@jbrowse/plugin-circular-view 2.1.7 → 2.2.0

package/esm/CircularView/models/CircularView.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-circular-view",
-  "version": "2.1.7",
+  "version": "2.2.0",
   "description": "JBrowse 2 circular view",
   "keywords": [
     "jbrowse",
@@ -55,5 +55,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "a1344081f61e22e0f597517efa7386023eef9f33"
+  "gitHead": "cf31db8d833117f8822510340664fb3f045975cb"
 }

package/src/BaseChordDisplay/models/BaseChordDisplayModel.ts

@@ -18,219 +18,261 @@ import {
 } from '@jbrowse/core/util/tracks'
 import { Region } from '@jbrowse/core/util/types'
 import { getParent, isAlive, types } from 'mobx-state-tree'
+
+// locals
 import { renderReactionData, renderReactionEffect } from './renderReaction'
 import { CircularViewModel } from '../../CircularView/models/CircularView'
 
-export const BaseChordDisplayModel = types
-  .compose(
-    'BaseChordDisplay',
-    BaseDisplay,
-    types.model({
-      bezierRadiusRatio: 0.1,
-      assemblyName: types.maybe(types.string),
-    }),
-  )
-  .volatile(() => {
-    return {
-      // NOTE: all this volatile stuff has to be filled in at once
-      // so that it stays consistent
-      filled: false,
-      reactElement: undefined as React.ReactElement | undefined,
-      data: undefined,
-      message: '',
-      renderingComponent: undefined as undefined | AnyReactComponentType,
-      refNameMap: undefined as Record<string, string> | undefined,
-    }
-  })
-  .actions(self => {
-    const { pluginManager } = getEnv(self)
-    const track = self
-    return {
-      onChordClick(feature: Feature) {
-        getConf(self, 'onChordClick', { feature, track, pluginManager })
-      },
-    }
-  })
-  .views(self => ({
-    get blockDefinitions() {
-      const origSlices = (getContainingView(self) as CircularViewModel)
-        .staticSlices
-      if (!self.refNameMap) {
-        return origSlices
+/**
+ * #stateModel BaseChordDisplay
+ * extends `BaseDisplay`
+ */
+function stateModelFactory() {
+  return types
+    .compose(
+      'BaseChordDisplay',
+      BaseDisplay,
+      types.model({
+        /**
+         * #property
+         */
+        bezierRadiusRatio: 0.1,
+        /**
+         * #property
+         */
+        assemblyName: types.maybe(types.string),
+      }),
+    )
+    .volatile(() => {
+      return {
+        // NOTE: all this volatile stuff has to be filled in at once
+        // so that it stays consistent
+        filled: false,
+        reactElement: undefined as React.ReactElement | undefined,
+        data: undefined,
+        message: '',
+        renderingComponent: undefined as undefined | AnyReactComponentType,
+        refNameMap: undefined as Record<string, string> | undefined,
+      }
+    })
+    .actions(self => {
+      const { pluginManager } = getEnv(self)
+      const track = self
+      return {
+        /**
+         * #action
+         */
+        onChordClick(feature: Feature) {
+          getConf(self, 'onChordClick', { feature, track, pluginManager })
+        },
       }
+    })
+    .views(self => ({
+      /**
+       * #getter
+       */
+      get blockDefinitions() {
+        const origSlices = (getContainingView(self) as CircularViewModel)
+          .staticSlices
+        if (!self.refNameMap) {
+          return origSlices
+        }
 
-      const slices = JSON.parse(JSON.stringify(origSlices))
+        const slices = JSON.parse(JSON.stringify(origSlices))
 
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      slices.forEach((slice: any) => {
-        const regions = slice.region.elided
-          ? slice.region.regions
-          : [slice.region]
-        regions.forEach((region: Region) => {
-          const renamed = self.refNameMap?.[region.refName]
-          if (renamed && region.refName !== renamed) {
-            region.refName = renamed
-          }
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        slices.forEach((slice: any) => {
+          const regions = slice.region.elided
+            ? slice.region.regions
+            : [slice.region]
+          regions.forEach((region: Region) => {
+            const renamed = self.refNameMap?.[region.refName]
+            if (renamed && region.refName !== renamed) {
+              region.refName = renamed
+            }
+          })
         })
-      })
-      return slices
-    },
+        return slices
+      },
 
