@jbrowse/plugin-linear-genome-view 2.2.0 → 2.2.2

package/src/LinearGenomeView/{index.tsx → model.ts}

@@ -22,7 +22,7 @@ import { BlockSet, BaseBlock } from '@jbrowse/core/util/blockTypes'
 import calculateDynamicBlocks from '@jbrowse/core/util/calculateDynamicBlocks'
 import calculateStaticBlocks from '@jbrowse/core/util/calculateStaticBlocks'
 import { getParentRenderProps } from '@jbrowse/core/util/tracks'
-import { transaction, autorun } from 'mobx'
+import { when, transaction, autorun } from 'mobx'
 import {
   addDisposer,
   cast,
@@ -59,6 +59,7 @@ import Header from './components/Header'
 import ZoomControls from './components/ZoomControls'
 import LinearGenomeView from './components/LinearGenomeView'
 
+// lazies
 const SequenceSearchDialog = lazy(
   () => import('./components/SequenceSearchDialog'),
 )
@@ -136,8 +137,11 @@ export function stateModelFactory(pluginManager: PluginManager) {
 
         /**
          * #property
+         * this is a string instead of the const literal 'LinearGenomeView' to reduce some
+         * typescripting strictness, but you should pass the string 'LinearGenomeView' to
+         * the model explicitly
          */
-        type: types.literal('LinearGenomeView'),
+        type: types.literal('LinearGenomeView') as unknown as string,
 
         /**
          * #property
@@ -274,16 +278,25 @@ export function stateModelFactory(pluginManager: PluginManager) {
       },
     }))
     .views(self => ({
+      /**
+       * #method
+       */
       // eslint-disable-next-line @typescript-eslint/no-explicit-any
       MiniControlsComponent(): React.FC<any> {
         return MiniControls
       },
 
+      /**
+       * #method
+       */
       // eslint-disable-next-line @typescript-eslint/no-explicit-any
       HeaderComponent(): React.FC<any> {
         return Header
       },
 
+      /**
+       * #getter
+       */
       get assemblyErrors() {
         const { assemblyManager } = getSession(self)
         const { assemblyNames } = self
@@ -293,23 +306,46 @@ export function stateModelFactory(pluginManager: PluginManager) {
           .join(', ')
       },
 
+      /**
+       * #getter
+       */
       get assembliesInitialized() {
         const { assemblyManager } = getSession(self)
         const { assemblyNames } = self
         return assemblyNames.every(a => assemblyManager.get(a)?.initialized)
       },
+
+      /**
+       * #getter
+       */
       get initialized() {
         return self.volatileWidth !== undefined && this.assembliesInitialized
       },
+
+      /**
+       * #getter
+       */
       get hasDisplayedRegions() {
         return self.displayedRegions.length > 0
       },
+
+      /**
+       * #getter
+       */
       get isSearchDialogDisplayed() {
         return self.searchResults !== undefined
       },
+
+      /**
+       * #getter
+       */
       get scaleBarHeight() {
         return SCALE_BAR_HEIGHT + RESIZE_HANDLE_HEIGHT
       },
+
+      /**
+       * #getter
+       */
       get headerHeight() {
         if (self.hideHeader) {
           return 0
@@ -319,15 +355,26 @@ export function stateModelFactory(pluginManager: PluginManager) {
         }
         return HEADER_BAR_HEIGHT + HEADER_OVERVIEW_HEIGHT
       },
+
+      /**
+       * #getter
+       */
       get trackHeights() {
         return self.tracks
           .map(t => t.displays[0].height)
           .reduce((a, b) => a + b, 0)
       },
 
+      /**
+       * #getter
+       */
       get trackHeightsWithResizeHandles() {
         return this.trackHeights + self.tracks.length * RESIZE_HANDLE_HEIGHT
       },
+
+      /**
+       * #getter
+       */
       get height() {
         return (
           this.trackHeightsWithResizeHandles +
@@ -335,38 +382,63 @@ export function stateModelFactory(pluginManager: PluginManager) {
           this.scaleBarHeight
         )
       },
+
+      /**
+       * #getter
+       */
       get totalBp() {
         return self.displayedRegions.reduce((a, b) => a + b.end - b.start, 0)
       },
 
+      /**
+       * #getter
+       */
       get maxBpPerPx() {
         return this.totalBp / (self.width * 0.9)
       },
 
+      /**
+       * #getter
+       */
       get minBpPerPx() {
         return 1 / 50
       },
 
+      /**
+       * #getter
+       */
       get error() {
         return self.volatileError || this.assemblyErrors
       },
 
