@jbrowse/plugin-sequence 1.5.8 → 1.6.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-sequence",
-  "version": "1.5.8",
+  "version": "1.6.2",
   "description": "JBrowse 2 sequence adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -55,5 +55,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "f16afc382629a4a830f9040410a9ff1a3a328918"
+  "gitHead": "92455c6021abd69548496a450983d89f8837860d"
 }

package/src/DivSequenceRenderer/components/DivSequenceRendering.tsx

@@ -1,11 +1,11 @@
 /* eslint-disable @typescript-eslint/no-explicit-any */
+import React from 'react'
 import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'
 import { contrastingTextColor } from '@jbrowse/core/util/color'
 import { Feature } from '@jbrowse/core/util/simpleFeature'
 import { Region } from '@jbrowse/core/util/types'
 import { createJBrowseTheme } from '@jbrowse/core/ui'
 import { observer } from 'mobx-react'
-import React from 'react'
 import {
   bpSpanPx,
   revcom,
@@ -273,6 +273,7 @@ const Wrapper = ({ exportSVG, width, totalHeight, children }: any) => {
     <>{children}</>
   ) : (
     <svg
+      data-testid="sequence_track"
       width={width}
       height={totalHeight}
       style={{ width, height: totalHeight }}

package/src/DivSequenceRenderer/components/__snapshots__/DivSequenceRendering.test.js.snap

@@ -3,6 +3,7 @@
 exports[`<DivSequenceRendering /> renders with no features 1`] = `
 <div>
   <svg
+    data-testid="sequence_track"
     height="200"
     style="width: 100px; height: 200px;"
     width="100"
@@ -13,6 +14,7 @@ exports[`<DivSequenceRendering /> renders with no features 1`] = `
 exports[`<DivSequenceRendering /> renders with one feature reversed with a correct seq, zoomed in, should render nicely 1`] = `
 <div>
   <svg
+    data-testid="sequence_track"
     height="200"
     style="width: 20000px; height: 200px;"
     width="20000"
@@ -23,6 +25,7 @@ exports[`<DivSequenceRendering /> renders with one feature reversed with a corre
 exports[`<DivSequenceRendering /> renders with one feature with a correct seq, zoomed in, should render nicely 1`] = `
 <div>
   <svg
+    data-testid="sequence_track"
     height="200"
     style="width: 20000px; height: 200px;"
     width="20000"
@@ -33,6 +36,7 @@ exports[`<DivSequenceRendering /> renders with one feature with a correct seq, z
 exports[`<DivSequenceRendering /> renders with one feature with an incorrect seq, zoomed in, should throw 1`] = `
 <div>
   <svg
+    data-testid="sequence_track"
     height="200"
     style="width: 20000px; height: 200px;"
     width="20000"
@@ -43,6 +47,7 @@ exports[`<DivSequenceRendering /> renders with one feature with an incorrect seq
 exports[`<DivSequenceRendering /> renders with one feature with no seq, zoomed in, should throw 1`] = `
 <div>
   <svg
+    data-testid="sequence_track"
     height="200"
     style="width: 20000px; height: 200px;"
     width="20000"
@@ -53,6 +58,7 @@ exports[`<DivSequenceRendering /> renders with one feature with no seq, zoomed i
 exports[`<DivSequenceRendering /> renders with one, zoomed way out 1`] = `
 <div>
   <svg
+    data-testid="sequence_track"
     height="200"
     style="width: 333.3333333333333px; height: 200px;"
     width="333.3333333333333"

package/src/GCContentAdapter/GCContentAdapter.ts

@@ -56,12 +56,13 @@ export default class extends BaseFeatureDataAdapter {
         return
       }
 
-      const ret = sequenceAdapter.getFeatures(
-        { ...query, start: queryStart, end: queryEnd },
-        opts,
-      )
-      const [feat] = await ret.pipe(toArray()).toPromise()
-      const residues = feat.get('seq')
+      const ret = sequenceAdapter.getFeatures({
+        ...query,
+        start: queryStart,
+        end: queryEnd,
+      })
+      const feats = await ret.pipe(toArray()).toPromise()
+      const residues = feats[0]?.get('seq') || ''
 
       for (let i = hw; i < residues.length - hw; i += this.windowDelta) {
         const r = f ? residues[i] : residues.slice(i - hw, i + hw)
@@ -86,7 +87,6 @@ export default class extends BaseFeatureDataAdapter {
           score = (ng - nc) / (ng + nc || 1)
         }
 
