@jbrowse/plugin-alignments 2.6.1 → 2.6.3

package/src/LinearSNPCoverageDisplay/components/Tooltip.tsx

@@ -1,128 +0,0 @@
-import React from 'react'
-import { observer } from 'mobx-react'
-import { Feature } from '@jbrowse/core/util'
-import { Tooltip } from '@jbrowse/plugin-wiggle'
-
-type Count = {
-  [key: string]: {
-    total: number
-    '-1': number
-    '0': number
-    '1': number
-  }
-}
-
-type SNPInfo = {
-  cov: Count
-  lowqual: Count
-  noncov: Count
-  delskips: Count
-  refbase: string
-  total: number
-  ref: number
-  all: number
-  '-1': number
-  '0': number
-  '1': number
-}
-
-const en = (n: number) => n.toLocaleString('en-US')
-const toP = (s = 0) => +(+s).toFixed(1)
-const pct = (n: number, total: number) => `${toP((n / (total || 1)) * 100)}%`
-interface Props {
-  feature: Feature
-}
-const TooltipContents = React.forwardRef<HTMLDivElement, Props>(function (
-  { feature },
-  reactRef,
-) {
-  const start = feature.get('start')
-  const end = feature.get('end')
-  const name = feature.get('refName')
-  const {
-    refbase,
-    all,
-    total,
-    ref,
-    '-1': rn1,
-    '1': r1,
-    '0': r0,
-    ...info
-  } = feature.get('snpinfo') as SNPInfo
-  const loc = [name, start === end ? en(start) : `${en(start)}..${en(end)}`]
-    .filter(f => !!f)
-    .join(':')
-
-  return (
-    <div ref={reactRef}>
-      <table>
-        <caption>{loc}</caption>
-        <thead>
-          <tr>
-            <th>Base</th>
-            <th>Count</th>
-            <th>% of Total</th>
-            <th>Strands</th>
-            <th>Source</th>
-          </tr>
-        </thead>
-        <tbody>
-          <tr>
-            <td>Total</td>
-            <td>{all}</td>
-          </tr>
-          <tr>
-            <td>REF {refbase ? `(${refbase.toUpperCase()})` : ''}</td>
-            <td>{ref}</td>
-            <td>{pct(ref, all)}</td>
-            <td>
-              {rn1 ? `${rn1}(-)` : ''}
-              {r1 ? `${r1}(+)` : ''}
-            </td>
-            <td />
-          </tr>
-
-          {Object.entries(info as unknown as Record<string, Count>).map(
-            ([key, entry]) =>
-              Object.entries(entry).map(([base, score]) => (
-                <tr key={base}>
-                  <td>{base.toUpperCase()}</td>
-                  <td>{score.total}</td>
-                  <td>
-                    {base === 'total' || base === 'skip'
-                      ? '---'
-                      : pct(score.total, all)}
-                  </td>
-                  <td>
-                    {score['-1'] ? `${score['-1']}(-)` : ''}
-                    {score['1'] ? `${score['1']}(+)` : ''}
-                  </td>
-                  <td>{key}</td>
-                </tr>
-              )),
-          )}
-        </tbody>
-      </table>
-    </div>
-  )
-})
-
-type Coord = [number, number]
-
-const SNPCoverageTooltip = observer(
-  (props: {
-    model: { featureUnderMouse: Feature }
-    height: number
-    offsetMouseCoord: Coord
-    clientMouseCoord: Coord
-    clientRect?: DOMRect
-  }) => {
-    const { model } = props
-    const { featureUnderMouse: feat } = model
-    return feat && feat.get('type') === 'skip' ? null : (
-      <Tooltip TooltipContents={TooltipContents} {...props} />
-    )
-  },
-)
-
-export default SNPCoverageTooltip

package/src/LinearSNPCoverageDisplay/index.ts

@@ -1,20 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import configSchemaFactory from './models/configSchema'
-import modelFactory from './models/model'
-import { LinearWiggleDisplayReactComponent } from '@jbrowse/plugin-wiggle'
-import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
-
-export default function register(pluginManager: PluginManager) {
-  pluginManager.addDisplayType(() => {
-    const configSchema = configSchemaFactory(pluginManager)
-    return new DisplayType({
-      name: 'LinearSNPCoverageDisplay',
-      displayName: 'SNPCoverage display',
-      configSchema,
-      stateModel: modelFactory(pluginManager, configSchema),
-      trackType: 'AlignmentsTrack',
-      viewType: 'LinearGenomeView',
-      ReactComponent: LinearWiggleDisplayReactComponent,
-    })
-  })
-}

