@jbrowse/plugin-gccontent 2.6.1 → 2.6.3

package/dist/GCContentAdapter/GCContentAdapter.js

@@ -87,4 +87,3 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
 }
 default_1.capabilities = ['hasLocalStats'];
 exports.default = default_1;
-//# sourceMappingURL=GCContentAdapter.js.map

package/dist/GCContentAdapter/configSchema.js

@@ -18,4 +18,3 @@ const GCContentAdapterF = (pluginManager) => {
     }, { explicitlyTyped: true });
 };
 exports.default = GCContentAdapterF;
-//# sourceMappingURL=configSchema.js.map

package/dist/GCContentAdapter/index.js

@@ -39,4 +39,3 @@ exports.default = (pluginManager) => {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./GCContentAdapter'))).then(r => r.default),
     }));
 };
-//# sourceMappingURL=index.js.map

package/dist/LinearGCContentDisplay/config.js

@@ -16,4 +16,3 @@ function WiggleConfigFactory(pluginManager) {
     });
 }
 exports.default = WiggleConfigFactory;
-//# sourceMappingURL=config.js.map

package/dist/LinearGCContentDisplay/index.js

@@ -22,4 +22,3 @@ exports.default = (pluginManager) => {
         });
     });
 };
-//# sourceMappingURL=index.js.map

package/dist/LinearGCContentDisplay/stateModel.d.ts

@@ -333,7 +333,7 @@ export default function stateModelFactory(pluginManager: PluginManager, configSc
 } & {
     renderProps(): any;
     readonly needsScalebar: boolean;
-    readonly fillSetting: 0 | 1 | 2;
+    readonly fillSetting: 1 | 2 | 0;
 } & {
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
         label: string;

package/dist/LinearGCContentDisplay/stateModel.js

@@ -38,4 +38,3 @@ function stateModelFactory(pluginManager, configSchema) {
     });
 }
 exports.default = stateModelFactory;
-//# sourceMappingURL=stateModel.js.map

package/dist/index.js

@@ -18,4 +18,3 @@ class GCContentPlugin extends Plugin_1.default {
     }
 }
 exports.default = GCContentPlugin;
-//# sourceMappingURL=index.js.map

package/esm/GCContentAdapter/GCContentAdapter.js

@@ -85,4 +85,3 @@ class default_1 extends BaseFeatureDataAdapter {
 }
 default_1.capabilities = ['hasLocalStats'];
 export default default_1;
-//# sourceMappingURL=GCContentAdapter.js.map

package/esm/GCContentAdapter/configSchema.js

@@ -16,4 +16,3 @@ const GCContentAdapterF = (pluginManager) => {
     }, { explicitlyTyped: true });
 };
 export default GCContentAdapterF;
-//# sourceMappingURL=configSchema.js.map

package/esm/GCContentAdapter/index.js

@@ -11,4 +11,3 @@ export default (pluginManager) => {
         getAdapterClass: () => import('./GCContentAdapter').then(r => r.default),
     }));
 };
-//# sourceMappingURL=index.js.map

package/esm/LinearGCContentDisplay/config.js

@@ -13,4 +13,3 @@ export default function WiggleConfigFactory(pluginManager) {
         explicitlyTyped: true,
     });
 }
-//# sourceMappingURL=config.js.map

package/esm/LinearGCContentDisplay/index.js

@@ -17,4 +17,3 @@ export default (pluginManager) => {
         });
     });
 };
-//# sourceMappingURL=index.js.map

package/esm/LinearGCContentDisplay/stateModel.d.ts

@@ -333,7 +333,7 @@ export default function stateModelFactory(pluginManager: PluginManager, configSc
 } & {
     renderProps(): any;
     readonly needsScalebar: boolean;
-    readonly fillSetting: 0 | 1 | 2;
+    readonly fillSetting: 1 | 2 | 0;
 } & {
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
         label: string;

package/esm/LinearGCContentDisplay/stateModel.js

@@ -35,4 +35,3 @@ export default function stateModelFactory(pluginManager, configSchema) {
         };
     });
 }
-//# sourceMappingURL=stateModel.js.map

