@jbrowse/plugin-dotplot-view 2.6.1 → 2.6.2

package/esm/DotplotView/model.js.map

@@ -1 +0,0 @@
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package/esm/DotplotView/svgcomponents/SVGBackground.js.map

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package/esm/DotplotView/svgcomponents/SVGDotplotView.js.map

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package/esm/LaunchDotplotView.js.map

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package/esm/ServerSideRenderedBlockContent.js.map

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package/esm/ServerSideSyntenyRendering.js.map

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package/esm/index.js.map

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package/esm/util.js.map

@@ -1 +0,0 @@
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package/src/ComparativeRenderer/index.ts

@@ -1,87 +0,0 @@
-import { checkAbortSignal } from '@jbrowse/core/util'
-import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType'
-import ComparativeRenderer, {
-  RenderArgs as ComparativeRenderArgs,
-  RenderArgsSerialized as ComparativeRenderArgsSerialized,
-  RenderResults,
-  ResultsSerialized,
-} from '@jbrowse/core/pluggableElementTypes/renderers/ComparativeServerSideRendererType'
-import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'
-
-interface RenderArgs extends ComparativeRenderArgs {
-  adapterConfig: {}
-  rendererType: string
-}
-
-interface RenderArgsSerialized extends ComparativeRenderArgsSerialized {
-  adapterConfig: {}
-  rendererType: string
-}
-
-/**
- * call a synteny renderer with the given args
- * param views: a set of views that each contain a set of regions
- * used instead of passing regions directly as in render()
- */
-export default class ComparativeRender extends RpcMethodType {
-  name = 'ComparativeRender'
-
-  async renameRegionsIfNeeded(args: RenderArgs, rend: ComparativeRenderer) {
-    return rend.renameRegionsIfNeeded(args)
-  }
-
-  getRenderer(rendererType: string) {
-    const pm = this.pluginManager
-    return pm.getRendererType(rendererType) as ComparativeRenderer
-  }
-
-  async serializeArguments(args: RenderArgs, rpcDriver: string) {
-    const { rendererType } = args
-    const renderer = this.getRenderer(rendererType)
-    const n = (await super.serializeArguments(args, rpcDriver)) as RenderArgs
-    const result = await this.renameRegionsIfNeeded(n, renderer)
-
-    return rpcDriver === 'MainThreadRpcDriver'
-      ? result
-      : renderer.serializeArgsInClient(result)
-  }
-
-  async execute(
-    args: RenderArgsSerialized & { signal?: RemoteAbortSignal },
-    rpcDriver: string,
-  ) {
-    let deserializedArgs = args
-    if (rpcDriver !== 'MainThreadRpcDriver') {
-      deserializedArgs = await this.deserializeArguments(args, rpcDriver)
-    }
-    const { sessionId, rendererType, signal } = deserializedArgs
-    if (!sessionId) {
-      throw new Error('must pass a unique session id')
-    }
-
-    checkAbortSignal(signal)
-
-    const renderer = this.getRenderer(rendererType)
-    return rpcDriver === 'MainThreadRpcDriver'
-      ? renderer.render(deserializedArgs)
-      : renderer.renderInWorker(deserializedArgs)
-  }
-
-  async deserializeReturn(
-    val: RenderResults | ResultsSerialized,
-    args: RenderArgs,
-    rpcDriver: string,
-  ): Promise<unknown> {
-    const ret = (await super.deserializeReturn(
-      val,
-      args,
-      rpcDriver,
-    )) as ResultsSerialized
-    if (rpcDriver === 'MainThreadRpcDriver') {
-      return ret
-    }
-
-    const renderer = this.getRenderer(args.rendererType)
-    return renderer.deserializeResultsInClient(ret, args)
-  }
-}

package/src/DotplotDisplay/components/DotplotDisplay.tsx

@@ -1,34 +0,0 @@
-import React from 'react'
-import { observer } from 'mobx-react'
-import { getContainingView } from '@jbrowse/core/util'
-
-// locals
-import { DotplotDisplayModel } from '../stateModelFactory'
-import { DotplotViewModel } from '../../DotplotView/model'
-
-function DotplotDisplay(props: {
-  model: DotplotDisplayModel
-  children?: React.ReactNode
-}) {
-  const { model, children } = props
-  const { offsetX = 0, offsetY = 0 } = model.data || {}
-  const view = getContainingView(model) as DotplotViewModel
-
-  const top = view.vview.offsetPx - offsetY
-  const left = -(view.hview.offsetPx - offsetX)
-  return (
-    <div style={{ position: 'relative' }}>
-      <model.ReactComponent2
-        {...props}
-        style={{
-          position: 'absolute',
-          top,
-          left,
-        }}
-      />
-      {children}
-    </div>
-  )
-}
-
-export default observer(DotplotDisplay)