+      /**
+       * #getter
+       */
       get maxOffset() {
         // objectively determined to keep the linear genome on the main screen
         const leftPadding = 10
         return this.displayedRegionsTotalPx - leftPadding
       },
 
+      /**
+       * #getter
+       */
       get minOffset() {
         // objectively determined to keep the linear genome on the main screen
         const rightPadding = 30
         return -self.width + rightPadding
       },
 
+      /**
+       * #getter
+       */
       get displayedRegionsTotalPx() {
         return this.totalBp / self.bpPerPx
       },
 
+      /**
+       * #method
+       */
       renderProps() {
         return {
           ...getParentRenderProps(self),
@@ -378,6 +450,9 @@ export function stateModelFactory(pluginManager: PluginManager) {
         }
       },
 
+      /**
+       * #method
+       */
       searchScope(assemblyName: string) {
         return {
           assemblyName,
@@ -386,10 +461,16 @@ export function stateModelFactory(pluginManager: PluginManager) {
         }
       },
 
+      /**
+       * #method
+       */
       getTrack(id: string) {
         return self.tracks.find(t => t.configuration.trackId === id)
       },
 
+      /**
+       * #method
+       */
       rankSearchResults(results: BaseResult[]) {
         // order of rank
         const openTrackIds = self.tracks.map(
@@ -403,7 +484,10 @@ export function stateModelFactory(pluginManager: PluginManager) {
         return results
       },
 
