@apollo-annotation/jbrowse-plugin-apollo 0.3.6 → 0.3.8

package/src/LinearApolloReferenceSequenceDisplay/stateModel/base.ts

@@ -0,0 +1,227 @@
+/* eslint-disable @typescript-eslint/unbound-method */
+/* eslint-disable @typescript-eslint/no-unsafe-return */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+import { type AnnotationFeature } from '@apollo-annotation/mst'
+import type PluginManager from '@jbrowse/core/PluginManager'
+import { ConfigurationReference, getConf } from '@jbrowse/core/configuration'
+import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
+import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes'
+import {
+  type AbstractSessionModel,
+  getContainingView,
+  getSession,
+} from '@jbrowse/core/util'
+import { getParentRenderProps } from '@jbrowse/core/util/tracks'
+// import type LinearGenomeViewPlugin from '@jbrowse/plugin-linear-genome-view'
+import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import { autorun } from 'mobx'
+import { addDisposer, getRoot, types } from 'mobx-state-tree'
+
+import { type ApolloInternetAccountModel } from '../../ApolloInternetAccount/model'
+import { type ApolloSessionModel, type HoveredFeature } from '../../session'
+import { type ApolloRootModel } from '../../types'
+
+const minDisplayHeight = 20
+
+export function baseModelFactory(
+  _pluginManager: PluginManager,
+  configSchema: AnyConfigurationSchemaType,
+) {
+  return BaseDisplay.named('BaseLinearApolloReferenceSequenceDisplay')
+    .props({
+      type: types.literal('LinearApolloReferenceSequenceDisplay'),
+      configuration: ConfigurationReference(configSchema),
+      showStartCodons: false,
+      showStopCodons: true,
+      highContrast: false,
+      heightPreConfig: types.maybe(
+        types.refinement(
+          'displayHeight',
+          types.number,
+          (n) => n >= minDisplayHeight,
+        ),
+      ),
+      sequenceRowHeight: 15,
+    })
+    .views((self) => {
+      const { configuration, renderProps: superRenderProps } = self
+      return {
+        renderProps() {
+          return {
+            ...superRenderProps(),
+            ...getParentRenderProps(self),
+            config: configuration.renderer,
+          }
+        },
+      }
+    })
+    .views((self) => ({
+      get lgv() {
+        return getContainingView(self) as unknown as LinearGenomeViewModel
+      },
+    }))
+    .views((self) => ({
+      get rendererTypeName() {
+        return self.configuration.renderer.type
+      },
+      get session() {
+        return getSession(self) as unknown as ApolloSessionModel
+      },
+      get regions() {
+        const regions = self.lgv.dynamicBlocks.contentBlocks.map(
+          ({ assemblyName, end, refName, start }) => ({
+            assemblyName,
+            refName,
+            start: Math.round(start),
+            end: Math.round(end),
+          }),
+        )
+        return regions
+      },
+      regionCannotBeRendered(/* region */) {
+        if (self.lgv && self.lgv.bpPerPx >= 3) {
+          return 'Zoom in to see sequence'
+        }
+        return
+      },
+    }))
+    .views((self) => ({
+      get apolloInternetAccount() {
+        const [region] = self.regions
+        const { internetAccounts } = getRoot<ApolloRootModel>(self)
+        const { assemblyName } = region
+        const { assemblyManager } =
+          self.session as unknown as AbstractSessionModel
+        const assembly = assemblyManager.get(assemblyName)
+        if (!assembly) {
+          throw new Error(`No assembly found with name ${assemblyName}`)
+        }
+        const { internetAccountConfigId } = getConf(assembly, [
+          'sequence',
+          'metadata',
+        ]) as { internetAccountConfigId: string }
+        return internetAccounts.find(
+          (ia) => getConf(ia, 'internetAccountId') === internetAccountConfigId,
+        ) as ApolloInternetAccountModel | undefined
+      },
+      get changeManager() {
+        return (self.session as unknown as ApolloSessionModel).apolloDataStore
+          .changeManager
+      },
+      getAssemblyId(assemblyName: string) {
+        const { assemblyManager } =
+          self.session as unknown as AbstractSessionModel
+        const assembly = assemblyManager.get(assemblyName)
+        if (!assembly) {
+          throw new Error(`Could not find assembly named ${assemblyName}`)