-        // if (r[Math.floor(r.length / 2)] !== 'N') {
         observer.next(
           new SimpleFeature({
             uniqueId: `${this.id}_${pos + i}`,
@@ -95,7 +95,6 @@ export default class extends BaseFeatureDataAdapter {
             score,
           }),
         )
-        // }
       }
       observer.complete()
     })

package/src/IndexedFastaAdapter/IndexedFastaAdapter.ts

@@ -1,7 +1,6 @@
 import { IndexedFasta } from '@gmod/indexedfasta'
 import {
-  BaseFeatureDataAdapter,
-  SequenceAdapter,
+  BaseSequenceAdapter,
   BaseOptions,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { FileLocation, NoAssemblyRegion } from '@jbrowse/core/util/types'
@@ -15,7 +14,7 @@ import LRU from '@jbrowse/core/util/QuickLRU'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
 
-export default class extends BaseFeatureDataAdapter implements SequenceAdapter {
+export default class extends BaseSequenceAdapter {
   protected fasta: IndexedFasta
 
   private seqCache = new AbortablePromiseCache({

package/src/TwoBitAdapter/TwoBitAdapter.ts

@@ -1,7 +1,4 @@
-import {
-  BaseFeatureDataAdapter,
-  SequenceAdapter,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
+import { BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { NoAssemblyRegion } from '@jbrowse/core/util/types'
 import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
@@ -12,10 +9,7 @@ import { AnyConfigurationModel } from '@jbrowse/core/configuration/configuration
 import PluginManager from '@jbrowse/core/PluginManager'
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
 
-export default class TwoBitAdapter
-  extends BaseFeatureDataAdapter
-  implements SequenceAdapter
-{
+export default class TwoBitAdapter extends BaseSequenceAdapter {
   private twobit: TwoBitFile
 
   // the chromSizesData can be used to speed up loading since TwoBit has to do

package/src/index.ts

@@ -71,11 +71,14 @@ export default class SequencePlugin extends Plugin {
           const regexGuess = /\.2bit$/i
           const adapterName = 'TwoBitAdapter'
           const fileName = getFileName(file)
-          if (regexGuess.test(fileName) || adapterHint === adapterName) {
-            return {
-              type: adapterName,
-              twoBitLocation: file,
-            }
+          const obj = {
+            type: adapterName,
+            twoBitLocation: file,
+          }
+          if (regexGuess.test(fileName) && !adapterHint) {
+            return obj
+          } else if (adapterHint === adapterName) {
+            return obj
           }
           return adapterGuesser(file, index, adapterHint)
         }
@@ -139,12 +142,16 @@ export default class SequencePlugin extends Plugin {
           const regexGuess = /\.(fa|fasta|fas|fna|mfa)$/i
           const adapterName = 'IndexedFastaAdapter'
           const fileName = getFileName(file)
-          if (regexGuess.test(fileName) || adapterHint === adapterName) {
-            return {
-              type: adapterName,
-              fastaLocation: file,
-              faiLocation: index || makeIndex(file, '.fai'),
-            }
+          const obj = {
+            type: adapterName,
+            fastaLocation: file,
+            faiLocation: index || makeIndex(file, '.fai'),
+          }
+
+          if (regexGuess.test(fileName) && !adapterHint) {
+            return obj
+          } else if (adapterHint === adapterName) {
+            return obj
           }
           return adapterGuesser(file, index, adapterHint)
         }
@@ -191,12 +198,16 @@ export default class SequencePlugin extends Plugin {
           const regexGuess = /\.(fa|fasta|fas|fna|mfa)\.b?gz$/i
           const adapterName = 'BgzipFastaAdapter'
           const fileName = getFileName(file)
-          if (regexGuess.test(fileName) || adapterHint === adapterName) {
-            return {
-              type: adapterName,
-              faiLocation: makeIndex(file, '.fai'),
-              gziLocation: makeIndex(file, '.gzi'),
-            }
+          const obj = {
+            type: adapterName,
+            faiLocation: makeIndex(file, '.fai'),
+            gziLocation: makeIndex(file, '.gzi'),
+          }
+
+          if (regexGuess.test(fileName) && !adapterHint) {
+            return obj
+          } else if (adapterHint === adapterName) {
+            return obj
           }
           return adapterGuesser(file, index, adapterHint)
         }