@jbrowse/plugin-variants 2.1.0 → 2.1.2

package/src/VcfTabixAdapter/index.ts

@@ -1 +1,16 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
+import configSchema from './configSchema'
+
 export { default as configSchema } from './configSchema'
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addAdapterType(
+    () =>
+      new AdapterType({
+        name: 'VcfTabixAdapter',
+        configSchema,
+        getAdapterClass: () => import('./VcfTabixAdapter').then(r => r.default),
+      }),
+  )
+}

package/src/__snapshots__/index.test.js.snap

@@ -5,14 +5,14 @@ exports[`plugin in a stock JBrowse 1`] = `Object {}`;
 exports[`plugin in a stock JBrowse 2`] = `
 Object {
   "displays": Array [
-    Object {
-      "displayId": "trackId0-ChordVariantDisplay",
-      "type": "ChordVariantDisplay",
-    },
     Object {
       "displayId": "trackId0-LinearVariantDisplay",
       "type": "LinearVariantDisplay",
     },
+    Object {
+      "displayId": "trackId0-ChordVariantDisplay",
+      "type": "ChordVariantDisplay",
+    },
   ],
   "trackId": "trackId0",
   "type": "VariantTrack",

package/src/extensionPoints.ts

@@ -0,0 +1,74 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import { FileLocation } from '@jbrowse/core/util/types'
+import {
+  makeIndex,
+  makeIndexType,
+  getFileName,
+  AdapterGuesser,
+  TrackTypeGuesser,
+} from '@jbrowse/core/util/tracks'
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addToExtensionPoint(
+    'Core-guessAdapterForLocation',
+    (adapterGuesser: AdapterGuesser) => {
+      return (
+        file: FileLocation,
+        index?: FileLocation,
+        adapterHint?: string,
+      ) => {
+        const regexGuess = /\.vcf\.b?gz$/i
+        const adapterName = 'VcfTabixAdapter'
+        const fileName = getFileName(file)
+        const indexName = index && getFileName(index)
+        const obj = {
+          type: adapterName,
+          vcfGzLocation: file,
+          index: {
+            location: index || makeIndex(file, '.tbi'),
+            indexType: makeIndexType(indexName, 'CSI', 'TBI'),
+          },
+        }
+        if (regexGuess.test(fileName) && !adapterHint) {
+          return obj
+        } else if (adapterHint === adapterName) {
+          return obj
+        }
+        return adapterGuesser(file, index, adapterHint)
+      }
+    },
+  )
+  pluginManager.addToExtensionPoint(
+    'Core-guessTrackTypeForLocation',
+    (trackTypeGuesser: TrackTypeGuesser) => {
+      return (adapterName: string) => {
+        if (adapterName === 'VcfTabixAdapter' || adapterName === 'VcfAdapter') {
+          return 'VariantTrack'
+        }
+        return trackTypeGuesser(adapterName)
+      }
+    },
+  )
+
+  pluginManager.addToExtensionPoint(
+    'Core-guessAdapterForLocation',
+    (adapterGuesser: AdapterGuesser) => {
+      return (
+        file: FileLocation,
+        index?: FileLocation,
+        adapterHint?: string,
+      ) => {
+        const regexGuess = /\.vcf$/i
+        const adapterName = 'VcfAdapter'
+        const fileName = getFileName(file)
+        if (regexGuess.test(fileName) || adapterHint === adapterName) {
+          return {
+            type: adapterName,
+            vcfLocation: file,
+          }
+        }
+        return adapterGuesser(file, index, adapterHint)
+      }
+    },
+  )
+}

package/src/index.ts

@@ -1,175 +1,32 @@
-import { lazy } from 'react'
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
-import {
-  createBaseTrackConfig,
-  createBaseTrackModel,
-} from '@jbrowse/core/pluggableElementTypes/models'
-import { FileLocation } from '@jbrowse/core/util/types'
-import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType'
-import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType'
+import VcfAdapterF from './VcfAdapter'
+import VcfTabixAdapterF from './VcfTabixAdapter'
+import ExtensionPointsF from './extensionPoints'
+import VariantTrackF from './VariantTrack'
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
-import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view'
 import ChordVariantDisplay from './ChordVariantDisplay'
-import {
-  configSchemaFactory as linearVariantDisplayConfigSchemaFactory,
-  modelFactory as linearVariantDisplayModelFactory,
-} from './LinearVariantDisplay'
+import LinearVariantDisplayF from './LinearVariantDisplay'
 import StructuralVariantChordRendererFactory from './StructuralVariantChordRenderer'
-import {
-  configSchema as variantFeatureWidgetConfigSchema,
-  stateModelFactory as variantFeatureWidgetStateModelFactory,
-} from './VariantFeatureWidget'
-import { configSchema as vcfTabixAdapterConfigSchema } from './VcfTabixAdapter'
-import { configSchema as vcfAdapterConfigSchema } from './VcfAdapter'
-import {
-  makeIndex,
-  makeIndexType,
-  AdapterGuesser,
-  getFileName,
-  TrackTypeGuesser,
-} from '@jbrowse/core/util/tracks'
+import VariantFeatureWidgetF from './VariantFeatureWidget'
 
