@jbrowse/plugin-linear-genome-view 1.7.9 → 2.0.0

package/src/LinearGenomeView/components/util.ts

@@ -1,4 +1,8 @@
+import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
+import { SearchType } from '@jbrowse/core/data_adapters/BaseAdapter'
 import BaseResult from '@jbrowse/core/TextSearch/BaseResults'
+import { SearchScope } from '@jbrowse/core/TextSearch/TextSearchManager'
+import { TextSearchManager } from '@jbrowse/core/util'
 
 export function dedupe(
   results: BaseResult[] = [],
@@ -8,3 +12,42 @@ export function dedupe(
     (elt, idx, self) => idx === self.findIndex(t => cb(t) === cb(elt)),
   )
 }
+
+export async function fetchResults({
+  queryString,
+  searchType,
+  searchScope,
+  rankSearchResults,
+  textSearchManager,
+  assembly,
+}: {
+  queryString: string
+  searchScope: SearchScope
+  rankSearchResults: (results: BaseResult[]) => BaseResult[]
+  searchType?: SearchType
+  textSearchManager?: TextSearchManager
+  assembly?: Assembly
+}) {
+  if (!textSearchManager) {
+    console.warn('No text search manager')
+  }
+
+  const textSearchResults = await textSearchManager?.search(
+    {
+      queryString,
+      searchType,
+    },
+    searchScope,
+    rankSearchResults,
+  )
+
+  const refNameResults = assembly?.allRefNames
+    ?.filter(ref => ref.toLowerCase().startsWith(queryString.toLowerCase()))
+    .slice(0, 10)
+    .map(r => new BaseResult({ label: r }))
+
+  return dedupe(
+    [...(refNameResults || []), ...(textSearchResults || [])],
+    elt => elt.getId(),
+  )
+}

package/src/LinearGenomeView/index.test.ts

@@ -72,7 +72,7 @@ function initialize() {
     })
     .actions(self => ({
       isValidRefName(str: string) {
-        return !str.includes(':')
+        return str === 'ctgA' || str === 'ctgB'
       },
       get(str: string) {
         return self.assemblies.get(str)
@@ -88,6 +88,7 @@ function initialize() {
       assemblyManager: types.optional(AssemblyManager, {
         assemblies: {
           volvox: {
+            // @ts-ignore
             regions: volvoxDisplayedRegions,
           },
         },
@@ -989,8 +990,23 @@ test('multi region', () => {
   model.navToLocString('ctgA ctgB')
   expect(model.displayedRegions[0].refName).toBe('ctgA')
   expect(model.displayedRegions[1].refName).toBe('ctgB')
-  // [
-  //   { refName: 'ctgA', start: 0, end: 50001 },
-  //   { refName: 'ctgB', start: 0, end: 6079 },
-  // ])
+})
+
+test('space separated locstring', () => {
+  const { Session, LinearGenomeModel } = initialize()
+  const model = Session.create({
+    configuration: {},
+  }).setView(
+    LinearGenomeModel.create({
+      type: 'LinearGenomeView',
+      tracks: [{ name: 'foo track', type: 'BasicTrack' }],
+    }),
+  )
+  model.setWidth(800)
+  model.setDisplayedRegions(volvoxDisplayedRegions.slice(0, 1))
+
+  model.navToLocString('ctgA 0 100')
+
+  expect(model.offsetPx).toBe(0)
+  expect(model.bpPerPx).toBe(0.125)
 })

package/src/LinearGenomeView/index.tsx

@@ -39,13 +39,13 @@ import { saveAs } from 'file-saver'
 