package/esm/index.js

@@ -12,4 +12,3 @@ export default class GCContentPlugin extends Plugin {
         LinearGCContentDisplayF(pluginManager);
     }
 }
-//# sourceMappingURL=index.js.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gccontent",
-  "version": "2.6.1",
+  "version": "2.6.3",
   "description": "JBrowse 2 gccontent concepts",
   "keywords": [
     "jbrowse",
@@ -20,7 +20,6 @@
   "main": "dist/index.js",
   "files": [
     "dist",
-    "src",
     "esm"
   ],
   "scripts": {
@@ -33,7 +32,7 @@
     "useSrc": "node ../../scripts/useSrc.js",
     "prebuild": "npm run clean",
     "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "peerDependencies": {
@@ -54,5 +53,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
+  "gitHead": "ed402c87efb0904858d602c363bd1757d5742129"
 }

package/dist/GCContentAdapter/GCContentAdapter.js.map

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package/dist/GCContentAdapter/configSchema.js.map

@@ -1 +0,0 @@
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package/dist/GCContentAdapter/index.js.map

@@ -1 +0,0 @@
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package/dist/LinearGCContentDisplay/config.js.map

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package/dist/LinearGCContentDisplay/index.js.map

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package/dist/LinearGCContentDisplay/stateModel.js.map

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package/dist/index.js.map

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package/esm/GCContentAdapter/GCContentAdapter.js.map

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package/src/GCContentAdapter/GCContentAdapter.ts

@@ -1,100 +0,0 @@
-import {
-  BaseFeatureDataAdapter,
-  BaseOptions,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
-import { firstValueFrom } from 'rxjs'
-import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import { SimpleFeature, Feature, Region } from '@jbrowse/core/util'
-import { toArray } from 'rxjs/operators'
-
-export default class extends BaseFeatureDataAdapter {
-  private windowSize = 1000
-
-  private windowDelta = 1000
-
-  private gcMode = 'content'
-
-  public static capabilities = ['hasLocalStats']
-
-  public async configure() {
-    const adapter = await this.getSubAdapter?.(this.getConf('sequenceAdapter'))
-    if (!adapter) {
-      throw new Error('Error getting subadapter')
-    }
-    return adapter.dataAdapter as BaseFeatureDataAdapter
-  }
-
-  public async getRefNames() {
-    const adapter = await this.configure()
-    return adapter.getRefNames()
-  }
-
-  public getFeatures(query: Region, opts: BaseOptions) {
-    return ObservableCreate<Feature>(async observer => {
-      const sequenceAdapter = await this.configure()
-      const hw = this.windowSize === 1 ? 1 : this.windowSize / 2 // Half the window size
-      const f = this.windowSize === 1
-
-      let { start: queryStart, end: queryEnd } = query
-      queryStart = Math.max(0, queryStart - hw)
-      queryEnd += hw
-
-      if (queryEnd < 0 || queryStart > queryEnd) {
-        observer.complete()
-        return
-      }
-
-      const ret = sequenceAdapter.getFeatures(
-        {
-          ...query,
-          start: queryStart,
-          end: queryEnd,
-        },
-        opts,
-      )
-      const feats = await firstValueFrom(ret.pipe(toArray()))
-      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)
-        let nc = 0
-        let ng = 0
-        let len = 0
-        for (let j = 0; j < r.length; j++) {
-          if (r[j] === 'c' || r[j] === 'C') {
-            nc++
-          } else if (r[j] === 'g' || r[j] === 'G') {
-            ng++
-          }
-          if (r[j] !== 'N') {
-            len++
-          }
-        }
-        const pos = queryStart
-        let score
-        if (this.gcMode === 'content') {
-          score = (ng + nc) / (len || 1)
-        } else if (this.gcMode === 'skew') {
-          score = (ng - nc) / (ng + nc || 1)
-        }
-
-        observer.next(
-          new SimpleFeature({
-            uniqueId: `${this.id}_${pos + i}`,
-            start: pos + i,
-            end: pos + i + this.windowDelta,
-            score,
-          }),
-        )
-      }
-      observer.complete()
-    })
-  }
-
-  /**
-   * called to provide a hint that data tied to a certain region
-   * will not be needed for the foreseeable future and can be purged
-   * from caches, etc
-   */
-  public freeResources(/* { region } */) {}
-}