package/src/LinearSNPCoverageDisplay/models/configSchema.test.ts

@@ -1,35 +0,0 @@
-import Plugin from '@jbrowse/core/Plugin'
-import PluginManager from '@jbrowse/core/PluginManager'
-import SNPCoverageRenderer from '../../SNPCoverageRenderer' // change renderer
-import configSchemaFactory from './configSchema'
-
-// mock warnings to avoid unnecessary outputs
-beforeEach(() => {
-  jest.spyOn(console, 'warn').mockImplementation(() => {})
-})
-
-afterEach(() => {
-  // @ts-expect-error
-  console.warn.mockRestore()
-})
-// change renderer
-class SNPCoverageRendererPlugin extends Plugin {
-  name = 'SNPCoverageRendererPlugin'
-  install(pluginManager: PluginManager) {
-    SNPCoverageRenderer(pluginManager)
-  }
-}
-
-test('has a type attr', () => {
-  const configSchema = configSchemaFactory(
-    new PluginManager([new SNPCoverageRendererPlugin()])
-      .createPluggableElements()
-      .configure(),
-  )
-  const config = configSchema.create({
-    type: 'LinearSNPCoverageDisplay',
-    displayId: 'display1',
-    name: 'SNPZonker Display',
-  })
-  expect(config.type).toEqual('LinearSNPCoverageDisplay')
-})

package/src/LinearSNPCoverageDisplay/models/configSchema.ts

@@ -1,82 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view'
-import { types } from 'mobx-state-tree'
-import PluginManager from '@jbrowse/core/PluginManager'
-
-/**
- * #config LinearSNPCoverageDisplay
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-export default function SNPCoverageConfigFactory(pluginManager: PluginManager) {
-  return ConfigurationSchema(
-    'LinearSNPCoverageDisplay',
-    {
-      /**
-       * #slot
-       */
-      autoscale: {
-        type: 'stringEnum',
-        defaultValue: 'local',
-        model: types.enumeration('Autoscale type', ['local']),
-        description:
-          'performs local autoscaling (no other options for SNP Coverage available)',
-      },
-      /**
-       * #slot
-       */
-      minScore: {
-        type: 'number',
-        defaultValue: Number.MIN_VALUE,
-        description: 'minimum value for the y-scale',
-      },
-      /**
-       * #slot
-       */
-      maxScore: {
-        type: 'number',
-        description: 'maximum value for the y-scale',
-        defaultValue: Number.MAX_VALUE,
-      },
-      /**
-       * #slot
-       */
-      scaleType: {
-        type: 'stringEnum',
-        model: types.enumeration('Scale type', ['linear', 'log']), // todo zscale
-        description: 'The type of scale to use',
-        defaultValue: 'linear',
-      },
-      /**
-       * #slot
-       */ inverted: {
-        type: 'boolean',
-        description: 'draw upside down',
-        defaultValue: false,
-      },
-      /**
-       * #slot
-       */
-      multiTicks: {
-        type: 'boolean',
-        description: 'Display multiple values for the ticks',
-        defaultValue: false,
-      },
-      /**
-       * #slot
-       */
-      renderers: ConfigurationSchema('RenderersConfiguration', {
-        SNPCoverageRenderer: pluginManager.getRendererType(
-          'SNPCoverageRenderer',
-        ).configSchema,
-      }),
-    },
-    {
-      /**
-       * #baseConfiguration
-       */
-      baseConfiguration: baseLinearDisplayConfigSchema,
-      explicitlyTyped: true,
-    },
-  )
-}