package/src/DotplotDisplay/index.ts

@@ -1,48 +0,0 @@
-/* eslint-disable @typescript-eslint/no-explicit-any */
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { types } from 'mobx-state-tree'
-import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
-import PluginManager from '@jbrowse/core/PluginManager'
-
-// locals
-import { stateModelFactory } from './stateModelFactory'
-import ReactComponent from './components/DotplotDisplay'
-
-export default (pm: PluginManager) => {
-  pm.addDisplayType(() => {
-    const configSchema = configSchemaFactory(pm)
-    return new DisplayType({
-      name: 'DotplotDisplay',
-      displayName: 'Dotplot display',
-      configSchema,
-      stateModel: stateModelFactory(configSchema),
-      trackType: 'SyntenyTrack',
-      viewType: 'DotplotView',
-      ReactComponent,
-    })
-  })
-}
-
-/**
- * #config DotplotDisplay
- */
-export function configSchemaFactory(pm: any) {
-  return ConfigurationSchema(
-    'DotplotDisplay',
-    {
-      /**
-       * #slot
-       */
-      renderer: types.optional(pm.pluggableConfigSchemaType('renderer'), {
-        type: 'DotplotRenderer',
-      }),
-    },
-    {
-      /**
-       * #identifier
-       */
-      explicitIdentifier: 'displayId',
-      explicitlyTyped: true,
-    },
-  )
-}

package/src/DotplotDisplay/renderDotplotBlock.ts

@@ -1,60 +0,0 @@
-import clone from 'clone'
-import { readConfObject } from '@jbrowse/core/configuration'
-import { getRpcSessionId } from '@jbrowse/core/util/tracks'
-import { getSnapshot, IAnyStateTreeNode } from 'mobx-state-tree'
-import { getContainingView, getSession } from '@jbrowse/core/util'
-
-import { DotplotViewModel } from '../DotplotView/model'
-
-export function renderBlockData(self: IAnyStateTreeNode) {
-  const { rpcManager } = getSession(self)
-  const { rendererType } = self
-  const { adapterConfig } = self
-  const parent = getContainingView(self) as DotplotViewModel
-
-  // Alternative to readConfObject(config) is below used because renderProps is
-  // something under our control.  Compare to serverSideRenderedBlock
-  readConfObject(self.configuration)
-  getSnapshot(parent)
-
-  if (parent.initialized) {
-    const { viewWidth, viewHeight, borderSize, borderX, borderY } = parent
-    return {
-      rendererType,
-      rpcManager,
-      renderProps: {
-        ...self.renderProps(),
-        view: clone(getSnapshot(parent)),
-        width: viewWidth,
-        height: viewHeight,
-        borderSize,
-        borderX,
-        borderY,
-        adapterConfig,
-        rendererType: rendererType.name,
-        sessionId: getRpcSessionId(self),
-        timeout: 1000000, // 10000,
-      },
-    }
-  }
-  return undefined
-}
-
-export async function renderBlockEffect(
-  props?: ReturnType<typeof renderBlockData>,
-) {
-  if (!props) {
-    return
-  }
-
-  const { rendererType, rpcManager, renderProps } = props
-  const { reactElement, ...data } = await rendererType.renderInClient(
-    rpcManager,
-    renderProps,
-  )
-  return {
-    reactElement,
-    data,
-    renderingComponent: rendererType.ReactComponent,
-  }
-}

