@jbrowse/plugin-linear-comparative-view 2.6.1 → 2.6.3

package/src/LinearComparativeView/model.ts

@@ -1,395 +0,0 @@
-import { lazy } from 'react'
-import {
-  addDisposer,
-  cast,
-  getParent,
-  getPath,
-  getRoot,
-  onAction,
-  resolveIdentifier,
-  types,
-  Instance,
-  SnapshotIn,
-} from 'mobx-state-tree'
-import { autorun, transaction } from 'mobx'
-
-// jbrowse
-import BaseViewModel from '@jbrowse/core/pluggableElementTypes/models/BaseViewModel'
-import { MenuItem } from '@jbrowse/core/ui'
-import { getSession, isSessionModelWithWidgets, avg } from '@jbrowse/core/util'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { AnyConfigurationModel } from '@jbrowse/core/configuration'
-import { ElementId } from '@jbrowse/core/util/types/mst'
-import {
-  LinearGenomeViewModel,
-  LinearGenomeViewStateModel,
-} from '@jbrowse/plugin-linear-genome-view'
-
-// icons
-import { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons'
-import FolderOpenIcon from '@mui/icons-material/FolderOpen'
-
-// lazies
-const ReturnToImportFormDialog = lazy(
-  () => import('@jbrowse/core/ui/ReturnToImportFormDialog'),
-)
-
-/**
- * #stateModel LinearComparativeView
- */
-function stateModelFactory(pluginManager: PluginManager) {
-  return types
-    .compose(
-      'LinearComparativeView',
-      BaseViewModel,
-      types.model({
-        /**
-         * #property
-         */
-        id: ElementId,
-        /**
-         * #property
-         */
-        type: types.literal('LinearComparativeView'),
-        /**
-         * #property
-         */
-        trackSelectorType: 'hierarchical',
-        /**
-         * #property
-         */
-        showIntraviewLinks: true,
-        /**
-         * #property
-         */
-        linkViews: false,
-        /**
-         * #property
-         */
-        interactToggled: false,
-        /**
-         * #property
-         */
-        middleComparativeHeight: 100,
-        /**
-         * #property
-         */
-        tracks: types.array(
-          pluginManager.pluggableMstType('track', 'stateModel'),
-        ),
-        /**
-         * #property
-         * currently this is limited to an array of two
-         */
-        views: types.array(
-          pluginManager.getViewType('LinearGenomeView')
-            .stateModel as LinearGenomeViewStateModel,
-        ),
-
-        /**
-         * #property
-         * this represents tracks specific to this view specifically used
-         * for read vs ref dotplots where this track would not really apply
-         * elsewhere
-         */
-        viewTrackConfigs: types.array(
-          pluginManager.pluggableConfigSchemaType('track'),
-        ),
-      }),
-    )
-    .volatile(() => ({
-      width: undefined as number | undefined,
-    }))
-    .views(self => ({
-      /**
-       * #getter
-       */
-      get highResolutionScaling() {
-        return 2
-      },
-      /**
-       * #getter
-       */
-      get initialized() {
-        return (
-          self.width !== undefined &&
-          self.views.length > 0 &&
-          self.views.every(view => view.initialized)
-        )
-      },
-
-      /**
-       * #getter
-       */
-      get refNames() {
-        return self.views.map(v => [
-          ...new Set(v.staticBlocks.map(m => m.refName)),
-        ])
-      },
-
-      /**
-       * #getter
-       */
-      get assemblyNames() {
-        return [...new Set(self.views.flatMap(v => v.assemblyNames))]
-      },
-    }))
-    .actions(self => ({
-      afterAttach() {
-        addDisposer(
-          self,
-          onAction(self, param => {
-            if (self.linkViews) {
-              const { name, path, args } = param
-
-              // doesn't link showTrack/hideTrack, doesn't make sense in
-              // synteny views most time
-              const actions = ['horizontalScroll', 'zoomTo', 'setScaleFactor']
-              if (actions.includes(name) && path) {
-                this.onSubviewAction(name, path, args)
-              }
-            }
-          }),
-        )
-      },
-
-      // automatically removes session assemblies associated with this view
-      // e.g. read vs ref
-      beforeDestroy() {
-        const session = getSession(self)
-        self.assemblyNames.forEach(asm => session.removeTemporaryAssembly(asm))
-      },
-
-      onSubviewAction(actionName: string, path: string, args?: unknown[]) {
-        self.views.forEach(view => {
-          const ret = getPath(view)
-          if (ret.lastIndexOf(path) !== ret.length - path.length) {
-            // @ts-expect-error
-            view[actionName](args?.[0])
-          }
-        })
-      },
-
-      /**
-       * #action
-       */
-      setWidth(newWidth: number) {
-        self.width = newWidth
-      },
-
-      /**
-       * #action
-       */
-      setViews(views: SnapshotIn<LinearGenomeViewModel>[]) {
-        self.views = cast(views)
-      },
-
-      /**
-       * #action
-       */
-      removeView(view: LinearGenomeViewModel) {
-        self.views.remove(view)
-      },
-
-      /**
-       * #action
-       * removes the view itself from the state tree entirely by calling the
-       * parent removeView
-       */
-      closeView() {
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        getParent<any>(self, 2).removeView(self)
-      },
-
-      /**
-       * #action
-       */
-      setMiddleComparativeHeight(n: number) {
-        self.middleComparativeHeight = n
