@jbrowse/plugin-linear-comparative-view 2.6.1 → 2.6.2

package/esm/LinearSyntenyDisplay/index.js.map

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package/esm/LinearSyntenyDisplay/model.js.map

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package/esm/LinearSyntenyView/components/ExportSvgDialog.js.map

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package/esm/LinearSyntenyView/components/Icons.js.map

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package/esm/LinearSyntenyView/components/ImportCustomTrack.js.map

@@ -1 +0,0 @@
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package/esm/LinearSyntenyView/components/ImportForm.js.map

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package/esm/LinearSyntenyView/components/ImportSyntenyTrackSelector.js.map

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package/esm/SyntenyFeatureDetail/SyntenyFeatureDetail.js.map

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package/esm/util.js.map

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package/src/LGVSyntenyDisplay/configSchemaF.ts

@@ -1,22 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { linearPileupDisplayConfigSchemaFactory } from '@jbrowse/plugin-alignments'
-
-/**
- * #config LGVSyntenyDisplay
- */
-function configSchemaF(pluginManager: PluginManager) {
-  return ConfigurationSchema(
-    'LGVSyntenyDisplay',
-    {},
-    {
-      /**
-       * #baseConfiguration
-       */
-      baseConfiguration: linearPileupDisplayConfigSchemaFactory(pluginManager),
-      explicitlyTyped: true,
-    },
-  )
-}
-
-export default configSchemaF

package/src/LGVSyntenyDisplay/index.ts

@@ -1,20 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
-import configSchemaF from './configSchemaF'
-import stateModelF from './model'
-import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addDisplayType(() => {
-    const configSchema = configSchemaF(pluginManager)
-    const stateModel = stateModelF(configSchema)
-    return new DisplayType({
-      name: 'LGVSyntenyDisplay',
-      configSchema,
-      stateModel,
-      trackType: 'SyntenyTrack',
-      viewType: 'LinearGenomeView',
-      ReactComponent: BaseLinearDisplayComponent,
-    })
-  })
-}

package/src/LGVSyntenyDisplay/model.ts

@@ -1,177 +0,0 @@
-import {
-  ConfigurationReference,
-  AnyConfigurationSchemaType,
-} from '@jbrowse/core/configuration'
-import {
-  getSession,
-  getContainingTrack,
-  getContainingView,
-  Feature,
-} from '@jbrowse/core/util'
-import {
-  MismatchParser,
-  linearPileupDisplayStateModelFactory,
-} from '@jbrowse/plugin-alignments'
-import { IAnyStateTreeNode, types } from 'mobx-state-tree'
-import { when } from 'mobx'
-
-// locals
-import { LinearSyntenyViewModel } from '../LinearSyntenyView/model'
-
-type LSV = LinearSyntenyViewModel
-
-const { parseCigar } = MismatchParser
-
-function findPosInCigar(cigar: string[], startX: number) {
-  let featX = 0
-  let mateX = 0
-  for (let i = 0; i < cigar.length; i++) {
-    const len = +cigar[i]
-    const op = cigar[i + 1]
-    const min = Math.min(len, startX - featX)
-
-    if (featX >= startX) {
-      break
-    } else if (op === 'I') {
-      mateX += len
-    } else if (op === 'D') {
-      featX += min
-    } else if (op === 'M') {
-      mateX += min
-      featX += min
-    }
-  }
-  return [featX, mateX]
-}
-
-async function navToSynteny(feature: Feature, self: IAnyStateTreeNode) {
-  const session = getSession(self)
-  const track = getContainingTrack(self)
-  const view = getContainingView(self)
-  const reg = view.dynamicBlocks.contentBlocks[0]
-  const cigar = feature.get('CIGAR')
-  const strand = feature.get('strand')
-  const regStart = reg.start
-  const regEnd = reg.end
-  const featStart = feature.get('start')
-  const featEnd = feature.get('end')
-  const mate = feature.get('mate')
-  const mateStart = mate.start
-  const mateEnd = mate.end
-  const mateAsm = mate.assemblyName
-  const mateRef = mate.refName
-  const featAsm = reg.assemblyName
-  const featRef = reg.refName
-
-  let rMateStart: number
-  let rMateEnd: number
-  let rFeatStart: number
-  let rFeatEnd: number
-
-  if (cigar) {
-    const p = parseCigar(cigar)
-    const [fStartX, mStartX] = findPosInCigar(p, regStart - featStart)
-    const [fEndX, mEndX] = findPosInCigar(p, regEnd - featStart)
-
-    // avoid multiply by 0 with strand undefined
-    const flipper = strand === -1 ? -1 : 1
-    rFeatStart = featStart + fStartX
-    rFeatEnd = featStart + fEndX
-    rMateStart = (strand === -1 ? mateEnd : mateStart) + mStartX * flipper
-    rMateEnd = (strand === -1 ? mateEnd : mateStart) + mEndX * flipper
-  } else {
-    rFeatStart = featStart
-    rFeatEnd = featEnd
-    rMateStart = mateStart
-    rMateEnd = mateEnd
-  }
-  const trackId = track.configuration.trackId
-
-  const view2 = session.addView('LinearSyntenyView', {
-    type: 'LinearSyntenyView',
-    views: [
-      {
-        id: `${Math.random()}`,
-        type: 'LinearGenomeView',
-        hideHeader: true,
-      },
-      {
-        id: `${Math.random()}`,
-        type: 'LinearGenomeView',
-        hideHeader: true,
-      },
-    ],
-    tracks: [
-      {
-        configuration: trackId,
-        type: 'SyntenyTrack',
-        displays: [
-          {
-            type: 'LinearSyntenyDisplay',
-            configuration: `${trackId}-LinearSyntenyDisplay`,
-          },
-        ],
-      },
-    ],
-  }) as LSV
-  const f = (n: number) => Math.floor(n)
-  const l1 = `${featRef}:${f(rFeatStart)}-${f(rFeatEnd)}`
-  const m1 = Math.min(rMateStart, rMateEnd)
-  const m2 = Math.max(rMateStart, rMateEnd)
-  const l2 = `${mateRef}:${f(m1)}-${f(m2)}${strand === -1 ? '[rev]' : ''}`
-  await when(() => view2.width !== undefined)
-  await Promise.all([
-    view2.views[0].navToLocString(l1, featAsm),
-    view2.views[1].navToLocString(l2, mateAsm),
-  ])
-}
-
-/**
- * #stateModel LGVSyntenyDisplay
- * extends `LinearPileupDisplay`, displays location of "synteny" feature in a
- * plain LGV, allowing linking out to external synteny views
- */
-function stateModelFactory(schema: AnyConfigurationSchemaType) {
-  return types
-    .compose(
-      'LGVSyntenyDisplay',
-      linearPileupDisplayStateModelFactory(schema),
-      types.model({
-        /**
-         * #property
-         */
-        type: types.literal('LGVSyntenyDisplay'),
-        /**
-         * #property
-         */
-        configuration: ConfigurationReference(schema),
-      }),
-    )
-    .views(self => {
-      const superContextMenuItems = self.contextMenuItems
-      return {
-        contextMenuItems() {
-          const feature = self.contextMenuFeature
-          return [
-            ...superContextMenuItems(),
-            ...(feature
-              ? [
-                  {
-                    label: 'Open synteny view for this position',
-                    onClick: () => navToSynteny(feature, self),
-                  },
-                ]
-              : []),
-          ]
-        },
-      }
-    })
-    .actions(self => ({
-      afterCreate() {
-        // use color by strand to help indicate inversions better
-        self.setColorScheme({ type: 'strand' })
-      },
-    }))
-}
-
-export default stateModelFactory

