@jbrowse/plugin-circular-view 2.6.1 → 2.6.2

package/src/CircularView/svgcomponents/SVGBackground.tsx

@@ -1,21 +0,0 @@
-import React from 'react'
-import { useTheme } from '@mui/material'
-
-export default function SVGBackground({
-  width,
-  height,
-  shift,
-}: {
-  width: number
-  height: number
-  shift: number
-}) {
-  const theme = useTheme()
-  return (
-    <rect
-      width={width + shift * 2}
-      height={height}
-      fill={theme.palette.background.default}
-    />
-  )
-}

package/src/CircularView/svgcomponents/SVGCircularView.tsx

@@ -1,58 +0,0 @@
-import React from 'react'
-import { ThemeProvider } from '@mui/material'
-import { renderToStaticMarkup } from 'react-dom/server'
-import { when } from 'mobx'
-import { getSession, radToDeg } from '@jbrowse/core/util'
-import { createJBrowseTheme } from '@jbrowse/core/ui'
-
-// locals
-import { ExportSvgOptions, CircularViewModel } from '../models/CircularView'
-import SVGBackground from './SVGBackground'
-import Ruler from '../components/Ruler'
-
-type CGV = CircularViewModel
-
-export async function renderToSvg(model: CGV, opts: ExportSvgOptions) {
-  await when(() => model.initialized)
-  const { themeName = 'default', Wrapper = ({ children }) => <>{children}</> } =
-    opts
-  const session = getSession(model)
-  const theme = session.allThemes?.()[themeName]
-  const { width, tracks, height } = model
-  const shift = 50
-  const displayResults = await Promise.all(
-    tracks.map(async track => {
-      const display = track.displays[0]
-      await when(() => (display.ready !== undefined ? display.ready : true))
-      return { track, result: await display.renderSvg({ ...opts, theme }) }
-    }),
-  )
-
-  const { staticSlices, offsetRadians, centerXY } = model
-  const deg = radToDeg(offsetRadians)
-
-  // the xlink namespace is used for rendering <image> tag
-  return renderToStaticMarkup(
-    <ThemeProvider theme={createJBrowseTheme(theme)}>
-      <Wrapper>
-        <svg
-          width={width}
-          height={height}
-          xmlns="http://www.w3.org/2000/svg"
-          xmlnsXlink="http://www.w3.org/1999/xlink"
-          viewBox={[0, 0, width + shift * 2, height].toString()}
-        >
-          <SVGBackground width={width} height={height} shift={shift} />
-          <g transform={`translate(${centerXY}) rotate(${deg})`}>
-            {staticSlices.map((slice, i) => (
-              <Ruler key={i} model={model} slice={slice} />
-            ))}
-            {displayResults.map(({ result }, i) => (
-              <React.Fragment key={i}>{result}</React.Fragment>
-            ))}
-          </g>
-        </svg>
-      </Wrapper>
-    </ThemeProvider>,
-  )
-}

package/src/LaunchCircularView/index.ts

@@ -1,48 +0,0 @@
-import { when } from 'mobx'
-import { AbstractSessionModel } from '@jbrowse/core/util'
-import PluginManager from '@jbrowse/core/PluginManager'
-
-// locals
-import { CircularViewModel } from '../CircularView/models/CircularView'
-
-type CGV = CircularViewModel
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addToExtensionPoint(
-    'LaunchView-CircularView',
-    // @ts-expect-error
-    async ({
-      session,
-      assembly,
-      loc,
-      tracks = [],
-    }: {
-      session: AbstractSessionModel
-      assembly?: string
-      loc: string
-      tracks?: string[]
-    }) => {
-      const { assemblyManager } = session
-      const view = session.addView('CircularView', {}) as CGV
-
-      await when(() => view.initialized)
-
-      if (!assembly) {
-        throw new Error(
-          'No assembly provided when launching circular genome view',
-        )
-      }
-
-      const asm = await assemblyManager.waitForAssembly(assembly)
-      if (!asm) {
-        throw new Error(
-          `Assembly "${assembly}" not found when launching circular genome view`,
-        )
-      }
-
-      view.setDisplayedRegions(asm.regions || [])
-
-      tracks.forEach(track => view.showTrack(track))
-    },
-  )
-}

package/src/index.ts

@@ -1,43 +0,0 @@
-import { AbstractSessionModel, isAbstractMenuManager } from '@jbrowse/core/util'
-import PluginManager from '@jbrowse/core/PluginManager'
-import Plugin from '@jbrowse/core/Plugin'
-
-// locals
-
-import CircularViewF from './CircularView'
-import LaunchCircularViewF from './LaunchCircularView'
-
-// icons
-import DataUsageIcon from '@mui/icons-material/DataUsage'
-
-export default class CircularViewPlugin extends Plugin {
-  name = 'CircularViewPlugin'
-
-  install(pluginManager: PluginManager) {
-    CircularViewF(pluginManager)
-    LaunchCircularViewF(pluginManager)
-  }
-
-  configure(pluginManager: PluginManager) {
-    if (isAbstractMenuManager(pluginManager.rootModel)) {
-      pluginManager.rootModel.appendToSubMenu(['Add'], {
-        label: 'Circular view',
-        icon: DataUsageIcon,
-        onClick: (session: AbstractSessionModel) => {
-          session.addView('CircularView', {})
-        },
-      })
-    }
-  }
-}
-
-export {
-  baseChordDisplayConfig,
-  BaseChordDisplayModel,
-  BaseChordDisplayComponent,
-} from './BaseChordDisplay'
-
-export {
-  type CircularViewModel,
-  type CircularViewStateModel,
-} from './CircularView/models/CircularView'