-    renderProps() {
-      const view = getContainingView(self) as CircularViewModel
-      return {
-        ...getParentRenderProps(self),
-        rpcDriverName: self.rpcDriverName,
-        displayModel: self,
-        bezierRadius: view.radiusPx * self.bezierRadiusRatio,
-        radius: view.radiusPx,
-        blockDefinitions: this.blockDefinitions,
-        onChordClick: self.onChordClick,
-      }
-    },
+      /**
+       * #method
+       */
+      renderProps() {
+        const view = getContainingView(self) as CircularViewModel
+        return {
+          ...getParentRenderProps(self),
+          rpcDriverName: self.rpcDriverName,
+          displayModel: self,
+          bezierRadius: view.radiusPx * self.bezierRadiusRatio,
+          radius: view.radiusPx,
+          blockDefinitions: this.blockDefinitions,
+          onChordClick: self.onChordClick,
+        }
+      },
 
-    /**
-     * the pluggable element type object for this diplay's
-     * renderer
-     */
-    get rendererType() {
-      const display = self
-      const { pluginManager } = getEnv(self)
-      const ThisRendererType = pluginManager.getRendererType(
-        self.rendererTypeName,
-      )
-      if (!ThisRendererType) {
-        throw new Error(`renderer "${display.rendererTypeName}" not found`)
-      }
-      if (!ThisRendererType.ReactComponent) {
-        throw new Error(
-          `renderer ${display.rendererTypeName} has no ReactComponent, it may not be completely implemented yet`,
+      /**
+       * #getter
+       * the pluggable element type object for this diplay's
+       * renderer
+       */
+      get rendererType() {
+        const display = self
+        const { pluginManager } = getEnv(self)
+        const ThisRendererType = pluginManager.getRendererType(
+          self.rendererTypeName,
         )
-      }
-      return ThisRendererType
-    },
+        if (!ThisRendererType) {
+          throw new Error(`renderer "${display.rendererTypeName}" not found`)
+        }
+        if (!ThisRendererType.ReactComponent) {
+          throw new Error(
+            `renderer ${display.rendererTypeName} has no ReactComponent, it may not be completely implemented yet`,
+          )
+        }
+        return ThisRendererType
+      },
 
-    isCompatibleWithRenderer(renderer: RendererType) {
-      return !!(renderer instanceof CircularChordRendererType)
-    },
+      /**
+       * #method
+       */
+      isCompatibleWithRenderer(renderer: RendererType) {
+        return !!(renderer instanceof CircularChordRendererType)
+      },
 
-    /**
-     * returns a string feature ID if the globally-selected object
-     * is probably a feature
-     */
-    get selectedFeatureId() {
-      if (!isAlive(self)) {
+      /**
+       * #getter
+       * returns a string feature ID if the globally-selected object
+       * is probably a feature
+       */
+      get selectedFeatureId() {
+        if (!isAlive(self)) {
+          return undefined
+        }
+        const session = getSession(self)
+        if (!session) {
+          return undefined
+        }
+        const { selection } = session
+        // does it quack like a feature?
+        if (isFeature(selection)) {
+          return selection.id()
+        }
         return undefined
-      }
-      const session = getSession(self)
-      if (!session) {
-        return undefined
-      }
-      const { selection } = session
-      // does it quack like a feature?
-      if (isFeature(selection)) {
-        return selection.id()
-      }
-      return undefined
-    },
-  }))
-  .actions(self => ({
-    renderStarted() {
-      self.filled = false
-      self.message = ''
-      self.reactElement = undefined
-      self.data = undefined
-      self.error = undefined
-      self.renderingComponent = undefined
-    },
-    renderSuccess({
-      message,
-      data,
-      reactElement,
-      renderingComponent,
-    }: {
-      message: string
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      data: any
-      reactElement: React.ReactElement
-      renderingComponent: AnyReactComponentType
-    }) {
-      if (message) {
+      },
+    }))
+    .actions(self => ({
+      /**
+       * #action
+       */
+      renderStarted() {
         self.filled = false
-        self.message = message
+        self.message = ''
         self.reactElement = undefined
         self.data = undefined
         self.error = undefined
         self.renderingComponent = undefined
-      } else {
-        self.filled = true
+      },
+      /**
+       * #action
+       */
+      renderSuccess({
+        message,
+        data,
+        reactElement,
+        renderingComponent,
+      }: {
+        message: string
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        data: any
+        reactElement: React.ReactElement
+        renderingComponent: AnyReactComponentType
+      }) {
+        if (message) {
+          self.filled = false
+          self.message = message
+          self.reactElement = undefined
+          self.data = undefined
+          self.error = undefined
+          self.renderingComponent = undefined
+        } else {
+          self.filled = true
+          self.message = ''
+          self.reactElement = reactElement
+          self.data = data
+          self.error = undefined
+          self.renderingComponent = renderingComponent
+        }
+      },
+      /**
+       * #action
+       */
+      renderError(error: unknown) {
+        console.error(error)
+        // the rendering failed for some reason
+        self.filled = false
         self.message = ''
-        self.reactElement = reactElement
-        self.data = data
-        self.error = undefined
-        self.renderingComponent = renderingComponent
-      }
-    },
-    renderError(error: unknown) {
-      console.error(error)
-      // the rendering failed for some reason
-      self.filled = false
-      self.message = ''
-      self.reactElement = undefined
-      self.data = undefined
-      self.error = error
-      self.renderingComponent = undefined
-    },
+        self.reactElement = undefined
+        self.data = undefined
+        self.error = error
+        self.renderingComponent = undefined
+      },
 