-      // modifies view menu action onClick to apply to all tracks of same type
+      /**
+       * #method
+       * modifies view menu action onClick to apply to all tracks of same type
+       */
       rewriteOnClicks(trackType: string, viewMenuActions: MenuItem[]) {
         viewMenuActions.forEach(action => {
           // go to lowest level menu
@@ -422,7 +506,9 @@ export function stateModelFactory(pluginManager: PluginManager) {
           }
         })
       },
-
+      /**
+       * #getter
+       */
       get trackTypeActions() {
         const allActions: Map<string, MenuItem[]> = new Map()
         self.tracks.forEach(track => {
@@ -609,7 +695,9 @@ export function stateModelFactory(pluginManager: PluginManager) {
         }
         return t[0]
       },
-
+      /**
+       * #action
+       */
       hideTrack(trackId: string) {
         const schema = pluginManager.pluggableConfigSchemaType('track')
         const conf = resolveIdentifier(schema, getRoot(self), trackId)
@@ -973,59 +1061,57 @@ export function stateModelFactory(pluginManager: PluginManager) {
             icon: SyncAltIcon,
             onClick: self.horizontallyFlip,
           },
-          { type: 'divider' },
-          {
-            label: 'Show all regions in assembly',
-            icon: VisibilityIcon,
-            onClick: self.showAllRegionsInAssembly,
-          },
-          {
-            label: 'Show center line',
-            icon: VisibilityIcon,
-            type: 'checkbox',
-            checked: self.showCenterLine,
-            onClick: self.toggleCenterLine,
-          },
-          {
-            label: 'Show header',
-            icon: VisibilityIcon,
-            type: 'checkbox',
-            checked: !self.hideHeader,
-            onClick: self.toggleHeader,
-          },
-          {
-            label: 'Show header overview',
-            icon: VisibilityIcon,
-            type: 'checkbox',
-            checked: !self.hideHeaderOverview,
-            onClick: self.toggleHeaderOverview,
-            disabled: self.hideHeader,
-          },
-          {
-            label: 'Show no tracks active button',
-            icon: VisibilityIcon,
-            type: 'checkbox',
-            checked: !self.hideNoTracksActive,
-            onClick: self.toggleNoTracksActive,
-          },
           {
-            label: 'Show guidelines',
+            label: 'Show...',
             icon: VisibilityIcon,
-            type: 'checkbox',
-            checked: self.showGridlines,
-            onClick: self.toggleShowGridlines,
+            subMenu: [
+              {
+                label: 'Show all regions in assembly',
+                onClick: self.showAllRegionsInAssembly,
+              },
+              {
+                label: 'Show center line',
+                type: 'checkbox',
+                checked: self.showCenterLine,
+                onClick: self.toggleCenterLine,
+              },
+              {
+                label: 'Show header',
+                type: 'checkbox',
+                checked: !self.hideHeader,
+                onClick: self.toggleHeader,
+              },
+              {
+                label: 'Show header overview',
+                type: 'checkbox',
+                checked: !self.hideHeaderOverview,
+                onClick: self.toggleHeaderOverview,
+                disabled: self.hideHeader,
+              },
+              {
+                label: 'Show no tracks active button',
+                type: 'checkbox',
+                checked: !self.hideNoTracksActive,
+                onClick: self.toggleNoTracksActive,
+              },
+              {
+                label: 'Show guidelines',
+                type: 'checkbox',
+                checked: self.showGridlines,
+                onClick: self.toggleShowGridlines,
+              },
+              ...(canShowCytobands
+                ? [
+                    {
+                      label: 'Show ideogram',
+                      type: 'checkbox' as const,
+                      checked: self.showCytobands,
+                      onClick: () => self.setShowCytobands(!showCytobands),
+                    },
+                  ]
+                : []),
+            ],
           },
-          ...(canShowCytobands
-            ? [
-                {
-                  label: 'Show ideogram',
-                  icon: VisibilityIcon,
-                  type: 'checkbox' as const,
-                  checked: self.showCytobands,
-                  onClick: () => self.setShowCytobands(!showCytobands),
-                },
-              ]
-            : []),
           {
             label: 'Track labels',
             icon: LabelIcon,
@@ -1181,6 +1267,7 @@ export function stateModelFactory(pluginManager: PluginManager) {
         const { assemblyNames } = self
         const { assemblyManager } = getSession(self)
         const { isValidRefName } = assemblyManager
+        await when(() => self.volatileWidth !== undefined)
         const assemblyName = optAssemblyName || assemblyNames[0]
         let parsedLocStrings
         const inputs = locString
@@ -1195,8 +1282,8 @@ export function stateModelFactory(pluginManager: PluginManager) {
         // first try interpreting as a whitespace-separated sequence of
         // multiple locstrings
         try {
-          parsedLocStrings = inputs.map(l =>
-            parseLocString(l, ref => isValidRefName(ref, assemblyName)),
+          parsedLocStrings = inputs.map(loc =>
+            parseLocString(loc, ref => isValidRefName(ref, assemblyName)),
           )
         } catch (e) {
           // if this fails, try interpreting as a whitespace-separated refname,
@@ -1375,18 +1462,14 @@ export function stateModelFactory(pluginManager: PluginManager) {
               )
               return
             }
-            let locationIndex = 0
-            let locationStart = 0
-            let locationEnd = 0
-            for (
-              locationIndex;
-              locationIndex < locations.length;
-              locationIndex++
-            ) {
-              const location = locations[locationIndex]
-              const region = self.displayedRegions[index + locationIndex]
-              locationStart = location.start || region.start
-              locationEnd = location.end || region.end
+            let idx = 0
+            let start = 0
+            let end = 0
+            for (idx; idx < locations.length; idx++) {
+              const location = locations[idx]
+              const region = self.displayedRegions[index + idx]
+              start = location.start || region.start
+              end = location.end || region.end
               if (location.refName !== region.refName) {
                 throw new Error(
                   `Entered location ${assembleLocString(
@@ -1395,10 +1478,9 @@ export function stateModelFactory(pluginManager: PluginManager) {
                 )
               }
             }
-            locationIndex -= 1
+            idx -= 1
             const startDisplayedRegion = self.displayedRegions[index]
-            const endDisplayedRegion =
-              self.displayedRegions[index + locationIndex]
+            const endDisplayedRegion = self.displayedRegions[index + idx]
             this.moveTo(
               {
                 index,
@@ -1407,10 +1489,10 @@ export function stateModelFactory(pluginManager: PluginManager) {
                   : s - startDisplayedRegion.start,
               },
               {
-                index: index + locationIndex,
+                index: index + idx,
                 offset: endDisplayedRegion.reversed
-                  ? endDisplayedRegion.end - locationStart
-                  : locationEnd - endDisplayedRegion.start,
+                  ? endDisplayedRegion.end - start
+                  : end - endDisplayedRegion.start,
               },
             )
             return
@@ -1503,6 +1585,8 @@ export {
   ZoomControls,
   LinearGenomeView,
 }
+
 export type LinearGenomeViewStateModel = ReturnType<typeof stateModelFactory>
 export type LinearGenomeViewModel = Instance<LinearGenomeViewStateModel>
+
 export { default as ReactComponent } from './components/LinearGenomeView'

