jbrowse-plugin-mafviewer 1.0.8 → 1.1.1

package/src/TaffyAdapter/TaffyAdapter.ts

@@ -1,112 +0,0 @@
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { getSnapshot } from 'mobx-state-tree'
-import { Feature, Region, SimpleFeature } from '@jbrowse/core/util'
-import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import { openLocation } from '@jbrowse/core/util/io'
-
-interface OrganismRecord {
-  chr: string
-  start: number
-  srcSize: number
-  strand: number
-  unknown: number
-  data: string
-}
-
-interface ByteRange {
-  chrStart: number
-  fileOffst: number
-}
-type IndexData = Record<string, ByteRange[]>
-
-export default class TaffyAdapter extends BaseFeatureDataAdapter {
-  public setupP?: Promise<IndexData>
-
-  async getRefNames() {
-    const data = await this.setup()
-    return Object.keys(data)
-  }
-
-  setup() {
-    if (!this.setupP) {
-      this.setupP = this.readTaiFile().catch((e: unknown) => {
-        this.setupP = undefined
-        throw e
-      })
-    }
-    return this.setupP
-  }
-
-  async readTaiFile() {
-    const text = await openLocation(this.getConf('taiLocation')).readFile(
-      'utf8',
-    )
-    const entries = {} as IndexData
-    let lastChr = ''
-    for (const line of text.split('\n').filter(line => line.trim())) {
-      const [chr, chrStart, fileOffset] = line.split('\t')
-      const ref = chr === '*' ? lastChr : chr
-      const r2 = ref.split('.').at(-1)!
-
-      if (!entries[r2]) {
-        entries[r2] = []
-      }
-      entries[r2].push({
-        chrStart: +chrStart,
-        fileOffst: +fileOffset,
-      })
-      lastChr = ref
-    }
-    return entries
-  }
-
-  getFeatures(query: Region) {
-    return ObservableCreate<Feature>(async observer => {
-      try {
-        // const { tafLocation } = getSnapshot(this.config)
-        // const byteRanges = await this.setup()
-        //
-        // for (const range of byteRanges[query.refName] || []) {
-        //   const response = await fetch(tafLocation, {
-        //     headers: {
-        //       Range: `bytes=${range.start}-${range.start + range.length - 1}`,
-        //     },
-        //   })
-        //
-        //   const text = await response.text()
-        //   const lines = text.split('\n').filter(line => line.trim())
-        //
-        //   for (const line of lines) {
-        //     const [chr, start, srcSize, strand, unknown, data] =
-        //       line.split('\t')
-        //
-        //     // Only emit features that overlap with query region
-        //     const featureStart = parseInt(start, 10)
-        //     const featureEnd = featureStart + parseInt(srcSize, 10)
-        //
-        //     if (
-        //       chr === query.refName &&
-        //       featureEnd >= query.start &&
-        //       featureStart <= query.end
-        //     ) {
-        //       observer.next(
-        //         new SimpleFeature({
-        //           uniqueId: `${chr}-${start}-${data}`,
-        //           refName: chr,
-        //           start: featureStart,
-        //           end: featureEnd,
-        //           strand: parseInt(strand, 10),
-        //           data: data,
-        //         }),
-        //       )
-        //     }
-        //   }
-        // }
-        observer.complete()
-      } catch (e) {
-        observer.error(e)
-      }
-    })
-  }
-  freeResources(): void {}
-}