+        }
+        return assembly.name
+      },
+      get selectedFeature(): AnnotationFeature | undefined {
+        return (self.session as unknown as ApolloSessionModel)
+          .apolloSelectedFeature
+      },
+      get hoveredFeature(): HoveredFeature | undefined {
+        return (self.session as unknown as ApolloSessionModel)
+          .apolloHoveredFeature
+      },
+      get height() {
+        const { sequenceRowHeight } = self
+        return self.lgv.bpPerPx <= 1
+          ? sequenceRowHeight * 8
+          : sequenceRowHeight * 6
+      },
+    }))
+    .volatile(() => ({
+      scrollTop: 0,
+    }))
+    .actions((self) => ({
+      setScrollTop(scrollTop: number) {
+        self.scrollTop = scrollTop
+      },
+      setHeight(displayHeight: number) {
+        self.heightPreConfig = Math.max(displayHeight, minDisplayHeight)
+        return self.height
+      },
+      resizeHeight(distance: number) {
+        const oldHeight = self.height
+        const newHeight = this.setHeight(self.height + distance)
+        return newHeight - oldHeight
+      },
+      toggleShowStartCodons() {
+        self.showStartCodons = !self.showStartCodons
+      },
+      toggleShowStopCodons() {
+        self.showStopCodons = !self.showStopCodons
+      },
+      toggleHighContrast() {
+        self.highContrast = !self.highContrast
+      },
+    }))
+    .views((self) => {
+      const { trackMenuItems: superTrackMenuItems } = self
+      return {
+        trackMenuItems() {
+          const { showStartCodons, showStopCodons, highContrast } = self
+          return [
+            ...superTrackMenuItems(),
+            {
+              type: 'subMenu',
+              label: 'Appearance',
+              subMenu: [
+                {
+                  label: 'Show start codons',
+                  type: 'checkbox',
+                  checked: showStartCodons,
+                  onClick: () => {
+                    self.toggleShowStartCodons()
+                  },
+                },
+                {
+                  label: 'Show stop codons',
+                  type: 'checkbox',
+                  checked: showStopCodons,
+                  onClick: () => {
+                    self.toggleShowStopCodons()
+                  },
+                },
+                {
+                  label: 'Use high contrast colors',
+                  type: 'checkbox',
+                  checked: highContrast,
+                  onClick: () => {
+                    self.toggleHighContrast()
+                  },
+                },
+              ],
+            },
+          ]
+        },
+      }
+    })
+    .actions((self) => ({
+      afterAttach() {
+        addDisposer(
+          self,
+          autorun(
+            () => {
+              if (!self.lgv.initialized || self.regionCannotBeRendered()) {
+                return
+              }
+              if (self.lgv.bpPerPx <= 3) {
+                void (
+                  self.session as unknown as ApolloSessionModel
+                ).apolloDataStore.loadRefSeq(self.regions)
+              }
+            },
+            {
+              name: 'LinearApolloReferenceSequenceDisplayLoadFeatures',
+              delay: 1000,
+            },
+          ),
+        )
+      },
+    }))
+}

package/src/LinearApolloReferenceSequenceDisplay/stateModel/index.ts

@@ -0,0 +1,25 @@
+import type PluginManager from '@jbrowse/core/PluginManager'
+import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
+import { type Instance } from 'mobx-state-tree'
+
+import { renderingModelFactory } from './rendering'
+
+export function stateModelFactory(
+  pluginManager: PluginManager,
+  configSchema: AnyConfigurationSchemaType,
+) {
+  // TODO: this needs to be refactored so that the final composition of the
+  // state model mixins happens here in one central place
+  return renderingModelFactory(pluginManager, configSchema).named(
+    'LinearApolloReferenceSequenceDisplay',
+  )
+}
+
+export type LinearApolloReferenceSequenceDisplayStateModel = ReturnType<
+  typeof stateModelFactory
+>
+// eslint disable because of
+// https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time
+// eslint-disable-next-line @typescript-eslint/no-empty-object-type
+export interface LinearApolloReferenceSequenceDisplay
+  extends Instance<LinearApolloReferenceSequenceDisplayStateModel> {}