@jbrowse/plugin-linear-genome-view 2.5.0 → 2.6.2

package/src/LinearGenomeView/util.ts

@@ -1,182 +0,0 @@
-import {
-  AssemblyManager,
-  ParsedLocString,
-  parseLocString,
-} from '@jbrowse/core/util'
-
-/**
- * Given a scale ( bp/px ) and minimum distances (px) between major and minor
- * gridlines, return an object like `{ majorPitch: bp, minorPitch: bp }` giving
- * the gridline pitches to use.
- */
-export function chooseGridPitch(
-  scale: number,
-  minMajorPitchPx: number,
-  minMinorPitchPx: number,
-) {
-  scale = Math.abs(scale)
-  const minMajorPitchBp = minMajorPitchPx * scale
-  const majorMagnitude = Number.parseInt(
-    Number(minMajorPitchBp).toExponential().split(/e/i)[1],
-    10,
-  )
-
-  let majorPitch = 10 ** majorMagnitude
-  while (majorPitch < minMajorPitchBp) {
-    majorPitch *= 2
-    if (majorPitch >= minMajorPitchBp) {
-      break
-    }
-    majorPitch *= 2.5
-  }
-
-  majorPitch = Math.max(majorPitch, 5)
-
-  const majorPitchPx = majorPitch / scale
-
-  let minorPitch = 0
-  if (!(majorPitch % 10) && majorPitchPx / 10 >= minMinorPitchPx) {
-    minorPitch = majorPitch / 10
-  } else if (!(majorPitch % 5) && majorPitchPx / 5 >= minMinorPitchPx) {
-    minorPitch = majorPitch / 5
-  } else if (!(majorPitch % 2) && majorPitchPx / 2 >= minMinorPitchPx) {
-    minorPitch = majorPitch / 2
-  }
-
-  return { majorPitch, minorPitch }
-}
-
-export function makeTicks(
-  start: number,
-  end: number,
-  bpPerPx: number,
-  emitMajor = true,
-  emitMinor = true,
-) {
-  const gridPitch = chooseGridPitch(bpPerPx, 60, 15)
-
-  let minBase = start
-  let maxBase = end
-  if (minBase === null || maxBase === null) {
-    return []
-  }
-
-  if (bpPerPx < 0) {
-    ;[minBase, maxBase] = [maxBase, minBase]
-  }
-
-  // add 20px additional on the right and left to allow us to draw the ends
-  // of labels that lie a little outside our region
-  minBase -= Math.abs(20 * bpPerPx) - 1
-  maxBase += Math.abs(20 * bpPerPx) + 1
-
-  const iterPitch = gridPitch.minorPitch || gridPitch.majorPitch
-  let index = 0
-  const ticks = []
-  for (
-    let base = Math.floor(minBase / iterPitch) * iterPitch;
-    base < Math.ceil(maxBase / iterPitch) * iterPitch + 1;
-    base += iterPitch
-  ) {
-    if (emitMinor && base % (gridPitch.majorPitch * 2)) {
-      ticks.push({ type: 'minor', base: base - 1, index })
-      index += 1
-    } else if (emitMajor && !(base % (gridPitch.majorPitch * 2))) {
-      ticks.push({ type: 'major', base: base - 1, index })
-      index += 1
-    }
-  }
-  return ticks
-}
-
-/**
- * Generate location objects for a set of parsed locstrings, which includes
- * translating the refNames to assembly-canonical refNames and adding the
- * 'parentRegion'
- *
- * Used by navToLocations and navToLocString
- */
-export async function generateLocations(
-  regions: ParsedLocString[] = [],
-  assemblyManager: AssemblyManager,
-  assemblyName?: string,
-) {
-  return Promise.all(
-    regions.map(async region => {
-      const asmName = region.assemblyName || assemblyName
-      if (!asmName) {
-        throw new Error('no assembly provided')
-      }
-      const asm = await assemblyManager.waitForAssembly(asmName)
-      const { refName } = region
-      if (!asm) {
-        throw new Error(`assembly ${asmName} not found`)
-      }
-      const { regions } = asm
-      if (!regions) {
-        throw new Error(`regions not loaded yet for ${asmName}`)
-      }
-      const canonicalRefName = asm.getCanonicalRefName(region.refName)
-      if (!canonicalRefName) {
-        throw new Error(`Could not find refName ${refName} in ${asm.name}`)
-      }
-      const parentRegion = regions.find(r => r.refName === canonicalRefName)
-      if (!parentRegion) {
-        throw new Error(`Could not find refName ${refName} in ${asmName}`)
-      }
-
-      return {
-        ...(region as Omit<typeof region, symbol>),
-        assemblyName: asmName,
-        parentRegion,
-      }
-    }),
-  )
-}
-
-/**
- * Parses locString or space separated set of locStrings into location objects
- * Example inputs:
- * "chr1"
- * "chr1:1-100"
- * "chr1:1..100"
- * "chr1 chr2"
- * "chr1:1-100 chr2:1-100"
- * "chr1 100 200" equivalent to "chr1:1-100"
- *
- * Used by navToLocString
- */
-export function parseLocStrings(
-  input: string,
-  assemblyName: string,
-  isValidRefName: (str: string, assemblyName: string) => boolean,
-) {
-  const inputs = input
-    .split(/(\s+)/)
-    .map(f => f.trim())
-    .filter(f => !!f)
-  // first try interpreting as a whitespace-separated sequence of
-  // multiple locstrings
-  try {
-    return inputs.map(loc =>
-      parseLocString(loc, ref => isValidRefName(ref, assemblyName)),
-    )
-  } catch (e) {
-    // if this fails, try interpreting as a whitespace-separated refname,
-    // start, end if start and end are integer inputs
-    const [refName, start, end] = inputs
-    if (
-      `${e}`.match(/Unknown reference sequence/) &&
-      Number.isInteger(+start) &&
-      Number.isInteger(+end)
-    ) {
-      return [
-        parseLocString(refName + ':' + start + '..' + end, ref =>
-          isValidRefName(ref, assemblyName),
-        ),
-      ]
-    } else {
-      throw e
-    }
-  }
-}