 export default class VariantsPlugin extends Plugin {
   name = 'VariantsPlugin'
 
   install(pluginManager: PluginManager) {
-    pluginManager.addAdapterType(
-      () =>
-        new AdapterType({
-          name: 'VcfTabixAdapter',
-          configSchema: vcfTabixAdapterConfigSchema,
-          getAdapterClass: () =>
-            import('./VcfTabixAdapter/VcfTabixAdapter').then(r => r.default),
-        }),
-    )
-    pluginManager.addToExtensionPoint(
-      'Core-guessAdapterForLocation',
-      (adapterGuesser: AdapterGuesser) => {
-        return (
-          file: FileLocation,
-          index?: FileLocation,
-          adapterHint?: string,
-        ) => {
-          const regexGuess = /\.vcf\.b?gz$/i
-          const adapterName = 'VcfTabixAdapter'
-          const fileName = getFileName(file)
-          const indexName = index && getFileName(index)
-          const obj = {
-            type: adapterName,
-            vcfGzLocation: file,
-            index: {
-              location: index || makeIndex(file, '.tbi'),
-              indexType: makeIndexType(indexName, 'CSI', 'TBI'),
-            },
-          }
-          if (regexGuess.test(fileName) && !adapterHint) {
-            return obj
-          } else if (adapterHint === adapterName) {
-            return obj
-          }
-          return adapterGuesser(file, index, adapterHint)
-        }
-      },
-    )
-    pluginManager.addToExtensionPoint(
-      'Core-guessTrackTypeForLocation',
-      (trackTypeGuesser: TrackTypeGuesser) => {
-        return (adapterName: string) => {
-          if (
-            adapterName === 'VcfTabixAdapter' ||
-            adapterName === 'VcfAdapter'
-          ) {
-            return 'VariantTrack'
-          }
-          return trackTypeGuesser(adapterName)
-        }
-      },
-    )
-
-    pluginManager.addAdapterType(
-      () =>
-        new AdapterType({
-          name: 'VcfAdapter',
-          configSchema: vcfAdapterConfigSchema,
-          getAdapterClass: () =>
-            import('./VcfAdapter/VcfAdapter').then(r => r.default),
-        }),
-    )
-
-    pluginManager.addToExtensionPoint(
-      'Core-guessAdapterForLocation',
-      (adapterGuesser: AdapterGuesser) => {
-        return (
-          file: FileLocation,
-          index?: FileLocation,
-          adapterHint?: string,
-        ) => {
-          const regexGuess = /\.vcf$/i
-          const adapterName = 'VcfAdapter'
-          const fileName = getFileName(file)
-          if (regexGuess.test(fileName) || adapterHint === adapterName) {
-            return {
-              type: adapterName,
-              vcfLocation: file,
-            }
-          }
-          return adapterGuesser(file, index, adapterHint)
-        }
-      },
-    )
+    VcfAdapterF(pluginManager)
+    VcfTabixAdapterF(pluginManager)
+    VariantFeatureWidgetF(pluginManager)
+    VariantTrackF(pluginManager)
+    ExtensionPointsF(pluginManager)
+    LinearVariantDisplayF(pluginManager)
 
     pluginManager.addRendererType(() =>
       pluginManager.jbrequire(StructuralVariantChordRendererFactory),
     )
-    pluginManager.addTrackType(() => {
-      const configSchema = ConfigurationSchema(
-        'VariantTrack',
-        {},
-        { baseConfiguration: createBaseTrackConfig(pluginManager) },
-      )
-      return new TrackType({
-        name: 'VariantTrack',
-        configSchema,
-        stateModel: createBaseTrackModel(
-          pluginManager,
-          'VariantTrack',
-          configSchema,
-        ),
-      })
-    })
 
     pluginManager.addDisplayType(() =>
       pluginManager.jbrequire(ChordVariantDisplay),
     )
-
-    pluginManager.addDisplayType(() => {
-      const configSchema =
-        linearVariantDisplayConfigSchemaFactory(pluginManager)
-      return new DisplayType({
-        name: 'LinearVariantDisplay',
-        configSchema,
-        stateModel: linearVariantDisplayModelFactory(configSchema),
-        trackType: 'VariantTrack',
-        viewType: 'LinearGenomeView',
-        ReactComponent: BaseLinearDisplayComponent,
-      })
-    })
-
-    pluginManager.addWidgetType(
-      () =>
-        new WidgetType({
-          name: 'VariantFeatureWidget',
-          heading: 'Feature details',
-          configSchema: variantFeatureWidgetConfigSchema,
-          stateModel: variantFeatureWidgetStateModelFactory(pluginManager),
-          ReactComponent: lazy(
-            () => import('./VariantFeatureWidget/VariantFeatureWidget'),
-          ),
-        }),
-    )
   }
 }