package/src/GCContentAdapter/configSchema.ts

@@ -1,26 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config GCContentAdapter
- * #category adapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const GCContentAdapterF = (pluginManager: PluginManager) => {
-  return ConfigurationSchema(
-    'GCContentAdapter',
-    {
-      /**
-       * #slot
-       */
-      sequenceAdapter: {
-        type: 'frozen',
-        defaultValue: null,
-      },
-    },
-    { explicitlyTyped: true },
-  )
-}
-
-export default GCContentAdapterF

package/src/GCContentAdapter/index.ts

@@ -1,20 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-
-import configSchemaF from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(
-    () =>
-      new AdapterType({
-        name: 'GCContentAdapter',
-        displayName: 'GC content adapter',
-        adapterMetadata: {
-          hiddenFromGUI: true,
-        },
-        configSchema: configSchemaF(pluginManager),
-        getAdapterClass: () =>
-          import('./GCContentAdapter').then(r => r.default),
-      }),
-  )
-}

package/src/LinearGCContentDisplay/config.ts

@@ -1,21 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import PluginManager from '@jbrowse/core/PluginManager'
-
-/**
- * #config LinearGCContentDisplay
- * #category display
- */
-export default function WiggleConfigFactory(pluginManager: PluginManager) {
-  return ConfigurationSchema(
-    'LinearGCContentDisplay',
-    {},
-    {
-      /**
-       * #baseConfiguration
-       */
-      baseConfiguration: pluginManager.getDisplayType('LinearWiggleDisplay')
-        .configSchema,
-      explicitlyTyped: true,
-    },
-  )
-}

package/src/LinearGCContentDisplay/index.ts

@@ -1,22 +0,0 @@
-import { DisplayType } from '@jbrowse/core/pluggableElementTypes'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { LinearWiggleDisplayReactComponent } from '@jbrowse/plugin-wiggle'
-
-import configSchemaFactory from './config'
-import stateModelFactory from './stateModel'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addDisplayType(() => {
-    const configSchema = configSchemaFactory(pluginManager)
-    const stateModel = stateModelFactory(pluginManager, configSchema)
-    return new DisplayType({
-      name: 'LinearGCContentDisplay',
-      configSchema,
-      stateModel,
-      displayName: 'GC content display',
-      trackType: 'ReferenceSequenceTrack',
-      viewType: 'LinearGenomeView',
-      ReactComponent: LinearWiggleDisplayReactComponent,
-    })
-  })
-}

package/src/LinearGCContentDisplay/stateModel.ts

@@ -1,49 +0,0 @@
-import {
-  getConf,
-  AnyConfigurationSchemaType,
-} from '@jbrowse/core/configuration'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { linearWiggleDisplayModelFactory } from '@jbrowse/plugin-wiggle'
-import { types } from 'mobx-state-tree'
-
-/**
- * #stateModel LinearGCContentDisplay
- * #category display
- * base model `BaseWiggleDisplayModel`
- */
-export default function stateModelFactory(
-  pluginManager: PluginManager,
-  configSchema: AnyConfigurationSchemaType,
-) {
-  return types
-    .compose(
-      'LinearGCContentDisplay',
-      linearWiggleDisplayModelFactory(pluginManager, configSchema),
-      types.model({
-        /**
-         * #property
-         */
-        type: types.literal('LinearGCContentDisplay'),
-      }),
-    )
-    .views(self => {
-      const { renderProps: superRenderProps } = self
-      return {
-        /**
-         * #method
-         * retrieves the sequence adapter from parent track, and puts it as a
-         * subadapter on a GCContentAdapter
-         */
-        renderProps() {
-          const sequenceAdapter = getConf(self.parentTrack, 'adapter')
-          return {
-            ...superRenderProps(),
-            adapterConfig: {
-              type: 'GCContentAdapter',
-              sequenceAdapter,
-            },
-          }
-        },
-      }
-    })
-}

package/src/index.ts

@@ -1,15 +0,0 @@
-import Plugin from '@jbrowse/core/Plugin'
-import PluginManager from '@jbrowse/core/PluginManager'
-
-// locals
-import GCContentAdapterF from './GCContentAdapter'
-import LinearGCContentDisplayF from './LinearGCContentDisplay'
-
-export default class GCContentPlugin extends Plugin {
-  name = 'GCContentPlugin'
-
-  install(pluginManager: PluginManager) {
-    GCContentAdapterF(pluginManager)
-    LinearGCContentDisplayF(pluginManager)
-  }
-}