package/src/LinearGenomeView/volvoxDisplayedRegions.json

@@ -1,16 +0,0 @@
-[
-  {
-    "assemblyName": "volvox",
-    "start": 0,
-    "end": 50001,
-    "refName": "ctgA",
-    "reversed": false
-  },
-  {
-    "assemblyName": "volvox",
-    "start": 0,
-    "end": 6079,
-    "refName": "ctgB",
-    "reversed": false
-  }
-]

package/src/index.ts

@@ -1,85 +0,0 @@
-import Plugin from '@jbrowse/core/Plugin'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { AbstractSessionModel, isAbstractMenuManager } from '@jbrowse/core/util'
-
-// icons
-import LineStyleIcon from '@mui/icons-material/LineStyle'
-
-// locals
-import {
-  BaseLinearDisplay,
-  BaseLinearDisplayComponent,
-  baseLinearDisplayConfigSchema,
-} from './BaseLinearDisplay'
-import LinearBareDisplayF from './LinearBareDisplay'
-import LinearGenomeViewF, {
-  SearchBox,
-  ZoomControls,
-  LinearGenomeView,
-} from './LinearGenomeView'
-
-import LinearBasicDisplayF from './LinearBasicDisplay'
-
-import FeatureTrackF from './FeatureTrack'
-import BasicTrackF from './BasicTrack'
-import LaunchLinearGenomeViewF from './LaunchLinearGenomeView'
-
-export default class LinearGenomeViewPlugin extends Plugin {
-  name = 'LinearGenomeViewPlugin'
-
-  exports = {
-    BaseLinearDisplayComponent,
-    BaseLinearDisplay,
-    baseLinearDisplayConfigSchema,
-    SearchBox,
-    ZoomControls,
-    LinearGenomeView,
-  }
-
-  install(pluginManager: PluginManager) {
-    FeatureTrackF(pluginManager)
-    BasicTrackF(pluginManager)
-    LinearBasicDisplayF(pluginManager)
-    LinearGenomeViewF(pluginManager)
-    LinearBareDisplayF(pluginManager)
-    LaunchLinearGenomeViewF(pluginManager)
-  }
-
-  configure(pluginManager: PluginManager) {
-    if (isAbstractMenuManager(pluginManager.rootModel)) {
-      pluginManager.rootModel.appendToSubMenu(['Add'], {
-        label: 'Linear genome view',
-        icon: LineStyleIcon,
-        onClick: (session: AbstractSessionModel) => {
-          session.addView('LinearGenomeView', {})
-        },
-      })
-    }
-  }
-}
-
-export type { BaseLinearDisplayModel, BlockModel } from './BaseLinearDisplay'
-
-export { configSchemaFactory as linearBareDisplayConfigSchemaFactory } from './LinearBareDisplay'
-export {
-  BlockMsg,
-  baseLinearDisplayConfigSchema,
-  BaseLinearDisplayComponent,
-  BaseLinearDisplay,
-} from './BaseLinearDisplay'
-export {
-  type LinearGenomeViewModel,
-  RefNameAutocomplete,
-  type LinearGenomeViewStateModel,
-  SearchBox,
-} from './LinearGenomeView'
-export {
-  renderToSvg,
-  SVGTracks,
-  totalHeight,
-  SVGRuler,
-} from './LinearGenomeView/svgcomponents/SVGLinearGenomeView'
-export {
-  configSchema as linearBasicDisplayConfigSchemaFactory,
-  modelFactory as linearBasicDisplayModelFactory,
-} from './LinearBasicDisplay'