package/src/DotplotDisplay/stateModelFactory.tsx

@@ -1,196 +0,0 @@
-/* eslint-disable @typescript-eslint/no-explicit-any */
-import React from 'react'
-import { ThemeOptions } from '@mui/material'
-import { types, Instance } from 'mobx-state-tree'
-import {
-  getConf,
-  ConfigurationReference,
-  AnyConfigurationSchemaType,
-} from '@jbrowse/core/configuration'
-import { getParentRenderProps } from '@jbrowse/core/util/tracks'
-import {
-  getContainingView,
-  makeAbortableReaction,
-  ReactRendering,
-} from '@jbrowse/core/util'
-import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes/models'
-
-// locals
-import ServerSideRenderedBlockContent from '../ServerSideRenderedBlockContent'
-import { renderBlockData, renderBlockEffect } from './renderDotplotBlock'
-import { DotplotViewModel, ExportSvgOptions } from '../DotplotView/model'
-
-/**
- * #stateModel DotplotDisplay
- * #category display
- */
-export function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
-  return types
-    .compose(
-      'DotplotDisplay',
-      BaseDisplay,
-      types
-        .model({
-          /**
-           * #property
-           */
-          type: types.literal('DotplotDisplay'),
-          /**
-           * #property
-           */
-          configuration: ConfigurationReference(configSchema),
-        })
-        .volatile(() => ({
-          warnings: [] as { message: string; effect: string }[],
-          renderInProgress: undefined as AbortController | undefined,
-          filled: false,
-          data: undefined as any,
-          reactElement: undefined as React.ReactElement | undefined,
-          message: undefined as string | undefined,
-          renderingComponent: undefined as any,
-          ReactComponent2:
-            ServerSideRenderedBlockContent as unknown as React.FC<any>,
-        })),
-    )
-    .views(self => ({
-      get shouldDisplay() {
-        const view = getContainingView(self)
-        return (
-          view.vview.bpPerPx === self.data.bpPerPxY &&
-          view.hview.bpPerPx === self.data.bpPerPxX
-        )
-      },
-      /**
-       * #getter
-       */
-      get rendererTypeName() {
-        return getConf(self, ['renderer', 'type'])
-      },
-      /**
-       * #method
-       */
-      renderProps() {
-        return {
-          ...getParentRenderProps(self),
-          rpcDriverName: self.rpcDriverName,
-          displayModel: self,
-          config: self.configuration.renderer,
-        }
-      },
-    }))
-    .views(self => ({
-      /**
-       * #method
-       */
-      async renderSvg(opts: ExportSvgOptions & { theme: ThemeOptions }) {
-        const props = renderBlockData(self)
-        if (!props) {
-          return null
-        }
-
-        const { rendererType, rpcManager, renderProps } = props
-        const rendering = await rendererType.renderInClient(rpcManager, {
-          ...renderProps,
-          exportSVG: opts,
-          theme: opts.theme || renderProps.theme,
-        })
-        const { hview, vview } = getContainingView(self) as DotplotViewModel
-        const offX = -hview.offsetPx + rendering.offsetX
-        const offY = -vview.offsetPx + rendering.offsetY
-        return (
-          <g transform={`translate(${offX} ${-offY})`}>
-            <ReactRendering rendering={rendering} />
-          </g>
-        )
-      },
-    }))
-    .actions(self => {
-      let renderInProgress: undefined | AbortController
-
-      return {
-        afterAttach() {
-          makeAbortableReaction(
-            self,
-            () => renderBlockData(self),
-            blockData => renderBlockEffect(blockData),
-            {
-              name: `${self.type} ${self.id} rendering`,
-              delay: 500,
-              fireImmediately: true,
-            },
-            this.setLoading,
-            this.setRendered,
-            this.setError,
-          )
-        },
-        /**
-         * #action
-         */
-        setLoading(abortController: AbortController) {
-          self.filled = false
-          self.message = undefined
-          self.reactElement = undefined
-          self.data = undefined
-          self.error = undefined
-          self.renderingComponent = undefined
-          renderInProgress = abortController
-        },
-        /**
-         * #action
-         */
-        setMessage(messageText: string) {
-          if (renderInProgress && !renderInProgress.signal.aborted) {
-            renderInProgress.abort()
-          }
-          self.filled = false
-          self.message = messageText
-          self.reactElement = undefined
-          self.data = undefined
-          self.error = undefined
-          self.renderingComponent = undefined
-          renderInProgress = undefined
-        },
-        /**
-         * #action
-         */
-        setRendered(args?: {
-          data: any
-          reactElement: React.ReactElement
-          renderingComponent: React.Component
-        }) {
-          if (args === undefined) {
-            return
-          }
-          const { data, reactElement, renderingComponent } = args
-          self.warnings = data.warnings
-          self.filled = true
-          self.message = undefined
-          self.reactElement = reactElement
-          self.data = data
-          self.error = undefined
-          self.renderingComponent = renderingComponent
-          renderInProgress = undefined
-        },
-        /**
-         * #action
-         */
-        setError(error: unknown) {
-          console.error(error)
-          if (renderInProgress && !renderInProgress.signal.aborted) {
-            renderInProgress.abort()
-          }
-          // the rendering failed for some reason
-          self.filled = false
-          self.message = undefined
-          self.reactElement = undefined
-          self.data = undefined
-          self.error = error
-          self.renderingComponent = undefined
-          renderInProgress = undefined
-        },
-      }
-    })
-}
-
-export type DotplotDisplayStateModel = ReturnType<typeof stateModelFactory>
-export type DotplotDisplayModel = Instance<DotplotDisplayStateModel>