package/src/LaunchLinearSyntenyView.ts

@@ -1,86 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import { AbstractSessionModel } from '@jbrowse/core/util'
-import { LinearSyntenyViewModel } from './LinearSyntenyView/model'
-import { when } from 'mobx'
-
-type LSV = LinearSyntenyViewModel
-
-export default function LaunchLinearSyntenyView(pluginManager: PluginManager) {
-  pluginManager.addToExtensionPoint(
-    'LaunchView-LinearSyntenyView',
-    // @ts-expect-error
-    async ({
-      session,
-      views,
-      tracks = [],
-    }: {
-      session: AbstractSessionModel
-      views: { loc: string; assembly: string; tracks?: string[] }[]
-      tracks?: string[]
-    }) => {
-      try {
-        const { assemblyManager } = session
-        const model = session.addView('LinearSyntenyView', {}) as LSV
-
-        await when(() => !!model.width)
-
-        model.setViews(
-          await Promise.all(
-            views.map(async view => {
-              const asm = await assemblyManager.waitForAssembly(view.assembly)
-              if (!asm) {
-                throw new Error(`Assembly ${view.assembly} failed to load`)
-              }
-              return {
-                type: 'LinearGenomeView' as const,
-                bpPerPx: 1,
-                offsetPx: 0,
-                hideHeader: true,
-                displayedRegions: asm.regions,
-              }
-            }),
-          ),
-        )
-
-        await Promise.all(model.views.map(view => when(() => view.initialized)))
-
-        const idsNotFound = [] as string[]
-        await Promise.all(
-          views.map(async (data, idx) => {
-            const view = model.views[idx]
-            const { loc, tracks = [] } = data
-            await view.navToLocString(loc)
-            tracks.forEach(track => tryTrack(view, track, idsNotFound))
-          }),
-        )
-
-        tracks.forEach(track => tryTrack(model, track, idsNotFound))
-
-        if (idsNotFound.length) {
-          throw new Error(
-            `Could not resolve identifiers: ${idsNotFound.join(',')}`,
-          )
-        }
-      } catch (e) {
-        session.notify(`${e}`, 'error')
-        throw e
-      }
-    },
-  )
-}
-
-function tryTrack(
-  model: { showTrack: (arg: string) => void },
-  trackId: string,
-  idsNotFound: string[],
-) {
-  try {
-    model.showTrack(trackId)
-  } catch (e) {
-    if (`${e}`.match('Could not resolve identifier')) {
-      idsNotFound.push(trackId)
-    } else {
-      throw e
-    }
-  }
-}

package/src/LinearComparativeDisplay/configSchemaF.ts

@@ -1,22 +0,0 @@
-/* eslint-disable @typescript-eslint/no-explicit-any */
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config LinearComparativeDisplay
- */
-function configSchemaFactory(pluginManager: any) {
-  return ConfigurationSchema(
-    'LinearComparativeDisplay',
-    {},
-    {
-      explicitlyTyped: true,
-
-      /**
-       * #identifier
-       */
-      explicitIdentifier: 'displayId',
-    },
-  )
-}
-
-export default configSchemaFactory

package/src/LinearComparativeDisplay/index.ts

@@ -1,21 +0,0 @@
-import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
-import PluginManager from '@jbrowse/core/PluginManager'
-
-import configSchemaFactory from './configSchemaF'
-import stateModelFactory from './stateModelFactory'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addDisplayType(() => {
-    const configSchema = configSchemaFactory(pluginManager)
-    return new DisplayType({
-      name: 'LinearComparativeDisplay',
-      configSchema,
-      stateModel: stateModelFactory(configSchema),
-      trackType: 'SyntenyTrack',
-      viewType: 'LinearComparativeView',
-      ReactComponent: () => {
-        return null
-      },
-    })
-  })
-}