 // icons
 import { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons'
-import SyncAltIcon from '@material-ui/icons/SyncAlt'
-import VisibilityIcon from '@material-ui/icons/Visibility'
-import LabelIcon from '@material-ui/icons/Label'
-import FolderOpenIcon from '@material-ui/icons/FolderOpen'
-import PhotoCameraIcon from '@material-ui/icons/PhotoCamera'
-import ZoomInIcon from '@material-ui/icons/ZoomIn'
-import MenuOpenIcon from '@material-ui/icons/MenuOpen'
+import SyncAltIcon from '@mui/icons-material/SyncAlt'
+import VisibilityIcon from '@mui/icons-material/Visibility'
+import LabelIcon from '@mui/icons-material/Label'
+import FolderOpenIcon from '@mui/icons-material/FolderOpen'
+import PhotoCameraIcon from '@mui/icons-material/PhotoCamera'
+import ZoomInIcon from '@mui/icons-material/ZoomIn'
+import MenuOpenIcon from '@mui/icons-material/MenuOpen'
 
 // locals
 import { renderToSvg } from './components/LinearGenomeViewSvg'
@@ -127,6 +127,7 @@ export function stateModelFactory(pluginManager: PluginManager) {
         ),
         hideHeader: false,
         hideHeaderOverview: false,
+        hideNoTracksActive: false,
         trackSelectorType: types.optional(
           types.enumeration(['hierarchical']),
           'hierarchical',
@@ -177,11 +178,18 @@ export function stateModelFactory(pluginManager: PluginManager) {
       get interRegionPaddingWidth() {
         return INTER_REGION_PADDING_WIDTH
       },
+
+      get assemblyNames() {
+        return [
+          ...new Set(self.displayedRegions.map(region => region.assemblyName)),
+        ]
+      },
     }))
     .views(self => ({
       get assemblyErrors() {
         const { assemblyManager } = getSession(self)
-        return this.assemblyNames
+        const { assemblyNames } = self
+        return assemblyNames
           .map(a => assemblyManager.get(a)?.error)
           .filter(f => !!f)
           .join(', ')
@@ -189,9 +197,8 @@ export function stateModelFactory(pluginManager: PluginManager) {
 
       get assembliesInitialized() {
         const { assemblyManager } = getSession(self)
-        return this.assemblyNames.every(
-          a => assemblyManager.get(a)?.initialized,
-        )
+        const { assemblyNames } = self
+        return assemblyNames.every(a => assemblyManager.get(a)?.initialized)
       },
       get initialized() {
         return self.volatileWidth !== undefined && this.assembliesInitialized
@@ -273,11 +280,6 @@ export function stateModelFactory(pluginManager: PluginManager) {
         }
       },
 
-      get assemblyNames() {
-        return [
-          ...new Set(self.displayedRegions.map(region => region.assemblyName)),
-        ]
-      },
       searchScope(assemblyName: string) {
         return {
           assemblyName,
@@ -286,13 +288,6 @@ export function stateModelFactory(pluginManager: PluginManager) {
         }
       },
 
-      /**
-       * @param refName - refName of the displayedRegion
-       * @param coord - coordinate at the displayed Region
-       * @param regionNumber - optional param used as identifier when
-       * there are multiple displayedRegions with the same refName
-       * @returns offsetPx of the displayed region that it lands in
-       */
       bpToPx({
         refName,
         coord,
@@ -316,8 +311,10 @@ export function stateModelFactory(pluginManager: PluginManager) {
         if (bp < 0) {
           const region = self.displayedRegions[0]
           const offset = bp
+          const snap = getSnapshot(region)
           return {
-            ...getSnapshot(region),
+            // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
+            ...(snap as Omit<typeof snap, symbol>),
             oob: true,
             coord: region.reversed
               ? Math.floor(region.end - offset) + 1
@@ -335,8 +332,10 @@ export function stateModelFactory(pluginManager: PluginManager) {
           const len = region.end - region.start
           const offset = bp - bpSoFar
           if (len + bpSoFar > bp && bpSoFar <= bp) {
+            const snap = getSnapshot(region)
             return {
-              ...getSnapshot(region),
+              // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
+              ...(snap as Omit<typeof snap, symbol>),
               oob: false,
               offset,
               coord: region.reversed
@@ -363,8 +362,10 @@ export function stateModelFactory(pluginManager: PluginManager) {
           const region = self.displayedRegions[n - 1]
           const len = region.end - region.start
           const offset = bp - bpSoFar + len
+          const snap = getSnapshot(region)
           return {
-            ...getSnapshot(region),
+            // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
+            ...(snap as Omit<typeof snap, symbol>),
             oob: true,
             offset,
             coord: region.reversed
@@ -396,10 +397,8 @@ export function stateModelFactory(pluginManager: PluginManager) {
           track => track.configuration.trackId,
         )
         results.forEach(result => {
-          if (openTrackIds !== []) {
-            if (openTrackIds.includes(result.trackId)) {
-              result.updateScore(result.getScore() + 1)
-            }
+          if (openTrackIds.includes(result.trackId)) {
+            result.updateScore(result.getScore() + 1)
           }
         })
         return results
@@ -407,7 +406,7 @@ export function stateModelFactory(pluginManager: PluginManager) {
 