package/src/index.ts

@@ -1,42 +1,36 @@
-import { lazy } from 'react'
-import { when } from 'mobx'
-
-import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
-import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType'
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { AbstractSessionModel, isAbstractMenuManager } from '@jbrowse/core/util'
+
+// icons
 import LineStyleIcon from '@mui/icons-material/LineStyle'
+
 import {
   BaseLinearDisplay,
   BaseLinearDisplayComponent,
-  baseLinearDisplayConfigSchema,
   BlockModel,
+  baseLinearDisplayConfigSchema,
 } from './BaseLinearDisplay'
-import {
+import LinearBareDisplayF, {
   configSchemaFactory as linearBareDisplayConfigSchemaFactory,
-  stateModelFactory as LinearBareDisplayStateModelFactory,
 } from './LinearBareDisplay'
-import {
+import LinearGenomeViewF, {
+  renderToSvg,
   LinearGenomeViewModel,
   LinearGenomeViewStateModel,
-  stateModelFactory as linearGenomeViewStateModelFactory,
-  renderToSvg,
   RefNameAutocomplete,
   SearchBox,
   ZoomControls,
   LinearGenomeView,
 } from './LinearGenomeView'
-
-import {
+import LinearBasicDisplayF, {
   configSchema as linearBasicDisplayConfigSchemaFactory,
   modelFactory as linearBasicDisplayModelFactory,
 } from './LinearBasicDisplay'
 
 import FeatureTrackF from './FeatureTrack'
 import BasicTrackF from './BasicTrack'
-
-type LGV = LinearGenomeViewModel
+import LaunchLinearGenomeViewF from './LaunchLinearGenomeView'
 
 export default class LinearGenomeViewPlugin extends Plugin {
   name = 'LinearGenomeViewPlugin'
@@ -53,99 +47,10 @@ export default class LinearGenomeViewPlugin extends Plugin {
   install(pluginManager: PluginManager) {
     FeatureTrackF(pluginManager)
     BasicTrackF(pluginManager)
-    pluginManager.addDisplayType(() => {
-      const configSchema = linearBareDisplayConfigSchemaFactory(pluginManager)
-      return new DisplayType({
-        name: 'LinearBareDisplay',
-        configSchema,
-        stateModel: LinearBareDisplayStateModelFactory(configSchema),
-        trackType: 'BasicTrack',
-        viewType: 'LinearGenomeView',
-        ReactComponent: BaseLinearDisplayComponent,
-      })
-    })
-
-    pluginManager.addDisplayType(() => {
-      const configSchema = linearBasicDisplayConfigSchemaFactory(pluginManager)
-      return new DisplayType({
-        name: 'LinearBasicDisplay',
-        configSchema,
-        stateModel: linearBasicDisplayModelFactory(configSchema),
-        trackType: 'FeatureTrack',
-        viewType: 'LinearGenomeView',
-        ReactComponent: BaseLinearDisplayComponent,
-      })
-    })
-
-    pluginManager.addViewType(
-      () =>
-        new ViewType({
-          name: 'LinearGenomeView',
-          stateModel: linearGenomeViewStateModelFactory(pluginManager),
-          ReactComponent: lazy(
-            () => import('./LinearGenomeView/components/LinearGenomeView'),
-          ),
-        }),
-    )
-
-    pluginManager.addToExtensionPoint(
-      'LaunchView-LinearGenomeView',
-      // @ts-ignore
-      async ({
-        session,
-        assembly,
-        loc,
-        tracks = [],
-      }: {
-        session: AbstractSessionModel
-        assembly?: string
-        loc: string
-        tracks?: string[]
-      }) => {
-        try {
-          const { assemblyManager } = session
-          const view = session.addView('LinearGenomeView', {}) as LGV
-
-          await when(() => !!view.volatileWidth)
-
-          if (!assembly) {
-            throw new Error(
-              'No assembly provided when launching linear genome view',
-            )
-          }
-
-          const asm = await assemblyManager.waitForAssembly(assembly)
-          if (!asm) {
-            throw new Error(
-              `Assembly "${assembly}" not found when launching linear genome view`,
-            )
-          }
-
-          view.navToLocString(loc, assembly)
-
-          const idsNotFound = [] as string[]
-          tracks.forEach(track => {
-            try {
-              view.showTrack(track)
-            } catch (e) {
-              if (`${e}`.match('Could not resolve identifier')) {
-                idsNotFound.push(track)
-              } else {
-                throw e
-              }
-            }
-          })
-          if (idsNotFound.length) {
-            throw new Error(
-              `Could not resolve identifiers: ${idsNotFound.join(',')}`,
-            )
-          }
-        } catch (e) {
-          session.notify(`${e}`, 'error')
-          throw e
-        }
-      },
-    )
+    LinearBasicDisplayF(pluginManager)
+    LinearGenomeViewF(pluginManager)
+    LinearBareDisplayF(pluginManager)
+    LaunchLinearGenomeViewF(pluginManager)
   }
 
   configure(pluginManager: PluginManager) {

package/dist/LinearGenomeView/components/OverviewRubberBand.js.map

@@ -1 +0,0 @@
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package/dist/LinearGenomeView/components/OverviewScaleBar.js.map

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