jbrowse-plugin-mafviewer 1.0.6 → 1.0.8

package/src/TaffyAdapter/TaffyAdapter.ts

@@ -0,0 +1,112 @@
+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 {}
+}

package/src/TaffyAdapter/configSchema.ts

@@ -0,0 +1,44 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+
+/**
+ * #config TaffyAdapter
+ * used to configure Taffy adapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const configSchema = ConfigurationSchema(
+  'TaffyAdapter',
+  {
+    /**
+     * #slot
+     */
+    samples: {
+      type: 'frozen',
+      description: 'string[] or {id:string,label:string,color?:string}[]',
+      defaultValue: [],
+    },
+    /**
+     * #slot
+     */
+    tafLocation: {
+      type: 'fileLocation',
+      defaultValue: {
+        uri: '/path/to/my.taf',
+        locationType: 'UriLocation',
+      },
+    },
+    /**
+     * #slot
+     */
+    taiLocation: {
+      type: 'fileLocation',
+      defaultValue: {
+        uri: '/path/to/my.taf.tai',
+        locationType: 'UriLocation',
+      },
+    },
+  },
+  { explicitlyTyped: true },
+)
+
+export default configSchema

package/src/TaffyAdapter/index.ts

@@ -0,0 +1,15 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import { AdapterType } from '@jbrowse/core/pluggableElementTypes'
+import configSchema from './configSchema'
+import TaffyAdapter from './TaffyAdapter'
+
+export default function TaffyAdapterF(pluginManager: PluginManager) {
+  return pluginManager.addAdapterType(
+    () =>
+      new AdapterType({
+        name: 'TaffyAdapter',
+        AdapterClass: TaffyAdapter,
+        configSchema,
+      }),
+  )
+}

package/src/index.ts

@@ -7,6 +7,7 @@ import MafTrackF from './MafTrack'
 import LinearMafDisplayF from './LinearMafDisplay'
 import LinearMafRendererF from './LinearMafRenderer'
 import MafTabixAdapterF from './MafTabixAdapter'
+import TaffyAdapterF from './TaffyAdapter'
 import MafAddTrackWorkflowF from './MafAddTrackWorkflow'
 
 export default class MafViewerPlugin extends Plugin {
@@ -19,6 +20,7 @@ export default class MafViewerPlugin extends Plugin {
     LinearMafDisplayF(pluginManager)
     LinearMafRendererF(pluginManager)
     MafTabixAdapterF(pluginManager)
+    TaffyAdapterF(pluginManager)
     MafAddTrackWorkflowF(pluginManager)
   }