       // modifies view menu action onClick to apply to all tracks of same type
       rewriteOnClicks(trackType: string, viewMenuActions: MenuItem[]) {
-        viewMenuActions.forEach((action: MenuItem) => {
+        viewMenuActions.forEach(action => {
           // go to lowest level menu
           if ('subMenu' in action) {
             this.rewriteOnClicks(trackType, action.subMenu)
@@ -464,6 +463,9 @@ export function stateModelFactory(pluginManager: PluginManager) {
       toggleHeaderOverview() {
         self.hideHeaderOverview = !self.hideHeaderOverview
       },
+      toggleNoTracksActive() {
+        self.hideNoTracksActive = !self.hideNoTracksActive
+      },
 
       scrollTo(offsetPx: number) {
         const newOffsetPx = clamp(offsetPx, self.minOffset, self.maxOffset)
@@ -533,26 +535,19 @@ export function stateModelFactory(pluginManager: PluginManager) {
         initialSnapshot = {},
         displayInitialSnapshot = {},
       ) {
-        const trackConfigSchema =
-          pluginManager.pluggableConfigSchemaType('track')
-        const configuration = resolveIdentifier(
-          trackConfigSchema,
-          getRoot(self),
-          trackId,
-        )
-        if (!configuration) {
+        const schema = pluginManager.pluggableConfigSchemaType('track')
+        const conf = resolveIdentifier(schema, getRoot(self), trackId)
+        if (!conf) {
           throw new Error(`Could not resolve identifier "${trackId}"`)
         }
-        const trackType = pluginManager.getTrackType(configuration?.type)
+        const trackType = pluginManager.getTrackType(conf?.type)
         if (!trackType) {
-          throw new Error(`Unknown track type ${configuration.type}`)
+          throw new Error(`Unknown track type ${conf.type}`)
         }
         const viewType = pluginManager.getViewType(self.type)
-        const supportedDisplays = viewType.displayTypes.map(
-          displayType => displayType.name,
-        )
-        const displayConf = configuration.displays.find(
-          (d: AnyConfigurationModel) => supportedDisplays.includes(d.type),
+        const supportedDisplays = viewType.displayTypes.map(d => d.name)
+        const displayConf = conf.displays.find((d: AnyConfigurationModel) =>
+          supportedDisplays.includes(d.type),
         )
         if (!displayConf) {
           throw new Error(
@@ -560,14 +555,12 @@ export function stateModelFactory(pluginManager: PluginManager) {
           )
         }
 
-        const shownTracks = self.tracks.filter(
-          t => t.configuration === configuration,
-        )
-        if (shownTracks.length === 0) {
+        const t = self.tracks.filter(t => t.configuration === conf)
+        if (t.length === 0) {
           const track = trackType.stateModel.create({
             ...initialSnapshot,
-            type: configuration.type,
-            configuration,
+            type: conf.type,
+            configuration: conf,
             displays: [
               {
                 type: displayConf.type,
@@ -579,38 +572,26 @@ export function stateModelFactory(pluginManager: PluginManager) {
           self.tracks.push(track)
           return track
         }
-        return shownTracks[0]
+        return t[0]
       },
 