-    setRefNameMap(refNameMap: Record<string, string>) {
-      self.refNameMap = refNameMap
-    },
-  }))
-  .actions(self => ({
-    afterAttach() {
-      makeAbortableReaction(
-        self,
-        renderReactionData,
+      /**
+       * #action
+       */
+      setRefNameMap(refNameMap: Record<string, string>) {
+        self.refNameMap = refNameMap
+      },
+    }))
+    .actions(self => ({
+      afterAttach() {
+        makeAbortableReaction(
+          self,
+          renderReactionData,
 
-        // @ts-ignore
-        renderReactionEffect,
-        {
-          name: `${self.type} ${self.id} rendering`,
-          // delay: self.renderDelay || 300,
-          fireImmediately: true,
-        },
-        self.renderStarted,
-        self.renderSuccess,
-        self.renderError,
-      )
-      makeAbortableReaction(
-        self,
-        () => ({
-          assemblyNames: getTrackAssemblyNames(self.parentTrack) as string[],
+          // @ts-ignore
+          renderReactionEffect,
+          {
+            name: `${self.type} ${self.id} rendering`,
+            // delay: self.renderDelay || 300,
+            fireImmediately: true,
+          },
+          self.renderStarted,
+          self.renderSuccess,
+          self.renderError,
+        )
+        makeAbortableReaction(
+          self,
+          () => ({
+            assemblyNames: getTrackAssemblyNames(self.parentTrack) as string[],
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            adapter: getConf(getParent<any>(self, 2), 'adapter'),
+            assemblyManager: getSession(self).assemblyManager,
+          }),
           // eslint-disable-next-line @typescript-eslint/no-explicit-any
-          adapter: getConf(getParent<any>(self, 2), 'adapter'),
-          assemblyManager: getSession(self).assemblyManager,
-        }),
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        async ({ assemblyNames, adapter, assemblyManager }: any, signal) => {
-          return assemblyManager.getRefNameMapForAdapter(
-            adapter,
-            assemblyNames[0],
-            { signal, sessionId: getRpcSessionId(self) },
-          )
-        },
-        {
-          name: `${self.type} ${self.id} getting refNames`,
-          fireImmediately: true,
-        },
-        () => {},
-        refNameMap => {
-          self.setRefNameMap(refNameMap)
-        },
-        error => {
-          console.error(error)
-          self.setError(error)
-        },
-      )
-    },
-  }))
+          async ({ assemblyNames, adapter, assemblyManager }: any, signal) => {
+            return assemblyManager.getRefNameMapForAdapter(
+              adapter,
+              assemblyNames[0],
+              { signal, sessionId: getRpcSessionId(self) },
+            )
+          },
+          {
+            name: `${self.type} ${self.id} getting refNames`,
+            fireImmediately: true,
+          },
+          () => {},
+          refNameMap => {
+            self.setRefNameMap(refNameMap)
+          },
+          error => {
+            console.error(error)
+            self.setError(error)
+          },
+        )
+      },
+    }))
+}
+
+export const BaseChordDisplayModel = stateModelFactory()

package/src/BaseChordDisplay/models/baseChordDisplayConfig.ts

@@ -1,8 +1,16 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 
+/**
+ * #config BaseChordDisplay
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
 const baseChordDisplayConfig = ConfigurationSchema(
   'BaseChordDisplay',
   {
+    /**
+     * #slot
+     */
     onChordClick: {
       type: 'boolean',
       description:
@@ -11,7 +19,12 @@ const baseChordDisplayConfig = ConfigurationSchema(
       contextVariable: ['feature', 'track', 'pluginManager'],
     },
   },
-  { explicitIdentifier: 'displayId' },
+  {
+    /**
+     * #identifier
+     */
+    explicitIdentifier: 'displayId',
+  },
 )
 
 export { baseChordDisplayConfig }

package/src/CircularView/components/ImportForm.tsx

@@ -54,7 +54,7 @@ const ImportForm = observer(({ model }: { model: any }) => {
             variant="contained"
             color="primary"
           >
-            {regions.length ? 'Open' : 'Loading…'}
+            {regions.length ? 'Open' : 'Loading…'}
           </Button>
         </Grid>
       </Grid>