@jbrowse/plugin-variants 2.6.1 → 2.6.3

package/dist/extensionPoints.js.map

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package/dist/index.js.map

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package/esm/ChordVariantDisplay/index.js.map

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package/esm/ChordVariantDisplay/models/configSchema.js.map

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package/esm/ChordVariantDisplay/models/stateModelFactory.js.map

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package/esm/LinearVariantDisplay/configSchema.js.map

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package/esm/LinearVariantDisplay/index.js.map

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package/esm/LinearVariantDisplay/model.js.map

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package/esm/StructuralVariantChordRenderer/Chord.js.map

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package/esm/StructuralVariantChordRenderer/ReactComponent.js.map

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package/esm/StructuralVariantChordRenderer/configSchema.js.map

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package/esm/StructuralVariantChordRenderer/index.js.map

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package/esm/VariantFeatureWidget/AnnotGrid.js.map

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package/esm/VariantFeatureWidget/BreakendOptionDialog.js.map

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package/esm/VariantFeatureWidget/BreakendPanel.js.map

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package/esm/VariantFeatureWidget/VariantAnnotationTable.js.map

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package/esm/VariantFeatureWidget/VariantFeatureWidget.js.map

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package/esm/VariantFeatureWidget/VariantSampleGrid.js.map

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package/esm/VariantFeatureWidget/index.js.map

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package/esm/VariantTrack/configSchema.js.map

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package/esm/VariantTrack/index.js.map

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package/esm/VcfAdapter/VcfAdapter.js.map

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package/esm/VcfAdapter/configSchema.js.map

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package/esm/VcfAdapter/index.js.map

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package/esm/VcfFeature/index.js.map

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package/esm/VcfFeature/util.js.map

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package/esm/VcfTabixAdapter/VcfTabixAdapter.js.map

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package/esm/VcfTabixAdapter/configSchema.js.map

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package/esm/extensionPoints.js.map

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package/src/ChordVariantDisplay/index.ts

@@ -1,23 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import { BaseChordDisplayComponent } from '@jbrowse/plugin-circular-view'
-import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
-
-// locals
-import configSchemaF from './models/configSchema'
-import stateModelF from './models/stateModelFactory'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addDisplayType(() => {
-    const configSchema = configSchemaF(pluginManager)
-    const stateModel = stateModelF(configSchema)
-    return new DisplayType({
-      name: 'ChordVariantDisplay',
-      displayName: 'Chord variant display',
-      configSchema,
-      stateModel,
-      trackType: 'VariantTrack',
-      viewType: 'CircularView',
-      ReactComponent: BaseChordDisplayComponent,
-    })
-  })
-}

package/src/ChordVariantDisplay/models/configSchema.ts

@@ -1,33 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { baseChordDisplayConfig } from '@jbrowse/plugin-circular-view'
-import { types } from 'mobx-state-tree'
-
-/**
- * #config ChordVariantDisplay
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-function stateModelFactory(pluginManager: PluginManager) {
-  return ConfigurationSchema(
-    'ChordVariantDisplay',
-    {
-      /**
-       * #slot
-       */
-      renderer: types.optional(
-        pluginManager.pluggableConfigSchemaType('renderer'),
-        { type: 'StructuralVariantChordRenderer' },
-      ),
-    },
-    {
-      /**
-       * #baseConfiguration
-       */
-      baseConfiguration: baseChordDisplayConfig,
-      explicitlyTyped: true,
-    },
-  )
-}
-
-export default stateModelFactory