       hideTrack(trackId: string) {
-        const trackConfigSchema =
-          pluginManager.pluggableConfigSchemaType('track')
-        const configuration = resolveIdentifier(
-          trackConfigSchema,
-          getRoot(self),
-          trackId,
-        )
-        // if we have any tracks with that configuration, turn them off
-        const shownTracks = self.tracks.filter(
-          t => t.configuration === configuration,
-        )
-        transaction(() => shownTracks.forEach(t => self.tracks.remove(t)))
-        return shownTracks.length
+        const schema = pluginManager.pluggableConfigSchemaType('track')
+        const conf = resolveIdentifier(schema, getRoot(self), trackId)
+        const t = self.tracks.filter(t => t.configuration === conf)
+        transaction(() => t.forEach(t => self.tracks.remove(t)))
+        return t.length
       },
     }))
     .actions(self => ({
-      moveTrack(movingTrackId: string, targetTrackId: string) {
-        const oldIndex = self.tracks.findIndex(
-          track => track.id === movingTrackId,
-        )
+      moveTrack(movingId: string, targetId: string) {
+        const oldIndex = self.tracks.findIndex(track => track.id === movingId)
         if (oldIndex === -1) {
-          throw new Error(`Track ID ${movingTrackId} not found`)
+          throw new Error(`Track ID ${movingId} not found`)
         }
-        const newIndex = self.tracks.findIndex(
-          track => track.id === targetTrackId,
-        )
+        const newIndex = self.tracks.findIndex(track => track.id === targetId)
         if (newIndex === -1) {
-          throw new Error(`Track ID ${targetTrackId} not found`)
+          throw new Error(`Track ID ${targetId} not found`)
         }
         const track = getSnapshot(self.tracks[oldIndex])
         self.tracks.splice(oldIndex, 1)
@@ -675,13 +656,38 @@ export function stateModelFactory(pluginManager: PluginManager) {
         const { assemblyManager } = getSession(self)
         const { isValidRefName } = assemblyManager
         const assemblyName = optAssemblyName || assemblyNames[0]
+        let parsedLocStrings
+        const inputs = locString
+          .split(/(\s+)/)
+          .map(f => f.trim())
+          .filter(f => !!f)
 
-        const parsedLocStrings = locString
-          .split(' ')
-          .filter(f => !!f.trim())
-          .map(l => parseLocString(l, ref => isValidRefName(ref, assemblyName)))
+        // first try interpreting as a whitespace-separated sequence of
+        // multiple locstrings
+        try {
+          parsedLocStrings = inputs.map(l =>
+            parseLocString(l, ref => isValidRefName(ref, assemblyName)),
+          )
+        } catch (e) {
+          // if this fails, try interpreting as a whitespace-separated refname,
+          // start, end if start and end are integer inputs
+          const [refName, start, end] = inputs
+          if (
+            `${e}`.match(/Unknown reference sequence/) &&
+            Number.isInteger(+start) &&
+            Number.isInteger(+end)
+          ) {
+            parsedLocStrings = [
+              parseLocString(refName + ':' + start + '..' + end, ref =>
+                isValidRefName(ref, assemblyName),
+              ),
+            ]
+          } else {
+            throw e
+          }
+        }
 
-        const locations = parsedLocStrings.map(region => {
+        const locations = parsedLocStrings?.map(region => {
           const asmName = region.assemblyName || assemblyName
           const asm = assemblyManager.get(asmName)
           const { refName } = region
@@ -932,21 +938,21 @@ export function stateModelFactory(pluginManager: PluginManager) {
         leftOffset: BpOffset | undefined,
         rightOffset: BpOffset | undefined,
       ) {
+        const snap = getSnapshot(self)
         const simView = Base1DView.create({
-          ...getSnapshot(self),
+          // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
+          ...(snap as Omit<typeof self, symbol>),
           interRegionPaddingWidth: self.interRegionPaddingWidth,
         })
 
         simView.setVolatileWidth(self.width)
         simView.zoomToDisplayedRegions(leftOffset, rightOffset)
 