package/src/LinearSNPCoverageDisplay/models/model.ts

@@ -1,336 +0,0 @@
-import { types, cast, getEnv, getSnapshot, isAlive } from 'mobx-state-tree'
-import { observable } from 'mobx'
-
-// jbrowse
-import PluginManager from '@jbrowse/core/PluginManager'
-import {
-  getConf,
-  readConfObject,
-  AnyConfigurationSchemaType,
-  AnyConfigurationModel,
-} from '@jbrowse/core/configuration'
-import { linearWiggleDisplayModelFactory } from '@jbrowse/plugin-wiggle'
-import { getContainingView } from '@jbrowse/core/util'
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-
-// locals
-import Tooltip from '../components/Tooltip'
-import { FilterModel, getUniqueModificationValues } from '../../shared'
-import { createAutorun, modificationColors } from '../../util'
-import { randomColor } from '../../util'
-
-// using a map because it preserves order
-const rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']])
-
-type LGV = LinearGenomeViewModel
-
-/**
- * #stateModel LinearSNPCoverageDisplay
- * extends `LinearWiggleDisplay`
- */
-function stateModelFactory(
-  pluginManager: PluginManager,
-  configSchema: AnyConfigurationSchemaType,
-) {
-  return types
-    .compose(
-      'LinearSNPCoverageDisplay',
-      linearWiggleDisplayModelFactory(pluginManager, configSchema),
-      types.model({
-        /**
-         * #property
-         */
-        type: types.literal('LinearSNPCoverageDisplay'),
-        /**
-         * #property
-         */
-        drawInterbaseCounts: types.maybe(types.boolean),
-        /**
-         * #property
-         */
-        drawIndicators: types.maybe(types.boolean),
-        /**
-         * #property
-         */
-        drawArcs: types.maybe(types.boolean),
-        /**
-         * #property
-         */
-        filterBy: types.optional(FilterModel, {}),
-        /**
-         * #property
-         */
-        colorBy: types.maybe(
-          types.model({
-            type: types.string,
-            tag: types.maybe(types.string),
-          }),
-        ),
-      }),
-    )
-    .volatile(() => ({
-      modificationTagMap: observable.map<string, string>({}),
-      modificationsReady: false,
-    }))
-    .actions(self => ({
-      /**
-       * #action
-       */
-      setConfig(configuration: AnyConfigurationModel) {
-        self.configuration = configuration
-      },
-      /**
-       * #action
-       */
-      setFilterBy(filter: {
-        flagInclude: number
-        flagExclude: number
-        readName?: string
-        tagFilter?: { tag: string; value: string }
-      }) {
-        self.filterBy = cast(filter)
-      },
-      /**
-       * #action
-       */
-      setColorBy(colorBy?: { type: string; tag?: string }) {
-        self.colorBy = cast(colorBy)
-      },
-
-      /**
-       * #action
-       */
-      updateModificationColorMap(uniqueModifications: string[]) {
-        uniqueModifications.forEach(value => {
-          if (!self.modificationTagMap.has(value)) {
-            self.modificationTagMap.set(
-              value,
-              modificationColors[value] || randomColor(),
-            )
-          }
-        })
-      },
-    }))
-    .views(self => {
-      const { renderProps: superRenderProps } = self
-      return {
-        /**
-         * #getter
-         */
-        get rendererConfig() {
-          const configBlob =
-            getConf(self, ['renderers', self.rendererTypeName]) || {}
-
-          return self.rendererType.configSchema.create(
-            {
-              ...configBlob,
-              drawInterbaseCounts:
-                self.drawInterbaseCounts ?? configBlob.drawInterbaseCounts,
-              drawIndicators: self.drawIndicators ?? configBlob.drawIndicators,
-              drawArcs: self.drawArcs ?? configBlob.drawArcs,
-            },
-            getEnv(self),
-          )
-        },
-        /**
-         * #getter
-         */
-        get drawArcsSetting() {
-          return (
-            self.drawArcs ?? readConfObject(this.rendererConfig, 'drawArcs')
-          )
-        },
-        /**
-         * #getter
-         */
-        get drawInterbaseCountsSetting() {
-          return (
-            self.drawInterbaseCounts ??
-            readConfObject(this.rendererConfig, 'drawInterbaseCounts')
-          )
-        },
-        /**
-         * #getter
-         */
-        get drawIndicatorsSetting() {
-          return (
-            self.drawIndicators ??
-            readConfObject(this.rendererConfig, 'drawIndicators')
-          )
-        },
-
-        /**
-         * #getter
