentRegion) {\n        regions.push(currentRegion)\n      }\n    }\n\n    return regions\n  }\n\n  /**\n   * called to provide a hint that data tied to a certain region\n   * will not be needed for the foreseeable future and can be purged\n   * from caches, etc\n   */\n  freeResources(/* { region } */): void {}\n}\n"],"names":["makeFeatures","fdata","features","Map","entry","f","SimpleFeature","refName","get","bucket","set","push","refFeatures","values","sort","a","b","FromConfigAdapter","BaseFeatureDataAdapter","constructor","conf","getSubAdapter","pluginManager","super","feats","readConfObject","this","getRefNames","keys","getRefNameAliases","map","featureArray","aliases","getFeatures","region","start","end","ObservableCreate","async","observer","next","complete","freeResources","FromConfigSequenceAdapter","feat","firstValueFrom","pipe","toArray","toJSON","uniqueId","id","seq","slice","Math","max","getRegions","regions","currentRegion","feature"],"sourceRoot":""}