package/src/ChordVariantDisplay/models/stateModelFactory.ts

@@ -1,63 +0,0 @@
-import { BaseChordDisplayModel } from '@jbrowse/plugin-circular-view'
-import {
-  AnyConfigurationSchemaType,
-  ConfigurationReference,
-} from '@jbrowse/core/configuration'
-import { types } from 'mobx-state-tree'
-import { Feature, getContainingView } from '@jbrowse/core/util'
-import { getParentRenderProps } from '@jbrowse/core/util/tracks'
-
-/**
- * #stateModel ChordVariantDisplay
- * extends `BaseChordDisplay`
- */
-const stateModelFactory = (configSchema: AnyConfigurationSchemaType) => {
-  return types
-    .compose(
-      'ChordVariantDisplay',
-      BaseChordDisplayModel,
-      types.model({
-        /**
-         * #property
-         */
-        type: types.literal('ChordVariantDisplay'),
-        /**
-         * #property
-         */
-        configuration: ConfigurationReference(configSchema),
-      }),
-    )
-    .views(self => ({
-      /**
-       * #getter
-       */
-      get rendererTypeName() {
-        return self.configuration.renderer.type
-      },
-
-      /**
-       * #method
-       */
-      renderProps(): Record<string, unknown> {
-        const view = getContainingView(self)
-        return {
-          ...getParentRenderProps(self),
-          rpcDriverName: self.rpcDriverName,
-          displayModel: self,
-          bezierRadius: view.radiusPx * self.bezierRadiusRatio,
-          radius: view.radiusPx,
-          blockDefinitions: self.blockDefinitions,
-          config: self.configuration.renderer,
-          onChordClick: (arg: Feature) => self.onChordClick(arg),
-        }
-      },
-    }))
-}
-
-// http://localhost:3000/test_data/hs37d5.HG002-SequelII-CCS.sv.vcf.gz.tbi
-
-// render request is for 1.5x the current viewing window
-
-// tracks all have a height
-//
-export default stateModelFactory

package/src/LinearVariantDisplay/configSchema.ts

@@ -1,30 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { Instance } from 'mobx-state-tree'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { linearBasicDisplayConfigSchemaFactory } from '@jbrowse/plugin-linear-genome-view'
-
-/**
- * #config LinearVariantDisplay
- * mostly empty, this display type is very much
- * like a `FeatureTrack` with a `LinearBasicDisplay` except it has a custom
- * feature details widget
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-export default function configSchemaF(pluginManager: PluginManager) {
-  return ConfigurationSchema(
-    'LinearVariantDisplay',
-    {},
-    {
-      /**
-       * #baseConfiguration
-       */
-      baseConfiguration: linearBasicDisplayConfigSchemaFactory(pluginManager),
-      explicitlyTyped: true,
-    },
-  )
-}
-
-export type LinearVariantDisplayConfigModel = ReturnType<typeof configSchemaF>
-export type LinearVariantDisplayConfig =
-  Instance<LinearVariantDisplayConfigModel>

package/src/LinearVariantDisplay/index.ts

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

package/src/LinearVariantDisplay/model.ts

@@ -1,76 +0,0 @@
-import { getConf, ConfigurationReference } from '@jbrowse/core/configuration'
-import { getRpcSessionId } from '@jbrowse/core/util/tracks'
-import {
-  getContainingTrack,
-  getSession,
-  getContainingView,
-  isSessionModelWithWidgets,
-  Feature,
-} from '@jbrowse/core/util'
-
-import { linearBasicDisplayModelFactory } from '@jbrowse/plugin-linear-genome-view'
-import { Instance, types } from 'mobx-state-tree'
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
-
-/**
- * #stateModel LinearVariantDisplay
- * extends `LinearBasicDisplay`
- * very similar to basic display, but provides custom widget on feature click
- */
-export default function stateModelFactory(
-  configSchema: AnyConfigurationSchemaType,
-) {
-  return types
-    .compose(
-      'LinearVariantDisplay',
-      linearBasicDisplayModelFactory(configSchema),
-      types.model({
-        /**
-         * #property
-         */
-        type: types.literal('LinearVariantDisplay'),
-        /**
-         * #property
-         */
-        configuration: ConfigurationReference(configSchema),
-      }),
-    )
-
-    .actions(self => ({
-      /**
-       * #action
-       */
-      async selectFeature(feature: Feature) {
-        const session = getSession(self)
-        if (isSessionModelWithWidgets(session)) {
-          const { rpcManager } = session
-          const sessionId = getRpcSessionId(self)
-          const track = getContainingTrack(self)
-          const view = getContainingView(self)
-          const adapterConfig = getConf(track, 'adapter')
-          const descriptions = await rpcManager.call(
-            sessionId,
-            'CoreGetMetadata',
-            {
-              adapterConfig,
-            },
-          )
-          session.showWidget(
-            session.addWidget('VariantFeatureWidget', 'variantFeature', {
-              featureData: feature.toJSON(),
-              view,
-              track,
-              descriptions,
-            }),
-          )
-        }
-
-        session.setSelection(feature)
-      },
-    }))
-}
-
-export type LinearVariantDisplayStateModel = ReturnType<
-  typeof stateModelFactory
->
-export type LinearVariantDisplayModel = Instance<LinearVariantDisplayStateModel>