-        return self.middleComparativeHeight
-      },
-
-      /**
-       * #action
-       */
-      toggleLinkViews() {
-        self.linkViews = !self.linkViews
-      },
-
-      /**
-       * #action
-       */
-      activateTrackSelector() {
-        if (self.trackSelectorType === 'hierarchical') {
-          const session = getSession(self)
-          if (isSessionModelWithWidgets(session)) {
-            const selector = session.addWidget(
-              'HierarchicalTrackSelectorWidget',
-              'hierarchicalTrackSelector',
-              { view: self },
-            )
-            session.showWidget(selector)
-            return selector
-          }
-          return undefined
-        }
-        throw new Error(`invalid track selector type ${self.trackSelectorType}`)
-      },
-
-      /**
-       * #action
-       */
-      toggleTrack(trackId: string) {
-        // if we have any tracks with that configuration, turn them off
-        const hiddenCount = this.hideTrack(trackId)
-
-        // if none had that configuration, turn one on
-        if (!hiddenCount) {
-          this.showTrack(trackId)
-        }
-      },
-
-      /**
-       * #action
-       */
-      showTrack(trackId: string, initialSnapshot = {}) {
-        const schema = pluginManager.pluggableConfigSchemaType('track')
-        const configuration = resolveIdentifier(schema, getRoot(self), trackId)
-        if (!configuration) {
-          throw new Error(`track not found ${trackId}`)
-        }
-        const trackType = pluginManager.getTrackType(configuration.type)
-        if (!trackType) {
-          throw new Error(`unknown track type ${configuration.type}`)
-        }
-        const viewType = pluginManager.getViewType(self.type)
-        const supportedDisplays = new Set(
-          viewType.displayTypes.map(d => d.name),
-        )
-        const displayConf = configuration.displays.find(
-          (d: AnyConfigurationModel) => supportedDisplays.has(d.type),
-        )
-        if (!displayConf) {
-          throw new Error(
-            `could not find a compatible display for view type ${self.type}`,
-          )
-        }
-        self.tracks.push(
-          trackType.stateModel.create({
-            ...initialSnapshot,
-            type: configuration.type,
-            configuration,
-            displays: [{ type: displayConf.type, configuration: displayConf }],
-          }),
-        )
-      },
-
-      /**
-       * #action
-       */
-      hideTrack(trackId: string) {
-        const schema = pluginManager.pluggableConfigSchemaType('track')
-        const config = resolveIdentifier(schema, getRoot(self), trackId)
-        const shownTracks = self.tracks.filter(t => t.configuration === config)
-        transaction(() => shownTracks.forEach(t => self.tracks.remove(t)))
-        return shownTracks.length
-      },
-      /**
-       * #action
-       */
-      squareView() {
-        const average = avg(self.views.map(v => v.bpPerPx))
-        self.views.forEach(view => {
-          const center = view.pxToBp(view.width / 2)
-          view.setNewView(average, view.offsetPx)
-          if (!center.refName) {
-            return
-          }
-          view.centerAt(center.coord, center.refName, center.index)
-        })
-      },
-      /**
-       * #action
-       */
-      clearView() {
-        self.views = cast([])
-        self.tracks = cast([])
-      },
-    }))
-    .views(() => ({
-      /**
-       * #method
-       * includes a subset of view menu options because the full list is a
-       * little overwhelming. overridden by subclasses
-       */
-      headerMenuItems(): MenuItem[] {
-        return []
-      },
-    }))
-    .views(self => ({
-      /**
-       * #method
-       */
-      menuItems(): MenuItem[] {
-        return [
-          ...self.views
-            .map((view, idx) => [idx, view.menuItems?.()] as const)
-            .filter(f => !!f[1])
-            .map(f => ({ label: `View ${f[0] + 1} Menu`, subMenu: f[1] })),
-          {
-            label: 'Return to import form',
-            onClick: () => {
-              getSession(self).queueDialog(handleClose => [
-                ReturnToImportFormDialog,
-                { model: self, handleClose },
-              ])
-            },
-            icon: FolderOpenIcon,
-          },
-          {
-            label: 'Open track selector',
-            onClick: self.activateTrackSelector,
-            icon: TrackSelectorIcon,
-          },
-        ]
-      },
-      /**
-       * #method
-       */
-      rubberBandMenuItems() {
-        return [
-          {
-            label: 'Zoom to region(s)',
-            onClick: () => {
-              self.views.forEach(view => {
-                const { leftOffset, rightOffset } = view
-                if (leftOffset && rightOffset) {
-                  view.moveTo(leftOffset, rightOffset)
-                }
-              })
-            },
-          },
-        ]
-      },
-    }))
-    .actions(self => ({
-      afterAttach() {
-        addDisposer(
-          self,
-          autorun(() => {
-            if (self.width) {
-              self.views.forEach(v => v.setWidth(self.width))
-            }
-          }),
-        )
-      },
-    }))
-}
-
-export type LinearComparativeViewStateModel = ReturnType<
-  typeof stateModelFactory
->
-export type LinearComparativeViewModel =
-  Instance<LinearComparativeViewStateModel>
-
-export default stateModelFactory