-        return simView.dynamicBlocks.contentBlocks.map(region => {
-          return {
-            ...region,
-            start: Math.floor(region.start),
-            end: Math.ceil(region.end),
-          }
-        })
+        return simView.dynamicBlocks.contentBlocks.map(region => ({
+          ...region,
+          start: Math.floor(region.start),
+          end: Math.ceil(region.end),
+        }))
       },
 
       // schedule something to be run after the next time displayedRegions is set
@@ -1207,6 +1213,13 @@ export function stateModelFactory(pluginManager: PluginManager) {
             onClick: self.toggleHeaderOverview,
             disabled: self.hideHeader,
           },
+          {
+            label: 'Show no tracks active button',
+            icon: VisibilityIcon,
+            type: 'checkbox',
+            checked: !self.hideNoTracksActive,
+            onClick: self.toggleNoTracksActive,
+          },
           {
             label: 'Track labels',
             icon: LabelIcon,

package/src/index.ts

@@ -11,7 +11,7 @@ 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'
-import LineStyleIcon from '@material-ui/icons/LineStyle'
+import LineStyleIcon from '@mui/icons-material/LineStyle'
 import {
   BaseLinearDisplay,
   BaseLinearDisplayComponent,
@@ -137,42 +137,47 @@ export default class LinearGenomeViewPlugin extends Plugin {
         loc: string
         tracks?: string[]
       }) => {
-        const { assemblyManager } = session
-        const view = session.addView('LinearGenomeView', {}) as LGV
+        try {
+          const { assemblyManager } = session
+          const view = session.addView('LinearGenomeView', {}) as LGV
 
-        await when(() => !!view.volatileWidth)
+          await when(() => !!view.volatileWidth)
 
-        if (!assembly) {
-          throw new Error(
-            'No assembly provided when launching linear genome view',
-          )
-        }
+          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 "${assembly}" not found when launching linear genome view`,
-          )
-        }
+          const asm = await assemblyManager.waitForAssembly(assembly)
+          if (!asm) {
+            throw new Error(
+              `Assembly "${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 (`${e}`.match('Could not resolve identifier')) {
-              idsNotFound.push(track)
-            } else {
-              throw e
+          view.navToLocString(loc, assembly)
+
+          const idsNotFound = [] as string[]
+          tracks.forEach(track => {
+            try {
+              view.showTrack(track)
+            } catch (e) {
+              if (`${e}`.match('Could not resolve identifier')) {
+                idsNotFound.push(track)
+              } else {
+                throw e
+              }
             }
+          })
+          if (idsNotFound.length) {
+            throw new Error(
+              `Could not resolve identifiers: ${idsNotFound.join(',')}`,
+            )
           }
-        })
-        if (idsNotFound.length) {
-          throw new Error(
-            `Could not resolve identifiers: ${idsNotFound.join(',')}`,
-          )
+        } catch (e) {
+          session.notify(`${e}`, 'error')
+          throw e
         }
       },
     )

package/dist/LinearBareDisplay/index.test.js

@@ -1,33 +0,0 @@
-"use strict";
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _ = require(".");
-
-test('config schema renderer type', function () {
-  var stubPluginManager = {
-    pluggableConfigSchemaType: function pluggableConfigSchemaType(type) {
-      var one = (0, _configuration.ConfigurationSchema)("".concat(type, "_TypeOne"), {}, {
-        explicitlyTyped: true
-      });
-      var two = (0, _configuration.ConfigurationSchema)("".concat(type, "_TypeTwo"), {}, {
-        explicitlyTyped: true
-      });
-      var three = (0, _configuration.ConfigurationSchema)("".concat(type, "_TypeThree"), {}, {
-        explicitlyTyped: true
-      });
-      return _mobxStateTree.types.union(one, two, three);
-    }
-  };
-  var configSchema = (0, _.configSchemaFactory)(stubPluginManager);
-  var instance = configSchema.create({
-    type: 'LinearBareDisplay',
-    displayId: 'displayId0',
-    renderer: {
-      type: 'renderer_TypeTwo'
-    }
-  });
-  expect(instance.renderer.type).toBe('renderer_TypeTwo');
-});