package/src/StructuralVariantChordRenderer/Chord.tsx

@@ -1,141 +0,0 @@
-import React from 'react'
-import { observer } from 'mobx-react'
-import { polarToCartesian, Feature } from '@jbrowse/core/util'
-import {
-  AnyConfigurationModel,
-  readConfObject,
-} from '@jbrowse/core/configuration'
-import { parseBreakend } from '@gmod/vcf'
-
-export interface Region {
-  end: number
-  start: number
-  refName: string
-  elided?: false
-}
-
-export interface ElidedRegion {
-  elided: true
-  regions: Region[]
-}
-
-export type AnyRegion = Region | ElidedRegion
-
-export interface Block {
-  flipped: boolean
-  bpPerRadian: number
-  startRadians: number
-  region: AnyRegion
-}
-
-function bpToRadians(block: Block, pos: number) {
-  const blockStart = block.region.elided ? 0 : block.region.start
-  const blockEnd = block.region.elided ? 0 : block.region.end
-  const bpOffset = block.flipped ? blockEnd - pos : pos - blockStart
-  return bpOffset / block.bpPerRadian + block.startRadians
-}
-
-const Chord = observer(function Chord({
-  feature,
-  blocksForRefs,
-  radius,
-  config,
-  bezierRadius,
-  selected,
-  onClick,
-}: {
-  feature: Feature
-  blocksForRefs: { [key: string]: Block }
-  radius: number
-  config: AnyConfigurationModel
-  bezierRadius: number
-  selected: boolean
-  onClick: (
-    feature: Feature,
-    reg: AnyRegion,
-    endBlock: AnyRegion,
-    evt: unknown,
-  ) => void
-}) {
-  // find the blocks that our start and end points belong to
-  const startBlock = blocksForRefs[feature.get('refName')]
-  if (!startBlock) {
-    return null
-  }
-  let svType
-  if (feature.get('INFO')) {
-    ;[svType] = feature.get('INFO').SVTYPE || []
-  } else if (feature.get('mate')) {
-    svType = 'mate'
-  }
-  let endPosition
-  let endBlock: Block | undefined
-  const alt = feature.get('ALT')?.[0]
-  const bnd = alt && parseBreakend(alt)
-  if (bnd) {
-    // VCF BND
-    const matePosition = bnd.MatePosition.split(':')
-    endPosition = +matePosition[1]
-    endBlock = blocksForRefs[matePosition[0]]
-  } else if (alt === '<TRA>') {
-    // VCF TRA
-    const chr2 = feature.get('INFO')?.CHR2?.[0]
-    const end = feature.get('INFO')?.END?.[0]
-    endPosition = parseInt(end, 10)
-    endBlock = blocksForRefs[chr2]
-  } else if (svType === 'mate') {
-    // generic simplefeatures arcs
-    const mate = feature.get('mate')
-    const chr2 = mate.refName
-    endPosition = mate.start
-    endBlock = blocksForRefs[chr2]
-  }
-
-  if (endBlock) {
-    const startPos = feature.get('start')
-    const startRadians = bpToRadians(startBlock, startPos)
-    const endRadians = bpToRadians(endBlock, endPosition)
-    const startXY = polarToCartesian(radius, startRadians)
-    const endXY = polarToCartesian(radius, endRadians)
-    const controlXY = polarToCartesian(
-      bezierRadius,
-      (endRadians + startRadians) / 2,
-    )
-
-    const strokeColor = selected
-      ? readConfObject(config, 'strokeColorSelected', { feature })
-      : readConfObject(config, 'strokeColor', { feature })
-
-    const hoverStrokeColor = readConfObject(config, 'strokeColorHover', {
-      feature,
-    })
-    return (
-      <path
-        data-testid={`chord-${feature.id()}`}
-        d={['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' ')}
-        style={{ stroke: strokeColor }}
-        onClick={evt => {
-          if (endBlock && startBlock) {
-            onClick(feature, startBlock.region, endBlock.region, evt)
-          }
-        }}
-        onMouseOver={evt => {
-          if (!selected) {
-            evt.currentTarget.style.stroke = hoverStrokeColor
-            evt.currentTarget.style.strokeWidth = '3px'
-          }
-        }}
-        onMouseOut={evt => {
-          if (!selected) {
-            evt.currentTarget.style.stroke = strokeColor
-            evt.currentTarget.style.strokeWidth = '1px'
-          }
-        }}
-      />
-    )
-  }
-
-  return null
-})
-
-export default Chord