package/src/DotplotReadVsRef/DotplotReadVsRef.ts

@@ -1,115 +0,0 @@
-import { getConf } from '@jbrowse/core/configuration'
-import { getSession, Feature, gatherOverlaps } from '@jbrowse/core/util'
-import {
-  LinearPileupDisplayModel,
-  MismatchParser,
-} from '@jbrowse/plugin-alignments'
-
-// locals
-import { ReducedFeature } from '../util'
-
-const { featurizeSA, getClip, getTag, getLength, getLengthSansClipping } =
-  MismatchParser
-
-export function onClick(feature: Feature, self: LinearPileupDisplayModel) {
-  const session = getSession(self)
-  try {
-    const cigar = feature.get('CIGAR')
-    const clipPos = getClip(cigar, 1)
-    const flags = feature.get('flags')
-    const strand = feature.get('strand')
-    const readName = feature.get('name')
-    const readAssembly = `${readName}_assembly_${Date.now()}`
-    const { parentTrack } = self
-    const [trackAssembly] = getConf(parentTrack, 'assemblyNames')
-    const assemblyNames = [trackAssembly, readAssembly]
-    const trackId = `track-${Date.now()}`
-    const trackName = `${readName}_vs_${trackAssembly}`
-    const SA = (getTag(feature, 'SA') as string) || ''
-    const SA2 = featurizeSA(SA, feature.id(), strand, readName, true)
-
-    const feat = feature.toJSON()
-    feat.strand = 1
-    feat.mate = {
-      refName: readName,
-      start: clipPos,
-      end: clipPos + getLengthSansClipping(cigar),
-    }
-
-    // if secondary alignment or supplementary, calculate length from SA[0]'s
-    // CIGAR which is the primary alignments. otherwise it is the primary
-    // alignment just use seq.length if primary alignment
-    const totalLength = getLength(flags & 2048 ? SA2[0].CIGAR : cigar)
-
-    const features = [feat, ...SA2] as ReducedFeature[]
-
-    features.sort((a, b) => a.clipPos - b.clipPos)
-
-    const refLength = features.reduce((a, f) => a + f.end - f.start, 0)
-
-    session.addView('DotplotView', {
-      type: 'DotplotView',
-      hview: {
-        offsetPx: 0,
-        bpPerPx: refLength / 800,
-        displayedRegions: gatherOverlaps(
-          features.map((f, index) => {
-            const { start, end, refName } = f
-            return {
-              start,
-              end,
-              refName,
-              index,
-              assemblyName: trackAssembly,
-            }
-          }),
-        ),
-      },
-      vview: {
-        offsetPx: 0,
-        bpPerPx: totalLength / 400,
-        minimumBlockWidth: 0,
-        interRegionPaddingWidth: 0,
-        displayedRegions: [
-          {
-            assemblyName: readAssembly,
-            start: 0,
-            end: totalLength,
-            refName: readName,
-          },
-        ],
-      },
-
-      viewTrackConfigs: [
-        {
-          type: 'SyntenyTrack',
-          assemblyNames,
-          adapter: {
-            type: 'FromConfigAdapter',
-            features,
-          },
-          trackId,
-          name: trackName,
-        },
-      ],
-      assemblyNames,
-      tracks: [
-        {
-          configuration: trackId,
-          type: 'SyntenyTrack',
-          displays: [
-            {
-              type: 'DotplotDisplay',
-              configuration: `${trackId}-DotplotDisplay`,
-            },
-          ],
-        },
-      ],
-
-      displayName: `${readName} vs ${trackAssembly}`,
-    })
-  } catch (e) {
-    console.error(e)
-    session.notify(`${e}`, 'error')
-  }
-}

package/src/DotplotReadVsRef/index.ts

@@ -1,50 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import {
-  PluggableElementType,
-  ViewType,
-} from '@jbrowse/core/pluggableElementTypes'
-import { LinearPileupDisplayModel } from '@jbrowse/plugin-alignments'
-
-// icons
-import AddIcon from '@mui/icons-material/Add'
-
-// local
-import { onClick } from './DotplotReadVsRef'
-
-export default function DotplotReadVsRefMenuItem(pluginManager: PluginManager) {
-  pluginManager.addToExtensionPoint(
-    'Core-extendPluggableElement',
-    (pluggableElement: PluggableElementType) => {
-      if (pluggableElement.name === 'LinearPileupDisplay') {
-        const { stateModel } = pluggableElement as ViewType
-        const newStateModel = stateModel.extend(
-          (self: LinearPileupDisplayModel) => {
-            const superContextMenuItems = self.contextMenuItems
-            return {
-              views: {
-                contextMenuItems() {
-                  const feature = self.contextMenuFeature
-                  return [
-                    ...superContextMenuItems(),
-                    ...(feature
-                      ? [
-                          {
-                            label: 'Dotplot of read vs ref',
-                            icon: AddIcon,
-                            onClick: () => onClick(feature, self),
-                          },
-                        ]
-                      : []),
-                  ]
-                },
-              },
-            }
-          },
-        )
-
-        ;(pluggableElement as ViewType).stateModel = newStateModel
-      }
-      return pluggableElement
-    },
-  )
-}