-         */
-        get autorunReady() {
-          const view = getContainingView(self) as LGV
-          return (
-            view.initialized &&
-            self.featureDensityStatsReady &&
-            !self.regionTooLarge &&
-            !self.error
-          )
-        },
-
-        get renderReady() {
-          const superProps = superRenderProps()
-          return !superProps.notReady && self.modificationsReady
-        },
-
-        get ready() {
-          return this.renderReady
-        },
-
-        /**
-         * #method
-         */
-        renderProps() {
-          const superProps = superRenderProps()
-          const { colorBy, filterBy, modificationTagMap } = self
-          return {
-            ...superProps,
-            notReady: !this.ready,
-            modificationTagMap: Object.fromEntries(modificationTagMap.toJSON()),
-
-            // must use getSnapshot because otherwise changes to e.g. just the
-            // colorBy.type are not read
-            colorBy: colorBy ? getSnapshot(colorBy) : undefined,
-            filterBy: filterBy ? getSnapshot(filterBy) : undefined,
-          }
-        },
-      }
-    })
-    .actions(self => ({
-      /**
-       * #action
-       */
-      setModificationsReady(flag: boolean) {
-        self.modificationsReady = flag
-      },
-      /**
-       * #action
-       */
-      toggleDrawIndicators() {
-        self.drawIndicators = !self.drawIndicatorsSetting
-      },
-      /**
-       * #action
-       */
-      toggleDrawInterbaseCounts() {
-        self.drawInterbaseCounts = !self.drawInterbaseCountsSetting
-      },
-      /**
-       * #action
-       */
-      toggleDrawArcs() {
-        self.drawArcs = !self.drawArcsSetting
-      },
-    }))
-    .actions(self => ({
-      afterAttach() {
-        createAutorun(
-          self,
-          async () => {
-            self.setModificationsReady(false)
-            if (!self.autorunReady) {
-              return
-            }
-            const view = getContainingView(self) as LGV
-            const { staticBlocks } = view
-            const { colorBy } = self
-            if (colorBy?.type === 'modifications') {
-              const adapter = getConf(self.parentTrack, 'adapter')
-              const vals = await getUniqueModificationValues(
-                self,
-                adapter,
-                colorBy,
-                staticBlocks,
-              )
-              if (isAlive(self)) {
-                self.updateModificationColorMap(vals)
-                self.setModificationsReady(true)
-              }
-            } else {
-              self.setModificationsReady(true)
-            }
-          },
-          { delay: 1000 },
-        )
-      },
-    }))
-
-    .views(self => {
-      const { trackMenuItems: superTrackMenuItems } = self
-      return {
-        /**
-         * #getter
-         */
-        get TooltipComponent() {
-          return Tooltip
-        },
-
-        /**
-         * #getter
-         */
-        get adapterConfig() {
-          const subadapter = getConf(self.parentTrack, 'adapter')
-          return {
-            type: 'SNPCoverageAdapter',
-            subadapter,
-          }
-        },
-
-        /**
-         * #getter
-         */
-        get rendererTypeName() {
-          return rendererTypes.get('snpcoverage')
-        },
-
-        /**
-         * #getter
-         */
-        get needsScalebar() {
-          return true
-        },
-
-        /**
-         * #method
-         */
-        contextMenuItems() {
-          return []
-        },
-
-        /**
-         * #method
-         */
-        trackMenuItems() {
-          return [
-            ...superTrackMenuItems(),
-            {
-              label: 'Draw insertion/clipping indicators',
-              type: 'checkbox',
-              checked: self.drawIndicatorsSetting,
-              onClick: () => self.toggleDrawIndicators(),
-            },
-            {
-              label: 'Draw insertion/clipping counts',
-              type: 'checkbox',
-              checked: self.drawInterbaseCountsSetting,
-              onClick: () => self.toggleDrawInterbaseCounts(),
-            },
-            {
-              label: 'Draw arcs',
-              type: 'checkbox',
-              checked: self.drawArcsSetting,
-              onClick: () => self.toggleDrawArcs(),
-            },
-          ]
-        },
-      }
-    })
-}
-
-export type SNPCoverageDisplayModel = ReturnType<typeof stateModelFactory>
-
-export default stateModelFactory